Scientific Programming for QCB

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General Info

The contacts to reach me can be found at this page.

Timetable and lecture rooms

Practicals will take place on Tuesdays from 15:30 to 17:30 (in lecture room A107) and on Thursdays from 15:30 to 17:30 (in lecture room A107). This first part of the course will tentatively run from 23/09/2019 to 05/11/2019.

Tutoring

Samuel Valentini (samuel.valentini) at unitn.it is the tutor for this part of the course. You can contact him and go to his office on Wednesdays from 10:00 to 11:00.

Slides

Slides of the practicals will be available on the top part of each practical page.

Acknowledgements

I would like to thank Dr. David Leoni for all his help and for sharing Jupman with me. I would also like to thank Dr. Stefano Teso for allowing us to use some of his material of a previous course.

Practical 1

In this practical we will set up a working Python3 development environment and will start familiarizing a bit with Python.

Slides

The slides shown in the introduction can be found here: Intro

Setting up the environment

We will need to install several pieces of software to get a working programming environment suitable for this practical. In this section we will install everything that we are going to need in the next few weeks.

Python3 is available for Windows, Linux and Mac.

Our toolbox

If you work on Windows or Mac, you can safely skip the following and go straight to the section “Windows/Mac installation”. Note that, regardless your operating system, a useful source of information on how to install python can be found here.

Linux on windows

If your computer has Windows installed you have several options to get it to run Linux:

1. This video tutorial (only in Italian) shows you how to set up a usb stick to run Linux from it: https://youtu.be/8_SK8iEMyJk
2. You can install a virtualization software like vmware player and download the .iso file of a linux distribution like ubuntu. and install/run it from vmware player. For more information you can look at this tutorial. Another option is to install virtual box.

Here you can find some VDI images that you can load in virtual box or in vmware player with several different operating systems. Please refer to this guide for more information (for information on vmware please click on VM IMAGES –> VMware IMAGES in the menu of the page).

Linux installation

1. The Python interpreter. In this course we will use python version 3.x. A lot of information on python can be found on the python web page. Open a terminal and try typing in:

   python3

   if you get an error like “python3 command not found” you need to install it, while if you get something like this (note that the version might be different):

   

   you are already sorted, just press Ctrl-D to exit.

   Installation on a debian-like linux distribution (e.g. Ubuntu) can be done by typing the following commands on a terminal:

   sudo apt-get update

   sudo apt-get install python3

   While if you are using Fedora you can use:

   sudo dnf install python3

2. Install now the package manager pip, which is a very convenient tool to install python packages, with the following command (on Fedora, the command above should have already installed it):

   sudo apt-get install python3-pip

   Note:

   If pip is already installed in your system you will get a message like: python3-pip is already the newest version (3.x.y)

3. Finally, install the Integrated Development Environment (IDE) that we will be using. This is called Visual Studio Code and is available for all platforms. You can read about it here. Downloads for all platforms can be found here. On a debian-like distribution go to the folder where you downloaded the .deb package and type:

   sudo dpkg -i code*.deb

   While if you are using Fedora you can use:

   sudo dnf install code*.rpm

Windows/Mac installation

OPTION 1:

1. The python interpreter. In this course we will use python version 3.x. A lot of information on python can be found on the python web page. Installers for Windows and Mac can be downloaded from this page. Click on Download Python 3.7.x. Please refrain from double-clicking on the installer and read below first.

   Attention! Important note

   When executing the installer, please remember to tick the flag “Add Python 3.7.x to PATH” and then click on Install now (see picture below).

2. Install now the Integrated Development Environment (IDE) that we will be using. This is called Visual Studio Code and is available for all platforms. You can read about it here. Downloads for all platforms can be found here.

OPTION 2 (easier):

Additional Information:

It is also possible to install python through the Anaconda package manager. You can install Visual Studio Code together with Anaconda(the Anaconda installer will ask if you want it, just say yes!).

Anaconda is available here

Upon launching the installer you should be prompted something like:

at the next step flag the correct items as in the figure below:

When installation is complete, start anaconda through the Anaconda Navigator in the windows menu. When the navigator starts, you should see a screen like:

from which you can install Visual Studio Code as IDE.

For more information please have a look here.

The console

To access the console on Linux just open a terminal and type:

python3

while in Windows you have to look for “Python” and run “Python 3.7”. The console should look like this:

Now we are all set to start interacting with the Python interpreter. In the console, type the following instructions:

5 + 3

8

All as expected. The “In [1]” line is the input, while the “Out [1]” reports the output of the interpreter. Let’s challenge python with some other operations:

12 / 5

2.4

1/133

0.007518796992481203

2**1000

10715086071862673209484250490600018105614048117055336074437503883703510511249361224931983788156958581275946729175531468251871452856923140435984577574698574803934567774824230985421074605062371141877954182153046474983581941267398767559165543946077062914571196477686542167660429831652624386837205668069376

And some assignments:

a = 10
b = 7
s = a + b
d = a / b

print("sum is:",s, " division is:",d)

sum is: 17  division is: 1.4285714285714286

In the first four lines, values have been assigned to variables through the = operator. In the last line, the print function is used to display the output. For the time being, we will skip all the details and just notice that the print function somehow managed to get text and variables in input and coherently merged them in an output text. Although quite useful in some occasions, the console is quite limited therefore you can close it for now. To exit press Ctrl-D or exit().

Visual Studio Code

Once you open the IDE Visual Studio Code you will see the welcome screen:

You can find useful information on this tool here. Please spend some time having a look at that page.

Once you are done with it you can close this window pressing on the “x”. First thing to do is to set the python interpreter to use. Click on View –> Command Palette and type “Python” in the text search space. Select Python: Select Workspace Interpreter as shown in the picture below.

Finally, select the python version you want to use (e.g. Python3).

Now you can click on Open Folder to create a new folder to place all the scripts you are going to create. You can call it something like “exercises”. Next you can create a new file, example1.py (.py extension stands for python).

Visual Studio Code will understand that you are writing Python code and will help you writing valid syntax in your scripts.

Warning:

If you get the following error message:

click on Install Pylint which is a useful tool to help your coding experience.

Add the following text to your example1.py file.

"""
This is the first example of Python script.
"""
a = 10 # variable a
b = 33 # variable b
c = a / b # variable c holds the ratio

# Let's print the result to screen.
print("a:", a, " b:", b, " a/b=", c)

a: 10  b: 33  a/b= 0.30303030303030304

A couple of things worth nothing. The first three lines opened and closed by “”” are some text describing the content of the script. Moreover, comments are proceeded by the hash key (#) and they are just ignored by the python interpreter.

Note

Good Pythonic code follows some syntactic rules on how to write things, naming conventions etc. The IDE will help you writing pythonic code even though we will not enforce this too much in this course. If you are interested in getting more details on this, you can have a look at the PEP8 Python Style Guide (Python Enanchement Proposals - index 8).

Warning

Please remember to comment your code, as it helps readability and will make your life easier when you have to modify or just understand the code you wrote some time in the past.**

Please notice that Visual Studio Code will help you writing your Python scripts. For example, when you start writing the print line it will complete the code for you (if the Pylint extension mentioned above is installed), suggesting the functions that match the letters written. This useful feature is called code completion and, alongside suggesting possible matches, it also visualizes a description of the function and parameters it needs. Here is an example:

Save the file (Ctrl+S as shortcut). It is convenient to ask the IDE to highlight potential syntactic problems found in the code. You can toggle this function on/off by clicking on View –> Problems. The Problems panel should look like this

Visual Studio Code is warning us that the variable names a,b,c at lines 4,5,6 do not follow Python naming conventions for constants. This is because they have been defined at the top level (there is no structure to our script yet) and therefore are interpreted as constants. The naming convention for constants states that they should be in capital letters. To amend the code, you can just replace all the names with the corresponding capitalized name (i.e. A,B,C). If you do that, and you save the file again (Ctrl+S), you will see all these problems disappearing as well as the green underlining of the variable names. If your code does not have an empty line before the end, you might get another warning “Final new line missing”.

Info

Note that these were just warnings and the interpreter in this case will happily and correctly execute the code anyway, but it is always good practice to understand what the warnings are telling us before deciding to ignore them!

Had we by mistake mispelled the print function name (something that should not happen with the code completion tool that suggests functions names!) writing printt (note the double t), upon saving the file, the IDE would have underlined in red the function name and flagged it up as a problem.

This is because the builtin function printt does not exist and the python interpreter does not know what to do when it reads it. Note that printt is actually underlined in red, meaning that there is an error which will cause the interpreter to stop the execution with a failure. Please remember that before running any piece of code all errors must be fixed.

Now it is time to execute the code. By right-clicking in the code panel and selecting Run Python File in Terminal (see picture below) you can execute the code you have just written.

Upon clicking on Run Python File in Terminal a terminal panel should pop up in the lower section of the coding panel and the result shown above should be reported.

Saving script files like the example1.py above is also handy because they can be invoked several times (later on we will learn how to get inputs from the command line to make them more useful…). To do so, you just need to call the python intepreter passing the script file as parameter. From the folder containing the example1.py script:

python3 example1.py

will in fact return:

a: 10 b: 33 a/b= 0.30303030303030304

Before ending this section, let me add another note on errors. The IDE will diligently point you out syntactic warnings and errors (i.e. errors/warnings concerning the structure of the written code like name of functions, number and type of parameters, etc.) but it will not detect semantic or runtime errors (i.e. connected to the meaning of your code or to the value of your variables). These sort of errors will most probably make your code crash or may result in unexpected results/behaviours. In the next section we will introduce the debugger, which is a useful tool to help detecting these errors.

Before getting into that, consider the following lines of code (do not focus on the import line, this is only to load the mathematics module and use its method sqrt):

"""
Runtime error example, compute square root of numbers
"""
import math

A = 16
B = math.sqrt(A)
C = 5*B
print("A:", A, " B:", B, " C:", C)

D = math.sqrt(A-C) # whoops, A-C is now -4!!!
print(D)

A: 16  B: 4.0  C: 20.0

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-7-5d4ed1b10924> in <module>
      9 print("A:", A, " B:", B, " C:", C)
     10
---> 11 D = math.sqrt(A-C) # whoops, A-C is now -4!!!
     12 print(D)

ValueError: math domain error

If you add that code to a python file (e.g. sqrt_example.py), you save it and you try to execute it, you should get an error message as reported above. You can see that the interpreter has happily printed off the vaule of A,B and C but then stumbled into an error at line 9 (math domain error) when trying to compute \(\sqrt{A-C} = \sqrt{-4}\), because the sqrt method of the math module cannot be applied to negative values (i.e. it works in the domain of real numbers).

Please take some time to familiarize with Visual Studio Code (creating files, saving files etc.) as in the next practicals we will take this ability for granted.

The debugger

Another important feature of advanced Integrated Development Environments (IDEs) is their debugging capabilities. Visual Studio Code comes with a debugging tool that can help you trace the execution of your code and understand where possible errors hide.

Write the following code on a new file (let’s call it integer_sum.py) and execute it to get the result.

""" integer_sum.py is a script to
 compute the sum of the first 1200 integers. """

S = 0
for i in range(0, 1201):
    S = S + i

print("The sum of the first 1200 integers is: ", S)

The sum of the first 1200 integers is:  720600

Without getting into too many details, the code you just wrote starts initializing a variable S to zero, and then loops from 0 to 1200 assigning each time the value to a variable i, accumulating the sum of S + i in the variable S.

A final thing to notice is indentation.

Info

In Python it is important to indent the code properly as this provides the right scope for variables (e.g. see that the line S = S + 1 starts more to the right than the previous and following line – this is because it is inside the for loop). You do not have to worry about this for the time being, we will get to this in a later practical…

How does this code work? How does the value of S and i change as the code is executed? These are questions that can be answered by the debugger.

To start the debugger, click on Debug –> Start Debugging (shortcut F5). The following small panel should pop up:

We will use it shortly, but before that, let’s focus on what we want to track. On the left hand side of the main panel, a Watch panel appeared. This is where we need to add the things we want to monitor as the execution of the program goes. With respect to the code written above, we are interested in keeping an eye on the variables S, i and also of the expression S+i (that will give us the value of S of the next iteration). Add these three expressions in the watch panel (click on + to add new expressions). The watch panel should look like this:

do not worry about the message “name X is not defined”, this is normal as no execution has taken place yet and the interpreter still does not know the value of these expressions.

The final thing before starting to debug is to set some breakpoints, places where the execution will stop so that we can check the value of the watched expressions. This can be done by hovering with the mouse on the left of the line number. A small reddish dot should appear, place the mouse over the correct line (e.g. the line corresponding to S = S + 1 and click to add the breakpoint (a red dot should appear once you click).

Now we are ready to start debugging the code. Click on the green triangle on the small debug panel and you will see that the yellow arrow moved to the breakpoint and that the watch panel updated the value of all our expressions.

The value of all expressions is zero because the debugger stopped before executing the code specified at the breakpoint line (recall that S is initialized to 0 and that i will range from 0 to 1200). If you click again on the green arrow, execution will continue until the next breakpoint (we are in a for loop, so this will be again the same line - trust me for the time being).

Now i has been increased to 1, S is still 0 (remember that the execution stopped before executing the code at the breakpoint) and therefore S + i is now 1. Click one more time on the green arrow and values should update accordingly (i.e. S to 1, i to 2 and S + i to 3), another round of execution should update S to 3, i to 3 and S + i to 6. Got how this works? Variable i is increased by one each time, while S increases by i. You can go on for a few more iterations and see if this makes any sense to you, once you are done with debugging you can stop the execution by pressing the red square on the small debug panel.

Other editors are available, if you already have your favourite one you can stick to it. Some examples are:

• Spyder
• PyCharm Community Edition
• Jupyter Notebook. Note: we might use it later on in the course.

A quick Jupyter primer (just for your information)

Jupyter allows to write notebooks organized in cells (these can be saved in files with .ipynb extension). Notebooks contain both the code, some text describing the code and the output of the code execution, they are quite useful to produce some quick reports on data analysis. where there is both code, output of running that code and text. The code by default is Python, but can also support other languages like R). The text is formatted using the **Markdown language** - see cheatsheet for its details. Jupyter is becoming the de-facto standard for writing technical documentation.

Installation

To install it (if you have not installed python with Anaconda otherwise you should have it already):

python3 -m pip install jupyter

you can find more information here

Upon successful installation, you can run it with:

jupyter-notebook

This should fire up a browser on a page where you can start creating your notebooks or modifying existing ones. To create a new notebook you simply click on New:

and then you can start adding cells (i.e. containers of code and text). The type of each cell is specified by selecting the cell and selecting the right type in the dropdown list:

Cells can be executed by clicking on the Run button. This will get the code to execute (and output to be written) and text to be processed to provide the final page layout. To go back to the edit mode, just double click on an executed cell.

Please take some more time to familiarize with Visual Studio Code (creating files, saving files, interacting with the debugger etc.) as in the next practicals we will take this ability for granted. Once you are done you can move on and do the following exercises.

Exercises

1. Compute the area of a triangle having base 120 units (B) and height 33 (H). Assign the result to a variable named area and print it.

Show/Hide Solution

B = 120
H = 33
Area = B*H/2
print("Triangle area is:", Area)

Triangle area is: 1980.0

2. Compute the area of a square having side (S) equal to 145 units. Assign the result to a variable named area and print it.

Show/Hide Solution

S = 145
Area = S*S
print("Square area is:",Area)

Square area is: 21025

3. Modify the program at point 2. to acquire the side S from the user at runtime. (Hint: use the input function and remember to covert the acquired value into an int).

Show/Hide Solution

S_str = input("Insert size: ")
print(type(S_str))
print(S_str)
S = int(S_str)
print(type(S))
print(S)
Area = S**2
print("Square area is:",Area)

Insert size: 33
<class 'str'>
33
<class 'int'>
33
Square area is: 1089

4. If you have not done so already, put the two previous scripts in two separate files (e.g. triangle_area.py and square_area.py and execute them from the terminal).
5. Write a small script (trapezoid.py) that computes the area of a trapezoid having major base (MB) equal to 30 units, minor base (mb) equal to 12 and height (H) equal to 17. Print the resulting area. Try executing the script from inside Visual Studio Code and from the terminal.

Show/Hide Solution

"""trapezoid.py"""
MB = 30
mb = 12
H = 17
Area = (MB + mb)*H/2
print("Trapezoid area is: ", Area)

Trapezoid area is:  357.0

6. Rewrite the example of the sum of the first 1200 integers by using the following equation: \(\sum\limits_{i=1}^n i = \frac{n (n+1)}{2}\).

Show/Hide Solution

N = 1200

print("Sum of first 1200 integers: ", N*(N+1)/2)

Sum of first 1200 integers:  720600.0

7. Modify the program at point 6. to make it acquire the number of integers to sum N from the user at runtime.

Show/Hide Solution

print("Input number N:")
N = int(input())
print("Sum of first ", N, " integers: ", N*(N+1)/2)

Input number N:
77
Sum of first  77  integers:  3003.0

8. Write a small script to compute the length of the hypotenuse (c) of a right triangle having sides a=133 and b=72 units (see picture below). Hint: remember the Pythagorean theorem and use math.sqrt).

Show/Hide Solution

import math

a = 133
b = 72

c = math.sqrt(a**2 + b**2)

print("Hypotenuse: ", c)

Hypotenuse:  151.23822268196622

9. Rewrite the trapezoid script making it compute the area of the trapezoid starting from the major base (MB), minor base (mb) and height (H) taken in input. (Hint: use the input function and remember to convert the acquired value into an int).

Show/Hide Solution

"""trapezoidV2.py"""
MB = int(input("Input the major base (MB):"))
mb = int(input("Input the minor base (mb):"))
H = int(input("Input the height (H):"))
Area = (MB + mb)*H/2
print("Given MB:", str(MB) , " mb:", str(mb) , " and H:", H)
print("The trapezoid area is: ", Area)

Input the major base (MB):33
Input the minor base (mb):22
Input the height (H):10
Given MB: 33  mb: 22  and H: 10
The trapezoid area is:  275.0

10. Write a script that reads the side of an heagon in input and computes its perimeter and area printing them to the screen. Hint: \(Area = \frac{3*\sqrt{3}*side^{2}}{2}\)

Show/Hide Solution

import math

side = int(input("Please insert the side of the hexagon: "))

P = 6*side
A = (3*math.sqrt(3)*side**2)/2
print("Perimeter: ", P, " Area: ", A)

Please insert the side of the hexagon: 9
Perimeter:  54  Area:  210.4441731196186

Practical 2

In this practical we will start interacting more with Python, practicing on how to handle data, functions and methods. We will see several built-in data types and then dive deeper into strings.

Slides

The slides of the introduction can be found here: Intro

Modules

Python modules are simply text files having the extension .py (e.g. exercise.py). When you were writing the code in the IDE in the previous practical, you were in fact implementing the corresponding module.

As said in the previous practical, once you implemented and saved the code of the module, you can execute it by typing

python3 exercise1.py

or, in Visual Studio Code, by right clicking on the code panel and selecting Run Python File in Terminal.

A Module A can be loaded from another module B so that B can use the functions defined in A. Remember when we used the sqrt function? It is defined in the module math. To import it and use it we indeed wrote something like:

import math

A = math.sqrt(4)
print(A)

2.0

Note

When importing modules we do not need to specify the extension “.py” of the file.

Objects

Python understands very well objects, and in fact everything is an object in Python.

Objects have properties (characteristic features) and methods (things they can do). For example, an object car caould be defined to have the properties model, make, color, number of doors, position etc., and the methods steer right, steer left, accelerate, break, stop, change gear, repaint,… whose application might affect the state of the object.

According to Python’s official documentation:

“Objects are Python’s abstraction for data. All data in a Python program is represented by objects or by relations between objects.”

All you need to know for now is that in Python objects have an identifier (ID) (i.e. their name), a type (numbers, text, collections,…) and a value (the actual data represented by the objects). Once an object has been created the identifier and the type never change, while its value can either change (mutable objects) or stay constant (immutable objects).

Python provides the following built-in data types:

We will stick with the simplest ones for now, but later on we will dive deeper into the all of them.

Variables

Variables are just references to objects, in other words they are the name given to an object. Variables can be assigned to objects by using the assignment operator =.

The instruction

sides = 4

might represent the number of sides of a square. What happens when we execute it in Python? An object is created, it is given an identifier, its type is set to “int” (an integer number), it value to 4 and a name sides is placed in the current namespace to point to that object, so that after that instruction we can access that object through its name. The type of an object can be accessed with the function type() and the identifier with the function id():

sides = 4
print( type(sides) )
print( id(sides) )

<class 'int'>
10919520

Consider now the following code:

sides = 4 #a square
print ("value:", sides, " type:", type(sides), " id:", id(sides))
sides = 5 #a pentagon
print ("value:", sides, " type:", type(sides), " id:", id(sides))

value: 4  type: <class 'int'>  id: 10919520
value: 5  type: <class 'int'>  id: 10919552

The value of the variable sides has been changed from 4 to 5, but as stated in the table above, the type int is immutable. Luckily, this did not prevent us to change the value of sides from 4 to 5. What happened behind the scenes when we executed the instruction sides = 5 is that a new object has been created of type int (5 is still an integer) and it has been made accessible with the same name sides, but since it is a different object (i.e. the integer 5) you can see that the identifier is actually different.

Note: You do not have to really worry about what happens behind the scenes, as the Python interpreter will take care of these aspects for you, but it is nice to know what it does.

You can even change the type of a variable during execution but that is normally a bad idea as it makes understanding the code more complicated.

You can do (but, please, refrain!):

sides = 4 #a square
print ("value:", sides, " type:", type(sides), " id:", id(sides))
sides = "four" #the sides in text format
print ("value:", sides, " type:", type(sides), " id:", id(sides))

value: 4  type: <class 'int'>  id: 10919520
value: four  type: <class 'str'>  id: 139909167957192

IMPORTANT NOTE: You can chose the name that you like for your variables (I advise to pick something reminding their meaning), but you need to adhere to some simple rules.

1. Names can only contain upper/lower case digits (A-Z, a-z), numbers (0-9) or underscores _;
2. Names cannot start with a number;
3. Names cannot be equal to reserved keywords:

Numeric types

We already mentioned that numbers are immutable objects. Python provides different numeric types: integers, booleans, reals (floats) and even complex numbers and fractions (but we will not get into those).

Integers

Their range of values is limited only by the memory available. As we have already seen, python provides also a set of standard operators to work with numbers:

a = 7
b = 4

a + b # 11
a - b # 3
a // b # integer division: 1
a * b # 28
a ** b # power: 2401
a / b # division 0.8333333333333334
type(a / b)

float

Note that in the latter case the result is no more an integer, but a float (we will get to that later).

Booleans

These objects are used for the boolean algebra. Truth values are represented with the keywords True and False in Python. A boolean object can only have value True or False. We can convert booleans into integers with the builtin function int. Any integer can be converted into a boolean (and vice-versa) with:

a = bool(1)
b = bool(0)
c = bool(72)
d = bool(-5)
t = int(True)
f = int(False)

print("a: ", a, " b: ", b, " c: ", c, " d: ", d , " t: ", t, " f: ", f)

a:  True  b:  False  c:  True  d:  True  t:  1  f:  0

any integer is evaluated to true, except 0. Note that, the truth values True and False respectively behave like the integers 1 and 0.

We can operate on boolean values with the boolean operators and, or, not. Recall boolean algebra for their use:

T = True
F = False

print ("T: ", T, " F:", F)

print ("T and F: ", T and F) #False
print ("T and T: ", T and T) #True
print ("F and F: ", F and F) #False
print ("not T: ", not T) # False
print ("not F: ", not F) # True
print ("T or F: ", T or F) # True
print ("T or T: ", T or T) # True
print ("F or F: ", F or F) # False

T:  True  F: False
T and F:  False
T and T:  True
F and F:  False
not T:  False
not F:  True
T or F:  True
T or T:  True
F or F:  False

Numeric comparators are operators that return a boolean value. Here are some examples (from the lecture):

Example: Given a variable a = 10 and a variable b = 77, let’s swap their values (i.e. at the end a will be equal to 77 and b to 10). Let’s also check the values at the beginning and at the end.

a = 10
b =  77
print("a: ", a, " b:", b)
print("is a equal to 10?", a == 10)
print("is b equal to 77?", b == 77)

TMP = b  #we need to store the value of b safely
b = a    #ok, the old value of b is gone... is it?
a = TMP  #a gets the old value of b... :-)

print("a: ", a, " b:", b)
print("is a equal to 10?", a == 10)
print("is a equal to 77?", a == 77)
print("is b equal to 10?", b == 10)
print("is b equal to 77?", b == 77)

a:  10  b: 77
is a equal to 10? True
is b equal to 77? True
a:  77  b: 10
is a equal to 10? False
is a equal to 77? True
is b equal to 10? True
is b equal to 77? False

Real numbers

Python stores real numbers (floating point numbers) in 64 bits of information divided in sign, exponent and mantissa.

Example: Let’s calculate the area of the center circle of a football pitch (radius = 9.15m) recalling that \(area= Pi*R^2\):

R = 9.15
Pi = 3.1415926536
Area = Pi*(R**2)
print (Area)

263.02199094102605

Note that the parenthesis around the R**2 are not necessary as operator ** has the precedence, but I personally think it helps readability.

Here is a reminder of the precedence of operators:

Example: Let’s compute the GC content of a DNA sequence 33 base pairs long, having 12 As, 9 Ts, 5 Cs and 7Gs. The GC content can be expressed by the formula: \(gc = \frac{G+C}{A+T+C+G}\) where A,T,C,G represent the number of nucleotides of each kind. What is the AT content? Is the GC content higher than the AT content?

A = 12
T = 9
C = 5
G = 7

gc = (G+C)/(A+T+C+G)

print("The GC content is: ", gc)

at = 1 - gc

print (gc > at)

The GC content is:  0.36363636363636365
False

Strings

Strings are immutable objects (note the actual type is str) used by python to handle text data. Strings are sequences of unicode code points that can represent characters, but also formatting information (e.g. ‘\n’ for new line). Unlike other programming languages, python does not have the data type character, which is represented as a string of length 1.

There are several ways to define a string:

S = "my first string, in double quotes"

S1 = 'my second string, in single quotes'

S2 = '''my third string is
in triple quotes
therefore it can span several lines'''

S3 = """my fourth string, in triple double-quotes
can also span
several lines"""

print(S, '\n') #let's add a new line at the end of the string with \n
print(S1,'\n')
print(S2, '\n')
print(S3, '\n')

my first string, in double quotes

my second string, in single quotes

my third string is
in triple quotes
therefore it can span several lines

my fourth string, in triple double-quotes
can also span
several lines

To put special characters like ‘,” and so on you need to “escape them” (i.e. write them following a back-slash).

Example: Let’s print a string containing a quote and double quote (i.e. ‘ and “).

myString = "This is how I \'quote\' and \"double quote\" things in strings"
print(myString)

This is how I 'quote' and "double quote" things in strings

Strings can be converted to and from numbers with the functions str(), int() or float().

Example: Let’s define a string myString with the value “47001” and convert it into an int. Try adding one and print the result.

myString = "47001"
print(myString, " has type ", type(myString))

myInt = int(myString)

print(myInt, " has type ", type(myInt))

myInt = myInt + 1   #adds one

myString = myString + "1" #cannot add 1 (we need to use a string).
                          #This will append 1 at the end of the string

print(myInt)
print(myString)

47001  has type  <class 'str'>
47001  has type  <class 'int'>
47002
470011

Python defines some operators to work with strings. Recall the slides shown during the lecture:

Example A tandem repeat is a short sequence of DNA that is repeated several times in a row. Let’s create a string representing the tandem repeat of the motif “ATTCG” repeated 5 times. What is the length of the whole repetitive region? Is the motif “TCGAT” (m1) present in the region? The motif “TCCT” (m2)? Let’s give an orientation to the tandem repeat by adding the string “5’-” (5’ end) on the left and “-3’” (3’ end) to the right.

motif = "ATTCG"

tandem_repeat = motif * 5

print(motif)
print(tandem_repeat, " has length", len(tandem_repeat))
m1 = "TCGAT"
m2 = "TCCT"

print("Is ", m1, " in ", tandem_repeat, " ? ", m1 in tandem_repeat )
print("Is ", m2, " in ", tandem_repeat, " ? ", m2 in tandem_repeat )
oriented_tr = "5\'-" + tandem_repeat + "-3\'"
print(oriented_tr)

ATTCG
ATTCGATTCGATTCGATTCGATTCG  has length 25
Is  TCGAT  in  ATTCGATTCGATTCGATTCGATTCG  ?  True
Is  TCCT  in  ATTCGATTCGATTCGATTCGATTCG  ?  False
5'-ATTCGATTCGATTCGATTCGATTCG-3'

We can access strings at specific positions (indexing) or get a substring starting from a position S to a position E. The only thing to remember is that numbering starts from 0. Thei-th character of a string can be accessed as str[i-1]. Substrings can be accessed as str[S:E], optionally a third parameter can be specified to set the step (i.e. str[S:E:STEP]).

Important note. Remember that when you do str[S:E], S is inclusive, while E is exclusive (see S[0:6] below).

Let’s see these aspects in action with an example:

S = "Luther College"

print(S) #print the whole string
print(S == S[:]) #a fancy way of making a copy of the original string
print(S[0]) #first character
print(S[3]) #fourth character
print(S[-1]) #last character
print(S[0:6]) #first six characters
print(S[-7:]) #final seven characters
print(S[0:len(S):2]) #every other character starting from the first
print(S[1:len(S):2]) #every other character starting from the second

Luther College
True
L
h
e
Luther
College
Lte olg
uhrClee

Methods for the str object

The object str has some methods that can be applied to it (remember methods are things you can do on objects). Recall from the lecture that the main methods are:

IMPORTANT NOTE: Since Strings are immutable, every operation that changes the string actually produces a new str object having the modified string as value.

Recall that strings are immutable. For this reason we cannot directly change them with an assignment operator.

Example: Since the genetic code is degenerate, there are many codons encoding for the same aminoacid. Consider Proline, it can be encoded by the following codons: CCU, CCA,CCG, CCC. Let’s create a string proline and assign it to its possible codons one after the other.

"""
Wrong solution. We cannot directly replace the value of a string
"""

proline = "CCU"
print("Proline can be encoded by: ", proline)
proline[2]="A"
print(".. or by: ", proline)

Proline can be encoded by:  CCU

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-17-9750dcfa1cbd> in <module>()
      5 proline = "CCU"
      6 print("Proline can be encoded by: ", proline)
----> 7 proline[2]="A"
      8 print(".. or by: ", proline)
      9

TypeError: 'str' object does not support item assignment

"""
Correct solution. Using str.replace
"""
proline = "CCU"
print("Proline can be encoded by: ", proline)
proline = proline.replace("U","A")
print(".. or by: ", proline)
proline = proline.replace("A","G")
print(".. or by: ", proline)
proline = proline.replace("G","C")
print(".. or by: ", proline)

Proline can be encoded by:  CCU
.. or by:  CCA
.. or by:  CCG
.. or by:  CCC

"""
Another correct solution. Using string slicing and catenation.
"""
proline = "CCU"
print("Proline can be encoded by: ", proline)
proline = proline[:-1]+"A" #equal to proline[0:-1] or proline[0:2]
print(".. or by: ", proline)
proline = proline[:-1]+"G"
print(".. or by: ", proline)
proline = proline[:-1]+"C"
print(".. or by: ", proline)

Proline can be encoded by:  CCU
.. or by:  CCA
.. or by:  CCG
.. or by:  CCC

Example: Given the DNA sequence S = ” aTATGCCCATatcgctAAATTGCTGCCATTACA “. Print its length (removing any blank spaces at either sides), the number of adenines, cytosines, guanines and thymines present. Is the sequence “ATCG” present in S? Print how many times the substring “TGCC” appears in S and all the corresponding indexes.

S = "   aTATGCCCATatcgctAAATTGCTGCCATTACA    "

print(S)
S = S.strip(" ")
print(S)

print(len(S))
tmpS = S.upper() #for simplicity to count only 4 different nucleotides
print("A count: ", tmpS.count("A"))
print("C count: ", tmpS.count("C"))
print("T count: ", tmpS.count("T"))
print("G count: ", tmpS.count("G"))
print("Is ATCG in ", tmpS, "? ", tmpS.find("ATCG") != -1) #or tmpS.count("ATCG") > 0
print("TGCC is present ", tmpS.count("TGCC"), " times in ", tmpS)
print("TGCC is present at pos ", tmpS.find("TGCC"))
print("TGCC is present at pos ", tmpS.rfind("TGCC")) #or tmpS.find("TGCC",4)

   aTATGCCCATatcgctAAATTGCTGCCATTACA
aTATGCCCATatcgctAAATTGCTGCCATTACA
33
A count:  10
C count:  9
T count:  10
G count:  4
Is ATCG in  ATATGCCCATATCGCTAAATTGCTGCCATTACA ?  True
TGCC is present  2  times in  ATATGCCCATATCGCTAAATTGCTGCCATTACA
TGCC is present at pos  3
TGCC is present at pos  23

Exercises

1. Given the following string on two lines:

text = """Nobody said it was easy
No one ever said it would be this hard"""

write some python code that a)prints the whole string; b) prints the first and last character; c) prints the first 10 characters; d) prints from the 19th character to the 31st; e) prints the string all in capital letters.

Show/Hide Solution

text = """Nobody said it was easy
No one ever said it would be this hard"""
# a) prints the whole text
print(text)

#some empty space...
print("")

# b) 1st and last character
print("1st char: ", text[0], " last char: ", text[-1])

#c) the 1st 10 characters:
print("1st 10 chars:", text[0:10])

#d) from the 20th to the 31st char
print("\nCharacters from 19 to 31:")
print(text[18:31])
print("\nAll upper case:")
print(text.upper())

Nobody said it was easy
No one ever said it would be this hard

1st char:  N  last char:  d
1st 10 chars: Nobody sai

Characters from 19 to 31:
easy
No one e

All upper case:
NOBODY SAID IT WAS EASY
NO ONE EVER SAID IT WOULD BE THIS HARD

2. An exon of a gene starts from position 12030 on a genome and ends at position 12174. Does an A/T SNP present at position 12111 affect this exon (i.e. is it inside the exon)? And what about a SNP present at position 12188? Hint: test a suitable boolean expression to answer this question.

Show/Hide Solution

E_start = 12030
E_end = 12174
SNP1_pos = 12111
SNP2_pos = 12188

Test1 = (SNP1_pos >= E_start and SNP1_pos <=E_end)
Test2 = (SNP2_pos >= E_start and SNP2_pos <=E_end)
print ("SNP1 (", SNP1_pos,") in [", E_start, ",", E_end, "]?", Test1)
print ("SNP2 (", SNP2_pos,") in [", E_start, ",", E_end, "]?", Test2)

SNP1 ( 12111 ) in [ 12030 , 12174 ]? True
SNP2 ( 12188 ) in [ 12030 , 12174 ]? False

3. SNP FB_AFFY_0000024 of the Apple 480K SNP chip has 5’ flanking region (i.e. the forward probe) CATTATTTTCACTTGGGTCGAGGCCAGATTCCATC and 3’ flanking region (i.e. the reverse probe) GGATTGCCCGAAATCAGAGAAAAGTCG. The SNP is a G/A transversion. Answer the following questions:
   1. What is the length of the 5’ flanking region? And that of the 3’ flanking region?
   2. The IUPAC code of the G/A transversion is R. What is the sequence of the whole region using the “[G/A]” notation for the SNP (hint: concatenate it in a new string called region) and the iupac notation R (region_iupac)?
   3. Retrive and print only the SNP from region and iupac_region

Show/Hide Solution

SNP_5prime =  "CATTATTTTCACTTGGGTCGAGGCCAGATTCCATC"
SNP_3prime = "GGATTGCCCGAAATCAGAGAAAAGTCG"

SNPseq = "G/A"
SNPiupac = "R"

print("Length of 5' end: ", len(SNP_5prime))
print("Length of 3' end: ", len(SNP_3prime))
region = SNP_5prime + "[" + SNPseq + "]" + SNP_3prime
region_iupac = SNP_5prime + SNPiupac + SNP_3prime
print(region)
print(region_iupac)

#string slicing and indexing!

snp_from_region = region[ len(SNP_5prime) + 1 : len(SNP_5prime) + 4 ]
snp_from_iupac = region_iupac[ len(SNP_5prime) ]

print("SNP from region: ", snp_from_region)
print("SNP from iupac region: ", snp_from_iupac)

# Another way:
#L_ind = region.find("[")
#R_ind = region.find("]")
#print(L_ind)
#print(R_ind)

#print(region[L_ind + 1 : R_ind])

Length of 5' end:  35
Length of 3' end:  27
CATTATTTTCACTTGGGTCGAGGCCAGATTCCATC[G/A]GGATTGCCCGAAATCAGAGAAAAGTCG
CATTATTTTCACTTGGGTCGAGGCCAGATTCCATCRGGATTGCCCGAAATCAGAGAAAAGTCG
SNP from region:  G/A
SNP from iupac region:  R
35
39
G/A

4. Compute the melting temperature \(T_m\) of the primer with sequence “TTAGCACACGTGAGCCAATGGAGCAAACGGGTAATT”. The melting temperature \(T_m\) (in degrees Celtius) can be computed as: \(T_m = 64.9 + 41(GC - 16.4)/N\), where \(GC\) is the total number of G and C in the primer and \(N\) is its length.

Show/Hide Solution

primer = "TTAGCACACGTGAGCCAATGGAGCAAACGGGTAATT"
N = len(primer)

gc = (primer.count("G") + primer.count("C"))

Tm = 64.9 + 41 * (gc - 16.4)/N

print("The melting T for primer ", primer, " is: ", Tm, "°C")

The melting T for primer  TTAGCACACGTGAGCCAATGGAGCAAACGGGTAATT  is:  65.58333333333334 °C

5. Convert the following extract of the PalB2 gene into mRNA (i.e. replace thymine with uracile): CTGTCTCCCTCACTGTATGTAAATTGCATCTAGAATAGCA TCTGGAGCACTAATTGACACATAGTGGGTATCAATTATTA TTCCAGGTACTAGAGATACCTGGACCATTAACGGATAAAT AGAAGATTCATTTGTTGAGTGACTGAGGATGGCAGTTCCT GCTACCTTCAAGGATCTGGATGATGGGGAGAAACAGAGAA CATAGTGTGAGAATACTGTGGTAAGGAAAGTACAGAGGAC TGGTAGAGTGTCTAACCTAGATTTGGAGAAGGACCTAGAA GTCTATCCCAGGGAAATAAAAATCTAAGCTAAGGTTTGAG GAATCAGTAGGAATTGGCAAAGGAAGGACATGTTCCAGAT GATAGGAACAGGTTATGCAAAGATCCTGAAATGGTCAGAG CTTGGTGCTTTTTGAGAACCAAAAGTAGATTGTTATGGAC CAGTGCTACTCCCTGCCTCTTGCCAAGGGACCCCGCCAAG CACTGCATCCCTTCCCTCTGACTCCACCTTTCCACTTGCC CAGTATTGTTGGTGT

and print the number of uracils present and the total length of the sequence (remember to remove newlines).

Considering the genetic code and all the possible open reading frames, answer the following questions:

1. How many stop codons are present in the sequence?
2. How many Glycines (Gly)?
3. Is Tryptophane (Trp) present?
4. What is the position of the leftmost Trp? Print the codon to double check correctness (hint: slicing).
5. What is the position of the rightmost Trp? Print the codon to double check correctness (hint: slicing).

Show/Hide Solution

seq ="""CTGTCTCCCTCACTGTATGTAAATTGCATCTAGAATAGCA
TCTGGAGCACTAATTGACACATAGTGGGTATCAATTATTA
TTCCAGGTACTAGAGATACCTGGACCATTAACGGATAAAT
AGAAGATTCATTTGTTGAGTGACTGAGGATGGCAGTTCCT
GCTACCTTCAAGGATCTGGATGATGGGGAGAAACAGAGAA
CATAGTGTGAGAATACTGTGGTAAGGAAAGTACAGAGGAC
TGGTAGAGTGTCTAACCTAGATTTGGAGAAGGACCTAGAA
GTCTATCCCAGGGAAATAAAAATCTAAGCTAAGGTTTGAG
GAATCAGTAGGAATTGGCAAAGGAAGGACATGTTCCAGAT
GATAGGAACAGGTTATGCAAAGATCCTGAAATGGTCAGAG
CTTGGTGCTTTTTGAGAACCAAAAGTAGATTGTTATGGAC
CAGTGCTACTCCCTGCCTCTTGCCAAGGGACCCCGCCAAG
CACTGCATCCCTTCCCTCTGACTCCACCTTTCCACTTGCC
CAGTATTGTTGGTGT"""

seq = seq.replace("\n","")
mRNA = seq.replace("T","U")

print("Number of uracils: ", mRNA.count("U"))
print("Total length of the sequence: ", len(seq))
stopc = mRNA.count("UAA") + mRNA.count("UGA") + mRNA.count("UAG")
print("Number of stop codons: ", stopc)
gly = mRNA.count("GGU") + mRNA.count("GGC") + mRNA.count("GGA") + mRNA.count("GGG")
print("Number of glycines: ", gly)
print("Is Trp present? ", mRNA.find("UGG")> 0)
rmTrp = mRNA.find("UGG")
print("Leftmost Trp at pos:", rmTrp, " Codon: ", mRNA[rmTrp : rmTrp + 3])
lmTrp = mRNA.rfind("UGG")
print("Rightmost Trp at pos:", mRNA.rfind("UGG"), " Codon: ", mRNA[lmTrp:lmTrp+3])

Number of uracils:  140
Total length of the sequence:  535
Number of stop codons:  32
Number of glycines:  34
Is Trp present?  True
Leftmost Trp at pos: 42  Codon:  UGG
Rightmost Trp at pos: 529  Codon:  UGG

6. Consider the following Illumina HiSeq 4000 read: “”“AATGATACGGCGACCACCGAGATCTACACGCCTCCCTCGCGC CATCAGAGAGTCTGGGTCTCAGGTACCGCAGTTGTATCTTGCGCGACTATA ATCCACGGCTCTTATTCTAGCGTGCGCGTACGGCGGTGGGCGTCGTTACGCTATATT”“”.

Answer the following questions:

1. How long is the read (beware of newlines)?
2. What is the GC content of the read (remember $gc = \frac{G+C}{A+T+C+G}$)?
3. A Nextera adapter is "AATGATACGGCGACCACCGAGATCTACACGCCTCCCTCGCGCCATCAG".
Is it present in the read? How long is it?
4. Remove the Nextera adapter from the read and recompute the GC content.
Has GC content increased after adapter trimmming?

Show/Hide Solution

read = """AATGATACGGCGACCACCGAGATCTACACGCCTCCCTCGCGC
CATCAGAGAGTCTGGGTCTCAGGTACCGCAGTTGTATCTTGCGCGACTATA
ATCCACGGCTCTTATTCTAGCGTGCGCGTACGGCGGTGGGCGTCGTTACGCTATATT"""

read = read.replace("\n","")
print("Read length is: ", len(read), " base pairs")
g = read.count("G")
c = read.count("C")
t = read.count("T")
a = read.count("A")

gc = (g + c) / (a + t + c + g)

print("GC content of read: ", gc)

adapter = "AATGATACGGCGACCACCGAGATCTACACGCCTCCCTCGCGCCATCAG"

print("Is the adapter present? ", adapter in read)
print("Adapter length: ", len(adapter))
print("The adapter starts at: ", read.find(adapter))

trimmed_read = read.replace(adapter,"")

tr_g = trimmed_read.count("G")
tr_c = trimmed_read.count("C")
tr_t = trimmed_read.count("T")
tr_a = trimmed_read.count("A")

tr_gc = (tr_g + tr_c) / (tr_a + tr_t + tr_c + tr_g)
print("GC content of trimmed read: ", tr_gc)
print("GC content has increased after trimming: ", tr_gc > gc)

Read length is:  150  base pairs
GC content of read:  0.56
Is the adapter present?  True
Adapter length:  48
The adapter starts at:  0
GC content of trimmed read:  0.5392156862745098
GC content has increased after trimming:  False

7. Given geneA starting at position 1000 and ending at position 3400, and geneB starting at position 3700 and ending at position 6000. Randomly select a position (pos) from 1 to 5202 and check the following: a. is pos in geneA? b. is pos in geneB? c. is pos in between the two genes? d. is pos within one of the two genes? e. is pos outside both genes? f. is pos within 100 bases before the start of geneA? To pick a random number you can import the random module and use the random.randint(start,end) function:

   import random

   pos = random.randint(1,6000)

Show/Hide Solution

import random

geneA_start = 1000
geneA_end = 3400
geneB_start = 3700
geneB_end = 5201

pos = random.randint(1,6000)
print("Random position is: ", pos)

answerA = (pos >= geneA_start and pos <= geneA_end)
answerB = (pos >= geneB_start and pos <= geneB_end)
answerC = (pos >geneA_end and pos <geneB_start)
answerD = (answerA or answerB)
answerE = (pos < geneA_start or (pos > geneA_end and pos < geneB_start) or (pos > geneB_end))
answerF = (pos >= geneA_start - 100 ) and (pos < geneA_start)
print("Is ", pos, " in geneA [", geneA_start, ",", geneA_end, "]? ", answerA)
print("Is ", pos, " in geneB [", geneB_start, ",", geneB_end, "]? ", answerB)
print("Is ", pos, " between the two genes? ", answerC)
print("Is ", pos, " in one of the two genes? ", answerD)
print("Is ", pos, " outside of both genes? ", answerE)
print("Is ", pos, " within 100 bases from the start of geneA? ", answerF)

Random position is:  3729
Is  3729  in geneA [ 1000 , 3400 ]?  False
Is  3729  in geneB [ 3700 , 5201 ]?  True
Is  3729  between the two genes?  False
Is  3729  in one of the two genes?  True
Is  3729  outside of both genes?  False
Is  3729  within 100 bases from the start of geneA?  False

8. The DNA-binding domain of the Tumor Suppressor Protein TP53 can be represented by the string:

chain_a = “”“SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKM FCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVV RRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFR HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILT IITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKG EPHHELPPGSTKRALPNNT”“”

Answer the following questions:

1. How many lines is the sequence written on?
2. How long is the sequence (remove newlines)?
3. Create a new sequence with all new lines removed
4. How many cysteines "C" and histidines "H" are there in the sequence?
5. Does the chain contain the sub-sequence "NLRVEYLDDRN"? Where?
6. Extract the first line of the sequence (Hint: use find and string slicing).

Show/Hide Solution

chain_a = """SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKM
FCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVV
RRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFR
HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILT
IITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKG
EPHHELPPGSTKRALPNNT"""

print(chain_a)
lines = chain_a.count('\n') + 1
print("The sequence is in ", lines, " lines")

sequence = chain_a.replace("\n","")
print("The sequence has ", len(sequence), " aminoacids")
print("The sequence counts ", sequence.count('C'), " cysteins")
print("The sequence counts ", sequence.count('H'), " histidines")
subseq = "NLRVEYLDDRN"
print("Does the sequence contain ", subseq, "?", subseq in sequence )
pos = sequence.find(subseq)
getS = sequence[pos:pos+len(subseq)]
print(subseq, " is present at pos: ", pos , "[check:", getS , "]")

end_first_line = chain_a.find('\n')
print("The first line is: ", chain_a[0:end_first_line])

SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKM
FCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVV
RRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFR
HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILT
IITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKG
EPHHELPPGSTKRALPNNT
The sequence is in  6  lines
The sequence has  219  aminoacids
The sequence counts  10  cysteins
The sequence counts  9  histidines
Does the sequence contain  NLRVEYLDDRN ? True
NLRVEYLDDRN  is present at pos:  106 [check: NLRVEYLDDRN ]
The first line is:  SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKM

9. Calculate the zeros of the equation \(ax^2-b = 0\) where a = 10 and b = 1. Hint: use math.sqrt or ** 0.5. Finally check that substituting the obtained value of x in the equation gives zero.

Show/Hide Solution

import math

A = 10
B = 1

X = math.sqrt(B/A)

print("10X**2 - 1 = 0 for X:", X)
print(10*X**2 -1 == 0)

10X**2 - 1 = 0 for X: 0.31622776601683794
True

Practical 3

In this practical we will work with lists and tuples.

Slides

The slides of the introduction can be found here: Intro

Lists

Python lists are ordered collections of (homogeneous) objects, but they can hold also non-homogeneous data. List are mutable objects. Elements of the collection are specified within two square brackets [] and are comma separated.

We can use the function print to print the content of lists. Some examples of list definitions follow:

my_first_list = [1,2,3]
print("first:" , my_first_list)

my_second_list = [1,2,3,1,3] #elements can appear several times
print("second: ", my_second_list)

fruits = ["apple", "pear", "peach", "strawberry", "cherry"] #elements can be strings
print("fruits:", fruits)

an_empty_list = []
print("empty:" , an_empty_list)

another_empty_list = list()
print("another empty:", another_empty_list)

a_list_containing_other_lists = [[1,2], [3,4,5,6]] #elements can be other lists
print("list of lists:", a_list_containing_other_lists)

my_final_example = [my_first_list, a_list_containing_other_lists]
print("a list of lists of lists:", my_final_example)

first: [1, 2, 3]
second:  [1, 2, 3, 1, 3]
fruits: ['apple', 'pear', 'peach', 'strawberry', 'cherry']
empty: []
another empty: []
list of lists: [[1, 2], [3, 4, 5, 6]]
a list of lists of lists: [[1, 2, 3], [[1, 2], [3, 4, 5, 6]]]

Operators for lists

Python provides several operators to handle lists. The following behave like on strings (remember that as in strings, the first position is 0!):

While this requires that the whole tested obj is present in the list

and

can also change the corresponding value of the list (lists are mutable objects).

Some examples follow.

A = [1, 2, 3 ]
B = [1, 2, 3, 1, 2]

print("A is a ", type(A))

print(A, " has length: ", len(A))
print("A[0]: ", A[0], " A[1]:", A[1], " A[-1]:", A[-1])

print(B, " has length: ", len(B))
print("Is A equal to B?", A == B)

C = A + [1, 2]
print(C)
print("Is C equal to B?", B == C)
D = [1, 2, 3]*8
print(D)

E = D[12:18] #slicing
print(E)
print("Is A*2 equal to E?", A*2 == E)

A is a  <class 'list'>
[1, 2, 3]  has length:  3
A[0]:  1  A[1]: 2  A[-1]: 3
[1, 2, 3, 1, 2]  has length:  5
Is A equal to B? False
[1, 2, 3, 1, 2]
Is C equal to B? True
[1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3]
[1, 2, 3, 1, 2, 3]
Is A*2 equal to E? True

A = [1, 2, 3, 4, 5, 6]
B = [1, 3, 5]
print("A:", A)
print("B:", B)

print("Is B in A?", B in A)
print("A\'s ID:", id(A))
A[5] = [1,3,5] #we can add elements
print(A)
print("A\'s ID:", id(A))
print("A has length:", len(A))
print("Is now B in A?", B in A)

A: [1, 2, 3, 4, 5, 6]
B: [1, 3, 5]
Is B in A? False
A's ID: 140546986337864
[1, 2, 3, 4, 5, [1, 3, 5]]
A's ID: 140546986337864
A has length: 6
Is now B in A? True

Note: When slicing do not exceed the list boundaries (or you will be prompted a list index out of range error).

Consider the following example:

A = [1, 2, 3, 4, 5, 6]
print("A has length:", len(A))

print("First element:", A[0])
print("7th-element: ", A[6])

A has length: 6
First element: 1

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-4-699e5f04cae0> in <module>()
      3
      4 print("First element:", A[0])
----> 5 print("7th-element: ", A[6])

IndexError: list index out of range

Example: Consider the matrix \(M = \begin{bmatrix}1 & 2 & 3\\ 1 & 2 & 1\\ 1 & 1 & 3\end{bmatrix}\) and the vector \(v=[10, 5, 10]^T\). What is the matrix-vector product \(M*v\)?

\[\begin{split}\begin{bmatrix}1 & 2 & 3\\ 1 & 2 & 1\\ 1 & 1 & 3\end{bmatrix}*[10,5,10]^T = [50, 30, 45]^T\end{split}\]

M = [[1, 2, 3], [1, 2, 1], [1, 1, 3]]
v = [10, 5, 10]
prod = [0, 0 ,0] #at the beginning the product is the null vector

prod[0]=M[0][0]*v[0] + M[0][1]*v[1] + M[0][2]*v[2]
prod[1]=M[1][0]*v[0] + M[1][1]*v[1] + M[1][2]*v[2]
prod[2]=M[2][0]*v[0] + M[2][1]*v[1] + M[2][2]*v[2]

print("M: ", M)
print("v: ", v)
print("M*v: ", prod)

M:  [[1, 2, 3], [1, 2, 1], [1, 1, 3]]
v:  [10, 5, 10]
M*v:  [50, 30, 45]

Methods of the class list

The class list has some methods to operate on it. Recall from the lecture the following methods:

Note: Lists are mutable objects and therefore virtually all the previous methods (except count) do not have an output value, but they modify the list.

Some usage examples follow:

#A numeric list
A = [1, 2, 3]
print(A)
print("A has id:", id(A))
A.append(72) #appends one and only one object
print(A)
print("A has id:", id(A))
A.extend([1, 5, 124, 99]) #adds all these objects, one after the other.
print(A)
A.reverse()
print(A)
A.sort()
print(A)
print("Min value: ", A[0]) # In this simple case, could have used min(A)
print("Max value: ", A[-1]) #In this simple case, could have used max(A)
print("Number 1 appears:", A.count(1), " times")
print("While number 837: ", A.count(837))

print("\nDone with numbers, let's go strings...\n")
#A string list
fruits = ["apple", "banana", "pineapple", "cherry","pear", "almond", "orange"]
#Let's get a reverse lexicographic order:
print(fruits)
fruits.sort()
fruits.reverse()
print(fruits)
fruits.remove("banana")
print(fruits)
fruits.insert(5, "wild apple") #put wild apple after apple.
print(fruits)
print("\nSorted fruits:")
fruits.sort() # does not return anything. Modifies list!
print(fruits)

[1, 2, 3]
A has id: 140547045876232
[1, 2, 3, 72]
A has id: 140547045876232
[1, 2, 3, 72, 1, 5, 124, 99]
[99, 124, 5, 1, 72, 3, 2, 1]
[1, 1, 2, 3, 5, 72, 99, 124]
Min value:  1
Max value:  124
Number 1 appears: 2  times
While number 837:  0

Done with numbers, let's go strings...

['apple', 'banana', 'pineapple', 'cherry', 'pear', 'almond', 'orange']
['pineapple', 'pear', 'orange', 'cherry', 'banana', 'apple', 'almond']
['pineapple', 'pear', 'orange', 'cherry', 'apple', 'almond']
['pineapple', 'pear', 'orange', 'cherry', 'apple', 'wild apple', 'almond']

Sorted fruits:
['almond', 'apple', 'cherry', 'orange', 'pear', 'pineapple', 'wild apple']

Some things to remember

1. append and extend work quite differently:

A = [1, 2, 3]

A.extend([4, 5])
print(A)
B = [1, 2, 3]
B.append([4,5])
print(B)

[1, 2, 3, 4, 5]
[1, 2, 3, [4, 5]]

2. To remove an object it must exist:

A = [1,2,3, [[4],[5,6]], 8]
print(A)
A.remove(2)
print(A)
A.remove([[4],[5,6]])
print(A)
A.remove(7)

[1, 2, 3, [[4], [5, 6]], 8]
[1, 3, [[4], [5, 6]], 8]
[1, 3, 8]

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-8-cef337401de9> in <module>()
      5 A.remove([[4],[5,6]])
      6 print(A)
----> 7 A.remove(7)

ValueError: list.remove(x): x not in list

3. To sort a list, its elements must be sortable (i.e. homogeneous)!

A = [4,3, 1,7, 2]
print(A)
A.sort()
print(A)
A.append("banana")
print(A)
A.sort()
print(A)

[4, 3, 1, 7, 2]
[1, 2, 3, 4, 7]
[1, 2, 3, 4, 7, 'banana']

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-1-91b77adb823f> in <module>
      5 A.append("banana")
      6 print(A)
----> 7 A.sort()
      8 print(A)

TypeError: '<' not supported between instances of 'str' and 'int'

Important to remember:

Lists are mutable objects and this has some consequences! Since lists are mutable objects, they hold references to objects rather than objects.

Take a look at the following examples:

l1 = [1, 2]
l2 = [4, 3]
LL = [l1, l2]
print("l1:", l1)
print("l2:",l2)
print("LL:", LL)
l1.append(7)
print("\nAppending 7 to l1...")
print("l1:", l1)
print("LL now: ", LL)

LL[0][1] = -1
print("\nSetting LL[0][1]=-1...")
print("LL now:" , LL)
print("l1 now", l1)
#but the list can point also to a different object,
#without affecting the original list.
LL[0] = 100
print("\nSetting LL[0] = 100")
print("LL now:", LL)
print("l1 now", l1)

l1: [1, 2]
l2: [4, 3]
LL: [[1, 2], [4, 3]]

Appending 7 to l1...
l1: [1, 2, 7]
LL now:  [[1, 2, 7], [4, 3]]

Setting LL[0][1]=-1...
LL now: [[1, -1, 7], [4, 3]]
l1 now [1, -1, 7]

Setting LL[0] = 100
LL now: [100, [4, 3]]
l1 now [1, -1, 7]

Making copies

A = ["hi", "there"]
B = A
print("A:", A)
print("B:", B)
A.extend(["from", "python"])
print("A now: ", A)
print("B now: ", B)

print("\n---- copy example -------")
#Let's make a distinct copy of A.
C = A[:] #all the elements of A have been copied in C
print("C:", C)
A[3] = "java"
print("A now:", A)
print("C now:", C)

print("\n---- be careful though -------")
#Watch out though that...
D = [A, A]
E = D[:]
print("D:", D)
print("E:", E)

D[0][0] = "hello"
print("\nD now:", D)
print("E now:", E)
print("A now:", A)

A: ['hi', 'there']
B: ['hi', 'there']
A now:  ['hi', 'there', 'from', 'python']
B now:  ['hi', 'there', 'from', 'python']

---- copy example -------
C: ['hi', 'there', 'from', 'python']
A now: ['hi', 'there', 'from', 'java']
C now: ['hi', 'there', 'from', 'python']

---- be careful though -------
D: [['hi', 'there', 'from', 'java'], ['hi', 'there', 'from', 'java']]
E: [['hi', 'there', 'from', 'java'], ['hi', 'there', 'from', 'java']]

D now: [['hello', 'there', 'from', 'java'], ['hello', 'there', 'from', 'java']]
E now: [['hello', 'there', 'from', 'java'], ['hello', 'there', 'from', 'java']]
A now: ['hello', 'there', 'from', 'java']

Equality and identity

A = [1, 2, 3]
B = A
C = [1, 2, 3]
print("Is A equal to B?", A == B)
print("Is A actually B?", A is B)
print("Is A equal to C?", A == C)
print("Is A actually C?", A is C)
#in fact:
print("\nA's id:", id(A))
print("B's id:", id(B))
print("C's id:", id(C))
#just to confirm that:
A.append(4)
B.append(5)
print("\nA now: ", A)
print("B now: ", A)

Is A equal to B? True
Is A actually B? True
Is A equal to C? True
Is A actually C? False

A's id: 140546986339208
B's id: 140546986339208
C's id: 140546977413576

A now:  [1, 2, 3, 4, 5]
B now:  [1, 2, 3, 4, 5]

From strings to lists, the split method

Strings have a method split that can literally split the string at specific characters.

Example Recall the protein seen in the previous practical:

chain_a = “”“SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKM FCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVV RRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFR HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILT IITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKG EPHHELPPGSTKRALPNNT”“”

how can we split it into several lines?

chain_a = """SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKM
FCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVV
RRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFR
HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILT
IITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKG
EPHHELPPGSTKRALPNNT"""

lines = chain_a.split('\n')
print("Original sequence:")
print( chain_a, "\n") #some spacing to keep things clear
print("line by line:")
print("1st line:" ,lines[0])
print("2nd line:" ,lines[1])
print("3rd line:" ,lines[2])
print("4th line:" ,lines[3])
print("5th line:" ,lines[4])
print("6th line:" ,lines[5])

print("\nSplit the 1st line in correspondence to FRL:\n",lines[0].split("FRL"))

Original sequence:
SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKM
FCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVV
RRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFR
HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILT
IITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKG
EPHHELPPGSTKRALPNNT

line by line:
1st line: SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKM
2nd line: FCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVV
3rd line: RRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFR
4th line: HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILT
5th line: IITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKG
6th line: EPHHELPPGSTKRALPNNT

Split the 1st line in correspondence to FRL:
 ['SSSVPSQKTYQGSYG', 'GFLHSGTAKSVTCTYSPALNKM']

Note that in the last instruction, the substring FRL is disappeared (as happened to the newline).

And back to strings with the join method

Given a list, one can join the elements of the list together into a string by using the join method of the class string. The syntax is the following: str.join(list) which joins together all the elements in the list in a string separating them with the string str.

Example Given the list [‘Oct’, ‘5’, ‘2018’, ‘15:30’], let’s combine all its elements in a string joining the elements with a dash (“-“) and print them. Let’s finally join them with a tab (“\t”) and print them.

vals = ['Oct', '5th', '2018', '15:30']
print(vals)
myStr = "-".join(vals)
print("\n" + myStr)
myStr = "\t".join(vals)
print("\n" + myStr)

['Oct', '5th', '2018', '15:30']

Oct-5th-2018-15:30

Oct     5th     2018    15:30

Tuples

Tuples are the immutable version of lists (i.e. it is not possible to change their content without actually changing the object). They are sequential collections of objects, and elements of tuples are assumed to be in a particular order. They can hold heterogeneous information. They are defined with the brackets (). Some examples:

first_tuple = (1,2,3)
print(first_tuple)

second_tuple = (1,) #this contains one element only, but we need the comma!
var = (1) #This is not a tuple!!!
print(second_tuple, " type:", type(second_tuple))
print(var, " type:", type(var))
empty_tuple = () #fairly useless
print(empty_tuple, "\n")
third_tuple = ("January", 1 ,2007) #heterogeneous info
print(third_tuple)

days = (third_tuple,("February",2,1998), ("March",2,1978),("June",12,1978))
print(days, "\n")

#Remember tuples are immutable objects...
print("Days has id: ", id(days))
days = ("Mon","Tue","Wed","Thu","Fri","Sat","Sun")
#...hence reassignment creates a new object
print("Days now has id: ", id(days))

(1, 2, 3)
(1,)  type: <class 'tuple'>
1  type: <class 'int'>
()

('January', 1, 2007)
(('January', 1, 2007), ('February', 2, 1998), ('March', 2, 1978), ('June', 12, 1978))

Days has id:  140546977398040
Days now has id:  140546995078232

The following operators work on tuples and they behave exactly as on lists:

practical1 = ("Friday", "28/09/2018")
practical2 = ("Tuesday", "02/10/2018")
practical3 = ("Friday", "05/10/2018")

#A tuple containing 3 tuples
lectures = (practical1, practical2, practical3)
#One tuple only
mergedLectures = practical1 + practical2 + practical3

print("The first three lectures:\n", lectures, "\n")
print("mergedLectures:\n", mergedLectures)

#This returns the whole tuple
print("1st lecture was on: ", lectures[0], "\n")
#2 elements from the same tuple
print("1st lecture was on ", mergedLectures[0], ", ", mergedLectures[1], "\n")
# Return type is tuple!
print("3rd lecture was on: ", lectures[2])
#2 elements from the same tuple returned in tuple
print("3rd lecture was on ", mergedLectures[4:], "\n")

The first three lectures:
 (('Friday', '28/09/2018'), ('Tuesday', '02/10/2018'), ('Friday', '05/10/2018'))

mergedLectures:
 ('Friday', '28/09/2018', 'Tuesday', '02/10/2018', 'Friday', '05/10/2018')
1st lecture was on:  ('Friday', '28/09/2018')

1st lecture was on  Friday ,  28/09/2018

3rd lecture was on:  ('Friday', '05/10/2018')
3rd lecture was on  ('Friday', '05/10/2018')

The following methods are available for tuples:

practical1 = ("Friday", "28/09/2018")
practical2 = ("Tuesday", "02/10/2018")
practical3 = ("Friday", "05/10/2018")


mergedLectures = practical1 + practical2 + practical3  #One tuple only
print(mergedLectures.count("Friday"), " lectures were on Friday")
print(mergedLectures.count("Tuesday"), " lecture was on Tuesday")

print("Index:", practical2.index("Tuesday"))
print("Index:", practical2.index("Wednesday"))

2  lectures were on Friday
1  lecture was on Tuesday
Index: 0

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-16-fc543d476575> in <module>()
      9
     10 print("Index:", practical2.index("Tuesday"))
---> 11 print("Index:", practical2.index("Wednesday"))

ValueError: tuple.index(x): x not in tuple

Exercises

1. Given the following text string:

   """this is a text
   string on
   several lines that does not say anything."""
   

1. print it; b) print how many lines, words and characters it contains. Finally, c)sort the words alphabetically and print the first and the last in lexicographic order.

Show/Hide Solution

T = """this is a text
string on
several lines that does not say anything."""

#a) print it
print(T)
print("")
#b) print the lines, words and characters
lines = T.split('\n')

#NOTE: words are split by a space or a newline!

words = lines[0].split(' ') + lines[1].split(' ') + lines[2].split(' ')

num_chars = len(T)
print("Lines:", len(lines), "words:", len(words), "chars:", num_chars)
# alternative way for number of characters:
print("")
characters = list(T)
num_chars2 = len(characters)
print(characters)
print(num_chars2)

words.sort(reverse = True) #NOTE: it does not return ANYTHING!!!
print(words)
print("")
print("First word: ", words[-1])
print("Last word:", words[0])

this is a text
string on
several lines that does not say anything.

Lines: 3 words: 13 chars: 66

['t', 'h', 'i', 's', ' ', 'i', 's', ' ', 'a', ' ', 't', 'e', 'x', 't', '\n', 's', 't', 'r', 'i', 'n', 'g', ' ', 'o', 'n', '\n', 's', 'e', 'v', 'e', 'r', 'a', 'l', ' ', 'l', 'i', 'n', 'e', 's', ' ', 't', 'h', 'a', 't', ' ', 'd', 'o', 'e', 's', ' ', 'n', 'o', 't', ' ', 's', 'a', 'y', ' ', 'a', 'n', 'y', 't', 'h', 'i', 'n', 'g', '.']
66
['this', 'that', 'text', 'string', 'several', 'say', 'on', 'not', 'lines', 'is', 'does', 'anything.', 'a']

First word:  a
Last word: this

2. The variant calling format (VCF) is a format to represent structural variants of genomes (i.e. SNPs, insertions, deletions) . Each line of this format represents a variant, every piece of information within a line is separated by a tab (\t in python). The first 5 fields of this format report the chromosome (chr), the position (pos), the name of the variant (name), the reference allele (REF) and the alternative allele (ALT). Assuming to have a variable VCF defined containing the following three lines (representing three SNPs):

VCF = “”“MDC000001.124\t7112\tFB_AFFY_0000024\tG\tA MDC000002.328\t941\tFB_AFFY_0000144\tC\tT MDC000004.272\t2015\tFB_AFFY_0000222\tG\tA”“”

1. Store these three variants as a list of lists, where each one of the fields is kept separate
(e.g. the list should be similar to:
[[chr1,pos1,name1,ref1,alt1], [chr2, pos2, name2, ref2, alt2], ...] where all the elements
are as specified in the string VCF (note that "..." means that the list is not complete).

2. Print each variant changing its format in:  "name|chr|pos|REF/ALT".

Show/Hide Solution

VCF="""MDC000001.124\t7112\tFB_AFFY_0000024\tG\tA
MDC000002.328\t941\tFB_AFFY_0000144\tC\tT
MDC000004.272\t2015\tFB_AFFY_0000222\tG\tA"""

variants = VCF.split('\n')

variants[0] = variants[0].split('\t')
variants[1] = variants[1].split('\t')
variants[2] = variants[2].split('\t')

print(variants)

print(variants[0])
print(variants[1])
print(variants[2], "\n")

info = variants[0]
print(info[2] + "|" + info[0] + "|" + info[1] + "|" + info[3] +"/" + info[4])
info = variants[1]
print(info[2] + "|" + info[0] + "|" + info[1] + "|" + info[3] +"/" + info[4])
info = variants[2]
print(info[2] + "|" + info[0] + "|" + info[1] + "|" + info[3] +"/" + info[4])

[['MDC000001.124', '7112', 'FB_AFFY_0000024', 'G', 'A'], ['MDC000002.328', '941', 'FB_AFFY_0000144', 'C', 'T'], ['MDC000004.272', '2015', 'FB_AFFY_0000222', 'G', 'A']]
['MDC000001.124', '7112', 'FB_AFFY_0000024', 'G', 'A']
['MDC000002.328', '941', 'FB_AFFY_0000144', 'C', 'T']
['MDC000004.272', '2015', 'FB_AFFY_0000222', 'G', 'A']

FB_AFFY_0000024|MDC000001.124|7112|G/A
FB_AFFY_0000144|MDC000002.328|941|C/T
FB_AFFY_0000222|MDC000004.272|2015|G/A
FB_AFFY_0000024|MDC000001.124|7112|G/A
FB_AFFY_0000144|MDC000002.328|941|C/T
FB_AFFY_0000222|MDC000004.272|2015|G/A

3. Given the list L = [“walnut”, “eggplant”, “lemon”, “lime”, “date”, “onion”, “nectarine”, “endive” ]:

   1. Create another list (called newList) containing the first letter of each element of L
   (e.g newList =["w", "e", ...]).
   2. Add a space to newList at position 4 and append an exclamation mark (!) at the end.
   3. Print the list.
   4. Print the content of the list joining all the elements with an empty space
   (i.e. use the method join: "".join(newList) )
   

Show/Hide Solution

L = ["walnut", "eggplant", "lemon", "lime", "date", "onion", "nectarine", "endive" ]

newList = []
newList.append(L[0][0])
newList.append(L[1][0])
newList.append(L[2][0])
newList.append(L[3][0])
newList.append(L[4][0])
newList.append(L[5][0])
newList.append(L[6][0])
newList.append(L[7][0])

newList.insert(4," ")
newList.append("!")

print(newList)
print("\n", "".join(newList))

['w', 'e', 'l', 'l', ' ', 'd', 'o', 'n', 'e', '!']

 well done!

4. Fastq is a standard format for storing sequences and quality information. More information on the format can be found here. This format can be used to store sequencing information coming from the sequencer. Each entry represents a read (i.e. a sequence) and carries four different pieces of information. A sample entry is the following:

@HWI-ST1296:75:C3F7CACXX:1:1101:19142:14904 CCAACAACTTTGACGCTAAGGATAGCTCCATGGCAGCATATCTGGCACAA + FHIIJIJJGIJJJJJIHHHFFFFFEE:;CIDDDDDDDDDDDDEDDDDDDB”“”

where:

• 1. the first line is the read identifier starts with a “@” and carries several types of information regarding the instrument used for sequencing (the reported example is an illumina read - if you are interested, you can find more info on the format of the ID here.
• (ii). the second information is the sequence of the read (note that it can span several lines, not in our simple example though);
• 3. a “+” sign to mark the end of the sequence information (optionally the read identifier can be repeated);
• 4. the phred quality score of the read encoded as a text string. It must contain the same number of elements that are in the sequence. To decode each character into a the corresponding phred score, one needs to convert it into the unicode integer representation of it - 33. For example, the conversion of a character “I” in python can be done using the ord built in function in the following way: ord(“I”) - 33 = 40. Finally the phred score can be converted into probability of the base to be wrong with the following formula: \(P = 10^{-Q/10}\), where \(Q\) is the phred quality score.

Given the entry above:

1. Check that the ID starts with a @
2. Store the sequence as a string and as list where each element is one single base
(e.g. sequence =['T', 'A',...])
3. Store the quality as a list where each element is one single quality character
(e.g. qualChar = ['C', 'C', ...])
4. Check that the length of the sequence and quality are the same
(hint: use the sequence string, not the list)
5. Count how many times the sequence "TCCA" appears in the read
6. Retrieve the sub-list containing the quality values corresponding to the "TCCA" string
7. Convert each value in the list at point 6 in the corresponding probability of the base
being wrong

Show/Hide Solution

entry = """@HWI-ST1296:75:C3F7CACXX:1:1101:19142:14904
CCAACAACTTTGACGCTAAGGATAGCTCCATGGCAGCATATCTGGCACAA
+
FHIIJIJJGIJJJJJIHHHFFFFFEE:;CIDDDDDDDDDDDDEDDDDDDB
"""

print("Does header start with @?", entry.startswith("@"))
entryList = entry.split('\n')

sequence = list(entryList[1])
qualChar = list(entryList[3])


print("Sequence and quality have the same length:", len(sequence) == len(qualChar))
print("Sequence \"ACAA\" is present ", entryList[1].count("TCCA"), " times" )

pos = entryList[1].find("TCCA")

qVals = qualChar[pos:pos+4]
print("Sequence: ", entryList[1][pos:pos+4])
print("Quality: ", qVals)

phredS = []

phredS.append(ord(qVals[0]) - 33)
phredS.append(ord(qVals[1]) - 33)
phredS.append(ord(qVals[2]) - 33)
phredS.append(ord(qVals[3]) - 33)

print("Phred score:", phredS)

probVals = []
probVals.append(10**(0-phredS[0]/10))
probVals.append(10**(0-phredS[1]/10))
probVals.append(10**(0-phredS[2]/10))
probVals.append(10**(0-phredS[3]/10))

print("Error Probabilities:\n", probVals)

Does header start with @? True
Sequence and quality have the same length: True
Sequence "ACAA" is present  1  times
Sequence:  TCCA
Quality:  [':', ';', 'C', 'I']
Phred score: [25, 26, 34, 40]
Error Probabilities:
 [0.0031622776601683794, 0.0025118864315095794, 0.00039810717055349735, 0.0001]

5. Given the list L = [10, 60, 72, 118, 11, 71, 56, 89, 120, 175] find the min, max and median value (hint: sort it and extract the right values). Create a list with only the elements at even indexes (i.e. [10, 72, 11, ..], note that the “..” means that the list is not complete) and re-compute min, max and median values. Finally, re-do the same for the elements located at odd indexes (i.e. [60, 118,..]).

Show/Hide Solution

L = [10, 60, 72, 118, 11, 71, 56, 89, 120, 175]
Lodd = L[1::2] #get only odd-indexed elements
Leven = L[0::2] #get only even-indexed elements

print("original:" , L)
print("Lodd:", Lodd)
print("Leven:", Leven)
L.sort()
Lodd.sort()
Leven.sort()


print("sorted:  " , L)
print("sorted Lodd:  " , Lodd)
print("sorted Leven:  " , Leven)

print("L: Min: ", L[0], " Max." , L[-1], " Median: ", L[len(L) // 2])
print("Lodd: Min: ", Lodd[0], " Max." , Lodd[-1], " Median: ", Lodd[len(Lodd) // 2])
print("Leven: Min: ", Leven[0], " Max." , Leven[-1], " Median: ", Leven[len(Leven) // 2])

original: [10, 60, 72, 118, 11, 71, 56, 89, 120, 175]
Lodd: [60, 118, 71, 89, 175]
Leven: [10, 72, 11, 56, 120]
sorted:   [10, 11, 56, 60, 71, 72, 89, 118, 120, 175]
sorted Lodd:   [60, 71, 89, 118, 175]
sorted Leven:   [10, 11, 56, 72, 120]
L: Min:  10  Max. 175  Median:  72
Lodd: Min:  60  Max. 175  Median:  89
Leven: Min:  10  Max. 120  Median:  56

6. Given the string pets = “siamese cat,dog,songbird,guinea pig,rabbit,hampster” convert it into a list. Create then a tuple of tuples where each tuple has two information: the name of the pet and the length of the name. E.g. ((“dog”,3), ( “hampster”,8)). Print the tuple.

Show/Hide Solution

pets = "cat,dog,bird,guinea pig,rabbit,hampster"

pet_list = pets.split(',')

print(pet_list)

pet_tuples = ((pet_list[0], len(pet_list[0])),
              (pet_list[1], len(pet_list[1])),
              (pet_list[2], len(pet_list[2])),
              (pet_list[3], len(pet_list[3])),
              (pet_list[4], len(pet_list[4])),
              (pet_list[5], len(pet_list[5])))

print(pet_tuples)

['cat', 'dog', 'bird', 'guinea pig', 'rabbit', 'hampster']
(('cat', 3), ('dog', 3), ('bird', 4), ('guinea pig', 10), ('rabbit', 6), ('hampster', 8))

7. Given the string S=”apple|pear|apple|cherry|pear|apple|pear|pear|cherry|pear|strawberry”. Store the elements separated by the “|” in a list.
   1. How many elements does the list have?
   2. Knowing that the list created at the previous point has only four distinct elements (i.e. “apple”,”pear”,”cherry” and “strawberry”), create another list where each element is a tuple containing the name of the fruit and its multiplicity (that is how many times it appears in the original list). Ex. list_of_tuples = [(“apple”, 3), (“pear”, “5”),…]
   3. Print the content of each tuple in a separate line (ex. first line: apple is present 3 times)

Show/Hide Solution

S="apple|pear|apple|cherry|pear|apple|pear|pear|cherry|pear|strawberry"

Slist = S.split("|")
print(Slist)

appleT = ("apple", Slist.count("apple"))
pearT = ("pear", Slist.count("pear"))
cherryT = ("cherry", Slist.count("cherry"))
strawberryT = ("strawberry", Slist.count("strawberry"))
list_of_tuples =[appleT, pearT, cherryT, strawberryT]

print(list_of_tuples, "\n") #adding newline to separate elements

print(appleT[0], " is present ", appleT[1], " times")
print(pearT[0], " is present ", pearT[1], " times")
print(cherryT[0], " is present ", cherryT[1], " times")
print(strawberryT[0], " is present ", strawberryT[1], " times")

['apple', 'pear', 'apple', 'cherry', 'pear', 'apple', 'pear', 'pear', 'cherry', 'pear', 'strawberry']
[('apple', 3), ('pear', 5), ('cherry', 2), ('strawberry', 1)]

apple  is present  3  times
pear  is present  5  times
cherry  is present  2  times
strawberry  is present  1  times

8. Define three tuples representing points in the 3D space: A = (10,20,30), B = (1,72, 100) and C = (4, 9, 20).
   1. Compute the Euclidean distance between A and B (let’s call it AB), A and C (AC), B and C (BC) and print them. Remember that the distance \(d\) between two points \(X_1 = (x_1,y_1,z_1)\) and \(X_2 = (x_2,y_2,z_2)\) is \(d = \sqrt{(x_2-x_1)^2 + (y_2 - y_1)^2 + (z_2-z_1)^2}\). Hint: remember to import math to use the sqrt method.
   2. Create a point D multiplying every element of C by 10. (Hint: do not use C*10, as this will repeat C 10 times). And compute the distance AD, BD, CD.
   3. Answer to the following questions (writing a suitable boolean expression and printing the result):
      1. Is A closer to B than to C?
      2. Is A closer to C than to B or to D?
      3. Is B closer to A than to C to D?

Show/Hide Solution

import math

A = (10,20,30)
B = (1,72, 100)
C = (4,9,20)
D = (C[0]*10, C[1]*10, C[2]*10)

AB = math.sqrt( (B[0]-A[0])**2 + (B[1] - A[1])**2 + (B[2] - A[2])**2)
AC = math.sqrt( (C[0]-A[0])**2 + (C[1] - A[1])**2 + (C[2] - A[2])**2)
BC = math.sqrt( (C[0]-B[0])**2 + (C[1] - B[1])**2 + (C[2] - B[2])**2)
AD = math.sqrt( (D[0]-A[0])**2 + (D[1] - A[1])**2 + (D[2] - A[2])**2)
BD = math.sqrt( (D[0]-B[0])**2 + (D[1] - B[1])**2 + (D[2] - B[2])**2)
CD = math.sqrt( (D[0]-C[0])**2 + (D[1] - C[1])**2 + (D[2] - C[2])**2)

print("Distance AB: ", AB)
print("Distance AC: ", AC)
print("Distance AD: ", AD)
print("Distance BC: ", BC)
print("Distance BD: ", BD)
print("Distance CD: ", CD)

print("A is closer to B than to C: ", AB < AC)
print("A is closer to C than to B or D:", AC < AB and AC < AD)
print("B is closer to A than C to D:", AB < CD)

Distance AB:  87.66413177577246
Distance AC:  16.0312195418814
Distance AD:  186.27936010197158
Distance BC:  101.87246929372037
Distance BD:  108.83473710171766
Distance CD:  200.64147128647159
A is closer to B than to C:  False
A is closer to C than to B or D: True
B is closer to A than C to D: True

9. Given the matrix \(M =\begin{bmatrix}1 & 2 & 3\\ 4 & 5 & 6\\ 7 & 8 & 9\end{bmatrix}\) compute \(M^2 = \begin{bmatrix}1 & 2 & 3\\ 4 & 5 & 6\\ 7 & 8 & 9\end{bmatrix} \times \begin{bmatrix}1 & 2 & 3\\ 4 & 5 & 6\\ 7 & 8 & 9\end{bmatrix} = \begin{bmatrix}30 & 36 & 42\\ 66 & 81 & 96\\ 102 & 126 & 150\end{bmatrix}\)

Show/Hide Solution

M = [[1, 2, 3], [4, 5, 6], [7, 8, 9]]

Msq = [[0, 0, 0], [0, 0,0], [0, 0, 0]]# the output is initialized to the zero matrix
#Msq[i,j] is represented as Msq[i][j]
Msq[0][0] = M[0][0]*M[0][0] + M[0][1]*M[1][0] + M[0][2] * M[2][0]
Msq[0][1] = M[0][0]*M[0][1] + M[0][1]*M[1][1] + M[0][2] * M[2][1]
Msq[0][2] = M[0][0]*M[0][2] + M[0][1]*M[1][2] + M[0][2] * M[2][2]
Msq[1][0] = M[1][0]*M[0][0] + M[1][1]*M[1][0] + M[1][2] * M[2][0]
Msq[1][1] = M[1][0]*M[0][1] + M[1][1]*M[1][1] + M[1][2] * M[2][1]
Msq[1][2] = M[1][0]*M[0][2] + M[1][1]*M[1][2] + M[1][2] * M[2][2]
Msq[2][0] = M[2][0]*M[0][0] + M[2][1]*M[1][0] + M[2][2] * M[2][0]
Msq[2][1] = M[2][0]*M[0][1] + M[2][1]*M[1][1] + M[2][2] * M[2][1]
Msq[2][2] = M[2][0]*M[0][2] + M[2][1]*M[1][2] + M[2][2] * M[2][2]

print(Msq)

[[30, 36, 42], [66, 81, 96], [102, 126, 150]]

Practical 4

In this practical we will work with conditionals (branching) and loops.

Slides

The slides of the introduction can be found here: Intro

Execution flow

Recall from the lecture that there are at least three types of execution flows. Our statements can be simple and structured sequentially, when one instruction is executed right after the previous one, but some more complex flows involve conditional branching (when the portion of the code to be executed depends on the value of some condition), or loops when a portion of the code is executed multiple times until a certain condition becomes False.

These portions of code are generally called blocks and Python, unlike most of the programming languages, uses indentation (and some keywords like else, ‘:’, ‘next’, etc.) to define blocks.

Conditionals

We can use conditionals any time a decision needs to be made depending on the value of some condition. A block of code will be executed if the condition is evaluated to the boolean True and another one if the condition is evaluated to False.

The basic if - else statement

The basic syntax of conditionals is an if statement like:

if condition :

    #This is the True branch
    #do something

else:

    #This is the False branch (or else branch)
    #do something else

where condition is a boolean expression that tells the interpreter which of the two blocks should be executed. If and only if the condition is True the first branch is executed, otherwise execution goes to the second branch (i.e. the else branch). Note that the condition is followed by a “:” character and that the two branches are indented. This is the way Python uses to identify the block of instructions that belong to the same branch. The else keyword is followed by “:” and is not indented (i.e. it is at the same level of the if statement. There is no keyword at the end of the “else branch”, but indentation tells when the block of code is finished.

Example: Let’s get an integer from the user and test if it is even or odd, printing the result to the screen.

print("Dear user give me an integer:")
num = int(input())
res = ""
if num % 2 == 0:
    #The number is even
    res = "even"
else:
    #The number is odd
    res = "odd"

print("Number ", num, " is ", res)

Dear user give me an integer:
121
Number  121  is  odd

Note that the execution is sequential until the if keyword, then it branches until the indentation goes back to the same level of the if (i.e. the two branches rejoin at the print statement in the final line). Remember that the else branch is optional.

The if - elif - else statement

If statements can be chained in such a way that there are more than two possible branches to be followed. Chaining them with the if - elif - else statement will make execution follow only one of the possible paths.

The syntax is the following:

if condition :

    #This is branch 1
    #do something

elif condition1 :

    #This is branch 2
    #do something

elif condition2 :

    #This is branch 3
    #do something

else:

    #else branch. Executed if all other conditions are false
    #do something else

Note that branch 1 is executed if condition is True, branch 2 if and only if condition is False and condition1 is True, branch 3 if condition is False, condition 1 is False and condition2 is True. If all conditions are False the else branch is executed.

Example: The tax rate of a salary depends on the income. If the income is < 10000 euros, no tax is due, if the income is between 10000 euros and 20000 the tax rate is 25%, if between 20000 and 45000 it is 35% otherwise it is 40%. What is the tax due by a person earning 35000 euros per year?

income = 35000
rate = 0.0

if income < 10000:
    rate = 0
elif income < 20000:
    rate = 0.2
elif income < 45000:
    rate = 0.35
else:
    rate = 0.4

tax = income*rate

print("The tax due is ", tax, " euros (i.e ", rate*100, "%)")

The tax due is  12250.0  euros (i.e  35.0 %)

Note the difference in the two following cases:

#Example 1

val = 10

if val > 5:
    print("Value >5")
elif val > 5:
    print("I said value is >5!")
else:
    print("Value is <= 5")

#Example 2

val = 10

if(val > 5):
    print("\n\nValue is >5")

if(val > 5):
    print("I said Value is >5!!!")

Value >5


Value is >5
I said Value is >5!!!

Loops

Looping is the ability of repeating a specific block of code several times (i.e. until a specific condition is True or there are no more elements to process).

For loop

The for loop is used to loop over a collection of objects (e.g. a string, list, tuple, …). The basic syntax of the for loop is the following:

for elem in collection :
    #OK, do something with elem
    # instruction 1
    # instruction 2

the variable elem will get the value of each one of the elements present in collection one after the other. The end of the block of code to be executed for each element in the collection is again defined by indentation.

Depending on the type of the collection elem will get different values. Recall from the lecture that:

Let’s see this in action:

S = "Hi there from python"
Slist = S.split(" ")
Stuple = ("Hi","there","from","python")
print("String:", S)
print("List:", Slist)
print("Tuple:", Stuple)

#for loop on string
print("On strings:")
for c in S:
    print(c)

print("\nOn lists:")
#for loop on list
for item in Slist:
    print(item)

print("\nOn tuples:")
#for loop on list
for item in Stuple:
    print(item)

String: Hi there from python
List: ['Hi', 'there', 'from', 'python']
Tuple: ('Hi', 'there', 'from', 'python')
On strings:
H
i

t
h
e
r
e

f
r
o
m

p
y
t
h
o
n

On lists:
Hi
there
from
python

On tuples:
Hi
there
from
python

Looping over a range

It is possible to loop over a range of values with the pythom built-in function range. The range function accepts either two or three parameters (all of them are integers). Similarly to the slicing operator, it needs the starting point, end point and an optional step. Three distinct syntaxes are available:

range(E)        # ranges from 0 to E-1
range(S,E)      # ranges from S to E-1
range(S,E,step) # ranges from S to E-1 with +step jumps

Remember that S is included while E is excluded. Let’s see some examples.

Example: Given a list of integers, return a list with all the even numbers.

myList = [1, 7, 9, 121, 77, 82]
onlyEven = []

for i in range(0, len(myList)):  #this is equivalent to range(len(myList)):
    if( myList[i] % 2 == 0 ):
        onlyEven.append(myList[i])

print("original list:", myList)
print("only even numbers:", onlyEven)

original list: [1, 7, 9, 121, 77, 82]
only even numbers: [82]

Example: Store in a list the multiples of 19 between 1 and 100.

multiples = []

for i in range(19,101,19):
    multiples.append(i)

print("multiples of 19: ", multiples)

#alternative way:
multiples = []
for i in range(1, (100//19) + 1):
    multiples.append(i*19)
print("multiples of 19:", multiples)

multiples of 19:  [19, 38, 57, 76, 95]
multiples of 19: [19, 38, 57, 76, 95]

Note: range works differently in Python 2.x and 3.x

In Python 3 the range function returns an iterator rather storing the entire list.

#Check out the difference:
print(range(0,10))

print(list(range(0,10)))

range(0, 10)
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9]

Example: Let’s consider the two DNA strings s1 = “ATACATATAGGGCCAATTATTATAAGTCAC” and s2 = “CGCCACTTAAGCGCCCTGTATTAAAGTCGC” that have the same length. Let’s create a third string \(out\) such that \(out[i]\) is \("|"\) if \(s1[i]==s2[i]\), \("\ "\) otherwise.

s1 = "ATACATATAGGGCCAATTATTATAAGTCAC"
s2 = "CGCCACTTAAGCGCCCTGTATTAAAGTCGC"

outSTR = ""
for i in range(len(s1)):
    if(s1[i] == s2[i]):
        outSTR = outSTR + "|"
    else:
        outSTR = outSTR + " "

print(s1)
print(outSTR)
print(s2)

ATACATATAGGGCCAATTATTATAAGTCAC
   ||  || |  |  |   |  ||||| |
CGCCACTTAAGCGCCCTGTATTAAAGTCGC

Nested for loops

In some occasions it is useful to nest one (or more) for loops into another one. The basic syntax is:

for i in collection:
    for j in another_collection:
        #do some stuff with i and j

Example:

Given the matrix \(\begin{bmatrix}1 & 2 & 3\\4 & 5 & 6\\7 & 8 & 9\end{bmatrix}\) stored as a list of lists (i.e. matrix = [[1, 2, 3], [4, 5, 6], [7, 8, 9]].

Print it out as: \(\begin{matrix}1 & 2 & 3\\4 & 5 & 6\\7 & 8 & 9\end{matrix}\)

matrix = [[1, 2, 3], [4, 5, 6], [7, 8, 9]]

for i in range(len(matrix)):
    line = ""
    for j in range(len(matrix[i])):
        line = line + str(matrix[i][j]) + " " #note int --> str conversion!
    print(line)

1 2 3
4 5 6
7 8 9

While loops

The for loop is great when we have to iterate over a finite sequence of elements. But when one needs to loop until a specific condition holds true, another construct must be used: the while statement. The loop will end when the condition becomes false.

The basic syntax is the following:

while condition:

    #do something
    #update the value of condition

An example follows:

i = 0
while (i < 5):
    print("i now is:", i)
    i = i + 1 #THIS IS VERY IMPORTANT!

i now is: 0
i now is: 1
i now is: 2
i now is: 3
i now is: 4

Note that if condition is false at the beginning the block of code is never executed.

Note: The loop will continue until condition holds true and the only code executed is the block defined through the indentation. This block of code must update the value of condition otherwise the interpreter will get stuck in the loop and will never exit.

We can combine for loops and while loops one into the code block of the other:

for i in range(1,10):                       # or without string output
    j = 1                                   # for i in range(1,10):
    output = ""                             #     j = 1
    while(j<= i):                           #     while(j<=i):
        output = str(j) + " " + output      #         print(j, end = " ")
        j = j + 1                           #         j = j + 1
    print(output)                           #     print("")

1
2 1
3 2 1
4 3 2 1
5 4 3 2 1
6 5 4 3 2 1
7 6 5 4 3 2 1
8 7 6 5 4 3 2 1
9 8 7 6 5 4 3 2 1

Exercises

1. Given the integer 134479170, print if it is divisible for the numbers from 2 to 16. Hint: use for and if.

Show/Hide Solution

val = 134479170
flag = False

for divisor in range(2,17):
    if val % divisor == 0:
        print(val, " can be divided by ", divisor)
        print("\t", divisor, "*", val//divisor, "=", val )
        flag = True

if flag == False:
    print("Sorry, could not find divisors")

134479170  can be divided by  2
         2 * 67239585 = 134479170
134479170  can be divided by  3
         3 * 44826390 = 134479170
134479170  can be divided by  5
         5 * 26895834 = 134479170
134479170  can be divided by  6
         6 * 22413195 = 134479170
134479170  can be divided by  7
         7 * 19211310 = 134479170
134479170  can be divided by  9
         9 * 14942130 = 134479170
134479170  can be divided by  10
         10 * 13447917 = 134479170
134479170  can be divided by  14
         14 * 9605655 = 134479170
134479170  can be divided by  15
         15 * 8965278 = 134479170

2. Given the DNA string “GATTACATATATCAGTACAGATATATACGCGCGGGCTTACTATTAAAAACCCC”, write a Python script that reverse-complements it. To reverse-complement a string of DNA, one needs to replace and A with T, T with A, C with G and G with C, while any other character is complemented in N. Finally, the sequence has to be reversed (e.g. the first base becomes the last). For example, ATCG becomes CGAT.

Show/Hide Solution

DNA = "GATTACATATATCAGTACAGATATATACGCGCGGGCTTACTATTAAAAACCCC"

revComp = ""
for base in DNA:
    if base == "T":
        revComp = "A"+ revComp
    elif base == "A":
        revComp = "T"+ revComp
    elif base == "C":
        revComp = "G"+ revComp
    elif base == "G":
        revComp = "C" + revComp
    else:
        revComp = "N" + revComp

print("5'-", DNA, "-3'")
print("3'-", revComp, "-5'")

5'- GATTACATATATCAGTACAGATATATACGCGCGGGCTTACTATTAAAAACCCC -3'
3'- GGGGTTTTTAATAGTAAGCCCGCGCGTATATATCTGTACTGATATATGTAATC -5'

""" Another solution"""

DNA = "GATTACATATATCAGTACAGATATATACGCGCGGGCTTACTATTAAAAACCCC"


dna_list = list(DNA)
print(dna_list)
compl = []
for el in dna_list:
    if el == 'A':
        compl.append('T')
    elif el == 'T':
        compl.append('A')
    elif el == 'C':
        compl.append('G')
    elif el == 'G':
        compl.append('C')
    else:
        compl.append('N')
print(compl)
compl.reverse()
print(compl)
print("".join(compl))

['G', 'A', 'T', 'T', 'A', 'C', 'A', 'T', 'A', 'T', 'A', 'T', 'C', 'A', 'G', 'T', 'A', 'C', 'A', 'G', 'A', 'T', 'A', 'T', 'A', 'T', 'A', 'C', 'G', 'C', 'G', 'C', 'G', 'G', 'G', 'C', 'T', 'T', 'A', 'C', 'T', 'A', 'T', 'T', 'A', 'A', 'A', 'A', 'A', 'C', 'C', 'C', 'C']
['C', 'T', 'A', 'A', 'T', 'G', 'T', 'A', 'T', 'A', 'T', 'A', 'G', 'T', 'C', 'A', 'T', 'G', 'T', 'C', 'T', 'A', 'T', 'A', 'T', 'A', 'T', 'G', 'C', 'G', 'C', 'G', 'C', 'C', 'C', 'G', 'A', 'A', 'T', 'G', 'A', 'T', 'A', 'A', 'T', 'T', 'T', 'T', 'T', 'G', 'G', 'G', 'G']
['G', 'G', 'G', 'G', 'T', 'T', 'T', 'T', 'T', 'A', 'A', 'T', 'A', 'G', 'T', 'A', 'A', 'G', 'C', 'C', 'C', 'G', 'C', 'G', 'C', 'G', 'T', 'A', 'T', 'A', 'T', 'A', 'T', 'C', 'T', 'G', 'T', 'A', 'C', 'T', 'G', 'A', 'T', 'A', 'T', 'A', 'T', 'G', 'T', 'A', 'A', 'T', 'C']
GGGGTTTTTAATAGTAAGCCCGCGCGTATATATCTGTACTGATATATGTAATC

3. Write a python script that creates the following pattern:

+
++
+++
++++
+++++
++++++
+++++++ <-- 7
++++++
+++++
++++
+++
++
+

Show/Hide Solution

outStr = ""
for i in range(0,7):
    outStr = ""
    for j in range(0,i+1):
        outStr = outStr + "+"
    if(i == 6):
        outStr = outStr + " <-- 7"

    print(outStr)

for i in range(1,7):
    outStr = ""
    for j in range(0, 7-i):
        outStr = outStr + "+"
    print(outStr)

+
++
+++
++++
+++++
++++++
+++++++ <-- 7
++++++
+++++
++++
+++
++
+

4. Count how many of the first 100 integers are divisible by 2, 3, 5, 7 but not by 10 and print these counts. Be aware that a number can be divisible by more than one of these numbers (e.g. 6) and therefore it must be counted as divisible by all of them (e.g. 6 must be counted as divisible by 2 and 3).

Show/Hide Solution

cnts = [0,0,0,0] #cnts[0] counts for 2, cnts[1] counts for 3...
vals = [2,3,5,7]
for i in range(1,101):
    if ( i % 2 == 0 and i % 10 != 0 ):
        cnts[0] = cnts[0] + 1

    if ( i % 3 == 0 and i % 10 != 0):
        cnts[1] = cnts[1] + 1

    if ( i % 5 == 0 and i % 10 != 0):
        cnts[2] = cnts[2] + 1

    if ( i % 7 == 0 and i % 10 != 0):
        cnts[3] = cnts[3] + 1

for i in range(0, len(cnts)):
    print(cnts[i], " numbers are divisible by ", vals[i], "(but not 10) in the first 100")

40  numbers are divisible by  2 (but not 10) in the first 100
30  numbers are divisible by  3 (but not 10) in the first 100
10  numbers are divisible by  5 (but not 10) in the first 100
13  numbers are divisible by  7 (but not 10) in the first 100

5. Given the following fastq entry:

@HWI-ST1296:75:C3F7CACXX:1:1101:19142:14904
CCAACAACTTTGACGCTAAGGATAGCTCCATGGCAGCATATCTGGCACAA
+
FHIIJIJJGIJJJJJ1HHHFFFFFEE:;CIDDDDDDDDDDDDEDDD-./0

Store the sequence and the quality in two strings. Create a list with all the quality phred scores (given a quality character “X” the phred score is: ord(“X”) -33. Finally print all the bases that have quality lower than 25, reporting the base, its position, quality character and phred score. Output example: base: C index: 14 qual:1 phred: 16).

Show/Hide Solution

entry = """@HWI-ST1296:75:C3F7CACXX:1:1101:19142:14904
CCAACAACTTTGACGCTAAGGATAGCTCCATGGCAGCATATCTGGCACAA
+
FHIIJIJJGIJJJJJ1HHHFFFFFEE:;CIDDDDDDDDDDDDEDDD-./0"""

lines = entry.split("\n")
seq = lines[1]
qual = lines[3]

phredScores = []
for i in range(len(qual)):
    phredScores.append(ord(qual[i]) - 33)


for i in range(len(seq)):
    if(phredScores[i] <25):
        print("base:",seq[i],"index:",i,"qual:",qual[i],"phredScore:",phredScores[i])

base: C index: 15 qual: 1 phredScore: 16
base: A index: 46 qual: - phredScore: 12
base: C index: 47 qual: . phredScore: 13
base: A index: 48 qual: / phredScore: 14
base: A index: 49 qual: 0 phredScore: 15

6. Given the following sequence:

AUGCUGUCUCCCUCACUGUAUGUAAAUUGCAUCUAGAAUAGCA
UCUGGAGCACUAAUUGACACAUAGUGGGUAUCAAUUAUUA
UUCCAGGUACUAGAGAUACCUGGACCAUUAACGGAUAAAU
AGAAGAUUCAUUUGUUGAGUGACUGAGGAUGGCAGUUCCU
GCUACCUUCAAGGAUCUGGAUGAUGGGGAGAAACAGAGAA
CAUAGUGUGAGAAUACUGUGGUAAGGAAAGUACAGAGGAC
UGGUAGAGUGUCUAACCUAGAUUUGGAGAAGGACCUAGAA
GUCUAUCCCAGGGAAAUAAAAAUCUAAGCUAAGGUUUGAG
GAAUCAGUAGGAAUUGGCAAAGGAAGGACAUGUUCCAGAU
GAUAGGAACAGGUUAUGCAAAGAUCCUGAAAUGGUCAGAG
CUUGGUGCUUUUUGAGAACCAAAAGUAGAUUGUUAUGGAC
CAGUGCUACUCCCUGCCUCUUGCCAAGGGACCCCGCCAAG
CACUGCAUCCCUUCCCUCUGACUCCACCUUUCCACUUGCC
CAGUAUUGUUGGUGU

Considering the genetic code and the first forward open reading frame (i.e. the string as it is remembering to remove newlines).

1. How many start codons are present in the whole sequence (i.e. AUG)?
2. How many stop codons (i.e. UAA,UAG, UGA)
3. Create another string in which any codon with except the start and stop codons are substituted with “—” and print the resulting string.

Show/Hide Solution

seq ="""AUGCUGUCUCCCUCACUGUAUGUAAAUUGCAUCUAGAAUAGCA
UCUGGAGCACUAAUUGACACAUAGUGGGUAUCAAUUAUUA
UUCCAGGUACUAGAGAUACCUGGACCAUUAACGGAUAAAU
AGAAGAUUCAUUUGUUGAGUGACUGAGGAUGGCAGUUCCU
GCUACCUUCAAGGAUCUGGAUGAUGGGGAGAAACAGAGAA
CAUAGUGUGAGAAUACUGUGGUAAGGAAAGUACAGAGGAC
UGGUAGAGUGUCUAACCUAGAUUUGGAGAAGGACCUAGAA
GUCUAUCCCAGGGAAAUAAAAAUCUAAGCUAAGGUUUGAG
GAAUCAGUAGGAAUUGGCAAAGGAAGGACAUGUUCCAGAU
GAUAGGAACAGGUUAUGCAAAGAUCCUGAAAUGGUCAGAG
CUUGGUGCUUUUUGAGAACCAAAAGUAGAUUGUUAUGGAC
CAGUGCUACUCCCUGCCUCUUGCCAAGGGACCCCGCCAAG
CACUGCAUCCCUUCCCUCUGACUCCACCUUUCCACUUGCC
CAGUAUUGUUGGUG"""

seq = seq.replace("\n","")


countStart = 0
countEnd = 0

newSeq = ""
i = 0
while i < len(seq):
    codon = seq[i:i+3]
    if(codon == "AUG"):
            countStart = countStart + 1

    elif (codon == "UAA" or codon == "UAG" or codon == "UGA"):
        countEnd = countEnd + 1
    else:
        codon = "---"

    newSeq = newSeq + codon
    i = i + 3


print("\nNumber of start codons:", countStart)
print("Number of end codons:", countEnd)
print("\n")
print(seq)
print("\n")
print(newSeq)

Number of start codons: 2
Number of end codons: 12


AUGCUGUCUCCCUCACUGUAUGUAAAUUGCAUCUAGAAUAGCAUCUGGAGCACUAAUUGACACAUAGUGGGUAUCAAUUAUUAUUCCAGGUACUAGAGAUACCUGGACCAUUAACGGAUAAAUAGAAGAUUCAUUUGUUGAGUGACUGAGGAUGGCAGUUCCUGCUACCUUCAAGGAUCUGGAUGAUGGGGAGAAACAGAGAACAUAGUGUGAGAAUACUGUGGUAAGGAAAGUACAGAGGACUGGUAGAGUGUCUAACCUAGAUUUGGAGAAGGACCUAGAAGUCUAUCCCAGGGAAAUAAAAAUCUAAGCUAAGGUUUGAGGAAUCAGUAGGAAUUGGCAAAGGAAGGACAUGUUCCAGAUGAUAGGAACAGGUUAUGCAAAGAUCCUGAAAUGGUCAGAGCUUGGUGCUUUUUGAGAACCAAAAGUAGAUUGUUAUGGACCAGUGCUACUCCCUGCCUCUUGCCAAGGGACCCCGCCAAGCACUGCAUCCCUUCCCUCUGACUCCACCUUUCCACUUGCCCAGUAUUGUUGGUG


AUG------------------------------UAG---------------------UGA---------------------------------UAG---------------UAA------------------------UGA------------------------------------------UGA------------------------UGA---------------------------------UAG------UAA------------------------------------------------------UAA---------------UAG------------------------------------------------------------AUG---------------------------------------------------------------------------------------------------------UGA---------------------------------

7. Playing time! Write a python scripts that:
   1. Picks a random number from 1 to 10, with: import random myInt = random.randint(1,10)
   2. Asks the user to guess a number and checks if the user has guessed the right one
   3. If the guess is right the program will stop with a congratulation message
   4. If the guess is wrong the program will continue asking a number, reporting the numbers already guessed (hint: store them in a list and print it).
   5. Modify the program to notify the user if he/she inputs the same number more than once.

Show/Hide Solution

import random
myInt = random.randint(1,10)
guessedNumbers = []

found = False
while (found == False):
    userInt = int(input("Guess a number from 1 to 10: "))
    if(userInt == myInt):
        print("Congratulations. The number I guessed was ", myInt)
        found = True
    else:
        if(userInt in guessedNumbers):
            print("You already guessed ", userInt)
        else:
            guessedNumbers.append(userInt)
        guessedNumbers.sort()
        print("Nope, try again. So far you guessed: ", guessedNumbers)

Guess a number from 1 to 10: 7
Nope, try again. So far you guessed:  [7]
Guess a number from 1 to 10: 5
Nope, try again. So far you guessed:  [5, 7]
Guess a number from 1 to 10: 2
Nope, try again. So far you guessed:  [2, 5, 7]
Guess a number from 1 to 10: 3
Congratulations. The number I guessed was  3

Practical 5

In this practical we will add some information on loops and introduce dictionaries.

Slides

The slides of the introduction can be found here: Intro

More on loops

As seen in the previous practical and in the lecture, there are three different ways of execution flow:

We have already seen the if, for and while loops and their variants. The code block of each of these statements is defined by the indentation (i.e. spacing).

Ternary operator

In some cases it is handy to be able to initialize a variable depending on the value of another one.

Example: The discount rate applied to a purchase depends on the amount of the sale. Create a variable discount setting its value to 0 if the variable amount is lower than 100 euros, to 10% if it is higher.

amount = 110
discount = 0

if(amount >100):
    discount = 0.1
else:
    discount = 0 # not necessary

print("Total amount:", amount, "discount:", discount)

Total amount: 110 discount: 0.1

The previous code can be written more coincisely as:

amount = 110
discount = 0.1 if amount > 100 else 0
print("Total amount:", amount, "discount:", discount)

Total amount: 110 discount: 0.1

The basic syntax of the ternary operator is:

variable = value if condition else other_value

meaning that the variable is initialized to value if the condition holds, otherwise to other_value.

Python also allows in line operations separated by a “;”

a = 10; b = a + 1; c = b +2
print(a,b,c)

10 11 13

Note: Although the ternary operator and in line operations are sometimes useful and less verbose than the explicit definition, they are considered “non-pythonic” and advised against.

Break and continue

Sometimes it is useful to skip an entire iteration of a loop or end the loop before its supposed end. This can be achieved with two different statements: continue and break.

Continue statement

Within a for or while loop, continue makes the interpreter skip that iteration and move to the next.

Example: Print all the odd numbers from 1 to 20.

#Two equivalent ways
#1. Testing remainder == 1
for i in range(21):
    if(i % 2 == 1):
        print(i, end = " ")

print("")

#2. Skipping if remainder == 0 in for
for i in range(21):
    if(i % 2 == 0):
        continue
    print(i, end = " ")

1 3 5 7 9 11 13 15 17 19
1 3 5 7 9 11 13 15 17 19

Continue can be used also within while loops but we need to be careful to update the value of the variable before reaching the continue statement or we will get stuck in never-ending loops. Example: Print all the odd numbers from 1 to 20.

#Wrong code:
i = 0
while (i < 21):
    if(i % 2 == 0):
        continue
    print(i, end = " ")
    i = i + 1 # NEVER EXECUTED IF i % 2 == 0!!!!

a possible correct solution using while:

i = -1
while( i< 20):       #i is incremented in the loop, so 20!!!
    i = i + 1        #the variable is updated no matter what
    if(i % 2 == 0 ):
        continue
    print(i, end = " ")

1 3 5 7 9 11 13 15 17 19

Break statement

Within a for or while loop, break makes the interpreter exit the loop and continue with the sequential execution. Sometimes it is useful to get out of the loop if to complete our task we do not need to get to the end of the loop.

Example: Given the following list of integers [1,5,6,4,7,1,2,3,7] print them until a number already printed is found.

L = [1,5,6,4,7,1,2,3,7]
found = []
for i in L:
    if(i in found):
        break

    found.append(i)
    print(i, end = " ")

1 5 6 4 7

Example: Pick a random number from 1 and 50 and count how many times it takes to randomly choose number 27. Limit the number of random picks to 40 (i.e. if more than 40 picks have been done and 27 has not been found exit anyway with a message).

import random

iterations = 1
picks = []
while(iterations <= 40):
    pick = random.randint(1,50)
    picks.append(pick)

    if(pick == 27):
        break
    iterations += 1

if(iterations == 41):
    print("Sorry number 27 was never found!")
else:
    print("27 found in ", iterations, "iterations")

print(picks)

27 found in  7 iterations
[30, 29, 16, 3, 42, 1, 27]

An alternative way without using the break statement makes use of a flag variable (that when changes value will make the loop end):

import random
found = False # This is called flag
iterations = 1
picks = []
while iterations <= 40 and found == False: #the flag is used to exit
    pick = random.randint(1,50)
    picks.append(pick)
    if pick == 27:
        found = True     #update the flag, will exit at next iteration
    iterations += 1

if iterations == 41 and not found:
    print("Sorry number 27 was never found!")
else:
    print("27 found in ", iterations -1, "iterations")

print(picks)

27 found in  20 iterations
[29, 13, 17, 14, 45, 21, 39, 26, 34, 17, 23, 10, 49, 13, 39, 6, 4, 2, 22, 27]

List comprehension

List comprehension is a quick way of creating a list. The resulting list is normally obtained by applying a function or a method to the elements of another list that remains unchanged.

The basic syntax is:

new_list = [ some_function (x) for x in start_list]

or

new_list = [ x.some_method() for x in start_list]

List comprehension can also be used to filter elements of a list and produce another list as sublist of the first one (remember that the original list is not changed).

In this case the syntax is:

new_list = [ some_function (x) for x in start_list if condition]

or

new_list = [ x.some_method() for x in start_list if condition]

where the element x in start_list becomes part of new_list if and only if the condition holds True.

Let’s see some examples:

Example: Given a list of strings [“hi”, “there”, “from”, “python”] create a list with the length of the corresponding element (i.e. the one with the same index).

elems = ["hi", "there", "from", "python"]

newList = [len(x) for x in elems]

for i in range(0,len(elems)):
    print(elems[i], " has length ", newList[i])

hi  has length  2
there  has length  5
from  has length  4
python  has length  6

Example: Given a list of strings [“dog”, “cat”, “rabbit”, “guinea pig”, “hamster”, “canary”, “goldfish”] create a list with the elements starting with a “c” or “g”.

pets = ["dog", "cat", "rabbit", "guinea pig", "hamster", "canary", "goldfish"]

cg_pets = [x for x in pets if x.startswith("c") or x.startswith("g")]

print("Original:")
print(pets)
print("Filtered:")
print(cg_pets)

Original:
['dog', 'cat', 'rabbit', 'guinea pig', 'hamster', 'canary', 'goldfish']
Filtered:
['cat', 'guinea pig', 'canary', 'goldfish']

Example: Create a list with all the numbers divisible by 17 from 1 to 200.

values = [ x for x in range(1,200) if x % 17 == 0]
print(values)

[17, 34, 51, 68, 85, 102, 119, 136, 153, 170, 187]

Example: Transpose the matrix \(\begin{bmatrix}1 & 10\\2 & 20\\3 & 30\\4 & 40\end{bmatrix}\) stored as a list of lists (i.e. matrix = [[1, 10], [2,20], [3,30], [4,40]]). The output matrix should be: \(\begin{bmatrix}1 & 2 & 3 & 4\\10 & 20 & 30 & 40\end{bmatrix}\), represented as [[1, 2, 3, 4], [10, 20, 30, 40]]

matrix = [[1, 10], [2,20], [3,30], [4,40]]
print(matrix)
transpose = [[row[i] for row in matrix] for i in range(2)]
print (transpose)

[[1, 10], [2, 20], [3, 30], [4, 40]]
[[1, 2, 3, 4], [10, 20, 30, 40]]

Example: Given the list: [“Hotel”, “Icon”,” Bus”,”Train”, “Hotel”, “Eye”, “Rain”, “Elephant”] create a list with all the first letters.

myList = ["Hotel", "Icon"," Bus","Train", "Hotel", "Eye", "Rain", "Elephant"]
initials = [x[0] for x in myList]

print(myList)
print(initials)
print("".join(initials))

['Hotel', 'Icon', ' Bus', 'Train', 'Hotel', 'Eye', 'Rain', 'Elephant']
['H', 'I', ' ', 'T', 'H', 'E', 'R', 'E']
HI THERE

Dictionaries

A dictionary is a map between one object, the key, and another object, the value. Dictionaries are mutable objects and contain sequences of mappings key –> object but there is not specific ordering among them. Dictionaries are defined using the curly braces {key1 : value1, key2 : value2} and : to separate keys from values.

Some examples on how to define dictionaries follow:

first_dict = {"one" : 1, "two": 2, "three" : 3, "four" : 4}
print("First:", first_dict)

empty_dict = dict()
print("Empty:",empty_dict)

second_dict = {1 : "one", 2 : "two", "three" :3 } #BAD IDEA BUT POSSIBLE!!!
print(second_dict)

third_dict = dict(zip(["one","two","three","four"],[1,2,3,4]))
print(third_dict)
print(first_dict == third_dict)

First: {'one': 1, 'two': 2, 'three': 3, 'four': 4}
Empty: {}
{1: 'one', 2: 'two', 'three': 3}
{'one': 1, 'two': 2, 'three': 3, 'four': 4}
True

Note that there is no ordering of the keys, and that the order in which they have been inserted is not preserved. Moreover, keys and values can be dishomogeneous (e.g. keys strings and values integers). An interesting case is third_dict where the function zip followed by dict is used to map the keys of the first list into the values present in the second.

Note that keys can be dishomogeneous, even though this is a bad idea normally. The only requirement for the keys is that they must be immutable objects. Trying to use a mutable object as a key will make the interpreter crash with the error: unhashable type. Finally, keys must be unique. We cannot associate more than one value to the same key.

a = (1,2,3) #a,b are tuples: hence immutable
b = (1,3,5)

my_dict = {a : 6, b : 9 }
print(my_dict)

c = [1,2,3] #c,d are lists: hence mutable
d = [1,3,5]

dict2 = {c : 6, d : 9}
print(dict2)

{(1, 2, 3): 6, (1, 3, 5): 9}

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-21-0fe98c7f5acd> in <module>
      8 d = [1,3,5]
      9
---> 10 dict2 = {c : 6, d : 9}
     11 print(dict2)

TypeError: unhashable type: 'list'

Functions working on dictionaries

As for the other data types, python provides several operators that can be applied to dictionaries. The following operators are available and they basically work as in lists. The only exception being that the operator in checks whether the specified object is present among the keys.

Some usage examples follow:

myDict = {"one" : 1, "two" : 2, "twentyfive" : 25}

print(myDict)
myDict["ten"] = 10
myDict["twenty"] = 20
print(myDict)
myDict["ten"] = "10-again"
print(myDict)
print("The dictionary has ", len(myDict), " elements")
print("The value of \"ten\" is:", myDict["ten"])
print("The value of \"two\" is:", myDict["two"])

print("Is \"twentyfive\" in dictionary?", "twentyfive" in myDict)
print("Is \"seven\" in dictionary?", "seven" in myDict)

{'one': 1, 'two': 2, 'twentyfive': 25}
{'one': 1, 'two': 2, 'twentyfive': 25, 'ten': 10, 'twenty': 20}
{'one': 1, 'two': 2, 'twentyfive': 25, 'ten': '10-again', 'twenty': 20}
The dictionary has  5  elements
The value of "ten" is: 10-again
The value of "two" is: 2
Is "twentyfive" in dictionary? True
Is "seven" in dictionary? False

Dictionary methods

Recall what seen in the lecture, the following methods are available for dictionaries:

These methods are new to dictionaries and can be used to loop through the elements in them.

ERRATUM: dict.keys() returns a dict_keys object not a list. To cast it to list, we need to call list(dict.keys()). The same applies to dict.values() that returns a dict_values object that needs conversion to a list with list(dict.values()).

Example Given the protein sequence below, store in a dictionary all the aminoacids present and count how many times they appear. Finally print out the stats (e.g. how many amino-acids are present, the most frequent, the least frequent and the frequency of all of them in alphabetical order).

>sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinase catalytic subunit alpha
MGNAAAAKKGSEQESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVML
VKHMETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMV
MEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGY
IQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFF
ADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFAT
TDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF

protein = """MGNAAAAKKGSEQESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVML
VKHMETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMV
MEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGY
IQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFF
ADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFAT
TDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF"""

protein = protein.replace("\n","")

print(protein)

amino_acids = dict()

for a in protein:
    if( a in amino_acids):
        amino_acids[a] = amino_acids[a] + 1
    else:
        amino_acids[a] = 1


num_aminos = len(amino_acids)

print("The number of amino-acids present is ", num_aminos)
#let's get all aminoacids
#and sort them alphabetically
a_keys = list(amino_acids.keys())

a_keys.sort()

mostF = {"frequency" : 0, "aminoacid" : "-"}
leastF = {"frequency" : len(protein), "aminoacid" : "-"}

for a in a_keys:
    freq = amino_acids[a]
    if(mostF["frequency"] < freq):
        mostF["frequency"] = freq
        mostF["aminoacid"] = a

    if(leastF["frequency"] > freq):
        leastF["frequency"] = freq
        leastF["aminoacid"] = a
    print(a, " is present", freq, "times")

print("Amino", leastF["aminoacid"], "has the lowest freq. (",leastF["frequency"],")")
print("Amino", mostF["aminoacid"], "has the highest freq. (",mostF["frequency"],")")

MGNAAAAKKGSEQESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVMLVKHMETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
The number of amino-acids present is  20
A  is present 23 times
C  is present 2 times
D  is present 18 times
E  is present 27 times
F  is present 25 times
G  is present 22 times
H  is present 9 times
I  is present 21 times
K  is present 34 times
L  is present 32 times
M  is present 8 times
N  is present 17 times
P  is present 14 times
Q  is present 14 times
R  is present 15 times
S  is present 16 times
T  is present 14 times
V  is present 20 times
W  is present 6 times
Y  is present 14 times
Amino C has the lowest freq. ( 2 )
Amino K has the highest freq. ( 34 )

Important NOTE. Accessing a value through the key of a dictionary requires that the pair key-value one searches for is present in the dictionary. If the searched key is not present the interpreter crashes out throwing a KeyError as follows:

myDict = {"one" : 1, "two" : 2, "three" : 3}

print(myDict["one"])
print(myDict["seven"])

1

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-24-a05b31e54a02> in <module>
      2
      3 print(myDict["one"])
----> 4 print(myDict["seven"])

KeyError: 'seven'

This could be avoided by checking that the key is present in the dictionary beforehand:

myDict = {"one" : 1, "two" : 2, "three" : 3}

search_keys = ["one", "seven"]

for s in search_keys:
    if s in myDict:
        print("key:", s, "value:", myDict[s])
    else:
        print("key", s, "not found in dictionary")

key: one value: 1
key seven not found in dictionary

or by using the dictionary method get that has two inputs: the key and a default value to return in case key is not present in the dictionary:

myDict = {"one" : 1, "two" : 2, "three" : 3}

search_keys = ["one", "seven"]

for s in search_keys:
    print("key:", s, "value:", myDict.get(s, "not found"))

key: one value: 1
key: seven value: not found

Exercises

1. Given the following two lists of integers: [1, 13, 22, 7, 43, 81, 77, 12, 15,21, 84,100] and [44,32,7, 100, 81, 13, 1, 21, 71]:
   1. Sort the two lists
   2. Create a third list as intersection of the two lists (i.e. an element is in the intersection if it is present in both lists).
   3. Print the three lists.

Show/Hide Solution

L1 = [1, 13, 22, 7, 43, 81, 77, 12, 15,21, 84,100]
L2 = [44,32,7, 100, 81, 13, 1, 21, 71]

L1.sort()
L2.sort()
intersection = [x for x in L1 if x in L2]

print("L1:    ", L1)
print("L2:    ", L2)
print("inters:", intersection)

L1:     [1, 7, 12, 13, 15, 21, 22, 43, 77, 81, 84, 100]
L2:     [1, 7, 13, 21, 32, 44, 71, 81, 100]
inters: [1, 7, 13, 21, 81, 100]

2. Given the string “nOBody Said iT was eAsy, No oNe Ever saId it WoulD be tHis hArd…”
   1. Create a list with all the letters that are capitalized (use str.isupper)
   2. Print the list
   3. Use the string method join to concatenate all the letters in a string, using “*” as separator. The syntax of join is str.join(list) and it outputs a string with all the elements in list joined with the character in str (es. “+”.join([1,2,3]) returns “1+2+3”).

The expected output:

['O', 'B', 'S', 'T', 'A', 'N', 'N', 'E', 'I', 'W', 'D', 'H', 'A']
O*B*S*T*A*N*N*E*I*W*D*H*A

Show/Hide Solution

text = "nOBody Said iT was eAsy, No oNe Ever saId it WoulD be tHis hArd…"
initials = [x for x in text if x.isupper()]

print(initials)
print("*".join(initials))

['O', 'B', 'S', 'T', 'A', 'N', 'N', 'E', 'I', 'W', 'D', 'H', 'A']
O*B*S*T*A*N*N*E*I*W*D*H*A

3. Given the following sequence:

AUGCUGUCUCCCUCACUGUAUGUAAAUUGCAUCUAGAAUAGCA
UCUGGAGCACUAAUUGACACAUAGUGGGUAUCAAUUAUUA
UUCCAGGUACUAGAGAUACCUGGACCAUUAACGGAUAAAU
AGAAGAUUCAUUUGUUGAGUGACUGAGGAUGGCAGUUCCU
GCUACCUUCAAGGAUCUGGAUGAUGGGGAGAAACAGAGAA
CAUAGUGUGAGAAUACUGUGGUAAGGAAAGUACAGAGGAC
UGGUAGAGUGUCUAACCUAGAUUUGGAGAAGGACCUAGAA
GUCUAUCCCAGGGAAAUAAAAAUCUAAGCUAAGGUUUGAG
GAAUCAGUAGGAAUUGGCAAAGGAAGGACAUGUUCCAGAU
GAUAGGAACAGGUUAUGCAAAGAUCCUGAAAUGGUCAGAG
CUUGGUGCUUUUUGAGAACCAAAAGUAGAUUGUUAUGGAC
CAGUGCUACUCCCUGCCUCUUGCCAAGGGACCCCGCCAAG
CACUGCAUCCCUUCCCUCUGACUCCACCUUUCCACUUGCC
CAGUAUUGUUGGUG

considering only first forward open reading frame (i.e. the string as it is remembering to remove newlines): 1. create a list of all the codons and print it.

2. create then a dictionary in which codons are keys and values are how many times that codon is present in the first forward open reading frame and print it; 3. retrieve from the dictionary and print the number of times codons: “AUG”, “AGA”, “GGG”, “AUA” are present. If a codon is not present the script should print “NOT present” rather than crash.

Show/Hide Solution

seq= """AUGCUGUCUCCCUCACUGUAUGUAAAUUGCAUCUAGAAUAGCA
UCUGGAGCACUAAUUGACACAUAGUGGGUAUCAAUUAUUA
UUCCAGGUACUAGAGAUACCUGGACCAUUAACGGAUAAAU
AGAAGAUUCAUUUGUUGAGUGACUGAGGAUGGCAGUUCCU
GCUACCUUCAAGGAUCUGGAUGAUGGGGAGAAACAGAGAA
CAUAGUGUGAGAAUACUGUGGUAAGGAAAGUACAGAGGAC
UGGUAGAGUGUCUAACCUAGAUUUGGAGAAGGACCUAGAA
GUCUAUCCCAGGGAAAUAAAAAUCUAAGCUAAGGUUUGAG
GAAUCAGUAGGAAUUGGCAAAGGAAGGACAUGUUCCAGAU
GAUAGGAACAGGUUAUGCAAAGAUCCUGAAAUGGUCAGAG
CUUGGUGCUUUUUGAGAACCAAAAGUAGAUUGUUAUGGAC
CAGUGCUACUCCCUGCCUCUUGCCAAGGGACCCCGCCAAG
CACUGCAUCCCUUCCCUCUGACUCCACCUUUCCACUUGCC
CAGUAUUGUUGGUG"""


seq = seq.replace("\n","")

codons = [seq[i:i+3] for i in range(0,len(seq),3)]

count_dict = dict()

for el in codons:
    if el not in count_dict:
        count_dict[el] = codons.count(el)

print("1st fwd ORF codons:")
print(codons)
print("Codon counts:")
print(count_dict)
print("\n")
to_check = ["AUG", "AGA", "GGG", "AUA"]
for c in to_check:
    if c in count_dict:
        print(c , "is present", count_dict[c], "times")
    else:
        print(c, "is NOT present")

1st fwd ORF codons:
['AUG', 'CUG', 'UCU', 'CCC', 'UCA', 'CUG', 'UAU', 'GUA', 'AAU', 'UGC', 'AUC', 'UAG', 'AAU', 'AGC', 'AUC', 'UGG', 'AGC', 'ACU', 'AAU', 'UGA', 'CAC', 'AUA', 'GUG', 'GGU', 'AUC', 'AAU', 'UAU', 'UAU', 'UCC', 'AGG', 'UAC', 'UAG', 'AGA', 'UAC', 'CUG', 'GAC', 'CAU', 'UAA', 'CGG', 'AUA', 'AAU', 'AGA', 'AGA', 'UUC', 'AUU', 'UGU', 'UGA', 'GUG', 'ACU', 'GAG', 'GAU', 'GGC', 'AGU', 'UCC', 'UGC', 'UAC', 'CUU', 'CAA', 'GGA', 'UCU', 'GGA', 'UGA', 'UGG', 'GGA', 'GAA', 'ACA', 'GAG', 'AAC', 'AUA', 'GUG', 'UGA', 'GAA', 'UAC', 'UGU', 'GGU', 'AAG', 'GAA', 'AGU', 'ACA', 'GAG', 'GAC', 'UGG', 'UAG', 'AGU', 'GUC', 'UAA', 'CCU', 'AGA', 'UUU', 'GGA', 'GAA', 'GGA', 'CCU', 'AGA', 'AGU', 'CUA', 'UCC', 'CAG', 'GGA', 'AAU', 'AAA', 'AAU', 'CUA', 'AGC', 'UAA', 'GGU', 'UUG', 'AGG', 'AAU', 'CAG', 'UAG', 'GAA', 'UUG', 'GCA', 'AAG', 'GAA', 'GGA', 'CAU', 'GUU', 'CCA', 'GAU', 'GAU', 'AGG', 'AAC', 'AGG', 'UUA', 'UGC', 'AAA', 'GAU', 'CCU', 'GAA', 'AUG', 'GUC', 'AGA', 'GCU', 'UGG', 'UGC', 'UUU', 'UUG', 'AGA', 'ACC', 'AAA', 'AGU', 'AGA', 'UUG', 'UUA', 'UGG', 'ACC', 'AGU', 'GCU', 'ACU', 'CCC', 'UGC', 'CUC', 'UUG', 'CCA', 'AGG', 'GAC', 'CCC', 'GCC', 'AAG', 'CAC', 'UGC', 'AUC', 'CCU', 'UCC', 'CUC', 'UGA', 'CUC', 'CAC', 'CUU', 'UCC', 'ACU', 'UGC', 'CCA', 'GUA', 'UUG', 'UUG', 'GUG']
Codon counts:
{'AUG': 2, 'CUG': 3, 'UCU': 2, 'CCC': 3, 'UCA': 1, 'UAU': 3, 'GUA': 2, 'AAU': 8, 'UGC': 7, 'AUC': 4, 'UAG': 4, 'AGC': 3, 'UGG': 5, 'ACU': 4, 'UGA': 5, 'CAC': 3, 'AUA': 3, 'GUG': 4, 'GGU': 3, 'UCC': 5, 'AGG': 5, 'UAC': 4, 'AGA': 8, 'GAC': 3, 'CAU': 2, 'UAA': 3, 'CGG': 1, 'UUC': 1, 'AUU': 1, 'UGU': 2, 'GAG': 3, 'GAU': 4, 'GGC': 1, 'AGU': 6, 'CUU': 2, 'CAA': 1, 'GGA': 7, 'GAA': 7, 'ACA': 2, 'AAC': 2, 'AAG': 3, 'GUC': 2, 'CCU': 4, 'UUU': 2, 'CUA': 2, 'CAG': 2, 'AAA': 3, 'UUG': 7, 'GCA': 1, 'GUU': 1, 'CCA': 3, 'UUA': 2, 'GCU': 2, 'ACC': 2, 'CUC': 3, 'GCC': 1}


AUG is present 2 times
AGA is present 8 times
GGG is NOT present
AUA is present 3 times

4. Given the following list of gene correlations:

   geneCorr = [["G1C2W9", "G1C2Q7", 0.2], ["G1C2W9", "G1C2Q4", 0.9],
   ["Q6NMS1", "G1C2W9", 0.8],["G1C2W9", "Q6NMS1",0.4], ["G1C2Q7", "G1C2Q4",0.76]]
   

   where each sublist [“gene1”, “gene2”, corr] represents a correlation between gene1 and gene2 with correlation corr, create another list containing only the elements having an high correlation (i.e. > 0.75). Print this list.

Expected result:

[['G1C2W9', 'G1C2Q4', 0.9], ['Q6NMS1', 'G1C2W9', 0.8], ['G1C2Q7', 'G1C2Q4', 0.76]]

Show/Hide Solution

geneCorr = [["G1C2W9", "G1C2Q7", 0.2], ["G1C2W9", "G1C2Q4", 0.9], ["Q6NMS1", "G1C2W9", 0.8],
            ["G1C2W9", "Q6NMS1",0.4], ["G1C2Q7", "G1C2Q4",0.76]]

highlyCorr = [x for x in geneCorr if x[2] > 0.75]

print(geneCorr, "\n")
print(highlyCorr)

[['G1C2W9', 'G1C2Q7', 0.2], ['G1C2W9', 'G1C2Q4', 0.9], ['Q6NMS1', 'G1C2W9', 0.8], ['G1C2W9', 'Q6NMS1', 0.4], ['G1C2Q7', 'G1C2Q4', 0.76]]

[['G1C2W9', 'G1C2Q4', 0.9], ['Q6NMS1', 'G1C2W9', 0.8], ['G1C2Q7', 'G1C2Q4', 0.76]]

5. Given the following sequence of DNA:

DNA = “GATTACATATATCAGTACAGATATATACGCGCGGGCTTACTATTAAAAACCCC”

1. Create a dictionary reporting the frequency of each base (i.e. key is the
base and value is the frequency).
2. Create a dictionary representing an index of all possible dimers (i.e. 2
bases, 16 dimers in total): AA, AT, AC, AG, TA, TT, TC, TG, ... . In this case,
keys of the dictionary are dimers and values are lists with all possible starting
positions of the dimer.
3. Print the DNA string.
4. Print for each base its frequency
4. Print all positions of the dimer "AT"

The expected result is:

sequence: GATTACATATATCAGTACAGATATATACGCGCGGGCTTACTATTAAAAACCCC
G has frequency: 0.1509433962264151
C has frequency: 0.22641509433962265
A has frequency: 0.3584905660377358
T has frequency: 0.2641509433962264
{'GG': [32, 33], 'TC': [11], 'GT': [14], 'CA': [5, 12, 17], 'TT': [2, 36, 42],
'CG': [27, 29, 31], 'TA': [3, 7, 9, 15, 21, 23, 25, 37, 40, 43], 'AG': [13, 18],
'GA': [0, 19], 'CT': [35, 39], 'GC': [28, 30, 34], 'AT': [1, 6, 8, 10, 20, 22, 24, 41],
'CC': [49, 50, 51], 'AA': [44, 45, 46, 47], 'AC': [4, 16, 26, 38, 48]}

Dimer AT is found at: [1, 6, 8, 10, 20, 22, 24, 41]

Show/Hide Solution

DNA = "GATTACATATATCAGTACAGATATATACGCGCGGGCTTACTATTAAAAACCCC"

n = len(DNA)

baseFreq = {"A" : DNA.count("A")/n, "T" : DNA.count("T")/n,
            "C": DNA.count("C")/n, "G" : DNA.count("G")/n }

dimersDict ={}

print("sequence:", DNA)

for base in baseFreq:
    print(base, "has frequency:", baseFreq[base])

for ind in range(len(DNA) -1 ): #need -1 because at each iteration I get the dimer [ind:ind+1]
    dimer = DNA[ind:ind+2]
    if(dimer in dimersDict):
        dimersDict[dimer].append(ind)
    else:
        dimersDict[dimer] = [ind]
print(dimersDict, "\n")
print("Dimer AT is found at:", dimersDict["AT"])

sequence: GATTACATATATCAGTACAGATATATACGCGCGGGCTTACTATTAAAAACCCC
A has frequency: 0.3584905660377358
T has frequency: 0.2641509433962264
C has frequency: 0.22641509433962265
G has frequency: 0.1509433962264151
{'GA': [0, 19], 'AT': [1, 6, 8, 10, 20, 22, 24, 41], 'TT': [2, 36, 42], 'TA': [3, 7, 9, 15, 21, 23, 25, 37, 40, 43], 'AC': [4, 16, 26, 38, 48], 'CA': [5, 12, 17], 'TC': [11], 'AG': [13, 18], 'GT': [14], 'CG': [27, 29, 31], 'GC': [28, 30, 34], 'GG': [32, 33], 'CT': [35, 39], 'AA': [44, 45, 46, 47], 'CC': [49, 50, 51]}

Dimer AT is found at: [1, 6, 8, 10, 20, 22, 24, 41]

6. Given the following table, reporting molecular weights for each amino acid, store them in a dictionary where the key is the one letter code and the value is the molecular weight (e.g. {“A” : 89, “R”:174”}).

Write a python script to answer the following questions:

1. What is the average molecular weight of an amino acid?
2. What is the total molecular weight and number of aminoacids
of the P53 peptide GSRAHSSHLKSKKGQSTSRHK?
3. What is the total molecular weight and number of aminoacids
of the peptide YTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWF?

Show/Hide Solution

mws = {"A" : 89, "R" : 174, "N" : 132, "D" : 133, "B": 133, "C": 121, "Q": 146,
       "E": 147, "Z": 147, "G": 75, "H": 155, "I": 131, "L" : 131,
      "K" : 146, "M" : 149, "F" : 165, "P" : 115, "S" : 105, "T" : 119,
       "W" : 204, "Y": 181, "V" : 117
      }
avgW = 0
for amino in mws:
    avgW = avgW + mws[amino]

avgW = avgW/len(mws)
print("The average molecular weight of amino acids is:", avgW)

P53amino = "GSRAHSSHLKSKKGQSTSRHK"

totW = 0
for amino in P53amino:
    totW += mws[amino]
print("Peptide ", P53amino, "has",len(P53amino), "amino acids and a total mw of",totW, "Da")

totW = 0 #reusing same variable name
peptide = "YTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWF"
for amino in peptide:
    totW += mws[amino]

print("Peptide ", peptide, "has",len(peptide), "amino acids and a total mw of",totW, "Da")

The average molecular weight of amino acids is: 137.04545454545453
Peptide  GSRAHSSHLKSKKGQSTSRHK has 21 amino acids and a total mw of 2662 Da
Peptide  YTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWF has 36 amino acids and a total mw of 5076 Da

7. The following string is an extract of a blast alignment with compacted textual output. This is a comma (“,”) separated text file where the columns report the following info: the first column is the query_id, the second the subject_id (i.e. the reference on which we aligned the query), the third is the percentage of identity and then we have the alignment length, number of mismatches, gap opens, start point of the alignment on the query, end point of the alignment on the query, start point of the alignment on the subject, end point of the alignment on the subject and evalue of the alignment.

#Fields:q.id,s.id,% ident,align len,mismatches,gap opens,q.start,q.end,s.start,s.end,evalue
ab1_400a,scaffold16155,98.698,384,4,1,12,394,6700,7083,0.0
ab1_400b,scaffold14620,98.698,384,4,1,12,394,1240,857,0.0
92A2_SP6_344a,scaffold14394,95.575,113,5,0,97,209,250760,250648,2.92e-44
92A2_SP6_344b,scaffold10682,97.849,93,2,0,18,110,898,990,3.81e-38
92A2_T7_558a,scaffold277,88.746,311,31,3,21,330,26630,26937,5.81e-103
92A2_T7_558b,scaffold277,89.545,220,21,2,27,246,27167,26950,6.06e-73
92A2_T7_558c,scaffold1125,88.125,320,31,5,30,346,231532,231847,7.51e-102
ab1_675a,scaffold4896,100.000,661,0,0,15,675,79051,78391,0.0
ab1_676b,scaffold4896,99.552,670,0,3,7,673,78421,79090,0.0

1. For each alignment, store the subject id, the percentage of identity and evalue, subject start and end in a dictionary using the query id as key. All this information can be stored in a dictionary having subject id as key and a dictionary with all the information as value:

   alignments["ab1_400"] = {"subjectid" : scaffold16155, "perc_id" : 98.698, "evalue" : 0.0}
   

2. Print the whole dictionary

3. Print only the alignments having percentage of identity > 90%

Note: skip the first comment line (i.e. skip line if starts with “#”). Note1: when storing the percentage of identity remember to convert the string into a float.

The expected output is:

{'92A2_T7_558a': {'perc_id': 88.746, 'subjectid': 'scaffold277', 'evalue': '5.81e-103'},
'92A2_T7_558b': {'perc_id': 89.545, 'subjectid': 'scaffold277', 'evalue': '6.06e-73'},
'92A2_SP6_344b': {'perc_id': 97.849, 'subjectid': 'scaffold10682', 'evalue': '3.81e-38'},
'92A2_T7_558c': {'perc_id': 88.125, 'subjectid': 'scaffold1125', 'evalue': '7.51e-102'},
'ab1_400a': {'perc_id': 98.698, 'subjectid': 'scaffold16155', 'evalue': '0.0'},
'ab1_675a': {'perc_id': 100.0, 'subjectid': 'scaffold4896', 'evalue': '0.0'},
'ab1_400b': {'perc_id': 98.698, 'subjectid': 'scaffold14620', 'evalue': '0.0'},
'92A2_SP6_344a': {'perc_id': 95.575, 'subjectid': 'scaffold14394', 'evalue': '2.92e-44'},
'ab1_676b': {'perc_id': 99.552, 'subjectid': 'scaffold4896', 'evalue': '0.0'}}


Alignments with identity > 90%:

Query id    Subject id  % ident evalue
92A2_SP6_344b    scaffold10682   97.849      3.81e-38
ab1_400a     scaffold16155   98.698      0.0
ab1_675a     scaffold4896    100.0   0.0
ab1_400b     scaffold14620   98.698      0.0
92A2_SP6_344a    scaffold14394   95.575      2.92e-44
ab1_676b     scaffold4896    99.552      0.0

Show/Hide Solution

blast_out = """#Fields:q.id,s.id,% ident,align len,mismatches,gap opens,q.start,q.end,s.start,s.end,evalue
ab1_400a,scaffold16155,98.698,384,4,1,12,394,6700,7083,0.0
ab1_400b,scaffold14620,98.698,384,4,1,12,394,1240,857,0.0
92A2_SP6_344a,scaffold14394,95.575,113,5,0,97,209,250760,250648,2.92e-44
92A2_SP6_344b,scaffold10682,97.849,93,2,0,18,110,898,990,3.81e-38
92A2_T7_558a,scaffold277,88.746,311,31,3,21,330,26630,26937,5.81e-103
92A2_T7_558b,scaffold277,89.545,220,21,2,27,246,27167,26950,6.06e-73
92A2_T7_558c,scaffold1125,88.125,320,31,5,30,346,231532,231847,7.51e-102
ab1_675a,scaffold4896,100.000,661,0,0,15,675,79051,78391,0.0
ab1_676b,scaffold4896,99.552,670,0,3,7,673,78421,79090,0.0"""



alignments = dict()

for align in blast_out.split("\n"):
    if(align.startswith("#") == False):
        align_info = align.split(",")
        alignments[align_info[0]] = {"subjectid" : align_info[1],
                                     "perc_id" : float(align_info[2]),
                                    "evalue" : align_info[-1]
                                    }

print(alignments, "\n\n")
print("Alignments with identity > 90%:\n")
print("Query id\tSubject id\t% ident\tevalue")
for a in alignments:
    if(alignments[a]["perc_id"]>90):
        print(a,"\t", alignments[a]["subjectid"],"\t", alignments[a]["perc_id"],"\t", alignments[a]["evalue"])

{'ab1_400a': {'subjectid': 'scaffold16155', 'perc_id': 98.698, 'evalue': '0.0'}, 'ab1_400b': {'subjectid': 'scaffold14620', 'perc_id': 98.698, 'evalue': '0.0'}, '92A2_SP6_344a': {'subjectid': 'scaffold14394', 'perc_id': 95.575, 'evalue': '2.92e-44'}, '92A2_SP6_344b': {'subjectid': 'scaffold10682', 'perc_id': 97.849, 'evalue': '3.81e-38'}, '92A2_T7_558a': {'subjectid': 'scaffold277', 'perc_id': 88.746, 'evalue': '5.81e-103'}, '92A2_T7_558b': {'subjectid': 'scaffold277', 'perc_id': 89.545, 'evalue': '6.06e-73'}, '92A2_T7_558c': {'subjectid': 'scaffold1125', 'perc_id': 88.125, 'evalue': '7.51e-102'}, 'ab1_675a': {'subjectid': 'scaffold4896', 'perc_id': 100.0, 'evalue': '0.0'}, 'ab1_676b': {'subjectid': 'scaffold4896', 'perc_id': 99.552, 'evalue': '0.0'}}


Alignments with identity > 90%:

Query id        Subject id      % ident evalue
ab1_400a         scaffold16155   98.698          0.0
ab1_400b         scaffold14620   98.698          0.0
92A2_SP6_344a    scaffold14394   95.575          2.92e-44
92A2_SP6_344b    scaffold10682   97.849          3.81e-38
ab1_675a         scaffold4896    100.0   0.0
ab1_676b         scaffold4896    99.552          0.0

8. The following text (separated with a comma “,”) is an extract of protein-protein interactions network stored in the database STRING involving PKLR (Pyruvate kinase, liver and RBC) that plays a key role in glycolysis:

#node1,node2,node1_ext_id,node2_ext_id,
ENO1,TPI1,ENSP00000234590,ENSP00000229270
PKLR,ENO1,ENSP00000339933,ENSP00000234590
PKLR,ENO3,ENSP00000339933,ENSP00000324105
PGK1,ENO1,ENSP00000362413,ENSP00000234590
PGK1,TPI1,ENSP00000362413,ENSP00000229270
GPI,TPI1,ENSP00000405573,ENSP00000229270
PKLR,ENO2,ENSP00000339933,ENSP00000229277
PGK1,ENO3,ENSP00000362413,ENSP00000324105
PGK1,ENO2,ENSP00000362413,ENSP00000229277
GPI,PKLR,ENSP00000405573,ENSP00000339933
ENO2,TPI1,ENSP00000229277,ENSP00000229270
PGK2,ENO1,ENSP00000305995,ENSP00000234590
ENO3,PGK2,ENSP00000324105,ENSP00000305995
PGK2,TPI1,ENSP00000305995,ENSP00000229270
ENO3,TPI1,ENSP00000324105,ENSP00000229270
PGK2,ENO2,ENSP00000305995,ENSP00000229277
GPI,ENO3,ENSP00000405573,ENSP00000324105
PKLR,LDHB,ENSP00000339933,ENSP00000229319
PKLR,LDHC,ENSP00000339933,ENSP00000280704
PKLR,TPI1,ENSP00000339933,ENSP00000229270
PGK1,PKLR,ENSP00000362413,ENSP00000339933
GPI,ENO2,ENSP00000405573,ENSP00000229277
PKLR,PGK2,ENSP00000339933,ENSP00000305995
GPI,PGK1,ENSP00000405573,ENSP00000362413
ME3,PKLR,ENSP00000352657,ENSP00000339933
ME3,LDHB,ENSP00000352657,ENSP00000229319
ME3,LDHC,ENSP00000352657,ENSP00000280704
GPI,PGK2,ENSP00000405573,ENSP00000305995
GPI,ENO1,ENSP00000405573,ENSP00000234590
GPI,LDHB,ENSP00000405573,ENSP00000229319
ENO3,ENO2,ENSP00000324105,ENSP00000229277
GPI,LDHC,ENSP00000405573,ENSP00000280704
ENO3,LDHB,ENSP00000324105,ENSP00000229319
ENO3,LDHC,ENSP00000324105,ENSP00000280704
ENO1,LDHB,ENSP00000234590,ENSP00000229319
LDHB,TPI1,ENSP00000229319,ENSP00000229270
LDHC,TPI1,ENSP00000280704,ENSP00000229270
PGK2,LDHC,ENSP00000305995,ENSP00000280704
PGK1,LDHB,ENSP00000362413,ENSP00000229319
PGK1,PGK2,ENSP00000362413,ENSP00000305995
ENO1,ENO2,ENSP00000234590,ENSP00000229277
LDHC,ENO1,ENSP00000280704,ENSP00000234590
LDHB,ENO2,ENSP00000229319,ENSP00000229277
LDHC,ENO2,ENSP00000280704,ENSP00000229277
ENO3,ENO1,ENSP00000324105,ENSP00000234590
PGK1,LDHC,ENSP00000362413,ENSP00000280704
GPI,ME3,ENSP00000405573,ENSP00000352657
PGK2,LDHB,ENSP00000305995,ENSP00000229319
ME3,TPI1,ENSP00000352657,ENSP00000229270

Here is a graphic representation of the protein-protein interactions:

Note: we can assume that relations between nodes are transitive. node1 --> node2
implies node2 --> node1.

1. Store the network information in a dictionary having node1 as key and
the list of all nodes2 associated to it as value (remember to skip the first
line that is the header). Remember transitivity, therefore add also node2 -->node1
2. Find all first neighbours of "PKLR" (i.e. the nodes that are directly connected
to "PKLR") and print them
3. Find all first neighbours of "ME3" (i.e. the nodes that are directly connected
to "PKLR") and print them
4. Find all the second neighbours of "ME3" (i.e. the nodes that are connected to nodes
directly connected to "ME3", but not directly to "ME3").

Show/Hide Solution

networkStr = """#node1,node2,node1_ext_id,node2_ext_id,
ENO1,TPI1,ENSP00000234590,ENSP00000229270
PKLR,ENO1,ENSP00000339933,ENSP00000234590
PKLR,ENO3,ENSP00000339933,ENSP00000324105
PGK1,ENO1,ENSP00000362413,ENSP00000234590
PGK1,TPI1,ENSP00000362413,ENSP00000229270
GPI,TPI1,ENSP00000405573,ENSP00000229270
PKLR,ENO2,ENSP00000339933,ENSP00000229277
PGK1,ENO3,ENSP00000362413,ENSP00000324105
PGK1,ENO2,ENSP00000362413,ENSP00000229277
GPI,PKLR,ENSP00000405573,ENSP00000339933
ENO2,TPI1,ENSP00000229277,ENSP00000229270
PGK2,ENO1,ENSP00000305995,ENSP00000234590
ENO3,PGK2,ENSP00000324105,ENSP00000305995
PGK2,TPI1,ENSP00000305995,ENSP00000229270
ENO3,TPI1,ENSP00000324105,ENSP00000229270
PGK2,ENO2,ENSP00000305995,ENSP00000229277
GPI,ENO3,ENSP00000405573,ENSP00000324105
PKLR,LDHB,ENSP00000339933,ENSP00000229319
PKLR,LDHC,ENSP00000339933,ENSP00000280704
PKLR,TPI1,ENSP00000339933,ENSP00000229270
PGK1,PKLR,ENSP00000362413,ENSP00000339933
GPI,ENO2,ENSP00000405573,ENSP00000229277
PKLR,PGK2,ENSP00000339933,ENSP00000305995
GPI,PGK1,ENSP00000405573,ENSP00000362413
ME3,PKLR,ENSP00000352657,ENSP00000339933
ME3,LDHB,ENSP00000352657,ENSP00000229319
ME3,LDHC,ENSP00000352657,ENSP00000280704
GPI,PGK2,ENSP00000405573,ENSP00000305995
GPI,ENO1,ENSP00000405573,ENSP00000234590
GPI,LDHB,ENSP00000405573,ENSP00000229319
ENO3,ENO2,ENSP00000324105,ENSP00000229277
GPI,LDHC,ENSP00000405573,ENSP00000280704
ENO3,LDHB,ENSP00000324105,ENSP00000229319
ENO3,LDHC,ENSP00000324105,ENSP00000280704
ENO1,LDHB,ENSP00000234590,ENSP00000229319
LDHB,TPI1,ENSP00000229319,ENSP00000229270
LDHC,TPI1,ENSP00000280704,ENSP00000229270
PGK2,LDHC,ENSP00000305995,ENSP00000280704
PGK1,LDHB,ENSP00000362413,ENSP00000229319
PGK1,PGK2,ENSP00000362413,ENSP00000305995
ENO1,ENO2,ENSP00000234590,ENSP00000229277
LDHC,ENO1,ENSP00000280704,ENSP00000234590
LDHB,ENO2,ENSP00000229319,ENSP00000229277
LDHC,ENO2,ENSP00000280704,ENSP00000229277
ENO3,ENO1,ENSP00000324105,ENSP00000234590
PGK1,LDHC,ENSP00000362413,ENSP00000280704
GPI,ME3,ENSP00000405573,ENSP00000352657
PGK2,LDHB,ENSP00000305995,ENSP00000229319
ME3,TPI1,ENSP00000352657,ENSP00000229270"""

netData = dict()

for line in networkStr.split("\n"):

    if(not line.startswith("#") ):
        info = line.split(",")
        #insert node1
        if(info[0] in netData):
            netData[info[0]].append(info[1])
        else:
            netData[info[0]] = [info[1]]
        #insert node2
        if(info[1] in netData):
            netData[info[1]].append(info[0])
        else:
            netData[info[1]] = [info[0]]


print(netData)

print("\nPKLR is directly connected to:", netData["PKLR"] )

firstNeigh = netData["ME3"]
print("\nME3 is directly connected to:", firstNeigh  )

secondNeigh = []
for node in firstNeigh:
    if(node in netData): #important, the node might not have connections
        neighbours = netData[node]
        for n in neighbours:
            if(n not in secondNeigh and  n not in firstNeigh and n != "ME3"):
                secondNeigh.append(n)

print("\nME3's second neighbours:", secondNeigh  )

{'ENO1': ['TPI1', 'PKLR', 'PGK1', 'PGK2', 'GPI', 'LDHB', 'ENO2', 'LDHC', 'ENO3'], 'TPI1': ['ENO1', 'PGK1', 'GPI', 'ENO2', 'PGK2', 'ENO3', 'PKLR', 'LDHB', 'LDHC', 'ME3'], 'PKLR': ['ENO1', 'ENO3', 'ENO2', 'GPI', 'LDHB', 'LDHC', 'TPI1', 'PGK1', 'PGK2', 'ME3'], 'ENO3': ['PKLR', 'PGK1', 'PGK2', 'TPI1', 'GPI', 'ENO2', 'LDHB', 'LDHC', 'ENO1'], 'PGK1': ['ENO1', 'TPI1', 'ENO3', 'ENO2', 'PKLR', 'GPI', 'LDHB', 'PGK2', 'LDHC'], 'GPI': ['TPI1', 'PKLR', 'ENO3', 'ENO2', 'PGK1', 'PGK2', 'ENO1', 'LDHB', 'LDHC', 'ME3'], 'ENO2': ['PKLR', 'PGK1', 'TPI1', 'PGK2', 'GPI', 'ENO3', 'ENO1', 'LDHB', 'LDHC'], 'PGK2': ['ENO1', 'ENO3', 'TPI1', 'ENO2', 'PKLR', 'GPI', 'LDHC', 'PGK1', 'LDHB'], 'LDHB': ['PKLR', 'ME3', 'GPI', 'ENO3', 'ENO1', 'TPI1', 'PGK1', 'ENO2', 'PGK2'], 'LDHC': ['PKLR', 'ME3', 'GPI', 'ENO3', 'TPI1', 'PGK2', 'ENO1', 'ENO2', 'PGK1'], 'ME3': ['PKLR', 'LDHB', 'LDHC', 'GPI', 'TPI1']}

PKLR is directly connected to: ['ENO1', 'ENO3', 'ENO2', 'GPI', 'LDHB', 'LDHC', 'TPI1', 'PGK1', 'PGK2', 'ME3']

ME3 is directly connected to: ['PKLR', 'LDHB', 'LDHC', 'GPI', 'TPI1']

ME3's second neighbours: ['ENO1', 'ENO3', 'ENO2', 'PGK1', 'PGK2']

Practical 6

In this practical we will see how to define functions to reuse code, we will talk about the scope of variables and finally will see how to deal with files in Python.

Slides

The slides of the introduction can be found here: Intro

Functions

A function is a block of code that has a name and that performs a task. A function can be thought of as a box that gets an input and returns an output.

Why should we use functions? For a lot of reasons including:

1. Reduce code duplication: put in functions parts of code that are needed several times in the whole program so that you don’t need to repeat the same code over and over again;
2. Decompose a complex task: make the code easier to write and understand by splitting the whole program in several easier functions;

both things improve code readability and make your code easier to understand.

The basic definition of a function is:

def function_name(input) :
    #code implementing the function
    ...
    ...
    return return_value

Functions are defined with the def keyword that proceeds the function_name and then a list of parameters is passed in the brackets. A colon : is used to end the line holding the definition of the function. The code implementing the function is specified by using indentation. A function might or might not return a value. In the first case a return statement is used.

Example: Define a function that implements the sum of two integer lists (note that there is no check that the two lists actually contain integers and that they have the same size).

def int_list_sum(l1,l2):
    """implements the sum of two lists of integers having the same size
    """
    ret =[]
    for i in range(len(l1)):
        ret.append(l1[i] + l2[i])
    return ret

L1 = list(range(1,10))
L2 = list(range(20,30))
print("L1:", L1)
print("L2:", L2)

res = int_list_sum(L1,L2)

print("L1+L2:", res)

res = int_list_sum(L1,L1)

print("L1+L1", res)

L1: [1, 2, 3, 4, 5, 6, 7, 8, 9]
L2: [20, 21, 22, 23, 24, 25, 26, 27, 28, 29]
L1+L2: [21, 23, 25, 27, 29, 31, 33, 35, 37]
L1+L1 [2, 4, 6, 8, 10, 12, 14, 16, 18]

Note that once the function has been defined, it can be called as many times as wanted with different input parameters. Moreover, a function does not do anything until it is actually called. A function can return 0 (in this case the return value would be “None”), 1 or more results. Notice also that collecting the results of a function is not mandatory.

Example: Let’s write a function that, given a list of elements, prints only the even-placed ones without returning anything.

def get_even_placed(myList):
    """returns the even placed elements of myList"""
    ret = [myList[i] for i in range(len(myList)) if i % 2 == 0]
    print(ret)

L1 = ["hi", "there", "from","python","!"]
L2 = list(range(13))

print("L1:", L1)
print("L2:", L2)

print("even L1:")
get_even_placed(L1)
print("even L2:")
get_even_placed(L2)

L1: ['hi', 'there', 'from', 'python', '!']
L2: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
even L1:
['hi', 'from', '!']
even L2:
[0, 2, 4, 6, 8, 10, 12]

Note that the function above is polymorphic (i.e. it works on several data types, provided that we can iterate through them).

Example: Let’s write a function that, given a list of integers, returns the number of elements, the maximum and minimum.

def get_info(myList):
    """returns len of myList, min and max value (assumes elements are integers)"""
    tmp = myList[:] #copy the input list
    tmp.sort()
    return len(tmp), tmp[0], tmp[-1] #return type is a tuple

A = [7, 1, 125, 4, -1, 0]

print("Original A:", A, "\n")
result = get_info(A)
print("Len:", result[0], "Min:", result[1], "Max:",result[2], "\n" )

print("A now:", A)

Original A: [7, 1, 125, 4, -1, 0]

Len: 6 Min: -1 Max: 125

A now: [7, 1, 125, 4, -1, 0]

def my_sum(myList):
    ret = 0
    for el in myList:
        ret += el # == ret = ret + el
    return ret

A = [1,2,3,4,5,6]
B = [7, 9, 4]
s = my_sum(A)

print("List A:", A)
print("Sum:", s)
s = my_sum(B)
print("List B:", B)
print("Sum:", s)

List A: [1, 2, 3, 4, 5, 6]
Sum: 21
List B: [7, 9, 4]
Sum: 20

Please note that the return value above is actually a tuple. Importantly enough, a function needs to be defined (i.e. its code has to be written) before it can actually be used.

A = [1,2,3]
my_sum(A)

def my_sum(myList):
    ret = 0
    for el in myList:
        ret += el
    return ret

Namespace and variable scope

Namespaces are mappings from names to objects, or in other words places where names are associated to objects. Namespaces can be considered as the context. According to Python’s reference a scope is a textual region of a Python program, where a namespace is directly accessible, which means that Python will look into that namespace to find the object associated to a name. Four namespaces are made available by Python:

1. **Local**: the innermost that contains local names (inside a function or a class);

2. **Enclosing**: the scope of the enclosing function,
it does not contain local nor global names (nested functions) ;

3. **Global**: contains the global names;

4. **Built-in**: contains all built in names
(e.g. print, if, while, for,...)

When one refers to a name, Python tries to find it in the current namespace, if it is not found it continues looking in the namespace that contains it until the built-in namespace is reached. If the name is not found there either, the Python interpreter will throw a NameError exception, meaning it cannot find the name. The order in which namespaces are considered is: Local, Enclosing, Global and Built-in (LEGB).

Consider the following example:

def my_function():
    var = 1  #local variable
    print("Local:", var)
    b = "my string"
    print("Local:", b)

var = 7 #global variable
my_function()
print("Global:", var)
print(b)

Local: 1
Local: my string
Global: 7

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-6-da11a41b34ff> in <module>()
      8 my_function()
      9 print("Global:", var)
---> 10 print(b)
     11

NameError: name 'b' is not defined

Variables defined within a function can only be seen within the function. That is why variable b is defined only within the function. Variables defined outside all functions are global to the whole program. The namespace of the local variable is within the function my_function, while outside it the variable will have its global value.

And the following:

def outer_function():
    var = 1 #outer

    def inner_function():
        var = 2 #inner
        print("Inner:", var)
        print("Inner:", B)

    inner_function()
    print("Outer:", var)


var = 3 #global
B = "This is B"
outer_function()
print("Global:", var)
print("Global:", B)

Inner: 2
Inner: This is B
Outer: 1
Global: 3
Global: This is B

Note in particular that the variable B is global, therefore it is accessible everywhere and also inside the inner_function. On the contrary, the value of var defined within the inner_function is accessible only in the namespace defined by it, outside it will assume different values as shown in the example.

In a nutshell, remember the three simple rules seen in the lecture. Within a def:

1. Name assignments create local names by default;
2. Name references search the following four scopes in the order:
local, enclosing functions (if any), then global and finally built-in (LEGB)
3. Names declared in global and nonlocal statements map assigned names to
enclosing module and function scopes.

Argument passing

Arguments are the parameters and data we pass to functions. When passing arguments, there are three important things to bear in mind are:

1. Passing an argument is actually assigning an object to a local variable name;
2. Assigning an object to a variable name within a function does not affect the caller;
3. Changing a mutable object variable name within a function affects the caller

Consider the following examples:

"""Assigning the argument does not affect the caller"""

def my_f(x):
    x = "local value" #local
    print("Local: ", x)

x = "global value" #global
my_f(x)
print("Global:", x)
my_f(x)

Local:  local value
Global: global value
Local:  local value

"""Changing a mutable affects the caller"""

def my_f(myList):
    myList[1] = "new value1"
    myList[3] = "new value2"
    print("Local: ", myList)

myList = ["old value"]*4
print("Global:", myList)
my_f(myList)
print("Global now: ", myList)

Global: ['old value', 'old value', 'old value', 'old value']
Local:  ['old value', 'new value1', 'old value', 'new value2']
Global now:  ['old value', 'new value1', 'old value', 'new value2']

Recall what seen in the lecture:

The behaviour above is because immutable objects are passed by value (therefore it is like making a copy), while mutable objects are passed by reference (therefore changing them effectively changes the original object).

To avoid making changes to a mutable object passed as parameter one needs to explicitely make a copy of it.

Consider the example seen before. Example: Let’s write a function that, given a list of integers, returns the number of elements, the maximum and minimum.

def get_info(myList):
    """returns len of myList, min and max value (assumes elements are integers)"""
    myList.sort()
    return len(myList), myList[0], myList[-1] #return type is a tuple


def get_info_copy(myList):
    """returns len of myList, min and max value (assumes elements are integers)"""
    tmp = myList[:] #copy the input list!!!!
    tmp.sort()
    return len(tmp), tmp[0], tmp[-1] #return type is a tuple

A = [7, 1, 125, 4, -1, 0]
B = [70, 10, 1250, 40, -10, 0, 10]

print("A:", A)
result = get_info(A)
print("Len:", result[0], "Min:", result[1], "Max:",result[2] )

print("A now:", A) #whoops A is changed!!!

print("\n###### With copy now ########")

print("\nB:", B)
result = get_info_copy(B)
print("Len:", result[0], "Min:", result[1], "Max:",result[2] )

print("B now:", B) #B is not changed!!!

A: [7, 1, 125, 4, -1, 0]
Len: 6 Min: -1 Max: 125
A now: [-1, 0, 1, 4, 7, 125]

###### With copy now ########

B: [70, 10, 1250, 40, -10, 0, 10]
Len: 7 Min: -10 Max: 1250
B now: [70, 10, 1250, 40, -10, 0, 10]

Positional arguments

Arguments can be passed to functions following the order in which they appear in the function definition.

Consider the following example:

def print_parameters(a,b,c,d):
    print("1st param:", a)
    print("2nd param:", b)
    print("3rd param:", c)
    print("4th param:", d)


print_parameters("A", "B", "C", "D")

1st param: A
2nd param: B
3rd param: C
4th param: D

Passing arguments by keyword

Given the name of an argument as specified in the definition of the function, parameters can be passed using the name = value syntax.

For example:

def print_parameters(a,b,c,d):
    print("1st param:", a)
    print("2nd param:", b)
    print("3rd param:", c)
    print("4th param:", d)


print_parameters(a = 1, c=3, d=4, b=2)
print("\n###############\n")
print_parameters("first","second",d="fourth",c="third")
print("\n###############\n")

1st param: 1
2nd param: 2
3rd param: 3
4th param: 4

###############

1st param: first
2nd param: second
3rd param: third
4th param: fourth

###############

Arguments passed positionally and by name can be used at the same time, but parameters passed by name must always be to the left of those passed by name. The following code in fact is not accepted by the Python interpreter:

def print_parameters(a,b,c,d):
    print("1st param:", a)
    print("2nd param:", b)
    print("3rd param:", c)
    print("4th param:", d)

print_parameters(d="fourth",c="third", "first","second")

  File "<ipython-input-13-4991b2c31842>", line 7
    print_parameters(d="fourth",c="third", "first","second")
                                          ^
SyntaxError: positional argument follows keyword argument

Specifying default values

During the definition of a function it is possible to specify default values. The syntax is the following:

def my_function(par1 = val1, par2 = val2, par3 = val3):

Consider the following example:

def print_parameters(a="defaultA", b="defaultB",c="defaultC"):
    print("a:",a)
    print("b:",b)
    print("c:",c)

print_parameters("param_A")
print("\n#################\n")
print_parameters(b="PARAMETER_B")
print("\n#################\n")
print_parameters()
print("\n#################\n")
print_parameters(c="PARAMETER_C", b="PAR_B")

a: param_A
b: defaultB
c: defaultC

#################

a: defaultA
b: PARAMETER_B
c: defaultC

#################

a: defaultA
b: defaultB
c: defaultC

#################

a: defaultA
b: PAR_B
c: PARAMETER_C

File input and output

Files are non volatile data stored at specific locations in memory. To read or write from/to a file, one first needs to create a reference to the file. This is called the handle to the file.

Recall from the lecture that Python provides programmers with the following functions and methods:

To read or write to a file one first needs to open it with the python’s built-in function open that returns a handler to the file. The handler can then be used to read or write the content of the file.

Example: Download the file textFile.txt to your favourite location and read it from python, printing out all its content. NOTE: the path of your file might be different from mine.

fh = open("file_samples/textFile.txt", "r") #read-only mode

print("--- File content ---")

for line in fh:
    print(line, end ="") #no need to add a new line

fh.close()

print("\n--- File closed ---")

--- File content ---
Hi everybody,
This is my first file
and it contains a total of
four lines!
--- File closed ---

The usual interaction with files is done in three steps: open the file, read or write its content, close the file.

Opening a file

As said, a file needs to be opened before working with it. This can be done by using the function open.

The standard syntax is:

file_handle = open("file_name", "file_mode")

where file_name is a string representing the path to reach the file (either absolute or relative to the .py module we are writing) and file_mode is the string representing the opening mode of the file. file_mode can be:

1. "r" which is the default and opens the file in read only mode;
2. "w" write only mode. Note that this would overwrite an existing file;
3. "a" append mode (i.e. add information at the end of an existing file or create a new file)
4. "t" text mode. The file will be a text file (this is the default).
5. "b" binary mode. The file will not be a textual file.
6. "x" exclusive creation. This will fail if the file already exists.
7. "+" update mode. The file will be opened with read and write permissions.

Opening modes can be combined (ex. "ra" would read and append, "wb" would write (and overwrite) a binary file, "r+b" read and write a binary file).

Closing a file

A opened file always needs to be closed. The basic syntax is:

file_handle.close()

this will free up resources and will not allow any more operations on the same file.

The following code will in fact crash, because the file has been closed and therefore no more operations can be performed on it.

fh = open("file_samples/textFile.txt", "r") #read-only mode

print("--- File content ---")

for line in fh:
    print(line, end ="") #no need to add a new line

fh.close()

print("\n--- File closed ---")

print(fh.readline())

--- File content ---
Hi everybody,
This is my first file
and it contains a total of
four lines!
--- File closed ---

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-16-0367c74d60af> in <module>()
     10 print("\n--- File closed ---")
     11
---> 12 print(fh.readline())

ValueError: I/O operation on closed file.

An alternative way to open and implicitly close the file is by using the with keyword. The basic syntax is:

with open("file") as f:
    #do some stuff
    #until done with it

The previous example would become:

print("--- File content ---")

with open("file_samples/textFile.txt", "r") as f:
    for line in f:
        print(line, end ="") #no need to add a new line

print("\n--- File closed ---")

--- File content ---
Hi everybody,
This is my first file
and it contains a total of
four lines!
--- File closed ---

Reading from a file

There are several ways for reading a file that has been opened in read mode having file handle fh:

1. content = fh.read() reads the whole file in the content string. Good for small and not structured files.

2. line = fh.readline() reads the file one line at a time storing it in the string line

3. lines = fh.readlines() reads all the lines of the file storing them as a list lines

4. using the iterator:

   for line in f:
   #process the information
   

   which is the most convenient way for big files.

Let’s see some examples. Note that to restart reading a file from the beginning we need to close it and open it gain.

fh = open("file_samples/textFile.txt", "r") #read-only mode

content = fh.read()
print("--- Mode1 (the whole file in a string) ---")
print(content)
fh.close()
print("")
print("--- Mode2 (line by line) ---")
with open("file_samples/textFile.txt","r") as f:
    print("Line1: ", f.readline(), end = "")
    print("Line2: ", f.readline(), end = "")

print("")
print("--- Mode3 (all lines as a list) ---")
with open("file_samples/textFile.txt","r") as f:
    print(f.readlines())

print("")
print("--- Mode4 (as a stream) ---")
with open("file_samples/textFile.txt","r") as f:
    for line in f:
        print(line, end = "")

--- Mode1 (the whole file in a string) ---
Hi everybody,
This is my first file
and it contains a total of
four lines!

--- Mode2 (line by line) ---
Line1:  Hi everybody,
Line2:  This is my first file

--- Mode3 (all lines as a list) ---
['Hi everybody,\n', 'This is my first file\n', 'and it contains a total of\n', 'four lines!']

--- Mode4 (as a stream) ---
Hi everybody,
This is my first file
and it contains a total of
four lines!

Writing to a file

To write some data to a file it must first be opened in write mode (i.e. “w”) or append mode (“a”, “+”). The actual writing can be performed by the method write that has the following basic syntax:

file_handle.write(data_to_be_written)

To make sure all data is written to the file, we must remember to close the file after writing on it.

Example: Given the matrix represented as list of lists, M = [[1,2,3], [4,5,6], [7,8,9]] let’s write it on a file my_matrix.txt as \(\begin{matrix}1 & 2 & 3\\4 & 5 & 6\\7 & 8 & 9\end{matrix}\)

M =  [[1,2,3], [4,5,6], [7,8,9]]

with open("file_samples/my_matrix.txt", "w") as f:
    for line in M:
        str_line = [str(x) for x in line] #to make this "joinable"
        f.write(" ".join(str_line))
        f.write("\n")

#no need to put the close because we used with

String formatting with format

Strings can be formatted with the method format. A lot of information on the use of format can be found here.

Format can be used to add values to a string in specific placeholders (normally defined with the syntax {}) or to format values according to the user specifications (e.g. number of decimal places for floating point numbers).

In the following we will see some simple examples.

#simple empty placeholders
print("I like {} more than {}.\n".format("python", "java"))

#indexed placeholders, note order
print("I like {0} more than {1} or {2}.\n".format("python", "java", "C++"))
print("I like {2} more than {1} or {0}.\n".format("python", "java", "C++"))

#indexed and named placeholders
print("I like {1} more than {c} or {0}.\n".format("python", "java", c="C++"))

#with type specification
import math
print("The square root of {0} is {1:f}.\n".format(2, math.sqrt(2)))

#with type and format specification (NOTE: {.2f})
print("The square root of {0} is {1:.2f}.\n".format(2, math.sqrt(2)))

#spacing data properly
print("{:2s}|{:5}|{:6}".format("N","sqrt","square"))
for i in range(0,20):
    print("{:2d}|{:5.3f}|{:6d}".format(i,math.sqrt(i),i*i))

I like python more than java.

I like python more than java or C++.

I like C++ more than java or python.

I like java more than C++ or python.

The square root of 2 is 1.414214.

The square root of 2 is 1.41.

N |sqrt |square
 0|0.000|     0
 1|1.000|     1
 2|1.414|     4
 3|1.732|     9
 4|2.000|    16
 5|2.236|    25
 6|2.449|    36
 7|2.646|    49
 8|2.828|    64
 9|3.000|    81
10|3.162|   100
11|3.317|   121
12|3.464|   144
13|3.606|   169
14|3.742|   196
15|3.873|   225
16|4.000|   256
17|4.123|   289
18|4.243|   324
19|4.359|   361

Exercises

1. Implement a function that takes in input a string representing a DNA sequence and computes its reverse-complement. Take care to reverse complement any character other than (A,T,C,G,a,t,c,g) to N. The function should preserve the case of each letter (i.e. A becomes T, but a becomes t). For simplicity all bases that do not represent nucleotides are converted to a capital N. Hint: create a dictionary revDict with bases as keys and their complements as values. Ex. revDict = {“A” : “T” , “a” : “t”, …}.
   1. Apply the function to the DNA sequence “ATTACATATCATACTATCGCNTTCTAAATA”
   2. Apply the function to the DNA sequence “acaTTACAtagataATACTaccataGCNTTCTAAATA”
   3. Apply the function to the DNA sequence “TTTTACCKKKAKTUUUITTTARRRRRAIUTYYA”
   4. Check that the reverse complement of the reverse complement of the sequence in 1. is exactly as the original sequence.

Show/Hide Solution

def reverse_complement(DNA):
    """the function reverse complements a string of DNA"""
    revDict = {"A" : "T", "a" : "t",
             "C" : "G", "c" : "g",
             "G" : "C", "g" : "c",
             "T" : "A", "t" : "a"
            }
    result = ""
    for base in DNA:
        ### dict.get(val, default) : returns default if val not in
        result = revDict.get(base, "N") + result

    return result

# Second version (equivalent)
def reverse_complement2(DNA):
    """the function reverse complements a string of DNA"""
    revDict = {"A" : "T", "a" : "t",
             "C" : "G", "c" : "g",
             "G" : "C", "g" : "c",
             "T" : "A", "t" : "a"
            }

    result = ""
    DNAlist = list(DNA)
    DNAlist.reverse()
    revComp =[revDict.get(x, "N") for x in DNAlist]
    result = "".join(revComp)
    return result

# Third version (equivalent)
def reverse_complement3(DNA):
    """the function reverse complements a string of DNA"""
    k = "AaTtCcGg"
    v = "TtAaGgCc"
    revDict  = dict()
    for i in range(0,len(k)):
        revDict[k[i]] = v[i]
    result = ""
    DNAlist = list(DNA)
    DNAlist.reverse()
    revComp =[revDict.get(x, "N") for x in DNAlist]
    result = "".join(revComp)
    return result


S1 = "ATTACATATCATACTATCGCNTTCTAAATA"
S2 = "acaTTACAtagataATACTaccataGCNTTCTAAATA"
S3 = "TTTTACCKKKAKTUUUITTTARRRRRAIUTYYA"

print("S1 {}".format(S1) )
print("rc S1", reverse_complement(S1))

print("\nS2   ", S2)
print("rc S2", reverse_complement(S2))

print("\nS3   ", S3)
print("rc S3", reverse_complement(S3))

print("\nrev_comp(rev_comp(S1)): {}".format(reverse_complement(reverse_complement(S1))))
print("\nrev_comp(rev_comp(S1) == S1?)", reverse_complement(reverse_complement(S1)) == S1)

S1 ATTACATATCATACTATCGCNTTCTAAATA
rc S1 TATTTAGAANGCGATAGTATGATATGTAAT

S2    acaTTACAtagataATACTaccataGCNTTCTAAATA
rc S2 TATTTAGAANGCtatggtAGTATtatctaTGTAAtgt

S3    TTTTACCKKKAKTUUUITTTARRRRRAIUTYYA
rc S3 TNNANNTNNNNNTAAANNNNANTNNNGGTAAAA

rev_comp(rev_comp(S1)): ATTACATATCATACTATCGCNTTCTAAATA

rev_comp(rev_comp(S1) == S1?) True

2. Write the following python functions and test them with some parameters of your choice:
   1. getDivisors: the function has a positive integer as parameter and returns a list of all the positive divisors of the integer in input (excluding the number itself). Example: getDivisors(6) --> [1,2,3]
   2. checkSum: the function has a list and an integer as parameters and returns True if the sum of all elements in the list equals the integer, False otherwise. Example: checkSum([1,2,3], 6) --> True, checkSum([1,2,3],1) --> False.
   3. checkPerfect: the function gets an integer as parameter and returns True if the integer is a perfect number, False otherwise. A number is perfect if all its divisors (excluding itself) sum to its value. Example: checkPerfect(6) --> True because 1+2+3 = 6. Hint: use the functions implemented before.

Use the three implemented functions to write a fourth function:

getFirstNperfects: the function gets an integer N as parameter and returns a dictionary with the first N perfect numbers. The key of the dictionary is the perfect number, while the value of the dictionary is the list of its divisors. Example: getFirstNperfects(1) --> {6 : [1,2,3]}

Get and print the first 4 perfect numbers and finally test if 33550336 is a perfect number.

WARNING: do not try to find more than 4 perfect numbers as it might take a while!!!

Show/Hide Solution

def getDivisors(intVal):
    """returns the integer divisors of intVal"""
    ret = [x for x in range(1,intVal//2 + 1) if intVal % x == 0]
    #OR:
    #for i in range(1,intVal//2+1):
    #    if(intVal % i == 0):
    #        ret.append(i)
    return ret

def checkSum(intList, intVal):
    """checks if the sum of elements in intList equals intVal"""
    s = 0
    for x in intList:
        s += x
    return s == intVal

def checkPerfect(intVal):
    """checks if intVal is a perfect number"""
    divisors = getDivisors(intVal)
    return checkSum(divisors,intVal)

def getFirstNPerfects(N):
    """Finds the first N perfect numbers"""
    i = 0
    val = 2
    ret = {}
    while(i<N):
        if(checkPerfect(val)):
            i+=1
            ret[val] = getDivisors(val)
            val += 1
        else:
            val += 1


    return ret


perfects = getFirstNPerfects(4) #do not go higher than 4, or it might take a while
perKeys = list(perfects.keys())
perKeys.sort()
for p in perKeys:
    print(p, " = ", "+".join([str(x) for x in perfects[p]]))

print("Is 33550336 a perfect number?", checkPerfect(33550336))

6  =  1+2+3
28  =  1+2+4+7+14
496  =  1+2+4+8+16+31+62+124+248
8128  =  1+2+4+8+16+32+64+127+254+508+1016+2032+4064
Is 33550336 a perfect number? True

3. Blast is a well known tool to perform sequence alignment between a pool of query sequences and a pool of subject sequences. Among the other formats, it can produce an text output that is tab separated (\t) capturing user specified output. Comments in the file are written in lines starting with an hash key (“#”). A sample blast output file is blast_sample.tsv, please download it and spend some time to look at it. The meaning of all columns is specified in the file header:

   # Fields: query id, subject id, query length, % identity, alignment length,
   identical, gap opens, q. start, q. end, s. start, s. end, evalue
   

   Write a python program with:

   1. A function (readBlast) that reads in the blast .tsv file (storing each line in a list) ignoring comment lines;
   2. A function (filterBlast) that gets a string in input representing a blast alignment and filters it according to the user specified parameters below. It should return True if all filters are passed, false otherwise:
      1. % identity > identity_threshold (default 0%)
      2. evalue < evalue_thrshold (default 0.5)
      3. alignment length / query length > align_threshold (default 0)

The program should report how many entries out of the total passed the filter.

Test several combinations of filters like:

1. identity_theshold = 97, all others default
2. evalue_threshold = 0.5, all others default
3. align_threshold = 0.9, all others default
4. align_threshold = 0.9, identity_threshold = 97

Show/Hide Solution

def filterBlast(seq, id_thr = 0, eval_thr = 1, al_thr = 0):
    """filters an alignment represented as a string. Returns True if filters OK, False otherwise"""
    infos = seq.split("\t")
    return float(infos[3]) > id_thr and float(infos[-1]) < eval_thr and float(infos[4])/int(infos[2]) > al_thr

def readBlast(inFile):
    """Reads the blast .tsv file and returns a list"""
    fh = open(inFile, "r")
    alignments = []
    for line in fh:
        if not line.startswith("#"):
            alignments.append(line)
    return alignments

def filterAndCount(alignList, id_thr = 0, eval_thr = 1, al_thr = 0):
    """filters alignments and counts the ones passing the filter"""
    passed = [x for x in alignList if filterBlast(x, id_thr, eval_thr, al_thr)]
    print("{} out of {} aligns passed filter (id_thr:{},eval_thr:{},al_thr:{})".format(
        len(passed), len(alignList), id_thr,eval_thr,al_thr))

blastF = "file_samples/blast_sample.tsv"

myAligns = readBlast(blastF)

filterAndCount(myAligns, id_thr=97)
filterAndCount(myAligns, eval_thr=1)
filterAndCount(myAligns, al_thr=0.9)
filterAndCount(myAligns, al_thr=0.9, id_thr=97)

8390 out of 90790 aligns passed filter (id_thr:97,eval_thr:1,al_thr:0)
90780 out of 90790 aligns passed filter (id_thr:0,eval_thr:1,al_thr:0)
27711 out of 90790 aligns passed filter (id_thr:0,eval_thr:1,al_thr:0.9)
804 out of 90790 aligns passed filter (id_thr:97,eval_thr:1,al_thr:0.9)

4. Fasta is a format representing nucleotide or peptide sequences. Each entry of a fasta file starts with a “>” followed by the identifier of the entry (the header of the sequence). All the lines following a header represent the sequence belonging to that identifier. Here you can find an example of fasta file: contigs82.fasta. Please download it and have a look at its content.

Write a python program that reads a fasta file and prints to screen the identifier of the sequence and the frequency of all the characters in the sequence (note that sequences might contain all IUPAC codes in case of SNPs). Hint: use a dictionary.

Sample output:

MDC020656.85 :
     N has freq 0.052
     T has freq 0.273
     A has freq 0.308
     G has freq 0.203
     C has freq 0.163
MDC001115.177 :
     N has freq 0.018
     G has freq 0.157
     A has freq 0.302
     T has freq 0.316
     C has freq 0.207
     ...

Show/Hide Solution

def countFrequency(seq):
    """gets a sequence in input and returns
    a dictionary with bases as keys and frequence as value"""
    bases = {}
    for b in seq:
        if b not in bases:
            bases[b] = 1
        else:
            bases[b] += 1

    for b in bases:
        bases[b] = bases[b]/len(seq)
    return bases

def printData(ident, freqDict):
    """get the identifier and a dictionary with all frequencies
    and prints both information on the screen"""
    print(ident,":")
    for f in freqDict:
        print("\t {} has freq {:.3f}".format(f,freqDict[f]))

def processFasta(file):
    header = ""
    seq = ""
    with open(file, "r") as f:
        for line in f:
            line = line.strip()
            if(line.startswith(">")):
                if(len(header) == 0 ):
                    #first entry:
                    header = line[1:]
                else:
                    #this is a new entry
                    freqData = countFrequency(seq)
                    printData(header,freqData)
                    seq = ""
                    header = line[1:]
            else:
                seq +=line
    #processing the final entry
    freqData = countFrequency(seq)
    printData(header,freqData)


inFasta = "file_samples/contigs82.fasta"
processFasta(inFasta)

MDC020656.85 :
         C has freq 0.163
         T has freq 0.273
         A has freq 0.308
         N has freq 0.052
         G has freq 0.203
MDC001115.177 :
         C has freq 0.207
         T has freq 0.316
         A has freq 0.302
         N has freq 0.018
         G has freq 0.157
MDC013284.379 :
         C has freq 0.171
         T has freq 0.321
         A has freq 0.309
         N has freq 0.005
         G has freq 0.194
MDC018185.243 :
         S has freq 0.000
         W has freq 0.000
         K has freq 0.000
         G has freq 0.181
         N has freq 0.001
         M has freq 0.000
         R has freq 0.001
         C has freq 0.204
         T has freq 0.304
         A has freq 0.307
         Y has freq 0.001
MDC018185.241 :
         S has freq 0.000
         W has freq 0.000
         K has freq 0.001
         G has freq 0.183
         N has freq 0.006
         M has freq 0.001
         R has freq 0.001
         C has freq 0.168
         T has freq 0.304
         A has freq 0.335
         Y has freq 0.002
MDC004527.213 :
         C has freq 0.273
         T has freq 0.332
         A has freq 0.227
         N has freq 0.013
         G has freq 0.155
MDC003661.174 :
         C has freq 0.213
         T has freq 0.301
         A has freq 0.246
         N has freq 0.007
         G has freq 0.232
MDC012176.157 :
         C has freq 0.240
         T has freq 0.253
         A has freq 0.343
         N has freq 0.001
         G has freq 0.163
MDC001204.812 :
         C has freq 0.221
         T has freq 0.298
         A has freq 0.293
         N has freq 0.000
         G has freq 0.187
MDC001204.810 :
         C has freq 0.182
         T has freq 0.340
         A has freq 0.297
         N has freq 0.017
         G has freq 0.164
MDC004389.256 :
         C has freq 0.277
         T has freq 0.203
         A has freq 0.285
         N has freq 0.028
         G has freq 0.207
MDC024257.15 :
         C has freq 0.144
         T has freq 0.331
         A has freq 0.319
         N has freq 0.022
         G has freq 0.184
MDC018297.229 :
         C has freq 0.181
         T has freq 0.305
         A has freq 0.275
         N has freq 0.031
         G has freq 0.209
MDC001802.364 :
         C has freq 0.203
         T has freq 0.328
         A has freq 0.252
         N has freq 0.037
         G has freq 0.180
MDC016621.241 :
         C has freq 0.206
         T has freq 0.262
         A has freq 0.302
         N has freq 0.063
         G has freq 0.168
MDC014057.243 :
         C has freq 0.263
         T has freq 0.212
         A has freq 0.291
         N has freq 0.016
         G has freq 0.217
MDC021015.302 :
         C has freq 0.143
         T has freq 0.223
         A has freq 0.302
         N has freq 0.081
         G has freq 0.251
MDC018185.242 :
         S has freq 0.000
         W has freq 0.000
         K has freq 0.000
         G has freq 0.189
         N has freq 0.000
         M has freq 0.001
         R has freq 0.002
         C has freq 0.200
         T has freq 0.289
         A has freq 0.316
         Y has freq 0.001
MDC051782.000 :
         N has freq 0.044
         W has freq 0.001
         K has freq 0.001
         S has freq 0.001
         G has freq 0.177
         M has freq 0.000
         R has freq 0.002
         C has freq 0.180
         T has freq 0.306
         A has freq 0.285
         Y has freq 0.002
MDC017187.314 :
         C has freq 0.206
         T has freq 0.276
         A has freq 0.289
         N has freq 0.003
         G has freq 0.225
MDC017187.311 :
         S has freq 0.000
         W has freq 0.001
         K has freq 0.000
         G has freq 0.185
         N has freq 0.068
         M has freq 0.000
         R has freq 0.002
         C has freq 0.179
         T has freq 0.315
         A has freq 0.248
         Y has freq 0.001
MDC012865.410 :
         C has freq 0.162
         T has freq 0.328
         A has freq 0.289
         N has freq 0.003
         G has freq 0.218
MDC000427.83 :
         C has freq 0.165
         T has freq 0.274
         A has freq 0.392
         N has freq 0.010
         G has freq 0.159
MDC017187.319 :
         C has freq 0.181
         T has freq 0.331
         A has freq 0.282
         N has freq 0.006
         G has freq 0.200
MDC017187.318 :
         K has freq 0.000
         N has freq 0.001
         G has freq 0.232
         C has freq 0.187
         T has freq 0.305
         A has freq 0.275
MDC004081.319 :
         C has freq 0.106
         T has freq 0.197
         A has freq 0.172
         G has freq 0.098
         N has freq 0.428
MDC021913.275 :
         C has freq 0.155
         T has freq 0.169
         A has freq 0.199
         N has freq 0.334
         G has freq 0.143
MDC015147.205 :
         C has freq 0.154
         T has freq 0.350
         A has freq 0.298
         N has freq 0.002
         G has freq 0.196
MDC000038.355 :
         S has freq 0.000
         W has freq 0.000
         K has freq 0.000
         G has freq 0.158
         N has freq 0.025
         M has freq 0.000
         R has freq 0.000
         C has freq 0.170
         T has freq 0.315
         A has freq 0.331
         Y has freq 0.000
MDC016032.95 :
         S has freq 0.001
         W has freq 0.001
         K has freq 0.002
         G has freq 0.222
         N has freq 0.003
         R has freq 0.002
         C has freq 0.142
         T has freq 0.286
         A has freq 0.342
         Y has freq 0.001
MDC052568.000 :
         N has freq 0.008
         W has freq 0.001
         K has freq 0.000
         S has freq 0.001
         G has freq 0.178
         M has freq 0.001
         R has freq 0.002
         C has freq 0.207
         T has freq 0.302
         A has freq 0.300
         Y has freq 0.001
MDC008119.414 :
         C has freq 0.245
         T has freq 0.316
         A has freq 0.209
         N has freq 0.001
         G has freq 0.229
MDC026201.7 :
         C has freq 0.247
         T has freq 0.250
         A has freq 0.313
         G has freq 0.191
MDC003995.601 :
         S has freq 0.000
         W has freq 0.001
         K has freq 0.000
         G has freq 0.167
         N has freq 0.006
         M has freq 0.001
         R has freq 0.001
         C has freq 0.166
         T has freq 0.334
         A has freq 0.323
         Y has freq 0.001
MDC009211.561 :
         C has freq 0.237
         T has freq 0.286
         A has freq 0.306
         N has freq 0.001
         G has freq 0.171
MDC009211.567 :
         C has freq 0.167
         T has freq 0.327
         A has freq 0.318
         N has freq 0.006
         G has freq 0.181
MDC054294.001 :
         W has freq 0.001
         K has freq 0.001
         S has freq 0.000
         G has freq 0.186
         M has freq 0.001
         R has freq 0.002
         C has freq 0.186
         T has freq 0.318
         A has freq 0.303
         Y has freq 0.002
MDC004364.265 :
         S has freq 0.000
         W has freq 0.000
         K has freq 0.000
         G has freq 0.198
         N has freq 0.007
         R has freq 0.001
         C has freq 0.170
         T has freq 0.302
         A has freq 0.323
         Y has freq 0.001
MDC002360.219 :
         C has freq 0.204
         T has freq 0.303
         A has freq 0.316
         N has freq 0.003
         G has freq 0.173
MDC003408.117 :
         C has freq 0.215
         T has freq 0.247
         A has freq 0.329
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MDC007018.186 :
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         N has freq 0.016
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5. Write a python program that reads two files. The first is a one column text file (contig_ids.txt) with the identifiers of some contigs that are present in the second file, which is a fasta formatted file (contigs82.fasta). The program will write on a third, fasta formatted file (e.g. filtered_contigs.fasta) only those entries in contigs82.fasta having identifier in contig_ids.txt.

Show/Hide Solution

def readIDS(f):
    """reads a one column file in and stores
    the ids in a dictionary that is returned at the end"""
    ret = dict()
    with open(f, "r") as file:
        for line in file:
            line = line.strip()
            if(line not in ret):
                ret[line] = 1
    return ret

def filterFasta(inF, outF, ids2keep):
    oF = open(outF, "w")

    outputME = False
    with open(inF, "r") as file:
        for line in file:
            line = line.strip()
            if(line.startswith(">")):
                #this is the header
                if(line[1:] in ids2keep):
                    oF.write(line +"\n")
                    outputME = True
                    print("Writing contig ", line[1:])
                else:
                    outputME = False
            else:
                if(outputME):
                    oF.write(line +"\n")

    oF.close()


idsFile = "file_samples/contig_ids.txt"
inFasta = "file_samples/contigs82.fasta"
outFasta = "file_samples/filtered_contigs.fasta"

ids = readIDS(idsFile)
filterFasta(inFasta,outFasta, ids)

Writing contig  MDC001115.177
Writing contig  MDC013284.379
Writing contig  MDC018185.243
Writing contig  MDC018185.241
Writing contig  MDC004527.213
Writing contig  MDC012176.157
Writing contig  MDC001204.810
Writing contig  MDC004389.256
Writing contig  MDC018297.229
Writing contig  MDC001802.364
Writing contig  MDC014057.243
Writing contig  MDC021015.302
Writing contig  MDC017187.314
Writing contig  MDC012865.410
Writing contig  MDC000427.83
Writing contig  MDC017187.319
Writing contig  MDC004364.265
Writing contig  MDC002360.219
Writing contig  MDC015155.172
Writing contig  MDC019140.398
Writing contig  MDC019140.399
Writing contig  MDC011390.337
Writing contig  MDC007154.375
Writing contig  MDC010588.505
Writing contig  MDC002519.240
Writing contig  MDC006346.711
Writing contig  MDC011551.182
Writing contig  MDC002717.156
Writing contig  MDC006346.719
Writing contig  MDC007838.447
Writing contig  MDC007018.186
Writing contig  MDC017873.233
Writing contig  MDC016296.138
Writing contig  MDC019067.226
Writing contig  MDC014019.318
Writing contig  MDC007995.528
Writing contig  MDC026961.60
Writing contig  MDC020963.161
Writing contig  MDC005174.220
Writing contig  MDC040033.7
Writing contig  MDC019674.147
Writing contig  MDC010450.877
Writing contig  MDC007097.457
Writing contig  MDC016278.70

6. Write a python program that:
   1. reads the text file sample_text.txt and stores in a dictionary how many times each word appears (hint: the key is the word and the count is the value);
   2. prints to screen how many lines the file has and how many distinct words are in the file;
   3. writes to a text file (scientist_histo.csv) the histogram of the words in comma separated value format (i.e. word,count). Words must be sorted alphabetically;
   4. Finally, write a function that prints to screen (alphabetically) all the words that have a count higher than a threshold N and apply it with N = 5.

Show/Hide Solution

def wordHisto(myText):
    """this function returns a dictionary
    with the count of each word in myText (separated by " " or "\n")
    """
    myDict = dict()
    tmp = myText.replace("\n"," ")

    for word in tmp.split(" "):
        if(word not in myDict):
            myDict[word] = 1
        else:
            myDict[word] += 1
    return myDict

def writeWordHisto(outF, data):
    """this function writes to outFile
    the word histogram data contained in the dictionary data
    the output format is comma separated
    """
    fh = open(outF, "w")
    dictKeys = list(data.keys())
    dictKeys.sort()
    fh.write("#word,count\n")
    for k in dictKeys:
        curVal = data[k]
        myStr = k + "," + str(curVal)+"\n" #string to write in file
        fh.write(myStr)
    fh.close() #remember to close the file

def printWords(N, data):
    """prints the words in data that have a count higher than N"""
    dictKeys = list(data.keys())
    dictKeys.sort()
    for w in dictKeys:
        cnt = data[w]
        if(cnt > N):
            print("Word \"{}\" is present {} times".format( w, cnt))


file = "file_samples/sample_text.txt"
outFile = "file_samples/sample_text_histo.csv"
wholeText = ""
fh = open(file,"r")
wholeText = fh.read()
wholeText = wholeText.strip() #to remove the final newline character

fh.close()
print("The file {} has {} lines".format(file, wholeText.count("\n") +1 )) #n lines have n-1 \n

#Let's do the job:
wordD = wordHisto(wholeText)
writeWordHisto(outFile, wordD)
print("The total number of distinct words is ", len(wordD))
printWords(5,wordD)

The file file_samples/sample_text.txt has 28 lines
The total number of distinct words is  308
Word "challenge" is present 6 times
Word "future" is present 22 times
Word "reply" is present 7 times
Word "shop" is present 6 times
Word "thunder" is present 11 times
Word "umbrella" is present 10 times

Practical 7

In this practical we will keep practicing with functions and will see how to get input from the command line.

Slides

The slides of the introduction can be found here: Intro

Functions

Reminder. The basic definition of a function is:

def function_name(input) :
    #code implementing the function
    ...
    ...
    return return_value

Functions are defined with the def keyword that proceeds the function_name and then a list of parameters is passed in the brackets. A colon : is used to end the line holding the definition of the function. The code implementing the function is specified by using indentation. A function might or might not return a value. In the first case a return statement is used.

Getting input from the command line

To call a program my_python_program.py from command line, you just have to open a terminal (in Linux) or the command prompt (in Windows) and, assuming that python is present in the path, you can cd into the folder containing your python program, (eg. cd C:\python\my_exercises\) and just type in python3 my_python_program.py or python my_python_program.py In case of arguments to be passed by command line, one has to put them after the specification of the program name (eg. python my_python_program.py parm1 param2 param3).

Python provides the module sys to interact with the interpreter. In particular, sys.argv is a list representing all the arguments passed to the python script from the command line.

Consider the following code:

import sys
"""Test input from command line in systest.py"""

if(len(sys.argv) != 4):
    print("Dear user, I was expecting 3 params. You gave me ",len(sys.argv)-1)
    exit(1)
else:
    for i in range(0,len(sys.argv)):
        print("Param {}:{} ({})".format(i,sys.argv[i],type(sys.argv[i])))

Dear user, I was expecting 3 params. You gave me  2

Invoking the systest.py script from command line with the command python3 exercises/systest.py 1st_param 2nd 3 will return:

Param 0: exercises/systest.py (<class 'str'>)
Param 1: 1st_param (<class 'str'>)
Param 2: 2nd (<class 'str'>)
Param 3: 3 (<class 'str'>)

Invoking the systest.py script from command line with the command python3 exercises/systest.py 1st_param will return:

Dear user, I was expecting three parameters. You gave me  1

Note that the parameter at index 0, sys.argv[0] holds the name of the script, and that all parameters are actually strings (and therefore need to be cast to numbers if we want to do mathematical operations on them).

Example: Write a script that takes two integers in input, i1 and i2, and computes the sum, difference, multiplication and division on them.

import sys
"""Maths example with input from command line"""

if(len(sys.argv) != 3):
    print("Dear user, I was expecting 2 params. You gave me ",len(sys.argv)-1)
    exit(1)
else:
    i1 = int(sys.argv[1])
    i2 = int(sys.argv[2])
    print("{} + {} = {}".format(i1,i2, i1 + i2))
    print("{} - {} = {}".format(i1,i2, i1 - i2))
    print("{} * {} = {}".format(i1,i2, i1 * i2))
    if(i2 != 0):
        print("{} / {} = {}".format(i1,i2, i1 / i2))
    else:
        print("{} / {} = Infinite".format(i1,i2))

Which, depending on user input, should give something like:

note that we need to check if the values given in input are actually numbers, otherwise the execution will crash (third example). This is easy in case of integers (str.isdigit()) but in case of floats it is more complex and might require Exception handling.

A more flexible and powerful way of getting input from command line makes use of the Argparse module.

Argparse

Argparse is a command line parsing module which deals with user specified parameters (positional arguments) and optional arguments.

Very briefly, the basic syntax of the Argparse module (for more information check the official documentation) is the following.

1. Import the module:

import argparse

2. Define a argparse object:

parser = argparse.ArgumentParser(description="This is the description of the program")

note the parameter description that is a string to describe the program;

3. Add positional arguments:

   parser.add_argument("arg_name", type = obj,
                   help = "Description of the parameter)
   

   where arg_name is the name of the argument (which will be used to retrieve its value). The argument has type obj (the type will be automatically checked for us) and a description specified in the helpstring.

4. Add optional arguments:

   parser.add_argument("-p", "--optional_arg", type = obj, default = def_val,
                       help = "Description of the parameter)
   

   where -p is a short form of the parameter (and it is optional), --optional_arg is the extended name and it requires a value after it is specified, default is optional and gives a default value to the parameter. If not specified and no argument is passed, the argument will get the value “None”. Help is again the description string.

5. Parse the arguments:

   args = parser.parse_args()
   

   the parser checks the arguments and stores their values in the argparse object that we called args.

6. Retrieve and process arguments:

   myArgName = args.arg_name
   myOptArg = args.optional_arg
   

   now variables contain the values specified by the user and we can use them.

Example: Let’s write a program that gets a string (S) and an integer (N) in input and prints the string repeated N times. Three optional parameters are specified: verbosity (-v) to make the software print a more descriptive output, separator (-s) to separate each copy of the string (defaults to ” “) and trailpoints (-p) to add several “.” at the end of the string (defaults to 1).

import argparse
parser = argparse.ArgumentParser(description="""This script gets a string
                                 and an integer and repeats the string N times""")
parser.add_argument("string", type=str,
                    help="The string to be repeated")
parser.add_argument("N", type=int,
                    help="The number of times to repeat the string")

parser.add_argument("-v", "--verbose", action="store_true",
                    help="increase output verbosity")

parser.add_argument("-p", "--trailpoints", type = int, default = 1,
                    help="Adds these many trailing points")
parser.add_argument("-s", "--separator", type = str, default = " ",
                    help="The separator between repeated strings")

args = parser.parse_args()

mySTR = args.string+args.separator
trailP = "." * args.trailpoints
answer = mySTR * args.N

answer = answer[:-len(args.separator)] + trailP #to remove the last separator

if args.verbose:
    print("the string {} repeated {} is:".format(args.str, args.N, answer))
else:
    print(answer)

Executing the program from command line without parameters gives the message:

Calling it with the -h flag:

With the positional arguments "ciao a tutti" and 3:

With the positional arguments "ciao a tutti" and 3, and with the optional parameters -s "___" -p 3 -v

Example: Let’s write a program that reads and prints to screen a text file specified by the user. Optionally, the file might be compressed with gzip to save space. The user should be able to read also gzipped files. Hint: use the module gzip which is very similar to the standard file management method (more info here). You can find a text file here textFile.txt and its gzipped version here text.gz:

import argparse
import gzip

parser = argparse.ArgumentParser(description="""Reads and prints a text file""")
parser.add_argument("filename", type=str, help="The file name")
parser.add_argument("-z", "--gzipped", action="store_true",
                    help="If set, input file is assumed gzipped")

args = parser.parse_args()
inputFile = args.filename
fh = ""
if(args.gzipped):
    fh = gzip.open(inputFile, "rt")
else:
    fh = open(inputFile, "r")

for line in fh:
    line = line.strip("\n")
    print(line)

fh.close()

The output:

Example: Let’s write a program that reads the content of a file and prints to screen some stats like the number of lines, the number of characters and maximum number of characters in one line. Optionally (if flag -v is set) it should print the content of the file. You can find a text file here textFile.txt:

import argparse


def readText(f):
    """reads the file and returns a list with
    each line as separate element"""
    myF = open(f, "r")
    ret = myF.readlines()
    return ret


def computeStats(fileList):
    """returns a tuple (num.lines, num.characters,max_char.line)"""
    num_lines = len(fileList)
    lines_len = [len(x.replace("\n", "")) for x in fileList]
    num_char = sum(lines_len)
    max_char = max(lines_len)
    return (num_lines, num_char, max_char)


parser = argparse.ArgumentParser(description="Computes file stats")
parser.add_argument("inputFile", type=str, help="The input file")
parser.add_argument(
    "-v", "--verbose", action="store_true", help="if set, prints the file content")

args = parser.parse_args()

inFile = args.inputFile
lines = readText(inFile)
stats = computeStats(lines)
if args.verbose:
    print("File content:\n{}\n".format("".join(lines)))
print(
    "Stats:\nN.lines:{}\nN.chars:{}\nMax. char in line:{}".format(
        stats[0], stats[1], stats[2]))

Output with -v flag:

Output without -v flag:

Exercises

1. Modify the program of Exercise 5 of Practical 6 in order to allow users to specify the input and output files from command line. Then test it with the provided files. The text of the exercise follows:

Write a python program that reads two files. The first is a one column text file (contig_ids.txt) with the identifiers of some contigs that are present in the second file, which is a fasta formatted file (contigs82.fasta). The program will write on a third, fasta formatted file (e.g. filtered_contigs.fasta) only those entries in contigs82.fasta having identifier in contig_ids.txt.

Show/Hide Solution

"""exercises/filterFasta.py"""

import argparse

def readIDS(f):
    """reads a one column file in and stores
    the ids in a dictionary that is returned at the end"""
    ret = dict()
    with open(f, "r") as file:
        for line in file:
            line = line.strip()
            if(line not in ret):
                ret[line] = 1
    return ret

def filterFasta(inF, outF, ids2keep):
    oF = open(outF, "w")

    outputME = False
    with open(inF, "r") as file:
        for line in file:
            line = line.strip()
            if line.startswith(">"):
                #this is the header
                if ids2keep.get(line[1:],False):
                    oF.write(line +"\n")
                    outputME = True
                    print("Writing contig ", line[1:])
                else:
                    outputME = False
            else:
                if outputME:
                    oF.write(line +"\n")

    oF.close()


parser = argparse.ArgumentParser(description="Filters a fasta file")
parser.add_argument("inputFasta", type = str, help = "The input fasta file")
parser.add_argument("inputIDS", type = str, help = "The IDS to keep")
parser.add_argument("outputFasta", type = str,
                    help = "The output fasta file with filtered entries")
args = parser.parse_args()
idsFile = args.inputIDS
inFasta = args.inputFasta
outFasta = args.outputFasta

ids = readIDS(idsFile)
filterFasta(inFasta,outFasta, ids)

2. Cytoscape is a well known tool to perform network analysis. It is well integrated with several online databases housing for example protein-protein interactions like EBI’s IntAct. It is also able to read and write a very simple text file called .sif to represent interactions between the nodes of a network. Sif formatted files are tab separated (\t) and each line represents a connection between the nodes of the network. For example:

   node1 interaction1 node2
   node1 interaction2 node3
   node2 interaction1 node3
   

   represents two types of interactions between node1, node2 and node3. Normally nodes are represented as circles in a network (graph) and interactions as lines (that can be of different kinds) connecting nodes (edges). The following is an extract from the file pka.sif that has been downloaded by Cytoscape from the database IntAct and represents the interactions of the Protein Kinase A (PKA) of E.coli:

   P75742  EBI-9168813 P76594
   P21513  EBI-888473  P76594
   P21513  EBI-15543881    P76594
   

   the first and third columns represent proteins and the second is the interaction joining them. All the values are identifiers from the IntAct database. The cytoscape representation of the full set of interactions is:

Write a python script that reads in the .sif file (pka.sif is here but even better if any .sif file specified in input by the user) and stores the information in one (or more) suitable objects to be able to:

1. Print the interaction that is more present among the nodes;
2. Print the node that is connected to the highest number of
other nodes (no matter if on the left or right of the interaction);

Hint: you can store the information in a dictionary having the interaction as key and a list of tuples (node1,node2) as value. Although redundant, it is convenient to keep a list of unique nodes. Note: This will use more memory but it is acceptable for small examples as it allows to quickly answer the questions.

Optional: check what these ids refer to on the IntAct database.

Show/Hide Solution

"""exercises/parseSif.py"""

import argparse

def readSif(fn):
    """reads in the sif file fn and ouptputs a
    dictionary and a list:
    interDict : has "interaction" as key
    and [(node1,node2), (node3,node4)] as values
    nodes list : is the list of unique node names
    (both on the right or left hand of an interaction)
    """
    interDict = {}
    nodes = []
    with open(fn, "r") as myfile:
        for line in myfile:
            line = line.strip()
            [n1,inter,n2] = line.split("\t")
            if inter not in interDict:
                interDict[inter] = [(n1,n2)]
            else:
                interDict[inter].append((n1,n2))

            if n1 not in nodes:
                nodes.append(n1)
            if n2 not in nodes:
                nodes.append(n2)

    return interDict,nodes

def getMostPresentInteraction(iDict):
    """gets the interaction dictionary as defined above and returns the
    most present interaction (with its count). If more than one, all are
    returned comma separated"""
    mpInter = ""
    mpInterCount = 0
    for inter in iDict:

        cnt = len(iDict[inter])

        if mpInterCount < cnt:
            mpInterCount = cnt
            mpInter = inter
        elif mpInterCount == cnt:
            #mpInterCount = cnt #not necessary
            mpInter = mpInter + "," + inter
    return (mpInter,mpInterCount)

def getMostPresentNode(iDict, nodeList):
    """gets the most highly connected node (or nodes, comma separated)
    and returns it with its count
    iDict : the interaction dictionary seen above
    nodeList : the node of unique node names seen above
    """
    mostPresentNode = ""
    mostPresentCount = 0
    #NOTE: iDict : {"inter1" : [(n1,n2), (n2,n3),(n3,n1), (n1,n3)],
    #               "inter2" : [(n5,n1), (n1,n2)] }
    #
    for n in nodeList:
        #the number of times a node is present is the sum of its count
        #in all interactions
        #both as first or second member of the couple
        curCnt = 0
        for i in iDict:
            pairsContainingN = [x for x in iDict[i] if n in x]
            curCnt = curCnt + len(pairsContainingN)
        if(curCnt > mostPresentCount):
            mostPresentNode = n
            mostPresentCount = curCnt
        elif curCnt == mostPresentCount:
            postPresentNode += "," + n
            mostPresentCount = curCnt

    return (mostPresentNode,mostPresentCount)

parser = argparse.ArgumentParser(description="""Reads and processes a .sif file""")
parser.add_argument("filename", type=str, help="The .sif file name")

args = parser.parse_args()
inputFile = args.filename
#inputFile = "file_samples/pka.sif"
interactions, nodeL = readSif(inputFile)
(mpI,mpICount) = getMostPresentInteraction(interactions)
print("The most present interaction(s): {}. Present {} times".format(mpI,mpICount))
(mpN, mpNCount) = getMostPresentNode(interactions,nodeL)
print("The most present node(s) {}. Present {} times".format(mpN,mpNCount))

3. Given a fasta file like contigs82.fasta specified in input by a user, write a python script that counts, for each sequence, the number of times that a DNA or protein string specified in input appears.

If we run something like: python3 find_stringInFasta.py contigs82.fasta TGCTCACAG

the result should print lines like:

TGCTCACAG in MDC052568.000: 1 times
TGCTCACAG in MDC002479.192: 1 times
TGCTCACAG in MDC040033.7: 1 times

Modify the program so that it outputs also the list of all the indexes where the string appears in each sequence in the fasta file. Try to look for the following sequences:

TTTTCCTAGG
TGCTCCGAGCATGTGATAATCATTCCAAGCTCCAT
TAAACAT
GATTACA

Show/Hide Solution

"""exercises/find_stringInFasta.py"""


import argparse

def getIndexes(string1,string2):
    """checks if string2 is present in string1 and returns
    all the positions at which string2 occurs in string1"""
    ret = []
    ind = string1.find(string2)

    while (ind > -1 and ind < len(string1)):
        ret.append(ind)
        ind = string1.find(string2,ind + 1)

    return ret

def processFasta(file,testStr):
    """reads a fasta file entry by entry checks if the input string
       testStr is present in each sequence. Reporting how many times and where.
    """
    header = ""
    seq = ""
    with open(file, "r") as f:
        for line in f:
            line = line.strip()
            if(line.startswith(">")):
                if(len(header) == 0 ):
                    #first entry:
                    header = line[1:]
                else:
                    #this is a new entry
                    indexes = getIndexes(seq,testStr)
                    if len(indexes) > 0:
                        print("{} in {}: {} times ({})".format(testStr,
                                                               header,
                                                               len(indexes),
                                                               indexes))
                    seq = ""
                    header = line[1:]
            else:
                seq +=line
    #processing the final entry
    indexes = getIndexes(seq,testStr)
    if len(indexes) > 0:
        print("{} in {}: {} times ({})".format(testStr,
                                               header,
                                               len(indexes),
                                               indexes))

parser = argparse.ArgumentParser(
    description="""Checks if a sequence is exactly contained in a fasta file"""
)
parser.add_argument("filename", type=str, help="The fasta file name")
parser.add_argument("query", type=str, help="The query string")

args = parser.parse_args()
#inFasta = args.filename
#testS = args.query
inFasta = "file_samples/contigs82.fasta"
testS = "TAAACAT"
processFasta(inFasta, testS)

4. The Fisher’s dataset regarding Petal and Sepal length and width in csv format can be found here. These are the measurements of the flowers of fifty plants each of the two species Iris setosa and Iris versicolor.

The header of the file is:

Species Number,Species Name,Petal width,Petal length,Sepal length,Sepal width

Write a python script that reads this file in input (feel free to hard-code the filename in the code) and computes the average petal length and width and sepal length and width for each of the three different Iris species. Print them to the screen alongside the number of elements.

Show/Hide Solution

def readCSV(f):
    """reads the csv dataset and returns a dictionary with
    species name as key and, as value, a dictionary with
    four keys : petalLen, sepalLen, petalWidth, sepalWidth
    """
    ret = dict()
    with open(f, "r") as file:
        for line in file:
            line = line.strip()
            if not line.startswith("Species Number"):
                data = line.split(",")
                speciesName = data[1]
                pWidth = int(data[2])
                pLen = int(data[3])
                sLen = int(data[4])
                sWidth = int(data[5])
                if(speciesName not in ret):
                    ret[speciesName] = {"petalLen" : [], "sepalLen" : [],
                                        "petalWidth" : [], "sepalWidth" : []
                                       }
                ret[speciesName]["petalLen"].append(pLen)
                ret[speciesName]["sepalLen"].append(sLen)
                ret[speciesName]["sepalWidth"].append(sWidth)
                ret[speciesName]["petalWidth"].append(pWidth)
    return ret

def printData(dataDict):
    for s in dataDict:
        avgPlen = sum(dataDict[s]["petalLen"])/len(dataDict[s]["petalLen"])
        avgPwid = sum(dataDict[s]["petalWidth"])/len(dataDict[s]["petalWidth"])
        avgSlen = sum(dataDict[s]["sepalLen"])/len(dataDict[s]["sepalLen"])
        avgSwid = sum(dataDict[s]["sepalWidth"])/len(dataDict[s]["sepalWidth"])
        print("Species {} has {} measurements:".format(s, len(dataDict[s]["petalLen"])))
        print("\t petal length {}".format(avgPlen))
        print("\t petal width {}".format(avgPwid))
        print("\t sepal length {}".format(avgSlen))
        print("\t sepal width {}".format(avgSwid))




inFile = "file_samples/Fishers_Iris.csv"

data = readCSV(inFile)
printData(data)

Species I. Setosa has 50 measurements:
         petal length 14.62
         petal width 2.46
         sepal length 34.28
         sepal width 50.1
Species I. Verginica has 50 measurements:
         petal length 55.52
         petal width 20.06
         sepal length 29.74
         sepal width 65.88
Species I. Versicolor has 50 measurements:
         petal length 43.22
         petal width 13.26
         sepal length 27.64
         sepal width 59.36

Practical 8

In this practical we will will practice Pandas.

Slides

The slides of the introduction can be found here: Intro

Libraries installation

First things first. Let’s start off by installing the required libraries. In particular we will need three libraries. Try and see if they are already available by typing the following commands in the console or put them in a python script:

import pandas as pd
import matplotlib.pyplot as plt
import numpy as np

if, upon execution, you do not get any error messages, you are sorted. Otherwise, you need to install them.

In Linux you can install the libraries by typing in a terminal sudo pip3 install matplotlib, sudo pip3 install pandas and sudo pip3 install numpy (or sudo python3.X -m pip install matplotlib, sudo python3.X -m pip install pandas and sudo python3.X -m pip install numpy), where X is your python version.

In Windows you can install the libraries by typing in the command prompt (to open it type cmd in the search) pip3 install matplotlib, pip3 install pandas and pip3 install numpy. If you are using anaconda you need to run these commands from the anaconda prompt.

Please install them in this order. You might not need to install numpy as matplotlib requires it. Once done that, try to perform the above imports again and they should work this time around.

Pandas

Pandas (the name comes from panel data) is a very efficient library to deal with numerical tables and time series. It is a quite complex library and here we will only scratch the surface of it. You can find a lot of information including the documentation on the Pandas website.

In particular the library pandas provides two data structures: Series and DataFrames.

Series

Series are 1-dimensional structures (like lists) containing data. Series are characterized by two types of information: the values and the index (a list of labels associated to the data), therefore they are a bit like a list and a bit like a dictionary. The index is optional and can be added by the library if not specified.

How to define and access a Series

There are several ways to define a Series. We can specify both the values and the index esplicitly, or through a dictionary, or let python add the default index for us. We can access the index with the Series.index method and the values with the Series.values.

import pandas as pd
import random

print("Values and index explicitly defined")
#values and index explicitely defined
S = pd.Series([random.randint(0,20) for x in range(0,10)],
              index = list("ABCDEFGHIL"))

print(S)
print("The index:", S.index)
print("The values:", S.values)

print("------------------------\n")
print("From dictionary")
#from a dictionary
S1 = pd.Series({"one" : 1, "two" : 2, "ten": 10,
                "three" : 3, "four": 4, "forty" : 40})
print(S1)
print(S1.index)
print(S1.values)
print("------------------------\n")
print("Default index")
#index added by default
myData = [random.randint(0,10) for x in range(10)]
S2 = pd.Series(myData)

print(S2)
print(S2.index)
print(S2.values)

print("------------------------\n")
print("Same value repeated")
S3 = pd.Series(1.27, range(10))
print(S3)
print(S3.index)
print(S3.values)

Values and index explicitly defined
A     9
B     6
C    20
D    10
E     0
F    13
G    10
H     4
I    14
L    15
dtype: int64
The index: Index(['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'L'], dtype='object')
The values: [ 9  6 20 10  0 13 10  4 14 15]
------------------------

From dictionary
one       1
two       2
ten      10
three     3
four      4
forty    40
dtype: int64
Index(['one', 'two', 'ten', 'three', 'four', 'forty'], dtype='object')
[ 1  2 10  3  4 40]
------------------------

Default index
0     8
1     2
2     8
3    10
4     1
5     5
6     3
7     8
8     9
9     5
dtype: int64
RangeIndex(start=0, stop=10, step=1)
[ 8  2  8 10  1  5  3  8  9  5]
------------------------

Same value repeated
0    1.27
1    1.27
2    1.27
3    1.27
4    1.27
5    1.27
6    1.27
7    1.27
8    1.27
9    1.27
dtype: float64
RangeIndex(start=0, stop=10, step=1)
[1.27 1.27 1.27 1.27 1.27 1.27 1.27 1.27 1.27 1.27]

Data in a series can be accessed by using the label (i.e. the index) as in a dictionary or through its position as in a list. Slicing is also allowed both by position and index. In the latter case, we can do Series[S:E] with S and E indexes, both S and E are included.

It is also possible to retrieve some elements by passing a list of positions or indexes. Head and tail methods can also be used to retrieve the top or bottom N elements with Series.head(N) or Series.tail(N).

Note: When the method returns more than one element, the return type is a Series.

import pandas as pd
import random

#values and index explicitely defined
S = pd.Series([random.randint(0,20) for x in range(0,10)],
              index = list("ABCDEFGHIL"))
print(S)
print("")

print("Value at label \"A\":", S["A"])
print("Value at index 1:", S[1])
print("")

print("Slicing from 1 to 3:") #note 3 excluded
print(S[1:3])
print("")
print("Slicing from C to H:") #note H included!
print(S["C":"H"])
print("")

print("Retrieving from list:")
print(S[[1,3,5,7,9]])
print(S[["A","C","E","G"]])
print("")

print("Top 3")
print(S.head(3))
print("")
print("Bottom 3")
print(S.tail(3))

A    15
B    11
C     4
D     7
E     1
F     4
G    15
H    14
I    14
L    17
dtype: int64

Value at label "A": 15
Value at index 1: 11

Slicing from 1 to 3:
B    11
C     4
dtype: int64

Slicing from C to H:
C     4
D     7
E     1
F     4
G    15
H    14
dtype: int64

Retrieving from list:
B    11
D     7
F     4
H    14
L    17
dtype: int64
A    15
C     4
E     1
G    15
dtype: int64

Top 3
A    15
B    11
C     4
dtype: int64

Bottom 3
H    14
I    14
L    17
dtype: int64

Operator broadcasting

Operations can automatically be broadcast to the entire Series. This is a quite cool feature and saves us from looping through the elements of the Series.

Example: Given a list of 10 integers and we want to divide them by 2. Without using pandas we would:

import random

listS = [random.randint(0,20) for x in range(0,10)]

print(listS)

for el in range(0,len(listS)):
    listS[el] /=2  #compact of X = X / 2

print(listS)

[6, 4, 5, 19, 14, 16, 9, 3, 13, 11]
[3.0, 2.0, 2.5, 9.5, 7.0, 8.0, 4.5, 1.5, 6.5, 5.5]

With pandas instead:

import pandas as pd
import random

S = pd.Series([random.randint(0,20) for x in range(0,10)],
              index = list("ABCDEFGHIL"))

print(S)
print("")
S1 = S / 2
print(S1)

A     4
B    13
C    14
D     6
E    13
F     2
G    13
H    19
I    20
L     7
dtype: int64

A     2.0
B     6.5
C     7.0
D     3.0
E     6.5
F     1.0
G     6.5
H     9.5
I    10.0
L     3.5
dtype: float64

Filtering

We can also apply boolean operators to obtain only the sub-Series with all the values satisfying a specific condition. This allows us to filter the Series.

Calling the boolean operator on the series alone (e.g. S > 10) will return a Series with True at the indexes where the condition is met, False at the others. Passing such a Series to a Series of the same lenght will return only the elements where the condition is True. Check the code below to see this in action.

import pandas as pd
import random

S = pd.Series([random.randint(0,20) for x in range(0,10)],
              index = list("ABCDEFGHIL"))

print(S)
print("")
S1 = S>10
print(S1)
print("")
S2 = S[S > 10]
print(S2)

A    14
B    18
C    10
D     6
E    17
F    14
G     2
H    17
I     4
L    15
dtype: int64

A     True
B     True
C    False
D    False
E     True
F     True
G    False
H     True
I    False
L     True
dtype: bool

A    14
B    18
E    17
F    14
H    17
L    15
dtype: int64

Missing data

Operations involving Series might have to deal with missing data or non-valid values (both cases are represented as NaN, that is not a number). Operations are carried out by aligning the Series based on their indexes. Indexes not in common end up in NaN values. Although most the operations that can be performed on series quite happily deal with NaNs, it is possible to drop NaN values or to fill them (i.e. replace their value with some other value). The sytax is:

Series.dropna()

or

Series.fillna(some_value)

Note that these operations do not modify the Series but rather return a new Series.

import pandas as pd
import random

S = pd.Series([random.randint(0,10) for x in range(0,10)],
              index = list("ABCDEFGHIL"))

S1 = pd.Series([random.randint(0,10) for x in range(0,8)],
              index = list("DEFGHAZY"))

print("The dimensions of these Series:", S.shape)
print("")
print(S1)
print("---- S + S1 ----")
Ssum = S + S1
print(Ssum)
print("---- Dropping NaNs ----")
print(Ssum.dropna())
print("---- Filling NaNs ----")
print(Ssum.fillna("my_value"))

The dimensions of these Series: (10,)

D     4
E     2
F     7
G     2
H     0
A     6
Z     1
Y    10
dtype: int64
---- S + S1 ----
A    10.0
B     NaN
C     NaN
D    14.0
E     4.0
F    14.0
G     8.0
H     1.0
I     NaN
L     NaN
Y     NaN
Z     NaN
dtype: float64
---- Dropping NaNs ----
A    10.0
D    14.0
E     4.0
F    14.0
G     8.0
H     1.0
dtype: float64
---- Filling NaNs ----
A          10
B    my_value
C    my_value
D          14
E           4
F          14
G           8
H           1
I    my_value
L    my_value
Y    my_value
Z    my_value
dtype: object

Computing stats

Pandas offer several operators to compute stats on the data stored in a Series. These include basic stats like min, max (and relative indexes with argmin and argmax) mean, std, quantile (to get the quantiles. A description of the data can be obtained by using the method describe and the counts for each value can be obtained by value_counts. Other methods available are sum and cumsum (for the sum and cumulative sum of the elements), autocorr and corr (for autocorrelation and correlation) and many others. For a complete list check the Pandas reference.

Note: as said before, when these methods do not return a single value, they return a Series.

Example: Fill the previous Series with the mean values of the series rather than NaNs.

Ssum = S + S1
print(Ssum)
print("---- Filling with avg value ----")
print(Ssum.fillna(Ssum.mean()))

A    10.0
B     NaN
C     NaN
D    14.0
E     4.0
F    14.0
G     8.0
H     1.0
I     NaN
L     NaN
Y     NaN
Z     NaN
dtype: float64
---- Filling with avg value ----
A    10.0
B     8.5
C     8.5
D    14.0
E     4.0
F    14.0
G     8.0
H     1.0
I     8.5
L     8.5
Y     8.5
Z     8.5
dtype: float64

Let’s see some operators introduced above in action.

import pandas as pd
import random

S = pd.Series([random.randint(0,10) for x in range(0,10)],
              index = list("ABCDEFGHIL"))
print("The data:")
print(S)
print("")
print("Its description")
print(S.describe())
print("")
print("Specifying different quantiles:")
print(S.quantile([0.1,0.2,0.8,0.9]))
print("")
print("Histogram:")
print(S.value_counts())
print("")
print("The type is a Series:")
print(type(S.value_counts()))
print("Summing the values:")
print(S.sum())
print("")
print("The cumulative sum:")
print(S.cumsum())

The data:
A     3
B    10
C     3
D     4
E     9
F     9
G     5
H     0
I    10
L     5
dtype: int64

Its description
count    10.000000
mean      5.800000
std       3.489667
min       0.000000
25%       3.250000
50%       5.000000
75%       9.000000
max      10.000000
dtype: float64

Specifying different quantiles:
0.1     2.7
0.2     3.0
0.8     9.2
0.9    10.0
dtype: float64

Histogram:
10    2
9     2
5     2
3     2
4     1
0     1
dtype: int64

The type is a Series:
<class 'pandas.core.series.Series'>
Summing the values:
58

The cumulative sum:
A     3
B    13
C    16
D    20
E    29
F    38
G    43
H    43
I    53
L    58
dtype: int64

Example:

Create two Series from the lists [2, 4, 6, 8, 10, 12, 13, 14, 15, 16], [1, 3, 5, 7, 9, 11, 13, 14, 15, 16] using the same index for both: [‘9B47’, ‘468B’, ‘B228’, ‘3C52’, ‘AE2E’, ‘DFF6’, ‘C38B’, ‘2CE5’, ‘0325’, ‘398F’].

Let’s compare the distribution stats of the two Series (mean value, max, min, quantiles) and get the index and value of the positions where the two series are the same. Finally, let’s get the sub-series where the first has an higher value than the first quartile of the second and compute its stats.

import pandas as pd

L1 = [2, 4, 6, 8, 10, 12, 13, 14, 15, 16]
L2 = [1, 3, 5, 7, 9, 11, 13, 14, 15, 16]
I = ['9B47', '468B', 'B228', '3C52', 'AE2E', 'DFF6', 'C38B', '2CE5', '0325', '398F']
L1Series = pd.Series(L1,index = I)
L2Series = pd.Series(L2, index = I)
#Let's describe the stats
print("Stats of L1Series")
print(L1Series.describe())
print("")
print("Stats of L2Series")
print(L2Series.describe())
print("")
#This is a Series with boolean values (True means the two Series where the same)
Leq = L1Series == L2Series
print("Equality series")
print(Leq)
print("")
#Get the subseries where both are the same
Lsub = L1Series[Leq]
print("Subseries of identicals")
print(Lsub)
print("")
#Get the values that are the same
print("Identical values:")
print(Lsub.values)
print("")
#Get the indexes where the two series are the same
print("Indexes of identical values:")
print(Lsub.index)
print("")
firstQuartile = L2Series.quantile(0.25)
print("The first quartile of L2Series:",firstQuartile)
print("")
#Get the subseries in which L1 is bigger than L2
Lbig = L1Series[L1Series > firstQuartile]
print("The subseries with L1 > L2")
print(Lbig)

Stats of L1Series
count    10.000000
mean     10.000000
std       4.830459
min       2.000000
25%       6.500000
50%      11.000000
75%      13.750000
max      16.000000
dtype: float64

Stats of L2Series
count    10.00000
mean      9.40000
std       5.25357
min       1.00000
25%       5.50000
50%      10.00000
75%      13.75000
max      16.00000
dtype: float64

Equality series
9B47    False
468B    False
B228    False
3C52    False
AE2E    False
DFF6    False
C38B     True
2CE5     True
0325     True
398F     True
dtype: bool

Subseries of identicals
C38B    13
2CE5    14
0325    15
398F    16
dtype: int64

Identical values:
[13 14 15 16]

Indexes of identical values:
Index(['C38B', '2CE5', '0325', '398F'], dtype='object')

The first quartile of L2Series: 5.5

The subseries with L1 > L2
B228     6
3C52     8
AE2E    10
DFF6    12
C38B    13
2CE5    14
0325    15
398F    16
dtype: int64

Plotting data

Using python’s matplotlib it is possible to plot data. The basic syntax is Series.plot(kind = "type") the parameter kind can be used to produce several types of plots (examples include line, hist, pie, bar, see here for all possible choices). Note that matplotlib needs to be imported and the pyplot needs to be shown with pyplot.show() to display the plot.

import pandas as pd
import matplotlib.pyplot as plt
import random
S = pd.Series([random.randint(0,10) for x in range(0,10)],
              index = list("ABCDEFGHIL"))
print("The data:")
print(S)
S1 = pd.Series([random.randint(0,10) for x in range(0,100)])

S.plot()
plt.show()
plt.close()
S1.plot(kind = "hist")
plt.show()
plt.close()
S.plot(kind = "pie")
plt.show()
plt.close()

The data:
A     2
B     6
C     4
D    10
E     0
F     7
G     3
H     8
I     5
L     2
dtype: int64

Example: Let’s create a series representing the sin, cos and sqrt functions and plot them.

import math
import matplotlib.pyplot as plt
import pandas as pd

x = [i/10 for i in range(0,500)]


y =  [math.sin(2*i/3.14 ) for i in x]
y1 = [math.cos(2*i/3.14 ) for i in x]
y2 = [math.sqrt(i) for i in x]
#print(x)

ySeries = pd.Series(y)
ySeries1 = pd.Series(y1)
ySeries2 = pd.Series(y2)

ySeries.plot()
plt.title("Sin function")
plt.show()
plt.close()
ySeries1.plot()
plt.title("Cos function")
plt.show()
plt.close()
ySeries2.plot()
plt.title("Sqrt function")
plt.show()
plt.close()
ySeries2 = (ySeries + 2*ySeries1)/ySeries2
ySeries2.plot()
plt.title("(sin(x) + 2cos(x)) / sqrt(x)")
plt.show()

Pandas DataFrames

DataFrames in pandas are the 2D analogous of Series. Dataframes are spreadsheet-like data structures with an ordered set of columns that can also be dishomogeneous. We can think about Dataframes as dictionaries of Series, each one representing a named column. Dataframes are described by an index that contains the labels of rows and a columns structure that holds the labels of the columns.

Note that the operation of extracting a column from a DataFrame returns a Series. Moreover, most (but not all!) of the operations that apply to Series also apply to DataFrames.

Define a DataFrame

There are several different ways to define a DataFrame. It is possible to create a DataFrame starting from a dictionary having Series as values. In this case, they keys of the dictionary are the columns of the DataFrame.

import pandas as pd

myData = {
    "temperature" : pd.Series([1, 3, 8, 13, 17, 20, 22, 22,18 ,13,6,2],
                            index = ["Jan","Feb", "Mar","Apr","May","Jun",
                                     "Jul","Aug","Sep","Oct","Nov","Dec"]
                             ),
    "dayLength" : pd.Series([9.7, 10.9, 12.5, 14.1, 15.6, 16.3, 15.9,
                             14.6,13,11.4,10,9.3],
                            index = ["Jan","Feb", "Mar","Apr","May","Jun",
                                     "Jul","Aug","Sep","Oct","Nov","Dec"]
                             )

}

DF = pd.DataFrame(myData)
print(DF)

print(DF.columns)
print(DF.index)

     dayLength  temperature
Jan        9.7            1
Feb       10.9            3
Mar       12.5            8
Apr       14.1           13
May       15.6           17
Jun       16.3           20
Jul       15.9           22
Aug       14.6           22
Sep       13.0           18
Oct       11.4           13
Nov       10.0            6
Dec        9.3            2
Index(['dayLength', 'temperature'], dtype='object')
Index(['Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', 'Oct',
       'Nov', 'Dec'],
      dtype='object')

If the index is not specified, it is given by default:

import pandas as pd
import matplotlib.pyplot as plt

myData = {
    "temperature" : pd.Series([1, 3, 8, 13, 17, 20,
                               22, 22,18 ,13,6,2]),
    "dayLength" : pd.Series([9.7, 10.9, 12.5, 14.1, 15.6,
                             16.3,15.9,14.6,13,11.4,10,9.3])

}

DF = pd.DataFrame(myData)
print(DF)
print(DF.index)

DF.plot()
plt.show()
plt.close()
DF.plot(kind ="box")
plt.show()

    dayLength  temperature
0         9.7            1
1        10.9            3
2        12.5            8
3        14.1           13
4        15.6           17
5        16.3           20
6        15.9           22
7        14.6           22
8        13.0           18
9        11.4           13
10       10.0            6
11        9.3            2
RangeIndex(start=0, stop=12, step=1)

It is also possible to define a DataFrame from a list of dictionaries holding a set of values rather than Series. Note that when columns do not have the corresponding information a NaN is added. Indexes and columns can be changed after they have been defined.

import pandas as pd

myData = [{"A" : 1, "B" : 2, "C" : 3.2, "D" : 10},
          {"A" : 1, "B" : 2, "F" : 3.2, "G" : 10, "H":1},
          {"A" : 1, "B" : 2, "C" : 3.2, "D" : 1,
           "E": 4.1, "F" : 3.2, "G" : 10, "H":1}

         ]

DF = pd.DataFrame(myData)
print(DF)
print("")
#Let's change the columns and indexes
columns = "val1,val2,val3,val4,val5,val6,val7,val8".split(',')
inds = ["Day1", "Day2", "Day3"]

DF.columns = columns
DF.index = inds
print(DF)

   A  B    C     D    E    F     G    H
0  1  2  3.2  10.0  NaN  NaN   NaN  NaN
1  1  2  NaN   NaN  NaN  3.2  10.0  1.0
2  1  2  3.2   1.0  4.1  3.2  10.0  1.0

      val1  val2  val3  val4  val5  val6  val7  val8
Day1     1     2   3.2  10.0   NaN   NaN   NaN   NaN
Day2     1     2   NaN   NaN   NaN   3.2  10.0   1.0
Day3     1     2   3.2   1.0   4.1   3.2  10.0   1.0

Loading data from external files

Pandas also provide methods to load data from external files. In particular, to load data from a .cvs file, we can use the method pandas.read_csv(filename). This method has a lot of parameters, you can see all the details on its usage on the official documentation. Some useful optional parameters are the separator (to specify the column separator like sep="\t" for tab separated files), the character to identify comments (comment="#") or that to skip some lines (like the header for example or any initial comments to the file) skiprows=N. The rows to use as column header can be specified with the parameter header that accepts a number or a list of numbers. Similarly, the columns to use as index can be specified with the parameter index_col.

Other methods to read data in are pandas.read_excel(filename) that works in a similar way but can load excel files (see here).

Example: Let’s load the data stored in a csv datafile sampledata_orders.csv in a pandas DataFrame.

import pandas as pd

orders = pd.read_csv("file_samples/sampledata_orders.csv",
                     sep=",", index_col = 0, header = 0)
print("First 5 entries:")
print(orders.head())
print("")
print("The index:")
print(orders.index)
print("")
print("The column names:")
print(orders.columns)
print("")
print("A description of the numerical values:")
print(orders.describe())

First 5 entries:
        Order ID  Order Date Order Priority  Order Quantity       Sales  \
Row ID
1              3  10/13/2010            Low               6    261.5400
49           293   10/1/2012           High              49  10123.0200
50           293   10/1/2012           High              27    244.5700
80           483   7/10/2011           High              30   4965.7595
85           515   8/28/2010  Not Specified              19    394.2700

        Discount       Ship Mode   Profit  Unit Price  Shipping Cost  \
Row ID
1           0.04     Regular Air  -213.25       38.94          35.00
49          0.07  Delivery Truck   457.81      208.16          68.02
50          0.01     Regular Air    46.71        8.69           2.99
80          0.08     Regular Air  1198.97      195.99           3.99
85          0.08     Regular Air    30.94       21.78           5.94

             Customer Name Province   Region Customer Segment  \
Row ID
1       Muhammed MacIntyre  Nunavut  Nunavut   Small Business
49            Barry French  Nunavut  Nunavut         Consumer
50            Barry French  Nunavut  Nunavut         Consumer
80           Clay Rozendal  Nunavut  Nunavut        Corporate
85          Carlos Soltero  Nunavut  Nunavut         Consumer

       Product Category            Product Sub-Category  \
Row ID
1       Office Supplies          Storage & Organization
49      Office Supplies                      Appliances
50      Office Supplies  Binders and Binder Accessories
80           Technology    Telephones and Communication
85      Office Supplies                      Appliances

                                             Product Name Product Container  \
Row ID
1        Eldon Base for stackable storage shelf, platinum         Large Box
49      1.7 Cubic Foot Compact "Cube" Office Refrigera...        Jumbo Drum
50       Cardinal Slant-D® Ring Binder, Heavy Gauge Vinyl         Small Box
80                                                   R380         Small Box
85                               Holmes HEPA Air Purifier        Medium Box

        Product Base Margin   Ship Date
Row ID
1                      0.80  10/20/2010
49                     0.58   10/2/2012
50                     0.39   10/3/2012
80                     0.58   7/12/2011
85                     0.50   8/30/2010

The index:
Int64Index([   1,   49,   50,   80,   85,   86,   97,   98,  103,  107,
            ...
            6492, 6526, 6657, 7396, 7586, 7765, 7766, 7906, 7907, 7914],
           dtype='int64', name='Row ID', length=8399)

The column names:
Index(['Order ID', 'Order Date', 'Order Priority', 'Order Quantity', 'Sales',
       'Discount', 'Ship Mode', 'Profit', 'Unit Price', 'Shipping Cost',
       'Customer Name', 'Province', 'Region', 'Customer Segment',
       'Product Category', 'Product Sub-Category', 'Product Name',
       'Product Container', 'Product Base Margin', 'Ship Date'],
      dtype='object')

A description of the numerical values:
           Order ID  Order Quantity         Sales     Discount        Profit  \
count   8399.000000     8399.000000   8399.000000  8399.000000   8399.000000
mean   29965.179783       25.571735   1775.878179     0.049671    181.184423
std    17260.883447       14.481071   3585.050525     0.031823   1196.653372
min        3.000000        1.000000      2.240000     0.000000 -14140.700000
25%    15011.500000       13.000000    143.195000     0.020000    -83.315000
50%    29857.000000       26.000000    449.420000     0.050000     -1.500000
75%    44596.000000       38.000000   1709.320000     0.080000    162.750000
max    59973.000000       50.000000  89061.050000     0.250000  27220.690000

        Unit Price  Shipping Cost  Product Base Margin
count  8399.000000    8399.000000          8336.000000
mean     89.346259      12.838557             0.512513
std     290.354383      17.264052             0.135589
min       0.990000       0.490000             0.350000
25%       6.480000       3.300000             0.380000
50%      20.990000       6.070000             0.520000
75%      85.990000      13.990000             0.590000
max    6783.020000     164.730000             0.850000

Extract values by row and column

Once a DataFrame is populated we can access its content. Several options are available:

1. Select by column DataFrame[col] returns a Series
2. Select by row label DataFrame.loc[row_label] returns a Series
3. Select row by integer location DataFrame.iloc[row_position] returns a Series
4. Slice rows DataFrame[S:E] (S and E are labels, both included) returns a DataFrame
5. Select rows by boolean vector DataFrame[bool_vect] returns a DataFrame

Note that if names are well formed (i.e. no spaces, no strange characters…) we can use DataFrame.col instead of DataFrame[col]. Here are some ways to extract data from the orders dataframe:

import pandas as pd

orders = pd.read_csv("file_samples/sampledata_orders.csv", sep=",", index_col =0, header=0)

print("The Order Quantity column (top 5)")
print(orders["Order Quantity"].head(5))
print("")
print("The Sales column (top 10)")
print(orders.Sales.head(10))
print("")
print("The row with ID:50")
r50 = orders.loc[50]
print(r50)
print("")
print("The third row:")
print(orders.iloc[3])

print("The Order Quantity, Sales, Discount and Profit of the 2nd,4th, 6th and 8th row:")
print(orders[1:8:2][["Order Quantity", "Sales","Discount", "Profit"]])
print("The Order Quantity, Sales, Discount and  Profit of orders with discount > 10%:")
print(orders[orders["Discount"] > 0.1][["Order Quantity", "Sales","Discount", "Profit"]])

The Order Quantity column (top 5)
Row ID
1      6
49    49
50    27
80    30
85    19
Name: Order Quantity, dtype: int64

The Sales column (top 10)
Row ID
1        261.5400
49     10123.0200
50       244.5700
80      4965.7595
85       394.2700
86       146.6900
97        93.5400
98       905.0800
103     2781.8200
107      228.4100
Name: Sales, dtype: float64

The row with ID:50
Order ID                                                             293
Order Date                                                     10/1/2012
Order Priority                                                      High
Order Quantity                                                        27
Sales                                                             244.57
Discount                                                            0.01
Ship Mode                                                    Regular Air
Profit                                                             46.71
Unit Price                                                          8.69
Shipping Cost                                                       2.99
Customer Name                                               Barry French
Province                                                         Nunavut
Region                                                           Nunavut
Customer Segment                                                Consumer
Product Category                                         Office Supplies
Product Sub-Category                      Binders and Binder Accessories
Product Name            Cardinal Slant-D® Ring Binder, Heavy Gauge Vinyl
Product Container                                              Small Box
Product Base Margin                                                 0.39
Ship Date                                                      10/3/2012
Name: 50, dtype: object

The third row:
Order ID                                         483
Order Date                                 7/10/2011
Order Priority                                  High
Order Quantity                                    30
Sales                                        4965.76
Discount                                        0.08
Ship Mode                                Regular Air
Profit                                       1198.97
Unit Price                                    195.99
Shipping Cost                                   3.99
Customer Name                          Clay Rozendal
Province                                     Nunavut
Region                                       Nunavut
Customer Segment                           Corporate
Product Category                          Technology
Product Sub-Category    Telephones and Communication
Product Name                                    R380
Product Container                          Small Box
Product Base Margin                             0.58
Ship Date                                  7/12/2011
Name: 80, dtype: object
The Order Quantity, Sales, Discount and Profit of the 2nd,4th, 6th and 8th row:
        Order Quantity       Sales  Discount   Profit
Row ID
49                  49  10123.0200      0.07   457.81
80                  30   4965.7595      0.08  1198.97
86                  21    146.6900      0.05     4.43
98                  22    905.0800      0.09   127.70
The Order Quantity, Sales, Discount and  Profit of orders with discount > 10%:
        Order Quantity    Sales  Discount  Profit
Row ID
176                 11  663.784      0.25 -481.04
3721                22  338.520      0.21  -17.75
37                  43  586.110      0.11   98.44
2234                 1   27.960      0.17   -9.13
4900                49  651.900      0.16  -74.51

Broadcasting, filtering and computing stats

These work pretty much like on Series and pandas takes care of adding NaNs when it cannot perform some operations due to missing values and so on.

Obviously some operators, when applied to entire tables might not always make sense (like mean or sum of strings).

import pandas as pd

orders = pd.read_csv("file_samples/sampledata_orders.csv", sep=",", index_col =0, header=0)

orders_10 = orders[["Sales","Profit", "Product Category"]].head(10)
orders_5 = orders[["Sales","Profit", "Product Category"]].head()
orders_20 = orders[["Sales","Profit", "Product Category"]].head(20)
print(orders_20)
print("")

#Summing over the entries, does not make sense but...
print("Top10 + Top5:")
print(orders_10 + orders_5)
print("")

prod_cost = orders_20["Sales"] - orders_20["Profit"]
print(prod_cost)

print("")
print("Technology orders")
print(orders_20[orders_20["Product Category"] == "Technology"])
print("")
print("Office Supplies positive profit")
print(orders_20[ (orders_20["Product Category"] == "Office Supplies") & (orders_20["Profit"] >0) ])

             Sales   Profit Product Category
Row ID
1         261.5400  -213.25  Office Supplies
49      10123.0200   457.81  Office Supplies
50        244.5700    46.71  Office Supplies
80       4965.7595  1198.97       Technology
85        394.2700    30.94  Office Supplies
86        146.6900     4.43        Furniture
97         93.5400   -54.04  Office Supplies
98        905.0800   127.70  Office Supplies
103      2781.8200  -695.26  Office Supplies
107       228.4100  -226.36  Office Supplies
127       196.8500  -166.85  Office Supplies
128       124.5600   -14.33  Office Supplies
134       716.8400   134.72  Office Supplies
135      1474.3300   114.46       Technology
149        80.6100    -4.72  Office Supplies
160      1815.4900   782.91        Furniture
161       248.2600    93.80  Office Supplies
175      4462.2300   440.72        Furniture
176       663.7840  -481.04        Furniture
203       834.9040   -11.68       Technology

Top10 + Top5:
            Sales   Profit                Product Category
Row ID
1         523.080  -426.50  Office SuppliesOffice Supplies
49      20246.040   915.62  Office SuppliesOffice Supplies
50        489.140    93.42  Office SuppliesOffice Supplies
80       9931.519  2397.94            TechnologyTechnology
85        788.540    61.88  Office SuppliesOffice Supplies
86            NaN      NaN                             NaN
97            NaN      NaN                             NaN
98            NaN      NaN                             NaN
103           NaN      NaN                             NaN
107           NaN      NaN                             NaN

Row ID
1       474.7900
49     9665.2100
50      197.8600
80     3766.7895
85      363.3300
86      142.2600
97      147.5800
98      777.3800
103    3477.0800
107     454.7700
127     363.7000
128     138.8900
134     582.1200
135    1359.8700
149      85.3300
160    1032.5800
161     154.4600
175    4021.5100
176    1144.8240
203     846.5840
dtype: float64

Technology orders
            Sales   Profit Product Category
Row ID
80      4965.7595  1198.97       Technology
135     1474.3300   114.46       Technology
203      834.9040   -11.68       Technology

Office Supplies positive profit
           Sales  Profit Product Category
Row ID
49      10123.02  457.81  Office Supplies
50        244.57   46.71  Office Supplies
85        394.27   30.94  Office Supplies
98        905.08  127.70  Office Supplies
134       716.84  134.72  Office Supplies
161       248.26   93.80  Office Supplies

Statistics can be computed by column (normally the default) or by row (specifying axis=1) or on the entire table.

Here you can find the complete list of methods that can be applied.

import pandas as pd

data = pd.read_csv("file_samples/random.csv", sep=",", header=0)

print("Global description")
print(data.describe())
print("")

print(data)
print("")

print("Let's reduce A in [0,1]")
print(data["A"]/ data["A"].max())

print("Let's reduce first row in [0,1]")
print(data.iloc[0]/ data.loc[0].max())

print("Mean and std values (by column)")
print(data.mean())
print(data.std())
print("")
print("Mean and std values (by column) - top 10 values")
print(data.head(10).mean(axis=1))
print(data.head(10).std(axis=1))

print("Cumulative sum (by column)- top 10 rows")
print(data.head(10).cumsum())

print("Cumulative sum (by row) - top 10 rows")
print(data.head(10).cumsum(axis = 1 ))

Global description
               A          B           C          D           E          F  \
count  50.000000  50.000000   50.000000  50.000000   50.000000  50.000000
mean   45.240000  49.760000   54.120000  50.500000   57.860000  49.180000
std    28.393417  32.193015   25.165282  28.321226   32.443364  28.488229
min     0.000000   0.000000    5.000000   1.000000    2.000000   1.000000
25%    21.750000  18.000000   35.750000  28.250000   29.250000  25.000000
50%    42.000000  49.500000   52.500000  49.500000   68.000000  52.000000
75%    63.250000  76.250000   73.750000  76.000000   86.750000  75.500000
max    99.000000  99.000000  100.000000  95.000000  100.000000  97.000000

                G         H          I           L
count   50.000000  50.00000  50.000000   50.000000
mean    49.780000  47.78000  46.920000   51.780000
std     29.673248  29.75978  31.056788   30.613649
min      1.000000   1.00000   0.000000    3.000000
25%     26.500000  24.50000  19.000000   26.250000
50%     51.000000  42.50000  44.000000   46.500000
75%     76.750000  72.00000  73.000000   82.000000
max    100.000000  99.00000  98.000000  100.000000

     A   B    C   D    E   F    G   H   I    L
0   28  69    5  41   12  62   90  32  33   85
1   91  59   64  94    4  51   45  52  96    5
2   54  74   53  92   20  84   85  21  98   73
3   99   0   39  12   90  15   62  38   4   67
4   98  10   35  77   46  97   88  72  15   37
5   44   9   91  57   98  63   52  77  62    7
6   76  17   12  41   69  34  100  29   0   91
7   52  25   43  59   87  91    1  90  23   90
8   56  33   38  91   13   1   34  17  22   82
9   29  18   42  48   34  16   64   7  46    9
10  81  77   38  93   63  90   57  58  52  100
11  57  97   23  59   38  93   46  49  88   86
12  57   0   79  78  100  76   16  31  79    8
13  18   1   67  44    2  17   53  51   6   23
14  77  95   94  88    9  25   54  23  36   35
15  87  42   63  33   95  53   11  58  53    3
16  34  24   24  28   74  79   86  98  42   90
17   1  31   20  63   70   3   29  39   5   87
18  35  17   77  15    9  63   86  95  95   21
19   0  85   13  13   60  74   44  78   7   56
20  61  20   47  21   85  78   53  14  37   70
21  81  15   89  54   38  59   72  35  59   12
22  20  81   76  15   64  18    9  47  11   81
23  57  94   73  19   21  79   81  45  71   40
24   2  58   83  67   99  46   76  70  50   45
25  64  13   52  60   32  70   32   4  73   20
26  27  49  100  48   70  30   58  48  42   36
27  82  89   93  73   30  64   18  54  93   82
28  19  85   98   7   84  71   77  20  18   63
29  34  95   68  23   68  38   73   1  28   10
30  33  60   66  80   94  41   53  99  29   57
31   0  99   18   2   29  28   11  30  36   56
32  20  61   33  89   52  59   50  55   4   33
33  82  72   41  33   92  16   18  99  73   91
34   8  28   22  29   83  53   47  10  42   34
35  64  50   24  59    6  83   92  91  87   98
36  42  73   50  17   91   9   39  37  97   50
37  27  49   67  61   21  25   94  96  16   98
38  44  44   48  70   86  85    9  31   4   46
39  36  93   64   1   96  89   14  75  10   84
40  20  13   34  87   11  10    2   5  91   27
41  54   2   61  80   98  53   96  40   2   26
42  42  88   79  31   41  23   50  95  77   26
43   7  14   56  95   70  28   78  31  34   95
44  40  65   34  44   97  36    3  90  55   13
45  97  61   45  32   91  26   84  33  57   80
46  60  49   47  92   81  51    7  18  66   47
47  39  98   90  33   68   5   26  72  76   37
48   6  18   74  51   77  19   28  21  81   46
49  20  69   54  26   25  80   36   8  65   31

Let's reduce A in [0,1]
0     0.282828
1     0.919192
2     0.545455
3     1.000000
4     0.989899
5     0.444444
6     0.767677
7     0.525253
8     0.565657
9     0.292929
10    0.818182
11    0.575758
12    0.575758
13    0.181818
14    0.777778
15    0.878788
16    0.343434
17    0.010101
18    0.353535
19    0.000000
20    0.616162
21    0.818182
22    0.202020
23    0.575758
24    0.020202
25    0.646465
26    0.272727
27    0.828283
28    0.191919
29    0.343434
30    0.333333
31    0.000000
32    0.202020
33    0.828283
34    0.080808
35    0.646465
36    0.424242
37    0.272727
38    0.444444
39    0.363636
40    0.202020
41    0.545455
42    0.424242
43    0.070707
44    0.404040
45    0.979798
46    0.606061
47    0.393939
48    0.060606
49    0.202020
Name: A, dtype: float64
Let's reduce first row in [0,1]
A    0.311111
B    0.766667
C    0.055556
D    0.455556
E    0.133333
F    0.688889
G    1.000000
H    0.355556
I    0.366667
L    0.944444
Name: 0, dtype: float64
Mean and std values (by column)
A    45.24
B    49.76
C    54.12
D    50.50
E    57.86
F    49.18
G    49.78
H    47.78
I    46.92
L    51.78
dtype: float64
A    28.393417
B    32.193015
C    25.165282
D    28.321226
E    32.443364
F    28.488229
G    29.673248
H    29.759780
I    31.056788
L    30.613649
dtype: float64

Mean and std values (by column) - top 10 values
0    45.7
1    56.1
2    65.4
3    42.6
4    57.5
5    56.0
6    46.9
7    56.1
8    38.7
9    31.3
dtype: float64
0    29.424291
1    33.013297
2    27.785688
3    35.647035
4    33.069792
5    30.342489
6    34.853503
7    32.942543
8    29.431842
9    18.826990
dtype: float64
Cumulative sum (by column)- top 10 rows
     A    B    C    D    E    F    G    H    I    L
0   28   69    5   41   12   62   90   32   33   85
1  119  128   69  135   16  113  135   84  129   90
2  173  202  122  227   36  197  220  105  227  163
3  272  202  161  239  126  212  282  143  231  230
4  370  212  196  316  172  309  370  215  246  267
5  414  221  287  373  270  372  422  292  308  274
6  490  238  299  414  339  406  522  321  308  365
7  542  263  342  473  426  497  523  411  331  455
8  598  296  380  564  439  498  557  428  353  537
9  627  314  422  612  473  514  621  435  399  546
Cumulative sum (by row) - top 10 rows
    A    B    C    D    E    F    G    H    I    L
0  28   97  102  143  155  217  307  339  372  457
1  91  150  214  308  312  363  408  460  556  561
2  54  128  181  273  293  377  462  483  581  654
3  99   99  138  150  240  255  317  355  359  426
4  98  108  143  220  266  363  451  523  538  575
5  44   53  144  201  299  362  414  491  553  560
6  76   93  105  146  215  249  349  378  378  469
7  52   77  120  179  266  357  358  448  471  561
8  56   89  127  218  231  232  266  283  305  387
9  29   47   89  137  171  187  251  258  304  313

Merging DataFrames

It is possible to merge together DataFrames having a common column name. The merge can be done with the pandas merge method. Upon merging, the two tables will be concatenated into a bigger one containing information from both DataFrames. The basic syntax is:

pandas.merge(DataFrame1, DataFrame2, on="col_name", how="inner/outer/left/right")

The column on which perform the merge is specified with the parameter on followed by the column name, while the behaviour of the merging depends on the parameter how that tells pandas how to behave when dealing with non-matching data. In particular:

1. how = inner : non-matching entries are discarded;
2. how = left : ids are taken from the first DataFrame;
3. how = right : ids are taken from the second DataFrame;
4. how = outer : ids from both are retained.

import pandas as pd

Snp1 = {"id": ["SNP_FB_0411211","SNP_FB_0412425","SNP_FB_0942385",
               "CH01f09","Hi05f12x","SNP_FB_0942712" ],
        "type" : ["SNP","SNP","SNP","SSR","SSR","SNP"]
       }
Snp2 = {"id" : ["SNP_FB_0411211","SNP_FB_0412425",
                "SNP_FB_0942385", "CH01f09","SNP_FB_0428218" ],
      "chr" : ["1", "15","7","9","1"]
     }

DFs1 = pd.DataFrame(Snp1)
DFs2 = pd.DataFrame(Snp2)

print(DFs1)
print(DFs2)
print("")
print("Inner merge (only common in both)")
inJ = pd.merge(DFs1,DFs2, on = "id", how = "inner")
print(inJ)
print("")
print("Left merge (IDS from DFs1)")
leftJ = pd.merge(DFs1,DFs2, on = "id", how = "left")
print(leftJ)
print("")
print("Right merge (IDS from DFs2)")
rightJ = pd.merge(DFs1,DFs2, on = "id", how = "right")
print(rightJ)
print("")
print("Outer merge (IDS from both)")
outJ = pd.merge(DFs1,DFs2, on = "id", how = "outer")
print(outJ)

               id type
0  SNP_FB_0411211  SNP
1  SNP_FB_0412425  SNP
2  SNP_FB_0942385  SNP
3         CH01f09  SSR
4        Hi05f12x  SSR
5  SNP_FB_0942712  SNP
  chr              id
0   1  SNP_FB_0411211
1  15  SNP_FB_0412425
2   7  SNP_FB_0942385
3   9         CH01f09
4   1  SNP_FB_0428218

Inner merge (only common in both)
               id type chr
0  SNP_FB_0411211  SNP   1
1  SNP_FB_0412425  SNP  15
2  SNP_FB_0942385  SNP   7
3         CH01f09  SSR   9

Left merge (IDS from DFs1)
               id type  chr
0  SNP_FB_0411211  SNP    1
1  SNP_FB_0412425  SNP   15
2  SNP_FB_0942385  SNP    7
3         CH01f09  SSR    9
4        Hi05f12x  SSR  NaN
5  SNP_FB_0942712  SNP  NaN

Right merge (IDS from DFs2)
               id type chr
0  SNP_FB_0411211  SNP   1
1  SNP_FB_0412425  SNP  15
2  SNP_FB_0942385  SNP   7
3         CH01f09  SSR   9
4  SNP_FB_0428218  NaN   1

Outer merge (IDS from both)
               id type  chr
0  SNP_FB_0411211  SNP    1
1  SNP_FB_0412425  SNP   15
2  SNP_FB_0942385  SNP    7
3         CH01f09  SSR    9
4        Hi05f12x  SSR  NaN
5  SNP_FB_0942712  SNP  NaN
6  SNP_FB_0428218  NaN    1

Note that the columns we merge on do not necessarily need to be the same, we can specify a correspondence between the row of the first dataframe (the one on the left) and the second dataframe (the one on the right) specifying which columns must have the same values to perform the merge. This can be done by using the parameters right_on = column_name and left_on = column_name:

%reset -s -f

import pandas as pd

d = dict({"A" : [1,2,3,4], "B" : [3,4,73,13]})
d2 = dict({"E" : [1,4,3,13], "F" : [3,1,71,1]})

DF = pd.DataFrame(d)
DF2 = pd.DataFrame(d2)

merged_onBE = DF.merge(DF2, left_on = 'B', right_on = 'E', how = "inner")
merged_onAF = DF.merge(DF2, right_on = "F", left_on = "A", how = "outer")
print("DF:")
print(DF)
print("DF2:")
print(DF2)
print("\ninner merge on BE")
print(merged_onBE)
print("\nouter merge on AF:")
print(merged_onAF)

DF:
   A   B
0  1   3
1  2   4
2  3  73
3  4  13
DF2:
    E   F
0   1   3
1   4   1
2   3  71
3  13   1

inner merge on BE
   A   B   E   F
0  1   3   3  71
1  2   4   4   1
2  4  13  13   1

outer merge on AF:
     A     B     E     F
0  1.0   3.0   4.0   1.0
1  1.0   3.0  13.0   1.0
2  2.0   4.0   NaN   NaN
3  3.0  73.0   1.0   3.0
4  4.0  13.0   NaN   NaN
5  NaN   NaN   3.0  71.0

Grouping

Given a DataFrame, it is possible to apply the so called split-apply-aggregate processing method. Basically, this helps to group the data according to the value of some columns, apply a function on the different groups and aggregate the results in a new DataFrame.

Grouping of a DataFrame can be done by using the DataFrame.groupby(columnName) method which returns a pandas.DataFrameGroupBy object, which basically is composed of two information the name shared by each group and a DataFrame containing all the elements belonging to that group.

Given a grouped DataFrame, each group can be obtained with the get_group(groupName) it is also possible to loop over the groups:

for groupName, groupDataFrame in grouped:
    #do something

It is also possible to aggregate the groups by applying some functions to each of them (please refer to the documentation).

Let’s see these things in action.

Example Given a list of labels and integers group them by label and compute the mean of all values in each group.

import pandas as pd

test = {"x": ["a","a", "b", "b", "c", "c" ],
        "y" : [2,4,0,5,5,10]
       }

DF = pd.DataFrame(test)
print(DF)
print("")
gDF = DF.groupby("x")
for i,g in gDF:
    print("Group: ", i)
    print(g)
    print(type(g))

aggDF = gDF.aggregate(pd.DataFrame.mean)
print(aggDF)

   x   y
0  a   2
1  a   4
2  b   0
3  b   5
4  c   5
5  c  10

Group:  a
   x  y
0  a  2
1  a  4
<class 'pandas.core.frame.DataFrame'>
Group:  b
   x  y
2  b  0
3  b  5
<class 'pandas.core.frame.DataFrame'>
Group:  c
   x   y
4  c   5
5  c  10
<class 'pandas.core.frame.DataFrame'>
     y
x
a  3.0
b  2.5
c  7.5

Example Given the orders data seen above, let’s get the columns “Sales”, “Profit” and “Product Category” and compute the total sum and the mean of the sales and profits for each product category.

import pandas as pd
import matplotlib.pyplot as plt

orders = pd.read_csv("file_samples/sampledata_orders.csv", sep=",",
                     index_col =0, header=0)

SPC = orders[["Sales","Profit", "Product Category"]]
print(SPC.head())

SPC.plot(kind = "hist", bins = 10)
plt.show()

print("")
grouped = SPC.groupby("Product Category")
for i,g in grouped:
    print("Group: ", i)

print("")
print("Count elements per category:") #get the series corresponding to the column
                                      #and apply the value_counts() method
print(orders["Product Category"].value_counts())
print("")
print("Total values:")
print(grouped.aggregate(pd.DataFrame.sum)[["Sales"]])

print("Mean values (sorted by profit):")
mv_sorted = grouped.aggregate(pd.DataFrame.mean).sort_values(by="Profit")
print(mv_sorted)
print("")
print("The most profitable is {}".format(mv_sorted.index[-1]))

             Sales   Profit Product Category
Row ID
1         261.5400  -213.25  Office Supplies
49      10123.0200   457.81  Office Supplies
50        244.5700    46.71  Office Supplies
80       4965.7595  1198.97       Technology
85        394.2700    30.94  Office Supplies

Group:  Furniture
Group:  Office Supplies
Group:  Technology

Count elements per category:
Office Supplies    4610
Technology         2065
Furniture          1724
Name: Product Category, dtype: int64

Total values:
                        Sales
Product Category
Furniture         5178590.542
Office Supplies   3752762.100
Technology        5984248.182
Mean values (sorted by profit):
                        Sales      Profit
Product Category
Furniture         3003.822820   68.116607
Office Supplies    814.048178  112.369072
Technology        2897.941008  429.207516

The most profitable is Technology

Exercises

1. The file top_3000_words.txt is a one-column file representing the top 3000 English words. Read the file and for each letter, count how many words start with that letter. Store this information in a dictionary. Create a pandas series from the dictionary and plot an histogram of all initials counting more than 100 words starting with them.

Show/Hide Solution

import pandas as pd
import matplotlib.pyplot as plt


def readFile(file):
    fh = open(file, "r")
    initials = dict()
    for line in fh:
        line = line.strip().lower()
        init = line[0]
        if init in initials:
            initials[init] += 1
        else:
            initials[init] = 1
    fh.close()

    return initials

def filter_and_plot(data, minCount = 10):
    series = pd.Series(myDict)

    filt_series = series[series > minCount]
    filt_series.plot(kind = 'bar')
    plt.show()

inFile = "file_samples/top_3000_words.txt"

myDict = readFile(inFile)
filter_and_plot(myDict,100)

2. The file filt_aligns.tsv is a tab separated value file representing alignments of paired-end reads on some apple chromosomes. Paired end reads have the property of being X bases apart from each other as they have been sequenced from the two ends of some size-selected DNA molecules.

Each line of the file has the following information readID\tChrPE1\tAlignmentPosition1\tChrPE2\tAlignmentPosition2. The two ends of the same pair have the same readID. Load the read pairs aligning on the same chromosome into two dictionaries. The first (inserts) having readID as keys and the insert size (i.e. the absolute value of AlignmentPosition1 - AlignmentPosition2) as value. The second dictionary (chrs)will have readID as key and chromosome ID as value. Example:

readID Chr11 31120 Chr11 31472
readID1 Chr7 12000 Chr11 11680

will result in:

inserts = {"readID" : 352, "readID1" : 320}
chrs = {"readID" : "Chr11", "readID1" : "Chr7"}

Once you have the two dictionaries:

1. Create a Series with all the insert sizes and show some
of its stats with the method **describe**. What is the mean
insert size? How many paried end are we using to create
this distribution?
2. Display the first 5 values of the series
3. Make a box plot to assess the distribution of the values.
4. Make an histogram to see the values in a different way.
How does this distribution look like?
5. Create another series from the chromosome info and print
the first 10 elements
6. Create a DataFrame starting from the two Series and print
the first 10 elements
7. For each chromosome, get the average insert size of the
paired aligned to it (hint:use group by).
8. Make a box plot of the average insert size per chromosome.

Show/Hide Solution

import pandas as pd
import matplotlib.pyplot as plt

#Open the file and store the entries in the two dicts
f = open("file_samples/filt_aligns.tsv")
inserts = dict()
chrs = dict()

for line in f:
    line = line.strip()
    infos = line.split("\t")
    if(infos[1] == infos[3]):
        inserts[infos[0]] = abs(int(infos[2]) - int(infos[4]))
        chrs[infos[0]] = infos[1] # or infos[3], they are the same!
#Inserts series
inSeries = pd.Series(inserts)
descr = inSeries.describe()

print(descr)
print("")
print("Mean insert size:", descr["mean"])
#Question 2
print("")
print("First five elements:")
print(inSeries.head(5))
#Question 3
inSeries.plot(kind = "box")
plt.show()
#Question 4
inSeries.plot(kind = "hist", bins = 50)
plt.show()
#Question 5
#Chromosomes series
chrSeries = pd.Series(chrs)
print(chrSeries.head(10))
#Question 6
DF = pd.DataFrame({"inserts": inSeries,"chrs" : chrSeries})
print(DF.head(10))
#Question 7
grouped = DF.groupby("chrs")
print("Average insert size by Chr:")
ins_by_chr = grouped.aggregate(pd.DataFrame.mean).sort_index()
print(grouped.aggregate(pd.DataFrame.mean).sort_index())
#Question 8
plt.close()
ins_by_chr.plot(kind = "box")
plt.show()

count    246499.000000
mean        194.126950
std          70.277551
min           0.000000
25%         150.000000
50%         189.000000
75%         232.000000
max         605.000000
dtype: float64

Mean insert size: 194.1269498050702

First five elements:
HWI-ST1296:74:C3FU9ACXX:7:2314:5661:3000    132
HWI-ST1296:74:C3FU9ACXX:6:2108:3151:3000    284
HWI-ST1296:75:C3F7CACXX:2:2302:4462:4000    294
HWI-ST1296:75:C3F7CACXX:1:1107:4328:4000      4
HWI-ST1296:75:C3F7CACXX:6:1205:3248:5000     69
dtype: int64

HWI-ST1296:74:C3FU9ACXX:7:2314:5661:3000     Chr5
HWI-ST1296:74:C3FU9ACXX:6:2108:3151:3000     Chr3
HWI-ST1296:75:C3F7CACXX:2:2302:4462:4000    Chr11
HWI-ST1296:75:C3F7CACXX:1:1107:4328:4000    Chr13
HWI-ST1296:75:C3F7CACXX:6:1205:3248:5000    Chr11
HWI-ST1296:67:C2F0FACXX:6:2305:7251:7000     Chr6
HWI-ST1296:75:C3F7CACXX:6:1203:5851:3100    Chr13
HWI-ST1296:75:C3F7CACXX:4:2309:3769:8000    Chr14
HWI-ST1296:75:C3F7CACXX:4:1212:5969:8000     Chr6
HWI-ST1296:74:C3FU9ACXX:2:2215:1855:8000     Chr4
dtype: object
                                          inserts   chrs
HWI-ST1296:74:C3FU9ACXX:7:2314:5661:3000      132   Chr5
HWI-ST1296:74:C3FU9ACXX:6:2108:3151:3000      284   Chr3
HWI-ST1296:75:C3F7CACXX:2:2302:4462:4000      294  Chr11
HWI-ST1296:75:C3F7CACXX:1:1107:4328:4000        4  Chr13
HWI-ST1296:75:C3F7CACXX:6:1205:3248:5000       69  Chr11
HWI-ST1296:67:C2F0FACXX:6:2305:7251:7000      142   Chr6
HWI-ST1296:75:C3F7CACXX:6:1203:5851:3100      197  Chr13
HWI-ST1296:75:C3F7CACXX:4:2309:3769:8000      298  Chr14
HWI-ST1296:75:C3F7CACXX:4:1212:5969:8000      369   Chr6
HWI-ST1296:74:C3FU9ACXX:2:2215:1855:8000      519   Chr4
Average insert size by Chr:
          inserts
chrs
Chr1   195.351513
Chr10  193.678891
Chr11  194.374923
Chr12  193.983594
Chr13  192.804249
Chr14  194.400139
Chr15  194.937928
Chr16  193.533066
Chr17  194.559222
Chr2   193.905932
Chr3   193.937721
Chr4   193.858397
Chr5   195.052776
Chr6   194.336027
Chr7   193.766347
Chr8   194.482513
Chr9   193.195012

3. Download the train.csv dataset. As the name says it is a .csv file. The file contains information regarding loans given or refused to applicants. Information on the gender, marital status, education, work and income of the applicant is reported alongside the amount and length of the loan and credit history (i.e. 0 if no previous loan was given, 1 otherwise). Open it in a text editor or excel and inspect it first. Then, answer the following questions (if you have any doubts check here):
   0. Load it into a pandas DataFrame (use column Loan_ID as index. Hint: use parm index_col).
   1. Get an idea of the data by visualizing its first 5 entries;
   2. How many total entries are present in the file? How many males and females?
   3. What is the average applicant income? Does the gender affect the income? Compute the average of the applicant income on the whole dataset and the average of the data grouped by Gender. How many Females have an income > than the average?
   4. How many loans have been given (i.e. Loan_Status equals Y)? What is the percentage of the loans given and that of the loans refused?
   5. What is the percentage of given/refused loans in the case of married people?
   6. What is the percentage of given/refused loans in the case of applicants with positive credit history (i.e. Credit_History equals 1)?

Show/Hide Solution

import pandas as pd
import matplotlib.pyplot as plt

train = pd.read_csv("file_samples/train.csv", index_col = "Loan_ID")
#Question 1:
print(train.head())
#Question 2:
print("")
entries = train.shape[0]
print("The toal number of entries is {}".format(entries))
print("")
print("Males and Females")
print(train["Gender"].value_counts())

#Question 3:
print("")
avgIncome = train["ApplicantIncome"].mean()
print("The average income is {}".format(avgIncome))
train[["Gender", "ApplicantIncome"]].groupby("Gender").mean()
train.boxplot(column = "ApplicantIncome", by = "Gender")
plt.show()
females = train[train["Gender"] == "Female"]
fhi = females[females["ApplicantIncome"] > avgIncome][["Gender","ApplicantIncome"]]

print("Female applicants with income higher than avg ({}): {}".format(avgIncome,len(fhi)))
print(fhi)
print("")
#Question 4:
loanSt = train["Loan_Status"].value_counts()
print("The number of given loans is: {}".format(loanSt["Y"]))
#loanSt is a Series, I can apply operator broadcasting on it
#to get the percentage
loanSt = loanSt / entries
print("")
print("The percentage of loans is the following")
print(loanSt)

#Question 5:
loanSt =  train[train["Married"] == "Yes"]["Loan_Status"].value_counts()
married = train["Married"][train["Married"] == "Yes"].count()
print(married)
print("The percentage of loans to married people ({} applicants)".format(married))
print(loanSt/married)

#Question 6:
loanSt =  train[train["Credit_History"] == 1]["Loan_Status"].value_counts()
chist = train["Credit_History"][train["Credit_History"] == 1].count()
print(chist)
print("The percentage of loans to applicants with credit history ({} applicants)".format(chist))
print(loanSt/chist)

         Gender Married Dependents     Education Self_Employed  \
Loan_ID
LP001002   Male      No          0      Graduate            No
LP001003   Male     Yes          1      Graduate            No
LP001005   Male     Yes          0      Graduate           Yes
LP001006   Male     Yes          0  Not Graduate            No
LP001008   Male      No          0      Graduate            No

          ApplicantIncome  CoapplicantIncome  LoanAmount  Loan_Amount_Term  \
Loan_ID
LP001002             5849                0.0         NaN             360.0
LP001003             4583             1508.0       128.0             360.0
LP001005             3000                0.0        66.0             360.0
LP001006             2583             2358.0       120.0             360.0
LP001008             6000                0.0       141.0             360.0

          Credit_History Property_Area Loan_Status
Loan_ID
LP001002             1.0         Urban           Y
LP001003             1.0         Rural           N
LP001005             1.0         Urban           Y
LP001006             1.0         Urban           Y
LP001008             1.0         Urban           Y

The toal number of entries is 614

Males and Females
Male      489
Female    112
Name: Gender, dtype: int64

The average income is 5403.459283387622

/usr/local/lib/python3.5/dist-packages/numpy/core/fromnumeric.py:57: FutureWarning: reshape is deprecated and will raise in a subsequent release. Please use .values.reshape(...) instead
  return getattr(obj, method)(*args, **kwds)

Female applicants with income higher than avg (5403.459283387622): 21
          Gender  ApplicantIncome
Loan_ID
LP001186  Female            11500
LP001392  Female             7451
LP001422  Female            10408
LP001516  Female            14866
LP001519  Female            10000
LP001708  Female            10000
LP001776  Female             8333
LP001871  Female             7200
LP001945  Female             5417
LP002142  Female             5500
LP002194  Female            15759
LP002231  Female             6000
LP002301  Female             7441
LP002377  Female             8624
LP002393  Female            10047
LP002407  Female             7142
LP002582  Female            17263
LP002634  Female            13262
LP002731  Female            18165
LP002813  Female            19484
LP002959  Female            12000

The number of given loans is: 422

The percentage of loans is the following
Y    0.687296
N    0.312704
Name: Loan_Status, dtype: float64
398
The percentage of loans to married people (398 applicants)
Y    0.71608
N    0.28392
Name: Loan_Status, dtype: float64
475
The percentage of loans to applicants with credit history (475 applicants)
Y    0.795789
N    0.204211
Name: Loan_Status, dtype: float64

4. [Thanks to Stefano Teso] DNA transcription and translation into proteins follows this schema:

The file gene_table.csv is a comma separated value file representing a summary of the annotation of several human genes based on the Ensembl annotation. For each gene it contains the following information:

gene_name,gene_biotype,chromosome,strand,transcript_count

where gene_name is based on the HGNC nomenclature. gene_biotype represents the biotype (refer to VEGA like protein_coding, pseudogene, lincRNA, miRNA etc. chromosome is where the feature is located, strand is a + or a - for the forward or reverse strand and transcript_count reports the number of isoforms of the gene.

A sample of the file follows:

TSPAN6,protein_coding,chrX,-,5
TNMD,protein_coding,chrX,+,2
DPM1,protein_coding,chr20,-,6
SCYL3,protein_coding,chr1,-,5
C1orf112,protein_coding,chr1,+,9
FGR,protein_coding,chr1,-,7
CFH,protein_coding,chr1,+,6
FUCA2,protein_coding,chr6,-,3
GCLC,protein_coding,chr6,-,13

Write a python program that: 0. Loads the gene_table.csv in a DataFrame (inspect the first entries with head to check the content of the file); 1. Computes the number of genes annotated for the human genome; 2. Computes the minimum, maximum, average and median number of known isoforms per gene (consider the transcript_count column as a series). 3. Plots a histogram and a boxplot of the number of known isoforms per gene 4. Computes the number of different biotypes. How many genes do we have for each genotype? Plot the number of genes per biotype in a horizontal bar plot (hint: use also figsize = (10,10) to make it visible; 5. Computes the number of different chromosomes 6. Computes, for each chromosome, the number of genes it contains, and prints a horizontal barplot with the number of genes per chromosome. 7. Computes, for each chromosome, the percentage of genes located on the + strand 8. Computes, for each biotype, the average number of transcripts associated to genes belonging to the biotype. Finally, plots them in a vertical bar plot

Show/Hide Solution

import pandas as pd
import matplotlib.pyplot as plt

genes = pd.read_csv("file_samples/gene_table.csv", sep=",")
print(genes.head())
print("")
#Question 1
print("Total number of genes: {}".format(genes.shape[0]))
#Question 2
maxI = genes["transcript_count"].max()
minI = genes["transcript_count"].min()
avgI = genes["transcript_count"].mean()
medI = genes["transcript_count"].median()
print("")
print("Isoform per gene stats:")
print(" - max: {} min {} avg {} median {}".format(maxI, minI,avgI,medI))

#Question 3
genes["transcript_count"].plot(kind = "hist", bins = 100)
plt.show()
plt.close()
genes["transcript_count"].plot(kind = "box")
plt.show()
print("")
#Question 4
biot = genes["gene_biotype"].value_counts()
print("The number of different biotypes is", len(biot))
print("")
print(biot)
plt.close()
biot.plot(kind = "barh", figsize = (10,10))
plt.show()
#Question 5
chrs = genes["chromosome"].unique()
print("The total number of chromosomes is ", chrs.shape[0])

#Question 6
plt.close()
chrs = genes["chromosome"].value_counts()
chrs.plot(kind = "barh", figsize = (10,10))
plt.show()

#Question 7
#Let's group the data by chromosome and strand
#then loop through all the elements to count the
#total elements per chromosome
#to compute the percentage of the ones that are on + strand
#The totals go on a dictionary with key chr

grp_chrs = genes.groupby(["chromosome", "strand"])

print(type(grp_chrs))
for ind, grp in grp_chrs:
    print("{}({}) : {}".format(ind, type(ind), grp.shape[0]))

tot_byChr = {}

for ind, grp in grp_chrs:
    v = tot_byChr.get(ind[0],0)
    tot_byChr[ind[0]] = v + grp.shape[0]

print(tot_byChr)

for ind, grp in grp_chrs:
    if (ind[1] == "+"):

        print("% genes of {} on strand +: {:.2f}".format(ind[0], 100*grp.shape[0]/tot_byChr[ind[0]]))



#Question 8
biot= grp_chrs = genes.groupby(["gene_biotype"])
biot_transc = biot.aggregate(pd.DataFrame.mean)[["transcript_count"]]
print(biot_transc)

biot_transc.plot(kind = "bar", figsize = (10,10))
plt.show()

  gene_name    gene_biotype chromosome strand  transcript_count
0    TSPAN6  protein_coding       chrX      -                 5
1      TNMD  protein_coding       chrX      +                 2
2      DPM1  protein_coding      chr20      -                 6
3     SCYL3  protein_coding       chr1      -                 5
4  C1orf112  protein_coding       chr1      +                 9

Total number of genes: 51116

Isoform per gene stats:
 - max: 170 min 1 avg 3.7033218561702794 median 1.0

The number of different biotypes is 41

protein_coding                        19297
processed_pseudogene                   9826
lincRNA                                6645
antisense                              5086
unprocessed_pseudogene                 2143
snRNA                                  1802
miRNA                                  1173
misc_RNA                                955
sense_intronic                          686
transcribed_unprocessed_pseudogene      660
rRNA                                    512
processed_transcript                    438
transcribed_processed_pseudogene        425
snoRNA                                  403
sense_overlapping                       174
IG_V_pseudogene                         173
unitary_pseudogene                      141
IG_V_gene                               130
TR_V_gene                                93
TR_J_gene                                71
transcribed_unitary_pseudogene           53
IG_D_gene                                33
TR_V_pseudogene                          30
polymorphic_pseudogene                   28
3prime_overlapping_ncRNA                 26
Mt_tRNA                                  22
IG_J_gene                                18
scaRNA                                   16
IG_C_gene                                14
IG_C_pseudogene                           9
TEC                                       6
TR_C_gene                                 5
ribozyme                                  5
TR_J_pseudogene                           4
TR_D_gene                                 3
IG_J_pseudogene                           3
bidirectional_promoter_lncRNA             2
Mt_rRNA                                   2
pseudogene                                2
scRNA                                     1
vaultRNA                                  1
Name: gene_biotype, dtype: int64

The total number of chromosomes is  25

<class 'pandas.core.groupby.generic.DataFrameGroupBy'>
('chr1', '+')(<class 'tuple'>) : 2388
('chr1', '-')(<class 'tuple'>) : 2322
('chr10', '+')(<class 'tuple'>) : 999
('chr10', '-')(<class 'tuple'>) : 944
('chr11', '+')(<class 'tuple'>) : 1470
('chr11', '-')(<class 'tuple'>) : 1472
('chr12', '+')(<class 'tuple'>) : 1262
('chr12', '-')(<class 'tuple'>) : 1269
('chr13', '+')(<class 'tuple'>) : 537
('chr13', '-')(<class 'tuple'>) : 558
('chr14', '+')(<class 'tuple'>) : 1029
('chr14', '-')(<class 'tuple'>) : 976
('chr15', '+')(<class 'tuple'>) : 901
('chr15', '-')(<class 'tuple'>) : 883
('chr16', '+')(<class 'tuple'>) : 1077
('chr16', '-')(<class 'tuple'>) : 1036
('chr17', '+')(<class 'tuple'>) : 1227
('chr17', '-')(<class 'tuple'>) : 1306
('chr18', '+')(<class 'tuple'>) : 508
('chr18', '-')(<class 'tuple'>) : 491
('chr19', '+')(<class 'tuple'>) : 1361
('chr19', '-')(<class 'tuple'>) : 1303
('chr2', '+')(<class 'tuple'>) : 1803
('chr2', '-')(<class 'tuple'>) : 1786
('chr20', '+')(<class 'tuple'>) : 577
('chr20', '-')(<class 'tuple'>) : 592
('chr21', '+')(<class 'tuple'>) : 297
('chr21', '-')(<class 'tuple'>) : 342
('chr22', '+')(<class 'tuple'>) : 585
('chr22', '-')(<class 'tuple'>) : 505
('chr3', '+')(<class 'tuple'>) : 1345
('chr3', '-')(<class 'tuple'>) : 1395
('chr4', '+')(<class 'tuple'>) : 1152
('chr4', '-')(<class 'tuple'>) : 1145
('chr5', '+')(<class 'tuple'>) : 1303
('chr5', '-')(<class 'tuple'>) : 1295
('chr6', '+')(<class 'tuple'>) : 1222
('chr6', '-')(<class 'tuple'>) : 1237
('chr7', '+')(<class 'tuple'>) : 1320
('chr7', '-')(<class 'tuple'>) : 1187
('chr8', '+')(<class 'tuple'>) : 1039
('chr8', '-')(<class 'tuple'>) : 1113
('chr9', '+')(<class 'tuple'>) : 989
('chr9', '-')(<class 'tuple'>) : 952
('chrMT', '+')(<class 'tuple'>) : 28
('chrMT', '-')(<class 'tuple'>) : 9
('chrX', '+')(<class 'tuple'>) : 1078
('chrX', '-')(<class 'tuple'>) : 1031
('chrY', '+')(<class 'tuple'>) : 240
('chrY', '-')(<class 'tuple'>) : 230
{}
{'chr1': 2388}
{'chr1': 4710}
{'chr1': 4710, 'chr10': 999}
{'chr1': 4710, 'chr10': 1943}
{'chr1': 4710, 'chr10': 1943, 'chr11': 1470}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 1262}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 537}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 1029}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 901}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 1077}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 1227}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 508}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 1361}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 1803}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 577}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 297}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 585}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 1345}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 1152}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297, 'chr5': 1303}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297, 'chr5': 2598}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297, 'chr5': 2598, 'chr6': 1222}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297, 'chr5': 2598, 'chr6': 2459}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297, 'chr5': 2598, 'chr6': 2459, 'chr7': 1320}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297, 'chr5': 2598, 'chr6': 2459, 'chr7': 2507}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297, 'chr5': 2598, 'chr6': 2459, 'chr7': 2507, 'chr8': 1039}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297, 'chr5': 2598, 'chr6': 2459, 'chr7': 2507, 'chr8': 2152}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297, 'chr5': 2598, 'chr6': 2459, 'chr7': 2507, 'chr8': 2152, 'chr9': 989}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297, 'chr5': 2598, 'chr6': 2459, 'chr7': 2507, 'chr8': 2152, 'chr9': 1941}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297, 'chr5': 2598, 'chr6': 2459, 'chr7': 2507, 'chr8': 2152, 'chr9': 1941, 'chrMT': 28}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297, 'chr5': 2598, 'chr6': 2459, 'chr7': 2507, 'chr8': 2152, 'chr9': 1941, 'chrMT': 37}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297, 'chr5': 2598, 'chr6': 2459, 'chr7': 2507, 'chr8': 2152, 'chr9': 1941, 'chrMT': 37, 'chrX': 1078}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297, 'chr5': 2598, 'chr6': 2459, 'chr7': 2507, 'chr8': 2152, 'chr9': 1941, 'chrMT': 37, 'chrX': 2109}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297, 'chr5': 2598, 'chr6': 2459, 'chr7': 2507, 'chr8': 2152, 'chr9': 1941, 'chrMT': 37, 'chrX': 2109, 'chrY': 240}
{'chr1': 4710, 'chr10': 1943, 'chr11': 2942, 'chr12': 2531, 'chr13': 1095, 'chr14': 2005, 'chr15': 1784, 'chr16': 2113, 'chr17': 2533, 'chr18': 999, 'chr19': 2664, 'chr2': 3589, 'chr20': 1169, 'chr21': 639, 'chr22': 1090, 'chr3': 2740, 'chr4': 2297, 'chr5': 2598, 'chr6': 2459, 'chr7': 2507, 'chr8': 2152, 'chr9': 1941, 'chrMT': 37, 'chrX': 2109, 'chrY': 470}
% genes of chr1 on strand +: 50.70
% genes of chr10 on strand +: 51.42
% genes of chr11 on strand +: 49.97
% genes of chr12 on strand +: 49.86
% genes of chr13 on strand +: 49.04
% genes of chr14 on strand +: 51.32
% genes of chr15 on strand +: 50.50
% genes of chr16 on strand +: 50.97
% genes of chr17 on strand +: 48.44
% genes of chr18 on strand +: 50.85
% genes of chr19 on strand +: 51.09
% genes of chr2 on strand +: 50.24
% genes of chr20 on strand +: 49.36
% genes of chr21 on strand +: 46.48
% genes of chr22 on strand +: 53.67
% genes of chr3 on strand +: 49.09
% genes of chr4 on strand +: 50.15
% genes of chr5 on strand +: 50.15
% genes of chr6 on strand +: 49.69
% genes of chr7 on strand +: 52.65
% genes of chr8 on strand +: 48.28
% genes of chr9 on strand +: 50.95
% genes of chrMT on strand +: 75.68
% genes of chrX on strand +: 51.11
% genes of chrY on strand +: 51.06
                                    transcript_count
gene_biotype
3prime_overlapping_ncRNA                    1.153846
IG_C_gene                                   1.285714
IG_C_pseudogene                             1.000000
IG_D_gene                                   1.000000
IG_J_gene                                   1.000000
IG_J_pseudogene                             1.000000
IG_V_gene                                   1.053846
IG_V_pseudogene                             1.000000
Mt_rRNA                                     1.000000
Mt_tRNA                                     1.000000
TEC                                         1.166667
TR_C_gene                                   1.800000
TR_D_gene                                   1.000000
TR_J_gene                                   1.000000
TR_J_pseudogene                             1.000000
TR_V_gene                                   1.010753
TR_V_pseudogene                             1.000000
antisense                                   1.870232
bidirectional_promoter_lncRNA               2.000000
lincRNA                                     1.690143
miRNA                                       1.000000
misc_RNA                                    1.000000
polymorphic_pseudogene                      3.285714
processed_pseudogene                        1.000204
processed_transcript                        5.844749
protein_coding                              7.447893
pseudogene                                  1.000000
rRNA                                        1.000000
ribozyme                                    1.000000
scRNA                                       1.000000
scaRNA                                      1.000000
sense_intronic                              1.087464
sense_overlapping                           1.609195
snRNA                                       1.000000
snoRNA                                      1.027295
transcribed_processed_pseudogene            2.101176
transcribed_unitary_pseudogene              5.056604
transcribed_unprocessed_pseudogene          3.339394
unitary_pseudogene                          1.921986
unprocessed_pseudogene                      1.000467
vaultRNA                                    1.000000

5. Write a function that creates and returns a data frame having columns with the labels specified through a list taken in input and ten rows of random data between 1 and 100.
   1. Create two random DataFrames one with labels l = [“A”, “B”, “C” ,”D”,”E”] and l1 = [“W”, “X”,”Y”,”Z”]
   2. Print the first 5 elements to inspect the two DataFrames and plot the valuse of the two DataFrames;
   3. Create a new Series S1 with values: [1, 1, 1, 0, 0, 1, 1, 0, 0, 1]. Get the Series corresponding to the column “C” and multiply it point-to-point by the Series S1 (hint use: Series.multiply(S1))
   4. Add this new series as a “C” column of the second DataFrame.
   5. Merge the two DataFrames based on the value of C. Perform an inner, outer, left and right merge and see the difference

Show/Hide Solution

import pandas as pd
import matplotlib.pyplot as plt
import random

def createRandomDF(labels):
    """ returns a random dataframe with columns having names equal to the
    input labels"""
    tmp_dict = {}
    for l in labels:
        tmp_dict[l] = []
        for i in range(0,10):
            tmp_dict[l].append(random.randint(0,10))

    DF = pd.DataFrame(tmp_dict)
    return DF

#Question 1
l = ["A", "B", "C" ,"D","E"]
l1 = [ "W", "X","Y","Z"]
df = createRandomDF(l)
df1 = createRandomDF(l1)

#Question 2
print(df.head())
print("")
print(df1.head())
plt.close()
df.plot(kind = "line")
plt.show()
plt.close()
df1.plot(kind = "line")
plt.show()

#Question 3
S1 = pd.Series( [ 1, 1, 1, 0, 0, 1, 1, 0,0,1])
Sc = df["C"]
c1 = Sc.multiply(S1)
print(c1)

#Question 4
df1["C"] = c1
print(df1)
print(df)
#Question 5
inJ = pd.merge(df,df1, how ="inner")
print("")
print("Inner Join DF - DF1")
print(inJ)
outJ = pd.merge(df,df1, how ="outer")
print("")
print("Outer Join DF - DF1")
print(outJ)
print("")
print("Left Join DF - DF1")
lJ = pd.merge(df,df1, on = "C", how ="left")
print(lJ)
print("")
print("Right Join DF - DF1")
rJ = pd.merge(df,df1, on = "C", how ="right")
print(rJ)

   A   B  C  D  E
0  0   1  6  6  4
1  6   4  0  7  0
2  3  10  9  8  2
3  0   7  6  6  7
4  9   4  7  7  7

    W  X   Y   Z
0   2  7   9   3
1   5  1   3  10
2  10  5  10   7
3   8  7   3   7
4   3  3   7   2

0    6
1    0
2    9
3    0
4    0
5    2
6    2
7    0
8    0
9    1
dtype: int64
    W  X   Y   Z  C
0   2  7   9   3  6
1   5  1   3  10  0
2  10  5  10   7  9
3   8  7   3   7  0
4   3  3   7   2  0
5   2  0   7   8  2
6  10  3   2   4  2
7   4  2   0   8  0
8  10  4   0   1  0
9   2  2   3   5  1
    A   B  C   D  E
0   0   1  6   6  4
1   6   4  0   7  0
2   3  10  9   8  2
3   0   7  6   6  7
4   9   4  7   7  7
5  10   5  2   6  7
6   3  10  2   7  6
7   6   1  0  10  0
8   1   1  5   0  4
9   6   5  1   9  8

Inner Join DF - DF1
     A   B  C   D  E   W  X   Y   Z
0    0   1  6   6  4   2  7   9   3
1    0   7  6   6  7   2  7   9   3
2    6   4  0   7  0   5  1   3  10
3    6   4  0   7  0   8  7   3   7
4    6   4  0   7  0   3  3   7   2
5    6   4  0   7  0   4  2   0   8
6    6   4  0   7  0  10  4   0   1
7    6   1  0  10  0   5  1   3  10
8    6   1  0  10  0   8  7   3   7
9    6   1  0  10  0   3  3   7   2
10   6   1  0  10  0   4  2   0   8
11   6   1  0  10  0  10  4   0   1
12   3  10  9   8  2  10  5  10   7
13  10   5  2   6  7   2  0   7   8
14  10   5  2   6  7  10  3   2   4
15   3  10  2   7  6   2  0   7   8
16   3  10  2   7  6  10  3   2   4
17   6   5  1   9  8   2  2   3   5

Outer Join DF - DF1
     A   B  C   D  E     W    X     Y     Z
0    0   1  6   6  4   2.0  7.0   9.0   3.0
1    0   7  6   6  7   2.0  7.0   9.0   3.0
2    6   4  0   7  0   5.0  1.0   3.0  10.0
3    6   4  0   7  0   8.0  7.0   3.0   7.0
4    6   4  0   7  0   3.0  3.0   7.0   2.0
5    6   4  0   7  0   4.0  2.0   0.0   8.0
6    6   4  0   7  0  10.0  4.0   0.0   1.0
7    6   1  0  10  0   5.0  1.0   3.0  10.0
8    6   1  0  10  0   8.0  7.0   3.0   7.0
9    6   1  0  10  0   3.0  3.0   7.0   2.0
10   6   1  0  10  0   4.0  2.0   0.0   8.0
11   6   1  0  10  0  10.0  4.0   0.0   1.0
12   3  10  9   8  2  10.0  5.0  10.0   7.0
13   9   4  7   7  7   NaN  NaN   NaN   NaN
14  10   5  2   6  7   2.0  0.0   7.0   8.0
15  10   5  2   6  7  10.0  3.0   2.0   4.0
16   3  10  2   7  6   2.0  0.0   7.0   8.0
17   3  10  2   7  6  10.0  3.0   2.0   4.0
18   1   1  5   0  4   NaN  NaN   NaN   NaN
19   6   5  1   9  8   2.0  2.0   3.0   5.0

Left Join DF - DF1
     A   B  C   D  E     W    X     Y     Z
0    0   1  6   6  4   2.0  7.0   9.0   3.0
1    6   4  0   7  0   5.0  1.0   3.0  10.0
2    6   4  0   7  0   8.0  7.0   3.0   7.0
3    6   4  0   7  0   3.0  3.0   7.0   2.0
4    6   4  0   7  0   4.0  2.0   0.0   8.0
5    6   4  0   7  0  10.0  4.0   0.0   1.0
6    3  10  9   8  2  10.0  5.0  10.0   7.0
7    0   7  6   6  7   2.0  7.0   9.0   3.0
8    9   4  7   7  7   NaN  NaN   NaN   NaN
9   10   5  2   6  7   2.0  0.0   7.0   8.0
10  10   5  2   6  7  10.0  3.0   2.0   4.0
11   3  10  2   7  6   2.0  0.0   7.0   8.0
12   3  10  2   7  6  10.0  3.0   2.0   4.0
13   6   1  0  10  0   5.0  1.0   3.0  10.0
14   6   1  0  10  0   8.0  7.0   3.0   7.0
15   6   1  0  10  0   3.0  3.0   7.0   2.0
16   6   1  0  10  0   4.0  2.0   0.0   8.0
17   6   1  0  10  0  10.0  4.0   0.0   1.0
18   1   1  5   0  4   NaN  NaN   NaN   NaN
19   6   5  1   9  8   2.0  2.0   3.0   5.0

Right Join DF - DF1
     A   B  C   D  E   W  X   Y   Z
0    0   1  6   6  4   2  7   9   3
1    0   7  6   6  7   2  7   9   3
2    6   4  0   7  0   5  1   3  10
3    6   1  0  10  0   5  1   3  10
4    6   4  0   7  0   8  7   3   7
5    6   1  0  10  0   8  7   3   7
6    6   4  0   7  0   3  3   7   2
7    6   1  0  10  0   3  3   7   2
8    6   4  0   7  0   4  2   0   8
9    6   1  0  10  0   4  2   0   8
10   6   4  0   7  0  10  4   0   1
11   6   1  0  10  0  10  4   0   1
12   3  10  9   8  2  10  5  10   7
13  10   5  2   6  7   2  0   7   8
14   3  10  2   7  6   2  0   7   8
15  10   5  2   6  7  10  3   2   4
16   3  10  2   7  6  10  3   2   4
17   6   5  1   9  8   2  2   3   5

Practical 9

In this practical we will will practice Numpy and Matplotlib.

Slides

The slides of the introduction can be found here: Intro

Numpy

Numpy is a fundamental library for high performance scientific computations. It provides fast and memory efficient data structures like ndarray with broadcasting capabilities, standard mathematical functions that can be applied on the arrays avoiding loops, linear algebra functions, I/O methods and it is well integrated with programming languages like C.

To use the functionalities of the library we always need to import it with (standard name is np):

import numpy as np

The official documentation of the numpy library can be found at http://www.numpy.org/.

Numpy ndarray

Numpy ndarray is an N-dimensional array object designed to contain homogeneous data (i.e. all data must have the same type). Every array (also called tensor) comes with two information: the shape (a tuple describing the dimensions of the array) and a dtype (the data type of the array).

Given a list of homogeneous values the ndarray can be obtained by using the np.array(list) method. Given the numpy array its shape, dimensionality and dtype can be obtained with array.shape, array.ndim and array.dtype.

An example follows:

import numpy as np

Aint = np.array([[1,2,3], [4,5,6]])
Afloat = np.array([[1.1,2,3], [4.2,5,6], [1,2,3]])

print(Aint)
print(type(Aint))
print(Aint.shape)
print(Aint.dtype)
print("")
print(Afloat)
print(type(Afloat))
print(Afloat.shape)
print(Afloat.dtype)

[[1 2 3]
 [4 5 6]]
<class 'numpy.ndarray'>
(2, 3)
int64

[[1.1 2.  3. ]
 [4.2 5.  6. ]
 [1.  2.  3. ]]
<class 'numpy.ndarray'>
(3, 3)
float64

Example:

Let’s create a ndarray holding the square root and one with the cubic root of the first five integers. Let’s put them together in a 2-d array and check its dimensions.

import numpy as np
import math


mysqrt = [math.sqrt(x) for x in range(0,5)]
mycrt = [x**(1/3) for x in range(0,5)]
myOtherRt = [x**(1/5) for x in range(0,5)]
print("Original lists:")
print(mysqrt)
print(mycrt)
print("")
npData = np.array(mysqrt)
print("Numpy ndarray:")
print(npData)
print("")
print("The shape:", npData.shape)
print("The dimensionality:", npData.ndim)
print("The type:", npData.dtype)
print("")
twoDarray = np.array([mysqrt, mycrt, myOtherRt])
print("The 2D array:")
print(twoDarray)
print("")
print("The shape:", twoDarray.shape)
print("The dimensionality:", twoDarray.ndim)
print("The type:", twoDarray.dtype)

Original lists:
[0.0, 1.0, 1.4142135623730951, 1.7320508075688772, 2.0]
[0.0, 1.0, 1.2599210498948732, 1.4422495703074083, 1.5874010519681994]

Numpy ndarray:
[0.         1.         1.41421356 1.73205081 2.        ]

The shape: (5,)
The dimensionality: 1
The type: float64

The 2D array:
[[0.         1.         1.41421356 1.73205081 2.        ]
 [0.         1.         1.25992105 1.44224957 1.58740105]
 [0.         1.         1.14869835 1.24573094 1.31950791]]

The shape: (3, 5)
The dimensionality: 2
The type: float64

We can also create arrays (matrices) full of zeros or ones or even diagonal matrices with the following numpy methods:

1. Array: np.zeros(N) or matrix: np.zeros((N,M))
2. Array: np.ones(N) or matrix: np.ones((N,M))
3. Matrix: np.eye(N)

Numpy has its own range method that is called np.arange(N). Evenly spaced values in a range can be obtained also with np.linspace(S,E, num=N, endpoint=True/False) to obtain N linearly spaced values from S to E (included, unless endpoint = False is specified).

import numpy as np

zeros = np.zeros(3)
zMat = np.zeros((4,3))
ones = np.ones(3)
oMat = np.ones((3,2))
diag = np.eye(4)
rng = np.arange(5) #5 excluded!

print("Zero array (1x3)")
print(zeros)
print("")
D = zMat.shape
print("Zero matrix ({}x{})".format(D[0],D[1]))
print(zMat)
print("")
print("Ones array (1x3)")
print(ones)
print("")
print("Ones matrix (3x2)")
print(oMat)
print("")
print("Diagonal matrix")
print(diag)
print("")
print("Range 0-4")
print(rng)
print("A diagonal matrix:")
dm = np.diag(rng)
print(dm)
print("Its shape:")
print(dm.shape)

rng = np.arange(7)
print("Range 0-6")
print(rng)

myRange = np.linspace(-5,2.5,num =6)
print("6 linearly spaced elements in [-5 - 2.5]:")
print(myRange)

myRange = np.linspace(0,21,num =7, endpoint=False)
print("7 linearly spaced elements in [0 - 21):")
print(myRange)

Zero array (1x3)
[0. 0. 0.]

Zero matrix (4x3)
[[0. 0. 0.]
 [0. 0. 0.]
 [0. 0. 0.]
 [0. 0. 0.]]

Ones array (1x3)
[1. 1. 1.]

Ones matrix (3x2)
[[1. 1.]
 [1. 1.]
 [1. 1.]]

Diagonal matrix
[[1. 0. 0. 0.]
 [0. 1. 0. 0.]
 [0. 0. 1. 0.]
 [0. 0. 0. 1.]]

Range 0-4
[0 1 2 3 4]
A diagonal matrix:
[[0 0 0 0 0]
 [0 1 0 0 0]
 [0 0 2 0 0]
 [0 0 0 3 0]
 [0 0 0 0 4]]
Its shape:
(5, 5)
Range 0-6
[0 1 2 3 4 5 6]
6 linearly spaced elements in [-5 - 2.5]:
[-5.  -3.5 -2.  -0.5  1.   2.5]
7 linearly spaced elements in [0 - 21):
[ 0.  3.  6.  9. 12. 15. 18.]

Random arrays

Random arrays can be created from several different distributions (check here for all options). Some examples include uniform distribution, normal, binomial,…

Example:

Create a random array of 1000 values drawn from: 1. a gaussian distribution with \(\sigma = 20\) and \(\mu = 2\) 2. a uniform distribution from 0 to 5 3. a binomial distribution with \(p = 0.5\) and \(n = 12\)

and plot their histogram.

import numpy as np
import matplotlib.pyplot as plt

%matplotlib inline

#get the gaussian random array
g = np.random.normal(20,2, 1000)
#a uniform random array with vals in [0,5]
u = np.random.uniform(0,5, 1000)
#get the binomial random array
b = np.random.binomial(12,0.5, 1000)

plt.hist(g, bins = 30)
plt.title("Gaussian(20,2)")
plt.xlabel("Random #")
plt.ylabel("Count")
plt.show()

plt.hist(u, bins = 10)
plt.title("Uniform(0,5)")
plt.xlabel("Random #")
plt.ylabel("Count")
plt.show()
plt.hist(b, bins = 10)
plt.title("Binomial(12,0.5)")
plt.xlabel("Random #")
plt.ylabel("Count")
plt.show()

It is also possible to specify the the size of the output (with the tuple size)to get a matrix instead.

import numpy as np

u = np.random.uniform(0,1, size = (4,3))

print("Uniform distr. in (0,1). 4x3 matrix:")
print("")
print(u)

Uniform distr. in (0,1). 4x3 matrix:

[[0.01748314 0.68196938 0.7337711 ]
 [0.9061673  0.27011933 0.83324199]
 [0.13474732 0.21965773 0.24174557]
 [0.81930429 0.25657836 0.10198619]]

To always get the same values we need to initialize the random seed (a parameter of the pseudo-random sequence generator) always to the same value.

import numpy as np

u = np.random.uniform(0,1,size=(3,2))
u1 = np.random.uniform(0,1,size=(3,2))
u2 = np.random.uniform(0,1,size=(3,2))

print(" u: {}\n\n u1:{}\n\n u2:{}".format(u,u1,u2))

print("")
print("With random seed reinit.")
np.random.seed(0)
u = np.random.uniform(0,1,3)
np.random.seed(0)
u1 = np.random.uniform(0,1,3)
np.random.seed(0)
u2 = np.random.uniform(0,1,3)

print(" u: {}\n u1:{}\n u2:{}".format(u,u1,u2))

 u: [[0.1182575  0.88378038]
 [0.64969197 0.45585741]
 [0.0245672  0.28397606]]

 u1:[[0.43501974 0.6943427 ]
 [0.527252   0.96579963]
 [0.20484529 0.05242482]]

 u2:[[0.1545874  0.89794199]
 [0.75233458 0.56678759]
 [0.86651043 0.90583683]]

With random seed reinit.
 u: [0.5488135  0.71518937 0.60276338]
 u1:[0.5488135  0.71518937 0.60276338]
 u2:[0.5488135  0.71518937 0.60276338]

Numpy to and from pandas

Pandas Series and DataFrames are actually built on top of numpy ndarrays. Moreover, given a numpy matrix (or array) it is quite easy to convert it into a DataFrame (or Series).

import pandas as pd
import numpy as np

myDict = {"one" : 1, "two" : 2, "three" : 3, "four" : 4}

mySeries = pd.Series(myDict)

print(myDict)
print("")
print(type(mySeries))
print("")
print(type(mySeries.values))
print("")

myMat = np.diag(np.arange(6))
myDF = pd.DataFrame(myMat)
print("Numpy matrix")
print(myMat)
print("")
print("Pandas DataFrame")
print(myDF)
print("")
print("Reindexed DataFrame")
myDF = pd.DataFrame(myMat, index = list("ABCDEF"),
                    columns = ['a1','b2','c3','d4','e5','f6'])
print(myDF)

{'one': 1, 'two': 2, 'three': 3, 'four': 4}

<class 'pandas.core.series.Series'>

<class 'numpy.ndarray'>

Numpy matrix
[[0 0 0 0 0 0]
 [0 1 0 0 0 0]
 [0 0 2 0 0 0]
 [0 0 0 3 0 0]
 [0 0 0 0 4 0]
 [0 0 0 0 0 5]]

Pandas DataFrame
   0  1  2  3  4  5
0  0  0  0  0  0  0
1  0  1  0  0  0  0
2  0  0  2  0  0  0
3  0  0  0  3  0  0
4  0  0  0  0  4  0
5  0  0  0  0  0  5

Reindexed DataFrame
   a1  b2  c3  d4  e5  f6
A   0   0   0   0   0   0
B   0   1   0   0   0   0
C   0   0   2   0   0   0
D   0   0   0   3   0   0
E   0   0   0   0   4   0
F   0   0   0   0   0   5

Reshaping

The shape of a numpy ndarray can be changed at any time with the methods reshape((R,C)) where R and C are the rows and columns used to shape an array into a matrix, and ravel that is used to go the other way around from matrix to array.

import numpy as np

myA = np.arange(12)

print("The array:")
print(myA)
print("")
myB = myA.reshape((2,6))
print("Reshaped (2x6):")
print(myB)
print("")
myC = myA.reshape((3,4))
print("Reshaped: (3x4)")
print(myC)

myD = myB.ravel()
print("")
print("Back to array:")
print(myD)

The array:
[ 0  1  2  3  4  5  6  7  8  9 10 11]

Reshaped (2x6):
[[ 0  1  2  3  4  5]
 [ 6  7  8  9 10 11]]

Reshaped: (3x4)
[[ 0  1  2  3]
 [ 4  5  6  7]
 [ 8  9 10 11]]

Back to array:
[ 0  1  2  3  4  5  6  7  8  9 10 11]

Be careful though, if shapes don’t match an error cannot reshape array is returned:

Iterating over arrays and Indexing

It is possible to loop over the elements of an array by element or by row of the matrix. In the first case we use a the method np.ndarray.flat to make a matrix accessible as a one dimensional array. Check out the following examples:

import numpy as np

myA = np.arange(12)
print(myA)
print("")
print("Matrix:")
myA = myA.reshape((4,3))
print(myA)

print("Looping through elements:")# equivalent to:
for el in myA.flat:               # for el in myA.ravel():
    print("Element:", el)         #     print("Element:",el)


print("Looping row by row:")
for el in myA:
    print("Row: ", el, "is a", type(el))
    for j in el:
        print("\tel:", j)

[ 0  1  2  3  4  5  6  7  8  9 10 11]

Matrix:
[[ 0  1  2]
 [ 3  4  5]
 [ 6  7  8]
 [ 9 10 11]]
Looping through elements:
Element: 0
Element: 1
Element: 2
Element: 3
Element: 4
Element: 5
Element: 6
Element: 7
Element: 8
Element: 9
Element: 10
Element: 11
Looping row by row:
Row:  [0 1 2] is a <class 'numpy.ndarray'>
        el: 0
        el: 1
        el: 2
Row:  [3 4 5] is a <class 'numpy.ndarray'>
        el: 3
        el: 4
        el: 5
Row:  [6 7 8] is a <class 'numpy.ndarray'>
        el: 6
        el: 7
        el: 8
Row:  [ 9 10 11] is a <class 'numpy.ndarray'>
        el: 9
        el: 10
        el: 11

Indexing and slicing can be performed as usual with the [] operator. np.ndarray[i,j] returns the element at row i and column j.

A multi-dimensional matrix has more than 2 dimensions. They can be thought as several 2D matrices stacked one on top of the other:

Note that np.ndarray[0,:,:] is the whole first matrix. np.ndarray[:,0,:] is all the first rows, while np.ndarray[:,:,0] is all the first columns. Regarding slicing and indexing, the same reasoning applies to n-dimensional matrices. For example, myB below is a 3x3x3 matrix.

import numpy as np


myA = np.random.randint(0,10, size = (3,4))
print(myA)
print("")
print("myA[2,2] = ", myA[2,2])
print("myA[1,3] = ", myA[1,3])
print("myA[0,3] = ", myA[0,3])
print("second row:", myA[1,:])
print("")
print("3D matrix ",)
myB = np.random.randint(0,10, size = (3,3,3))
print(" - shape:", myB.shape)
print(myB)
print("")
print("myB[0,2,2] = ", myB[0,2,2])
print("Second matrix:")
print(myB[1,:,:])
print("Third row of second matrix:")
print(myB[1,2,:])
print("Second column of second matrix:")
print(myB[1,:,1])

[[3 7 9 3]
 [5 2 4 7]
 [6 8 8 1]]

myA[2,2] =  8
myA[1,3] =  7
myA[0,3] =  3
second row: [5 2 4 7]

3D matrix
 - shape: (3, 3, 3)
[[[6 7 7]
  [8 1 5]
  [9 8 9]]

 [[4 3 0]
  [3 5 0]
  [2 3 8]]

 [[1 3 3]
  [3 7 0]
  [1 9 9]]]

myB[0,2,2] =  9
Second matrix:
[[4 3 0]
 [3 5 0]
 [2 3 8]]
Third row of second matrix:
[2 3 8]
Second column of second matrix:
[3 5 3]

Broadcasting and arithmetic functions

Universal functions are very efficient element-wise functions that can be applied on ndarrays. As seen in Pandas, operations involving scalar values and arrays are broadcast to all the elements of the ndarray, while operations performed on arrays having the same size are done element by element.

Note also that it is possible to perform some operations only on a sub-part of an ndarray. Moreover, if operators are applied to differently sized, but compatible, ndarrays (es. matrix 3x3x3 and vector 3x1), numpy will perform broadcast of the operator. Let’s see some examples:

import numpy as np

A = np.random.randint(0,10, size = (3,2))
B = np.random.randint(0,10, size = (3,3,3))
C = np.random.randint(0,10, size = (3,1))
print("Matrix A 3x2")
print(A)
print("")
print("Matrix B 3x3x3")
print(B)
print("")
print("Matrix C 3x1")
print(C)
print("")
print("A squared")
print(A**2)
print("")
print("A square-rooted")
print(np.sqrt(A))

print("")
print("B square-rooted")
print(np.sqrt(B))

print("A + C ")
print(A + C)
print("")

print("B + C ")
print(B  + C)

print("")
print("B")
print(B)
print("Sub array B - 20")
B[:, 0:2 , 0:2 ] -= 20
print(B)

Matrix A 3x2
[[0 4]
 [7 3]
 [2 7]]

Matrix B 3x3x3
[[[2 0 0]
  [4 5 5]
  [6 8 4]]

 [[1 4 9]
  [8 1 1]
  [7 9 9]]

 [[3 6 7]
  [2 0 3]
  [5 9 4]]]

Matrix C 3x1
[[4]
 [6]
 [4]]

A squared
[[ 0 16]
 [49  9]
 [ 4 49]]

A square-rooted
[[0.         2.        ]
 [2.64575131 1.73205081]
 [1.41421356 2.64575131]]

B square-rooted
[[[1.41421356 0.         0.        ]
  [2.         2.23606798 2.23606798]
  [2.44948974 2.82842712 2.        ]]

 [[1.         2.         3.        ]
  [2.82842712 1.         1.        ]
  [2.64575131 3.         3.        ]]

 [[1.73205081 2.44948974 2.64575131]
  [1.41421356 0.         1.73205081]
  [2.23606798 3.         2.        ]]]
A + C
[[ 4  8]
 [13  9]
 [ 6 11]]

B + C
[[[ 6  4  4]
  [10 11 11]
  [10 12  8]]

 [[ 5  8 13]
  [14  7  7]
  [11 13 13]]

 [[ 7 10 11]
  [ 8  6  9]
  [ 9 13  8]]]

B
[[[2 0 0]
  [4 5 5]
  [6 8 4]]

 [[1 4 9]
  [8 1 1]
  [7 9 9]]

 [[3 6 7]
  [2 0 3]
  [5 9 4]]]
Sub array B - 20
[[[-18 -20   0]
  [-16 -15   5]
  [  6   8   4]]

 [[-19 -16   9]
  [-12 -19   1]
  [  7   9   9]]

 [[-17 -14   7]
  [-18 -20   3]
  [  5   9   4]]]

A lot of mathematical and statistical functions can be applied. Examples include trigonometric functions like sin, cos, tan,…, statistical functions like mean, std, max, min, cumsum,… see the documentation for a complete list.

Example: Let’s create and plot a sin, cos and \(\log_2 (2 + sin+cos)\) from -2Pi to 2Pi

import numpy as np
import matplotlib.pyplot as plt

A = np.arange(-2* np.pi, 2*np.pi, 0.01)

sA = np.sin(A)
cA = np.cos(A)


plt.plot(sA)
plt.plot(cA)
plt.plot(np.log2(2 + sA + cA))

plt.legend(["Sin(x)", "Cos(x)","$\log_2{2+sin(x)+cos(x)}$"])
plt.show()

Filtering

It is possible to filter np.ndarrays to retrieve the indexes (or the values) meeting specific conditions. The method where provides the index of those values. Note that if the np.ndarray is actually a matrix, where returns a tuple of indexes that are respectively the i and j coordinates of the elements fulfilling the condition.

Example: write a method that creates the np.ndarray with all the integers multiple of a certain number N that do not exceed M. The method should return also the indexes of those values in the original np.ndarray.

import numpy as np

def getMultiples(N,M):
    all = np.arange(1,M+1)
    ind = np.where(all % 27 == 0)
    filt = (all % 27 == 0)
    return ind, all[filt]


res = getMultiples(11, 1000)
print("Indexes: {}\nValues:{}".format(res[0],res[1]))

Indexes: (array([ 26,  53,  80, 107, 134, 161, 188, 215, 242, 269, 296, 323, 350,
       377, 404, 431, 458, 485, 512, 539, 566, 593, 620, 647, 674, 701,
       728, 755, 782, 809, 836, 863, 890, 917, 944, 971, 998]),)
Values:[ 27  54  81 108 135 162 189 216 243 270 297 324 351 378 405 432 459 486
 513 540 567 594 621 648 675 702 729 756 783 810 837 864 891 918 945 972
 999]

import numpy as np

myA = np.arange(12).reshape((3,4))
print(myA)
print("Elements divisible by 3")
indexes = np.where(myA % 3 == 0)
print(indexes)
for ind in range(len(indexes[0])):
    i = indexes[0][ind]
    j = indexes[1][ind]
    print("({},{}) -> {}".format(i,j, myA[i][j]))

[[ 0  1  2  3]
 [ 4  5  6  7]
 [ 8  9 10 11]]
Elements divisible by 3
(array([0, 0, 1, 2]), array([0, 3, 2, 1]))
(0,0) -> 0
(0,3) -> 3
(1,2) -> 6
(2,1) -> 9

Example: Let’s do some filtering on the sine and cosine series plotted above.

import numpy as np
import matplotlib.pyplot as plt

A = np.arange(-2* np.pi, 2*np.pi, 0.01)

sA = np.sin(A)
cA = np.cos(A)

plt.plot(sA)
plt.plot(cA)


s0A_Y = sA[sA < 0]
s0A_X = np.where(sA < 0)

c0A_Y = cA[np.all( [cA > 0.5 , cA < 0.75], axis = 0)]
c0A_X = np.where(np.all( [cA > 0.5 , cA < 0.75], axis = 0))

plt.scatter(s0A_X,s0A_Y, marker='o', c = 'red')
plt.scatter(c0A_X,c0A_Y, marker='X', c = 'green')

plt.legend(["Sin(x)",  "Cos(x)","Sin(x) < 0", "Cos(x) in[0.5,0.75]"])
plt.show()

Note that in the code above, np.all tests if the two conditions are True at the same time (i.e. AND). If we want to test if at least one is True we use np.any. See np.all and np.any for more info:

import numpy as np

v1 = [True, False,False, True]
v2 = [False, False,True, True]
v3 = [False, False, False, True]
print("vals:")
vals = np.array([v1,v2,v3])
print(vals)
print("\nANY(vals):")
print(np.any(vals, axis=0))
print("\nANY(vals) on rows:")
print(np.any(vals, axis=1))
print("\nALL(vals):")
print(np.all(vals, axis=0))

print("\nALL(vals) on rows:")
print(np.all(vals, axis=1))

vals:
[[ True False False  True]
 [False False  True  True]
 [False False False  True]]

ANY(vals):
[ True False  True  True]

ANY(vals) on rows:
[ True  True  True]

ALL(vals):
[False False False  True]

ALL(vals) on rows:
[False False False]

Linear algebra

In numpy the product operator * is used to perform element-wise product, and therefore the arrays in input must have the same size. Matrix-matrix multiplication can be done through the np.dot(x,y) method, which is also a method of the object np.ndarray and therefore if x is a np.ndarray of compatible size with y, we can perform their product with x.dot(y).

A ndarray can be transposed by using the method T.

import numpy as np

a = np.array([1, 2, 3, 1, 2, 3,1, 1 ,1])
A = a.reshape((3,3))
B = np.random.randint(0,10, size = (3,2))

print("A (3x3)")
print(A)
print("")
print("B (3x2)")
print(B)
print("")
print("AxB (3x2)")
print(A.dot(B))
print("")
print("A transposed:")
print(A.T)

A (3x3)
[[1 2 3]
 [1 2 3]
 [1 1 1]]

B (3x2)
[[4 3]
 [4 4]
 [8 4]]

AxB (3x2)
[[36 23]
 [36 23]
 [16 11]]

A transposed:
[[1 1 1]
 [2 2 1]
 [3 3 1]]

Numpy has a module called linalg providing several functions that implement matrix decompositions, inversions, determinant calculation and so on. Some of these methods are linalg.inv for the matrix inversion, linalg.qr for the QR decomposition, linalg.cholesky for the Cholesky decomposition, linalg.eig to find the eigenvalues of a matrix, linalg.solve to solve a system of linear equations and so on.

The complete list of all available methods can be found in the documentation.

Example: Let’s create a random 4x4 matrix and invert it. Let’s finally check that the product of the matrix by its inversion yields the 4x4 identity matrix.

import numpy as np
from numpy import linalg

A = np.random.randint(0,10, size = (4,4))
print("Matrix A:")
print(A)
print("")
print("inv(A)")
A_1 = linalg.inv(A)
print(A_1)
print("")
print(np.dot(A,A_1))

Matrix A:
[[3 7 5 5]
 [0 1 5 9]
 [3 0 5 0]
 [1 2 4 2]]

inv(A)
[[ 0.23121387  0.05780347  0.38150289 -0.83815029]
 [ 0.09537572 -0.10115607 -0.16763006  0.21676301]
 [-0.13872832 -0.03468208 -0.02890173  0.50289017]
 [ 0.06647399  0.1416185   0.03468208 -0.30346821]]

[[ 1.00000000e+00  2.77555756e-17  2.08166817e-17 -1.66533454e-16]
 [-4.16333634e-17  1.00000000e+00 -6.93889390e-18  5.55111512e-17]
 [ 2.77555756e-17  6.93889390e-18  1.00000000e+00  0.00000000e+00]
 [-2.77555756e-17  0.00000000e+00  6.93889390e-17  1.00000000e+00]]

Example: Let’s solve the following system of linear equations:\(\begin{cases} 2x + y - 2z = 3\\ x - y - z = 0\\ x + y + 3z = 12\end{cases}\)

import numpy as np
from numpy import linalg

A = np.array([[2, 1, -2],[1,-1,-1], [1, 1 ,3]])
b = np.array([3, 0, 12])

print("A")
print(A)
print("")
print("b")
print(b)
print("")
#Let's find x such that: Ax = b
x = linalg.solve(A,b)
print("X")
print(x)
#Let's double check Ax = b:
print("")
print("Ax:")
print(np.dot(A,x))

A
[[ 2  1 -2]
 [ 1 -1 -1]
 [ 1  1  3]]

b
[ 3  0 12]

X
[3.5 1.  2.5]

Ax:
[ 3.  0. 12.]

Matplotlib

Matplotlib is a library created for producing publication quality plots. To use matplotlib one has to import it in the python program. Typically this is done with

import matplotlib.pyplot as plt

Documentation and several examples can be found at the matplotlib website.

Figures can also be saved to files with plt.savefig('filename').

Example: [adapted from documentation] Let’s plot the function \(cos(2 * \Pi * x)*sin(2 * \Pi * x)\) for x ranging from 0 to 10, annotating the point (5,0).

import numpy as np
import matplotlib.pyplot as plt

x = np.arange(0, 10, 0.005)
y = np.cos(np.pi*x) * np.sin(2*np.pi*x)

fig = plt.figure()

ax = fig.add_subplot(111)
xdata = 5
ydata = 0

ax.plot(x, y)
ax.set_xlim(0, 10)
ax.set_ylim(-1, 1)

xdata = 5
ydata = 0

bbox = dict(boxstyle="round", fc="0.8")
arrowprops = dict(
    arrowstyle = "->")

offset = 92
ax.annotate('(%.1f, %.1f)'%(xdata, ydata),
            (xdata, ydata), xytext=(-1.5*offset, offset), textcoords='offset points',
            bbox=bbox, arrowprops=arrowprops)

plt.show()

Example: Let’s plot simultaneusly \(sin(2 * \Pi * x)\), \(cos(2 \Pi x)\) and \(sin(2 \Pi x)*cos(2 \Pi x)\) for x ranging from 0 to 5.

import numpy as np
import matplotlib.pyplot as plt

x = np.arange(0, 5, 0.005)
y = np.sin(2*np.pi*x)
y1 = np.cos(2*np.pi*x)
y2 = np.sin(2*np.pi*x)*np.cos(2*np.pi*x)

f, (ax1, ax2, ax3) = plt.subplots(3, sharex=True, sharey=True)
ax1.plot(x, y,'r')
ax2.plot(x, y1,'g')
ax3.plot(x,y2,'b')
ax1.legend(["sin"])
ax2.legend(["cos"])
ax3.legend(["sin * cos"])

plt.show()

Exercises

1. Create the following functions:
   • 1. createRadomList : with parameters, N, min, max. Creates a list of N random integers ranging from min to max;
   • 2. getIdentical : with parameters two lists of integers L1 and L2 having the same size. It returns the list of indexes I where L1[I] == L2[I]
   • 3. check : gets lists L1, L2, identities (as computed by getIdentical) and a number N and prints if the first N and last N values in identities correspond to indexes of identical values in L1 and L2;
   • 4. implement getIdentical using numpy.ndarrays. Call it getIdenticalNpy (hint: subtract the two arrays and find zeros).

Test the software creating two lists of 100,000 random numbers from 0 to 10. You should get something similar to:

100000
100000
9032
Index: 4 L: 1 L1: 1
Index: 21 L: 10 L1: 10
Index: 32 L: 6 L1: 6
Index: 37 L: 5 L1: 5
Index: 47 L: 1 L1: 1
Index: 99974 L: 8 L1: 8
Index: 99982 L: 6 L1: 6
Index: 99983 L: 3 L1: 3
Index: 99984 L: 4 L1: 4
Index: 99987 L: 0 L1: 0

Identities are OK!
9032
Index: 4 L: 1 L1: 1
Index: 21 L: 10 L1: 10
Index: 32 L: 6 L1: 6
Index: 37 L: 5 L1: 5
Index: 47 L: 1 L1: 1
Index: 99974 L: 8 L1: 8
Index: 99982 L: 6 L1: 6
Index: 99983 L: 3 L1: 3
Index: 99984 L: 4 L1: 4
Index: 99987 L: 0 L1: 0

Identities are OK!

Show/Hide Solution

%reset -s -f

import random
import numpy as np
import time


def createRandomList(N=0, min=0, max=10):
    """creates a list of N random numbers in [min,max]"""
    L = []
    for i in range(0,N):
        L.append(random.randint(min,max))
    #L = [random.randint(min,max) for i in range(0,N)]
    return L


def getIdentical(list1,list2):
    """return indexes of identical values
    (lists assumed of same size)"""

    return [i for i in range(0,len(list1)) if list1[i] == list2[i]]

def getIdenticalNpy(list1,list2):
    """return indexes of identical values
    (lists assumed of same size)"""
    nda1 = np.array(list1)
    nda2 = np.array(list2)
    diff = nda1 - nda2
    ret = np.where(diff == 0)
    return ret


def check(list1, list2, identical,N=10):
    ret = True
    for index in identical[0:5]:
        if(list1[index] !=list2[index]):
            ret = False

        print("Index: {} L: {} L1: {}".format(index, list1[index], list2[index]))
        #assert(L[index] ==  L1[index])
    for index in identical[-N:]:
        if(list1[index] !=list2[index]):
            ret = False
        print("Index: {} L: {} L1: {}".format(index, list1[index], list2[index]))
        #assert(L[index] ==  L1[index])

    return ret

def checkRND(list1, list2, identical,N=10):
    ret = True
    for index in createRandomList(N,0,len(identical)):
        I = identical[index]
        if(list1[I] !=list2[I]):
            ret = False

        print("Index: {} L: {} L1: {}".format(index, list1[index], list2[index]))
        #assert(L[index] ==  L1[index])

    return ret



L = createRandomList(100000)
L1 = createRandomList(100000)
print(len(L))
print(len(L1))

identical = getIdentical(L,L1)
print(len(identical))

if check(L,L1,identical,5):
    print("\nIdentities are OK!")
else:
    print("\nSomething went wrong!")


id1 = getIdenticalNpy(L,L1)
print(len(id1[0]))
if check(L,L1,identical,5):
    print("\nIdentities are OK!")
else:
    print("\nSomething went wrong!")

100000
100000
9143
Index: 16 L: 2 L1: 2
Index: 23 L: 6 L1: 6
Index: 51 L: 2 L1: 2
Index: 55 L: 1 L1: 1
Index: 84 L: 8 L1: 8
Index: 99935 L: 10 L1: 10
Index: 99957 L: 2 L1: 2
Index: 99966 L: 3 L1: 3
Index: 99992 L: 4 L1: 4
Index: 99995 L: 5 L1: 5

Identities are OK!
9143
Index: 16 L: 2 L1: 2
Index: 23 L: 6 L1: 6
Index: 51 L: 2 L1: 2
Index: 55 L: 1 L1: 1
Index: 84 L: 8 L1: 8
Index: 99935 L: 10 L1: 10
Index: 99957 L: 2 L1: 2
Index: 99966 L: 3 L1: 3
Index: 99992 L: 4 L1: 4
Index: 99995 L: 5 L1: 5

Identities are OK!

2. Write a function that converts a numpy ndarray of temperatures expressed in Degrees Celsius into Degrees Farenheit. The formula to convert a temperature C in Celsius into F in Farenheit is the following:

   \[F = C * 9/5 + 32\]

   Write then a function that converts a numpy ndarray of temperatures in Farenheit into Celsius.

   Finally:

   1. apply the Celsius to Farenheit conversion on an ndarray containing the following October’s minimum and maximum temperatures in Trento: tmin = [12, 11, 11, 8, 9, 10, 3, 8, 4, 5, 10, 9, 8, 9, 8, 7, 6, 4, 5, 6, 9, 9, 3, 3, 5] and tmax =[15, 22, 18, 20, 22, 22, 20, 21, 21, 21, 21, 23, 24, 24, 24, 25, 22, 22, 20, 20, 19, 15, 20, 23, 19];
   2. check that both functions work correctly by converting the values from Celsius to Farenheit and back to Celsius;
   3. plot the minimum and maximum temperatures in celsius on the same graph. Since the temperatures refer to the first 25 days of the month of October 2017, the x coordinate can be a range(1,26);

Show/Hide Solution

%reset -s -f
import numpy as np
import matplotlib.pyplot as plt

%matplotlib inline


def Celsius2Farenheit(CA):
    FA = CA * 9/5 + 32
    return FA

def Farenheit2Celsius(FA):
    CA = (FA - 32) * 5/9
    return CA

tmin = [12, 11, 11, 8, 9, 10, 3, 8, 4, 5, 10, 9, 8, 9, 8, 7, 6, 4, 5, 6, 9, 9, 3, 3, 5]
tmax =[15, 22, 18, 20, 22, 22, 20, 21, 21, 21, 21, 23, 24, 24, 24, 25, 22, 22, 20, 20, 19, 15, 20, 23, 19]

minC = np.array(tmin)
maxC = np.array(tmax)

minF = Celsius2Farenheit(minC)
maxF = Celsius2Farenheit(maxC)

print("T min in Celsius:")
print(minC)
print("")
print("T min in Farenheit")
print(minF)
print("T max in Celsius:")
print(maxC)
print("")
print("T max in Farenheit")
print(maxF)

print(Farenheit2Celsius(minF))

#plotting the data:
x = np.arange(1,26,1)

plt.plot(x, minC, 'r', x,maxC, 'b')
plt.title("Temperature in Trento: October 2017")
plt.ylabel('°C')
plt.xlabel('Day')
plt.show()
#plt.close()
plt.plot(x, minF, 'r', x,maxF, 'b')
plt.title("Temperature in Trento: October 2017")
plt.ylabel('°F')
plt.xlabel('Day')
plt.show()

T min in Celsius:
[12 11 11  8  9 10  3  8  4  5 10  9  8  9  8  7  6  4  5  6  9  9  3  3
  5]

T min in Farenheit
[53.6 51.8 51.8 46.4 48.2 50.  37.4 46.4 39.2 41.  50.  48.2 46.4 48.2
 46.4 44.6 42.8 39.2 41.  42.8 48.2 48.2 37.4 37.4 41. ]
T max in Celsius:
[15 22 18 20 22 22 20 21 21 21 21 23 24 24 24 25 22 22 20 20 19 15 20 23
 19]

T max in Farenheit
[59.  71.6 64.4 68.  71.6 71.6 68.  69.8 69.8 69.8 69.8 73.4 75.2 75.2
 75.2 77.  71.6 71.6 68.  68.  66.2 59.  68.  73.4 66.2]
[12. 11. 11.  8.  9. 10.  3.  8.  4.  5. 10.  9.  8.  9.  8.  7.  6.  4.
  5.  6.  9.  9.  3.  3.  5.]

3. Write some python code to solve the following system of linear equations:

   \[\begin{split}\begin{cases} 3x - 4y + 2z -5w = -9\\ -4x + 4y + 10z + w = 32\\ -x + 2y + -7z -w = -7\\ x + y + z + w = 1\end{cases}\end{split}\]

   Define then a function to compute the Euclidean norm of a ndarray in input. Hint: \(||X||_2 = \sqrt{{x_1}^2 + {x_2}^2 + ... + {x_n}^2}\)

   Compute then the Euclidean norm of the solution.

   Implement a function that takes two N-dimensional vectors and computes the euclidean distance between them. Compute the distance between the solution of the system of equations above and the vector V = [7,120,11,33]. Check also that the distance between a vector and itself is zero. The Euclidean distance between two vectors P and Q can be computed as: \(\sqrt{\sum\limits_{i=1}^n (q_i -p_i)^2}\).

Show/Hide Solution

import numpy as np
from numpy import linalg

def eucNorm(arr): ### equivalent to np.linalg.norm
    """computes the Euclidean norm of the array arr"""
    return np.sqrt(np.power(arr,2).sum())

def eucDist(v1, v2):
    """computes the Euclidean distance of two N-dimensional vectors"""
    dV = np.power(v2-v1,2)
    return np.sqrt(dV.sum())
#AX = b

A = [[3, 4, 2, -5],[4, 4, 10, 1],[-1, 2, -7, -1],[1, 1, 1, 1]]
Amat = np.array(A)

b = np.array([-9, 32, -7, 1])
print("A matrix")
print(Amat)
print("")
print("b vector")
print(b)
print("")
Xsol = linalg.solve(A,b)
print("Solution X:")
print(Xsol)
print(Amat.dot(Xsol))
print("")
#Euclidean norm:
print("Euclidean norm of {}:".format(Xsol))
print(eucNorm(Xsol))

#Euclidean distance
V = np.array([7,120,11,33])
print("\nThe Euclidean distance of")
print(Xsol)
print("\nand\n")
print(V)

print("\nis:")
print(eucDist(Xsol,V))

print("\neucDist(V,V) = {}".format(eucDist(V,V)))

A matrix
[[ 3  4  2 -5]
 [ 4  4 10  1]
 [-1  2 -7 -1]
 [ 1  1  1  1]]

b vector
[-9 32 -7  1]

Solution X:
[-15.88888889   9.28888889   5.64444444   1.95555556]
[-9. 32. -7.  1.]

Euclidean norm of [-15.88888889   9.28888889   5.64444444   1.95555556]:
19.35004386379691

The Euclidean distance of
[-15.88888889   9.28888889   5.64444444   1.95555556]

and

[  7 120  11  33]

is:
117.35966455387272

eucDist(V,V) = 0.0

4. Implement the following functions working on numpy ndarrays:

   1. The component form of a vector comp(A,B) starting in point A and ending in point B is \(\overline{AB}\). Hint: if \(A=(a_1,...,a_n)\) and \(B=(b_1,...,b_n)\), \(\overline{AB} = (b_1 - a_1, ..., b_n - a_n)\).
   2. The direction cosines of a 3D vector dirCos(A). If \(P=(x,y,z)\) the direction cosines are the cosines of the angles made by the vector with the three axes. They can be computed as:
   \[\frac{x}{\sqrt(x^2+y^2+z^2}, \frac{y}{\sqrt(x^2+y^2+z^2}, \frac{z}{\sqrt(x^2+y^2+z^2}\]
   
   3. The angle between two vectors angle(A,B). Given two vectors \(A = (a_x,a_y,a_z)\) and \(B = (b_x,b_y,b_z)\), \(cos(\alpha) = \frac{A \cdot B}{||A||_2||B||_2}\) where the Euclidean norms are computed as in the previous example.
   
   4. The volume of the pyramid described by three 3D vectors \(\overline{a},\overline{b},\overline{c}\):

   the volume pyrVol(a,b,c) can be computed as: \(\frac{1}{6} |det(M)|\), where \(M = \begin{bmatrix}\overline{a} \\ \overline{b} \\ \overline{c}\end{bmatrix}\), det is the determinant of the matrix anx || represents the absolute value.

   Define some numpy arrays starting from the following lists:

   1. A = [10, 3, 4, 7, 12], B = [6, 7, 8, 1, 1] and test comp(A,B)
   2. Va = [90,12,72] and test dirCos(Va)
   3. VA = [70,9,12] and VB = [1,-10,30] and test angle(VA,VB)
   4. a = [10, 20, 30], b = [ 4, 7, 21], c = [-5, 4, 12] and test pyrVol(a,b,c)

Check your solutions here.

Show/Hide Solution

import numpy as np
from numpy import linalg

def comp(p1,p2):
    """component of vector starting in p1 and ending in p2"""
    return p2 - p1

def dirCos(v1):
    """direction cosines of v1"""
    norm = np.sqrt(np.power(v1,2).sum())
    return v1[0]/norm, v1[1]/norm, v1[2]/norm

def eucNorm(arr):
    """computes the Euclidean norm of the array arr"""
    return np.sqrt(np.power(arr,2).sum())

def angle(v1,v2):
    """computes the angle between two vectors v1 and v2"""
    dp = np.dot(v1,v2)
    cosVal = dp / (eucNorm(v1) * eucNorm(v2))
    return cosVal

def pyrVol(v1,v2,v3):
    """returns the volume of the pyramid described by v1,v2 and v3"""
    matM = np.concatenate((v1,v2,v3))
    matM = matM.reshape((v1.shape[0], 3))
    return abs(np.linalg.det(matM))/6


#Testing the functions
#1. comp(A,B)
A = np.array([10, 3, 4, 7, 12])
B = np.array([6, 7, 8, 1, 1])
print("A")
print(A)
print("")
print("B")
print(B)
print("")
print("comp(A,B)")
print(comp(A,B))
#2. dirCos(Va)
print("")
Va = np.array([90,12,72])
print("Va")
print(Va)
print("")
print("dirCos(Va)")
print(dirCos(Va))
#3. angle(VA,VB)
VA = np.array([70,9,12])
VB = np.array([1,-10,30])
print("")
print("VA")
print(VA)
print("")
print("VB")
print(VB)
print("")
print("angle(VA,VB)")
print(angle(VA,VB))
print("")
#4. pyrVol(a,b,c)
a = np.array([10, 20, 30])
b = np.array([ 4,  7, 21])
c = np.array([-5,  4, 12])
print("a")
print(a)
print("")
print("b")
print(b)
print("")
print("c")
print(c)
print("")
print("pyrVol(a,b,c)")
print(pyrVol(a,b,c))

A
[10  3  4  7 12]

B
[6 7 8 1 1]

comp(A,B)
[ -4   4   4  -6 -11]

Va
[90 12 72]

dirCos(Va)
(0.7766705596177466, 0.10355607461569954, 0.6213364476941973)

VA
[70  9 12]

VB
[  1 -10  30]

angle(VA,VB)
0.15011183829724634

a
[10 20 30]

b
[ 4  7 21]

c
[-5  4 12]

pyrVol(a,b,c)
254.99999999999977

5. Implement the power iteration algorithm which is a method to obtain an approximation of the biggest (in absolute value) eigenvalue of a matrix A.

The algorithm starts from a random vector \(b_0\) and keeps computing \(b_{k+1} = \frac{A\cdot b_{k}}{min(A\cdot b_{k})}\). When the algorithm ends, the eigenvalue is actually the value: \(min(A\cdot b_{k})\)

The powerIteration function will have the maximum number of iterations and dThr as parameters powerIteration(A,maxIt, dThr). The computation will stop either when the maximum number of iterations maxIt is reached or when the Euclidean distance between b_{k-1} and b_k is lower than dThr.

Check the result against numpy eigenvalues obtained with np.linalg.eig() using various matrices.

Show/Hide Solution

import numpy as np
from numpy import linalg


def eucDist(v1, v2):
    """computes the Euclidean distance of two N-dimensional vectors"""
    dV = np.power(v2-v1,2)
    return np.sqrt(dV.sum())


def powerIteration(A,maxIt,dThr):
    b = np.random.randint(1,10,(A.shape[0]))
    it = 0
    dist = 1000000
    while( it < maxIt and dist > dThr ):
        tmp = np.dot(A,b)
        dist = eucDist(b,tmp)
        b = tmp/np.min(tmp)
        it += 1

    return np.min(tmp)



M = np.array([[1, 3, 7, 9], [ 4, 11, 7, 27], [22, 11, 57, 1], [4, 7, 27, 27]])

r = powerIteration(M,200, 0.0001)
print("Eigenvalue from power method: ", r)
print("FROM linalg:" , max(np.linalg.eig(M)[0]))

N = np.array([[0, 11, -5],[-2, 17, -7],[-4, 26, -10]])
print(N)
r = powerIteration(N,200, 0.0001)
print("Eigenvalue from power method: ", r)
print("FROM linalg:" , max(np.linalg.eig(N)[0]))
N1 = np.array([[2, -12],[1, -5]])
r = powerIteration(N1,200, 0.0001)
print("Eigenvalue from power method: ", r)
print("FROM linalg:" , max(np.linalg.eig(N1)[0]))
N2 = np.array([[1, 2, 0],[-2, 1, 2], [1,3,1]])

r = powerIteration(N2,200, 0.0001)
print("Eigenvalue from power method: ", r)
print("FROM linalg:" , max(np.linalg.eig(N2)[0]))

R = np.random.randint(0,20, size=(5,5))
r = powerIteration(R,200, 0.0001)
print("Eigenvalue from power method: ", r)
print("FROM linalg:" , max(np.linalg.eig(R)[0]))

Eigenvalue from power method:  68.24845123079758
FROM linalg: 68.24845123079754
[[  0  11  -5]
 [ -2  17  -7]
 [ -4  26 -10]]
Eigenvalue from power method:  3.9999999999999982
FROM linalg: 4.000000000000021
Eigenvalue from power method:  -2.0
FROM linalg: -0.9999999999999982
Eigenvalue from power method:  3.0
FROM linalg: (3.0000000000000004+0j)
Eigenvalue from power method:  50.69133949667758
FROM linalg: (50.69133949667753+0j)

6. Implement a function movingAvg(A,n) where A is a numpy one dimensional array and n is the window size on which computing the average, that outputs the moving average over a numpy one dimensional array. Es. A = [1,2,3,4,5] movingAvg(A,2) = [1.5, 2.5, 3.5, 4.5], while movingAvg(A,3) = [2,3,4] without using for loops. Hint: use cumsum and clever slicing. Assess the smoothing effect of the moving average by creating a numpy array containing a sinusoidal wave with some additional noise (i.e. use np.sin and np.random.rand) and testing several values of the window size n.

Show/Hide Solution

import numpy as np
import matplotlib.pyplot as plt

def movingAvg(v, n):
    """computes the moving average of n values in the array v"""
    cs = np.cumsum(v)
    print(cs)
    print("\t",cs[n:])
    print("\t", cs[:-n])
    cs[n:] = cs[n:] - cs[:-n]
    print("CS:", cs)
    return cs[n - 1:] / n



A = np.arange(1,8,1)

print("A:")
print(A)
print(movingAvg(A,2))
print(movingAvg(A,3))

X = np.arange(0, 5, 0.005)
#B = np.random(100)
B = np.sin(2*np.pi*X)
B += np.random.rand(1000)
C = movingAvg(B,5)
D = movingAvg(B,10)
E = movingAvg(B,20)
#X = np.arange(0,B.shape[0])

plt.plot(X,B)
plt.title("No moving average")
plt.show()
plt.close()
plt.plot(np.arange(0,C.shape[0]),C)
plt.title("Window size: 5")
plt.show()
plt.close()
plt.title("Window size: 10")
plt.plot(np.arange(0,D.shape[0]),D)
plt.show()
plt.close()
plt.title("Window size: 20")
plt.plot(np.arange(0,E.shape[0]),E)
plt.show()

A:
[1 2 3 4 5 6 7]
[ 1  3  6 10 15 21 28]
         [ 6 10 15 21 28]
         [ 1  3  6 10 15]
CS: [ 1  3  5  7  9 11 13]
[1.5 2.5 3.5 4.5 5.5 6.5]
[ 1  3  6 10 15 21 28]
         [10 15 21 28]
         [ 1  3  6 10]
CS: [ 1  3  6  9 12 15 18]
[2. 3. 4. 5. 6.]
[2.48753144e-01 8.56321237e-01 1.51115369e+00 2.17751391e+00
 2.52592877e+00 3.63511225e+00 4.26961894e+00 5.33417086e+00
 6.28234002e+00 6.85876808e+00 7.98158289e+00 8.71682655e+00
 9.96605430e+00 1.09444751e+01 1.22519897e+01 1.33985118e+01
 1.46055198e+01 1.56158856e+01 1.71077960e+01 1.83138696e+01
 1.93255099e+01 2.05448101e+01 2.12014273e+01 2.21643140e+01
 2.35090346e+01 2.45062190e+01 2.58532031e+01 2.70320829e+01
 2.79380702e+01 2.90265075e+01 3.04054894e+01 3.18234427e+01
 3.32420959e+01 3.47560388e+01 3.62844487e+01 3.76068737e+01
 3.94082473e+01 4.06935638e+01 4.20592052e+01 4.38920094e+01
 4.56492599e+01 4.73134421e+01 4.83822522e+01 5.02776516e+01
 5.19741801e+01 5.39607155e+01 5.51022785e+01 5.69659665e+01
 5.81264861e+01 5.97415523e+01 6.08653723e+01 6.27128870e+01
 6.45182327e+01 6.60828954e+01 6.74821934e+01 6.85390488e+01
 7.02187648e+01 7.16482242e+01 7.33388630e+01 7.51655390e+01
 7.70921170e+01 7.88888011e+01 7.98302917e+01 8.11080244e+01
 8.27428420e+01 8.38054782e+01 8.52028215e+01 8.61179015e+01
 8.71622260e+01 8.80078283e+01 8.96105430e+01 9.06246227e+01
 9.17404877e+01 9.34186800e+01 9.48520631e+01 9.55910088e+01
 9.64402500e+01 9.77230403e+01 9.89376929e+01 9.97884927e+01
 1.01310492e+02 1.02486541e+02 1.03558001e+02 1.04656952e+02
 1.05868828e+02 1.06634764e+02 1.07458764e+02 1.08065756e+02
 1.08620073e+02 1.09903183e+02 1.10951751e+02 1.11721201e+02
 1.12197306e+02 1.12669805e+02 1.12915216e+02 1.13506067e+02
 1.13943196e+02 1.14733648e+02 1.15174190e+02 1.15385205e+02
 1.15409883e+02 1.15445722e+02 1.16062324e+02 1.16421913e+02
 1.16833159e+02 1.17573396e+02 1.18376353e+02 1.18375107e+02
 1.18789495e+02 1.18773827e+02 1.18485461e+02 1.18905101e+02
 1.18856994e+02 1.18843310e+02 1.19005848e+02 1.19382906e+02
 1.19530134e+02 1.19893743e+02 1.19631459e+02 1.19867422e+02
 1.19465273e+02 1.19805157e+02 1.19855222e+02 1.19409417e+02
 1.19672241e+02 1.19695990e+02 1.19220963e+02 1.18684164e+02
 1.18431851e+02 1.17667359e+02 1.17065812e+02 1.16663417e+02
 1.16193259e+02 1.15796092e+02 1.15197414e+02 1.14893192e+02
 1.14852221e+02 1.14051998e+02 1.13639601e+02 1.12830788e+02
 1.12596591e+02 1.12032357e+02 1.11629195e+02 1.10836558e+02
 1.09999119e+02 1.09499487e+02 1.08862985e+02 1.08807855e+02
 1.08575153e+02 1.08324310e+02 1.08228030e+02 1.07311946e+02
 1.06866112e+02 1.06455026e+02 1.06424848e+02 1.05729307e+02
 1.04987848e+02 1.04112225e+02 1.03160072e+02 1.03129308e+02
 1.02848168e+02 1.02692440e+02 1.02044393e+02 1.01713049e+02
 1.00872177e+02 1.00466798e+02 1.00567987e+02 1.00583750e+02
 1.00077581e+02 1.00212070e+02 9.96347551e+01 9.97939189e+01
 9.99647834e+01 1.00013875e+02 9.99153542e+01 1.00082535e+02
 9.96910086e+01 9.98786403e+01 9.98590930e+01 9.92594228e+01
 9.90188711e+01 9.86049285e+01 9.90509311e+01 9.90202600e+01
 9.90358977e+01 9.92213797e+01 9.91641850e+01 9.89039374e+01
 9.93579306e+01 9.92090406e+01 9.94113426e+01 9.93566685e+01
 9.92058231e+01 9.98498714e+01 1.00635410e+02 1.01439810e+02
 1.02221032e+02 1.02900971e+02 1.03171326e+02 1.03221016e+02
 1.03628257e+02 1.03891902e+02 1.04087181e+02 1.04234716e+02
 1.05085644e+02 1.05253506e+02 1.06211468e+02 1.06576557e+02
 1.06904769e+02 1.07273364e+02 1.08254428e+02 1.08838534e+02
 1.09627198e+02 1.10581714e+02 1.11868045e+02 1.13049079e+02
 1.13801161e+02 1.14441685e+02 1.15032886e+02 1.15896568e+02
 1.16746472e+02 1.17815519e+02 1.19136225e+02 1.20493162e+02
 1.21461228e+02 1.22548262e+02 1.23458381e+02 1.24997038e+02
 1.25824399e+02 1.27311551e+02 1.28899264e+02 1.30503752e+02
 1.31607502e+02 1.32842058e+02 1.34305964e+02 1.35469792e+02
 1.36745472e+02 1.37860281e+02 1.39249914e+02 1.40235407e+02
 1.41986259e+02 1.43023509e+02 1.44510927e+02 1.45793654e+02
 1.47353485e+02 1.49300606e+02 1.50938291e+02 1.51969216e+02
 1.53397645e+02 1.54907168e+02 1.56443346e+02 1.58124245e+02
 1.59399868e+02 1.60524290e+02 1.61909080e+02 1.63853174e+02
 1.65022593e+02 1.66902493e+02 1.68414882e+02 1.69832088e+02
 1.71665185e+02 1.73064670e+02 1.74718614e+02 1.76035394e+02
 1.77844266e+02 1.79425297e+02 1.81001226e+02 1.82189688e+02
 1.83790795e+02 1.85253937e+02 1.86302974e+02 1.87253668e+02
 1.88820572e+02 1.90529850e+02 1.91716958e+02 1.93015049e+02
 1.94557318e+02 1.95675854e+02 1.97265152e+02 1.98453810e+02
 1.99862363e+02 2.01333290e+02 2.02684640e+02 2.03353096e+02
 2.04463748e+02 2.05316173e+02 2.05804665e+02 2.06625845e+02
 2.07252654e+02 2.08440430e+02 2.08782752e+02 2.10020726e+02
 2.10624785e+02 2.11199635e+02 2.11403344e+02 2.11745011e+02
 2.12271604e+02 2.13295004e+02 2.13457409e+02 2.14434121e+02
 2.15303610e+02 2.15726362e+02 2.15990272e+02 2.16128908e+02
 2.16618039e+02 2.16494679e+02 2.16322904e+02 2.16533557e+02
 2.16352941e+02 2.16325891e+02 2.16238035e+02 2.16152488e+02
 2.15915419e+02 2.15530307e+02 2.15220012e+02 2.15384502e+02
 2.15877004e+02 2.16358308e+02 2.16231535e+02 2.15832406e+02
 2.15883383e+02 2.15760781e+02 2.16112767e+02 2.15516759e+02
 2.15615446e+02 2.15196738e+02 2.14709188e+02 2.14621582e+02
 2.14097132e+02 2.13972836e+02 2.13681127e+02 2.13278136e+02
 2.12988496e+02 2.12414805e+02 2.12245073e+02 2.11768923e+02
 2.11224642e+02 2.11135544e+02 2.11130735e+02 2.10235861e+02
 2.09517432e+02 2.08905657e+02 2.08752041e+02 2.08761615e+02
 2.08748300e+02 2.08665560e+02 2.07970001e+02 2.07966451e+02
 2.07217844e+02 2.06324243e+02 2.06275196e+02 2.05509110e+02
 2.05200851e+02 2.04263646e+02 2.04002240e+02 2.03896272e+02
 2.03186422e+02 2.02589562e+02 2.01995275e+02 2.01783769e+02
 2.01070520e+02 2.00301492e+02 1.99821008e+02 1.99207721e+02
 1.99142083e+02 1.98488819e+02 1.98114902e+02 1.98196743e+02
 1.97986413e+02 1.98026622e+02 1.98157814e+02 1.98118424e+02
 1.98047486e+02 1.98265341e+02 1.98530773e+02 1.98275488e+02
 1.97661810e+02 1.97293292e+02 1.96808223e+02 1.96612802e+02
 1.96156307e+02 1.96198341e+02 1.96045322e+02 1.96431667e+02
 1.96917708e+02 1.97010602e+02 1.96859646e+02 1.97054729e+02
 1.97583366e+02 1.97651361e+02 1.97894422e+02 1.97887084e+02
 1.98093838e+02 1.98277408e+02 1.98338441e+02 1.98687873e+02
 1.98872920e+02 1.99151847e+02 1.99614027e+02 2.00333211e+02
 2.00666718e+02 2.01622288e+02 2.02547397e+02 2.02690196e+02
 2.03069171e+02 2.03671741e+02 2.03963750e+02 2.04530370e+02
 2.05519157e+02 2.06478663e+02 2.07410064e+02 2.08459330e+02
 2.09032379e+02 2.09771225e+02 2.10873246e+02 2.12206472e+02
 2.13231903e+02 2.14023645e+02 2.14589707e+02 2.15862127e+02
 2.16457796e+02 2.17443382e+02 2.18611343e+02 2.20194767e+02
 2.20968808e+02 2.22081858e+02 2.22835139e+02 2.23927861e+02
 2.25320606e+02 2.26389829e+02 2.27408596e+02 2.28351379e+02
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Practical 10

In this practical we will will get acquainted with Biopython.

Slides

The slides of the introduction can be found here: Intro

Biopython

From the Biopython tutorial: The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.

The goal of Biopython is to make it as easy as possible to use Python for bioinformatics by creating high-quality, reusable modules and classes. Biopython features include parsers for various Bioinformatics file formats (FASTA, FASTQ, BLAST, PDB, Clustalw, Genbank,…), access to online services (NCBI, Expasy,…), interfaces to common and not-so-common programs (Clustalw, DSSP, MSMS…), a standard sequence class, various clustering modules, a KD tree data structure etc. and even documentation.

In this practical we will see some features of Biopython but refer to biopython documentation to discover all its features, recipes etc.

These notes are largely based on what available here.

Installation of Biopython

To test if Biopython is installed in your system you can import the library with:

import Bio

if the execution gives:

Biopython needs to be installed.

In windows installing Biopython should be as easy as opening the command prompt as admininstrator (typing cmd and then right clicking on the link choosing run as admininstrator) and then pip3 install biopython. If that does not work, you should be able to install biopython with the following: python3.xx -m pip install biopython (where you should change python3.xx with the path to your python3.xx executable).

In linux sudo pip3 install biopython will install biopython for python3 up to python3.5. On python 3.6 and later the command is: python3.6 -m pip install biopython or, more in general, pythonX.X -m pip install biopython.

Detailed installation instructions can be found here.

General overview

Biopython provides the capability of parsing standard bioinformatics formats into python usable data structures. Some of the supported tools and formats are:

1. Blast output – both from standalone and WWW Blast
2. Clustalw
3. FASTA
4. GenBank
5. PubMed and Medline
6. ExPASy files, like Enzyme and Prosite
7. SCOP, including ‘dom’ and ‘lin’ files
8. UniGene
9. SwissProt

among the others. In particular it provides a sequence class to perform the most common operations on sequences, parsing of alignments, clustering etc. and it can quickly connect to the most popular databases to download data or parse information on the fly.

Sequence objects

Biopython has a specific object Seq to deal with biological sequences which is a lot more powerful than the str object of python when it comes to manage biological data. The object Seq has methods like translate() and reverse_complement() which are very handy.

As in the case of python’s str objects, the object Seq is immutable. The mutable version is MutableSeq.

All the information on Seq objects can be found here.

The alphabet

Seq objects are composed by two information: the actual sequence and the alphabet the sequence refers to. We normally will use the IUPAC alphabet as defined in the Bio.Alphabet.IUPAC which provides a suitable alphabet to deal with DNA, RNA and proteins. Several options are available, including Bio.Alphabet.generic_dna or Bio.Alphabet.generic_protein, Bio.Alphabet.ThreeLetterProtein and other.

Specifying an alphabet quickly tells you what information you are dealing with and moreover it provides a way to specify a constraint on the data.

If the definition of the alphabet is not specified, the default one is used (Alphabet).

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC

#No alphabet specified
s = Seq("GATTACATAATA")
dna_seq = Seq("GATTATACGTAC", IUPAC.unambiguous_dna)
print("S:", s)
print("S's alphabet:", s.alphabet)
print("dna_seq:", dna_seq)
print("dna_seq's alphabet:", dna_seq.alphabet)

my_prot = Seq("MGNAAAAKKGSEQE", IUPAC.protein)
print("my_prot:", my_prot)
print("my_prot's alphabet:", my_prot.alphabet)

S: GATTACATAATA
S's alphabet: Alphabet()
dna_seq: GATTATACGTAC
dna_seq's alphabet: IUPACUnambiguousDNA()
my_prot: MGNAAAAKKGSEQE
my_prot's alphabet: IUPACProtein()

Looping, slicing and concatenation

Note also that Seq objects behave like strings, but the consistency of the alphabet is checked too. For example we cannot concatenate a unambiguous_dna with a IUPAC.protein sequence. This is the error message we would get:

To do it one should change the alphabet to generic_alphabet:

from Bio.Seq import Seq
from Bio.Alphabet import generic_alphabet

dna_seq = Seq("GATTATACGTAC", IUPAC.unambiguous_dna)
my_prot = Seq("MGNAAAAKKGSEQE", IUPAC.protein)

my_prot.alphabet = generic_alphabet

#Does it really make sense though?!?
print(dna_seq + my_prot)

GATTATACGTACMGNAAAAKKGSEQE

We can also loop through the elements and slice strings with the usual [S:E:step] operator (and as usual S is included, E is excluded). We can also convert a Seq object into a string.

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC

dna_seq = Seq("GATTATACGTACGGCTA", IUPAC.unambiguous_dna)

for base in dna_seq:
    print(base, end = " ")

print("")

sub_seq = dna_seq[4:10]
print(sub_seq)

#Let's reverse the string:

print("Reversed: ", dna_seq[::-1])
#from Seq to string:
dna_str = str(dna_seq)
print("As string:", dna_str)
print(type(dna_str))

G A T T A T A C G T A C G G C T A
ATACGT
Reversed:  ATCGGCATGCATATTAG
As string: GATTATACGTACGGCTA
<class 'str'>

The object Seq provides several methods similar to the corresponding methods of strings:

1. Seq.count(s) : counts the number of times s appears in the sequence;
2. Seq.upper() : makes the sequence of the object Seq upper case
3. Seq.lower() : makes the sequence of the object Seq lower case

Example: Let’s compute the GC content of the sequence “GATTRWWACGTACGGCTASATTACSCCGGCTA”.

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
from Bio.SeqUtils import GC

dna_seq = Seq("GATTRWWACGTACGGCTASATTACSCCGGCTA", IUPAC.ambiguous_dna)

gc = (dna_seq.count("G") + dna_seq.count("C"))/len(dna_seq)
print("GC % is {:.2f}".format(100*gc))

correct_gc = GC(dna_seq)
print("GC % is {:.2f}".format(correct_gc))

print("original:", dna_seq)
print("lower_case:",dna_seq.lower())

GC % is 40.62
GC % is 46.88
original: GATTRWWACGTACGGCTASATTACSCCGGCTA
lower_case: gattrwwacgtacggctasattacsccggcta

The difference in the results goes down to the fact that Biopython’s GC method takes into account ambiguous nucleotides like (S which stands for C or G ref iupac). This is a method provided in the SeqUtils module (more info on all the methods here).

Complement and reverse complement

A usual operation on DNA strings is the reverse complement. Biopython provides two specific methods to do that:

1. Seq.complement() to complement the sequence
2. Seq.reverse_complement() to reverse complement the sequence.

Note that these methods will fail with a Value Error if we try to apply them to something that is not a nucleotide sequence (e.g. proteins).

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC

my_seq = Seq("GATCGATGGGCCTATATAGGATCGAAAATCGC", IUPAC.unambiguous_dna)

print("Sequence (alphabet: {}):".format(my_seq.alphabet))
print(my_seq)
comp  = my_seq.complement()
print("")
print("Complement (alphabet: {}):".format(comp.alphabet))
print(comp)
print("")
revcomp = my_seq.reverse_complement()
print("Rev Complement (alphabet: {}):".format(revcomp.alphabet))
print(revcomp)

Sequence (alphabet: IUPACUnambiguousDNA()):
GATCGATGGGCCTATATAGGATCGAAAATCGC

Complement (alphabet: IUPACUnambiguousDNA()):
CTAGCTACCCGGATATATCCTAGCTTTTAGCG

Rev Complement (alphabet: IUPACUnambiguousDNA()):
GCGATTTTCGATCCTATATAGGCCCATCGATC

Transcription and translation

Remember that:

[taken from the Biopython tutorial].

Biopython has a method to transcribe a DNA sequence into a mRNA sequence (and one to go back):

1. Seq.transcribe() that transcribes a DNA sequence into mRNA (converting Ts in Us).
2. Seq.back_transcribe() that back-transcribes a mRNA sequence into DNA (converting Us in Ts).

The alphabet of the transcribed sequence is converted into mRNA. Note that transcribing a protein will result in a ValueError.

Alike, a DNA or mRNA sequence can be translated into a protein with:

Seq.translate(table=N, to_stop=True/False, stop_symbol =symbol) that converts a DNA sequence or mRNA into the corresponding protein.

Optionally, the translate method accepts a parameter table to specify the NCBI translation table used (see below for codes). to_stop makes the translation stop at the first stop codon if True (in this case the stop codon is not translated!), stop_symbol to replace the asterisk with any other stop character (Es. “@”).

Stop codons will be represented by an asterisk.

Example: Let’s translate into mRNA the coding sequence: ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG.

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC

coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG",
                 IUPAC.unambiguous_dna)
print(coding_dna)

mrna = coding_dna.transcribe()
print(mrna)
print("")
print(mrna.alphabet)
print("")
print("... and back")
print(mrna.back_transcribe())
print("")
print("Translation to protein:")
prot = mrna.translate()
print(prot)
print("")
print("Up to first stop:")
print(mrna.translate(to_stop = True))
print("")
print("Mitocondrial translation: (TGA is W!)")
mit_prot = mrna.translate(table=2)
print(mit_prot)

ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG
AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG

IUPACUnambiguousRNA()

... and back
ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG

Translation to protein:
MAIVMGR*KGAR*

Up to first stop:
MAIVMGR

Mitocondrial translation: (TGA is W!)
MAIVMGRWKGAR*

Translation tables can be accessed at runtime through:

from Bio.Data import CodonTable
#equivalent to:
#standard_table = CodonTable.unambiguous_dna_by_id[1]
standard_table = CodonTable.unambiguous_dna_by_name["Standard"]
#equivalent to:
#standard_table = CodonTable.unambiguous_dna_by_id[2]
mito_table = CodonTable.unambiguous_dna_by_name["Vertebrate Mitochondrial"]


print(standard_table)
print(standard_table)

print(mito_table)

Table 1 Standard, SGC0

  |  T      |  C      |  A      |  G      |
--+---------+---------+---------+---------+--
T | TTT F   | TCT S   | TAT Y   | TGT C   | T
T | TTC F   | TCC S   | TAC Y   | TGC C   | C
T | TTA L   | TCA S   | TAA Stop| TGA Stop| A
T | TTG L(s)| TCG S   | TAG Stop| TGG W   | G
--+---------+---------+---------+---------+--
C | CTT L   | CCT P   | CAT H   | CGT R   | T
C | CTC L   | CCC P   | CAC H   | CGC R   | C
C | CTA L   | CCA P   | CAA Q   | CGA R   | A
C | CTG L(s)| CCG P   | CAG Q   | CGG R   | G
--+---------+---------+---------+---------+--
A | ATT I   | ACT T   | AAT N   | AGT S   | T
A | ATC I   | ACC T   | AAC N   | AGC S   | C
A | ATA I   | ACA T   | AAA K   | AGA R   | A
A | ATG M(s)| ACG T   | AAG K   | AGG R   | G
--+---------+---------+---------+---------+--
G | GTT V   | GCT A   | GAT D   | GGT G   | T
G | GTC V   | GCC A   | GAC D   | GGC G   | C
G | GTA V   | GCA A   | GAA E   | GGA G   | A
G | GTG V   | GCG A   | GAG E   | GGG G   | G
--+---------+---------+---------+---------+--
Table 1 Standard, SGC0

  |  T      |  C      |  A      |  G      |
--+---------+---------+---------+---------+--
T | TTT F   | TCT S   | TAT Y   | TGT C   | T
T | TTC F   | TCC S   | TAC Y   | TGC C   | C
T | TTA L   | TCA S   | TAA Stop| TGA Stop| A
T | TTG L(s)| TCG S   | TAG Stop| TGG W   | G
--+---------+---------+---------+---------+--
C | CTT L   | CCT P   | CAT H   | CGT R   | T
C | CTC L   | CCC P   | CAC H   | CGC R   | C
C | CTA L   | CCA P   | CAA Q   | CGA R   | A
C | CTG L(s)| CCG P   | CAG Q   | CGG R   | G
--+---------+---------+---------+---------+--
A | ATT I   | ACT T   | AAT N   | AGT S   | T
A | ATC I   | ACC T   | AAC N   | AGC S   | C
A | ATA I   | ACA T   | AAA K   | AGA R   | A
A | ATG M(s)| ACG T   | AAG K   | AGG R   | G
--+---------+---------+---------+---------+--
G | GTT V   | GCT A   | GAT D   | GGT G   | T
G | GTC V   | GCC A   | GAC D   | GGC G   | C
G | GTA V   | GCA A   | GAA E   | GGA G   | A
G | GTG V   | GCG A   | GAG E   | GGG G   | G
--+---------+---------+---------+---------+--
Table 2 Vertebrate Mitochondrial, SGC1

  |  T      |  C      |  A      |  G      |
--+---------+---------+---------+---------+--
T | TTT F   | TCT S   | TAT Y   | TGT C   | T
T | TTC F   | TCC S   | TAC Y   | TGC C   | C
T | TTA L   | TCA S   | TAA Stop| TGA W   | A
T | TTG L   | TCG S   | TAG Stop| TGG W   | G
--+---------+---------+---------+---------+--
C | CTT L   | CCT P   | CAT H   | CGT R   | T
C | CTC L   | CCC P   | CAC H   | CGC R   | C
C | CTA L   | CCA P   | CAA Q   | CGA R   | A
C | CTG L   | CCG P   | CAG Q   | CGG R   | G
--+---------+---------+---------+---------+--
A | ATT I(s)| ACT T   | AAT N   | AGT S   | T
A | ATC I(s)| ACC T   | AAC N   | AGC S   | C
A | ATA M(s)| ACA T   | AAA K   | AGA Stop| A
A | ATG M(s)| ACG T   | AAG K   | AGG Stop| G
--+---------+---------+---------+---------+--
G | GTT V   | GCT A   | GAT D   | GGT G   | T
G | GTC V   | GCC A   | GAC D   | GGC G   | C
G | GTA V   | GCA A   | GAA E   | GGA G   | A
G | GTG V(s)| GCG A   | GAG E   | GGG G   | G
--+---------+---------+---------+---------+--

MutableSeq

Seq objects are immutable and therefore we cannot change their value. If we need to do so, we need to convert them into MutableSeq objects to avoid a runtime TypeError that will occur when we try to change a Seq. Seq to MutableSeq conversion can be done by:

1. Seq.tomutable() to convert a Seq to a MutableSeq.
2. MutableSeq.toseq() to convert a MutableSeq to a Seq.

This will allow us to assign the value of characters within the MutableSeq with MutableSeq[ind] = newValue. Note also that methods like complement change the actual object if applied to a MutableSeq:

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC

coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG", IUPAC.unambiguous_dna)
print("Coding DNA:")
print(coding_dna)
mut_dna = coding_dna.tomutable()
print("Mutable DNA:")
print(mut_dna)
mut_dna[10:20] = "TATATATATA"
print("Mutable DNA now:")
print(mut_dna)
print("")
print("Rev comp (Seq not changed!):")
coding_dna.reverse_complement()
print(coding_dna)
print("Rev comp (MutableSeq changed!):")
mut_dna.reverse_complement()
print(mut_dna)

Coding DNA:
ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG
Mutable DNA:
ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG
Mutable DNA now:
ATGGCCATTGTATATATATACTGAAAGGGTGCCCGATAG

Rev comp (Seq not changed!):
ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG
Rev comp (MutableSeq changed!):
CTATCGGGCACCCTTTCAGTATATATATACAATGGCCAT

Sequence annotation

Sequence records are annotations associated to sequences. In biopython there is a SeqRecord object to store this information. SeqRecord are part of the Bio.SeqRecord module which therefore needs to be imported prior to be used.

The SeqRecord class has the following attributes:

1. SeqRecord.seq : the sequence (the Seq object)
2. SeqRecord.id : the identifier of the sequence, typically an accession number
3. SeqRecord.name : a “common” name or identifier sometimes identical to the accession number
4. SeqRecord.description : a human readable description of the sequence
5. SeqRecord.letter_annotations : a per letter annotation using a restricted dictionary (e.g. quality)
6. SeqRecord.annotations : a dictionary of unstructured annotation (e.g. organism, publications,…)
7. SeqRecord.features : a list of SeqFeature objects with more structured information (e.g. genes pos).
8. SeqRecord.dbxrefs : a list of database cross references.

Information on SeqFeature objects can be found here.

Although you can manually create a SeqRecord, normally you will access SeqRecords populated by methods like SeqIO, here you can find how to manually create a SeqRecord.

Example:

Read a fasta file NC005816.fna containing the whole sequence for Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1 and retrieve some information about the sequence.

from Bio import SeqIO

record = SeqIO.read("file_samples/NC_005816.fna", "fasta")

print(record)
print("")
print("Sequence [first 30 bases]:")
print(record.seq[0:30])
print("")
print("The id:")
print(record.id)
print("")
print("The description:")
print(record.description)
print("")
print("The record is a: ", type(record))

ID: gi|45478711|ref|NC_005816.1|
Name: gi|45478711|ref|NC_005816.1|
Description: gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence
Number of features: 0
Seq('TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGG...CTG', SingleLetterAlphabet())

Sequence [first 30 bases]:
TGTAACGAACGGTGCAATAGTGATCCACAC

The id:
gi|45478711|ref|NC_005816.1|

The description:
gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence

The record is a:  <class 'Bio.SeqRecord.SeqRecord'>

Sequence I/O

The Bio.SeqIO module aims to provide a simple way to work with several different sequence file formats. Detailed information on the module can be found here.

WARNING: When dealing with very large FASTA or FASTQ files, the overhead of working with all these objects can make scripts too slow. In this case SimpleFastaParser and FastqGeneralIterator parsers might be better as they return just a tuple of strings for each record.

For example, to use SimpleFastaParser:

from Bio.SeqIO.FastaIO import SimpleFastaParser


with open("file_samples/NC_005816.fna") as in_handle:
    for title, seq in SimpleFastaParser(in_handle):
        s = seq[0:50]+"\n"+seq[51:101]+"\n..."
        print("Header:\n{}\nSequence:\n{}".format(title,s))

#Another example:
print("\n")
labels = ["1st","2nd","3rd"]

with open("file_samples/contigs82.fasta") as cont_handle:
    for l in labels:
        ID, seq  = next(SimpleFastaParser(cont_handle))

        print(l, "entry:")
        print(ID, " has size ", len(seq))
        print(seq[:50]+"...")
        print("")

Header:
gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence
Sequence:
TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATC
AGGGGGTAATCTGCTCTCCTGATTCAGGAGAGTTTATGGTCACTTTTGAG
...


1st entry:
MDC020656.85  has size  2802
GAGGGGTTTAGTTCCTCATACTCGCAAAGCAAAGATACATAAATTTAGAA...

2nd entry:
MDC013284.379  has size  5173
TATCGTTTCCTCTGAGTAGAATATCGTTATAACAAGATTTTTTTTTTCCT...

3rd entry:
MDC018185.241  has size  23761
AAAACGAGGAAAATCCATCTTGATGAACAGGAGATGCGGAGGAAAAAAAT...

BioSeqIO.parse()

The method Bio.SeqIO.parse is used to parse some sequence data into a SeqRecord iterator. In particular, the basic syntax is:

SeqRecordIterator = Bio.SeqIO.parse(filename, file_format)

where filename is typically an open handle to a file and file_format is a lower case string describing the file format. Possible options include fasta, fastq-illumina, abi, ace, clustal… all the options are available here.

Example: Let’s read the first 10 entries in the .fasta file contigs82.fasta printing off the length of the sequence and the first 50 bases of each sequence followed by “…”.

from Bio import SeqIO
cnt = 0
for seq_record in SeqIO.parse("file_samples/contigs82.fasta", "fasta"):
    if(cnt == 10):
        break
    print("Seq {} has length {}".format(seq_record.id, len(seq_record)))
    print(seq_record.seq[:50]+"...")
    print("")
    cnt += 1

Seq MDC020656.85 has length 2802
GAGGGGTTTAGTTCCTCATACTCGCAAAGCAAAGATACATAAATTTAGAA...

Seq MDC001115.177 has length 3118
TGAATGGTGAAAATTAGCCAGAAGATCTTCTCCACACATGACATATGCAT...

Seq MDC013284.379 has length 5173
TATCGTTTCCTCTGAGTAGAATATCGTTATAACAAGATTTTTTTTTTCCT...

Seq MDC018185.243 has length 22724
CCATTAGTGACCCCCAATGCGGATTAACCAAGCACGGTCAAGATAACCAA...

Seq MDC018185.241 has length 23761
AAAACGAGGAAAATCCATCTTGATGAACAGGAGATGCGGAGGAAAAAAAT...

Seq MDC004527.213 has length 3551
CTTGTATGTTGAAGCTTTGTGAGTGGAGCATATAGGTTGAGGTAGTGTTC...

Seq MDC003661.174 has length 3334
AGTAAGGTTGTAGAATTCAATTTCCACGGAACTCCAGCACAGCTTAGGCA...

Seq MDC012176.157 has length 2236
ATAGTCACTGACAGCCGGTGACAGTTCGACAACAATAAGTTCAGGATGTT...

Seq MDC001204.812 has length 5804
TAATGTCCGAAAAAGATGAAAATGTAGTTTGCATGAAGAAGGAGCTGTCC...

Seq MDC001204.810 has length 9798
ATGCTGCTGACATATTCCAATCGACTACACGTCACATCCGTTGCTATTAT...

Note that Bio.SeqIO.parse returns an iterator, therefore it is possible to manually fetch one SeqRecord after the other with the next(iterator) method.

Example: Let’s get the first 3 entries of the .fasta file contigs82.fasta printing off the length of the sequence and the first 50 bases of each sequence followed by “…”.

from Bio import SeqIO

seqIterator = SeqIO.parse("file_samples/contigs82.fasta", "fasta")

labels = ["1st","2nd","3rd"]
for l in labels:
    seqRec = next(seqIterator)
    print(l, "entry:")
    print(seqRec.id, " has size ", len(seqRec.seq))
    print(seqRec.seq[:50]+"...")
    print("")

1st entry:
MDC020656.85  has size  2802
GAGGGGTTTAGTTCCTCATACTCGCAAAGCAAAGATACATAAATTTAGAA...

2nd entry:
MDC001115.177  has size  3118
TGAATGGTGAAAATTAGCCAGAAGATCTTCTCCACACATGACATATGCAT...

3rd entry:
MDC013284.379  has size  5173
TATCGTTTCCTCTGAGTAGAATATCGTTATAACAAGATTTTTTTTTTCCT...

Sequences as dictionaries

The module Bio.SeqIO also has three different ways to allow random access to elements:

1. Bio.SeqIO.to_dict(file_handle/iterator) : builds a dictionary of all the SeqRecords keeping them in memory and allowing modifications to the records. This potentially uses a lot of memory but is very fast;
2. Bio.SeqIO.index(filename,file_type) : builds a sort of read-only dictionary, parses the elements into SeqRecords on demand (i.e. it returns an iterator!). This method is slower, but more memory efficient;
3. Bio.SeqIO.index_db(indexName.idx,filenames, file_format) : builds a read-only dictionary, but stores ids and offsets on a SQLite3 database. It is slower but uses less memory.

The input of Bio.SeqIO.to_dict(file_handle/iterator) is a open file handler or the iterator to SeqRecords (like the output of Bio.SeqIO.parse()).

Example: Let’s read all the .fasta file contigs82.fasta in memory printing off the entry corresponding to contig “MDC019140.399”.

from Bio import SeqIO
seqDict = SeqIO.to_dict(SeqIO.parse("file_samples/contigs82.fasta", "fasta"))

print(list(seqDict.keys())[0:5])
print("")
print("Number of sequences: ", len(seqDict))
print("")
mySeq = seqDict["MDC019140.399"]
print("Description:", mySeq.description)
print("")
print(mySeq)

['MDC020656.85', 'MDC001115.177', 'MDC013284.379', 'MDC018185.243', 'MDC018185.241']

Number of sequences:  82

Description: MDC019140.399

ID: MDC019140.399
Name: MDC019140.399
Description: MDC019140.399
Number of features: 0
Seq('GACGGGCGGGGAGGGTTTGGTTTTTTTTGGTTTTTAAAAAATTCAGGTTTNNAA...TTT', SingleLetterAlphabet())

The input of Bio.SeqIO.index(filename,file_type) is the file name to read sequences from and the file type (like fasta, genebank,…).

Example: Let’s read all the .fasta file contigs82.fasta in memory (as an index) printing off the entry corresponding to contig “MDC019140.399”.

from Bio import SeqIO
seqDict =  SeqIO.index("file_samples/contigs82.fasta", "fasta")
print("SeqDict is an iterator:")
print(seqDict.keys())
print("")
print(list(seqDict.keys()))
print("")
print("Number of sequences: ", len(seqDict))
print("")
mySeq = seqDict["MDC019140.399"]
print("Description:", mySeq.description)
print("")
print(mySeq)

SeqDict is an iterator:
<odict_iterator object at 0x7fc4c416ff68>

['MDC020656.85', 'MDC001115.177', 'MDC013284.379', 'MDC018185.243', 'MDC018185.241', 'MDC004527.213', 'MDC003661.174', 'MDC012176.157', 'MDC001204.812', 'MDC001204.810', 'MDC004389.256', 'MDC024257.15', 'MDC018297.229', 'MDC001802.364', 'MDC016621.241', 'MDC014057.243', 'MDC021015.302', 'MDC018185.242', 'MDC051782.000', 'MDC017187.314', 'MDC017187.311', 'MDC012865.410', 'MDC000427.83', 'MDC017187.319', 'MDC017187.318', 'MDC004081.319', 'MDC021913.275', 'MDC015147.205', 'MDC000038.355', 'MDC016032.95', 'MDC052568.000', 'MDC008119.414', 'MDC026201.7', 'MDC003995.601', 'MDC009211.561', 'MDC009211.567', 'MDC054294.001', 'MDC004364.265', 'MDC002360.219', 'MDC003408.117', 'MDC015155.172', 'MDC053310.000', 'MDC019140.398', 'MDC019140.399', 'MDC011390.337', 'MDC007154.375', 'MDC006346.716', 'MDC010588.505', 'MDC002519.240', 'MDC031322.5', 'MDC010588.502', 'MDC006346.711', 'MDC011551.182', 'MDC002717.156', 'MDC006346.719', 'MDC007838.447', 'MDC007018.186', 'MDC017873.233', 'MDC016296.138', 'MDC019067.226', 'MDC036568.1', 'MDC014019.318', 'MDC007995.528', 'MDC026961.60', 'MDC013443.168', 'MDC022800.298', 'MDC021558.159', 'MDC002479.192', 'MDC010751.301', 'MDC000219.190', 'MDC020963.161', 'MDC020963.162', 'MDC051637.000', 'MDC005174.220', 'MDC040033.7', 'MDC019674.147', 'MDC010450.877', 'MDC007097.457', 'MDC016278.70', 'MDC013723.254', 'MDC002838.179', 'MDC009771.217']

Number of sequences:  82

Description: MDC019140.399

ID: MDC019140.399
Name: MDC019140.399
Description: MDC019140.399
Number of features: 0
Seq('GACGGGCGGGGAGGGTTTGGTTTTTTTTGGTTTTTAAAAAATTCAGGTTTNNAA...TTT', SingleLetterAlphabet())

The input of Bio.SeqIO.index_db(indexName.idx,filenames, file_format) is the name of the (SQLite3) index to store (.idx), the file (or files) to index and the format of those files like fasta, genebank,…

Example: Let’s read all the .fasta file contigs82.fasta in memory (as an index) printing off the entry corresponding to contig “MDC019140.399”.

from Bio import SeqIO
seqDict =  SeqIO.index_db("file_samples/ctgs.idx","file_samples/contigs82.fasta", "fasta")
print("SeqDict is an iterator:")
print(seqDict.keys())
print("")
print(list(seqDict.keys()))
print("")
print("Number of sequences: ", len(seqDict))
print("")
mySeq = seqDict["MDC019140.399"]
print("Description:", mySeq.description)
print("")
print(mySeq)

SeqDict is an iterator:
<generator object _SQLiteManySeqFilesDict.__iter__ at 0x7fc4c416fbf8>

['MDC020656.85', 'MDC001115.177', 'MDC013284.379', 'MDC018185.243', 'MDC018185.241', 'MDC004527.213', 'MDC003661.174', 'MDC012176.157', 'MDC001204.812', 'MDC001204.810', 'MDC004389.256', 'MDC024257.15', 'MDC018297.229', 'MDC001802.364', 'MDC016621.241', 'MDC014057.243', 'MDC021015.302', 'MDC018185.242', 'MDC051782.000', 'MDC017187.314', 'MDC017187.311', 'MDC012865.410', 'MDC000427.83', 'MDC017187.319', 'MDC017187.318', 'MDC004081.319', 'MDC021913.275', 'MDC015147.205', 'MDC000038.355', 'MDC016032.95', 'MDC052568.000', 'MDC008119.414', 'MDC026201.7', 'MDC003995.601', 'MDC009211.561', 'MDC009211.567', 'MDC054294.001', 'MDC004364.265', 'MDC002360.219', 'MDC003408.117', 'MDC015155.172', 'MDC053310.000', 'MDC019140.398', 'MDC019140.399', 'MDC011390.337', 'MDC007154.375', 'MDC006346.716', 'MDC010588.505', 'MDC002519.240', 'MDC031322.5', 'MDC010588.502', 'MDC006346.711', 'MDC011551.182', 'MDC002717.156', 'MDC006346.719', 'MDC007838.447', 'MDC007018.186', 'MDC017873.233', 'MDC016296.138', 'MDC019067.226', 'MDC036568.1', 'MDC014019.318', 'MDC007995.528', 'MDC026961.60', 'MDC013443.168', 'MDC022800.298', 'MDC021558.159', 'MDC002479.192', 'MDC010751.301', 'MDC000219.190', 'MDC020963.161', 'MDC020963.162', 'MDC051637.000', 'MDC005174.220', 'MDC040033.7', 'MDC019674.147', 'MDC010450.877', 'MDC007097.457', 'MDC016278.70', 'MDC013723.254', 'MDC002838.179', 'MDC009771.217']

Number of sequences:  82

Description: MDC019140.399

ID: MDC019140.399
Name: MDC019140.399
Description: MDC019140.399
Number of features: 0
Seq('GACGGGCGGGGAGGGTTTGGTTTTTTTTGGTTTTTAAAAAATTCAGGTTTNNAA...TTT', SingleLetterAlphabet())

Note that a file ctgs.idx has been created to store ids and offsets.

Writing sequence files

SeqRecords can be written out to files by using

N = Bio.SeqIO.write(records,out_filename, file_format)

where records is a list of the SeqRecords to write, out_filename is the string with the filename to write and file_format is the format of the file to write. N is the number of sequences written.

WARNING: If you write a file that is already present, SeqIO.write will just rewrite it without telling you.

Example: Write three protein records to file then read the file and print the three sequences.

from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import generic_protein

rec1 = SeqRecord(Seq("MMYQQGCFAGGTVLRLAKDLAENNRGARVLVVCSEITAVTFRGPSETHLDSMVGQALFGD" \
+"GAGAVIVGSDPDLSVERPLYELVWTGATLLPDSEGAIDGHLREVGLTFHLLKDVPGLISK" \
+"NIEKSLKEAFTPLGISDWNSTFWIAHPGGPAILDQVEAKLGLKEEKMRATREVLSEYGNM" \
+"SSAC", generic_protein),
id="gi|14150838|gb|AAK54648.1|AF376133_1",
description="chalcone synthase [Cucumis sativus]")

rec2 = SeqRecord(Seq("YPDYYFRITNREHKAELKEKFQRMCDKSMIKKRYMYLTEEILKENPSMCEYMAPSLDARQ" \
+"DMVVVEIPKLGKEAAVKAIKEWGQ", generic_protein),
id="gi|13919613|gb|AAK33142.1|",
description="chalcone synthase [Fragaria vesca subsp. bracteata]")

rec3 = SeqRecord(Seq("MVTVEEFRRAQCAEGPATVMAIGTATPSNCVDQSTYPDYYFRITNSEHKVELKEKFKRMC" \
+"EKSMIKKRYMHLTEEILKENPNICAYMAPSLDARQDIVVVEVPKLGKEAAQKAIKEWGQP" \
+"KSKITHLVFCTTSGVDMPGCDYQLTKLLGLRPSVKRFMMYQQGCFAGGTVLRMAKDLAEN" \
+"NKGARVLVVCSEITAVTFRGPNDTHLDSLVGQALFGDGAAAVIIGSDPIPEVERPLFELV" \
+"SAAQTLLPDSEGAIDGHLREVGLTFHLLKDVPGLISKNIEKSLVEAFQPLGISDWNSLFW" \
+"IAHPGGPAILDQVELKLGLKQEKLKATRKVLSNYGNMSSACVLFILDEMRKASAKEGLGT" \
+"TGEGLEWGVLFGFGPGLTVETVVLHSVAT", generic_protein),
id="gi|13925890|gb|AAK49457.1|",
description="chalcone synthase [Nicotiana tabacum]")

my_records = [rec1, rec2, rec3]
print(rec1)

seqWritten = SeqIO.write(my_records, "file_samples/my_proteins.fa", "fasta")
print(seqWritten, "sequences written!")
print("")
print("Reading file")
seqIT = SeqIO.parse("file_samples/my_proteins.fa", "fasta")

cnt = 1
for s in seqIT:
    print("Sequence ", cnt, "(", s.id, ")")
    print(s.seq)
    print("")
    cnt += 1

ID: gi|14150838|gb|AAK54648.1|AF376133_1
Name: <unknown name>
Description: chalcone synthase [Cucumis sativus]
Number of features: 0
Seq('MMYQQGCFAGGTVLRLAKDLAENNRGARVLVVCSEITAVTFRGPSETHLDSMVG...SAC', ProteinAlphabet())
3 sequences written!

Reading file
Sequence  1 ( gi|14150838|gb|AAK54648.1|AF376133_1 )
MMYQQGCFAGGTVLRLAKDLAENNRGARVLVVCSEITAVTFRGPSETHLDSMVGQALFGDGAGAVIVGSDPDLSVERPLYELVWTGATLLPDSEGAIDGHLREVGLTFHLLKDVPGLISKNIEKSLKEAFTPLGISDWNSTFWIAHPGGPAILDQVEAKLGLKEEKMRATREVLSEYGNMSSAC

Sequence  2 ( gi|13919613|gb|AAK33142.1| )
YPDYYFRITNREHKAELKEKFQRMCDKSMIKKRYMYLTEEILKENPSMCEYMAPSLDARQDMVVVEIPKLGKEAAVKAIKEWGQ

Sequence  3 ( gi|13925890|gb|AAK49457.1| )
MVTVEEFRRAQCAEGPATVMAIGTATPSNCVDQSTYPDYYFRITNSEHKVELKEKFKRMCEKSMIKKRYMHLTEEILKENPNICAYMAPSLDARQDIVVVEVPKLGKEAAQKAIKEWGQPKSKITHLVFCTTSGVDMPGCDYQLTKLLGLRPSVKRFMMYQQGCFAGGTVLRMAKDLAENNKGARVLVVCSEITAVTFRGPNDTHLDSLVGQALFGDGAAAVIIGSDPIPEVERPLFELVSAAQTLLPDSEGAIDGHLREVGLTFHLLKDVPGLISKNIEKSLVEAFQPLGISDWNSLFWIAHPGGPAILDQVELKLGLKQEKLKATRKVLSNYGNMSSACVLFILDEMRKASAKEGLGTTGEGLEWGVLFGFGPGLTVETVVLHSVAT

Multiple sequence alignment

Multiple Sequence Alignments, as the name says, are a collection of multiple sequences which have been aligned together – usually with the insertion of gap characters, and addition of leading or trailing gaps – such that all the sequence strings are the same length.

Such an alignment can be regarded as a matrix of letters, in biopython each row is a SeqRecord object. These alignments are stored in an object MultipleSeqAlignment

Parsing multiple sequence alignments

The function Bio.AlignIO.parse() returns an iterator of MultipleSeqAlignment objects. In the frequent case that we have to deal with a single alignment we will have to use the Bio.AlignIO.read() function.

The basic syntax of the two functions:

Bio.AlignIO.parse(file_handle, alignment_format)

Bio.AlignIO.read(file_handle, alignment_format)

where file_handle is the handler to the opened file, while the alignment_format is a lower case string with the alignment format (e.g. fasta, clustal, stockholm, mauve, phylip,…). Check here for all possible formats.

When more than one multiple alignment has to be read we will have to use the parse function, for single entries, we would use the function read.

Example: Load and visualize the seed alignment of the Piwi (PF02171) family stored in the pfam (stockholm) format. Information on the format can be found here. The file is available here: PF02171_seed.sth.

from Bio import AlignIO

alignments = AlignIO.read("file_samples/PF02171_seed.sth", "stockholm")

print(alignments)

SingleLetterAlphabet() alignment with 16 rows and 395 columns
YLFFILDK-NSPEP-YGSIKRVCNTMLGVPSQCAISKHILQS--...QDV AGO1_SCHPO/500-799
FILCILPERKTSDI-YGPWKKICLTEEGIHTQCICPIKI-----...FTK AGO6_ARATH/541-851
FILCVLPDKKNSDL-YGPWKKKNLTEFGIVTQCMAPTRQPND--...FMK AGO4_ARATH/577-885
CIIVVLQS-KNSDI-YMTVKEQSDIVHGIMSQCVLMKNVSRP--...HVK TAG76_CAEEL/660-966
LIVVVLPG--KTPI-YAEVKRVGDTVLGIATQCVQAKNAIRT--...HLV O16720_CAEEL/566-867
TFVFIITD-DSITT-LHQRYKMIEKDTKMIVQDMKLSKALSV--...LWN O62275_CAEEL/594-924
DILVGIAR-EKKPD-VHDILKYFEESIGLQTIQLCQQTVDKMMG...NYK YQ53_CAEEL/650-977
TIVFGIIA-EKRPD-MHDILKYFEEKLGQQTIQISSETADKFMR...NYK NRDE3_CAEEL/673-1001
MLVVMLAD-DNKTR-YDSLKKYLCVECPIPNQCVNLRTLAGKSK...SLH Q17567_CAEEL/397-708
IVMVVMRS-PNEEK-YSCIKKRTCVDRPVPSQVVTLKVIAPRQQ...SIN AUB_DROME/555-852
LILCLVPN-DNAER-YSSIKKRGYVDRAVPTQVVTLKTTKNRSL...NLH PIWI_DROME/538-829
IVVCLLSS-NRKDK-YDAIKKYLCTDCPTPSQCVVARTLGKQQT...SIH PIWL1_HUMAN/555-847
GIMLVLPE-YNTPL-YYKLKSYLINS--IPSQFMRYDILSNRNL...VNR PIWI_ARCFU/110-406
CFALIIGKEKYKDNDYYEILKKQLFDLKIISQNILWENWRKDDK...NWK Y1321_METJA/426-699
LVIVFLEEYPKVDP-YKSFLLYDFVKRELLKKMIPSQVILNRTL...GIE O67434_AQUAE/419-694
LLLAILPD-NNGSL-YGDLKRICETELGLISQCCLTKHVFKI--...YLE AGO10_ARATH/625-946

The code above prints a summary of the information, but each Bio.Align.MultipleSeqAlignment is composed of several alignment records (SeqRecord) that we can access with all their information looping through the object. Each SeqRecord contains several information like the ID, Name, Description, Number of features, start, end and sequence.

Example:

Load the seed alignment of the Piwi (PF02171) family stored in the pfam (stockholm) format PF02171_seed.sth. For each record print the description, start and the end point, the sequence and the external dbxrefs (if any).

from Bio import AlignIO

alignments = AlignIO.read("file_samples/PF02171_seed.sth", "stockholm")


for align in alignments:
    start = align.annotations["start"]
    end = align.annotations["end"]
    seq = align.seq
    desc = align.description
    dbref = ",".join([x for x in align.dbxrefs])
    print("{} S:{} E:{}".format(desc, start, end))
    if(len(dbref) > 0):
        print(dbref)
    print("{}".format(seq))
    print("")

ID: AGO1_SCHPO/500-799
Name: AGO1_SCHPO
Description: AGO1_SCHPO/500-799
Number of features: 0
/accession=O74957.1
/start=500
/end=799
Seq('YLFFILDK-NSPEP-YGSIKRVCNTMLGVPSQCAISKHILQS---------KPQ...QDV', SingleLetterAlphabet())
AGO1_SCHPO/500-799 S:500 E:799
YLFFILDK-NSPEP-YGSIKRVCNTMLGVPSQCAISKHILQS---------KPQYCANLGMKINVKVGGIN-CSLIPKSNP----LGNVPTL---------ILGGDVYHPGVGA----------TGVSIASIVASVD-LNGCKYTAVSRSQPRHQEVIEG-MKD------------IVVYLLQGFRAMTKQ-QPQRIIYFRDGTSEGQFLSVINDELSQIKEACH-------SLSPKYN--PKILVCTTQKRHHARFFIKNKSDG----------------------DRNGNPLPGTII---EKHVTHPYQYDFYLISHPSLQGVSVPVHYTVLHDEIQMPPDQF-QTL------CYNLCYVYARAT----SAVSLVPPVYYAHLVSNLARYQDV

ID: AGO6_ARATH/541-851
Name: AGO6_ARATH
Description: AGO6_ARATH/541-851
Number of features: 0
/accession=O48771.2
/start=541
/end=851
Seq('FILCILPERKTSDI-YGPWKKICLTEEGIHTQCICPIKI------------SDQ...FTK', SingleLetterAlphabet())
AGO6_ARATH/541-851 S:541 E:851
FILCILPERKTSDI-YGPWKKICLTEEGIHTQCICPIKI------------SDQYLTNVLLKINSKLGGIN-SLLGIEYSYNIPLINKIPTL---------ILGMDVSHGPPGR---------ADVPSVAAVVGSKCWPLISRYRAAVRTQSPRLEMIDSLFQPIENTE--KGDNGIMNELFVEFYRTSRARKPKQIIIFRDGVSESQFEQVLKIEVDQIIKAYQ-------RLGESDV--PKFTVIVAQKNHHTKLFQAKGPE---------------------------NVPAGTVV---DTKIVHPTNYDFYMCAHAGKIGTSRPAHYHVLLDEIGFSPDDL-QNL------IHSLSYVNQRST----TATSIVAPVRYAHLAAAQVAQFTK

ID: AGO4_ARATH/577-885
Name: AGO4_ARATH
Description: AGO4_ARATH/577-885
Number of features: 0
/accession=Q9ZVD5.2
/start=577
/end=885
Seq('FILCVLPDKKNSDL-YGPWKKKNLTEFGIVTQCMAPTRQPND-----------Q...FMK', SingleLetterAlphabet())
AGO4_ARATH/577-885 S:577 E:885
FILCVLPDKKNSDL-YGPWKKKNLTEFGIVTQCMAPTRQPND-----------QYLTNLLLKINAKLGGLN-SMLSVERTPAFTVISKVPTI---------ILGMDVSHGSPGQ---------SDVPSIAAVVSSREWPLISKYRASVRTQPSKAEMIESLVKKNGT-----EDDGIIKELLVDFYTSSNKRKPEHIIIFRDGVSESQFNQVLNIELDQIIEACK-------LLDANWN--PKFLLLVAQKNHHTKFFQPTSPE---------------------------NVPPGTII---DNKICHPKNNDFYLCAHAGMIGTTRPTHYHVLYDEIGFSADEL-QEL------VHSLSYVYQRST----SAISVVAPICYAHLAAAQLGTFMK

ID: TAG76_CAEEL/660-966
Name: TAG76_CAEEL
Description: TAG76_CAEEL/660-966
Number of features: 0
/accession=P34681.2
/start=660
/end=966
Seq('CIIVVLQS-KNSDI-YMTVKEQSDIVHGIMSQCVLMKNVSRP---------TPA...HVK', SingleLetterAlphabet())
TAG76_CAEEL/660-966 S:660 E:966
CIIVVLQS-KNSDI-YMTVKEQSDIVHGIMSQCVLMKNVSRP---------TPATCANIVLKLNMKMGGIN--SRIVADKITNKYLVDQPTM---------VVGIDVTHPTQAEM-------RMNMPSVAAIVANVD-LLPQSYGANVKVQKKCRESVVY-LLD------------AIRERIITFYRHTKQ-KPARIIVYRDGVSEGQFSEVLREEIQSIRTACL-------AIAEDFR--PPITYIVVQKRHHARIFCKYQNDM---------------------VGKAKNVPPGTTV---DTGIVSPEGFDFYLCSHYGVQGTSRPARYHVLLDECKFTADEI-QSI------TYGMCHTYGRCT----RSVSIPTPVYYADLVATRARCHVK

ID: O16720_CAEEL/566-867
Name: O16720_CAEEL
Description: O16720_CAEEL/566-867
Number of features: 0
/accession=O16720.2
/start=566
/end=867
Seq('LIVVVLPG--KTPI-YAEVKRVGDTVLGIATQCVQAKNAIRT---------TPQ...HLV', SingleLetterAlphabet())
O16720_CAEEL/566-867 S:566 E:867
LIVVVLPG--KTPI-YAEVKRVGDTVLGIATQCVQAKNAIRT---------TPQTLSNLCLKMNVKLGGVN-SILLPNVRPR---IFNEPVI---------FLGCDITHPAAGD---------TRKPSIAAVVGSMD-AHPSRYAATVRVQQHRQEIITD-LTY------------MVRELLVQFYRNTRF-KPARIVVYRDGVSEGQLFNVLQYELRAIREACV-------MLESGYQ--PGITFIAVQKRHHTRLFAADKADQ---------------------VGKAFNIPPGTTV---DVGITHPTEFDFFLCSHAGIQGTSRPSHYHVLWDDNDLTADEL-QQL------TYQMCHTYVRCT----RSVSIPAPAYYAHLVAFRARYHLV

ID: O62275_CAEEL/594-924
Name: O62275_CAEEL
Description: O62275_CAEEL/594-924
Number of features: 0
/accession=O62275.1
/start=594
/end=924
Seq('TFVFIITD-DSITT-LHQRYKMIEKDTKMIVQDMKLSKALSV--IN---AGKRL...LWN', SingleLetterAlphabet())
O62275_CAEEL/594-924 S:594 E:924
TFVFIITD-DSITT-LHQRYKMIEKDTKMIVQDMKLSKALSV--IN---AGKRLTLENVINKTNVKLGGSN--YVFVDAKKQL-----DSHL---------IIGVGISAPPAGTKYAM-ENKGVLNPNVIGYAYNA--QHNQEFSGDFVLNSASQDTLAP-IED------------IVMHSLNEYQKFHDGGLPRRVIVYRTGTSEGNHGSIMAYEIPLARAAMR-------DFSPDIQ----LVYIVVSKDHSFRFFKPDLASLASRPQATSSTASRHSAMPAAPKAWDLNIAPGILV---DSIVTNPACKQFFLNSHITLQGTAKTPLYTVLADDAKVSMTAL-EDI------TYKLCHLHQIVG----LPTSLPTPLYVANEYAKRGRNLWN

ID: YQ53_CAEEL/650-977
Name: YQ53_CAEEL
Description: YQ53_CAEEL/650-977
Number of features: 0
/accession=Q09249.1
/start=650
/end=977
Seq('DILVGIAR-EKKPD-VHDILKYFEESIGLQTIQLCQQTVDKMMGG----QGGRQ...NYK', SingleLetterAlphabet())
YQ53_CAEEL/650-977 S:650 E:977
DILVGIAR-EKKPD-VHDILKYFEESIGLQTIQLCQQTVDKMMGG----QGGRQTIDNVMRKFNLKCGGTNFFVEIPNAVRGKAVCSNNETLRKKLLEHVQFIGFEISHGASRTLFDRSRSQMDGEPSVVGVSYSLT---NSTQLGGFTYLQTQKEYKLQKLDE------------FFPKCVRSYKEHSKT-LPTRIVIYRVGAGEGNFNRVKE-EVEEMRRTFD-------KIQPGYR--PHLVVIIAQRASHARVFPSCISGN---------------------RATDQNIPSGTCV---ENVLTSYGYDEFILSSQTPLIGTVRPCKYTILVNDAKWSKNEL-MHL------TYFRAFGHQVSY----QPPSVPDVLYAAENLAKRGRNNYK

ID: NRDE3_CAEEL/673-1001
Name: NRDE3_CAEEL
Description: NRDE3_CAEEL/673-1001
Number of features: 0
/accession=Q21691.1
/start=673
/end=1001
Seq('TIVFGIIA-EKRPD-MHDILKYFEEKLGQQTIQISSETADKFMRD----HGGKQ...NYK', SingleLetterAlphabet())
NRDE3_CAEEL/673-1001 S:673 E:1001
TIVFGIIA-EKRPD-MHDILKYFEEKLGQQTIQISSETADKFMRD----HGGKQTIDNVIRKLNPKCGGTNFLIDVPESVGHRVVCNNSAEMRAKLYAKTQFIGFEMSHTGARTRFDIQKVMFDGDPTVVGVAYSL--KHSAQLGGFSYFQESRLHKLTN-LQE------------KMQICLNAYEQSSSY-LPETVVVYRVGSGEGDYPQIVN-EVNEMKLAAR-------KKKHGYN--PKFLVICTQRNSHIRVFPEHINERG--------------------KSMEQNVKSGTCV---DVPGASHGYEEFILCCQTPLIGTVKPTKYTIIVNDCRWSKNEI-MNV------TYHLAFAHQVSY----APPAIPNVSYAAQNLAKRGHNNYK

ID: Q17567_CAEEL/397-708
Name: Q17567_CAEEL
Description: Q17567_CAEEL/397-708
Number of features: 0
/accession=Q17567.1
/start=397
/end=708
Seq('MLVVMLAD-DNKTR-YDSLKKYLCVECPIPNQCVNLRTLAGKSKDGGENKNLGS...SLH', SingleLetterAlphabet())
Q17567_CAEEL/397-708 S:397 E:708
MLVVMLAD-DNKTR-YDSLKKYLCVECPIPNQCVNLRTLAGKSKDGGENKNLGSIVLKIVLQMICKTGGA---LWKVNIPL-------KSTM---------IVGYDLYHDSTLK-----------GKTVGACVSTTS-NDFTQFYSQTRPHENPTQLGNN-LTH------------FVRKSLKQYYDNNDKTLPSRLILYRDGAGDGQIPYIKNTEVKLVRDACDAVTDKAAELSNKVQEKIKLAFIIVTKRVNMRILKQGSSS-----------------------KSAINPQPGTVV---DTTVTRPERMDFYLVPQFVNQGTVTPVSYNIIHDDTGLGPDKH-QQL------AFKLCHLYYNWQ----GTVRVPAPCQYAHKLAFLTAQSLH

ID: AUB_DROME/555-852
Name: AUB_DROME
Description: AUB_DROME/555-852
Number of features: 0
/accession=O76922.1
/start=555
/end=852
Seq('IVMVVMRS-PNEEK-YSCIKKRTCVDRPVPSQVVTLKVIAPRQQKP---TGLMS...SIN', SingleLetterAlphabet())
AUB_DROME/555-852 S:555 E:852
IVMVVMRS-PNEEK-YSCIKKRTCVDRPVPSQVVTLKVIAPRQQKP---TGLMSIATKVVIQMNAKLMGA---PWQVVIPL-------HGLM---------TVGFDVCHSPKNK-----------NKSYGAFVATMDQKESFRYFSTVNEHIKGQELSEQ-MSV------------NMACALRSYQEQHRS-LPERILFFRDGVGDGQLYQVVNSEVNTLKDRLDEI---YKSAGKQEG--CRMTFIIVSKRINSRYFT-----------------------------GHRNPVPGTVV---DDVITLPERYDFFLVSQAVRIGTVSPTSYNVISDNMGLNADKL-QML------SYKMTHMYYNYS----GTIRVPAVCHYAHKLAFLVAESIN

ID: PIWI_DROME/538-829
Name: PIWI_DROME
Description: PIWI_DROME/538-829
Number of features: 0
/accession=Q9VKM1.1
/start=538
/end=829
Seq('LILCLVPN-DNAER-YSSIKKRGYVDRAVPTQVVTLKTTKNRSL--------MS...NLH', SingleLetterAlphabet())
PIWI_DROME/538-829 S:538 E:829
LILCLVPN-DNAER-YSSIKKRGYVDRAVPTQVVTLKTTKNRSL--------MSIATKIAIQLNCKLGYT---PWMIELPL-------SGLM---------TIGFDIAKSTRDR-----------KRAYGALIASMDLQQNSTYFSTV-TECSAFDVLANTLWP------------MIAKALRQYQHEHRK-LPSRIVFYRDGVSSGSLKQLFEFEVKDIIEKLKTE---YARVQLSP---PQLAYIVVTRSMNTRFFLN-----------------------------GQNPPPGTIV---DDVITLPERYDFYLVSQQVRQGTVSPTSYNVLYSSMGLSPEKM-QKL------TYKMCHLYYNWS----GTTRVPAVCQYAKKLATLVGTNLH

ID: PIWL1_HUMAN/555-847
Name: PIWL1_HUMAN
Description: PIWL1_HUMAN/555-847
Number of features: 0
/accession=Q96J94.1
/start=555
/end=847
Seq('IVVCLLSS-NRKDK-YDAIKKYLCTDCPTPSQCVVARTLGKQQT-------VMA...SIH', SingleLetterAlphabet())
PIWL1_HUMAN/555-847 S:555 E:847
IVVCLLSS-NRKDK-YDAIKKYLCTDCPTPSQCVVARTLGKQQT-------VMAIATKIALQMNCKMGGE---LWRVDIPL-------KLVM---------IVGIDCYHDMTAG-----------RRSIAGFVASIN-EGMTRWFSRCIFQDRGQELVDG-LKV------------CLQAALRAW-NSCNEYMPSRIIVYRDGVGDGQLKTLVNYEVPQFLDCLK-------SIGRGYN--PRLTVIVVKKRVNTRFFAQSGGR-------------------------LQNPLPGTVI---DVEVTRPEWYDFFIVSQAVRSGSVSPTHYNVIYDNSGLKPDHI-QRL------TYKLCHIYYNWP----GVIRVPAPCQYAHKLAFLVGQSIH

ID: PIWI_ARCFU/110-406
Name: PIWI_ARCFU
Description: PIWI_ARCFU/110-406
Database cross-references: PDB; 2W42 B; 110-406;, PDB; 1YTU B; 110-406;, PDB; 2BGG B; 110-406;, PDB; 1W9H A; 110-406;, PDB; 2BGG A; 110-406;, PDB; 1YTU A; 110-406;, PDB; 2W42 A; 110-406;
Number of features: 0
/accession=O28951.1
/start=110
/end=406
Per letter annotation for: secondary_structure
Seq('GIMLVLPE-YNTPL-YYKLKSYLINS--IPSQFMRYDILSNRNL--------TF...VNR', SingleLetterAlphabet())
PIWI_ARCFU/110-406 S:110 E:406
PDB; 2W42 B; 110-406;,PDB; 1YTU B; 110-406;,PDB; 2BGG B; 110-406;,PDB; 1W9H A; 110-406;,PDB; 2BGG A; 110-406;,PDB; 1YTU A; 110-406;,PDB; 2W42 A; 110-406;
GIMLVLPE-YNTPL-YYKLKSYLINS--IPSQFMRYDILSNRNL--------TFYVDNLLVQFVSKLGGK---PWILNVDPEK--------------------GSDIIIGTGAT--------RIDNVNLFCFAMVFK-KDGTMLWNEISPIVTSSEYLTY-LKS------------TIKKVVYGFKKSNPDWDVEKLTLHVSG----KRPKMKDGETKILKETVE-------ELKKQEMVSRDVKYAILHLNETHPFWVMGDPN------------------------NRFHPYEGTKVKLSSKRYLLTLLQPYLKRNGLEMVTPIKPLSVEIVSDN--WTSEEYYHNVHEILDEIYYLSKMNWRGF----RSRNLPVTVNYPKLVAGIIANVNR

ID: Y1321_METJA/426-699
Name: Y1321_METJA
Description: Y1321_METJA/426-699
Number of features: 0
/accession=Q58717.1
/start=426
/end=699
Seq('CFALIIGKEKYKDNDYYEILKKQLFDLKIISQNILWENWRKDDK--------GY...NWK', SingleLetterAlphabet())
Y1321_METJA/426-699 S:426 E:699
CFALIIGKEKYKDNDYYEILKKQLFDLKIISQNILWENWRKDDK--------GYMTNNLLIQIMGKLGIK---YFILDSKTPYDY----------------IMGLDTGLGIFGN------------HRVGGCTVVYDSEGKIRRIQPIETPAPGERLHLP----------------YVIEYLEN--KANIDMENKNILFLRDG-------FIQNSERNDLKEISK-------ELN------SNIEVISIRKNNKYKVFTSDYRI------------------------GSVFGNDGIFLPHKTPFGSNPVKLSTWLRFNCGNEEGLK---IN----------ESI-MQL------LYDLTKMNYSALYGEGRYLRIPAPIHYADKFVKALGKNWK

ID: O67434_AQUAE/419-694
Name: O67434_AQUAE
Description: O67434_AQUAE/419-694
Database cross-references: PDB; 1YVU A; 419-694;, PDB; 2F8S A; 419-694;, PDB; 2F8T A; 419-694;, PDB; 2F8S B; 419-694;, PDB; 2NUB A; 419-694;, PDB; 2F8T B; 419-694;
Number of features: 0
/accession=O67434.1
/start=419
/end=694
Per letter annotation for: secondary_structure
Seq('LVIVFLEEYPKVDP-YKSFLLYDFVKRELLKKMIPSQVILNRTLKN---ENLKF...GIE', SingleLetterAlphabet())
O67434_AQUAE/419-694 S:419 E:694
PDB; 1YVU A; 419-694;,PDB; 2F8S A; 419-694;,PDB; 2F8T A; 419-694;,PDB; 2F8S B; 419-694;,PDB; 2NUB A; 419-694;,PDB; 2F8T B; 419-694;
LVIVFLEEYPKVDP-YKSFLLYDFVKRELLKKMIPSQVILNRTLKN---ENLKFVLLNVAEQVLAKTGNIP--YKLKEIEGKVDA----------------FVGIDISRITRDG----------KTVNAVAFTKIFNSKGELVRYYLTSYPAFGEKLTEK----------------AIGDVFSLLEKLGF-KKGSKIVVHRDG-------RLYRDEVAAFK-----------KYGELYG--YSLELLEIIKRNNPRFFSNEKFI------------------------------KGYFYKLSEDSVILATYNQVY-------EGTHQPIKVRKVYGE--LPVEVL-CSQ------ILSLTLMNYSSF----QPIKLPATVHYSDKITKLMLRGIE

ID: AGO10_ARATH/625-946
Name: AGO10_ARATH
Description: AGO10_ARATH/625-946
Number of features: 0
/accession=Q9XGW1.1
/start=625
/end=946
Seq('LLLAILPD-NNGSL-YGDLKRICETELGLISQCCLTKHVFKI---------SKQ...YLE', SingleLetterAlphabet())
AGO10_ARATH/625-946 S:625 E:946
LLLAILPD-NNGSL-YGDLKRICETELGLISQCCLTKHVFKI---------SKQYLANVSLKINVKMGGRN-TVLVDAISCRIPLVSDIPTI---------IFGADVTHPENGE---------ESSPSIAAVVASQDWPEVTKYAGLVCAQAHRQELIQDLYKTWQDPVRGTVSGGMIRDLLISFRKATGQ-KPLRIIFYRDGVSEGQFYQVLLYELDAIRKACA-------SLEPNYQ--PPVTFIVVQKRHHTRLFANNHRDKN-------------------STDRSGNILPGTVV---DTKICHPTEFDFYLCSHAGIQGTSRPAHYHVLWDENNFTADGI-QSL------TNNLCYTYARCT----RSVSIVPPAYYAHLAAFRARFYLE

Writing multiple alignments

Biopython provides a function Bio.AlignIO.write() to write alignments to file. The basic syntax is:

N = Bio.AlignIO.write(alignments,outfile,file_format)

where alignments are a MultipleSeqAlignment object with the alignments to write to the output file with name outfile that has format file_format (a low case string with the file format). N is the number of entries written to the file.

Example: Let’s create some multiple sequence alignments and store them in phylip format. The output file is present here my_malign.phy. Finally, read and print the content of the file.

from Bio.Alphabet import generic_dna
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Align import MultipleSeqAlignment
from Bio import AlignIO

align1 = MultipleSeqAlignment([
SeqRecord(Seq("ACTGCTAGCTAG", generic_dna), id="Alpha"),
SeqRecord(Seq("ACT-CTAGCTAG", generic_dna), id="Beta"),
SeqRecord(Seq("ACTGCTAGDTAG", generic_dna), id="Gamma"),
])
align2 = MultipleSeqAlignment([
SeqRecord(Seq("GTCAGC-AG", generic_dna), id="Delta"),
SeqRecord(Seq("GACAGCTAG", generic_dna), id="Epsilon"),
SeqRecord(Seq("GTCAGCTAG", generic_dna), id="Zeta"),
])
align3 = MultipleSeqAlignment([
SeqRecord(Seq("ACTAGTACAGCTG", generic_dna), id="Eta"),
SeqRecord(Seq("ACTAGTACAGCT-", generic_dna), id="Theta"),
SeqRecord(Seq("-CTACTACAGGTG", generic_dna), id="Iota"),
])

my_alignments = [align1, align2, align3]
N = AlignIO.write(my_alignments, "file_samples/my_malign.phy", "phylip")

print("{} entries written to the file".format(N))
print("")
alignments = AlignIO.parse("file_samples/my_malign.phy", "phylip")
for align in alignments:
    print(align)

3 entries written to the file

SingleLetterAlphabet() alignment with 3 rows and 12 columns
ACTGCTAGCTAG Alpha
ACT-CTAGCTAG Beta
ACTGCTAGDTAG Gamma
SingleLetterAlphabet() alignment with 3 rows and 9 columns
GTCAGC-AG Delta
GACAGCTAG Epsilon
GTCAGCTAG Zeta
SingleLetterAlphabet() alignment with 3 rows and 13 columns
ACTAGTACAGCTG Eta
ACTAGTACAGCT- Theta
-CTACTACAGGTG Iota

Note that it is also possible to convert one format into the other (provided that all information needed for the second format is available) by using the function:

Bio.AlignIO.convert(input_file, input_file_format, output_file, output_file_format)

basically by passing the input file name and format and output file name and format.

Ex:

Bio.AlignIO.convert("PF05371_seed.sth", "stockholm", "PF05371_seed.aln", "clustal")

converts a stockholm file into a clustal.

Manipulating alignments

It is possible to slice alignments using the [] operator applied on a SeqRecord. In particular:

1. SeqRecord[i,j] returns the jth character of alignment i as a string;
2. SeqRecord[:,j] returns all the jth characters of the multiple alignment as a string;
3. SeqRecord[:,i:j] returns a MultipleSeqAlignment with the sub-alignments going for i to j (excluded)
4. SeqRecord[a:b,i:j] similar to 3. but for alignments going from a to b (excluded) only

One can also combine different portions of the alignment by slicing and adding the slices together with

SeqRecord[:,i:j] + SeqRecord[:,t:k]

Example: Load the seed alignment of the Piwi (PF02171) family stored in the pfam (stockholm) format PF02171_seed.sth. For each record print the description, the first 20 bases and the final 20 bases of the sequence.

from Bio import AlignIO

alignments = AlignIO.read("file_samples/PF02171_seed.sth", "stockholm")

edited_aligns = alignments[:,0:20] + alignments[:,-20:]


for align in edited_aligns:
    print(align.description, "\t", align.seq)

AGO1_SCHPO/500-799       YLFFILDK-NSPEP-YGSIKLVPPVYYAHLVSNLARYQDV
AGO6_ARATH/541-851       FILCILPERKTSDI-YGPWKIVAPVRYAHLAAAQVAQFTK
AGO4_ARATH/577-885       FILCVLPDKKNSDL-YGPWKVVAPICYAHLAAAQLGTFMK
TAG76_CAEEL/660-966      CIIVVLQS-KNSDI-YMTVKIPTPVYYADLVATRARCHVK
O16720_CAEEL/566-867     LIVVVLPG--KTPI-YAEVKIPAPAYYAHLVAFRARYHLV
O62275_CAEEL/594-924     TFVFIITD-DSITT-LHQRYLPTPLYVANEYAKRGRNLWN
YQ53_CAEEL/650-977       DILVGIAR-EKKPD-VHDILVPDVLYAAENLAKRGRNNYK
NRDE3_CAEEL/673-1001     TIVFGIIA-EKRPD-MHDILIPNVSYAAQNLAKRGHNNYK
Q17567_CAEEL/397-708     MLVVMLAD-DNKTR-YDSLKVPAPCQYAHKLAFLTAQSLH
AUB_DROME/555-852        IVMVVMRS-PNEEK-YSCIKVPAVCHYAHKLAFLVAESIN
PIWI_DROME/538-829       LILCLVPN-DNAER-YSSIKVPAVCQYAKKLATLVGTNLH
PIWL1_HUMAN/555-847      IVVCLLSS-NRKDK-YDAIKVPAPCQYAHKLAFLVGQSIH
PIWI_ARCFU/110-406       GIMLVLPE-YNTPL-YYKLKLPVTVNYPKLVAGIIANVNR
Y1321_METJA/426-699      CFALIIGKEKYKDNDYYEILIPAPIHYADKFVKALGKNWK
O67434_AQUAE/419-694     LVIVFLEEYPKVDP-YKSFLLPATVHYSDKITKLMLRGIE
AGO10_ARATH/625-946      LLLAILPD-NNGSL-YGDLKIVPPAYYAHLAAFRARFYLE

Example: Convert the seed alignment of the Piwi (PF02171) family stored in the pfam (stockholm) format PF02171_seed.sth into phylip format. Print some stats on the data.

from Bio import AlignIO

alignments = AlignIO.read("file_samples/PF02171_seed.sth", "stockholm")

out = AlignIO.convert("file_samples/PF02171_seed.sth",
                      "stockholm",
                      "file_samples/PF02171_seed.aln",
                      "clustal")

print("N. of seq: {}\nLen of seq: {}".format(
                                                len(alignments),
                                                len(alignments[0])))
print("{} multiple alignments converted to phylip".format(out))

N. of seq: 16
Len of seq: 395
1 multiple alignments converted to phylip

Biopython’s pairwise2 alignment

Biopython supports running some classic multiple alignment tools like clustal, MUSCLE but these require to be installed in your system first.

Biopython has its own module to make pairwise alignment. It provides two algorithms: Smith-Waterman for local alignment and Needleman-Wunsch for global alignment. These methods are implemented in two Biopython functions of the Bio.pairwise2 module:

pairwise2.align.globalxx() and pairwise2.align.localxx().

The basic syntax of the two methods is the same:

aligns = pairwise2.align.globalxx(seq1,seq2)
aligns = pairwise2.align.localxx(seq1,seq2)

where seq1 and seq2 are two str objects. These methods return a list of alignments (at least one) that have the same optimal score. Each alignment is represented as tuples with the following 5 elements in order:

1. The alignment of the first sequence;
2. The alignment of the second sequence;
3. The alignment score;
4. The start of the alignment (for global alignments this is always 0);
5. The end of the alignment (for global alignments this is always the length of the alignment).

The xx in globalxx or localxx encodes the penalties and scores for gaps and matches (and mismatches) of the alignment. The first letter is the score for a match the second letter is the penalty for a gap:

Match parameters can be:

• x : means that a match scores 1 a mismatch 0;
• m : the match and mismatch score are passed as additional params after the sequence (es. aligns = pairwise2.align.globalmx(seq1,seq2, 1, -1) to set 1 as match score and -1 as mismatch penalty.

Gap parameters can be:

• x : gap penalty is 0;
• s : same gap open and gap extend penalties for the 2 sequences (passed as additional params after seqs).
• d : different gap open and gap extend penalties for the 2 seqs (additional params after the seqs).

Example:

Let’s perform the alignment of the two sequences “ACCGTTATATAGGCCA” and “ACGTACTAGTATAGGCCA”

from Bio import pairwise2
from Bio import SeqIO


alignments = pairwise2.align.globalxx("ACCGTTATATAGGCCA",
                                      "ACGTACTAGTATAGGCCA")

for i in range(len(alignments)):
    print(alignments[i])

print("")
print("Looping through aligns")
for align in alignments:
        print(align[0])
        print(align[1])
        print("Score: {}, Start: {}, End: {}".format(align[2],
                                                     align[3],
                                                     align[4]))
        print("")

alignments = pairwise2.align.globalms("ACCGTTATATAGGCCA",
                                      "ACGTACTAGTATAGGCCA",
                                      1,-1,-0.5,-0.2)
print("")
print("Match: 1, Mismatch: -1, Gap open: -0.5, Gap extend: -0.2")
for align in alignments:
    print(align[0])
    print(align[1])
    print("Score: {}, Start: {}, End: {}".format(align[2],
                                                 align[3],
                                                 align[4]))
    print("")

('ACCGT--TA-TATAGGCCA', 'A-CGTACTAGTATAGGCCA', 15.0, 0, 19)
('ACCGT--TA-TATAGGCCA', 'AC-GTACTAGTATAGGCCA', 15.0, 0, 19)

Looping through aligns
ACCGT--TA-TATAGGCCA
A-CGTACTAGTATAGGCCA
Score: 15.0, Start: 0, End: 19

ACCGT--TA-TATAGGCCA
AC-GTACTAGTATAGGCCA
Score: 15.0, Start: 0, End: 19


Match: 1, Mismatch: -1, Gap open: -0.5, Gap extend: -0.2
ACCGT--TA-TATAGGCCA
A-CGTACTAGTATAGGCCA
Score: 13.5, Start: 0, End: 19

ACCGT--TA-TATAGGCCA
AC-GTACTAGTATAGGCCA
Score: 13.5, Start: 0, End: 19

It is also possible to specify a substitution matrix like the BLOSUM to improve the alignment of protein sequences. Substitution matrices like the blosum62 are present in Biopython and before using it we need to import it with from Bio.SubsMat.MatrixInfo import blosum62.

You can find all the substitution matrices available here.

Example: Align the alpha and beta subunits of the human hemoglobin protein stored in hem_alpha.fasta and hem_beta.fasta with globalxx and with a blosum62 substitution matrix and gap open -10 and gap extension -0.5.

from Bio import pairwise2
from Bio import SeqIO
from Bio.pairwise2 import format_alignment
from Bio.SubsMat.MatrixInfo import blosum62



seq1 = SeqIO.read("file_samples/hem_alpha.fasta", "fasta")
seq2 = SeqIO.read("file_samples/hem_beta.fasta", "fasta")


alignments = pairwise2.align.globalxx(seq1.seq,seq2.seq)
print(len(alignments), "optimal alignments")

align = alignments[0]
print(align[0])
print(align[1])
print("Score: {}, Start: {}, End: {}".format(align[2],align[3],align[4]))
print("")

alignments = pairwise2.align.globalds(seq1.seq, seq2.seq, blosum62, -10, -0.5)
print(len(alignments), "optimal alignments")

align = alignments[0]
print(align[0])
print(align[1])
print("Score: {}, Start: {}, End: {}".format(align[2],align[3],align[4]))

80 optimal alignments
MV-LSPADKTNV---K-A--A-WGKVGAHAG---EY-GA-EALE-RMFLSF----PTTK-TY--FPHFDL-SH-G--S---AQVK-G------HGKKV--A--DA-LTNAVAHVD-DMPNALS----A-LSD-LHAH--KLR-VDPV-NFKL-LSHCL---LVT--LAAHLPA----EFTPA-VH-ASLDKFLAS---VSTV------LTS--KYR-
MVHL-----T--PEEKSAVTALWGKV-----NVDE-VG-GEAL-GR--L--LVVYP---WT-QRF--F--ES-FGDLSTPDA-V-MGNPKVKAHGKKVLGAFSD-GL----AH--LD--N-L-KGTFATLS-EL--HCDKL-HVDP-ENF--RL---LGNVLV-CVL-AH---HFGKEFTP-PV-QA------A-YQKV--VAGVANAL--AHKY-H
Score: 72.0, Start: 0, End: 217

2 optimal alignments
MV-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
MVHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
Score: 292.5, Start: 0, End: 149

Exercises

1. Write a python function that reads a genebank file given in input and prints off the following information:
   1. Identifier, name and description;
   2. The first 100 characters of the sequence;
   3. Number of external references (dbxrefs) and ids of the external refs.
   4. The name of the organism (hint: check the annotations dictionary at the key “organism”)
   5. Retrieve and print all (if any) associated publications (hint: annotation dictionary, key:”references”)
   6. Retrieve and print all the locations of “CDS” features of the sequence (hint: check the features )

Hint: go back and check the details of the SeqRecord object.

Test the program downloading some files from genebank like this or this

Show/Hide Solution

%reset -s -f

from Bio import SeqIO

def getGenBankInfo(filename):
    record = SeqIO.read(filename, "genbank")
    #print(record.annotations.keys())
    #print(record.annotations)

    ident = record.id
    name = record.name
    desc = record.description
    numDbrefs = len(record.dbxrefs)
    dbrefs = ",".join(record.dbxrefs)
    organism = record.annotations["organism"]
    pubs = record.annotations["references"]

    print("ID:{}".format(ident) )
    print("NAME:{}".format(name))
    print("DESC:{}".format(desc) )
    print("ORGANISM:{}".format(organism))
    print("")
    print("CDS features:")
    for f in record.features:
        if(f.type == "CDS"):
            print(f.type, f.location)
    print("num DBrefs {}:".format(numDbrefs))
    if(numDbrefs > 0):
        print("Refs:{}".format(dbrefs))
    print("")
    if(len(pubs) > 0):
        print("PUBLICATIONS:")
        pcount = 1
        for p in pubs:
            #print(p)
            print("REFERENCE [{}]".format(pcount))
            print("{}".format(p.title))
            print("{}".format(p.authors))
            print("{}".format(p.journal))
            print("")
            pcount += 1



fn = "file_samples/NC_005816.gb"
getGenBankInfo(fn)

ID:NC_005816.1
NAME:NC_005816
DESC:Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence
ORGANISM:Yersinia pestis biovar Microtus str. 91001

CDS features:
CDS [86:1109](+)
CDS [1105:1888](+)
CDS [2924:3119](+)
CDS [<3358:3442](+)
CDS [4354:4780](+)
CDS [4814:5888](-)
CDS [6004:6421](+)
CDS [6663:7602](+)
CDS [7788:8088](-)
CDS [8087:8435](-)
CDS [8507:8639](-)
CDS [9264:9558](-)
num DBrefs 3:
Refs:BioProject:PRJNA224116,BioSample:SAMN02602970,Assembly:GCF_000007885.1

PUBLICATIONS:
REFERENCE [1]
Genetics of metabolic variations between Yersinia pestis biovars and the proposal of a new biovar, microtus
Zhou,D., Tong,Z., Song,Y., Han,Y., Pei,D., Pang,X., Zhai,J., Li,M., Cui,B., Qi,Z., Jin,L., Dai,R., Du,Z., Wang,J., Guo,Z., Wang,J., Huang,P. and Yang,R.
J. Bacteriol. 186 (15), 5147-5152 (2004)

REFERENCE [2]
Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans
Song,Y., Tong,Z., Wang,J., Wang,L., Guo,Z., Han,Y., Zhang,J., Pei,D., Zhou,D., Qin,H., Pang,X., Han,Y., Zhai,J., Li,M., Cui,B., Qi,Z., Jin,L., Dai,R., Chen,F., Li,S., Ye,C., Du,Z., Lin,W., Wang,J., Yu,J., Yang,H., Wang,J., Huang,P. and Yang,R.
DNA Res. 11 (3), 179-197 (2004)

REFERENCE [3]
Direct Submission
Song,Y., Tong,Z., Wang,L., Han,Y., Zhang,J., Pei,D., Wang,J., Zhou,D., Han,Y., Pang,X., Zhai,J., Chen,F., Qin,H., Wang,J., Li,S., Guo,Z., Ye,C., Du,Z., Lin,W., Wang,J., Yu,J., Yang,H., Wang,J., Huang,P. and Yang,R.
Submitted (24-APR-2003) The Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, People's Republic of China

2. Write a python program that loads a pfam file (stockholm format .sth) and reports for each record of the alignment:
   1. the id of the entry
   2. the start and end points
   3. the number of gaps and the % of gaps on the total length of the alignment
   4. the number of external database references (dbxrefs), and the first 3 external references comma separated (hint: use join).

Print these information to the screen. Finally, write this information in a tab separated file (.tsv) having the following format: #ID\tstart\tend\tnum_gaps\tpercentage_gaps\tdbxrefs.

You can test the program using the TP53 family file PF00870_seed.sth.

Show/Hide Solution

%reset  -s -f

from Bio import AlignIO

def getStockholmInfo(fn):

    alignments = AlignIO.read(fn, "stockholm")
    print(alignments)
    retVals = []
    for align in alignments:
        ident = align.id
        start = align.annotations["start"]
        end = align.annotations["end"]
        gaps = align.seq.count("-")
        #percentage gaps
        percGaps = 100*gaps/(end - start)
        dbxrfsN = len(align.dbxrefs)
        #get top five external refs
        dbxrfs = ",".join(align.dbxrefs[0:3])
        print("ID: {} start: {} end: {} gaps: {} % gaps: {:.2f} refs: {} {}".format(
            ident, start, end, gaps, percGaps, dbxrfsN, dbxrfs))
        retVals.append([ident, start, end, gaps, "{:.2f}".format(percGaps), dbxrfsN, dbxrfs])
    return retVals

def writeStockholmInfo(outFile, data):
    fh = open(outFile, "w")
    fh.write("#ID\tstart\tend\tnum_gaps\tpercentage_gaps\tdbxrefs\n")
    for entry in data:
        fh.write("\t".join([str(x) for x in entry]) + "\n")
    fh.close()
    print("Written {} entries.".format(len(data)))

file = "file_samples/PF00870_seed.sth"
outFile = "file_samples/PF00870_seed.tsv"

infos = getStockholmInfo(file)
print("")
writeStockholmInfo(outFile, infos)

SingleLetterAlphabet() alignment with 5 rows and 197 columns
SSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLA...ENL P53_HUMAN/95-289
STVPETSDYPGDHGFRLRFPQSGTAKSVTCTYSPDLNKLFCQLA...SNF P53_DANRE/63-257
-AVPSTEDYAGSYGLKLEFQQNGTAKSVTCTYSTDLNKLFCQLA...DN- F7A9U0_XENTR/70-263
PVIPSNTDYPGPHHFEVTFQQSSTAKSATWTYSPLLKKLYCQIA...DHY P73_HUMAN/113-309
TTVPVTTDYPGSYELELRFQKSGTAKSVTSTYSETLNKLYCQLA...ESR P53_ORYLA/80-270
ID: P53_HUMAN/95-289 start: 95 end: 289 gaps: 2 % gaps: 1.03 refs: 210 PDB; 3Q06 B; 96-289;,PDB; 4MZR B; 95-289;,PDB; 5LAP B; 95-289;
ID: P53_DANRE/63-257 start: 63 end: 257 gaps: 2 % gaps: 1.03 refs: 0
ID: F7A9U0_XENTR/70-263 start: 70 end: 263 gaps: 3 % gaps: 1.55 refs: 0
ID: P73_HUMAN/113-309 start: 113 end: 309 gaps: 0 % gaps: 0.00 refs: 45 PDB; 4A63 E; 114-309;,PDB; 4G83 A; 115-309;,PDB; 3VD2 A; 115-309;
ID: P53_ORYLA/80-270 start: 80 end: 270 gaps: 6 % gaps: 3.16 refs: 0

Written 5 entries.

3. Given a multiple sequence alignment stored in “phylip” format, write three methods: readAlignment that reads the input file and prints the number of sequences present, printAlignments(alignments) that prints the alignments to the screen and computeConsensus(alignments,minFrequency) that creates the consensus of all the alignments. MinFrequency is the minimum frequency (that has to be > 0.5) to keep a base in the consensus. “?” is put put if frequency < minFrequency for all possible bases.

Ex. if alignments are:

ATC-G
AAC-G
AAG-G
ATCGT

computeConsensus(alignments,0.6) is:

A?C-G

Test the script with the file alpha-globin.phy.

Show/Hide Solution

%reset -s -f
"""
NOTE:
Three different solutions are provided for computeConsensus.
One with standard methods, one with set and one with collections.Counter
"""


from Bio import AlignIO
#needed for computeConsensusV3
from collections import Counter

def readAlignment(fn):

    alignments = AlignIO.read(fn, "phylip")
    print("{} alignments present in \"{}\"\n".format(len(alignments),fn))
    return alignments

def printAlignments(aldata):
    for align in aldata:
        print("{}\n{}".format(align.id, align.seq))

def computeConsensus(aldata, minFreq = 0.51):
    #this solution uses sets.
    #set(list("ATTTAC")) returns {'A', 'T', 'C'}
    consensus = ""
    if(minFreq < 0.51):
        print("Warning: minFreq ({}) not valid!".format(minFreq))
        return None
    for j in range(len(aldata[0])):
        chrSeq = aldata[:,j]
        singleChars = [(x,chrSeq.count(x)) for x in chrSeq ]
        if(len(singleChars) == 1):
            consensus +=chrSeq[0][0]
        else:
            cons = [x[0] for x in singleChars if x[1] > minFreq*len(chrSeq)]
            if(len(cons) == 1):
                consensus +=cons[0]
            else:
                consensus += "?"
    return consensus

def computeConsensusV2(aldata, minFreq = 0.51):
    #this solution uses sets.
    #set(list("ATTTAC")) returns {'A', 'T', 'C'}
    consensus = ""
    if(minFreq < 0.51):
        print("Warning: minFreq ({}) not valid!".format(minFreq))
        return None
    for j in range(len(aldata[0])):
        chrSeq = aldata[:,j]
        singleChars = set(list(chrSeq))
        if(len(singleChars) == 1):
            consensus +=chrSeq[0]
        else:
            cons = [x for x in singleChars if chrSeq.count(x) > minFreq*len(chrSeq)]
            if(len(cons) == 1):
                consensus +=cons[0]
            else:
                consensus += "?"
    return consensus

def computeConsensusV3(aldata, minFreq = 0.51):
    #this solution uses collections.Counter
    #collections.Counter("ATTTAC") returns the dictionary: {'T': 3, 'A': 2, 'C': 1}
    #
    consensus = ""
    if(minFreq < 0.51):
        print("Warning: minFreq ({}) not valid!".format(minFreq))
        return None
    for j in range(len(aldata[0])):
        chrSeq = aldata[:,j]
        singleChars = Counter(chrSeq)
        if(len(singleChars) == 1):
            consensus +=chrSeq[0]
        else:
            cons = [x for x in singleChars if singleChars[x] > minFreq*len(chrSeq)]
            if(len(cons) == 1):
                consensus +=cons[0]
            else:
                consensus += "?"
    return consensus

file = "file_samples/alpha-globin.phy"


als = readAlignment(file)
printAlignments(als)
out = computeConsensusV2(als,minFreq = 0.7)
print("Consensus:\n{}".format(out))
#out1 = computeConsensusV2(als,minFreq = 0.7)
#print("Consensus:\n{}".format(out1))
#out2 = computeConsensusV3(als,minFreq = 0.7)
#print("Consensus:\n{}".format(out2))
#assert(out1 == out2)
#assert(out == out1)

4 alignments present in "file_samples/alpha-globin.phy"

ENA|BAA205
ATGAGTCTCTCTGATAAGGACAAGGCTGCTGTGAAAGCCCTATGGGCTAAGATCAGCCCCAAAGCCGATGATATCGGCGCTGAAGCTCTCGGCAGAATGCTGACCGTCTACCCTCAGACCAAGACCTACTTCGCTCACTGGGATGACCTGAGCCCTGGGTCCGGTCCTGTGAAGAAGCATGGCAAGGTTATCATGGGTGCAGTGGCCGATGCCGTTTCAAAAATAGACGACCTTGTGGGAGGTCTGGCCTCCCTGAGCGAACTTCATGCTTCCAAGCTGCGTGTTGACCCGGCCAACTTCAAGATCCTCGCACACAATGTCATCGTGGTCATCGGCATGCTCTTCCCTGGAGACTTCCCCCCAGAGGTTCACATGTCAGTTGACAAGTTTTTCCAGAACTTGGCTCTGGCTCTCTCTGAGAAGTACCGCTAA
ENA|CAA284
ATGTCTCTGACCAGGACTGAGAGGACCATCATCCTGTCCCTGTGGAGCAAGATCTCCACACAGGCAGACGTCATTGGCACCGAGACCCTGGAGAGGCTCTTCTCCTGCTACCCGCAGGCCAAGACCTACTTCCCGCACTTCGAC---CTGCACTCGGGCTCCGCGCAGCTGCGCGCGCACGGCTCCAAGGTGGTGGCCGCCGTGGGCGACGCGGTCAAGAGCATCGACAACGTGACGAGCGCGCTGTCCAAGCTGAGCGAGCTGCACGCCTACGTGCTGCGCGTGGACCCGGTCAACTTCAAGTTCCTGTCCCACTGCCTGCTGGTCACGTTGGCCTCGCACTTCCCCGCCGACTTCACGGCCGACGCGCACGCCGCCTGGGACAAGTTCCTGTCCATCGTGTCCGGCGTCCTGACGGAGAAGTACCGCTGA
ENA|CAA237
ATGGTGCTGTCTCCTGCCGACAAGACCAACGTCAAGGCCGCCTGGGGTAAGGTCGGCGCGCACGCTGGCGAGTATGGTGCGGAGGCCCTGGAGAGGATGTTCCTGTCCTTCCCCACCACCAAGACCTACTTCCCGCACTTCGAC---CTGAGCCACGGCTCTGCCCAAGTTAAGGGCCACGGCAAGAAGGTGGCCGACGCGCTGACCAACGCCGTGGCGCACGTGGACGACATGCCCAACGCGCTGTCCGCCCTGAGCGACCTGCACGCGCACAAGCTTCGGGTGGACCCGGTCAACTTCAAGCTCCTAAGCCACTGCCTGCTGGTGACCCTGGCCGCCCACCTCCCCGCCGAGTTCACCCCTGCGGTGCACGCTTCCCTGGACAAGTTCCTGGCTTCTGTGAGCACCGTGCTGACCTCCAAATACCGTTAA
ENA|CAA240
ATGGTGCTCTCTGGGGAAGACAAAAGCAACATCAAGGCTGCCTGGGGGAAGATTGGTGGCCATGGTGCTGAATATGGAGCTGAAGCCCTGGAAAGGATGTTTGCTAGCTTCCCCACCACCAAGACCTACTTTCCTCACTTTGAT---GTAAGCCACGGCTCTGCCCAGGTCAAGGGTCACGGCAAGAAGGTCGCCGATGCGCTGGCCAGTGCTGCAGGCCACCTCGATGACCTGCCCGGTGCCTTGTCTGCTCTGAGCGACCTGCATGCCCACAAGCTGCGTGTGGATCCCGTCAACTTCAAGCTCCTGAGCCACTGCCTGCTGGTGACCTTGGCTAGCCACCACCCTGCCGATTTCACCCCCGCGGTACATGCCTCTCTGGACAAATTCCTTGCCTCTGTGAGCACCGTGCTGACCTCCAAGTACCGTTAA
Consensus:
ATG???CT?TCT??????GACAAGACCA?C?TCAAGGCC???TGGGG?AAGATC?GC?C?CA?GC?G??GA???TGG?GC?GA?GCCCTGGA?AGGATGTT??C???CT?CCC????ACCAAGACCTACTTCCC?CACTT?GA?---CTGAGCC??GGCTC?GC?CA?GT?AAGG??CACGGCAAGAAGGT?G??G??GC??TGGCC?A?GC?GT?????AC?T?GACGAC?TG?C??G?GC?CTGTCC?C?CTGAGCGA?CTGCA?GC??ACAAGCTGCG?GTGGACCCGGTCAACTTCAAG?TCCT???CCACTGCCTGCTGGTGACC?TGGCC???CAC?TCCC?GCCGA?TTCACCCC?G?GGT?CACGC?TC??TGGACAAGTTCCT??C????GTG??C??CGT?CTGAC????AAGTACCG?TAA

4. Load the contigs present in the filtered_contigs.fasta file and translate each DNA sequence into the corresponding protein. Count the number of stop codons (i.e. *) for each sequence and print them to the user (e.g. MDC020656.85 51). Finally, write the translated proteins in another .fasta file (e.g. filtered_contigs_translated.fasta).

Show/Hide Solution

%reset -s -f

from Bio import SeqIO

seqIterator = SeqIO.parse("file_samples/filtered_contigs.fasta", "fasta")

sRcds = []
for s in seqIterator:
    #to avoid problems if not divisible by 3!
    seq1 = s.seq.tomutable()
    if(len(seq1) % 3 != 0):
        while( len(seq1) % 3 != 0):
            seq1 +="N"
    transl = seq1.toseq().translate()
    stop_cnt = transl.count("*")
    print(s.id,"\t", stop_cnt)
    s.seq = transl
    sRcds.append(s)

N = SeqIO.write(sRcds,"file_samples/filtered_contigs_translated.fasta", "fasta")
print("")
print("{} sequences written to output file".format(N))

MDC001115.177    65
MDC013284.379    93
MDC018185.243    418
MDC018185.241    467
MDC004527.213    48
MDC012176.157    30
MDC001204.810    155
MDC004389.256    43
MDC018297.229    317
MDC001802.364    45
MDC014057.243    23
MDC021015.302    19
MDC017187.314    83
MDC012865.410    68
MDC000427.83     42
MDC017187.319    251
MDC004364.265    145
MDC002360.219    60
MDC015155.172    47
MDC019140.398    67
MDC019140.399    56
MDC011390.337    71
MDC007154.375    248
MDC010588.505    29
MDC002519.240    500
MDC006346.711    376
MDC011551.182    806
MDC002717.156    55
MDC006346.719    157
MDC007838.447    141
MDC007018.186    47
MDC017873.233    35
MDC016296.138    176
MDC019067.226    49
MDC014019.318    45
MDC007995.528    53
MDC026961.60     71
MDC020963.161    65
MDC005174.220    132
MDC040033.7      142
MDC019674.147    89
MDC010450.877    40
MDC007097.457    89
MDC016278.70     69

44 sequences written to output file

5. Write the following three functions:
   1. countMatches(s1,s2) that takes two sequences aligned with pairwise2 local or global of the same length and returns how many elements match;
   2. countMismatches(s1,s2) that takes two sequences aligned with pairwise2 local or global of the same length and returns how many elements are different (i.e. they are not gaps but the character is different);
   3. countGapOpens(s1,s2) that takes two sequences aligned with pairwise2 local or global of the same length and returns the number of gap opened in the alignment;
   4. countGapExtensions(s1,s2) that takes two sequences aligned with pairwise2 local or global of the same length and returns the number of gap extensions in the alignment
   5. getScore(s1,s2, matchScore, mismatchPenalty, gapOpenPenalty, gapExtensionPenalty) and returns the score of the alignment of s1 and s2 (aligned with pairwise2 as before) given the scores and penalties in input.

Finally, align the sequences of the Interleukin-12 chain A (let’s call it s1) IL12A.fasta and B IL12B.fasta (let’s call it s2) with the following parameters:

pairwise2.align.globalxx(s1,s2)
pairwise2.align.globalms(s1,s2,,1,-0.1,-1,-0.1)
pairwise2.align.globalxs(s1, s2,1,-0.5,-5,-0.5)
pairwise2.align.globalxd(s1, s2,1,-0.5,-5,-0.5,-5,-5)

and check the score as computed from pairwise2 and from your functions (use the first of all the alignments to check). Note the effect of changing parameters.

Show/Hide Solution

%reset -s -f

from Bio import pairwise2
from Bio import SeqIO


def countMatches(a1,a2):
    return sum([1 for i in range(len(a1)) if a1[i] == a2[i]])

def countMismatches(a1,a2):
    return sum([1 for i in range(len(a1)) if a1[i] != a2[i] and a1[i] != "-" and a2[i] != "-"])

def countGapOpens(a1,a2):
    gaps = [1 for i in range(1,len(a1)-1)
            #if ((a1[i] == "-" or a2[i] == "-") and a1[i-1] != "-" and a2[i-1] !="-")
            if ((a1[i] == "-" and a1[i-1] != "-") or (a2[i] == "-" and a2[i-1] !="-"))
           ]
    return sum(gaps)

def countGapExtensions(a1,a2):
    gaps = [ 1 for i in range(1,len(a1)-1)
            if ((a1[i] == "-" and a1[i-1] == "-") or (a2[i] == "-" and a2[i-1] =="-"))
           ]
    return sum(gaps)

def getScore(s1,s2, matchScore, mismatchPenalty, gapOpenPenalty, gapExtensionPenalty):
    mat = countMatches(s1,s2)
    mis = countMismatches(s1,s2)
    gapo = countGapOpens(s1,s2)
    gape = countGapExtensions(s1,s2)
    score = matchScore*mat + mis*mismatchPenalty + gapo*gapOpenPenalty + gape*gapExtensionPenalty
    return score

def getSequenceData(filename):
    record = SeqIO.read(filename, "fasta")
    return record.seq

def printInfo(a1,a2,computedScore,Mscore,mScore,goScore,geScore):
    print(a1)
    print(a2)
    print(computedScore)
    print("")
    M = countMatches(a1,a2)
    m = countMismatches(a1,a2)
    go = countGapOpens(a1,a2)
    ge = countGapExtensions(a1,a2)
    print("Matches:{} Mismatches:{} GapOpens:{} GapExtensions:{}".format(M,m,go,ge))
    print("Recomputed Score: {}".format(getScore(a1,a2,Mscore,mScore,goScore,geScore)))

s1 = getSequenceData("file_samples/IL12A.fasta")
s2 = getSequenceData("file_samples/IL12B.fasta")

aligns = pairwise2.align.globalxx(s1,s2)
a1 = aligns[0][0]
a2 = aligns[0][1]
sc = aligns[0][2]
printInfo(a1,a2,sc, 1,0,0,0)


print("")
aligns = pairwise2.align.globalms(s1,s2,1,-0.1,-1,-0.1)
a1 = aligns[0][0]
a2 = aligns[0][1]
sc = aligns[0][2]
printInfo(a1,a2,sc, 1,-0.1,-1,-0.1)


print("")
aligns = pairwise2.align.globalms(s1, s2,1,-0.5,-5,-0.5)

a1 = aligns[0][0]
a2 = aligns[0][1]
sc = aligns[0][2]
printInfo(a1,a2,sc, 1,-0.5,-5,-0.5)

aligns = pairwise2.align.globalmd(s1, s2,1,-0.5,-5,-0.5,-5,-5)

a1 = aligns[0][0]
a2 = aligns[0][1]
sc = aligns[0][2]
printInfo(a1,a2,sc, 1,-0.5,-5,-0.5)

MCPAR------S---L--L---LVAT---L---VL----LDHLSL----ARNLP---VA--TP-D-P---GMFPC----LHHS-QNLLRAVSNM---LQ---KARQTL-----EF-----YPCTSE-----EID---H--------ED-I--T---KD-KTSTVEACLP-----L--ELT-KNE-S----C--LNSRETSF-I-TN----------GS-------CL-A---S--R-----KT----SFMMAL--CL---S-------S--IYE---D----LKMYQVE-----F------KTMNA----K-L-LMD-P-K--RQIFLDQNMLAVIDELMQALNFN-S-E---TV---PQK-S--SLE------------EP--D--FYKT-K-----IKLCILLHAFR----I--RAVTI-DRVMSYLN--------AS----
MC---HQQLVISWFSLVFLASPLVA-IWELKKDV-YVVELD----WYPDA---PGEMV-VLT-CDTPEEDG----ITWTL---DQ------S--SEVL-GSGK---TLTIQVKEFGDAGQY--T--CHKGGE--VLSHSLLLLHKKEDGIWSTDILKDQK----E---PKNKTFLRCE--AKN-YSGRFTCWWL----T--TIST-DLTFSVKSSRGSSDPQGVTC-GAATLSAERVRGDNK-EYEYS-----VEC-QEDSACPAAEESLPI-EVMVDAVHKLK-Y--ENYTSSFFIRDIIK----PDPPKNLQL--KPLKNSR-----Q----V--E--------VSWEYPDT-WSTP--HSYFSL-TFCVQVQGKSKRE-KKDRVF--TDKTSATVI--C------RKNASISVRA---QDR---Y--YSSSWSEWASVPCS
103.0

Matches:103 Mismatches:0 GapOpens:117 GapExtensions:223
Recomputed Score: 103

MC------PARSL--L---LVA--TL------VLLDHLSLARNLPVA-TPD-P---GMFPCLHHSQNLLRAVSNM-LQKARQTLEF-----YPC------TS---------EE-IDHEDITKD-KTSTVEACLPLELTKNES----CLNSRETSFITNGSCLASRKTS-----FMMALCLS--SIYEDLK--MYQVEFKTMNA------------------KL---------------LMDP-KR-QIFLDQNMLAV------IDELMQALNFNSET----VPQKSSLEEPD--FY-KTKIKLCILLHAFRI--RAVTIDRVMS---YLNA----S
MCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVL--GSGKTL--TIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCE-AKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRGDNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKREKKDRVFTDKT-SATVICRKNASISVRA--QDRYYSSSWSEWASVPCS
28.19999999999986

Matches:84 Mismatches:127 GapOpens:34 GapExtensions:91
Recomputed Score: 28.199999999999996

MCPARSLLLVATLVLLDHLSLA----------RNLPVATPDPGMFPCLHHSQNLLRAVSNMLQKARQTL----EFYPCTSEEIDHEDITKDKTSTVEACLPLELTKNESCLNS-------RETSFITNGSCLASRKTSFMMALCLSSIYEDL----------------------------------KMYQVEFKTMNA------------------KLLMDPKRQIFLDQNMLAVIDELMQALNFNSETVPQKSSLEEPDFYKT------------------------------------KIKLCILLHAFRIRAVTIDRVMSYLNAS
MCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRGDNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPCS
-122.0

Matches:46 Mismatches:173 GapOpens:6 GapExtensions:103
Recomputed Score: -122.0
MCPARSLLLVATLVLLDHLSLA----------RNLPVATPDPGMFPCLHHSQNLLRAVSNMLQKARQTL----EFYPCTSEEIDHEDITKDKTSTVEACLPLELTKNESCLNS-------RETSFITNGSCLASRKTSFMMALCLSSIYEDL----------------------------------KMYQVEFKTMNA------------------KLLMDPKRQIFLDQNMLAVIDELMQALNFNSETVPQKSSLEEPDFYKT------------------------------------KIKLCILLHAFRIRAVTIDRVMSYLNAS
MCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRGDNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPCS
-122.0

Matches:46 Mismatches:173 GapOpens:6 GapExtensions:103
Recomputed Score: -122.0

Practical 11

In this practical we will will see some other functionalities of Biopython.

Slides

The slides of the introduction can be found here: Intro

Biopython

From the Biopython tutorial: The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. The goal of Biopython is to make it as easy as possible to use Python for bioinformatics by creating high-quality, reusable modules and classes. Biopython features include parsers for various Bioinformatics file formats (BLAST, Clustalw, FASTA, Genbank,…), access to online services (NCBI, Expasy,…), interfaces to common and not-so-common programs (Clustalw, DSSP, MSMS…), a standard sequence class, various clustering modules, a KD tree data structure etc. and even documentation.

In this practical we will see some features of Biopython but refer to biopython documentation to discover all its features, recipes etc.

These notes are largely based on what is available here.

BLAST

Blast (Basic logical alignment search tool) is a well known tool to find similarities between biological sequences. It compares DNA or protein sequences and calculates the statistical significance of the matches found.

The typical interaction with BLAST sees the user submit some sequences to the tool to get an alignment and then the hits are parsed to obtain information on the matches. Both these steps can be performed from within Biopython. Although it is possible to interact directly with a local installation of BLAST, in this practical we will work with the tool made available by NCBI (available here).

The function qblast

The online version of blast can be accessed through the Bio.Blast.NCBIWWW.qblast() function.

It’s basic syntax is the following (first import from Bio.Blast import NCBIWWW):

result_handle = Bio.Blast.NCBIWWW.qblast(blast_program, database, query_str)

where blast_program is the program to perform the alignment. The options are blastn, blastp, blastx, tblast or tblastx. database is the database to search against and query_str is a string containing the query to search against the database. The query can be a sequence or a fasta file entry or an identifier like a GI number (NCIBI’s sequence identification number). Among the others, some optional parameters are the output format (format_type that by default is “XML” which is the most stable output format but results can be stored also as text with “Text”). It is also possible to specify an expectation value cut-off to filter out alignments expect (the e-value threshold, default value is 10.0).

Some databases to search against are reported below:

The query string can be obtained in different ways, for example it is possible to load sequences from a fasta file with:

from Bio.Blast import NCBIWWW
fasta_string = open("myfile.fasta").read()
result_handle = NCBIWWW.qblast("blastn", "nt", fasta_string)

or we can give a SeqRecord:

from Bio.Blast import NCBIWWW
from Bio import SeqIO
record = SeqIO.read("myfile.fasta", format="fasta")
result_handle = NCBIWWW.qblast("blastn", "nt", record.seq)

It is also possible to specify some optional parameters in the entrez_query for example we can limit the search to specific organisms with: entrez_query='"Malus Domestica" [Organism]'.

Example: Let’s align the first 100 bases of the first entry of the file contigs82.fasta to the Malus Domestica genome.

NOTE: this can take several minutes.

from Bio.Blast import NCBIWWW
from Bio import SeqIO



records = SeqIO.parse("file_samples/contigs82.fasta", format="fasta")
rec = next(records)
seq = rec.seq[0:100]
print("Aligning {} [{}] to Malus Dom.".format(rec.id,
                                              seq[0:10]+"..."+seq[90:101]))
result_handle = NCBIWWW.qblast("blastn", "nt",
                               seq,
                               entrez_query='"Malus Domestica" [Organism]'
                              )

Aligning MDC020656.85 [GAGGGGTTTA...TTGGCAGCAA] to Malus Dom.

Note that the previous code does not output anything, it just returns a result_handle. We need to parse it to get some results.

Parsing qblast output

Once the qblast call returns, it gives the results in a handle object result_handle that we can parse or we can write to disk to avoid having to rerun the query other times. If we expect to get one alignment only, we can use the method read otherwise (if we have multiple query sequences) we should use the method parse:

blast_record = NCBIXML.read(result_handle)

or

blast_records = NCBIXML.parse(result_handle)

Note that to use these methods we first need to import the NCBIXML module with from Bio.Blast import NCBIXML.

These methods are analogous to what seen in the case of SeqIO and AlignIO. In the case of multiple entries we can loop through them with:

blast_records = NCBIXML.parse(result_handle)
for record in blast_records:
    #do something with it...

or we can retrieve one record at a time with record = next(blast_records).

Saving results to file

To save the results present in the result_handle we can simply write them to file. In case we have only one entry we can read it and write it to file:

out_f = open("my_blast_result.xml", "w")
out_f.write(result_handle.read())
out_f.close
result_handle.close()

If we have more than one entry we need to loop through all the entries and save them in the file:

out_f = open("my_blast_result.xml", "w")
for entry in result_handle.parse():
    out_f.write(entry)
out_f.close
result_handle.close()

Example:

Let’s BLAST the galactosidase alpha (gi number: 2717) against the human database on NCBI and save the results to file. (Note that it can take several seconds/minutes to run!).

from Bio.Blast import NCBIWWW

result_handle = NCBIWWW.qblast("blastn", "nt", "2717")


with open("file_samples/blast_res.xml","w") as out_f:
    out_f.write(result_handle.read())

result_handle.close()

Open a blast .XML file

A BLAST output file can be read by opening the file to get the handler and then parse it with the method parse seen above:

from Bio.Blast import NCBIXML
result_handle = open("my_blast.xml")
blast_records = NCBIXML.parse(result_handle)

This will end up in a handle to the blast results.

The BLAST record class

The Bio.Blast.Record.Blast class holds the results of the alignment. In particular it is composed of the following three information:

1. query: the identifier of the query (a string).
2. Descriptions : a list of Description objects. Each Description holds the following information:
   • Description.title : a string with the title of the hit;
   • Description.score : a float with the score of the alignment;
   • Description.num_alignments : an int with the number of alignments with the same subject;
   • Description.e : a float with the e-value of the alignment.
3. Alignments : a list of Alignment objects. Each Alignment holds the following information:
   • Alignment.title : a string with the title of the hit (identical to Description.title);
   • Alignment.length : an int with the length of the alignment;
   • Alignment.hsps : a list of HSP objects (High Scoring Pair). Each HSP has the following info:
     • HSP.score : the BLAST score of the hit
     • HSP.bits : the bits score of the hit (x: on average 2^x pairs to find such a good hit by chance)
     • HSP.expect : the evalue of the hit
     • HSP.num_alignments : the number of alignments for the same subject
     • HSP.identities : the number of identities between query and subject
     • HSP.positives : the number of identical bases/aminos or having similar chemical properties
     • HSP.gaps : the number of gaps between query and subject
     • HSP.strand : a tuple with (query,subject) strands
     • HSP.frame : a tuple with the frame shifts
     • HSP.query/HSP.sbjct : query/subject sequence
     • HSP.query_start/HSP.sbjct_start :query/subject start point
     • HSP.match : the match sequence (basically “|” for matches and spaces for mismatches)
     • HSP.align_length : the alignment length.

More information on the BLAST record can be found here.

Example:

Let’s blast the serum albumin sequence (gi number 23307792) on the human genome and report all the information reported by BLAST. (warning might take a while to run!)

from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML

result_handle = NCBIWWW.qblast("blastn", "nt", "23307792",
                               entrez_query='"Homo Sapiens" [Organism]'
                               )



for res in NCBIXML.parse(result_handle):
    for d in res.descriptions:

        print("TITLE:{}\nSCORE:{}\nN.ALIGN:{}\nE-VAL:{}".format(
            d.title,d.score, d.num_alignments,d.e))

    for a in res.alignments:
        print("Align Title:{}\nAlign Len: {}".format(a.title, a.length))



        for h in a.hsps:
            s = h.score
            b = h.bits
            e = h.expect
            n = h.num_alignments
            i = h.identities
            p = h.positives
            g = h.gaps
            st = h.strand
            f = h.frame
            q = h.query
            sb = h.sbjct
            qs = h.query_start
            ss = h.sbjct_start
            qe = h.query_end
            se = h.sbjct_end
            m = h.match
            al = h.align_length

            print("Score: {} Bits: {} E-val: {}".format(s,b,e))
            print("N.aligns:{} Ident:{} Pos.:{} Gaps:{} Align len:{}".format(
                n,i,p,g,al))
            print("Strand: {} Frame: {}".format(st,f))
            print("Query:", q, " start:", qs, " end:", qe)
            print("Match:",m)
            print("Subjc:",sb, " start:", ss, " end:", se)


result_handle.close()

TITLE:gi|23307792|gb|AF542069.1| Homo sapiens serum albumin (HSA) mRNA, complete cds
SCORE:4352.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|1519245814|ref|NM_000477.7| Homo sapiens albumin (ALB), mRNA
SCORE:4305.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|28591|emb|V00495.1| H.sapiens mRNA for serum albumin
SCORE:4253.0
N.ALIGN:2
E-VAL:0.0
TITLE:gi|7770116|gb|AF119840.1|AF119840 Homo sapiens PRO0903 mRNA, complete cds
SCORE:4062.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|25058738|gb|BC039235.1| Homo sapiens albumin, mRNA (cDNA clone IMAGE:4768004), containing frame-shift errors
SCORE:4056.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|23243417|gb|BC036003.1| Homo sapiens albumin, mRNA (cDNA clone MGC:32850 IMAGE:4724105), complete cds
SCORE:4052.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|158258946|dbj|AK292755.1| Homo sapiens cDNA FLJ78413 complete cds, highly similar to Homo sapiens albumin, mRNA
SCORE:4036.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|28589|emb|V00494.1| Human messenger RNA for serum albumin (HSA)
SCORE:4033.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|21706455|gb|BC034023.1| Homo sapiens albumin, mRNA (cDNA clone MGC:22784 IMAGE:4734617), complete cds
SCORE:4029.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|51476389|emb|CR749331.1| Homo sapiens mRNA; cDNA DKFZp779N1935 (from clone DKFZp779N1935)
SCORE:4027.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|21706470|gb|BC034026.1| Homo sapiens cDNA clone IMAGE:4734794, containing frame-shift errors
SCORE:4010.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|194391079|dbj|AK298437.1| Homo sapiens cDNA FLJ54371 complete cds, highly similar to Serum albumin precursor
SCORE:3994.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|408407943|gb|AF130077.2| Homo sapiens clone FLB9714 PRO2619 mRNA, complete cds
SCORE:3937.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|62113340|gb|AY960291.1| Homo sapiens serum albumin mRNA, complete cds
SCORE:3907.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|49176516|gb|AY550967.1| Homo sapiens cell growth inhibiting protein 42 mRNA, complete cds
SCORE:3848.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|115607206|gb|DQ986150.1| Homo sapiens serum albumin mRNA, complete cds
SCORE:3733.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|164692402|dbj|AK314794.1| Homo sapiens cDNA, FLJ95666, highly similar to Homo sapiens albumin (ALB), mRNA
SCORE:3676.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|52001696|gb|AY728024.1| Homo sapiens serum albumin precursor, mRNA, complete cds
SCORE:3630.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|123981021|gb|DQ891414.2| Synthetic construct clone IMAGE:100004044; FLH176691.01X; RZPDo839G03122D albumin (ALB) gene, encodes complete protein
SCORE:3626.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|123995824|gb|DQ894588.2| Synthetic construct Homo sapiens clone IMAGE:100009048; FLH176687.01L; RZPDo839G03121D albumin (ALB) gene, encodes complete protein
SCORE:3624.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|6013426|gb|AF190168.1|AF190168 Homo sapiens serum albumin precursor, mRNA, complete cds
SCORE:3615.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|332356379|gb|HQ537426.1| Homo sapiens albumin mRNA, partial cds
SCORE:3471.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|194391111|dbj|AK298461.1| Homo sapiens cDNA FLJ50830 complete cds, highly similar to Serum albumin precursor
SCORE:3084.0
N.ALIGN:2
E-VAL:0.0
TITLE:gi|763428|gb|U22961.1|HSU22961 Human mRNA clone with similarity to L-glycerol-3-phosphate:NAD oxidoreductase and albumin gene sequences
SCORE:2748.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|27692692|gb|BC041789.1| Homo sapiens albumin, mRNA (cDNA clone MGC:32888 IMAGE:4766983), complete cds
SCORE:2620.0
N.ALIGN:2
E-VAL:0.0
TITLE:gi|164694201|dbj|AK308044.1| Homo sapiens cDNA, FLJ97992
SCORE:2536.0
N.ALIGN:2
E-VAL:0.0
TITLE:gi|7770216|gb|AF119890.1|AF119890 Homo sapiens PRO2675 mRNA, complete cds
SCORE:2488.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|47118014|gb|AY544124.1| Homo sapiens growth-inhibiting protein 20 mRNA, complete cds
SCORE:2453.0
N.ALIGN:2
E-VAL:0.0
TITLE:gi|7959790|gb|AF116645.1|AF116645 Homo sapiens PRO1708 mRNA, complete cds
SCORE:2003.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|6650825|gb|AF118090.1|AF118090 Homo sapiens PRO2044 mRNA, complete cds
SCORE:1983.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|168745965|emb|CU691683.1| Synthetic construct Homo sapiens gateway clone IMAGE:100022016 3' read mRNA
SCORE:1951.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|168745964|emb|CU691682.1| Synthetic construct Homo sapiens gateway clone IMAGE:100022016 5' read mRNA
SCORE:1896.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|23241674|gb|BC035969.1| Homo sapiens albumin, mRNA (cDNA clone MGC:32581 IMAGE:4714468), complete cds
SCORE:1767.0
N.ALIGN:2
E-VAL:0.0
TITLE:gi|15679995|gb|BC014308.1|BC014308 Homo sapiens, clone IMAGE:3934797, mRNA, partial cds
SCORE:1571.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|649152310|gb|KJ905683.1| Synthetic construct Homo sapiens clone ccsbBroadEn_15353 ALB gene, encodes complete protein
SCORE:1387.0
N.ALIGN:2
E-VAL:0.0
TITLE:gi|168740012|emb|CU690239.1| Synthetic construct Homo sapiens gateway clone IMAGE:100022252 3' read ALB mRNA
SCORE:1182.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|37181745|gb|AY358313.1| Homo sapiens DNA66677 ALB (UNQ696) mRNA, partial cds
SCORE:1018.0
N.ALIGN:1
E-VAL:0.0
TITLE:gi|168740011|emb|CU690238.1| Synthetic construct Homo sapiens gateway clone IMAGE:100022252 5' read ALB mRNA
SCORE:982.0
N.ALIGN:2
E-VAL:0.0
TITLE:gi|6642751|gb|AF113014.1|AF113014 Homo sapiens clone FLB3512 mRNA sequence
SCORE:618.0
N.ALIGN:1
E-VAL:1.15187e-155
TITLE:gi|219842221|ref|NG_009291.1| Homo sapiens albumin (ALB), RefSeqGene on chromosome 4
SCORE:581.0
N.ALIGN:15
E-VAL:2.37628e-145
TITLE:gi|152112963|gb|EF649953.1| Homo sapiens albumin (ALB) gene, complete cds
SCORE:581.0
N.ALIGN:15
E-VAL:2.37628e-145
TITLE:gi|19387810|gb|AC108157.3| Homo sapiens BAC clone RP11-580P21 from 4, complete sequence
SCORE:581.0
N.ALIGN:16
E-VAL:2.37628e-145
TITLE:gi|178343|gb|M12523.1|HUMALBGC Human serum albumin (ALB) gene, complete cds
SCORE:581.0
N.ALIGN:15
E-VAL:2.37628e-145
TITLE:gi|1036032687|gb|AH007061.2| Homo sapiens chromosome 4 serum albumin (ALB) gene, partial cds; and serum albumin-alphafetoprotein intergenic spacer, partial sequence
SCORE:579.0
N.ALIGN:1
E-VAL:8.29405e-145
TITLE:gi|408407822|gb|AF116616.2| Homo sapiens PRO0998 mRNA, complete cds
SCORE:577.0
N.ALIGN:1
E-VAL:2.89491e-144
TITLE:gi|338858118|gb|AH002596.2|SEG_HUMALB Homo sapiens albumin (ALB) gene, partial cds
SCORE:573.0
N.ALIGN:2
E-VAL:3.52672e-143
TITLE:gi|1122817323|gb|DQ145726.2| Homo sapiens ARNT-interacting protein 2 (AINP2) mRNA, complete cds
SCORE:404.0
N.ALIGN:1
E-VAL:1.40699e-97
TITLE:gi|32428|emb|X51365.1| Homo sapiens mRNA for albumin (clone pHA19)
SCORE:232.0
N.ALIGN:1
E-VAL:6.8383e-51
TITLE:gi|1338686512|ref|NG_056261.1| Homo sapiens albumin (ALB) 5' regulatory region (LOC111832671) on chromosome 4
SCORE:221.0
N.ALIGN:1
E-VAL:1.23639e-47
TITLE:gi|7959920|gb|AF116711.1|AF116711 Homo sapiens PRO2646 mRNA, complete cds
SCORE:216.0
N.ALIGN:1
E-VAL:1.50624e-46
Align Title:gi|23307792|gb|AF542069.1| Homo sapiens serum albumin (HSA) mRNA, complete cds
Align Len: 2176
Score: 4352.0 Bits: 3925.42 E-val: 0.0
N.aligns:None Ident:2176 Pos.:2176 Gaps:0 Align len:2176
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTGTGGGC  start: 1  end: 2176
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTGTGGGC  start: 1  end: 2176
Align Title:gi|1519245814|ref|NM_000477.7| Homo sapiens albumin (ALB), mRNA
Align Len: 2285
Score: 4305.0 Bits: 3883.04 E-val: 0.0
N.aligns:None Ident:2168 Pos.:2168 Gaps:1 Align len:2177
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTC-TGTGGGC  start: 1  end: 2176
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTTGTGGGC  start: 9  end: 2185
Align Title:gi|28591|emb|V00495.1| H.sapiens mRNA for serum albumin
Align Len: 2251
Score: 4253.0 Bits: 3836.15 E-val: 0.0
N.aligns:None Ident:2159 Pos.:2159 Gaps:4 Align len:2177
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATC-ACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTGTGGGC  start: 1  end: 2176
Match: |||||||||||||||||||||  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACGC--CTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTAGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAATGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTGGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAGGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAACTGTGAGCTTTTTAAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACAAAATGCTGCACAGAGTCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCTACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTG-TTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTGTGGGC  start: 45  end: 2218
Score: 103.0 Bits: 94.1598 E-val: 1.32244e-15
N.aligns:None Ident:56 Pos.:56 Gaps:2 Align len:58
Strand: (None, None) Frame: (1, -1)
Query: TGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCT  start: 489  end: 546
Match: |||||  |||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TGACA--GAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCT  start: 56  end: 1
Align Title:gi|7770116|gb|AF119840.1|AF119840 Homo sapiens PRO0903 mRNA, complete cds
Align Len: 2720
Score: 4062.0 Bits: 3663.93 E-val: 0.0
N.aligns:None Ident:2043 Pos.:2043 Gaps:0 Align len:2051
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 1  end: 2051
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 649  end: 2699
Align Title:gi|25058738|gb|BC039235.1| Homo sapiens albumin, mRNA (cDNA clone IMAGE:4768004), containing frame-shift errors
Align Len: 2085
Score: 4056.0 Bits: 3658.52 E-val: 0.0
N.aligns:None Ident:2042 Pos.:2042 Gaps:1 Align len:2050
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGT-AAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT  start: 1  end: 2049
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT  start: 7  end: 2056
Align Title:gi|23243417|gb|BC036003.1| Homo sapiens albumin, mRNA (cDNA clone MGC:32850 IMAGE:4724105), complete cds
Align Len: 2087
Score: 4052.0 Bits: 3654.91 E-val: 0.0
N.aligns:None Ident:2041 Pos.:2041 Gaps:0 Align len:2051
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 1  end: 2051
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGTCCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCGAA  start: 9  end: 2059
Align Title:gi|158258946|dbj|AK292755.1| Homo sapiens cDNA FLJ78413 complete cds, highly similar to Homo sapiens albumin, mRNA
Align Len: 2054
Score: 4036.0 Bits: 3640.48 E-val: 0.0
N.aligns:None Ident:2037 Pos.:2037 Gaps:3 Align len:2049
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT  start: 1  end: 2049
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||   |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAA---AATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTTGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT  start: 9  end: 2054
Align Title:gi|28589|emb|V00494.1| Human messenger RNA for serum albumin (HSA)
Align Len: 2055
Score: 4033.0 Bits: 3637.78 E-val: 0.0
N.aligns:None Ident:2036 Pos.:2036 Gaps:0 Align len:2049
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT  start: 1  end: 2049
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGGGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCTTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTGTTAGTTCGTTACACCAAGAAAGTACCCGAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCTGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT  start: 7  end: 2055
Align Title:gi|21706455|gb|BC034023.1| Homo sapiens albumin, mRNA (cDNA clone MGC:22784 IMAGE:4734617), complete cds
Align Len: 2068
Score: 4029.0 Bits: 3634.17 E-val: 0.0
N.aligns:None Ident:2028 Pos.:2028 Gaps:0 Align len:2037
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAA  start: 1  end: 2037
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACGTTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAACAAAAAA  start: 9  end: 2045
Align Title:gi|51476389|emb|CR749331.1| Homo sapiens mRNA; cDNA DKFZp779N1935 (from clone DKFZp779N1935)
Align Len: 2075
Score: 4027.0 Bits: 3632.37 E-val: 0.0
N.aligns:None Ident:2036 Pos.:2036 Gaps:0 Align len:2051
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 1  end: 2051
Match: ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCATACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCCTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGCGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAGAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAGCTGCACTTGTTGAGCTTGTGAAACACAGGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATTACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCCAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 8  end: 2058
Align Title:gi|21706470|gb|BC034026.1| Homo sapiens cDNA clone IMAGE:4734794, containing frame-shift errors
Align Len: 2059
Score: 4010.0 Bits: 3617.04 E-val: 0.0
N.aligns:None Ident:2025 Pos.:2025 Gaps:1 Align len:2037
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAA  start: 1  end: 2037
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  || ||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAA-TTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCTTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAAAAAAAAAAAAA  start: 7  end: 2042
Align Title:gi|194391079|dbj|AK298437.1| Homo sapiens cDNA FLJ54371 complete cds, highly similar to Serum albumin precursor
Align Len: 2082
Score: 3994.0 Bits: 3602.61 E-val: 0.0
N.aligns:None Ident:2040 Pos.:2040 Gaps:27 Align len:2076
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCAC---------------------------ACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT  start: 1  end: 2049
Match: ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||                           |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACTATTTATTTTTTTCTTCCCTTGCCCAGACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGGAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGGATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT  start: 7  end: 2082
Align Title:gi|408407943|gb|AF130077.2| Homo sapiens clone FLB9714 PRO2619 mRNA, complete cds
Align Len: 2560
Score: 3937.0 Bits: 3551.22 E-val: 0.0
N.aligns:None Ident:1982 Pos.:1982 Gaps:0 Align len:1991
Strand: (None, None) Frame: (1, 1)
Query: CTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 61  end: 2051
Match: || || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CTGTTACTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCACGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 477  end: 2467
Align Title:gi|62113340|gb|AY960291.1| Homo sapiens serum albumin mRNA, complete cds
Align Len: 1981
Score: 3907.0 Bits: 3524.17 E-val: 0.0
N.aligns:None Ident:1970 Pos.:1970 Gaps:0 Align len:1981
Strand: (None, None) Frame: (1, 1)
Query: CTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAA  start: 2  end: 1982
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGGGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGGAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTGTCTATCCGTGTTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACGGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAA  start: 1  end: 1981
Align Title:gi|49176516|gb|AY550967.1| Homo sapiens cell growth inhibiting protein 42 mRNA, complete cds
Align Len: 1939
Score: 3848.0 Bits: 3470.97 E-val: 0.0
N.aligns:None Ident:1933 Pos.:1933 Gaps:0 Align len:1939
Strand: (None, None) Frame: (1, 1)
Query: TGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCA  start: 27  end: 1965
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCA  start: 1  end: 1939
Align Title:gi|115607206|gb|DQ986150.1| Homo sapiens serum albumin mRNA, complete cds
Align Len: 1884
Score: 3733.0 Bits: 3367.27 E-val: 0.0
N.aligns:None Ident:1877 Pos.:1877 Gaps:0 Align len:1884
Strand: (None, None) Frame: (1, 1)
Query: CCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGA  start: 23  end: 1906
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGA  start: 1  end: 1884
Align Title:gi|164692402|dbj|AK314794.1| Homo sapiens cDNA, FLJ95666, highly similar to Homo sapiens albumin (ALB), mRNA
Align Len: 1871
Score: 3676.0 Bits: 3315.88 E-val: 0.0
N.aligns:None Ident:1853 Pos.:1853 Gaps:0 Align len:1863
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAA  start: 1  end: 1863
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCCTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTTTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAATAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAA  start: 9  end: 1871
Align Title:gi|52001696|gb|AY728024.1| Homo sapiens serum albumin precursor, mRNA, complete cds
Align Len: 1842
Score: 3630.0 Bits: 3274.4 E-val: 0.0
N.aligns:None Ident:1824 Pos.:1824 Gaps:0 Align len:1830
Strand: (None, None) Frame: (1, 1)
Query: ATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAA  start: 34  end: 1863
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||
Subjc: ATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAA  start: 7  end: 1836
Align Title:gi|123981021|gb|DQ891414.2| Synthetic construct clone IMAGE:100004044; FLH176691.01X; RZPDo839G03122D albumin (ALB) gene, encodes complete protein
Align Len: 1870
Score: 3626.0 Bits: 3270.79 E-val: 0.0
N.aligns:None Ident:1825 Pos.:1825 Gaps:0 Align len:1833
Strand: (None, None) Frame: (1, 1)
Query: CACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATA  start: 30  end: 1862
Match: ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Subjc: CACCATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACGTTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATA  start: 19  end: 1851
Align Title:gi|123995824|gb|DQ894588.2| Synthetic construct Homo sapiens clone IMAGE:100009048; FLH176687.01L; RZPDo839G03121D albumin (ALB) gene, encodes complete protein
Align Len: 1870
Score: 3624.0 Bits: 3268.99 E-val: 0.0
N.aligns:None Ident:1824 Pos.:1824 Gaps:0 Align len:1832
Strand: (None, None) Frame: (1, 1)
Query: CACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTAT  start: 30  end: 1861
Match: ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Subjc: CACCATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACGTTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTAT  start: 19  end: 1850
Align Title:gi|6013426|gb|AF190168.1|AF190168 Homo sapiens serum albumin precursor, mRNA, complete cds
Align Len: 1830
Score: 3615.0 Bits: 3260.88 E-val: 0.0
N.aligns:None Ident:1821 Pos.:1821 Gaps:0 Align len:1830
Strand: (None, None) Frame: (1, 1)
Query: ATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAA  start: 34  end: 1863
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||
Subjc: ATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGTAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACCTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGGAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAA  start: 1  end: 1830
Align Title:gi|332356379|gb|HQ537426.1| Homo sapiens albumin mRNA, partial cds
Align Len: 1758
Score: 3471.0 Bits: 3131.03 E-val: 0.0
N.aligns:None Ident:1749 Pos.:1749 Gaps:0 Align len:1758
Strand: (None, None) Frame: (1, 1)
Query: GATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAA  start: 106  end: 1863
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||
Subjc: GATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCGTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGGGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAGAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAA  start: 1  end: 1758
Align Title:gi|194391111|dbj|AK298461.1| Homo sapiens cDNA FLJ50830 complete cds, highly similar to Serum albumin precursor
Align Len: 1799
Score: 3084.0 Bits: 2782.08 E-val: 0.0
N.aligns:None Ident:1551 Pos.:1551 Gaps:0 Align len:1557
Strand: (None, None) Frame: (1, 1)
Query: AATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT  start: 493  end: 2049
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGGGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCT  start: 243  end: 1799
Score: 472.0 Bits: 426.881 E-val: 4.90655e-116
N.aligns:None Ident:239 Pos.:239 Gaps:0 Align len:241
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAG  start: 1  end: 241
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAG  start: 9  end: 249
Align Title:gi|763428|gb|U22961.1|HSU22961 Human mRNA clone with similarity to L-glycerol-3-phosphate:NAD oxidoreductase and albumin gene sequences
Align Len: 3239
Score: 2748.0 Bits: 2479.12 E-val: 0.0
N.aligns:None Ident:1386 Pos.:1386 Gaps:0 Align len:1394
Strand: (None, None) Frame: (1, 1)
Query: CTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAA  start: 7  end: 1400
Match: ||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGGGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCTTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAA  start: 1846  end: 3239
Align Title:gi|27692692|gb|BC041789.1| Homo sapiens albumin, mRNA (cDNA clone MGC:32888 IMAGE:4766983), complete cds
Align Len: 1510
Score: 2620.0 Bits: 2363.7 E-val: 0.0
N.aligns:None Ident:1327 Pos.:1327 Gaps:1 Align len:1337
Strand: (None, None) Frame: (1, 1)
Query: AAAAATTTGG-AGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 716  end: 2051
Match: ||| |||||| ||||  |  |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Subjc: AAAGATTTGGGAGAAGAAAATTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCGGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCGAA  start: 147  end: 1483
Score: 329.0 Bits: 297.94 E-val: 5.98796e-77
N.aligns:None Ident:166 Pos.:166 Gaps:0 Align len:167
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGC  start: 1  end: 167
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGC  start: 9  end: 175
Align Title:gi|164694201|dbj|AK308044.1| Homo sapiens cDNA, FLJ97992
Align Len: 1544
Score: 2536.0 Bits: 2287.96 E-val: 0.0
N.aligns:None Ident:1279 Pos.:1279 Gaps:1 Align len:1285
Strand: (None, None) Frame: (1, 1)
Query: TGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACC-AAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAA  start: 378  end: 1661
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTTCCCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAA  start: 260  end: 1544
Score: 506.0 Bits: 457.539 E-val: 2.89746e-125
N.aligns:None Ident:256 Pos.:256 Gaps:0 Align len:258
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAA  start: 1  end: 258
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAA  start: 9  end: 266
Align Title:gi|7770216|gb|AF119890.1|AF119890 Homo sapiens PRO2675 mRNA, complete cds
Align Len: 1618
Score: 2488.0 Bits: 2244.68 E-val: 0.0
N.aligns:None Ident:1247 Pos.:1247 Gaps:0 Align len:1249
Strand: (None, None) Frame: (1, 1)
Query: AGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 803  end: 2051
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 350  end: 1598
Align Title:gi|47118014|gb|AY544124.1| Homo sapiens growth-inhibiting protein 20 mRNA, complete cds
Align Len: 1363
Score: 2453.0 Bits: 2213.12 E-val: 0.0
N.aligns:None Ident:1242 Pos.:1242 Gaps:1 Align len:1251
Strand: (None, None) Frame: (1, 1)
Query: AAAAATTTGG-AGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCA  start: 716  end: 1965
Match: ||| |||||| ||||  |  |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AAAGATTTGGGAGAAGAAAATTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCGGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCA  start: 113  end: 1363
Score: 282.0 Bits: 255.561 E-val: 1.83335e-64
N.aligns:None Ident:141 Pos.:141 Gaps:0 Align len:141
Strand: (None, None) Frame: (1, 1)
Query: TGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGC  start: 27  end: 167
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGC  start: 1  end: 141
Align Title:gi|7959790|gb|AF116645.1|AF116645 Homo sapiens PRO1708 mRNA, complete cds
Align Len: 1251
Score: 2003.0 Bits: 1807.36 E-val: 0.0
N.aligns:None Ident:1006 Pos.:1006 Gaps:0 Align len:1009
Strand: (None, None) Frame: (1, 1)
Query: TTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAA  start: 1029  end: 2037
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGCGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAA  start: 234  end: 1242
Align Title:gi|6650825|gb|AF118090.1|AF118090 Homo sapiens PRO2044 mRNA, complete cds
Align Len: 1759
Score: 1983.0 Bits: 1789.33 E-val: 0.0
N.aligns:None Ident:996 Pos.:996 Gaps:0 Align len:999
Strand: (None, None) Frame: (1, 1)
Query: CAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 1053  end: 2051
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 692  end: 1690
Align Title:gi|168745965|emb|CU691683.1| Synthetic construct Homo sapiens gateway clone IMAGE:100022016 3' read mRNA
Align Len: 1128
Score: 1951.0 Bits: 1760.47 E-val: 0.0
N.aligns:None Ident:1034 Pos.:1034 Gaps:9 Align len:1061
Strand: (None, None) Frame: (1, -1)
Query: TGTGCTGATGACAGGGCGGACCTTGCCAAGTATAT-CTGTGAAAATCAAGATT-CGATCTCCAGTAAACT-GAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAAT-CCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAA-GGATGTTTGCAAAAA-CTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAA-AAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATG  start: 862  end: 1915
Match: || |||||  ||||||| ||||||||||||| | | |||  |||||||||||| |||| ||||||||||| |||||||||| |||||||||||  ||||||||||| ||||||||||||| |||||||||||||||||||||| ||||||||  | |||||||||||||||||||||||||||||| ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TGGGCTGAGAACAGGGCCGACCTTGCCAAGTTTTTTCTGGAAAAATCAAGATTTCGATTTCCAGTAAACTAGAAGGAATGC-GTGAAAAACCTTCGTTGGAAAAATTCCCACTGCATTGC-GAAGTGGAAAATGATGAGATGCTTGCTGACTGCCTTTCATTAGCTGCTGATTTTGTTGAAAGTAAAGGATGTTTGCAAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAAGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATG  start: 1075  end: 17
Align Title:gi|168745964|emb|CU691682.1| Synthetic construct Homo sapiens gateway clone IMAGE:100022016 5' read mRNA
Align Len: 1251
Score: 1896.0 Bits: 1710.88 E-val: 0.0
N.aligns:None Ident:1082 Pos.:1082 Gaps:15 Align len:1153
Strand: (None, None) Frame: (1, 1)
Query: ATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAA-TTTGGAGAAAGAGCTTTCAAAGCATGGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGG-AAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTG  start: 34  end: 1184
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||| |||||||||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||  ||||||||||||||||||||||||||| |||||||||||| || |||||||||||||||||||||||||||||||||||| || | ||||| |||||| |||||||||| ||| ||| ||| ||  | || ||| ||||||| ||||||  |||  |||||||||| |||||||  | | ||||||| ||  |||| ||||||   ||||||| ||||| | ||| |||| |||| |||| | |||| | ||||  |  || | ||||  | |||| | ||||| ||| | ||| |||
Subjc: ATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTTGGAGAAAGAGCTTTC-AAGCATGGGCAGTAGCTCGCCTGAGCCAGAGA-TTCCCAAAGCTGAGTTTGCAGAAGTTTCC-AGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCCTGGAGATCTGCTTGAATGTGCTGATGACAAGGCGGACCTTTGCAAGTATATCTGTGAAAATCAAGATTCAATCTCCAGTAAA-TGGAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCCCTTCCTTGCCCAAGTGGAAAAATGATGAAATG-CTGGTGAATTTGCCTCCTTAACTGCTGAATTTGTTTGAAGATAGGATGTTTG-AAAAACTTAGTTCAGGCAAAAGAGTTCTT-CTGGGCGATTTTTTGT-TGAATTTCCAA-AAGGGATCCGGATT-CCCTGTGGGGCTGGGGGGGA-ATTTGC--AAACATTTTAAACCTCTCCAAAGAGGTG  start: 17  end: 1156
Align Title:gi|23241674|gb|BC035969.1| Homo sapiens albumin, mRNA (cDNA clone MGC:32581 IMAGE:4714468), complete cds
Align Len: 1449
Score: 1767.0 Bits: 1594.56 E-val: 0.0
N.aligns:None Ident:888 Pos.:888 Gaps:0 Align len:891
Strand: (None, None) Frame: (1, 1)
Query: ATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 1161  end: 2051
Match: |||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: ATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 530  end: 1420
Score: 1048.0 Bits: 946.252 E-val: 0.0
N.aligns:None Ident:527 Pos.:527 Gaps:0 Align len:529
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAA  start: 1  end: 529
Match: ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAA  start: 9  end: 537
Align Title:gi|15679995|gb|BC014308.1|BC014308 Homo sapiens, clone IMAGE:3934797, mRNA, partial cds
Align Len: 823
Score: 1571.0 Bits: 1417.83 E-val: 0.0
N.aligns:None Ident:790 Pos.:790 Gaps:0 Align len:793
Strand: (None, None) Frame: (1, 1)
Query: AGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 1259  end: 2051
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Subjc: AGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCCAA  start: 4  end: 796
Align Title:gi|649152310|gb|KJ905683.1| Synthetic construct Homo sapiens clone ccsbBroadEn_15353 ALB gene, encodes complete protein
Align Len: 1320
Score: 1387.0 Bits: 1251.92 E-val: 0.0
N.aligns:None Ident:698 Pos.:698 Gaps:0 Align len:701
Strand: (None, None) Frame: (1, 1)
Query: ATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTAT  start: 1161  end: 1861
Match: |||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Subjc: ATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTGTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTAT  start: 554  end: 1254
Score: 987.0 Bits: 891.249 E-val: 0.0
N.aligns:None Ident:495 Pos.:495 Gaps:0 Align len:496
Strand: (None, None) Frame: (1, 1)
Query: ATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAA  start: 34  end: 529
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: ATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAA  start: 66  end: 561
Align Title:gi|168740012|emb|CU690239.1| Synthetic construct Homo sapiens gateway clone IMAGE:100022252 3' read ALB mRNA
Align Len: 1356
Score: 1182.0 Bits: 1067.08 E-val: 0.0
N.aligns:None Ident:647 Pos.:647 Gaps:12 Align len:670
Strand: (None, None) Frame: (1, -1)
Query: CATGAATG-CTAT--GCCAAA-GTGTT-CGATG-AATTTAAA-CCTCTTGTGG-AAGAGCCTCAG-AATTTAAT-CAAACAAAATT-GTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATA  start: 1204  end: 1862
Match: |||||||| |||   |||||| ||||| ||||| |||||||| ||| |||||| ||||||||||| |||||||| ||||||||||| ||||||||||||  ||||||||||||||||| | |||||||||||||| ||||||| |||||  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Subjc: CATGAATGACTAATGGCCAAAAGTGTTTCGATGGAATTTAAAACCTTTTGTGGTAAGAGCCTCAGGAATTTAATTCAAACAAAATTTGTGAGCTTTTTGGCCAGCTTGGAGAGTACAATTCCCAGAATGCGCTATAAGTTCGT-ACACCCTGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAACTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATA  start: 685  end: 17
Align Title:gi|37181745|gb|AY358313.1| Homo sapiens DNA66677 ALB (UNQ696) mRNA, partial cds
Align Len: 524
Score: 1018.0 Bits: 919.201 E-val: 0.0
N.aligns:None Ident:517 Pos.:517 Gaps:0 Align len:523
Strand: (None, None) Frame: (1, 1)
Query: AACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCC  start: 12  end: 534
Match: |||||||   || || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AACCCCANANGCTTTGGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAATTGCC  start: 2  end: 524
Align Title:gi|168740011|emb|CU690238.1| Synthetic construct Homo sapiens gateway clone IMAGE:100022252 5' read ALB mRNA
Align Len: 1442
Score: 982.0 Bits: 886.74 E-val: 0.0
N.aligns:None Ident:494 Pos.:494 Gaps:0 Align len:496
Strand: (None, None) Frame: (1, 1)
Query: ATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTAGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATACTTATATGAAA  start: 34  end: 529
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||
Subjc: ATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTTGGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTTCATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACCTTTTTGAAAAAATACTTATATGAAA  start: 17  end: 512
Score: 143.0 Bits: 130.227 E-val: 1.83659e-26
N.aligns:None Ident:122 Pos.:122 Gaps:13 Align len:145
Strand: (None, None) Frame: (1, 1)
Query: ATATAAAACCACTCTAGAGAA-GTGCTGTGCC-GCTGCAGATCCTCATGAATGCTA-TGCCAAAGTGTTCGATGAATTTAAACC--TCTTGTGGAA-GAGCCTCAGAA--TTTAATCAAAC---AAAATTG-TGAG-CTTTTTGA  start: 1161  end: 1292
Match: |||| |||||||||||||||| |||||||||| ||||||||||||||||||||||| || || ||||| |||||||| ||||||   |||| |||| ||||||||| |  |||||||||||   | | ||| |||| ||||||||
Subjc: ATATGAAACCACTCTAGAGAAAGTGCTGTGCCCGCTGCAGATCCTCATGAATGCTATTGACATAGTGTACGATGAATCTAAACCCTCCTTGGGGAATGAGCCTCAGTACTTTTAATCAAACTCAACACTTGTTGAGCCTTTTTGA  start: 505  end: 649
Align Title:gi|6642751|gb|AF113014.1|AF113014 Homo sapiens clone FLB3512 mRNA sequence
Align Len: 1476
Score: 618.0 Bits: 558.527 E-val: 1.15187e-155
N.aligns:None Ident:312 Pos.:312 Gaps:0 Align len:314
Strand: (None, None) Frame: (1, 1)
Query: AAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 1738  end: 2051
Match: ||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AAAGCTGCTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 1153  end: 1466
Align Title:gi|219842221|ref|NG_009291.1| Homo sapiens albumin (ALB), RefSeqGene on chromosome 4
Align Len: 24158
Score: 581.0 Bits: 525.165 E-val: 2.37628e-145
N.aligns:None Ident:294 Pos.:294 Gaps:1 Align len:295
Strand: (None, None) Frame: (1, 1)
Query: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTC-TGTGGGC  start: 1883  end: 2176
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Subjc: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTTGTGGGC  start: 21834  end: 22128
Score: 449.0 Bits: 406.143 E-val: 1.60396e-109
N.aligns:None Ident:226 Pos.:226 Gaps:0 Align len:227
Strand: (None, None) Frame: (1, 1)
Query: TATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAAC  start: 1459  end: 1685
Match: || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TAGCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAAC  start: 18831  end: 19057
Score: 436.0 Bits: 394.421 E-val: 2.90002e-106
N.aligns:None Ident:218 Pos.:218 Gaps:0 Align len:218
Strand: (None, None) Frame: (1, 1)
Query: GGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGT  start: 876  end: 1093
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGT  start: 14165  end: 14382
Score: 425.0 Bits: 384.502 E-val: 5.24337e-103
N.aligns:None Ident:214 Pos.:214 Gaps:0 Align len:215
Strand: (None, None) Frame: (1, 1)
Query: CATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATA  start: 304  end: 518
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Subjc: CATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAGTA  start: 9340  end: 9554
Score: 278.0 Bits: 251.955 E-val: 2.23348e-63
N.aligns:None Ident:139 Pos.:139 Gaps:0 Align len:139
Strand: (None, None) Frame: (1, 1)
Query: GCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTAT  start: 1323  end: 1461
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTAT  start: 18277  end: 18415
Score: 264.0 Bits: 239.331 E-val: 1.40948e-59
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:132
Strand: (None, None) Frame: (1, 1)
Query: GTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTT  start: 172  end: 303
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTT  start: 7376  end: 7507
Score: 264.0 Bits: 239.331 E-val: 1.40948e-59
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:132
Strand: (None, None) Frame: (1, 1)
Query: GGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGG  start: 746  end: 877
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGG  start: 12741  end: 12872
Score: 264.0 Bits: 239.331 E-val: 1.40948e-59
N.aligns:None Ident:138 Pos.:138 Gaps:0 Align len:142
Strand: (None, None) Frame: (1, 1)
Query: AAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGG  start: 1678  end: 1819
Match: ||||  | ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AAACTCAGTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGG  start: 20245  end: 20386
Score: 261.0 Bits: 236.626 E-val: 1.7171e-58
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:133
Strand: (None, None) Frame: (1, 1)
Query: GTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTG  start: 1092  end: 1224
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTG  start: 15781  end: 15913
Score: 256.0 Bits: 232.118 E-val: 2.09185e-57
N.aligns:None Ident:131 Pos.:131 Gaps:0 Align len:133
Strand: (None, None) Frame: (1, 1)
Query: ATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAG  start: 516  end: 648
Match: |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
Subjc: ATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAG  start: 10101  end: 10233
Score: 221.0 Bits: 200.559 E-val: 1.23639e-47
N.aligns:None Ident:115 Pos.:115 Gaps:0 Align len:118
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGA  start: 1  end: 118
Match: ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  ||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACGTAAGA  start: 5041  end: 5158
Score: 200.0 Bits: 181.623 E-val: 3.3177e-42
N.aligns:None Ident:100 Pos.:100 Gaps:0 Align len:100
Strand: (None, None) Frame: (1, 1)
Query: GTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCG  start: 1224  end: 1323
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCG  start: 17001  end: 17100
Score: 197.0 Bits: 178.918 E-val: 4.04179e-41
N.aligns:None Ident:100 Pos.:100 Gaps:0 Align len:101
Strand: (None, None) Frame: (1, 1)
Query: AGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGG  start: 647  end: 747
Match: ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGG  start: 11056  end: 11156
Score: 135.0 Bits: 123.014 E-val: 2.72574e-24
N.aligns:None Ident:69 Pos.:69 Gaps:0 Align len:70
Strand: (None, None) Frame: (1, 1)
Query: AGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAG  start: 1817  end: 1886
Match: ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Subjc: AGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAG  start: 20998  end: 21067
Score: 117.0 Bits: 106.783 E-val: 2.09555e-19
N.aligns:None Ident:60 Pos.:60 Gaps:0 Align len:61
Strand: (None, None) Frame: (1, 1)
Query: CACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTT  start: 110  end: 170
Match: || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CAGACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTT  start: 5859  end: 5919
Align Title:gi|152112963|gb|EF649953.1| Homo sapiens albumin (ALB) gene, complete cds
Align Len: 21070
Score: 581.0 Bits: 525.165 E-val: 2.37628e-145
N.aligns:None Ident:294 Pos.:294 Gaps:1 Align len:295
Strand: (None, None) Frame: (1, 1)
Query: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTC-TGTGGGC  start: 1883  end: 2176
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Subjc: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTTGTGGGC  start: 18784  end: 19078
Score: 449.0 Bits: 406.143 E-val: 1.60396e-109
N.aligns:None Ident:226 Pos.:226 Gaps:0 Align len:227
Strand: (None, None) Frame: (1, 1)
Query: TATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAAC  start: 1459  end: 1685
Match: || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TAGCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAAC  start: 15781  end: 16007
Score: 436.0 Bits: 394.421 E-val: 2.90002e-106
N.aligns:None Ident:218 Pos.:218 Gaps:0 Align len:218
Strand: (None, None) Frame: (1, 1)
Query: GGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGT  start: 876  end: 1093
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGT  start: 11115  end: 11332
Score: 425.0 Bits: 384.502 E-val: 5.24337e-103
N.aligns:None Ident:214 Pos.:214 Gaps:0 Align len:215
Strand: (None, None) Frame: (1, 1)
Query: CATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATA  start: 304  end: 518
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Subjc: CATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAGTA  start: 6290  end: 6504
Score: 278.0 Bits: 251.955 E-val: 2.23348e-63
N.aligns:None Ident:139 Pos.:139 Gaps:0 Align len:139
Strand: (None, None) Frame: (1, 1)
Query: GCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTAT  start: 1323  end: 1461
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTAT  start: 15227  end: 15365
Score: 264.0 Bits: 239.331 E-val: 1.40948e-59
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:132
Strand: (None, None) Frame: (1, 1)
Query: GTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTT  start: 172  end: 303
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTT  start: 4326  end: 4457
Score: 264.0 Bits: 239.331 E-val: 1.40948e-59
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:132
Strand: (None, None) Frame: (1, 1)
Query: GGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGG  start: 746  end: 877
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGG  start: 9691  end: 9822
Score: 264.0 Bits: 239.331 E-val: 1.40948e-59
N.aligns:None Ident:138 Pos.:138 Gaps:0 Align len:142
Strand: (None, None) Frame: (1, 1)
Query: AAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGG  start: 1678  end: 1819
Match: ||||  | ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AAACTCAGTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGG  start: 17195  end: 17336
Score: 261.0 Bits: 236.626 E-val: 1.7171e-58
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:133
Strand: (None, None) Frame: (1, 1)
Query: GTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTG  start: 1092  end: 1224
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTG  start: 12731  end: 12863
Score: 256.0 Bits: 232.118 E-val: 2.09185e-57
N.aligns:None Ident:131 Pos.:131 Gaps:0 Align len:133
Strand: (None, None) Frame: (1, 1)
Query: ATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAG  start: 516  end: 648
Match: |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
Subjc: ATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAG  start: 7051  end: 7183
Score: 221.0 Bits: 200.559 E-val: 1.23639e-47
N.aligns:None Ident:115 Pos.:115 Gaps:0 Align len:118
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGA  start: 1  end: 118
Match: ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  ||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACGTAAGA  start: 1991  end: 2108
Score: 200.0 Bits: 181.623 E-val: 3.3177e-42
N.aligns:None Ident:100 Pos.:100 Gaps:0 Align len:100
Strand: (None, None) Frame: (1, 1)
Query: GTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCG  start: 1224  end: 1323
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCG  start: 13951  end: 14050
Score: 197.0 Bits: 178.918 E-val: 4.04179e-41
N.aligns:None Ident:100 Pos.:100 Gaps:0 Align len:101
Strand: (None, None) Frame: (1, 1)
Query: AGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGG  start: 647  end: 747
Match: ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGG  start: 8006  end: 8106
Score: 135.0 Bits: 123.014 E-val: 2.72574e-24
N.aligns:None Ident:69 Pos.:69 Gaps:0 Align len:70
Strand: (None, None) Frame: (1, 1)
Query: AGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAG  start: 1817  end: 1886
Match: ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Subjc: AGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAG  start: 17948  end: 18017
Score: 117.0 Bits: 106.783 E-val: 2.09555e-19
N.aligns:None Ident:60 Pos.:60 Gaps:0 Align len:61
Strand: (None, None) Frame: (1, 1)
Query: CACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTT  start: 110  end: 170
Match: || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CAGACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTT  start: 2809  end: 2869
Align Title:gi|19387810|gb|AC108157.3| Homo sapiens BAC clone RP11-580P21 from 4, complete sequence
Align Len: 167001
Score: 581.0 Bits: 525.165 E-val: 2.37628e-145
N.aligns:None Ident:294 Pos.:294 Gaps:1 Align len:295
Strand: (None, None) Frame: (1, 1)
Query: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTC-TGTGGGC  start: 1883  end: 2176
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Subjc: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTTGTGGGC  start: 86936  end: 87230
Score: 449.0 Bits: 406.143 E-val: 1.60396e-109
N.aligns:None Ident:226 Pos.:226 Gaps:0 Align len:227
Strand: (None, None) Frame: (1, 1)
Query: TATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAAC  start: 1459  end: 1685
Match: || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TAGCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAAC  start: 83933  end: 84159
Score: 436.0 Bits: 394.421 E-val: 2.90002e-106
N.aligns:None Ident:218 Pos.:218 Gaps:0 Align len:218
Strand: (None, None) Frame: (1, 1)
Query: GGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGT  start: 876  end: 1093
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGT  start: 79267  end: 79484
Score: 425.0 Bits: 384.502 E-val: 5.24337e-103
N.aligns:None Ident:214 Pos.:214 Gaps:0 Align len:215
Strand: (None, None) Frame: (1, 1)
Query: CATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATA  start: 304  end: 518
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Subjc: CATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAGTA  start: 74442  end: 74656
Score: 278.0 Bits: 251.955 E-val: 2.23348e-63
N.aligns:None Ident:139 Pos.:139 Gaps:0 Align len:139
Strand: (None, None) Frame: (1, 1)
Query: GCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTAT  start: 1323  end: 1461
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTAT  start: 83379  end: 83517
Score: 264.0 Bits: 239.331 E-val: 1.40948e-59
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:132
Strand: (None, None) Frame: (1, 1)
Query: GTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTT  start: 172  end: 303
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTT  start: 72478  end: 72609
Score: 264.0 Bits: 239.331 E-val: 1.40948e-59
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:132
Strand: (None, None) Frame: (1, 1)
Query: GGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGG  start: 746  end: 877
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGG  start: 77843  end: 77974
Score: 264.0 Bits: 239.331 E-val: 1.40948e-59
N.aligns:None Ident:138 Pos.:138 Gaps:0 Align len:142
Strand: (None, None) Frame: (1, 1)
Query: AAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGG  start: 1678  end: 1819
Match: ||||  | ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AAACTCAGTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGG  start: 85347  end: 85488
Score: 261.0 Bits: 236.626 E-val: 1.7171e-58
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:133
Strand: (None, None) Frame: (1, 1)
Query: GTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTG  start: 1092  end: 1224
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTG  start: 80883  end: 81015
Score: 256.0 Bits: 232.118 E-val: 2.09185e-57
N.aligns:None Ident:131 Pos.:131 Gaps:0 Align len:133
Strand: (None, None) Frame: (1, 1)
Query: ATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAG  start: 516  end: 648
Match: |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
Subjc: ATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAG  start: 75203  end: 75335
Score: 221.0 Bits: 200.559 E-val: 1.23639e-47
N.aligns:None Ident:115 Pos.:115 Gaps:0 Align len:118
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGA  start: 1  end: 118
Match: ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  ||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACGTAAGA  start: 70143  end: 70260
Score: 200.0 Bits: 181.623 E-val: 3.3177e-42
N.aligns:None Ident:100 Pos.:100 Gaps:0 Align len:100
Strand: (None, None) Frame: (1, 1)
Query: GTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCG  start: 1224  end: 1323
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCG  start: 82103  end: 82202
Score: 197.0 Bits: 178.918 E-val: 4.04179e-41
N.aligns:None Ident:100 Pos.:100 Gaps:0 Align len:101
Strand: (None, None) Frame: (1, 1)
Query: AGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGG  start: 647  end: 747
Match: ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGG  start: 76158  end: 76258
Score: 135.0 Bits: 123.014 E-val: 2.72574e-24
N.aligns:None Ident:69 Pos.:69 Gaps:0 Align len:70
Strand: (None, None) Frame: (1, 1)
Query: AGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAG  start: 1817  end: 1886
Match: ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Subjc: AGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAG  start: 86100  end: 86169
Score: 117.0 Bits: 106.783 E-val: 2.09555e-19
N.aligns:None Ident:60 Pos.:60 Gaps:0 Align len:61
Strand: (None, None) Frame: (1, 1)
Query: CACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTT  start: 110  end: 170
Match: || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CAGACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTT  start: 70961  end: 71021
Score: 60.0 Bits: 55.3874 E-val: 0.000332357
N.aligns:None Ident:45 Pos.:45 Gaps:0 Align len:55
Strand: (None, None) Frame: (1, 1)
Query: ATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAA  start: 893  end: 947
Match: |||| |||  ||| |||||||| |||||||| ||| | || || |||||||||||
Subjc: ATATTTGTTCAAAACAAGATTCTATCTCCAGCAAAATCAAAGAGTGCTGTGAAAA  start: 157736  end: 157790
Align Title:gi|178343|gb|M12523.1|HUMALBGC Human serum albumin (ALB) gene, complete cds
Align Len: 19002
Score: 581.0 Bits: 525.165 E-val: 2.37628e-145
N.aligns:None Ident:294 Pos.:294 Gaps:1 Align len:295
Strand: (None, None) Frame: (1, 1)
Query: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTC-TGTGGGC  start: 1883  end: 2176
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Subjc: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTTGTGGGC  start: 18522  end: 18816
Score: 449.0 Bits: 406.143 E-val: 1.60396e-109
N.aligns:None Ident:226 Pos.:226 Gaps:0 Align len:227
Strand: (None, None) Frame: (1, 1)
Query: TATCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAAC  start: 1459  end: 1685
Match: || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TAGCTATCCGTGGTCCTGAACCAGTTATGTGTGTTGCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGCACACTTTCTGAGAAGGAGAGACAAATCAAGAAACAAAC  start: 15531  end: 15757
Score: 436.0 Bits: 394.421 E-val: 2.90002e-106
N.aligns:None Ident:218 Pos.:218 Gaps:0 Align len:218
Strand: (None, None) Frame: (1, 1)
Query: GGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGT  start: 876  end: 1093
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGCGGACCTTGCCAAGTATATCTGTGAAAATCAAGATTCGATCTCCAGTAAACTGAAGGAATGCTGTGAAAAACCTCTGTTGGAAAAATCCCACTGCATTGCCGAAGTGGAAAATGATGAGATGCCTGCTGACTTGCCTTCATTAGCTGCTGATTTTGTTGAAAGTAAGGATGTTTGCAAAAACTATGCTGAGGCAAAGGATGTCTTCCTGGGCATGT  start: 10866  end: 11083
Score: 425.0 Bits: 384.502 E-val: 5.24337e-103
N.aligns:None Ident:214 Pos.:214 Gaps:0 Align len:215
Strand: (None, None) Frame: (1, 1)
Query: CATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAATA  start: 304  end: 518
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Subjc: CATACCCTTTTTGGAGACAAATTATGCACAGTTGCAACTCTTCGTGAAACCTATGGTGAAATGGCTGACTGCTGTGCAAAACAAGAACCTGAGAGAAATGAATGCTTCTTGCAACACAAAGATGACAACCCAAACCTCCCCCGATTGGTGAGACCAGAGGTTGATGTGATGTGCACTGCTTTTCATGACAATGAAGAGACATTTTTGAAAAAGTA  start: 6041  end: 6255
Score: 278.0 Bits: 251.955 E-val: 2.23348e-63
N.aligns:None Ident:139 Pos.:139 Gaps:0 Align len:139
Strand: (None, None) Frame: (1, 1)
Query: GCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTAT  start: 1323  end: 1461
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GCTATTAGTTCGTTACACCAAGAAAGTACCCCAAGTGTCAACTCCAACTCTTGTAGAGGTCTCAAGAAACCTAGGAAAAGTGGGCAGCAAATGTTGTAAACATCCTGAAGCAAAAAGAATGCCCTGTGCAGAAGACTAT  start: 14977  end: 15115
Score: 264.0 Bits: 239.331 E-val: 1.40948e-59
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:132
Strand: (None, None) Frame: (1, 1)
Query: GTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTT  start: 172  end: 303
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATCATGTAAAATTAGTGAATGAAGTAACTGAATTTGCAAAAACATGTGTTGCTGATGAGTCAGCTGAAAATTGTGACAAATCACTT  start: 4077  end: 4208
Score: 264.0 Bits: 239.331 E-val: 1.40948e-59
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:132
Strand: (None, None) Frame: (1, 1)
Query: GGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGG  start: 746  end: 877
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGGCAGTAGCTCGCCTGAGCCAGAGATTTCCCAAAGCTGAGTTTGCAGAAGTTTCCAAGTTAGTGACAGATCTTACCAAAGTCCACACGGAATGCTGCCATGGAGATCTGCTTGAATGTGCTGATGACAGGG  start: 9443  end: 9574
Score: 264.0 Bits: 239.331 E-val: 1.40948e-59
N.aligns:None Ident:138 Pos.:138 Gaps:0 Align len:142
Strand: (None, None) Frame: (1, 1)
Query: AAACAAACTGCACTTGTTGAGCTTGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGG  start: 1678  end: 1819
Match: ||||  | ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AAACTCAGTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTCGCAGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGG  start: 16933  end: 17074
Score: 261.0 Bits: 236.626 E-val: 1.7171e-58
N.aligns:None Ident:132 Pos.:132 Gaps:0 Align len:133
Strand: (None, None) Frame: (1, 1)
Query: GTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATAAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTG  start: 1092  end: 1224
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTTTTTGTATGAATATGCAAGAAGGCATCCTGATTACTCTGTCGTGCTGCTGCTGAGACTTGCCAAGACATATGAAACCACTCTAGAGAAGTGCTGTGCCGCTGCAGATCCTCATGAATGCTATGCCAAAGTG  start: 12481  end: 12613
Score: 256.0 Bits: 232.118 E-val: 2.09185e-57
N.aligns:None Ident:131 Pos.:131 Gaps:0 Align len:133
Strand: (None, None) Frame: (1, 1)
Query: ATACTTATATGAAATTGCCAGAAGACATCCTTACTTCTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAGGCTGCCTGCCTGTTGCCAAAG  start: 516  end: 648
Match: |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
Subjc: ATACTTATATGAAATTGCCAGAAGACATCCTTACTTTTATGCCCCGGAACTCCTTTTCTTTGCTAAAAGGTATAAAGCTGCTTTTACAGAATGTTGCCAAGCTGCTGATAAAGCTGCCTGCCTGTTGCCAAAG  start: 6802  end: 6934
Score: 221.0 Bits: 200.559 E-val: 1.23639e-47
N.aligns:None Ident:115 Pos.:115 Gaps:0 Align len:118
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGA  start: 1  end: 118
Match: ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  ||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACGTAAGA  start: 1743  end: 1860
Score: 200.0 Bits: 181.623 E-val: 3.3177e-42
N.aligns:None Ident:100 Pos.:100 Gaps:0 Align len:100
Strand: (None, None) Frame: (1, 1)
Query: GTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCG  start: 1224  end: 1323
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GTTCGATGAATTTAAACCTCTTGTGGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCG  start: 13701  end: 13800
Score: 197.0 Bits: 178.918 E-val: 4.04179e-41
N.aligns:None Ident:100 Pos.:100 Gaps:0 Align len:101
Strand: (None, None) Frame: (1, 1)
Query: AGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGGCTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGG  start: 647  end: 747
Match: ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AGCTCGATGAACTTCGGGATGAAGGGAAGGCTTCGTCTGCCAAACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGAGAAAGAGCTTTCAAAGCATGG  start: 7757  end: 7857
Score: 135.0 Bits: 123.014 E-val: 2.72574e-24
N.aligns:None Ident:69 Pos.:69 Gaps:0 Align len:70
Strand: (None, None) Frame: (1, 1)
Query: AGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAG  start: 1817  end: 1886
Match: ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Subjc: AGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAG  start: 17686  end: 17755
Score: 117.0 Bits: 106.783 E-val: 2.09555e-19
N.aligns:None Ident:60 Pos.:60 Gaps:0 Align len:61
Strand: (None, None) Frame: (1, 1)
Query: CACACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTT  start: 110  end: 170
Match: || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: CAGACAAGAGTGAGGTTGCTCATCGGTTTAAAGATTTGGGAGAAGAAAATTTCAAAGCCTT  start: 2561  end: 2621
Align Title:gi|1036032687|gb|AH007061.2| Homo sapiens chromosome 4 serum albumin (ALB) gene, partial cds; and serum albumin-alphafetoprotein intergenic spacer, partial sequence
Align Len: 523
Score: 579.0 Bits: 523.362 E-val: 8.29405e-145
N.aligns:None Ident:293 Pos.:293 Gaps:1 Align len:294
Strand: (None, None) Frame: (1, 1)
Query: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTGTGGGC  start: 1883  end: 2176
Match: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: TCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTT-CTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTGTGGGC  start: 4  end: 296
Align Title:gi|408407822|gb|AF116616.2| Homo sapiens PRO0998 mRNA, complete cds
Align Len: 1649
Score: 577.0 Bits: 521.558 E-val: 2.89491e-144
N.aligns:None Ident:290 Pos.:290 Gaps:0 Align len:291
Strand: (None, None) Frame: (1, -1)
Query: AGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCGAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 1761  end: 2051
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AGCTTTTGTAGAGAAGTGCTGCAAGGCTGACGATAAGGAGACCTGCTTTGCCGAGGAGGGTAAAAAACTTGTTGCTGCAAGTCAAGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 317  end: 27
Align Title:gi|338858118|gb|AH002596.2|SEG_HUMALB Homo sapiens albumin (ALB) gene, partial cds
Align Len: 1863
Score: 573.0 Bits: 517.951 E-val: 3.52672e-143
N.aligns:None Ident:290 Pos.:290 Gaps:1 Align len:291
Strand: (None, None) Frame: (1, 1)
Query: CCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTC-TGTGGGC  start: 1887  end: 2176
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Subjc: CCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGCTATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTTCGGTAGAGGATTTCTAGTTTCTTGTGGGC  start: 1387  end: 1677
Score: 221.0 Bits: 200.559 E-val: 1.23639e-47
N.aligns:None Ident:115 Pos.:115 Gaps:0 Align len:118
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGA  start: 1  end: 118
Match: ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  ||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACGTAAGA  start: 1059  end: 1176
Align Title:gi|1122817323|gb|DQ145726.2| Homo sapiens ARNT-interacting protein 2 (AINP2) mRNA, complete cds
Align Len: 1054
Score: 404.0 Bits: 365.567 E-val: 1.40699e-97
N.aligns:None Ident:205 Pos.:205 Gaps:0 Align len:207
Strand: (None, None) Frame: (1, 1)
Query: AGCTGCCTTAGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 1845  end: 2051
Match: ||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AGCTGCCTTTGGCTTATAACATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGATCAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGCCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGGAAAGAATCTAA  start: 836  end: 1042
Align Title:gi|32428|emb|X51365.1| Homo sapiens mRNA for albumin (clone pHA19)
Align Len: 117
Score: 232.0 Bits: 210.477 E-val: 6.8383e-51
N.aligns:None Ident:116 Pos.:116 Gaps:0 Align len:116
Strand: (None, None) Frame: (1, 1)
Query: AGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGG  start: 1925  end: 2040
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: AGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTAAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAAAAATGG  start: 2  end: 117
Align Title:gi|1338686512|ref|NG_056261.1| Homo sapiens albumin (ALB) 5' regulatory region (LOC111832671) on chromosome 4
Align Len: 6858
Score: 221.0 Bits: 200.559 E-val: 1.23639e-47
N.aligns:None Ident:115 Pos.:115 Gaps:0 Align len:118
Strand: (None, None) Frame: (1, 1)
Query: TCTCTTCTGTCAACCCCACGCGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACACAAGA  start: 1  end: 118
Match: ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  ||||
Subjc: TCTCTTCTGTCAACCCCACACGCCTTTGGCACAATGAAGTGGGTAACCTTTATTTCCCTTCTTTTTCTCTTTAGCTCGGCTTATTCCAGGGGTGTGTTTCGTCGAGATGCACGTAAGA  start: 6711  end: 6828
Align Title:gi|7959920|gb|AF116711.1|AF116711 Homo sapiens PRO2646 mRNA, complete cds
Align Len: 1160
Score: 216.0 Bits: 196.05 E-val: 1.50624e-46
N.aligns:None Ident:108 Pos.:108 Gaps:0 Align len:108
Strand: (None, None) Frame: (1, -1)
Query: GGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCA  start: 1248  end: 1355
Match: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Subjc: GGAAGAGCCTCAGAATTTAATCAAACAAAATTGTGAGCTTTTTGAGCAGCTTGGAGAGTACAAATTCCAGAATGCGCTATTAGTTCGTTACACCAAGAAAGTACCCCA  start: 274  end: 167

Example: Let’s align the first 100 bases of the first 5 entries of the file contigs82.fasta to the Malus Domestica genome, writing the results to a apple_first5.xml file. Sample output is here: apple_first5.xml. NOTE: this can take several minutes.

from Bio.Blast import NCBIWWW
from Bio import SeqIO

rc = SeqIO.parse("file_samples/contigs82.fasta", format="fasta")
fasta_string = ""
ids2align =[]
for i in range(5):
    entry = next(rc)
    fasta_string +=">" + entry.id +"\n"+entry.seq +"\n"
    ids2align.append(entry.id)
print("Aligning the following {} entries:\n\t{}".format(
                                                    len(ids2align),
                                                    "\n\t".join(ids2align)
                                                    ))
result_handle = NCBIWWW.qblast("blastn", "nt",
                               fasta_string,
                               entrez_query='"Malus Domestica" [Organism]'
                              )

with open("file_samples/blast_res_apple.xml","w") as out_f:
    out_f.write(result_handle.read())
print("Output written to \"blast_res_apple.xml\"")

Aligning the following 5 entries:
        MDC020656.85
        MDC001115.177
        MDC013284.379
        MDC018185.243
        MDC018185.241
Output written to "blast_res_apple.xml"

Getting data from NCBI

Biopython provides a module (Bio.Entrez) to pull data off resources like PubMed or GenBank, and other repositories programmatically through Entrez.

There are some limitations (mostly taken care directly by Biopython) that you should be aware of when you use NCBI’s services (e.g. they recommend not to run more than 3 requests per second on weekdays, …). Check here if you want to learn what these limitations are.

First of all we need to import the Entrez module with (from Bio import Entrez) and then we can start interacting with Entrez, then we should specify (optional) an email setting Entrez.email (this is optional but you get a warning if you do not specify it – the email would be used to notify the user in case of excessive usage).

In particular the module (complete info on Entrez module are here) provides, among the others, the following functions:

1. res_handle = Entrez.einfo(db) returns a summary of the Entez databases as a results handle. db is an optional parameter specifying the resource of interest;
2. res_handle = Entrez.esearch(db, term,id) returns all the entries in db having query matching the term term. It is also possible to specify an id to get the information relative to that resource id;
3. res_handle = Entrez.efetch(db, id, rettype, retmode) returns full record corresponding to the identifier id from the database db formatted in rettype (eg. gb, fasta,… complete list) and return mode retmode (eg. text);
4. res_handle = Entrez.esummary(db, id) returns the summary of the entry id from the database db as a handle;
5. result = Entrez.read(res_handle) reads the information on the XML handle res_handle and stores them in a dictionary, list or string, depending on the case.

Example:

Let’s get a list of all available databases in Entrez as a dictionary. Let’s then get a summary of the entries in ‘sra’.

from Bio import Entrez
import datetime


Entrez.email = "my_email"
handle = Entrez.einfo()
res = Entrez.read(handle)
#print(res)
print("")
print("As a list:")
print(res['DbList'])

res = Entrez.read(Entrez.einfo(db = "sra"))
#uncomment to see all the information captured
#print(res)
#for el in res["DbInfo"].keys():
#    print(el)
date = res["DbInfo"]["LastUpdate"]
dt = datetime.datetime.strptime(date, "%Y/%m/%d %H:%M")
print("")
print("Entries count: {:,}".format(int(res["DbInfo"]["Count"])))
print("LastUpdate: {}/{}/{} {}:{}".format(dt.day,
                                          dt.month,
                                          dt.year,
                                          dt.hour,
                                          dt.minute))
print("Description:", res["DbInfo"]["Description"])

As a list:
['pubmed', 'protein', 'nuccore', 'ipg', 'nucleotide', 'structure', 'sparcle', 'genome', 'annotinfo', 'assembly', 'bioproject', 'biosample', 'blastdbinfo', 'books', 'cdd', 'clinvar', 'gap', 'gapplus', 'grasp', 'dbvar', 'gene', 'gds', 'geoprofiles', 'homologene', 'medgen', 'mesh', 'ncbisearch', 'nlmcatalog', 'omim', 'orgtrack', 'pmc', 'popset', 'probe', 'proteinclusters', 'pcassay', 'biosystems', 'pccompound', 'pcsubstance', 'seqannot', 'snp', 'sra', 'taxonomy', 'biocollections', 'gtr']

Entries count: 9,274,756
LastUpdate: 28/10/2019 11:54
Description: SRA Database

Note that effectively einfo returned a handler to an object that can be read by the read function that produces a dictionary. This dictionary had one key only “DbList” that is the list of available databases in the first case, while the key when db was specified is “DbInfo”.

Example: Fetch the first three entries (retmax = 3) in pubmed that are related to the species “Malus Domestica” and report the title of the publication.

from Bio import Entrez

Entrez.email = "my_email"
handle = Entrez.esearch(db="pubmed", term="Malus Domestica", retmax = 3)
res = Entrez.read(handle)
for el in res.keys():
    print(el , " : ", res[el])

print("")
for ids in res["IdList"]:
    print("Results for id:", ids)
    handle = Entrez.esummary(db="pubmed",  id = ids)
    res = Entrez.read(handle)
    #uncomment to see all info
    #print(res)
    for r in res:
        print(r["Title"])
        print(r["Source"])
        print("")

Count  :  5900
RetMax  :  3
RetStart  :  0
IdList  :  ['31655474', '31655083', '31649709']
TranslationSet  :  [DictElement({'From': 'Malus Domestica', 'To': '"malus"[MeSH Terms] OR "malus"[All Fields] OR ("malus"[All Fields] AND "domestica"[All Fields]) OR "malus domestica"[All Fields]'}, attributes={})]
TranslationStack  :  [DictElement({'Term': '"malus"[MeSH Terms]', 'Field': 'MeSH Terms', 'Count': '5069', 'Explode': 'Y'}, attributes={}), DictElement({'Term': '"malus"[All Fields]', 'Field': 'All Fields', 'Count': '5907', 'Explode': 'N'}, attributes={}), 'OR', DictElement({'Term': '"malus"[All Fields]', 'Field': 'All Fields', 'Count': '5907', 'Explode': 'N'}, attributes={}), DictElement({'Term': '"domestica"[All Fields]', 'Field': 'All Fields', 'Count': '5891', 'Explode': 'N'}, attributes={}), 'AND', 'GROUP', 'OR', DictElement({'Term': '"malus domestica"[All Fields]', 'Field': 'All Fields', 'Count': '832', 'Explode': 'N'}, attributes={}), 'OR', 'GROUP']
QueryTranslation  :  "malus"[MeSH Terms] OR "malus"[All Fields] OR ("malus"[All Fields] AND "domestica"[All Fields]) OR "malus domestica"[All Fields]

Results for id: 31655474
The role of glucose-6-phosphate dehydrogenase in reactive oxygen species metabolism in apple exocarp induced by acibenzolar-S-methyl.
Food Chem

Results for id: 31655083
Construction of full-length infectious cDNA clones of Apple stem grooving virus using Gibson Assembly method.
Virus Res

Results for id: 31649709
Red to Brown: An Elevated Anthocyanic Response in Apple Drives Ethylene to Advance Maturity and Fruit Flesh Browning.
Front Plant Sci

Example: Retrieve genbank formatted information of the Malus x domestica MYB domain class transcription factor (MYB1) mRNA complete cds (nucleotide database id:HM122614.1). Parse it as a SeqRecord, printing only the sequence (remember previous practical’s SeqIO).

from Bio import Entrez
from Bio import SeqIO

Entrez.email = "my_email"
handle = Entrez.efetch(db="nucleotide",
                       id = "HM122614.1",
                       rettype = "gb",
                       retmode="text")
my_seq = SeqIO.read(handle, format = "genbank")
print(handle.read())
print(my_seq)
print("")
print("SEQUENCE:")
print(my_seq.seq)

ID: HM122614.1
Name: HM122614
Description: Malus x domestica MYB domain class transcription factor (MYB1) mRNA, complete cds
Number of features: 3
/molecule_type=mRNA
/topology=linear
/data_file_division=HTC
/date=15-AUG-2010
/accessions=['HM122614']
/sequence_version=1
/keywords=['HTC']
/source=Malus domestica (apple)
/organism=Malus domestica
/taxonomy=['Eukaryota', 'Viridiplantae', 'Streptophyta', 'Embryophyta', 'Tracheophyta', 'Spermatophyta', 'Magnoliophyta', 'eudicotyledons', 'Gunneridae', 'Pentapetalae', 'rosids', 'fabids', 'Rosales', 'Rosaceae', 'Maloideae', 'Maleae', 'Malus']
/references=[Reference(title='Transcription Factors in Apple', ...), Reference(title='The FruiTFul database; full length cDNAs of apple transcription factors', ...), Reference(title='Direct Submission', ...)]
Seq('TTTGGTCTGCTGGGTAGGTACTCATAAAAACAAACCAACCGAAGCCTCCGAACC...AAA', IUPACAmbiguousDNA())

SEQUENCE:
TTTGGTCTGCTGGGTAGGTACTCATAAAAACAAACCAACCGAAGCCTCCGAACCGACCACCAATGACGGCCCCAAACGGCGCCGTCCCCAAACAAGCCGACGACCGCCCCGGCACCGAGGCCGAGTTGAACGAGGGCGCAGTGCCCAACGGGAAAGTGAGGGGACCGTGGTCGCCCGAGGAGGACGCGGTGCTGAGCCGGCTCGTGAGCAACTTCGGGGCGAGGAATTGGAGCCTGATCGCCCGAGGAATTCCCGGACGGTCTGGGAAGTCGTGCCGGCTGAGGTGGTGTAATCAGCTTGACCCCTGCGTCAAGCGTAAACCCTTTTCTGAGGAAGAAGACCGTATTATAGTTTCAGCACATGCTATCCATGGGAACAAATGGGCAGTAATTGCAAAGCTTCTTCCAGGTAGAACAGATAACGGAATCAAGAACCATTGGAATTCTACACTAAGGCGCAAGTGCTTTGATAAAGGAAGGTTTAATACTGGACCTGGGGAAATGATGGAAGATGACACCTTTGACAGAAAAAATGCATCCTCAGAAGAAACCCTGTCAGTTGGGAATATCAGTTCATTCAAGACTCATGAAGGAAGAGAGGTCTTGATGGAAAATAGACCAAACCAGTTCGATGTAAGAAGTCATGCAAAGGAGGGCTCTGGCGCTGCCGAATCAAAGCACAATTCTACTCTTATTGCCGAGCCAAGAGACCATCCGACTCTCCAGTCCACCATTTGTTGTCCAGTGGCACGTGTTAGTGCATTTAGTGTTTATAACCGTCCAAGTGTTCCAGCAAATGCTTCATCGTTGTCAAGGACAGTCCCAAGTCATGGCCCTTTGGTCCCAATAACTAAACTAGATTTCGGCTTTGACAACTTCCTTGAAGGTGCATGCAATGAGCCTACGGTTCCTCAACGCTGTGGTCACGGTTGCTGTGATCGAATTGAGGGGCATTCTCAAAGCTCGTTGTTGGGGCCTGAGTTCGTTGAGTATGATGAGCCTCTCCCTTTCTCTAGCCACGAATTAATCTCCATTGCTACGGATTTGAACAAGATTGCATGGATTAAGGGTGGCCTTGAGAGTAATGGGATAAGGATGCCAGAGCACGTAGCAAGCCAGAGAGTCTTTCAAGCAGCTGCCACTACCTTGCAAATGGGGTTGCCAGCAAACACTCCGATGAATGACCATATGCGCTTTGAGGAAGGAAGAAACAAGTTGATGGGAATGATGACGGACGTGCTATCAACCCAGGTGCCTAGACAAACTTTTGCAATGCCAACTGAAGTTGAGGGATTGAGCTAGAACTCATGGCTGGTCTTCCTCAGTCTTCCGGGTGTTTCGGTTAATTTACAGCAGATTAAGTTGAAGTCTCCAGTTTCATTTAGAAGGCTTTTCACTTTTGACTTATCTCGTTTAAGAGGGCATTACATCAAAGATATATATGTAGGTACTTCTCTACCCCTTTTGTCATGAGCAAAGAAGCTGTTGACTAGTAAATGCTTTTATACAAGTGCTTTTATCTCAAATCCGAAAACATAATTGATAAAAAAAAAAAA

Getting data from ExPASy

Similarly to what done with Entrez, it is possible to pull data out of ExPASy (https://www.expasy.org/) through the Bio.ExPASy module. We will not cover this in detail. All information can be found here: Bio.ExPASy module.

As an example, we will see how to download a couple of SwissProt entries (the human, rhesus macaque and mouse P53 protein) and perform pairwise sequence alignment of Human vs Macaque and Human vs Mouse.

from Bio import ExPASy
from Bio import SwissProt
from Bio import pairwise2

#the ids of the human, rhesus and mouse proteins
accessions = ["P04637", "P56424", "P02340"]
sequences = []
for accession in accessions:
    handle = ExPASy.get_sprot_raw(accession)
    record = SwissProt.read(handle)
    print("Organism: {}".format(record.organism))
    print(record.entry_name)
    print(",".join(record.accessions))
    print(record.keywords)

    print(record.sequence[:30] + "...")
    sequences.append(record.sequence)

print("\n\nPairwise sequence alignment of Human vs Rhesus P53:")

aligns = pairwise2.align.globalxx(sequences[0],sequences[1])
for al in aligns[0:3]:
    print("Score {}:".format(al[2]))
    print(al[0][0:50])
    print(al[1][0:50])

print("\n\nPairwise sequence alignment of Human vs Mouse P53:")

aligns = pairwise2.align.globalxx(sequences[0],sequences[2])
for al in aligns[0:3]:
    print("Score {}:".format(al[2]))
    print(al[0][0:50])
    print(al[1][0:50])

Organism: Homo sapiens (Human).
P53_HUMAN
P04637,Q15086,Q15087,Q15088,Q16535,Q16807,Q16808,Q16809,Q16810,Q16811,Q16848,Q2XN98,Q3LRW1,Q3LRW2,Q3LRW3,Q3LRW4,Q3LRW5,Q86UG1,Q8J016,Q99659,Q9BTM4,Q9HAQ8,Q9NP68,Q9NPJ2,Q9NZD0,Q9UBI2,Q9UQ61
['3D-structure', 'Acetylation', 'Activator', 'Alternative promoter usage', 'Alternative splicing', 'Apoptosis', 'Biological rhythms', 'Cell cycle', 'Complete proteome', 'Cytoplasm', 'Direct protein sequencing', 'Disease mutation', 'DNA-binding', 'Endoplasmic reticulum', 'Glycoprotein', 'Host-virus interaction', 'Isopeptide bond', 'Li-Fraumeni syndrome', 'Metal-binding', 'Methylation', 'Mitochondrion', 'Necrosis', 'Nucleus', 'Phosphoprotein', 'Polymorphism', 'Reference proteome', 'Repressor', 'Transcription', 'Transcription regulation', 'Tumor suppressor', 'Ubl conjugation', 'Zinc']
MEEPQSDPSVEPPLSQETFSDLWKLLPENN...
Organism: Macaca mulatta (Rhesus macaque).
P53_MACMU
P56424
['Acetylation', 'Activator', 'Apoptosis', 'Biological rhythms', 'Cell cycle', 'Complete proteome', 'Cytoplasm', 'DNA-binding', 'Endoplasmic reticulum', 'Isopeptide bond', 'Metal-binding', 'Methylation', 'Mitochondrion', 'Necrosis', 'Nucleus', 'Phosphoprotein', 'Reference proteome', 'Repressor', 'Transcription', 'Transcription regulation', 'Tumor suppressor', 'Ubl conjugation', 'Zinc']
MEEPQSDPSIEPPLSQETFSDLWKLLPENN...
Organism: Mus musculus (Mouse).
P53_MOUSE
P02340,Q9QUP3
['3D-structure', 'Acetylation', 'Activator', 'Apoptosis', 'Biological rhythms', 'Cell cycle', 'Complete proteome', 'Cytoplasm', 'Disease mutation', 'DNA-binding', 'Endoplasmic reticulum', 'Isopeptide bond', 'Metal-binding', 'Methylation', 'Mitochondrion', 'Necrosis', 'Nucleus', 'Phosphoprotein', 'Reference proteome', 'Repressor', 'Transcription', 'Transcription regulation', 'Tumor suppressor', 'Ubl conjugation', 'Zinc']
MTAMEESQSDISLELPLSQETFSGLWKLLP...


Pairwise sequence alignment of Human vs Rhesus P53:
Score 376.0:
MEEPQSDPSV-EPPLSQETFSDLWKLLPENNVLSPLPSQAM-DDLMLSPD
MEEPQSDPS-IEPPLSQETFSDLWKLLPENNVLSPLPSQA-VDDLMLSPD
Score 376.0:
MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAM-DDLMLSPDD
MEEPQSDPSIEPPLSQETFSDLWKLLPENNVLSPLPSQA-VDDLMLSPDD
Score 376.0:
MEEPQSDPSV-EPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDD
MEEPQSDPS-IEPPLSQETFSDLWKLLPENNVLSPLPSQAVDDLMLSPDD


Pairwise sequence alignment of Human vs Mouse P53:
Score 315.0:
M---EEP-QSDP-SV-EP-PLSQETFSD-LWKLLPENNVLSP---LPSQA
MTAMEE-SQSD-IS-LE-LPLSQETFS-GLWKLLP------PEDILPS--
Score 315.0:
---MEEP-QSDP-SV-EP-PLSQETFSD-LWKLLPENNVLSP---LPSQA
MTAMEE-SQSD-IS-LE-LPLSQETFS-GLWKLLP------PEDILPS--
Score 315.0:
M---EEPQSDP-SV-EP-PLSQETFSD-LWKLLPENNVLSP---LPSQA-
MTAMEESQSD-IS-LE-LPLSQETFS-GLWKLLP------PEDILPS--P

You can find here all the details on how to deal with the SwissProt records.

3D structure and PDB

Biopython can also deal with data coming from the Protein Data Bank database. It is a database of structural information of 3D shapes of proteins, nucleic acids, and complex assemblies. The database currently contains more than 157,000 total structures.

To deal with this kind of data we first need to import Biopython’s module Bio.PDB with from Bio.PDB import *. All the information on this module can be found here.

It is possible to download a structure directly from PDB by using a PDBList object that features a function called download_pdb_files having the basic syntax:

PDBList.download_pdb_files(pdb_codes, pdir, file_format)

that downloads the file_format formatted structures defined in the pdb_codes list of 4 symbols structure Ids from PDB, stores them in the directory pdir. The safer file_format to use is “mmCif”. The function will not download the structures more than once. If a file is already present in the specified directory, a message Structure exists will be displayed.

Example:

Let’s programmatically download two different structures of the DNA polymerase 3C2K and 3C2L

from Bio.PDB import *

pdbl = PDBList()
structures = ["3C2K", "3C2L"]
el = pdbl.download_pdb_files(structures,
                             file_format = "mmCif",
                             pdir = "file_samples/")

Structure exists: 'file_samples/3c2k.cif'
Structure exists: 'file_samples/3c2l.cif'

Macromolecular Crystallographic Information Files (mmCif files .cif) is a paired collection of names (starting with “_”) and values.They also contain a description of the 3D placement of every crystalized atom of the structure. A detailed description of the format can be found here.

Once the structures are available locally, one can start parsing them to do something useful. Parsing can be done through the MMCIFParser object:

parser = MMCIFParser()

The parser object has several methods able to deal with structures. One of these is the get_structure that creates a PDB.Structure.Structure object with all the data present in the structure file.

The basic syntax is:

structure = parser.get_structure(pdb_code, filename)

where pdb_code is the PDB code of the structure contained in the file filename. The method returns a PDB.Structure.Structure that contains one or more models.

A Structure consists of a collection of one or more Model (different 3D conformations of the very same structure) that is a collection of Chain that is a collection of Residues that is a collection of Atoms. Look in the documentation to get the information on each of these classes. This is the diagram of a structure:

Given a Structure we can obtain iterators to models, chains, residues or atoms with:

Structure.get_models()
Structure.get_chains()
Structure.get_residues()
Structure.get_atoms()

For each model obtained with structure.get_models() function we can loop through its chains, residues and atoms. For atoms we can get the 3D coordinates with Atom.get_coord().

Example: Let’s loop through all the models, chain, residues and atoms of the DNA polymerase structure 3C2K. Print the 3D coordinates of each atom.

from Bio.PDB import *


parser = MMCIFParser(QUIET=True) #To disable warnings


filename = "file_samples/3c2l.cif"
structure = parser.get_structure("3c2l", filename)

for model in structure.get_models():
    print("model", model, "has {} chains".format(len(model)))

    for chain in model:
        print(" - chain ", chain, "has {} residues".format(len(chain)))

        for residue in chain:
            print ("      - residue", residue.get_resname(), "has {} atoms".format(len(residue)))

            for atom in residue:
                x,y,z = atom.get_coord()
                print("        - atom:", atom.get_name(), "x: {} y:{} z:{}".format(x,y,z))

model <Model id=0> has 4 chains
 - chain  <Chain id=T> has 41 residues
      - residue DC has 16 atoms
        - atom: O5' x: 30.740999221801758 y:-2.2209999561309814 z:16.618999481201172
        - atom: C5' x: 31.167999267578125 y:-0.9599999785423279 z:16.062999725341797
        - atom: C4' x: 29.996000289916992 y:-0.009999999776482582 z:15.932999610900879
        - atom: O4' x: 28.96299934387207 y:-0.6069999933242798 z:15.107000350952148
        - atom: C3' x: 29.320999145507812 y:0.38499999046325684 z:17.253000259399414
        - atom: O3' x: 29.166000366210938 y:1.8140000104904175 z:17.327999114990234
        - atom: C2' x: 27.96500015258789 y:-0.3019999861717224 z:17.187999725341797
        - atom: C1' x: 27.701000213623047 y:-0.3490000069141388 z:15.692000389099121
        - atom: N1 x: 26.76099967956543 y:-1.4010000228881836 z:15.24899959564209
        - atom: C2 x: 25.65999984741211 y:-1.034000039100647 z:14.456999778747559
        - atom: O2 x: 25.51300048828125 y:0.16200000047683716 z:14.140999794006348
        - atom: N3 x: 24.78499984741211 y:-1.9910000562667847 z:14.057000160217285
        - atom: C4 x: 24.97599983215332 y:-3.2660000324249268 z:14.414999961853027
        - atom: N4 x: 24.086000442504883 y:-4.172999858856201 z:14.0
        - atom: C5 x: 26.08799934387207 y:-3.6679999828338623 z:15.21399974822998
        - atom: C6 x: 26.94700050354004 y:-2.7139999866485596 z:15.604000091552734
      - residue DC has 19 atoms
        - atom: P x: 28.641000747680664 y:2.5 z:18.69099998474121
        - atom: OP1 x: 29.559999465942383 y:3.625 z:19.025999069213867
        - atom: OP2 x: 28.385000228881836 y:1.4290000200271606 z:19.698999404907227
        - atom: O5' x: 27.225000381469727 y:3.124000072479248 z:18.30299949645996
        - atom: C5' x: 27.128999710083008 y:4.366000175476074 z:17.600000381469727
        - atom: C4' x: 25.67799949645996 y:4.741000175476074 z:17.399999618530273
        - atom: O4' x: 24.954999923706055 y:3.5789999961853027 z:16.92799949645996
        - atom: C3' x: 24.93600082397461 y:5.171000003814697 z:18.663000106811523
        - atom: O3' x: 23.81800079345703 y:5.980000019073486 z:18.29800033569336
        - atom: C2' x: 24.413000106811523 y:3.8489999771118164 z:19.187999725341797
        - atom: C1' x: 23.961999893188477 y:3.2190001010894775 z:17.882999420166016
        - atom: N1 x: 23.832000732421875 y:1.7519999742507935 z:17.87299919128418
        - atom: C2 x: 22.68899917602539 y:1.1799999475479126 z:17.298999786376953
        - atom: O2 x: 21.812999725341797 y:1.9190000295639038 z:16.829999923706055
        - atom: N3 x: 22.569000244140625 y:-0.16200000047683716 z:17.268999099731445
        - atom: C4 x: 23.52899932861328 y:-0.9279999732971191 z:17.78700065612793
        - atom: N4 x: 23.367000579833984 y:-2.252000093460083 z:17.738000869750977
        - atom: C5 x: 24.697999954223633 y:-0.37400001287460327 z:18.3799991607666
        - atom: C6 x: 24.808000564575195 y:0.9559999704360962 z:18.40399932861328
      - residue DG has 22 atoms
        - atom: P x: 23.493000030517578 y:7.309000015258789 z:19.131000518798828
        - atom: OP1 x: 24.016000747680664 y:8.472999572753906 z:18.36199951171875
        - atom: OP2 x: 23.934999465942383 y:7.0960001945495605 z:20.5310001373291
        - atom: O5' x: 21.90399932861328 y:7.382999897003174 z:19.136999130249023
        - atom: C5' x: 21.174999237060547 y:7.506999969482422 z:17.922000885009766
        - atom: C4' x: 19.93899917602539 y:6.644999980926514 z:17.98200035095215
        - atom: O4' x: 20.363000869750977 y:5.269000053405762 z:18.142000198364258
        - atom: C3' x: 19.0310001373291 y:6.951000213623047 z:19.179000854492188
        - atom: O3' x: 17.66200065612793 y:6.968999862670898 z:18.77199935913086
        - atom: C2' x: 19.263999938964844 y:5.7769999504089355 z:20.11400032043457
        - atom: C1' x: 19.552000045776367 y:4.665999889373779 z:19.12700080871582
        - atom: N9 x: 20.26799964904785 y:3.5169999599456787 z:19.67300033569336
        - atom: C8 x: 21.375 y:3.5269999504089355 z:20.490999221801758
        - atom: N7 x: 21.760000228881836 y:2.3299999237060547 z:20.850000381469727
        - atom: C5 x: 20.85700035095215 y:1.4789999723434448 z:20.225000381469727
        - atom: C6 x: 20.763999938964844 y:0.06800000369548798 z:20.246999740600586
        - atom: O6 x: 21.47800064086914 y:-0.7459999918937683 z:20.850000381469727
        - atom: N1 x: 19.707000732421875 y:-0.382999986410141 z:19.465999603271484
        - atom: C2 x: 18.85099983215332 y:0.4169999957084656 z:18.756000518798828
        - atom: N2 x: 17.89900016784668 y:-0.20800000429153442 z:18.055999755859375
        - atom: N3 x: 18.92099952697754 y:1.7330000400543213 z:18.733999252319336
        - atom: C4 x: 19.940000534057617 y:2.194999933242798 z:19.485000610351562
      - residue DA has 21 atoms
        - atom: P x: 16.55500030517578 y:7.6579999923706055 z:19.7189998626709
        - atom: OP1 x: 16.44099998474121 y:9.088000297546387 z:19.329999923706055
        - atom: OP2 x: 16.868000030517578 y:7.307000160217285 z:21.135000228881836
        - atom: O5' x: 15.189000129699707 y:6.940000057220459 z:19.316999435424805
        - atom: C5' x: 14.980999946594238 y:6.421999931335449 z:18.000999450683594
        - atom: C4' x: 13.972000122070312 y:5.296999931335449 z:18.041000366210938
        - atom: O4' x: 14.60099983215332 y:4.105000019073486 z:18.56999969482422
        - atom: C3' x: 12.777000427246094 y:5.566999912261963 z:18.947999954223633
        - atom: O3' x: 11.604000091552734 y:4.940000057220459 z:18.440000534057617
        - atom: C2' x: 13.196000099182129 y:4.954999923706055 z:20.273000717163086
        - atom: C1' x: 14.07699966430664 y:3.7829999923706055 z:19.85700035095215
        - atom: N9 x: 15.21399974822998 y:3.496999979019165 z:20.743000030517578
        - atom: C8 x: 15.923999786376953 y:4.367000102996826 z:21.542999267578125
        - atom: N7 x: 16.92300033569336 y:3.805999994277954 z:22.18000030517578
        - atom: C5 x: 16.867000579833984 y:2.4760000705718994 z:21.781999588012695
        - atom: C6 x: 17.660999298095703 y:1.3539999723434448 z:22.099000930786133
        - atom: N6 x: 18.72599983215332 y:1.3949999809265137 z:22.900999069213867
        - atom: N1 x: 17.31800079345703 y:0.1720000058412552 z:21.548999786376953
        - atom: C2 x: 16.260000228881836 y:0.12600000202655792 z:20.73200035095215
        - atom: N3 x: 15.449000358581543 y:1.1030000448226929 z:20.347999572753906
        - atom: C4 x: 15.809000015258789 y:2.2679998874664307 z:20.913000106811523
      - residue DC has 19 atoms
        - atom: P x: 10.178999900817871 y:5.289999961853027 z:19.089000701904297
        - atom: OP1 x: 9.128999710083008 y:5.105999946594238 z:18.054000854492188
        - atom: OP2 x: 10.288999557495117 y:6.593999862670898 z:19.79800033569336
        - atom: O5' x: 9.972999572753906 y:4.1579999923706055 z:20.18600082397461
        - atom: C5' x: 9.642000198364258 y:2.8340001106262207 z:19.795000076293945
        - atom: C4' x: 9.98900032043457 y:1.8619999885559082 z:20.893999099731445
        - atom: O4' x: 11.369999885559082 y:1.9759999513626099 z:21.277000427246094
        - atom: C3' x: 9.21500015258789 y:2.0450000762939453 z:22.19499969482422
        - atom: O3' x: 8.050999641418457 y:1.2230000495910645 z:22.155000686645508
        - atom: C2' x: 10.194000244140625 y:1.5709999799728394 z:23.26799964904785
        - atom: C1' x: 11.472000122070312 y:1.246999979019165 z:22.483999252319336
        - atom: N1 x: 12.76099967956543 y:1.5789999961853027 z:23.125999450683594
        - atom: C2 x: 13.718000411987305 y:0.5619999766349792 z:23.277999877929688
        - atom: O2 x: 13.458999633789062 y:-0.578000009059906 z:22.86400032043457
        - atom: N3 x: 14.899999618530273 y:0.8500000238418579 z:23.868999481201172
        - atom: C4 x: 15.147000312805176 y:2.0880000591278076 z:24.297000885009766
        - atom: N4 x: 16.325000762939453 y:2.3239998817443848 z:24.8700008392334
        - atom: C5 x: 14.196999549865723 y:3.1410000324249268 z:24.152000427246094
        - atom: C6 x: 13.029999732971191 y:2.8459999561309814 z:23.56599998474121
      - residue DC has 19 atoms
        - atom: P x: 6.784999847412109 y:1.5880000591278076 z:23.06800079345703
        - atom: OP1 x: 7.255000114440918 y:1.5880000591278076 z:24.479000091552734
        - atom: OP2 x: 5.660999774932861 y:0.6949999928474426 z:22.66699981689453
        - atom: O5' x: 6.434000015258789 y:3.0880000591278076 z:22.659000396728516
        - atom: C5' x: 5.370999813079834 y:3.378000020980835 z:21.74799919128418
        - atom: C4' x: 4.375999927520752 y:4.328000068664551 z:22.378000259399414
        - atom: O4' x: 3.687000036239624 y:3.677000045776367 z:23.465999603271484
        - atom: C3' x: 4.9770002365112305 y:5.60699987411499 z:22.972999572753906
        - atom: O3' x: 4.706999778747559 y:6.71999979019165 z:22.107999801635742
        - atom: C2' x: 4.288000106811523 y:5.76200008392334 z:24.326000213623047
        - atom: C1' x: 3.2070000171661377 y:4.689000129699707 z:24.322999954223633
        - atom: N1 x: 2.882999897003174 y:4.071000099182129 z:25.628000259399414
        - atom: C2 x: 3.9179999828338623 y:3.555999994277954 z:26.45199966430664
        - atom: O2 x: 5.10099983215332 y:3.6510000228881836 z:26.08799934387207
        - atom: N3 x: 3.5899999141693115 y:2.9709999561309814 z:27.625
        - atom: C4 x: 2.311000108718872 y:2.88700008392334 z:27.996999740600586
        - atom: N4 x: 2.0390000343322754 y:2.2960000038146973 z:29.16200065612793
        - atom: C5 x: 1.2519999742507935 y:3.4059998989105225 z:27.194000244140625
        - atom: C6 x: 1.5789999961853027 y:3.9860000610351562 z:26.031999588012695
      - residue DG has 22 atoms
        - atom: P x: 5.339000225067139 y:8.164999961853027 z:22.430999755859375
        - atom: OP1 x: 5.185999870300293 y:9.013999938964844 z:21.215999603271484
        - atom: OP2 x: 6.695000171661377 y:7.960000038146973 z:23.01799964904785
        - atom: O5' x: 4.388999938964844 y:8.75 z:23.570999145507812
        - atom: C5' x: 2.9639999866485596 y:8.717000007629395 z:23.433000564575195
        - atom: C4' x: 2.2890000343322754 y:8.987000465393066 z:24.761999130249023
        - atom: O4' x: 2.5959999561309814 y:7.940000057220459 z:25.718000411987305
        - atom: C3' x: 2.671999931335449 y:10.305999755859375 z:25.44499969482422
        - atom: O3' x: 1.5190000534057617 y:10.883999824523926 z:26.075000762939453
        - atom: C2' x: 3.6530001163482666 y:9.859000205993652 z:26.516000747680664
        - atom: C1' x: 3.0190000534057617 y:8.543000221252441 z:26.93000030517578
        - atom: N9 x: 3.871000051498413 y:7.5920000076293945 z:27.639999389648438
        - atom: C8 x: 5.236999988555908 y:7.434000015258789 z:27.535999298095703
        - atom: N7 x: 5.703999996185303 y:6.49399995803833 z:28.315000534057617
        - atom: C5 x: 4.581999778747559 y:5.999000072479248 z:28.972000122070312
        - atom: C6 x: 4.456999778747559 y:4.964000225067139 z:29.95199966430664
        - atom: O6 x: 5.3429999351501465 y:4.252999782562256 z:30.444000244140625
        - atom: N1 x: 3.134000062942505 y:4.795000076293945 z:30.350000381469727
        - atom: C2 x: 2.063999891281128 y:5.514999866485596 z:29.8700008392334
        - atom: N2 x: 0.8629999756813049 y:5.197000026702881 z:30.371000289916992
        - atom: N3 x: 2.1649999618530273 y:6.474999904632568 z:28.964000701904297
        - atom: C4 x: 3.443000078201294 y:6.664000034332275 z:28.562999725341797
      - residue DC has 19 atoms
        - atom: P x: 0.33799999952316284 y:11.519000053405762 z:25.18000030517578
        - atom: OP1 x: 0.1550000011920929 y:10.725000381469727 z:23.934999465942383
        - atom: OP2 x: 0.6060000061988831 y:12.97599983215332 z:25.08799934387207
        - atom: O5' x: -0.9620000123977661 y:11.310999870300293 z:26.07699966430664
        - atom: C5' x: -1.5479999780654907 y:10.01099967956543 z:26.243999481201172
        - atom: C4' x: -2.0759999752044678 y:9.840999603271484 z:27.652999877929688
        - atom: O4' x: -1.0989999771118164 y:9.121000289916992 z:28.450000762939453
        - atom: C3' x: -2.3559999465942383 y:11.156999588012695 z:28.393999099731445
        - atom: O3' x: -3.6589999198913574 y:11.140999794006348 z:28.993000030517578
        - atom: C2' x: -1.2630000114440918 y:11.21500015258789 z:29.448999404907227
        - atom: C1' x: -1.0080000162124634 y:9.743000030517578 z:29.716999053955078
        - atom: N1 x: 0.3089999854564667 y:9.418000221252441 z:30.30299949645996
        - atom: C2 x: 0.3610000014305115 y:8.574000358581543 z:31.42300033569336
        - atom: O2 x: -0.6980000138282776 y:8.114999771118164 z:31.885000228881836
        - atom: N3 x: 1.565000057220459 y:8.277999877929688 z:31.972000122070312
        - atom: C4 x: 2.681999921798706 y:8.782999992370605 z:31.444000244140625
        - atom: N4 x: 3.8420000076293945 y:8.456999778747559 z:32.00699996948242
        - atom: C5 x: 2.6589999198913574 y:9.640000343322754 z:30.309999465942383
        - atom: C6 x: 1.4630000591278076 y:9.928999900817871 z:29.774999618530273
      - residue DG has 22 atoms
        - atom: P x: -4.367000102996826 y:12.529000282287598 z:29.423999786376953
        - atom: OP1 x: -5.24399995803833 y:12.972000122070312 z:28.31399917602539
        - atom: OP2 x: -3.3519999980926514 y:13.472999572753906 z:29.975000381469727
        - atom: O5' x: -5.328999996185303 y:12.105999946594238 z:30.618999481201172
        - atom: C5' x: -5.7230000495910645 y:10.743000030517578 z:30.81599998474121
        - atom: C4' x: -5.9730000495910645 y:10.482000350952148 z:32.2859992980957
        - atom: O4' x: -4.754000186920166 y:10.02400016784668 z:32.917999267578125
        - atom: C3' x: -6.394000053405762 y:11.713000297546387 z:33.08300018310547
        - atom: O3' x: -7.164999961853027 y:11.305000305175781 z:34.207000732421875
        - atom: C2' x: -5.059999942779541 y:12.281000137329102 z:33.53200149536133
        - atom: C1' x: -4.284999847412109 y:11.005999565124512 z:33.8380012512207
        - atom: N9 x: -2.8359999656677246 y:11.102999687194824 z:33.691001892089844
        - atom: C8 x: -2.1500000953674316 y:11.842000007629395 z:32.762001037597656
        - atom: N7 x: -0.8539999723434448 y:11.725000381469727 z:32.86600112915039
        - atom: C5 x: -0.6690000295639038 y:10.854999542236328 z:33.930999755859375
        - atom: C6 x: 0.5249999761581421 y:10.35200023651123 z:34.5099983215332
        - atom: O6 x: 1.6929999589920044 y:10.571999549865723 z:34.17399978637695
        - atom: N1 x: 0.25699999928474426 y:9.508999824523926 z:35.584999084472656
        - atom: C2 x: -0.9919999837875366 y:9.182999610900879 z:36.04100036621094
        - atom: N2 x: -1.0390000343322754 y:8.371000289916992 z:37.106998443603516
        - atom: N3 x: -2.114000082015991 y:9.626999855041504 z:35.5
        - atom: C4 x: -1.8799999952316284 y:10.461000442504883 z:34.457000732421875
      - residue DC has 19 atoms
        - atom: P x: -7.857999801635742 y:12.404000282287598 z:35.13100051879883
        - atom: OP1 x: -9.21500015258789 y:11.907999992370605 z:35.45399856567383
        - atom: OP2 x: -7.696000099182129 y:13.723999977111816 z:34.48099899291992
        - atom: O5' x: -6.958000183105469 y:12.425999641418457 z:36.45100021362305
        - atom: C5' x: -7.033999919891357 y:11.376999855041504 z:37.417999267578125
        - atom: C4' x: -5.870999813079834 y:11.456999778747559 z:38.382999420166016
        - atom: O4' x: -4.645999908447266 y:11.569000244140625 z:37.64799880981445
        - atom: C3' x: -5.867000102996826 y:12.637999534606934 z:39.358001708984375
        - atom: O3' x: -6.331999778747559 y:12.196000099182129 z:40.64400100708008
        - atom: C2' x: -4.410999774932861 y:13.088000297546387 z:39.395999908447266
        - atom: C1' x: -3.680999994277954 y:12.074999809265137 z:38.53200149536133
        - atom: N1 x: -2.5789999961853027 y:12.61400032043457 z:37.72200012207031
        - atom: C2 x: -1.2640000581741333 y:12.213000297546387 z:38.012001037597656
        - atom: O2 x: -1.0640000104904175 y:11.440999984741211 z:38.959999084472656
        - atom: N3 x: -0.24699999392032623 y:12.678999900817871 z:37.25299835205078
        - atom: C4 x: -0.4959999918937683 y:13.519000053405762 z:36.24800109863281
        - atom: N4 x: 0.5400000214576721 y:13.949999809265137 z:35.527000427246094
        - atom: C5 x: -1.8209999799728394 y:13.954999923706055 z:35.93899917602539
        - atom: C6 x: -2.822999954223633 y:13.482999801635742 z:36.69499969482422
      - residue DA has 21 atoms
        - atom: P x: -6.264999866485596 y:13.177000045776367 z:41.92599868774414
        - atom: OP1 x: -7.065999984741211 y:12.534000396728516 z:43.00299835205078
        - atom: OP2 x: -6.591000080108643 y:14.555000305175781 z:41.50400161743164
        - atom: O5' x: -4.739999771118164 y:13.109999656677246 z:42.375999450683594
        - atom: C5' x: -4.144000053405762 y:11.85200023651123 z:42.70800018310547
        - atom: C4' x: -2.9830000400543213 y:12.027999877929688 z:43.66400146484375
        - atom: O4' x: -1.7519999742507935 y:12.300000190734863 z:42.95500183105469
        - atom: C3' x: -3.1029999256134033 y:13.125 z:44.70899963378906
        - atom: O3' x: -2.431999921798706 y:12.666999816894531 z:45.887001037597656
        - atom: C2' x: -2.390000104904175 y:14.291999816894531 z:44.04800033569336
        - atom: C1' x: -1.2949999570846558 y:13.611000061035156 z:43.23400115966797
        - atom: N9 x: -0.9739999771118164 y:14.23900032043457 z:41.952999114990234
        - atom: C8 x: -1.8300000429153442 y:14.854999542236328 z:41.07400131225586
        - atom: N7 x: -1.25 y:15.282999992370605 z:39.97800064086914
        - atom: C5 x: 0.07800000160932541 y:14.930999755859375 z:40.14799880981445
        - atom: C6 x: 1.2029999494552612 y:15.083999633789062 z:39.32500076293945
        - atom: N6 x: 1.1610000133514404 y:15.645000457763672 z:38.11600112915039
        - atom: N1 x: 2.38700008392334 y:14.62600040435791 z:39.78900146484375
        - atom: C2 x: 2.4230000972747803 y:14.048999786376953 z:40.99599838256836
        - atom: N3 x: 1.430999994277954 y:13.84000015258789 z:41.85900115966797
        - atom: C4 x: 0.26899999380111694 y:14.305000305175781 z:41.36800003051758
      - residue DT has 20 atoms
        - atom: P x: -2.188999891281128 y:13.661999702453613 z:47.132999420166016
        - atom: OP1 x: -2.315999984741211 y:12.843000411987305 z:48.37300109863281
        - atom: OP2 x: -2.986999988555908 y:14.913000106811523 z:47.0
        - atom: O5' x: -0.6570000052452087 y:14.04800033569336 z:46.965999603271484
        - atom: C5' x: 0.3330000042915344 y:13.050999641418457 z:46.792999267578125
        - atom: C4' x: 1.6670000553131104 y:13.706999778747559 z:46.54499816894531
        - atom: O4' x: 1.6430000066757202 y:14.303999900817871 z:45.2239990234375
        - atom: C3' x: 1.9980000257492065 y:14.854999542236328 z:47.505001068115234
        - atom: O3' x: 3.4089999198913574 y:14.859000205993652 z:47.75600051879883
        - atom: C2' x: 1.628999948501587 y:16.091999053955078 z:46.70199966430664
        - atom: C1' x: 2.1050000190734863 y:15.644000053405762 z:45.33000183105469
        - atom: N1 x: 1.6460000276565552 y:16.400999069213867 z:44.13199996948242
        - atom: C2 x: 2.572999954223633 y:16.636999130249023 z:43.12900161743164
        - atom: O2 x: 3.7309999465942383 y:16.2810001373291 z:43.194000244140625
        - atom: N3 x: 2.0889999866485596 y:17.312999725341797 z:42.03900146484375
        - atom: C4 x: 0.8059999942779541 y:17.77199935913086 z:41.84700012207031
        - atom: O4 x: 0.5199999809265137 y:18.349000930786133 z:40.797000885009766
        - atom: C5 x: -0.11999999731779099 y:17.506999969482422 z:42.948001861572266
        - atom: C7 x: -1.534999966621399 y:17.979000091552734 z:42.840999603271484
        - atom: C6 x: 0.3440000116825104 y:16.844999313354492 z:44.018001556396484
      - residue DC has 19 atoms
        - atom: P x: 3.9679999351501465 y:15.352999687194824 z:49.18199920654297
        - atom: OP1 x: 4.440999984741211 y:14.140000343322754 z:49.9010009765625
        - atom: OP2 x: 2.9700000286102295 y:16.26300048828125 z:49.823001861572266
        - atom: O5' x: 5.254000186920166 y:16.208999633789062 z:48.83000183105469
        - atom: C5' x: 6.129000186920166 y:15.824000358581543 z:47.78900146484375
        - atom: C4' x: 6.697999954223633 y:17.05900001525879 z:47.137001037597656
        - atom: O4' x: 5.788000106811523 y:17.520000457763672 z:46.10200119018555
        - atom: C3' x: 6.85699987411499 y:18.238000869750977 z:48.10900115966797
        - atom: O3' x: 8.050000190734863 y:18.95199966430664 z:47.797000885009766
        - atom: C2' x: 5.665999889373779 y:19.121000289916992 z:47.775001525878906
        - atom: C1' x: 5.61899995803833 y:18.917999267578125 z:46.27199935913086
        - atom: N1 x: 4.400000095367432 y:19.339000701904297 z:45.55400085449219
        - atom: C2 x: 4.5269999504089355 y:19.80699920654297 z:44.236000061035156
        - atom: O2 x: 5.656000137329102 y:19.850000381469727 z:43.71200180053711
        - atom: N3 x: 3.4189999103546143 y:20.195999145507812 z:43.56399917602539
        - atom: C4 x: 2.2239999771118164 y:20.1200008392334 z:44.14899826049805
        - atom: N4 x: 1.159999966621399 y:20.499000549316406 z:43.44300079345703
        - atom: C5 x: 2.065999984741211 y:19.648000717163086 z:45.48500061035156
        - atom: C6 x: 3.1689999103546143 y:19.274999618530273 z:46.145999908447266
      - residue DA has 21 atoms
        - atom: P x: 9.348999977111816 y:18.784000396728516 z:48.71699905395508
        - atom: OP1 x: 9.670999526977539 y:17.33099937438965 z:48.79199981689453
        - atom: OP2 x: 9.105999946594238 y:19.55500030517578 z:49.965999603271484
        - atom: O5' x: 10.47599983215332 y:19.483999252319336 z:47.83599853515625
        - atom: C5' x: 10.871000289916992 y:18.892000198364258 z:46.59400177001953
        - atom: C4' x: 11.45199966430664 y:19.92099952697754 z:45.64799880981445
        - atom: O4' x: 10.427000045776367 y:20.615999221801758 z:44.90599822998047
        - atom: C3' x: 12.335000038146973 y:21.007999420166016 z:46.249000549316406
        - atom: O3' x: 13.369999885559082 y:21.326000213623047 z:45.31800079345703
        - atom: C2' x: 11.381999969482422 y:22.177000045776367 z:46.426998138427734
        - atom: C1' x: 10.312000274658203 y:21.95800018310547 z:45.35599899291992
        - atom: N9 x: 8.944000244140625 y:22.131000518798828 z:45.83399963378906
        - atom: C8 x: 8.444000244140625 y:21.815000534057617 z:47.073001861572266
        - atom: N7 x: 7.1620001792907715 y:22.04400062561035 z:47.196998596191406
        - atom: C5 x: 6.795000076293945 y:22.551000595092773 z:45.95899963378906
        - atom: C6 x: 5.565000057220459 y:22.979999542236328 z:45.452999114990234
        - atom: N6 x: 4.434999942779541 y:22.95800018310547 z:46.16299819946289
        - atom: N1 x: 5.5329999923706055 y:23.437000274658203 z:44.18199920654297
        - atom: C2 x: 6.673999786376953 y:23.458999633789062 z:43.481998443603516
        - atom: N3 x: 7.896999835968018 y:23.07699966430664 z:43.85300064086914
        - atom: C4 x: 7.885000228881836 y:22.624000549316406 z:45.11600112915039
      - residue DG has 22 atoms
        - atom: P x: 14.439000129699707 y:22.465999603271484 z:45.67100143432617
        - atom: OP1 x: 15.732000350952148 y:22.033000946044922 z:45.07500076293945
        - atom: OP2 x: 14.36400032043457 y:22.801000595092773 z:47.12300109863281
        - atom: O5' x: 13.901000022888184 y:23.725000381469727 z:44.86199951171875
        - atom: C5' x: 13.479999542236328 y:23.606000900268555 z:43.500999450683594
        - atom: C4' x: 12.72700023651123 y:24.849000930786133 z:43.0880012512207
        - atom: O4' x: 11.375 y:24.797000885009766 z:43.606998443603516
        - atom: C3' x: 13.336999893188477 y:26.138999938964844 z:43.637001037597656
        - atom: O3' x: 13.461999893188477 y:27.09600067138672 z:42.59199905395508
        - atom: C2' x: 12.329000473022461 y:26.611000061035156 z:44.67499923706055
        - atom: C1' x: 11.03499984741211 y:26.066999435424805 z:44.11199951171875
        - atom: N9 x: 9.951000213623047 y:25.892000198364258 z:45.073001861572266
        - atom: C8 x: 10.029000282287598 y:25.426000595092773 z:46.36800003051758
        - atom: N7 x: 8.871000289916992 y:25.405000686645508 z:46.97800064086914
        - atom: C5 x: 7.974999904632568 y:25.875999450683594 z:46.02299880981445
        - atom: C6 x: 6.565999984741211 y:26.079999923706055 z:46.090999603271484
        - atom: O6 x: 5.789000034332275 y:25.85099983215332 z:47.0369987487793
        - atom: N1 x: 6.070000171661377 y:26.593000411987305 z:44.902000427246094
        - atom: C2 x: 6.811999797821045 y:26.860000610351562 z:43.779998779296875
        - atom: N2 x: 6.139999866485596 y:27.356000900268555 z:42.720001220703125
        - atom: N3 x: 8.112000465393066 y:26.660999298095703 z:43.69499969482422
        - atom: C4 x: 8.626999855041504 y:26.17799949645996 z:44.845001220703125
      - residue DC has 19 atoms
        - atom: P x: 14.321999549865723 y:28.42799949645996 z:42.8380012512207
        - atom: OP1 x: 15.064000129699707 y:28.68000030517578 z:41.57600021362305
        - atom: OP2 x: 15.067000389099121 y:28.295000076293945 z:44.112998962402344
        - atom: O5' x: 13.229000091552734 y:29.56800079345703 z:43.03499984741211
        - atom: C5' x: 12.413000106811523 y:29.974000930786133 z:41.94300079345703
        - atom: C4' x: 11.097000122070312 y:30.51300048828125 z:42.446998596191406
        - atom: O4' x: 10.517000198364258 y:29.645000457763672 z:43.43600082397461
        - atom: C3' x: 11.199999809265137 y:31.851999282836914 z:43.159000396728516
        - atom: O3' x: 11.206000328063965 y:32.849998474121094 z:42.15399932861328
        - atom: C2' x: 9.986000061035156 y:31.849000930786133 z:44.07699966430664
        - atom: C1' x: 9.475000381469727 y:30.405000686645508 z:44.016998291015625
        - atom: N1 x: 9.112000465393066 y:29.808000564575195 z:45.314998626708984
        - atom: C2 x: 7.763000011444092 y:29.753999710083008 z:45.65299987792969
        - atom: O2 x: 6.926000118255615 y:30.17300033569336 z:44.83599853515625
        - atom: N3 x: 7.3979997634887695 y:29.2450008392334 z:46.8489990234375
        - atom: C4 x: 8.324999809265137 y:28.78700065612793 z:47.6870002746582
        - atom: N4 x: 7.909999847412109 y:28.29199981689453 z:48.85599899291992
        - atom: C5 x: 9.71399974822998 y:28.812999725341797 z:47.36399841308594
        - atom: C6 x: 10.059000015258789 y:29.32699966430664 z:46.17900085449219
      - residue MN has 1 atoms
        - atom: MN x: 23.54800033569336 y:1.0 z:22.975000381469727
      - residue HOH has 1 atoms
        - atom: O x: -0.03799999877810478 y:22.62299919128418 z:45.85499954223633
      - residue HOH has 1 atoms
        - atom: O x: -0.2680000066757202 y:6.394999980926514 z:26.27400016784668
      - residue HOH has 1 atoms
        - atom: O x: -2.617000102996826 y:17.14299964904785 z:38.38199996948242
      - residue HOH has 1 atoms
        - atom: O x: -2.8450000286102295 y:9.204000473022461 z:40.37200164794922
      - residue HOH has 1 atoms
        - atom: O x: -4.395999908447266 y:15.696999549865723 z:41.887001037597656
      - residue HOH has 1 atoms
        - atom: O x: 8.746000289916992 y:3.684000015258789 z:24.974000930786133
      - residue HOH has 1 atoms
        - atom: O x: 20.542999267578125 y:3.009999990463257 z:24.375
      - residue HOH has 1 atoms
        - atom: O x: -6.396999835968018 y:10.779000282287598 z:28.01799964904785
      - residue HOH has 1 atoms
        - atom: O x: -9.277000427246094 y:15.675000190734863 z:35.47200012207031
      - residue HOH has 1 atoms
        - atom: O x: 6.900000095367432 y:24.628000259399414 z:49.99599838256836
      - residue HOH has 1 atoms
        - atom: O x: 30.777999877929688 y:4.184000015258789 z:16.06800079345703
      - residue HOH has 1 atoms
        - atom: O x: 14.788999557495117 y:20.408000946044922 z:42.99700164794922
      - residue HOH has 1 atoms
        - atom: O x: -2.247999906539917 y:17.725000381469727 z:46.025001525878906
      - residue HOH has 1 atoms
        - atom: O x: 25.37700080871582 y:2.634999990463257 z:22.086999893188477
      - residue HOH has 1 atoms
        - atom: O x: 24.393999099731445 y:-1.1100000143051147 z:22.084999084472656
      - residue HOH has 1 atoms
        - atom: O x: 5.159999847412109 y:11.8100004196167 z:48.76900100708008
      - residue HOH has 1 atoms
        - atom: O x: -1.069000005722046 y:4.329999923706055 z:24.06399917602539
      - residue HOH has 1 atoms
        - atom: O x: -0.26600000262260437 y:7.039999961853027 z:23.948999404907227
      - residue HOH has 1 atoms
        - atom: O x: 7.377999782562256 y:9.512999534606934 z:17.650999069213867
      - residue HOH has 1 atoms
        - atom: O x: 9.468000411987305 y:9.222999572753906 z:19.29199981689453
      - residue HOH has 1 atoms
        - atom: O x: 10.92199993133545 y:19.01799964904785 z:41.494998931884766
      - residue HOH has 1 atoms
        - atom: O x: -5.491000175476074 y:14.925999641418457 z:35.11899948120117
      - residue HOH has 1 atoms
        - atom: O x: -8.88599967956543 y:16.402999877929688 z:38.94599914550781
      - residue HOH has 1 atoms
        - atom: O x: -9.723999977111816 y:17.750999450683594 z:33.974998474121094
 - chain  <Chain id=P> has 18 residues
      - residue DG has 19 atoms
        - atom: O5' x: -2.617000102996826 y:29.32900047302246 z:49.946998596191406
        - atom: C5' x: -3.3010001182556152 y:30.40399932861328 z:49.26599884033203
        - atom: C4' x: -2.434000015258789 y:30.941999435424805 z:48.154998779296875
        - atom: O4' x: -1.0850000381469727 y:30.972999572753906 z:48.6510009765625
        - atom: C3' x: -2.38700008392334 y:30.049999237060547 z:46.91699981689453
        - atom: O3' x: -3.3589999675750732 y:30.52400016784668 z:45.96099853515625
        - atom: C2' x: -0.9549999833106995 y:30.20599937438965 z:46.415000915527344
        - atom: C1' x: -0.17599999904632568 y:30.812999725341797 z:47.584999084472656
        - atom: N9 x: 0.9449999928474426 y:30.017000198364258 z:48.07699966430664
        - atom: C8 x: 0.9980000257492065 y:29.2549991607666 z:49.22100067138672
        - atom: N7 x: 2.1589999198913574 y:28.683000564575195 z:49.40299987792969
        - atom: C5 x: 2.9100000858306885 y:29.089000701904297 z:48.3129997253418
        - atom: C6 x: 4.244999885559082 y:28.812999725341797 z:47.972999572753906
        - atom: O6 x: 5.076000213623047 y:28.15399932861328 z:48.59700012207031
        - atom: N1 x: 4.5980000495910645 y:29.413999557495117 z:46.77299880981445
        - atom: C2 x: 3.7769999504089355 y:30.197999954223633 z:46.01499938964844
        - atom: N2 x: 4.291999816894531 y:30.69099998474121 z:44.88600158691406
        - atom: N3 x: 2.5409998893737793 y:30.482999801635742 z:46.33399963378906
        - atom: C4 x: 2.1710000038146973 y:29.89900016784668 z:47.481998443603516
      - residue DC has 19 atoms
        - atom: P x: -3.7049999237060547 y:29.652999877929688 z:44.64699935913086
        - atom: OP1 x: -4.730999946594238 y:30.423999786376953 z:43.893001556396484
        - atom: OP2 x: -3.9800000190734863 y:28.243000030517578 z:45.04199981689453
        - atom: O5' x: -2.365999937057495 y:29.698999404907227 z:43.7859992980957
        - atom: C5' x: -1.8380000591278076 y:30.945999145507812 z:43.33399963378906
        - atom: C4' x: -0.75 y:30.716999053955078 z:42.310001373291016
        - atom: O4' x: 0.4480000138282776 y:30.246000289916992 z:42.97100067138672
        - atom: C3' x: -1.0950000286102295 y:29.672000885009766 z:41.250999450683594
        - atom: O3' x: -0.6209999918937683 y:30.075000762939453 z:39.96699905395508
        - atom: C2' x: -0.3880000114440918 y:28.417999267578125 z:41.731998443603516
        - atom: C1' x: 0.8130000233650208 y:28.95599937438965 z:42.499000549316406
        - atom: N1 x: 1.187000036239624 y:28.141000747680664 z:43.66999816894531
        - atom: C2 x: 2.503999948501587 y:27.666000366210938 z:43.784000396728516
        - atom: O2 x: 3.3299999237060547 y:27.927000045776367 z:42.89099884033203
        - atom: N3 x: 2.8429999351501465 y:26.937000274658203 z:44.86800003051758
        - atom: C4 x: 1.9320000410079956 y:26.677000045776367 z:45.81399917602539
        - atom: N4 x: 2.319999933242798 y:25.972000122070312 z:46.88399887084961
        - atom: C5 x: 0.5879999995231628 y:27.132999420166016 z:45.71099853515625
        - atom: C6 x: 0.2630000114440918 y:27.854000091552734 z:44.63600158691406
      - residue DT has 20 atoms
        - atom: P x: -0.828000009059906 y:29.101999282836914 z:38.70800018310547
        - atom: OP1 x: -0.8669999837875366 y:29.930999755859375 z:37.46799850463867
        - atom: OP2 x: -1.9559999704360962 y:28.173999786376953 z:39.0099983215332
        - atom: O5' x: 0.5260000228881836 y:28.270999908447266 z:38.683998107910156
        - atom: C5' x: 1.777999997138977 y:28.93600082397461 z:38.53799819946289
        - atom: C4' x: 2.8570001125335693 y:27.93600082397461 z:38.20399856567383
        - atom: O4' x: 3.250999927520752 y:27.259000778198242 z:39.422000885009766
        - atom: C3' x: 2.3949999809265137 y:26.836000442504883 z:37.24700164794922
        - atom: O3' x: 3.496999979019165 y:26.400999069213867 z:36.444000244140625
        - atom: C2' x: 1.9589999914169312 y:25.736000061035156 z:38.19599914550781
        - atom: C1' x: 3.0169999599456787 y:25.868000030517578 z:39.27899932861328
        - atom: N1 x: 2.696000099182129 y:25.316999435424805 z:40.617000579833984
        - atom: C2 x: 3.7639999389648438 y:24.950000762939453 z:41.40399932861328
        - atom: O2 x: 4.928999900817871 y:25.084999084472656 z:41.055999755859375
        - atom: N3 x: 3.421999931335449 y:24.41900062561035 z:42.61800003051758
        - atom: C4 x: 2.1570000648498535 y:24.222000122070312 z:43.119998931884766
        - atom: O4 x: 2.010999917984009 y:23.68400001525879 z:44.21900177001953
        - atom: C5 x: 1.0809999704360962 y:24.665000915527344 z:42.263999938964844
        - atom: C7 x: -0.328000009059906 y:24.54599952697754 z:42.757999420166016
        - atom: C6 x: 1.3980000019073486 y:25.173999786376953 z:41.064998626708984
      - residue DG has 22 atoms
        - atom: P x: 3.2839999198913574 y:26.125 z:34.874000549316406
        - atom: OP1 x: 2.9730000495910645 y:27.427000045776367 z:34.23400115966797
        - atom: OP2 x: 2.3570001125335693 y:24.972999572753906 z:34.70800018310547
        - atom: O5' x: 4.7270002365112305 y:25.694000244140625 z:34.374000549316406
        - atom: C5' x: 5.872000217437744 y:26.429000854492188 z:34.78499984741211
        - atom: C4' x: 6.8429999351501465 y:25.516000747680664 z:35.494998931884766
        - atom: O4' x: 6.228000164031982 y:24.899999618530273 z:36.65399932861328
        - atom: C3' x: 7.355000019073486 y:24.358999252319336 z:34.64799880981445
        - atom: O3' x: 8.71399974822998 y:24.148000717163086 z:35.01499938964844
        - atom: C2' x: 6.465000152587891 y:23.198999404907227 z:35.07500076293945
        - atom: C1' x: 6.324999809265137 y:23.479999542236328 z:36.55500030517578
        - atom: N9 x: 5.156000137329102 y:22.92099952697754 z:37.22999954223633
        - atom: C8 x: 3.8529999256134033 y:22.968000411987305 z:36.803001403808594
        - atom: N7 x: 3.006999969482422 y:22.51300048828125 z:37.68600082397461
        - atom: C5 x: 3.7990000247955322 y:22.11199951171875 z:38.75199890136719
        - atom: C6 x: 3.437000036239624 y:21.558000564575195 z:40.00899887084961
        - atom: O6 x: 2.309999942779541 y:21.3439998626709 z:40.45800018310547
        - atom: N1 x: 4.552999973297119 y:21.260000228881836 z:40.77899932861328
        - atom: C2 x: 5.854000091552734 y:21.476999282836914 z:40.400001525878906
        - atom: N2 x: 6.788000106811523 y:21.107999801635742 z:41.284000396728516
        - atom: N3 x: 6.209000110626221 y:22.014999389648438 z:39.24100112915039
        - atom: C4 x: 5.132999897003174 y:22.309999465942383 z:38.47100067138672
      - residue DA has 21 atoms
        - atom: P x: 9.545999526977539 y:22.961999893188477 z:34.34600067138672
        - atom: OP1 x: 10.937999725341797 y:23.468000411987305 z:34.21900177001953
        - atom: OP2 x: 8.817999839782715 y:22.490999221801758 z:33.14099884033203
        - atom: O5' x: 9.5 y:21.81399917602539 z:35.448001861572266
        - atom: C5' x: 10.081000328063965 y:22.02400016784668 z:36.736000061035156
        - atom: C4' x: 10.329000473022461 y:20.70199966430664 z:37.426998138427734
        - atom: O4' x: 9.138999938964844 y:20.261999130249023 z:38.12099838256836
        - atom: C3' x: 10.741000175476074 y:19.54400062561035 z:36.52299880981445
        - atom: O3' x: 11.741999626159668 y:18.784000396728516 z:37.20500183105469
        - atom: C2' x: 9.444000244140625 y:18.773000717163086 z:36.327999114990234
        - atom: C1' x: 8.732000350952148 y:18.981000900268555 z:37.65599822998047
        - atom: N9 x: 7.264999866485596 y:18.985000610351562 z:37.60900115966797
        - atom: C8 x: 6.453999996185303 y:19.448999404907227 z:36.606998443603516
        - atom: N7 x: 5.175000190734863 y:19.384000778198242 z:36.88800048828125
        - atom: C5 x: 5.138000011444092 y:18.83099937438965 z:38.15700149536133
        - atom: C6 x: 4.072999954223633 y:18.517000198364258 z:39.018001556396484
        - atom: N6 x: 2.7899999618530273 y:18.732999801635742 z:38.7239990234375
        - atom: N1 x: 4.375 y:17.97100067138672 z:40.21099853515625
        - atom: C2 x: 5.659999847412109 y:17.757999420166016 z:40.50899887084961
        - atom: N3 x: 6.749000072479248 y:18.011999130249023 z:39.78799819946289
        - atom: C4 x: 6.415999889373779 y:18.558000564575195 z:38.606998443603516
      - residue DT has 20 atoms
        - atom: P x: 12.317000389099121 y:17.43600082397461 z:36.55500030517578
        - atom: OP1 x: 13.734999656677246 y:17.33300018310547 z:36.98099899291992
        - atom: OP2 x: 11.979999542236328 y:17.409000396728516 z:35.11199951171875
        - atom: O5' x: 11.479000091552734 y:16.302000045776367 z:37.290000915527344
        - atom: C5' x: 11.32800006866455 y:16.334999084472656 z:38.70600128173828
        - atom: C4' x: 10.307000160217285 y:15.317999839782715 z:39.159000396728516
        - atom: O4' x: 8.970999717712402 y:15.774999618530273 z:38.867000579833984
        - atom: C3' x: 10.42199993133545 y:13.913000106811523 z:38.55099868774414
        - atom: O3' x: 10.61299991607666 y:12.967000007629395 z:39.61199951171875
        - atom: C2' x: 9.071999549865723 y:13.696999549865723 z:37.87799835205078
        - atom: C1' x: 8.182999610900879 y:14.621000289916992 z:38.68199920654297
        - atom: N1 x: 6.90500020980835 y:15.03499984741211 z:38.07099914550781
        - atom: C2 x: 5.755000114440918 y:14.852999687194824 z:38.80699920654297
        - atom: O2 x: 5.739999771118164 y:14.33899974822998 z:39.91299819946289
        - atom: N3 x: 4.610000133514404 y:15.300000190734863 z:38.196998596191406
        - atom: C4 x: 4.497000217437744 y:15.899999618530273 z:36.95600128173828
        - atom: O4 x: 3.3940000534057617 y:16.273000717163086 z:36.55699920654297
        - atom: C5 x: 5.741000175476074 y:16.042999267578125 z:36.229000091552734
        - atom: C7 x: 5.723999977111816 y:16.673999786376953 z:34.87300109863281
        - atom: C6 x: 6.864999771118164 y:15.604000091552734 z:36.8129997253418
      - residue DG has 22 atoms
        - atom: P x: 11.225000381469727 y:11.51099967956543 z:39.29899978637695
        - atom: OP1 x: 12.70300006866455 y:11.628000259399414 z:39.255001068115234
        - atom: OP2 x: 10.50100040435791 y:10.935999870300293 z:38.132999420166016
        - atom: O5' x: 10.819999694824219 y:10.654000282287598 z:40.57899856567383
        - atom: C5' x: 10.031000137329102 y:11.215999603271484 z:41.62900161743164
        - atom: C4' x: 8.626999855041504 y:10.654999732971191 z:41.597999572753906
        - atom: O4' x: 7.829999923706055 y:11.324000358581543 z:40.608001708984375
        - atom: C3' x: 8.498000144958496 y:9.168999671936035 z:41.27399826049805
        - atom: O3' x: 8.227999687194824 y:8.444999694824219 z:42.47800064086914
        - atom: C2' x: 7.328999996185303 y:9.090999603271484 z:40.29499816894531
        - atom: C1' x: 6.724999904632568 y:10.484000205993652 z:40.34600067138672
        - atom: N9 x: 6.067999839782715 y:10.968999862670898 z:39.12699890136719
        - atom: C8 x: 6.690000057220459 y:11.46500015258789 z:38.00699996948242
        - atom: N7 x: 5.853000164031982 y:11.904000282287598 z:37.10599899291992
        - atom: C5 x: 4.598999977111816 y:11.670999526977539 z:37.6510009765625
        - atom: C6 x: 3.306999921798706 y:11.958000183105469 z:37.13800048828125
        - atom: O6 x: 2.999000072479248 y:12.503999710083008 z:36.073001861572266
        - atom: N1 x: 2.312000036239624 y:11.548999786376953 z:38.00899887084961
        - atom: C2 x: 2.5190000534057617 y:10.954000473022461 z:39.215999603271484
        - atom: N2 x: 1.4140000343322754 y:10.656999588012695 z:39.900001525878906
        - atom: N3 x: 3.7149999141693115 y:10.678999900817871 z:39.7130012512207
        - atom: C4 x: 4.704999923706055 y:11.067999839782715 z:38.88600158691406
      - residue DC has 19 atoms
        - atom: P x: 8.17199993133545 y:6.841000080108643 z:42.446998596191406
        - atom: OP1 x: 8.222999572753906 y:6.381999969482422 z:43.845001220703125
        - atom: OP2 x: 9.154999732971191 y:6.321000099182129 z:41.47800064086914
        - atom: O5' x: 6.704999923706055 y:6.544000148773193 z:41.90299987792969
        - atom: C5' x: 5.586999893188477 y:6.679999828338623 z:42.770999908447266
        - atom: C4' x: 4.313000202178955 y:6.329999923706055 z:42.04499816894531
        - atom: O4' x: 4.117000102996826 y:7.260000228881836 z:40.965999603271484
        - atom: C3' x: 4.315999984741211 y:4.946000099182129 z:41.40299987792969
        - atom: O3' x: 3.621000051498413 y:4.050000190734863 z:42.27799987792969
        - atom: C2' x: 3.617000102996826 y:5.1479997634887695 z:40.055999755859375
        - atom: C1' x: 3.2750000953674316 y:6.645999908447266 z:40.01100158691406
        - atom: N1 x: 3.4820001125335693 y:7.343999862670898 z:38.71900177001953
        - atom: C2 x: 2.378000020980835 y:7.947999954223633 z:38.071998596191406
        - atom: O2 x: 1.2549999952316284 y:7.870999813079834 z:38.58700180053711
        - atom: N3 x: 2.571000099182129 y:8.600000381469727 z:36.9109992980957
        - atom: C4 x: 3.7929999828338623 y:8.67300033569336 z:36.38600158691406
        - atom: N4 x: 3.941999912261963 y:9.338000297546387 z:35.24399948120117
        - atom: C5 x: 4.923999786376953 y:8.069000244140625 z:37.013999938964844
        - atom: C6 x: 4.724999904632568 y:7.420000076293945 z:38.16299819946289
      - residue DG has 22 atoms
        - atom: P x: 3.5369999408721924 y:2.490000009536743 z:41.92900085449219
        - atom: OP1 x: 3.2130000591278076 y:1.7960000038146973 z:43.191001892089844
        - atom: OP2 x: 4.730999946594238 y:2.0999999046325684 z:41.15800094604492
        - atom: O5' x: 2.25 y:2.365000009536743 z:41.00199890136719
        - atom: C5' x: 0.9470000267028809 y:2.680999994277954 z:41.50899887084961
        - atom: C4' x: -0.08699999749660492 y:2.5480000972747803 z:40.415000915527344
        - atom: O4' x: 0.22200000286102295 y:3.51200008392334 z:39.380001068115234
        - atom: C3' x: -0.08799999952316284 y:1.1829999685287476 z:39.724998474121094
        - atom: O3' x: -1.4179999828338623 y:0.8140000104904175 z:39.356998443603516
        - atom: C2' x: 0.7760000228881836 y:1.4210000038146973 z:38.50400161743164
        - atom: C1' x: 0.375 y:2.8369998931884766 z:38.14500045776367
        - atom: N9 x: 1.3359999656677246 y:3.5820000171661377 z:37.33599853515625
        - atom: C8 x: 2.7079999446868896 y:3.490000009536743 z:37.36399841308594
        - atom: N7 x: 3.2909998893737793 y:4.26800012588501 z:36.49399948120117
        - atom: C5 x: 2.243000030517578 y:4.920000076293945 z:35.858001708984375
        - atom: C6 x: 2.259000062942505 y:5.873000144958496 z:34.814998626708984
        - atom: O6 x: 3.2360000610351562 y:6.339000225067139 z:34.21500015258789
        - atom: N1 x: 0.9739999771118164 y:6.2789998054504395 z:34.470001220703125
        - atom: C2 x: -0.17900000512599945 y:5.818999767303467 z:35.04999923706055
        - atom: N2 x: -1.3250000476837158 y:6.327000141143799 z:34.58100128173828
        - atom: N3 x: -0.20900000631809235 y:4.921999931335449 z:36.020999908447266
        - atom: C4 x: 1.031999945640564 y:4.517000198364258 z:36.37200164794922
      - residue DC has 19 atoms
        - atom: P x: -1.694000005722046 y:-0.6140000224113464 z:38.65599822998047
        - atom: OP1 x: -2.994999885559082 y:-1.1480000019073486 z:39.14899826049805
        - atom: OP2 x: -0.46000000834465027 y:-1.430999994277954 z:38.821998596191406
        - atom: O5' x: -1.8730000257492065 y:-0.24400000274181366 z:37.11000061035156
        - atom: C5' x: -2.808000087738037 y:0.7670000195503235 z:36.698001861572266
        - atom: C4' x: -2.8580000400543213 y:0.8840000033378601 z:35.1879997253418
        - atom: O4' x: -1.7769999504089355 y:1.7239999771118164 z:34.69900131225586
        - atom: C3' x: -2.756999969482422 y:-0.4309999942779541 z:34.39899826049805
        - atom: O3' x: -3.569999933242798 y:-0.4269999861717224 z:33.20000076293945
        - atom: C2' x: -1.312000036239624 y:-0.4320000112056732 z:33.9370002746582
        - atom: C1' x: -1.125 y:1.0440000295639038 z:33.637001037597656
        - atom: N1 x: 0.2680000066757202 y:1.524999976158142 z:33.55699920654297
        - atom: C2 x: 0.5590000152587891 y:2.6029999256134033 z:32.71099853515625
        - atom: O2 x: -0.36800000071525574 y:3.1510000228881836 z:32.09000015258789
        - atom: N3 x: 1.8370000123977661 y:3.0220000743865967 z:32.59600067138672
        - atom: C4 x: 2.8010001182556152 y:2.4200000762939453 z:33.29399871826172
        - atom: N4 x: 4.046999931335449 y:2.8559999465942383 z:33.137001037597656
        - atom: C5 x: 2.5299999713897705 y:1.3420000076293945 z:34.178001403808594
        - atom: C6 x: 1.2660000324249268 y:0.9300000071525574 z:34.27899932861328
      - residue MN has 1 atoms
        - atom: MN x: -0.07199999690055847 y:21.77899932861328 z:37.319000244140625
      - residue HOH has 1 atoms
        - atom: O x: 6.046000003814697 y:3.1649999618530273 z:39.082000732421875
      - residue HOH has 1 atoms
        - atom: O x: 13.569999694824219 y:10.14799976348877 z:41.25299835205078
      - residue HOH has 1 atoms
        - atom: O x: -5.609000205993652 y:-0.41600000858306885 z:34.5
      - residue HOH has 1 atoms
        - atom: O x: 4.633999824523926 y:30.27400016784668 z:40.766998291015625
      - residue HOH has 1 atoms
        - atom: O x: -5.763999938964844 y:33.71799850463867 z:44.33599853515625
      - residue HOH has 1 atoms
        - atom: O x: 2.937000036239624 y:31.315000534057617 z:42.645999908447266
      - residue HOH has 1 atoms
        - atom: O x: 7.23199987411499 y:5.645999908447266 z:38.564998626708984
 - chain  <Chain id=D> has 9 residues
      - residue DG has 23 atoms
        - atom: OP3 x: 21.908000946044922 y:-5.788000106811523 z:31.12700080871582
        - atom: P x: 22.32200050354004 y:-5.873000144958496 z:29.663000106811523
        - atom: OP1 x: 23.104999542236328 y:-4.658999919891357 z:29.17799949645996
        - atom: OP2 x: 22.988000869750977 y:-7.199999809265137 z:29.34600067138672
        - atom: O5' x: 20.930999755859375 y:-5.881999969482422 z:28.815000534057617
        - atom: C5' x: 19.81999969482422 y:-6.675000190734863 z:29.256000518798828
        - atom: C4' x: 19.066999435424805 y:-7.238999843597412 z:28.073999404907227
        - atom: O4' x: 18.231000900268555 y:-6.247000217437744 z:27.457000732421875
        - atom: C3' x: 19.908000946044922 y:-7.807000160217285 z:26.941999435424805
        - atom: O3' x: 19.149999618530273 y:-8.842000007629395 z:26.315000534057617
        - atom: C2' x: 20.09000015258789 y:-6.60699987411499 z:26.030000686645508
        - atom: C1' x: 18.798999786376953 y:-5.822999954223633 z:26.229999542236328
        - atom: N9 x: 18.93199920654297 y:-4.373000144958496 z:26.301000595092773
        - atom: C8 x: 19.9060001373291 y:-3.635999917984009 z:26.934999465942383
        - atom: N7 x: 19.700000762939453 y:-2.3499999046325684 z:26.86199951171875
        - atom: C5 x: 18.525999069213867 y:-2.2360000610351562 z:26.134000778198242
        - atom: C6 x: 17.79400062561035 y:-1.0950000286102295 z:25.75200080871582
        - atom: O6 x: 18.014999389648438 y:0.0860000029206276 z:26.02899932861328
        - atom: N1 x: 16.68000030517578 y:-1.4359999895095825 z:24.983999252319336
        - atom: C2 x: 16.304000854492188 y:-2.7179999351501465 z:24.660999298095703
        - atom: N2 x: 15.206000328063965 y:-2.86299991607666 z:23.91699981689453
        - atom: N3 x: 16.96299934387207 y:-3.7890000343322754 z:25.04400062561035
        - atom: C4 x: 18.05699920654297 y:-3.4769999980926514 z:25.764999389648438
      - residue DT has 20 atoms
        - atom: P x: 19.722999572753906 y:-9.595000267028809 z:25.020999908447266
        - atom: OP1 x: 19.643999099731445 y:-11.03600025177002 z:25.367000579833984
        - atom: OP2 x: 21.0049991607666 y:-9.012999534606934 z:24.559999465942383
        - atom: O5' x: 18.625999450683594 y:-9.286999702453613 z:23.91699981689453
        - atom: C5' x: 17.94099998474121 y:-8.050000190734863 z:23.905000686645508
        - atom: C4' x: 17.011999130249023 y:-7.999000072479248 z:22.722000122070312
        - atom: O4' x: 16.64699935913086 y:-6.625 z:22.472999572753906
        - atom: C3' x: 17.648000717163086 y:-8.508000373840332 z:21.43199920654297
        - atom: O3' x: 16.665000915527344 y:-9.154999732971191 z:20.62299919128418
        - atom: C2' x: 18.21299934387207 y:-7.251999855041504 z:20.790000915527344
        - atom: C1' x: 17.34600067138672 y:-6.119999885559082 z:21.343000411987305
        - atom: N1 x: 18.05500030517578 y:-4.886000156402588 z:21.767000198364258
        - atom: C2 x: 17.41699981689453 y:-3.680999994277954 z:21.559999465942383
        - atom: O2 x: 16.343000411987305 y:-3.5769999027252197 z:20.979000091552734
        - atom: N3 x: 18.089000701904297 y:-2.5910000801086426 z:22.051000595092773
        - atom: C4 x: 19.31100082397461 y:-2.578000068664551 z:22.687000274658203
        - atom: O4 x: 19.77400016784668 y:-1.5240000486373901 z:23.097999572753906
        - atom: C5 x: 19.947999954223633 y:-3.859999895095825 z:22.822999954223633
        - atom: C7 x: 21.301000595092773 y:-3.927000045776367 z:23.461000442504883
        - atom: C6 x: 19.29599952697754 y:-4.940000057220459 z:22.368000030517578
      - residue DC has 19 atoms
        - atom: P x: 17.084999084472656 y:-9.819999694824219 z:19.219999313354492
        - atom: OP1 x: 16.177000045776367 y:-10.982000350952148 z:18.999000549316406
        - atom: OP2 x: 18.55699920654297 y:-10.012999534606934 z:19.167999267578125
        - atom: O5' x: 16.697999954223633 y:-8.699999809265137 z:18.16200065612793
        - atom: C5' x: 15.357000350952148 y:-8.246999740600586 z:18.04599952697754
        - atom: C4' x: 15.291000366210938 y:-7.078000068664551 z:17.093000411987305
        - atom: O4' x: 15.998000144958496 y:-5.955999851226807 z:17.679000854492188
        - atom: C3' x: 15.972000122070312 y:-7.322999954223633 z:15.744999885559082
        - atom: O3' x: 15.348999977111816 y:-6.510000228881836 z:14.746000289916992
        - atom: C2' x: 17.37299919128418 y:-6.801000118255615 z:15.98900032043457
        - atom: C1' x: 17.03700065612793 y:-5.560999870300293 z:16.798999786376953
        - atom: N1 x: 18.117000579833984 y:-4.954999923706055 z:17.600000381469727
        - atom: C2 x: 18.066999435424805 y:-3.5810000896453857 z:17.847000122070312
        - atom: O2 x: 17.121999740600586 y:-2.9189999103546143 z:17.381999969482422
        - atom: N3 x: 19.047000885009766 y:-3.00600004196167 z:18.57200050354004
        - atom: C4 x: 20.05699920654297 y:-3.744999885559082 z:19.03499984741211
        - atom: N4 x: 21.01300048828125 y:-3.13100004196167 z:19.738000869750977
        - atom: C5 x: 20.13599967956543 y:-5.1479997634887695 z:18.79599952697754
        - atom: C6 x: 19.152999877929688 y:-5.706999778747559 z:18.086000442504883
      - residue DG has 22 atoms
        - atom: P x: 15.234000205993652 y:-7.048999786376953 z:13.239999771118164
        - atom: OP1 x: 14.206999778747559 y:-8.126999855041504 z:13.246000289916992
        - atom: OP2 x: 16.608999252319336 y:-7.3379998207092285 z:12.744999885559082
        - atom: O5' x: 14.673999786376953 y:-5.798999786376953 z:12.423999786376953
        - atom: C5' x: 13.835000038146973 y:-4.823999881744385 z:13.045000076293945
        - atom: C4' x: 14.350000381469727 y:-3.431999921798706 z:12.758999824523926
        - atom: O4' x: 15.515000343322754 y:-3.1540000438690186 z:13.57800006866455
        - atom: C3' x: 14.777999877929688 y:-3.1989998817443848 z:11.3100004196167
        - atom: O3' x: 14.291000366210938 y:-1.9329999685287476 z:10.85200023651123
        - atom: C2' x: 16.29599952697754 y:-3.2109999656677246 z:11.37399959564209
        - atom: C1' x: 16.589000701904297 y:-2.687999963760376 z:12.770999908447266
        - atom: N9 x: 17.82900047302246 y:-3.2009999752044678 z:13.35200023651123
        - atom: C8 x: 18.270000457763672 y:-4.50600004196167 z:13.321000099182129
        - atom: N7 x: 19.4060001373291 y:-4.679999828338623 z:13.937999725341797
        - atom: C5 x: 19.740999221801758 y:-3.4179999828338623 z:14.406999588012695
        - atom: C6 x: 20.8700008392334 y:-2.99399995803833 z:15.142999649047852
        - atom: O6 x: 21.81599998474121 y:-3.6710000038146973 z:15.54800033569336
        - atom: N1 x: 20.833999633789062 y:-1.628999948501587 z:15.395999908447266
        - atom: C2 x: 19.836000442504883 y:-0.7789999842643738 z:14.994000434875488
        - atom: N2 x: 19.996999740600586 y:0.5090000033378601 z:15.331999778747559
        - atom: N3 x: 18.766000747680664 y:-1.1640000343322754 z:14.309000015258789
        - atom: C4 x: 18.785999298095703 y:-2.489000082015991 z:14.050000190734863
      - residue DG has 22 atoms
        - atom: P x: 14.321999549865723 y:-1.5820000171661377 z:9.281999588012695
        - atom: OP1 x: 13.01200008392334 y:-0.9649999737739563 z:8.95199966430664
        - atom: OP2 x: 14.77400016784668 y:-2.7820000648498535 z:8.529999732971191
        - atom: O5' x: 15.46500015258789 y:-0.47600001096725464 z:9.168999671936035
        - atom: C5' x: 15.302000045776367 y:0.796999990940094 z:9.78600025177002
        - atom: C4' x: 16.645999908447266 y:1.4179999828338623 z:10.090999603271484
        - atom: O4' x: 17.479999542236328 y:0.46399998664855957 z:10.789999961853027
        - atom: C3' x: 17.46299934387207 y:1.8680000305175781 z:8.876999855041504
        - atom: O3' x: 18.23699951171875 y:3.005000114440918 z:9.279000282287598
        - atom: C2' x: 18.448999404907227 y:0.7289999723434448 z:8.701000213623047
        - atom: C1' x: 18.743999481201172 y:0.4269999861717224 z:10.154000282287598
        - atom: N9 x: 19.35700035095215 y:-0.8669999837875366 z:10.437000274658203
        - atom: C8 x: 18.961999893188477 y:-2.0980000495910645 z:9.970000267028809
        - atom: N7 x: 19.707000732421875 y:-3.0769999027252197 z:10.41100025177002
        - atom: C5 x: 20.650999069213867 y:-2.4560000896453857 z:11.215999603271484
        - atom: C6 x: 21.711999893188477 y:-3.006999969482422 z:11.972000122070312
        - atom: O6 x: 22.041000366210938 y:-4.203999996185303 z:12.086999893188477
        - atom: N1 x: 22.422000885009766 y:-2.015000104904175 z:12.651000022888184
        - atom: C2 x: 22.142000198364258 y:-0.6679999828338623 z:12.607999801635742
        - atom: N2 x: 22.93899917602539 y:0.13600000739097595 z:13.335000038146973
        - atom: N3 x: 21.152999877929688 y:-0.1459999978542328 z:11.904999732971191
        - atom: C4 x: 20.45199966430664 y:-1.090000033378601 z:11.239999771118164
      - residue HOH has 1 atoms
        - atom: O x: 18.135000228881836 y:3.9839999675750732 z:12.008999824523926
      - residue HOH has 1 atoms
        - atom: O x: 13.862000465393066 y:-5.619999885559082 z:23.08300018310547
      - residue HOH has 1 atoms
        - atom: O x: 21.132999420166016 y:-7.02400016784668 z:13.020999908447266
      - residue HOH has 1 atoms
        - atom: O x: 24.173999786376953 y:-5.079999923706055 z:33.534000396728516
 - chain  <Chain id=A> has 427 residues
      - residue THR has 7 atoms
        - atom: N x: 3.50600004196167 y:-24.027999877929688 z:29.959999084472656
        - atom: CA x: 4.690999984741211 y:-23.68400001525879 z:30.798999786376953
        - atom: C x: 5.771999835968018 y:-24.729000091552734 z:30.599000930786133
        - atom: O x: 6.264999866485596 y:-25.347000122070312 z:31.542999267578125
        - atom: CB x: 4.321000099182129 y:-23.61400032043457 z:32.292999267578125
        - atom: OG1 x: 4.0879998207092285 y:-24.940000534057617 z:32.81100082397461
        - atom: CG2 x: 3.069000005722046 y:-22.75 z:32.46699905395508
      - residue LEU has 8 atoms
        - atom: N x: 6.114999771118164 y:-24.933000564575195 z:29.336999893188477
        - atom: CA x: 7.14900016784668 y:-25.878000259399414 z:28.98900032043457
        - atom: C x: 8.472999572753906 y:-25.23200035095215 z:29.381999969482422
        - atom: O x: 9.387999534606934 y:-25.909000396728516 z:29.861000061035156
        - atom: CB x: 7.109000205993652 y:-26.163999557495117 z:27.488000869750977
        - atom: CG x: 5.886000156402588 y:-26.91900062561035 z:26.95199966430664
        - atom: CD1 x: 6.002999782562256 y:-27.079999923706055 z:25.44099998474121
        - atom: CD2 x: 5.789999961853027 y:-28.275999069213867 z:27.613000869750977
      - residue ASN has 8 atoms
        - atom: N x: 8.552000045776367 y:-23.913999557495117 z:29.201000213623047
        - atom: CA x: 9.74899959564209 y:-23.145999908447266 z:29.527999877929688
        - atom: C x: 9.545999526977539 y:-22.253000259399414 z:30.756999969482422
        - atom: O x: 10.102999687194824 y:-21.159000396728516 z:30.836000442504883
        - atom: CB x: 10.137999534606934 y:-22.27899932861328 z:28.33799934387207
        - atom: CG x: 10.458000183105469 y:-23.090999603271484 z:27.111000061035156
        - atom: OD1 x: 11.486000061035156 y:-23.759000778198242 z:27.051000595092773
        - atom: ND2 x: 9.572999954223633 y:-23.04400062561035 z:26.121000289916992
      - residue GLY has 4 atoms
        - atom: N x: 8.763999938964844 y:-22.740999221801758 z:31.716999053955078
        - atom: CA x: 8.47599983215332 y:-21.97800064086914 z:32.922000885009766
        - atom: C x: 9.657999992370605 y:-21.47800064086914 z:33.73500061035156
        - atom: O x: 9.645999908447266 y:-20.341999053955078 z:34.20500183105469
      - residue GLY has 4 atoms
        - atom: N x: 10.67199993133545 y:-22.316999435424805 z:33.91999816894531
        - atom: CA x: 11.829999923706055 y:-21.899999618530273 z:34.689998626708984
        - atom: C x: 12.550999641418457 y:-20.709999084472656 z:34.073001861572266
        - atom: O x: 13.067000389099121 y:-19.834999084472656 z:34.7869987487793
      - residue ILE has 8 atoms
        - atom: N x: 12.583999633789062 y:-20.67799949645996 z:32.74399948120117
        - atom: CA x: 13.246000289916992 y:-19.611000061035156 z:32.01900100708008
        - atom: C x: 12.480999946594238 y:-18.308000564575195 z:32.0890007019043
        - atom: O x: 13.067999839782715 y:-17.257999420166016 z:32.32899856567383
        - atom: CB x: 13.434000015258789 y:-19.965999603271484 z:30.530000686645508
        - atom: CG1 x: 14.45300006866455 y:-21.104000091552734 z:30.38800048828125
        - atom: CG2 x: 13.859999656677246 y:-18.719999313354492 z:29.7450008392334
        - atom: CD1 x: 14.708000183105469 y:-21.54400062561035 z:28.957000732421875
      - residue THR has 7 atoms
        - atom: N x: 11.17199993133545 y:-18.36400032043457 z:31.886999130249023
        - atom: CA x: 10.392000198364258 y:-17.139999389648438 z:31.91200065612793
        - atom: C x: 10.234000205993652 y:-16.545000076293945 z:33.3129997253418
        - atom: O x: 9.973999977111816 y:-15.357000350952148 z:33.44300079345703
        - atom: CB x: 9.015999794006348 y:-17.327999114990234 z:31.190000534057617
        - atom: OG1 x: 8.112000465393066 y:-18.10099983215332 z:31.989999771118164
        - atom: CG2 x: 9.234999656677246 y:-18.034000396728516 z:29.868000030517578
      - residue ASP has 8 atoms
        - atom: N x: 10.395000457763672 y:-17.35700035095215 z:34.356998443603516
        - atom: CA x: 10.33899974822998 y:-16.850000381469727 z:35.73699951171875
        - atom: C x: 11.638999938964844 y:-16.07200050354004 z:35.959999084472656
        - atom: O x: 11.659000396728516 y:-14.982999801635742 z:36.53799819946289
        - atom: CB x: 10.298999786376953 y:-17.98699951171875 z:36.75400161743164
        - atom: CG x: 8.946999549865723 y:-18.631000518798828 z:36.85300064086914
        - atom: OD1 x: 7.943999767303467 y:-17.89299964904785 z:36.93299865722656
        - atom: OD2 x: 8.88599967956543 y:-19.878000259399414 z:36.87099838256836
      - residue MET has 8 atoms
        - atom: N x: 12.729999542236328 y:-16.667999267578125 z:35.49599838256836
        - atom: CA x: 14.029999732971191 y:-16.049999237060547 z:35.595001220703125
        - atom: C x: 13.96500015258789 y:-14.680999755859375 z:34.904998779296875
        - atom: O x: 14.3149995803833 y:-13.659000396728516 z:35.48699951171875
        - atom: CB x: 15.060999870300293 y:-16.926000595092773 z:34.89899826049805
        - atom: CG x: 16.468000411987305 y:-16.416000366210938 z:35.000999450683594
        - atom: SD x: 17.45599937438965 y:-17.030000686645508 z:33.643001556396484
        - atom: CE x: 18.0049991607666 y:-15.479999542236328 z:32.88600158691406
      - residue LEU has 8 atoms
        - atom: N x: 13.51099967956543 y:-14.67199993133545 z:33.659000396728516
        - atom: CA x: 13.411999702453613 y:-13.447999954223633 z:32.88999938964844
        - atom: C x: 12.569999694824219 y:-12.394000053405762 z:33.59400177001953
        - atom: O x: 12.833000183105469 y:-11.189000129699707 z:33.472999572753906
        - atom: CB x: 12.795000076293945 y:-13.741000175476074 z:31.5310001373291
        - atom: CG x: 13.562000274658203 y:-14.668999671936035 z:30.604000091552734
        - atom: CD1 x: 12.758000373840332 y:-14.875 z:29.336999893188477
        - atom: CD2 x: 14.91100025177002 y:-14.074000358581543 z:30.27899932861328
      - residue THR has 7 atoms
        - atom: N x: 11.553000450134277 y:-12.848999977111816 z:34.323001861572266
        - atom: CA x: 10.657999992370605 y:-11.9399995803833 z:35.02000045776367
        - atom: C x: 11.28600025177002 y:-11.27299976348877 z:36.21799850463867
        - atom: O x: 11.097000122070312 y:-10.074999809265137 z:36.4109992980957
        - atom: CB x: 9.369000434875488 y:-12.640999794006348 z:35.45600128173828
        - atom: OG1 x: 8.581999778747559 y:-12.916000366210938 z:34.29399871826172
        - atom: CG2 x: 8.564000129699707 y:-11.765999794006348 z:36.387001037597656
      - residue GLU has 9 atoms
        - atom: N x: 12.020999908447266 y:-12.038000106811523 z:37.02199935913086
        - atom: CA x: 12.682999610900879 y:-11.47599983215332 z:38.189998626708984
        - atom: C x: 13.690999984741211 y:-10.45199966430664 z:37.67300033569336
        - atom: O x: 13.807000160217285 y:-9.345000267028809 z:38.196998596191406
        - atom: CB x: 13.37399959564209 y:-12.588000297546387 z:38.98899841308594
        - atom: CG x: 14.23799991607666 y:-12.11400032043457 z:40.15599822998047
        - atom: CD x: 14.40999984741211 y:-13.187000274658203 z:41.233001708984375
        - atom: OE1 x: 14.732999801635742 y:-14.33899974822998 z:40.88600158691406
        - atom: OE2 x: 14.22599983215332 y:-12.878000259399414 z:42.43600082397461
      - residue LEU has 8 atoms
        - atom: N x: 14.407999992370605 y:-10.817999839782715 z:36.62200164794922
        - atom: CA x: 15.376999855041504 y:-9.906000137329102 z:36.029998779296875
        - atom: C x: 14.710000038146973 y:-8.588000297546387 z:35.63999938964844
        - atom: O x: 15.276000022888184 y:-7.519999980926514 z:35.840999603271484
        - atom: CB x: 16.006000518798828 y:-10.550999641418457 z:34.801998138427734
        - atom: CG x: 17.10099983215332 y:-11.543000221252441 z:35.15599822998047
        - atom: CD1 x: 17.541000366210938 y:-12.317999839782715 z:33.928001403808594
        - atom: CD2 x: 18.26300048828125 y:-10.758000373840332 z:35.744998931884766
      - residue ALA has 5 atoms
        - atom: N x: 13.50100040435791 y:-8.6850004196167 z:35.09000015258789
        - atom: CA x: 12.727999687194824 y:-7.525000095367432 z:34.66899871826172
        - atom: C x: 12.454999923706055 y:-6.618000030517578 z:35.85900115966797
        - atom: O x: 12.86400032043457 y:-5.453999996185303 z:35.887001037597656
        - atom: CB x: 11.416000366210938 y:-7.9730000495910645 z:34.04499816894531
      - residue ASN has 8 atoms
        - atom: N x: 11.75100040435791 y:-7.1519999504089355 z:36.84299850463867
        - atom: CA x: 11.447999954223633 y:-6.377999782562256 z:38.02799987792969
        - atom: C x: 12.694999694824219 y:-5.685999870300293 z:38.54800033569336
        - atom: O x: 12.654999732971191 y:-4.507999897003174 z:38.917999267578125
        - atom: CB x: 10.857000350952148 y:-7.275000095367432 z:39.09700012207031
        - atom: CG x: 9.361000061035156 y:-7.355999946594238 z:38.999000549316406
        - atom: OD1 x: 8.668000221252441 y:-6.34499979019165 z:39.154998779296875
        - atom: ND2 x: 8.843999862670898 y:-8.548999786376953 z:38.73500061035156
      - residue PHE has 11 atoms
        - atom: N x: 13.807000160217285 y:-6.414000034332275 z:38.56399917602539
        - atom: CA x: 15.053000450134277 y:-5.831999778747559 z:39.0260009765625
        - atom: C x: 15.369000434875488 y:-4.565999984741211 z:38.233001708984375
        - atom: O x: 15.411999702453613 y:-3.4700000286102295 z:38.79100036621094
        - atom: CB x: 16.20800018310547 y:-6.817999839782715 z:38.86600112915039
        - atom: CG x: 17.55500030517578 y:-6.203999996185303 z:39.13100051879883
        - atom: CD1 x: 18.569000244140625 y:-6.275000095367432 z:38.180999755859375
        - atom: CD2 x: 17.791000366210938 y:-5.498000144958496 z:40.30799865722656
        - atom: CE1 x: 19.79800033569336 y:-5.644000053405762 z:38.39899826049805
        - atom: CE2 x: 19.00200080871582 y:-4.873000144958496 z:40.52799987792969
        - atom: CZ x: 20.007999420166016 y:-4.941999912261963 z:39.57600021362305
      - residue GLU has 9 atoms
        - atom: N x: 15.581000328063965 y:-4.728000164031982 z:36.926998138427734
        - atom: CA x: 15.913999557495117 y:-3.611999988555908 z:36.04999923706055
        - atom: C x: 14.92199993133545 y:-2.4560000896453857 z:36.1609992980957
        - atom: O x: 15.28499984741211 y:-1.3009999990463257 z:35.96900177001953
        - atom: CB x: 16.007999420166016 y:-4.086999893188477 z:34.59299850463867
        - atom: CG x: 17.152000427246094 y:-5.060999870300293 z:34.27799987792969
        - atom: CD x: 18.538000106811523 y:-4.489999771118164 z:34.58700180053711
        - atom: OE1 x: 18.69700050354004 y:-3.260999917984009 z:34.5260009765625
        - atom: OE2 x: 19.479000091552734 y:-5.265999794006348 z:34.875
      - residue LYS has 9 atoms
        - atom: N x: 13.677000045776367 y:-2.7669999599456787 z:36.48400115966797
        - atom: CA x: 12.642999649047852 y:-1.753000020980835 z:36.61600112915039
        - atom: C x: 12.543999671936035 y:-1.121999979019165 z:37.99599838256836
        - atom: O x: 12.244000434875488 y:0.06400000303983688 z:38.12799835205078
        - atom: CB x: 11.277999877929688 y:-2.3440001010894775 z:36.2859992980957
        - atom: CG x: 10.192999839782715 y:-1.8370000123977661 z:37.207000732421875
        - atom: CD x: 8.888999938964844 y:-1.6490000486373901 z:36.49800109863281
        - atom: CE x: 8.100000381469727 y:-0.546999990940094 z:37.20000076293945
        - atom: NZ x: 8.9350004196167 y:0.6930000185966492 z:37.34199905395508
      - residue ASN has 8 atoms
        - atom: N x: 12.75100040435791 y:-1.9199999570846558 z:39.03200149536133
        - atom: CA x: 12.637999534606934 y:-1.3869999647140503 z:40.36899948120117
        - atom: C x: 13.968000411987305 y:-0.8429999947547913 z:40.900001525878906
        - atom: O x: 14.02299976348877 y:0.24799999594688416 z:41.45899963378906
        - atom: CB x: 12.067999839782715 y:-2.4579999446868896 z:41.319000244140625
        - atom: CG x: 10.592000007629395 y:-2.7790000438690186 z:41.04800033569336
        - atom: OD1 x: 9.795999526977539 y:-1.8949999809265137 z:40.73699951171875
        - atom: ND2 x: 10.22700023651123 y:-4.045000076293945 z:41.18899917602539
      - residue VAL has 7 atoms
        - atom: N x: 15.041999816894531 y:-1.590999960899353 z:40.698001861572266
        - atom: CA x: 16.341999053955078 y:-1.1859999895095825 z:41.19900131225586
        - atom: C x: 17.093000411987305 y:-0.3190000057220459 z:40.21500015258789
        - atom: O x: 17.384000778198242 y:0.828000009059906 z:40.51300048828125
        - atom: CB x: 17.204999923706055 y:-2.4189999103546143 z:41.53900146484375
        - atom: CG1 x: 18.464000701904297 y:-1.99399995803833 z:42.32699966430664
        - atom: CG2 x: 16.385000228881836 y:-3.4179999828338623 z:42.33000183105469
      - residue SER has 6 atoms
        - atom: N x: 17.406999588012695 y:-0.871999979019165 z:39.04600143432617
        - atom: CA x: 18.14699935913086 y:-0.14800000190734863 z:37.999000549316406
        - atom: C x: 17.43199920654297 y:1.0440000295639038 z:37.369998931884766
        - atom: O x: 18.065000534057617 y:1.8589999675750732 z:36.69300079345703
        - atom: CB x: 18.55500030517578 y:-1.0989999771118164 z:36.875
        - atom: OG x: 19.535999298095703 y:-2.0239999294281006 z:37.31100082397461
      - residue GLN has 9 atoms
        - atom: N x: 16.125 y:1.1460000276565552 z:37.58000183105469
        - atom: CA x: 15.355999946594238 y:2.244999885559082 z:37.012001037597656
        - atom: C x: 15.548999786376953 y:2.385999917984009 z:35.499000549316406
        - atom: O x: 15.527999877929688 y:3.4839999675750732 z:34.96200180053711
        - atom: CB x: 15.715999603271484 y:3.553999900817871 z:37.7140007019043
        - atom: CG x: 15.02299976348877 y:3.7219998836517334 z:39.07899856567383
        - atom: CD x: 15.668000221252441 y:4.795000076293945 z:39.96500015258789
        - atom: OE1 x: 16.8799991607666 y:4.752999782562256 z:40.2400016784668
        - atom: NE2 x: 14.861000061035156 y:5.743000030517578 z:40.42499923706055
      - residue ALA has 5 atoms
        - atom: N x: 15.746000289916992 y:1.2569999694824219 z:34.82899856567383
        - atom: CA x: 15.914999961853027 y:1.1920000314712524 z:33.37699890136719
        - atom: C x: 14.652999877929688 y:0.49300000071525574 z:32.85499954223633
        - atom: O x: 14.583000183105469 y:-0.7369999885559082 z:32.79999923706055
        - atom: CB x: 17.15399932861328 y:0.3790000081062317 z:33.03300094604492
      - residue ILE has 8 atoms
        - atom: N x: 13.656999588012695 y:1.2949999570846558 z:32.49599838256836
        - atom: CA x: 12.378000259399414 y:0.7940000295639038 z:32.0260009765625
        - atom: C x: 12.460000038146973 y:0.032999999821186066 z:30.702999114990234
        - atom: O x: 11.57699966430664 y:-0.7519999742507935 z:30.37299919128418
        - atom: CB x: 11.407999992370605 y:1.9550000429153442 z:31.85700035095215
        - atom: CG1 x: 10.034000396728516 y:1.4700000286102295 z:31.36199951171875
        - atom: CG2 x: 12.008999824523926 y:2.937000036239624 z:30.867000579833984
        - atom: CD1 x: 9.13700008392334 y:0.8830000162124634 z:32.4379997253418
      - residue HIS has 10 atoms
        - atom: N x: 13.517000198364258 y:0.2529999911785126 z:29.94099998474121
        - atom: CA x: 13.626999855041504 y:-0.42500001192092896 z:28.665000915527344
        - atom: C x: 14.244000434875488 y:-1.7960000038146973 z:28.760000228881836
        - atom: O x: 14.008999824523926 y:-2.6500000953674316 z:27.905000686645508
        - atom: CB x: 14.366999626159668 y:0.4620000123977661 z:27.674999237060547
        - atom: CG x: 13.645999908447266 y:1.7430000305175781 z:27.393999099731445
        - atom: ND1 x: 12.3100004196167 y:1.7760000228881836 z:27.051000595092773
        - atom: CD2 x: 14.04800033569336 y:3.0329999923706055 z:27.476999282836914
        - atom: CE1 x: 11.918999671936035 y:3.0320000648498535 z:26.941999435424805
        - atom: NE2 x: 12.954000473022461 y:3.813999891281128 z:27.19499969482422
      - residue LYS has 9 atoms
        - atom: N x: 15.031999588012695 y:-2.0220000743865967 z:29.798999786376953
        - atom: CA x: 15.621000289916992 y:-3.3359999656677246 z:29.981000900268555
        - atom: C x: 14.463000297546387 y:-4.136000156402588 z:30.52199935913086
        - atom: O x: 14.262999534606934 y:-5.2829999923706055 z:30.141000747680664
        - atom: CB x: 16.773000717163086 y:-3.299999952316284 z:30.996000289916992
        - atom: CG x: 17.975000381469727 y:-2.4779999256134033 z:30.540000915527344
        - atom: CD x: 19.246000289916992 y:-2.9200000762939453 z:31.253000259399414
        - atom: CE x: 20.474000930786133 y:-2.2990000247955322 z:30.60099983215332
        - atom: NZ x: 21.74799919128418 y:-2.9100000858306885 z:31.034000396728516
      - residue TYR has 12 atoms
        - atom: N x: 13.689000129699707 y:-3.5139999389648438 z:31.408000946044922
        - atom: CA x: 12.527999877929688 y:-4.175000190734863 z:31.989999771118164
        - atom: C x: 11.668999671936035 y:-4.672999858856201 z:30.836999893188477
        - atom: O x: 11.380999565124512 y:-5.86899995803833 z:30.731000900268555
        - atom: CB x: 11.722999572753906 y:-3.194999933242798 z:32.847999572753906
        - atom: CG x: 10.309000015258789 y:-3.6470000743865967 z:33.15999984741211
        - atom: CD1 x: 10.064000129699707 y:-4.732999801635742 z:33.992000579833984
        - atom: CD2 x: 9.215999603271484 y:-2.9639999866485596 z:32.64899826049805
        - atom: CE1 x: 8.758999824523926 y:-5.125 z:34.310001373291016
        - atom: CE2 x: 7.9070000648498535 y:-3.3469998836517334 z:32.96200180053711
        - atom: CZ x: 7.689000129699707 y:-4.423999786376953 z:33.79100036621094
        - atom: OH x: 6.39900016784668 y:-4.795000076293945 z:34.09600067138672
      - residue ASN has 8 atoms
        - atom: N x: 11.267000198364258 y:-3.75 z:29.965999603271484
        - atom: CA x: 10.454999923706055 y:-4.125 z:28.819000244140625
        - atom: C x: 11.135000228881836 y:-5.242000102996826 z:28.03499984741211
        - atom: O x: 10.5 y:-6.247000217437744 z:27.711999893188477
        - atom: CB x: 10.20300006866455 y:-2.9200000762939453 z:27.91200065612793
        - atom: CG x: 9.14900016784668 y:-2.003999948501587 z:28.468000411987305
        - atom: OD1 x: 8.194000244140625 y:-2.4619998931884766 z:29.083999633789062
        - atom: ND2 x: 9.305000305175781 y:-0.7049999833106995 z:28.249000549316406
      - residue ALA has 5 atoms
        - atom: N x: 12.42199993133545 y:-5.059999942779541 z:27.74799919128418
        - atom: CA x: 13.201000213623047 y:-6.046000003814697 z:27.020999908447266
        - atom: C x: 13.07800006866455 y:-7.461999893188477 z:27.60099983215332
        - atom: O x: 12.82699966430664 y:-8.409000396728516 z:26.867000579833984
        - atom: CB x: 14.645999908447266 y:-5.619999885559082 z:26.993999481201172
      - residue TYR has 12 atoms
        - atom: N x: 13.26200008392334 y:-7.61299991607666 z:28.910999298095703
        - atom: CA x: 13.152000427246094 y:-8.927000045776367 z:29.538000106811523
        - atom: C x: 11.708000183105469 y:-9.369000434875488 z:29.48699951171875
        - atom: O x: 11.395999908447266 y:-10.520000457763672 z:29.2189998626709
        - atom: CB x: 13.609999656677246 y:-8.871000289916992 z:31.00200080871582
        - atom: CG x: 15.104999542236328 y:-8.961999893188477 z:31.177000045776367
        - atom: CD1 x: 15.8100004196167 y:-10.065999984741211 z:30.708999633789062
        - atom: CD2 x: 15.821000099182129 y:-7.946000099182129 z:31.804000854492188
        - atom: CE1 x: 17.191999435424805 y:-10.159000396728516 z:30.85700035095215
        - atom: CE2 x: 17.207000732421875 y:-8.029999732971191 z:31.95599937438965
        - atom: CZ x: 17.881999969482422 y:-9.13700008392334 z:31.481000900268555
        - atom: OH x: 19.249000549316406 y:-9.23799991607666 z:31.62700080871582
      - residue ARG has 11 atoms
        - atom: N x: 10.82800006866455 y:-8.425999641418457 z:29.774999618530273
        - atom: CA x: 9.402000427246094 y:-8.663000106811523 z:29.78499984741211
        - atom: C x: 8.987000465393066 y:-9.234000205993652 z:28.422000885009766
        - atom: O x: 8.211000442504883 y:-10.1850004196167 z:28.336999893188477
        - atom: CB x: 8.715999603271484 y:-7.334000110626221 z:30.06999969482422
        - atom: CG x: 7.258999824523926 y:-7.432000160217285 z:30.378000259399414
        - atom: CD x: 7.006999969482422 y:-7.331999778747559 z:31.860000610351562
        - atom: NE x: 5.626999855041504 y:-6.922999858856201 z:32.09299850463867
        - atom: CZ x: 5.074999809265137 y:-5.839000225067139 z:31.549999237060547
        - atom: NH1 x: 5.791999816894531 y:-5.061999797821045 z:30.73699951171875
        - atom: NH2 x: 3.812000036239624 y:-5.519999980926514 z:31.82900047302246
      - residue LYS has 9 atoms
        - atom: N x: 9.53499984741211 y:-8.657999992370605 z:27.354999542236328
        - atom: CA x: 9.25 y:-9.10099983215332 z:25.996000289916992
        - atom: C x: 9.82699966430664 y:-10.49899959564209 z:25.763999938964844
        - atom: O x: 9.098999977111816 y:-11.430000305175781 z:25.424999237060547
        - atom: CB x: 9.835000038146973 y:-8.100000381469727 z:24.999000549316406
        - atom: CG x: 9.510000228881836 y:-8.36299991607666 z:23.541000366210938
        - atom: CD x: 9.970000267028809 y:-7.190000057220459 z:22.68400001525879
        - atom: CE x: 10.038000106811523 y:-7.559000015258789 z:21.20800018310547
        - atom: NZ x: 10.956999778747559 y:-8.722000122070312 z:20.97100067138672
      - residue ALA has 5 atoms
        - atom: N x: 11.128999710083008 y:-10.652999877929688 z:25.959999084472656
        - atom: CA x: 11.76200008392334 y:-11.949000358581543 z:25.777999877929688
        - atom: C x: 10.984999656677246 y:-13.067000389099121 z:26.46299934387207
        - atom: O x: 10.824000358581543 y:-14.14799976348877 z:25.902999877929688
        - atom: CB x: 13.173999786376953 y:-11.914999961853027 z:26.304000854492188
      - residue ALA has 5 atoms
        - atom: N x: 10.5 y:-12.812000274658203 z:27.672000885009766
        - atom: CA x: 9.753999710083008 y:-13.829999923706055 z:28.402000427246094
        - atom: C x: 8.461000442504883 y:-14.230999946594238 z:27.68199920654297
        - atom: O x: 8.182000160217285 y:-15.414999961853027 z:27.506999969482422
        - atom: CB x: 9.442999839782715 y:-13.34000015258789 z:29.815000534057617
      - residue SER has 6 atoms
        - atom: N x: 7.676000118255615 y:-13.246000289916992 z:27.266000747680664
        - atom: CA x: 6.428999900817871 y:-13.508999824523926 z:26.575000762939453
        - atom: C x: 6.638999938964844 y:-14.333000183105469 z:25.29599952697754
        - atom: O x: 5.808000087738037 y:-15.168999671936035 z:24.929000854492188
        - atom: CB x: 5.763000011444092 y:-12.182000160217285 z:26.229999542236328
        - atom: OG x: 4.60099983215332 y:-12.369999885559082 z:25.44099998474121
      - residue VAL has 7 atoms
        - atom: N x: 7.751999855041504 y:-14.08899974822998 z:24.615999221801758
        - atom: CA x: 8.069000244140625 y:-14.795999526977539 z:23.388999938964844
        - atom: C x: 8.357000350952148 y:-16.267000198364258 z:23.677000045776367
        - atom: O x: 7.839000225067139 y:-17.152999877929688 z:22.985000610351562
        - atom: CB x: 9.284000396728516 y:-14.144000053405762 z:22.694000244140625
        - atom: CG1 x: 10.064000129699707 y:-15.180999755859375 z:21.92300033569336
        - atom: CG2 x: 8.812999725341797 y:-13.031000137329102 z:21.76099967956543
      - residue ILE has 8 atoms
        - atom: N x: 9.189000129699707 y:-16.523000717163086 z:24.68899917602539
        - atom: CA x: 9.541000366210938 y:-17.88800048828125 z:25.08799934387207
        - atom: C x: 8.321999549865723 y:-18.58099937438965 z:25.70199966430664
        - atom: O x: 8.041000366210938 y:-19.75 z:25.413000106811523
        - atom: CB x: 10.6850004196167 y:-17.89900016784668 z:26.131999969482422
        - atom: CG1 x: 12.006999969482422 y:-17.5049991607666 z:25.482999801635742
        - atom: CG2 x: 10.8100004196167 y:-19.267000198364258 z:26.743000030517578
        - atom: CD1 x: 13.130999565124512 y:-17.316999435424805 z:26.476999282836914
      - residue ALA has 5 atoms
        - atom: N x: 7.605999946594238 y:-17.854999542236328 z:26.55299949645996
        - atom: CA x: 6.414000034332275 y:-18.388999938964844 z:27.195999145507812
        - atom: C x: 5.311999797821045 y:-18.68000030517578 z:26.170000076293945
        - atom: O x: 4.185999870300293 y:-19.033000946044922 z:26.5310001373291
        - atom: CB x: 5.906000137329102 y:-17.415000915527344 z:28.23200035095215
      - residue LYS has 9 atoms
        - atom: N x: 5.626999855041504 y:-18.524999618530273 z:24.888999938964844
        - atom: CA x: 4.650000095367432 y:-18.802000045776367 z:23.851999282836914
        - atom: C x: 5.250999927520752 y:-19.749000549316406 z:22.81100082397461
        - atom: O x: 4.5879998207092285 y:-20.131999969482422 z:21.847999572753906
        - atom: CB x: 4.186999797821045 y:-17.496999740600586 z:23.204999923706055
        - atom: CG x: 2.924999952316284 y:-17.617000579833984 z:22.378999710083008
        - atom: CD x: 2.450000047683716 y:-16.24799919128418 z:21.92099952697754
        - atom: CE x: 3.4739999771118164 y:-15.571999549865723 z:21.01799964904785
        - atom: NZ x: 3.049999952316284 y:-14.184000015258789 z:20.684999465942383
      - residue TYR has 12 atoms
        - atom: N x: 6.513000011444092 y:-20.1200008392334 z:23.009000778198242
        - atom: CA x: 7.193999767303467 y:-21.051000595092773 z:22.108999252319336
        - atom: C x: 6.574999809265137 y:-22.388999938964844 z:22.45599937438965
        - atom: O x: 6.429999828338623 y:-22.719999313354492 z:23.631000518798828
        - atom: CB x: 8.675000190734863 y:-21.06599998474121 z:22.42099952697754
        - atom: CG x: 9.553000450134277 y:-21.915000915527344 z:21.53700065612793
        - atom: CD1 x: 9.6850004196167 y:-21.6560001373291 z:20.166000366210938
        - atom: CD2 x: 10.39799976348877 y:-22.868000030517578 z:22.111000061035156
        - atom: CE1 x: 10.666999816894531 y:-22.320999145507812 z:19.39699935913086
        - atom: CE2 x: 11.368000030517578 y:-23.527999877929688 z:21.361000061035156
        - atom: CZ x: 11.506999969482422 y:-23.253999710083008 z:20.016000747680664
        - atom: OH x: 12.527999877929688 y:-23.892000198364258 z:19.347999572753906
      - residue PRO has 7 atoms
        - atom: N x: 6.186999797821045 y:-23.167999267578125 z:21.437999725341797
        - atom: CA x: 5.563000202178955 y:-24.483999252319336 z:21.61400032043457
        - atom: C x: 6.4720001220703125 y:-25.672000885009766 z:21.94700050354004
        - atom: O x: 5.98199987411499 y:-26.764999389648438 z:22.20800018310547
        - atom: CB x: 4.800000190734863 y:-24.670000076293945 z:20.30299949645996
        - atom: CG x: 5.709000110626221 y:-24.02400016784668 z:19.30900001525879
        - atom: CD x: 6.133999824523926 y:-22.7450008392334 z:20.025999069213867
      - residue HIS has 10 atoms
        - atom: N x: 7.7820000648498535 y:-25.472000122070312 z:21.944000244140625
        - atom: CA x: 8.687000274658203 y:-26.566999435424805 z:22.27199935913086
        - atom: C x: 9.373000144958496 y:-26.291000366210938 z:23.597000122070312
        - atom: O x: 9.204000473022461 y:-25.219999313354492 z:24.173999786376953
        - atom: CB x: 9.75100040435791 y:-26.72800064086914 z:21.19099998474121
        - atom: CG x: 9.192999839782715 y:-26.843000411987305 z:19.81100082397461
        - atom: ND1 x: 8.234000205993652 y:-27.770999908447266 z:19.472000122070312
        - atom: CD2 x: 9.461999893188477 y:-26.148000717163086 z:18.680999755859375
        - atom: CE1 x: 7.934999942779541 y:-27.64299964904785 z:18.191999435424805
        - atom: NE2 x: 8.666000366210938 y:-26.665000915527344 z:17.687999725341797
      - residue LYS has 9 atoms
        - atom: N x: 10.135000228881836 y:-27.26099967956543 z:24.09000015258789
        - atom: CA x: 10.866999626159668 y:-27.077999114990234 z:25.336000442504883
        - atom: C x: 12.291999816894531 y:-26.701000213623047 z:24.979000091552734
        - atom: O x: 13.027999877929688 y:-27.5 z:24.395999908447266
        - atom: CB x: 10.859999656677246 y:-28.347000122070312 z:26.18000030517578
        - atom: CG x: 12.022000312805176 y:-28.41900062561035 z:27.149999618530273
        - atom: CD x: 11.635000228881836 y:-29.1200008392334 z:28.43199920654297
        - atom: CE x: 10.968999862670898 y:-28.14699935913086 z:29.37700080871582
        - atom: NZ x: 11.902000427246094 y:-27.017000198364258 z:29.71500015258789
      - residue ILE has 8 atoms
        - atom: N x: 12.661999702453613 y:-25.47100067138672 z:25.326000213623047
        - atom: CA x: 13.979999542236328 y:-24.924999237060547 z:25.03700065612793
        - atom: C x: 15.112000465393066 y:-25.763999938964844 z:25.604999542236328
        - atom: O x: 15.272000312805176 y:-25.878999710083008 z:26.81800079345703
        - atom: CB x: 14.07800006866455 y:-23.479999542236328 z:25.554000854492188
        - atom: CG1 x: 13.07699966430664 y:-22.618000030517578 z:24.783000946044922
        - atom: CG2 x: 15.498000144958496 y:-22.948999404907227 z:25.399999618530273
        - atom: CD1 x: 13.050000190734863 y:-21.170000076293945 z:25.19499969482422
      - residue LYS has 9 atoms
        - atom: N x: 15.897000312805176 y:-26.341999053955078 z:24.70400047302246
        - atom: CA x: 17.009000778198242 y:-27.194000244140625 z:25.08300018310547
        - atom: C x: 18.363000869750977 y:-26.479000091552734 z:25.097000122070312
        - atom: O x: 19.3799991607666 y:-27.075000762939453 z:25.45400047302246
        - atom: CB x: 17.05900001525879 y:-28.413999557495117 z:24.1560001373291
        - atom: CG x: 15.869000434875488 y:-29.34600067138672 z:24.302000045776367
        - atom: CD x: 16.128000259399414 y:-30.667999267578125 z:23.60300064086914
        - atom: CE x: 15.015000343322754 y:-31.684999465942383 z:23.892000198364258
        - atom: NZ x: 15.324999809265137 y:-33.077999114990234 z:23.42300033569336
      - residue SER has 6 atoms
        - atom: N x: 18.378000259399414 y:-25.202999114990234 z:24.72100067138672
        - atom: CA x: 19.618999481201172 y:-24.429000854492188 z:24.722000122070312
        - atom: C x: 19.31399917602539 y:-22.95199966430664 z:24.527000427246094
        - atom: O x: 18.201000213623047 y:-22.58300018310547 z:24.15399932861328
        - atom: CB x: 20.55699920654297 y:-24.892000198364258 z:23.604000091552734
        - atom: OG x: 20.27899932861328 y:-24.198999404907227 z:22.398000717163086
      - residue GLY has 4 atoms
        - atom: N x: 20.309999465942383 y:-22.110000610351562 z:24.777999877929688
        - atom: CA x: 20.1200008392334 y:-20.68199920654297 z:24.617000579833984
        - atom: C x: 20.091999053955078 y:-20.316999435424805 z:23.14699935913086
        - atom: O x: 19.503999710083008 y:-19.30699920654297 z:22.756000518798828
      - residue ALA has 5 atoms
        - atom: N x: 20.73200035095215 y:-21.145999908447266 z:22.327999114990234
        - atom: CA x: 20.773000717163086 y:-20.899999618530273 z:20.902000427246094
        - atom: C x: 19.391000747680664 y:-21.14299964904785 z:20.302000045776367
        - atom: O x: 18.961999893188477 y:-20.430999755859375 z:19.392000198364258
        - atom: CB x: 21.799999237060547 y:-21.798999786376953 z:20.253000259399414
      - residue GLU has 9 atoms
        - atom: N x: 18.69300079345703 y:-22.150999069213867 z:20.809999465942383
        - atom: CA x: 17.35700035095215 y:-22.451000213623047 z:20.31999969482422
        - atom: C x: 16.514999389648438 y:-21.20599937438965 z:20.593000411987305
        - atom: O x: 15.798999786376953 y:-20.719999313354492 z:19.715999603271484
        - atom: CB x: 16.768999099731445 y:-23.655000686645508 z:21.06100082397461
        - atom: CG x: 15.47700023651123 y:-24.17300033569336 z:20.458999633789062
        - atom: CD x: 14.970999717712402 y:-25.433000564575195 z:21.138999938964844
        - atom: OE1 x: 15.795999526977539 y:-26.31999969482422 z:21.44700050354004
        - atom: OE2 x: 13.744999885559082 y:-25.54800033569336 z:21.347999572753906
      - residue ALA has 5 atoms
        - atom: N x: 16.632999420166016 y:-20.677000045776367 z:21.808000564575195
        - atom: CA x: 15.897000312805176 y:-19.48900032043457 z:22.211000442504883
        - atom: C x: 16.354000091552734 y:-18.23699951171875 z:21.452999114990234
        - atom: O x: 15.574999809265137 y:-17.315000534057617 z:21.225000381469727
        - atom: CB x: 16.05699920654297 y:-19.281999588012695 z:23.701000213623047
      - residue LYS has 9 atoms
        - atom: N x: 17.624000549316406 y:-18.20800018310547 z:21.069000244140625
        - atom: CA x: 18.18400001525879 y:-17.07699966430664 z:20.341999053955078
        - atom: C x: 17.55699920654297 y:-16.8799991607666 z:18.937999725341797
        - atom: O x: 17.700000762939453 y:-15.824000358581543 z:18.320999145507812
        - atom: CB x: 19.695999145507812 y:-17.263999938964844 z:20.235000610351562
        - atom: CG x: 20.41699981689453 y:-16.229000091552734 z:19.392000198364258
        - atom: CD x: 20.399999618530273 y:-14.847999572753906 z:20.023000717163086
        - atom: CE x: 21.18199920654297 y:-13.862000465393066 z:19.165000915527344
        - atom: NZ x: 22.56599998474121 y:-14.347000122070312 z:18.958999633789062
      - residue LYS has 9 atoms
        - atom: N x: 16.861000061035156 y:-17.892000198364258 z:18.434999465942383
        - atom: CA x: 16.226999282836914 y:-17.773000717163086 z:17.131000518798828
        - atom: C x: 15.065999984741211 y:-16.77199935913086 z:17.200000762939453
        - atom: O x: 14.831000328063965 y:-16.006999969482422 z:16.256999969482422
        - atom: CB x: 15.673999786376953 y:-19.125 z:16.680999755859375
        - atom: CG x: 16.683000564575195 y:-20.246999740600586 z:16.594999313354492
        - atom: CD x: 15.987000465393066 y:-21.54400062561035 z:16.172000885009766
        - atom: CE x: 16.908000946044922 y:-22.753999710083008 z:16.27899932861328
        - atom: NZ x: 16.2549991607666 y:-24.025999069213867 z:15.857000350952148
      - residue LEU has 8 atoms
        - atom: N x: 14.343999862670898 y:-16.790000915527344 z:18.32200050354004
        - atom: CA x: 13.184000015258789 y:-15.925999641418457 z:18.53700065612793
        - atom: C x: 13.527999877929688 y:-14.432999610900879 z:18.64699935913086
        - atom: O x: 14.597000122070312 y:-14.064000129699707 z:19.136999130249023
        - atom: CB x: 12.437000274658203 y:-16.3799991607666 z:19.795000076293945
        - atom: CG x: 12.102999687194824 y:-17.868000030517578 z:19.90399932861328
        - atom: CD1 x: 11.484999656677246 y:-18.17799949645996 z:21.260000228881836
        - atom: CD2 x: 11.161999702453613 y:-18.250999450683594 z:18.78499984741211
      - residue PRO has 7 atoms
        - atom: N x: 12.616000175476074 y:-13.555999755859375 z:18.187000274658203
        - atom: CA x: 12.782999992370605 y:-12.100000381469727 z:18.21500015258789
        - atom: C x: 12.5 y:-11.564000129699707 z:19.618000030517578
        - atom: O x: 11.369999885559082 y:-11.609999656677246 z:20.106000900268555
        - atom: CB x: 11.753000259399414 y:-11.631999969482422 z:17.20800018310547
        - atom: CG x: 10.605999946594238 y:-12.545000076293945 z:17.520000457763672
        - atom: CD x: 11.295999526977539 y:-13.909000396728516 z:17.631999969482422
      - residue GLY has 4 atoms
        - atom: N x: 13.532999992370605 y:-11.04699993133545 z:20.26300048828125
        - atom: CA x: 13.359999656677246 y:-10.550000190734863 z:21.61199951171875
        - atom: C x: 14.352999687194824 y:-11.239999771118164 z:22.52199935913086
        - atom: O x: 14.593999862670898 y:-10.791000366210938 z:23.634000778198242
      - residue VAL has 7 atoms
        - atom: N x: 14.920000076293945 y:-12.342000007629395 z:22.047000885009766
        - atom: CA x: 15.909000396728516 y:-13.072999954223633 z:22.801000595092773
        - atom: C x: 17.238000869750977 y:-12.873000144958496 z:22.11199951171875
        - atom: O x: 17.503000259399414 y:-13.482999801635742 z:21.072999954223633
        - atom: CB x: 15.623000144958496 y:-14.553999900817871 z:22.81399917602539
        - atom: CG1 x: 16.7549991607666 y:-15.277000427246094 z:23.52199935913086
        - atom: CG2 x: 14.295000076293945 y:-14.815999984741211 z:23.481000900268555
      - residue GLY has 4 atoms
        - atom: N x: 18.07200050354004 y:-12.015999794006348 z:22.69700050354004
        - atom: CA x: 19.378999710083008 y:-11.729999542236328 z:22.134000778198242
        - atom: C x: 20.488000869750977 y:-12.513999938964844 z:22.802000045776367
        - atom: O x: 20.222000122070312 y:-13.487000465393066 z:23.506000518798828
      - residue THR has 7 atoms
        - atom: N x: 21.72800064086914 y:-12.062999725341797 z:22.60300064086914
        - atom: CA x: 22.920000076293945 y:-12.718999862670898 z:23.145999908447266
        - atom: C x: 22.94099998474121 y:-12.92199993133545 z:24.6560001373291
        - atom: O x: 23.170000076293945 y:-14.029999732971191 z:25.128000259399414
        - atom: CB x: 24.21299934387207 y:-11.954999923706055 z:22.770000457763672
        - atom: OG1 x: 24.249000549316406 y:-11.710000038146973 z:21.356000900268555
        - atom: CG2 x: 25.434999465942383 y:-12.774999618530273 z:23.156999588012695
      - residue LYS has 9 atoms
        - atom: N x: 22.709999084472656 y:-11.857999801635742 z:25.413000106811523
        - atom: CA x: 22.726999282836914 y:-11.961000442504883 z:26.865999221801758
        - atom: C x: 21.701000213623047 y:-12.954000473022461 z:27.388999938964844
        - atom: O x: 22.0 y:-13.739999771118164 z:28.275999069213867
        - atom: CB x: 22.475000381469727 y:-10.595999717712402 z:27.5
        - atom: CG x: 23.288000106811523 y:-9.480999946594238 z:26.8700008392334
        - atom: CD x: 24.777000427246094 y:-9.682999610900879 z:27.093000411987305
        - atom: CE x: 25.266000747680664 y:-8.854999542236328 z:28.26300048828125
        - atom: NZ x: 25.291000366210938 y:-7.4070000648498535 z:27.913999557495117
      - residue ILE has 8 atoms
        - atom: N x: 20.489999771118164 y:-12.942000389099121 z:26.85099983215332
        - atom: CA x: 19.493000030517578 y:-13.871000289916992 z:27.351999282836914
        - atom: C x: 19.766000747680664 y:-15.331000328063965 z:26.969999313354492
        - atom: O x: 19.400999069213867 y:-16.253000259399414 z:27.704999923706055
        - atom: CB x: 18.073999404907227 y:-13.446999549865723 z:26.920000076293945
        - atom: CG1 x: 17.691999435424805 y:-12.152999877929688 z:27.6560001373291
        - atom: CG2 x: 17.062999725341797 y:-14.581000328063965 z:27.211999893188477
        - atom: CD1 x: 16.2549991607666 y:-11.734999656677246 z:27.492000579833984
      - residue ALA has 5 atoms
        - atom: N x: 20.427000045776367 y:-15.54800033569336 z:25.836999893188477
        - atom: CA x: 20.742000579833984 y:-16.9060001373291 z:25.4060001373291
        - atom: C x: 21.82200050354004 y:-17.413000106811523 z:26.351999282836914
        - atom: O x: 21.839000701904297 y:-18.582000732421875 z:26.763999938964844
        - atom: CB x: 21.256999969482422 y:-16.88800048828125 z:23.981000900268555
      - residue GLU has 9 atoms
        - atom: N x: 22.719999313354492 y:-16.493000030517578 z:26.68899917602539
        - atom: CA x: 23.83099937438965 y:-16.760000228881836 z:27.58300018310547
        - atom: C x: 23.28700065612793 y:-17.075000762939453 z:28.95800018310547
        - atom: O x: 23.738000869750977 y:-18.0049991607666 z:29.625999450683594
        - atom: CB x: 24.726999282836914 y:-15.53600025177002 z:27.64900016784668
        - atom: CG x: 25.850000381469727 y:-15.63599967956543 z:28.64299964904785
        - atom: CD x: 26.965999603271484 y:-14.670000076293945 z:28.30900001525879
        - atom: OE1 x: 27.51799964904785 y:-14.795999526977539 z:27.19700050354004
        - atom: OE2 x: 27.283000946044922 y:-13.788999557495117 z:29.141000747680664
      - residue LYS has 9 atoms
        - atom: N x: 22.308000564575195 y:-16.295000076293945 z:29.381999969482422
        - atom: CA x: 21.725000381469727 y:-16.541000366210938 z:30.672000885009766
        - atom: C x: 20.95199966430664 y:-17.840999603271484 z:30.590999603271484
        - atom: O x: 20.99799919128418 y:-18.648000717163086 z:31.51300048828125
        - atom: CB x: 20.82699966430664 y:-15.378999710083008 z:31.089000701904297
        - atom: CG x: 21.610000610351562 y:-14.130999565124512 z:31.437000274658203
        - atom: CD x: 20.827999114990234 y:-13.210000038146973 z:32.361000061035156
        - atom: CE x: 21.672000885009766 y:-12.029999732971191 z:32.82699966430664
        - atom: NZ x: 22.187999725341797 y:-11.217000007629395 z:31.687999725341797
      - residue ILE has 8 atoms
        - atom: N x: 20.256000518798828 y:-18.055999755859375 z:29.479000091552734
        - atom: CA x: 19.496000289916992 y:-19.285999298095703 z:29.30500030517578
        - atom: C x: 20.44300079345703 y:-20.496999740600586 z:29.367000579833984
        - atom: O x: 20.117000579833984 y:-21.52899932861328 z:29.961999893188477
        - atom: CB x: 18.714000701904297 y:-19.270000457763672 z:27.961999893188477
        - atom: CG1 x: 17.535999298095703 y:-18.297000885009766 z:28.06399917602539
        - atom: CG2 x: 18.194000244140625 y:-20.665000915527344 z:27.6299991607666
        - atom: CD1 x: 16.844999313354492 y:-18.011999130249023 z:26.757999420166016
      - residue ASP has 8 atoms
        - atom: N x: 21.618000030517578 y:-20.37299919128418 z:28.761999130249023
        - atom: CA x: 22.56999969482422 y:-21.466999053955078 z:28.795000076293945
        - atom: C x: 22.993999481201172 y:-21.802000045776367 z:30.23200035095215
        - atom: O x: 23.159000396728516 y:-22.97800064086914 z:30.573999404907227
        - atom: CB x: 23.785999298095703 y:-21.145999908447266 z:27.93199920654297
        - atom: CG x: 23.558000564575195 y:-21.47599983215332 z:26.459999084472656
        - atom: OD1 x: 22.81999969482422 y:-22.45199966430664 z:26.187999725341797
        - atom: OD2 x: 24.12299919128418 y:-20.783000946044922 z:25.57900047302246
      - residue GLU has 9 atoms
        - atom: N x: 23.165000915527344 y:-20.785999298095703 z:31.07900047302246
        - atom: CA x: 23.533000946044922 y:-21.05699920654297 z:32.4640007019043
        - atom: C x: 22.351999282836914 y:-21.722000122070312 z:33.15700149536133
        - atom: O x: 22.476999282836914 y:-22.834999084472656 z:33.65800094604492
        - atom: CB x: 23.89900016784668 y:-19.783000946044922 z:33.233001708984375
        - atom: CG x: 24.15999984741211 y:-20.05900001525879 z:34.72200012207031
        - atom: CD x: 24.485000610351562 y:-18.812999725341797 z:35.542999267578125
        - atom: OE1 x: 25.302000045776367 y:-17.989999771118164 z:35.09000015258789
        - atom: OE2 x: 23.93899917602539 y:-18.665000915527344 z:36.654998779296875
      - residue PHE has 11 atoms
        - atom: N x: 21.201000213623047 y:-21.04800033569336 z:33.17599868774414
        - atom: CA x: 20.01799964904785 y:-21.60300064086914 z:33.83700180053711
        - atom: C x: 19.79599952697754 y:-23.05900001525879 z:33.45500183105469
        - atom: O x: 19.496999740600586 y:-23.89900016784668 z:34.303001403808594
        - atom: CB x: 18.76099967956543 y:-20.81599998474121 z:33.494998931884766
        - atom: CG x: 17.554000854492188 y:-21.259000778198242 z:34.27399826049805
        - atom: CD1 x: 17.402999877929688 y:-20.89900016784668 z:35.61000061035156
        - atom: CD2 x: 16.577999114990234 y:-22.05699920654297 z:33.68299865722656
        - atom: CE1 x: 16.29599952697754 y:-21.326000213623047 z:36.34700012207031
        - atom: CE2 x: 15.472000122070312 y:-22.486000061035156 z:34.4119987487793
        - atom: CZ x: 15.331999778747559 y:-22.1200008392334 z:35.74599838256836
      - residue LEU has 8 atoms
        - atom: N x: 19.929000854492188 y:-23.354999542236328 z:32.16999816894531
        - atom: CA x: 19.76099967956543 y:-24.719999313354492 z:31.724000930786133
        - atom: C x: 20.87299919128418 y:-25.54400062561035 z:32.38100051879883
        - atom: O x: 20.597000122070312 y:-26.49799919128418 z:33.11199951171875
        - atom: CB x: 19.84000015258789 y:-24.78700065612793 z:30.19499969482422
        - atom: CG x: 18.53700065612793 y:-25.14900016784668 z:29.46299934387207
        - atom: CD1 x: 17.368999481201172 y:-24.40399932861328 z:30.06100082397461
        - atom: CD2 x: 18.67099952697754 y:-24.833999633789062 z:27.979999542236328
      - residue ALA has 5 atoms
        - atom: N x: 22.125 y:-25.1560001373291 z:32.15299987792969
        - atom: CA x: 23.2549991607666 y:-25.881000518798828 z:32.73099899291992
        - atom: C x: 23.19700050354004 y:-25.913000106811523 z:34.263999938964844
        - atom: O x: 22.674999237060547 y:-26.856000900268555 z:34.8650016784668
        - atom: CB x: 24.572999954223633 y:-25.256999969482422 z:32.26499938964844
      - residue THR has 7 atoms
        - atom: N x: 23.732999801635742 y:-24.874000549316406 z:34.891998291015625
        - atom: CA x: 23.746999740600586 y:-24.791000366210938 z:36.345001220703125
        - atom: C x: 22.393999099731445 y:-25.16200065612793 z:36.95800018310547
        - atom: O x: 22.26799964904785 y:-26.194000244140625 z:37.60900115966797
        - atom: CB x: 24.17799949645996 y:-23.371000289916992 z:36.810001373291016
        - atom: OG1 x: 23.086000442504883 y:-22.448999404907227 z:36.68899917602539
        - atom: CG2 x: 25.349000930786133 y:-22.87700080871582 z:35.946998596191406
      - residue GLY has 4 atoms
        - atom: N x: 21.3799991607666 y:-24.339000701904297 z:36.72800064086914
        - atom: CA x: 20.069000244140625 y:-24.611000061035156 z:37.29199981689453
        - atom: C x: 19.61400032043457 y:-23.41699981689453 z:38.10900115966797
        - atom: O x: 18.61400032043457 y:-23.454999923706055 z:38.83599853515625
      - residue LYS has 9 atoms
        - atom: N x: 20.375999450683594 y:-22.34000015258789 z:37.97700119018555
        - atom: CA x: 20.104999542236328 y:-21.104000091552734 z:38.680999755859375
        - atom: C x: 20.933000564575195 y:-20.047000885009766 z:37.987998962402344
        - atom: O x: 21.757999420166016 y:-20.365999221801758 z:37.137001037597656
        - atom: CB x: 20.530000686645508 y:-21.229999542236328 z:40.150001525878906
        - atom: CG x: 22.016000747680664 y:-21.55299949645996 z:40.37799835205078
        - atom: CD x: 22.30500030517578 y:-21.792999267578125 z:41.87099838256836
        - atom: CE x: 23.71500015258789 y:-22.350000381469727 z:42.15399932861328
        - atom: NZ x: 24.823999404907227 y:-21.365999221801758 z:41.97200012207031
      - residue LEU has 8 atoms
        - atom: N x: 20.711000442504883 y:-18.78700065612793 z:38.33000183105469
        - atom: CA x: 21.5 y:-17.73200035095215 z:37.724998474121094
        - atom: C x: 22.31999969482422 y:-17.052000045776367 z:38.80699920654297
        - atom: O x: 21.7810001373291 y:-16.632999420166016 z:39.83000183105469
        - atom: CB x: 20.608999252319336 y:-16.709999084472656 z:37.027000427246094
        - atom: CG x: 21.32699966430664 y:-15.911999702453613 z:35.935001373291016
        - atom: CD1 x: 21.85099983215332 y:-16.854000091552734 z:34.85599899291992
        - atom: CD2 x: 20.36400032043457 y:-14.904999732971191 z:35.32699966430664
      - residue ARG has 11 atoms
        - atom: N x: 23.6299991607666 y:-16.968000411987305 z:38.57899856567383
        - atom: CA x: 24.55500030517578 y:-16.33300018310547 z:39.516998291015625
        - atom: C x: 24.148000717163086 y:-14.880000114440918 z:39.749000549316406
        - atom: O x: 24.016000747680664 y:-14.442000389099121 z:40.891998291015625
        - atom: CB x: 25.979000091552734 y:-16.405000686645508 z:38.9640007019043
        - atom: CG x: 26.475000381469727 y:-17.833999633789062 z:38.73099899291992
        - atom: CD x: 27.805999755859375 y:-17.840999603271484 z:37.98899841308594
        - atom: NE x: 27.750999450683594 y:-16.979000091552734 z:36.808998107910156
        - atom: CZ x: 28.722999572753906 y:-16.86400032043457 z:35.904998779296875
        - atom: NH1 x: 29.840999603271484 y:-17.56399917602539 z:36.03200149536133
        - atom: NH2 x: 28.58300018310547 y:-16.033000946044922 z:34.875999450683594
      - residue LYS has 9 atoms
        - atom: N x: 23.94099998474121 y:-14.14799976348877 z:38.65700149536133
        - atom: CA x: 23.523000717163086 y:-12.746999740600586 z:38.71799850463867
        - atom: C x: 22.263999938964844 y:-12.520000457763672 z:39.571998596191406
        - atom: O x: 22.094999313354492 y:-11.446999549865723 z:40.1609992980957
        - atom: CB x: 23.275999069213867 y:-12.211000442504883 z:37.30699920654297
        - atom: CG x: 22.777999877929688 y:-10.774999618530273 z:37.26499938964844
        - atom: CD x: 22.426000595092773 y:-10.364999771118164 z:35.8489990234375
        - atom: CE x: 21.812000274658203 y:-8.97700023651123 z:35.79999923706055
        - atom: NZ x: 22.783000946044922 y:-7.9079999923706055 z:36.16999816894531
      - residue LEU has 8 atoms
        - atom: N x: 21.37700080871582 y:-13.51099967956543 z:39.630001068115234
        - atom: CA x: 20.15399932861328 y:-13.38599967956543 z:40.43600082397461
        - atom: C x: 20.409000396728516 y:-13.715999603271484 z:41.909000396728516
        - atom: O x: 19.76099967956543 y:-13.151000022888184 z:42.79199981689453
        - atom: CB x: 19.0310001373291 y:-14.29800033569336 z:39.91299819946289
        - atom: CG x: 18.204999923706055 y:-13.871000289916992 z:38.69599914550781
        - atom: CD1 x: 17.20599937438965 y:-14.956000328063965 z:38.374000549316406
        - atom: CD2 x: 17.489999771118164 y:-12.565999984741211 z:38.97100067138672
      - residue GLU has 9 atoms
        - atom: N x: 21.33099937438965 y:-14.642000198364258 z:42.17399978637695
        - atom: CA x: 21.6560001373291 y:-14.987000465393066 z:43.553001403808594
        - atom: C x: 22.179000854492188 y:-13.70199966430664 z:44.17900085449219
        - atom: O x: 21.764999389648438 y:-13.3149995803833 z:45.27199935913086
        - atom: CB x: 22.73900032043457 y:-16.07699966430664 z:43.624000549316406
        - atom: CG x: 22.267000198364258 y:-17.479999542236328 z:43.24599838256836
        - atom: CD x: 21.235000610351562 y:-18.04599952697754 z:44.209999084472656
        - atom: OE1 x: 20.523000717163086 y:-18.98900032043457 z:43.81399917602539
        - atom: OE2 x: 21.13599967956543 y:-17.562999725341797 z:45.36000061035156
      - residue LYS has 9 atoms
        - atom: N x: 23.073999404907227 y:-13.038000106811523 z:43.45399856567383
        - atom: CA x: 23.663999557495117 y:-11.78600025177002 z:43.90700149536133
        - atom: C x: 22.57200050354004 y:-10.781999588012695 z:44.24700164794922
        - atom: O x: 22.555999755859375 y:-10.211999893188477 z:45.334999084472656
        - atom: CB x: 24.594999313354492 y:-11.241999626159668 z:42.821998596191406
        - atom: CG x: 25.749000549316406 y:-12.201000213623047 z:42.54100036621094
        - atom: CD x: 26.69700050354004 y:-11.706000328063965 z:41.46500015258789
        - atom: CE x: 27.738000869750977 y:-12.774999618530273 z:41.16299819946289
        - atom: NZ x: 28.597999572753906 y:-12.456000328063965 z:39.9900016784668
      - residue ILE has 8 atoms
        - atom: N x: 21.650999069213867 y:-10.579999923706055 z:43.3129997253418
        - atom: CA x: 20.538999557495117 y:-9.666999816894531 z:43.53300094604492
        - atom: C x: 19.79400062561035 y:-10.114999771118164 z:44.78499984741211
        - atom: O x: 19.698999404907227 y:-9.368000030517578 z:45.75299835205078
        - atom: CB x: 19.576000213623047 y:-9.663000106811523 z:42.31800079345703
        - atom: CG1 x: 20.308000564575195 y:-9.105999946594238 z:41.09299850463867
        - atom: CG2 x: 18.336999893188477 y:-8.845999717712402 z:42.625
        - atom: CD1 x: 19.481000900268555 y:-9.064000129699707 z:39.84400177001953
      - residue ARG has 11 atoms
        - atom: N x: 19.283000946044922 y:-11.342000007629395 z:44.7599983215332
        - atom: CA x: 18.551000595092773 y:-11.920999526977539 z:45.88999938964844
        - atom: C x: 19.215999603271484 y:-11.687000274658203 z:47.249000549316406
        - atom: O x: 18.5310001373291 y:-11.527000427246094 z:48.262001037597656
        - atom: CB x: 18.378999710083008 y:-13.430000305175781 z:45.68199920654297
        - atom: CG x: 17.430999755859375 y:-13.803000450134277 z:44.56800079345703
        - atom: CD x: 17.413000106811523 y:-15.305000305175781 z:44.323001861572266
        - atom: NE x: 16.273000717163086 y:-15.689000129699707 z:43.492000579833984
        - atom: CZ x: 15.977999687194824 y:-16.937000274658203 z:43.132999420166016
        - atom: NH1 x: 16.740999221801758 y:-17.950000762939453 z:43.525001525878906
        - atom: NH2 x: 14.906000137329102 y:-17.176000595092773 z:42.38800048828125
      - residue GLN has 9 atoms
        - atom: N x: 20.548999786376953 y:-11.678999900817871 z:47.263999938964844
        - atom: CA x: 21.320999145507812 y:-11.486000061035156 z:48.492000579833984
        - atom: C x: 21.540000915527344 y:-10.038999557495117 z:48.88999938964844
        - atom: O x: 21.20199966430664 y:-9.645999908447266 z:50.005001068115234
        - atom: CB x: 22.667999267578125 y:-12.187999725341797 z:48.374000549316406
        - atom: CG x: 22.65399932861328 y:-13.574000358581543 z:48.97700119018555
        - atom: CD x: 23.506999969482422 y:-14.543000221252441 z:48.20399856567383
        - atom: OE1 x: 24.591999053955078 y:-14.189000129699707 z:47.731998443603516
        - atom: NE2 x: 23.027000427246094 y:-15.782999992370605 z:48.07099914550781
      - residue ASP has 8 atoms
        - atom: N x: 22.11400032043457 y:-9.253000259399414 z:47.983001708984375
        - atom: CA x: 22.3700008392334 y:-7.834000110626221 z:48.22999954223633
        - atom: C x: 21.216999053955078 y:-7.169000148773193 z:48.99300003051758
        - atom: O x: 20.115999221801758 y:-7.050000190734863 z:48.47700119018555
        - atom: CB x: 22.594999313354492 y:-7.125999927520752 z:46.89099884033203
        - atom: CG x: 22.950000762939453 y:-5.663000106811523 z:47.05400085449219
        - atom: OD1 x: 23.440000534057617 y:-5.063000202178955 z:46.07400131225586
        - atom: OD2 x: 22.735000610351562 y:-5.116000175476074 z:48.15800094604492
      - residue ASP has 8 atoms
        - atom: N x: 21.47599983215332 y:-6.7230000495910645 z:50.21699905395508
        - atom: CA x: 20.43600082397461 y:-6.09499979019165 z:51.03499984741211
        - atom: C x: 19.680999755859375 y:-4.929999828338623 z:50.38100051879883
        - atom: O x: 18.44499969482422 y:-4.921999931335449 z:50.34199905395508
        - atom: CB x: 21.023000717163086 y:-5.610000133514404 z:52.36600112915039
        - atom: CG x: 20.0 y:-4.864999771118164 z:53.21699905395508
        - atom: OD1 x: 19.062999725341797 y:-5.508999824523926 z:53.75
        - atom: OD2 x: 20.125 y:-3.630000114440918 z:53.34400177001953
      - residue THR has 7 atoms
        - atom: N x: 20.41900062561035 y:-3.941999912261963 z:49.88199996948242
        - atom: CA x: 19.788000106811523 y:-2.7799999713897705 z:49.266998291015625
        - atom: C x: 18.878999710083008 y:-3.131999969482422 z:48.10300064086914
        - atom: O x: 17.701000213623047 y:-2.7730000019073486 z:48.104000091552734
        - atom: CB x: 20.826000213623047 y:-1.7740000486373901 z:48.766998291015625
        - atom: OG1 x: 21.684999465942383 y:-1.3969999551773071 z:49.84700012207031
        - atom: CG2 x: 20.131000518798828 y:-0.531000018119812 z:48.229000091552734
      - residue SER has 6 atoms
        - atom: N x: 19.43400001525879 y:-3.8239998817443848 z:47.11199951171875
        - atom: CA x: 18.676000595092773 y:-4.2210001945495605 z:45.930999755859375
        - atom: C x: 17.445999145507812 y:-4.991000175476074 z:46.375999450683594
        - atom: O x: 16.354000091552734 y:-4.8429999351501465 z:45.827999114990234
        - atom: CB x: 19.527999877929688 y:-5.125999927520752 z:45.04399871826172
        - atom: OG x: 20.857999801635742 y:-4.6479997634887695 z:44.95500183105469
      - residue SER has 6 atoms
        - atom: N x: 17.650999069213867 y:-5.809000015258789 z:47.39699935913086
        - atom: CA x: 16.614999771118164 y:-6.6579999923706055 z:47.946998596191406
        - atom: C x: 15.543000221252441 y:-5.864999771118164 z:48.672000885009766
        - atom: O x: 14.366999626159668 y:-6.239999771118164 z:48.676998138427734
        - atom: CB x: 17.256999969482422 y:-7.659999847412109 z:48.895999908447266
        - atom: OG x: 16.29199981689453 y:-8.527000427246094 z:49.439998626708984
      - residue SER has 6 atoms
        - atom: N x: 15.956999778747559 y:-4.765999794006348 z:49.28799819946289
        - atom: CA x: 15.032999992370605 y:-3.927000045776367 z:50.02299880981445
        - atom: C x: 14.21399974822998 y:-3.0350000858306885 z:49.106998443603516
        - atom: O x: 13.001999855041504 y:-2.947000026702881 z:49.257999420166016
        - atom: CB x: 15.791999816894531 y:-3.0929999351501465 z:51.06100082397461
        - atom: OG x: 16.2549991607666 y:-3.9210000038146973 z:52.12300109863281
      - residue ILE has 8 atoms
        - atom: N x: 14.859999656677246 y:-2.371999979019165 z:48.159000396728516
        - atom: CA x: 14.121000289916992 y:-1.5190000534057617 z:47.24399948120117
        - atom: C x: 13.07699966430664 y:-2.390000104904175 z:46.57600021362305
        - atom: O x: 11.907999992370605 y:-2.01200008392334 z:46.41999816894531
        - atom: CB x: 15.031999588012695 y:-0.9359999895095825 z:46.16899871826172
        - atom: CG1 x: 16.11400032043457 y:-0.07800000160932541 z:46.83300018310547
        - atom: CG2 x: 14.199000358581543 y:-0.11400000005960464 z:45.18199920654297
        - atom: CD1 x: 17.23699951171875 y:0.3479999899864197 z:45.91999816894531
      - residue ASN has 8 atoms
        - atom: N x: 13.520000457763672 y:-3.5810000896453857 z:46.20199966430664
        - atom: CA x: 12.65999984741211 y:-4.548999786376953 z:45.5620002746582
        - atom: C x: 11.432000160217285 y:-4.789000034332275 z:46.38999938964844
        - atom: O x: 10.333999633789062 y:-4.831999778747559 z:45.874000549316406
        - atom: CB x: 13.383999824523926 y:-5.864999771118164 z:45.374000549316406
        - atom: CG x: 13.378999710083008 y:-6.310999870300293 z:43.948001861572266
        - atom: OD1 x: 12.390000343322754 y:-6.114999771118164 z:43.23500061035156
        - atom: ND2 x: 14.47599983215332 y:-6.923999786376953 z:43.51100158691406
      - residue PHE has 11 atoms
        - atom: N x: 11.60099983215332 y:-4.936999797821045 z:47.6879997253418
        - atom: CA x: 10.439000129699707 y:-5.195000171661377 z:48.50699996948242
        - atom: C x: 9.46399974822998 y:-4.026000022888184 z:48.55799865722656
        - atom: O x: 8.288000106811523 y:-4.184000015258789 z:48.26900100708008
        - atom: CB x: 10.843999862670898 y:-5.577000141143799 z:49.92599868774414
        - atom: CG x: 9.680000305175781 y:-5.688000202178955 z:50.8489990234375
        - atom: CD1 x: 8.789999961853027 y:-6.736999988555908 z:50.729000091552734
        - atom: CD2 x: 9.430999755859375 y:-4.703000068664551 z:51.792999267578125
        - atom: CE1 x: 7.666999816894531 y:-6.803999900817871 z:51.534000396728516
        - atom: CE2 x: 8.303000450134277 y:-4.763999938964844 z:52.60100173950195
        - atom: CZ x: 7.425000190734863 y:-5.815000057220459 z:52.47100067138672
      - residue LEU has 8 atoms
        - atom: N x: 9.954999923706055 y:-2.8559999465942383 z:48.935001373291016
        - atom: CA x: 9.11299991607666 y:-1.6629999876022339 z:49.029998779296875
        - atom: C x: 8.187000274658203 y:-1.444000005722046 z:47.8489990234375
        - atom: O x: 6.998000144958496 y:-1.2089999914169312 z:48.0359992980957
        - atom: CB x: 9.97599983215332 y:-0.42399999499320984 z:49.19599914550781
        - atom: CG x: 10.741999626159668 y:-0.367000013589859 z:50.50699996948242
        - atom: CD1 x: 11.949000358581543 y:0.5139999985694885 z:50.32600021362305
        - atom: CD2 x: 9.82699966430664 y:0.1289999932050705 z:51.612998962402344
      - residue THR has 7 atoms
        - atom: N x: 8.727999687194824 y:-1.5180000066757202 z:46.63600158691406
        - atom: CA x: 7.913000106811523 y:-1.3020000457763672 z:45.45000076293945
        - atom: C x: 6.660999774932861 y:-2.1670000553131104 z:45.41999816894531
        - atom: O x: 5.74399995803833 y:-1.86899995803833 z:44.67499923706055
        - atom: CB x: 8.699999809265137 y:-1.5509999990463257 z:44.16999816894531
        - atom: OG1 x: 8.991000175476074 y:-2.943000078201294 z:44.060001373291016
        - atom: CG2 x: 9.998000144958496 y:-0.7699999809265137 z:44.17599868774414
      - residue ARG has 11 atoms
        - atom: N x: 6.604000091552734 y:-3.2290000915527344 z:46.2239990234375
        - atom: CA x: 5.4070000648498535 y:-4.083000183105469 z:46.25
        - atom: C x: 4.270999908447266 y:-3.384000062942505 z:46.97600173950195
        - atom: O x: 3.1610000133514404 y:-3.9130001068115234 z:47.06999969482422
        - atom: CB x: 5.684999942779541 y:-5.426000118255615 z:46.926998138427734
        - atom: CG x: 6.485000133514404 y:-6.410999774932861 z:46.06700134277344
        - atom: CD x: 7.070000171661377 y:-7.552000045776367 z:46.89799880981445
        - atom: NE x: 6.085000038146973 y:-8.112000465393066 z:47.81800079345703
        - atom: CZ x: 6.336999893188477 y:-9.085000038146973 z:48.68600082397461
        - atom: NH1 x: 7.546000003814697 y:-9.621999740600586 z:48.762001037597656
        - atom: NH2 x: 5.382999897003174 y:-9.510000228881836 z:49.492000579833984
      - residue VAL has 7 atoms
        - atom: N x: 4.554999828338623 y:-2.2019999027252197 z:47.51300048828125
        - atom: CA x: 3.5380001068115234 y:-1.4140000343322754 z:48.19200134277344
        - atom: C x: 3.002000093460083 y:-0.4729999899864197 z:47.124000549316406
        - atom: O x: 3.7679998874664307 y:0.1459999978542328 z:46.38100051879883
        - atom: CB x: 4.129000186920166 y:-0.6010000109672546 z:49.367000579833984
        - atom: CG1 x: 3.115000009536743 y:0.40299999713897705 z:49.87699890136719
        - atom: CG2 x: 4.514999866485596 y:-1.5449999570846558 z:50.49800109863281
      - residue SER has 6 atoms
        - atom: N x: 1.6820000410079956 y:-0.3880000114440918 z:47.029998779296875
        - atom: CA x: 1.0529999732971191 y:0.453000009059906 z:46.0260009765625
        - atom: C x: 1.2309999465942383 y:1.902999997138977 z:46.388999938964844
        - atom: O x: 0.7540000081062317 y:2.3459999561309814 z:47.4370002746582
        - atom: CB x: -0.4350000023841858 y:0.12800000607967377 z:45.922000885009766
        - atom: OG x: -0.9639999866485596 y:0.6510000228881836 z:44.733001708984375
      - residue GLY has 4 atoms
        - atom: N x: 1.9040000438690186 y:2.6449999809265137 z:45.51599884033203
        - atom: CA x: 2.1429998874664307 y:4.053999900817871 z:45.7760009765625
        - atom: C x: 3.634999990463257 y:4.316999912261963 z:45.90299987792969
        - atom: O x: 4.10099983215332 y:5.461999893188477 z:45.915000915527344
      - residue ILE has 8 atoms
        - atom: N x: 4.392000198364258 y:3.2300000190734863 z:45.9900016784668
        - atom: CA x: 5.824999809265137 y:3.325000047683716 z:46.11600112915039
        - atom: C x: 6.491000175476074 y:2.7769999504089355 z:44.880001068115234
        - atom: O x: 6.464000225067139 y:1.5800000429153442 z:44.64099884033203
        - atom: CB x: 6.308000087738037 y:2.569000005722046 z:47.356998443603516
        - atom: CG1 x: 5.689000129699707 y:3.2200000286102295 z:48.59600067138672
        - atom: CG2 x: 7.823999881744385 y:2.5880000591278076 z:47.42300033569336
        - atom: CD1 x: 5.960000038146973 y:2.489000082015991 z:49.89400100708008
      - residue GLY has 4 atoms
        - atom: N x: 7.071000099182129 y:3.6670000553131104 z:44.08700180053711
        - atom: CA x: 7.74399995803833 y:3.2360000610351562 z:42.8849983215332
        - atom: C x: 9.239999771118164 y:3.2160000801086426 z:43.108001708984375
        - atom: O x: 9.706999778747559 y:3.369999885559082 z:44.23500061035156
      - residue PRO has 7 atoms
        - atom: N x: 10.027999877929688 y:3.0280001163482666 z:42.04600143432617
        - atom: CA x: 11.480999946594238 y:3.003999948501587 z:42.20600128173828
        - atom: C x: 11.973999977111816 y:4.1529998779296875 z:43.07600021362305
        - atom: O x: 12.366000175476074 y:3.944999933242798 z:44.2140007019043
        - atom: CB x: 11.97599983215332 y:3.0999999046325684 z:40.766998291015625
        - atom: CG x: 10.942999839782715 y:2.306999921798706 z:40.03300094604492
        - atom: CD x: 9.645000457763672 y:2.819000005722046 z:40.638999938964844
      - residue SER has 6 atoms
        - atom: N x: 11.925999641418457 y:5.367000102996826 z:42.54199981689453
        - atom: CA x: 12.390000343322754 y:6.557000160217285 z:43.24700164794922
        - atom: C x: 12.029000282287598 y:6.611000061035156 z:44.720001220703125
        - atom: O x: 12.913999557495117 y:6.75 z:45.55099868774414
        - atom: CB x: 11.88700008392334 y:7.824999809265137 z:42.54899978637695
        - atom: OG x: 12.267000198364258 y:9.003000259399414 z:43.255001068115234
      - residue ALA has 5 atoms
        - atom: N x: 10.75 y:6.5229997634887695 z:45.060001373291016
        - atom: CA x: 10.368000030517578 y:6.559999942779541 z:46.47700119018555
        - atom: C x: 11.04699993133545 y:5.427999973297119 z:47.2599983215332
        - atom: O x: 11.673999786376953 y:5.670000076293945 z:48.2869987487793
        - atom: CB x: 8.85200023651123 y:6.466000080108643 z:46.63600158691406
      - residue ALA has 5 atoms
        - atom: N x: 10.935999870300293 y:4.192999839782715 z:46.78499984741211
        - atom: CA x: 11.574999809265137 y:3.0989999771118164 z:47.499000549316406
        - atom: C x: 13.069999694824219 y:3.3540000915527344 z:47.66600036621094
        - atom: O x: 13.619000434875488 y:3.138000011444092 z:48.733001708984375
        - atom: CB x: 11.357000350952148 y:1.7940000295639038 z:46.77399826049805
      - residue ARG has 11 atoms
        - atom: N x: 13.737000465393066 y:3.808000087738037 z:46.617000579833984
        - atom: CA x: 15.163999557495117 y:4.068999767303467 z:46.73899841308594
        - atom: C x: 15.439000129699707 y:5.125999927520752 z:47.801998138427734
        - atom: O x: 16.441999435424805 y:5.046999931335449 z:48.50899887084961
        - atom: CB x: 15.765000343322754 y:4.5269999504089355 z:45.41400146484375
        - atom: CG x: 17.187000274658203 y:5.013999938964844 z:45.55500030517578
        - atom: CD x: 17.774999618530273 y:5.38100004196167 z:44.2130012512207
        - atom: NE x: 17.91900062561035 y:4.206999778747559 z:43.36199951171875
        - atom: CZ x: 18.624000549316406 y:3.128000020980835 z:43.6879997253418
        - atom: NH1 x: 19.253999710083008 y:3.075000047683716 z:44.85200119018555
        - atom: NH2 x: 18.694000244140625 y:2.1010000705718994 z:42.85100173950195
      - residue LYS has 9 atoms
        - atom: N x: 14.557000160217285 y:6.117000102996826 z:47.91299819946289
        - atom: CA x: 14.75 y:7.156000137329102 z:48.909000396728516
        - atom: C x: 14.637999534606934 y:6.564000129699707 z:50.31399917602539
        - atom: O x: 15.583000183105469 y:6.656000137329102 z:51.0880012512207
        - atom: CB x: 13.739999771118164 y:8.288999557495117 z:48.73099899291992
        - atom: CG x: 13.96399974822998 y:9.401000022888184 z:49.72600173950195
        - atom: CD x: 13.178999900817871 y:10.670000076293945 z:49.441001892089844
        - atom: CE x: 13.61400032043457 y:11.75100040435791 z:50.43299865722656
        - atom: NZ x: 12.967000007629395 y:13.07800006866455 z:50.22100067138672
      - residue PHE has 11 atoms
        - atom: N x: 13.501999855041504 y:5.952000141143799 z:50.64099884033203
        - atom: CA x: 13.32699966430664 y:5.343999862670898 z:51.95600128173828
        - atom: C x: 14.543999671936035 y:4.506999969482422 z:52.38100051879883
        - atom: O x: 15.128999710083008 y:4.742000102996826 z:53.430999755859375
        - atom: CB x: 12.090999603271484 y:4.448999881744385 z:51.974998474121094
        - atom: CG x: 10.807000160217285 y:5.189000129699707 z:51.819000244140625
        - atom: CD1 x: 10.470999717712402 y:6.210000038146973 z:52.6879997253418
        - atom: CD2 x: 9.913000106811523 y:4.8480000495910645 z:50.8129997253418
        - atom: CE1 x: 9.260000228881836 y:6.885000228881836 z:52.5629997253418
        - atom: CE2 x: 8.70199966430664 y:5.513000011444092 z:50.67900085449219
        - atom: CZ x: 8.378000259399414 y:6.534999847412109 z:51.560001373291016
      - residue VAL has 7 atoms
        - atom: N x: 14.911999702453613 y:3.5230000019073486 z:51.564998626708984
        - atom: CA x: 16.048999786376953 y:2.6570000648498535 z:51.86399841308594
        - atom: C x: 17.27199935913086 y:3.493000030517578 z:52.22100067138672
        - atom: O x: 17.93000030517578 y:3.2239999771118164 z:53.21799850463867
        - atom: CB x: 16.365999221801758 y:1.7050000429153442 z:50.66899871826172
        - atom: CG1 x: 17.589000701904297 y:0.8560000061988831 z:50.96099853515625
        - atom: CG2 x: 15.1850004196167 y:0.796999990940094 z:50.41600036621094
      - residue ASP has 8 atoms
        - atom: N x: 17.565000534057617 y:4.51800012588501 z:51.428001403808594
        - atom: CA x: 18.70800018310547 y:5.386000156402588 z:51.70800018310547
        - atom: C x: 18.582000732421875 y:6.093999862670898 z:53.05699920654297
        - atom: O x: 19.562000274658203 y:6.625999927520752 z:53.564998626708984
        - atom: CB x: 18.885000228881836 y:6.446000099182129 z:50.612998962402344
        - atom: CG x: 19.240999221801758 y:5.841000080108643 z:49.27000045776367
        - atom: OD1 x: 19.964000701904297 y:4.815999984741211 z:49.257999420166016
        - atom: OD2 x: 18.80900001525879 y:6.396999835968018 z:48.229000091552734
      - residue GLU has 9 atoms
        - atom: N x: 17.381000518798828 y:6.117000102996826 z:53.62699890136719
        - atom: CA x: 17.163999557495117 y:6.752999782562256 z:54.92300033569336
        - atom: C x: 16.847999572753906 y:5.6570000648498535 z:55.96799850463867
        - atom: O x: 16.23900032043457 y:5.9070000648498535 z:57.007999420166016
        - atom: CB x: 16.024999618530273 y:7.790999889373779 z:54.821998596191406
        - atom: CG x: 16.170000076293945 y:8.746000289916992 z:53.61800003051758
        - atom: CD x: 15.095000267028809 y:9.843000411987305 z:53.54600143432617
        - atom: OE1 x: 13.904000282287598 y:9.550999641418457 z:53.82699966430664
        - atom: OE2 x: 15.446000099182129 y:10.996000289916992 z:53.183998107910156
      - residue GLY has 4 atoms
        - atom: N x: 17.257999420166016 y:4.429999828338623 z:55.65800094604492
        - atom: CA x: 17.05900001525879 y:3.325000047683716 z:56.571998596191406
        - atom: C x: 15.710000038146973 y:2.6449999809265137 z:56.645999908447266
        - atom: O x: 15.593000411987305 y:1.6239999532699585 z:57.33100128173828
      - residue ILE has 8 atoms
        - atom: N x: 14.696999549865723 y:3.197999954223633 z:55.98099899291992
        - atom: CA x: 13.359000205993652 y:2.5959999561309814 z:55.972999572753906
        - atom: C x: 13.357000350952148 y:1.5210000276565552 z:54.89799880981445
        - atom: O x: 13.423999786376953 y:1.8480000495910645 z:53.7130012512207
        - atom: CB x: 12.27299976348877 y:3.614000082015991 z:55.59700012207031
        - atom: CG1 x: 12.300999641418457 y:4.796999931335449 z:56.5620002746582
        - atom: CG2 x: 10.91100025177002 y:2.947999954223633 z:55.63399887084961
        - atom: CD1 x: 11.234000205993652 y:5.835999965667725 z:56.28099822998047
      - residue LYS has 9 atoms
        - atom: N x: 13.265000343322754 y:0.25099998712539673 z:55.29199981689453
        - atom: CA x: 13.29800033569336 y:-0.828000009059906 z:54.305999755859375
        - atom: C x: 12.36299991607666 y:-2.01200008392334 z:54.54800033569336
        - atom: O x: 12.54699993133545 y:-3.068000078201294 z:53.96500015258789
        - atom: CB x: 14.72599983215332 y:-1.3580000400543213 z:54.194000244140625
        - atom: CG x: 15.210000038146973 y:-2.0199999809265137 z:55.479000091552734
        - atom: CD x: 16.617000579833984 y:-2.6059999465942383 z:55.35300064086914
        - atom: CE x: 17.683000564575195 y:-1.5269999504089355 z:55.19200134277344
        - atom: NZ x: 19.045000076293945 y:-2.1089999675750732 z:55.125999450683594
      - residue THR has 7 atoms
        - atom: N x: 11.362000465393066 y:-1.8580000400543213 z:55.39500045776367
        - atom: CA x: 10.472999572753906 y:-2.9719998836517334 z:55.65399932861328
        - atom: C x: 9.10200023651123 y:-2.507999897003174 z:56.108001708984375
        - atom: O x: 8.946999549865723 y:-1.378999948501587 z:56.555999755859375
        - atom: CB x: 11.092000007629395 y:-3.8940000534057617 z:56.70600128173828
        - atom: OG1 x: 11.718000411987305 y:-3.0959999561309814 z:57.71200180053711
        - atom: CG2 x: 12.14799976348877 y:-4.789000034332275 z:56.07899856567383
      - residue LEU has 8 atoms
        - atom: N x: 8.11299991607666 y:-3.38700008392334 z:55.98899841308594
        - atom: CA x: 6.741000175476074 y:-3.065000057220459 z:56.361000061035156
        - atom: C x: 6.663000106811523 y:-2.3540000915527344 z:57.698001861572266
        - atom: O x: 5.9079999923706055 y:-1.3930000066757202 z:57.867000579833984
        - atom: CB x: 5.900000095367432 y:-4.335999965667725 z:56.41899871826172
        - atom: CG x: 4.75600004196167 y:-4.4770002365112305 z:55.40999984741211
        - atom: CD1 x: 5.265999794006348 y:-4.355999946594238 z:53.98500061035156
        - atom: CD2 x: 4.0980000495910645 y:-5.828000068664551 z:55.604000091552734
      - residue GLU has 9 atoms
        - atom: N x: 7.443999767303467 y:-2.8399999141693115 z:58.652000427246094
        - atom: CA x: 7.4720001220703125 y:-2.259000062942505 z:59.97999954223633
        - atom: C x: 7.995999813079834 y:-0.824999988079071 z:59.93000030517578
        - atom: O x: 7.494999885559082 y:0.04899999871850014 z:60.625
        - atom: CB x: 8.338000297546387 y:-3.124000072479248 z:60.90299987792969
        - atom: CG x: 7.71999979019165 y:-4.488999843597412 z:61.23899841308594
        - atom: CD x: 7.673999786376953 y:-5.454999923706055 z:60.05400085449219
        - atom: OE1 x: 8.753000259399414 y:-5.8520002365112305 z:59.5629997253418
        - atom: OE2 x: 6.560999870300293 y:-5.826000213623047 z:59.61600112915039
      - residue ASP has 8 atoms
        - atom: N x: 9.005000114440918 y:-0.5849999785423279 z:59.104000091552734
        - atom: CA x: 9.571999549865723 y:0.7480000257492065 z:58.9739990234375
        - atom: C x: 8.531999588012695 y:1.718000054359436 z:58.41600036621094
        - atom: O x: 8.362000465393066 y:2.8380000591278076 z:58.92399978637695
        - atom: CB x: 10.795999526977539 y:0.6819999814033508 z:58.07600021362305
        - atom: CG x: 11.92300033569336 y:-0.08399999886751175 z:58.7140007019043
        - atom: OD1 x: 11.635000228881836 y:-1.0809999704360962 z:59.4010009765625
        - atom: OD2 x: 13.090999603271484 y:0.3059999942779541 z:58.529998779296875
      - residue LEU has 8 atoms
        - atom: N x: 7.834000110626221 y:1.2890000343322754 z:57.37099838256836
        - atom: CA x: 6.793000221252441 y:2.117000102996826 z:56.79399871826172
        - atom: C x: 5.763000011444092 y:2.321000099182129 z:57.895999908447266
        - atom: O x: 5.111000061035156 y:3.3589999675750732 z:57.95600128173828
        - atom: CB x: 6.164000034332275 y:1.4190000295639038 z:55.58599853515625
        - atom: CG x: 7.113999843597412 y:1.1069999933242798 z:54.428001403808594
        - atom: CD1 x: 6.370999813079834 y:0.3479999899864197 z:53.361000061035156
        - atom: CD2 x: 7.696000099182129 y:2.390000104904175 z:53.86399841308594
      - residue ARG has 11 atoms
        - atom: N x: 5.632999897003174 y:1.3179999589920044 z:58.76499938964844
        - atom: CA x: 4.715000152587891 y:1.3680000305175781 z:59.90700149536133
        - atom: C x: 5.168000221252441 y:2.438999891281128 z:60.90299987792969
        - atom: O x: 4.3460001945495605 y:3.1530001163482666 z:61.48099899291992
        - atom: CB x: 4.678999900817871 y:0.017999999225139618 z:60.619998931884766
        - atom: CG x: 3.812999963760376 y:-1.0190000534057617 z:59.95800018310547
        - atom: CD x: 2.361999988555908 y:-0.7979999780654907 z:60.33000183105469
        - atom: NE x: 1.4429999589920044 y:-1.5540000200271606 z:59.483001708984375
        - atom: CZ x: 1.4910000562667847 y:-2.869999885559082 z:59.29999923706055
        - atom: NH1 x: 2.4179999828338623 y:-3.5999999046325684 z:59.909000396728516
        - atom: NH2 x: 0.6159999966621399 y:-3.4560000896453857 z:58.4900016784668
      - residue LYS has 9 atoms
        - atom: N x: 6.4770002365112305 y:2.5450000762939453 z:61.104000091552734
        - atom: CA x: 7.011000156402588 y:3.5309998989105225 z:62.02199935913086
        - atom: C x: 6.9720001220703125 y:4.920000076293945 z:61.40399932861328
        - atom: O x: 6.544000148773193 y:5.894000053405762 z:62.04800033569336
        - atom: CB x: 8.460000038146973 y:3.2070000171661377 z:62.402000427246094
        - atom: CG x: 9.081999778747559 y:4.255000114440918 z:63.327999114990234
        - atom: CD x: 10.49899959564209 y:3.9030001163482666 z:63.790000915527344
        - atom: CE x: 11.552000045776367 y:4.183000087738037 z:62.72600173950195
        - atom: NZ x: 12.932000160217285 y:4.047999858856201 z:63.28200149536133
      - residue ASN has 8 atoms
        - atom: N x: 7.419000148773193 y:5.011000156402588 z:60.154998779296875
        - atom: CA x: 7.459000110626221 y:6.291999816894531 z:59.483001708984375
        - atom: C x: 6.232999801635742 y:6.5929999351501465 z:58.65599822998047
        - atom: O x: 6.293000221252441 y:7.327000141143799 z:57.68299865722656
        - atom: CB x: 8.72700023651123 y:6.385000228881836 z:58.63999938964844
        - atom: CG x: 9.965999603271484 y:6.585999965667725 z:59.49399948120117
        - atom: OD1 x: 11.059000015258789 y:6.823999881744385 z:58.986000061035156
        - atom: ND2 x: 9.795000076293945 y:6.491000175476074 z:60.81100082397461
      - residue GLU has 9 atoms
        - atom: N x: 5.109000205993652 y:6.044000148773193 z:59.08000183105469
        - atom: CA x: 3.8510000705718994 y:6.230999946594238 z:58.387001037597656
        - atom: C x: 3.5390000343322754 y:7.684000015258789 z:58.02299880981445
        - atom: O x: 3.0429999828338623 y:7.9670000076293945 z:56.933998107910156
        - atom: CB x: 2.7279999256134033 y:5.677000045776367 z:59.244998931884766
        - atom: CG x: 1.3849999904632568 y:5.681000232696533 z:58.58300018310547
        - atom: CD x: 0.2879999876022339 y:5.394999980926514 z:59.57400131225586
        - atom: OE1 x: 0.3709999918937683 y:4.359000205993652 z:60.27399826049805
        - atom: OE2 x: -0.6549999713897705 y:6.210999965667725 z:59.65399932861328
      - residue ASP has 8 atoms
        - atom: N x: 3.8320000171661377 y:8.607999801635742 z:58.926998138427734
        - atom: CA x: 3.5360000133514404 y:10.008000373840332 z:58.665000915527344
        - atom: C x: 4.449999809265137 y:10.621000289916992 z:57.61399841308594
        - atom: O x: 4.502999782562256 y:11.836999893188477 z:57.472999572753906
        - atom: CB x: 3.615000009536743 y:10.812000274658203 z:59.96900177001953
        - atom: CG x: 5.039000034332275 y:11.223999977111816 z:60.327999114990234
        - atom: OD1 x: 5.9720001220703125 y:10.38599967956543 z:60.19599914550781
        - atom: OD2 x: 5.216000080108643 y:12.392000198364258 z:60.75600051879883
      - residue LYS has 9 atoms
        - atom: N x: 5.159999847412109 y:9.774999618530273 z:56.874000549316406
        - atom: CA x: 6.084000110626221 y:10.223999977111816 z:55.83000183105469
        - atom: C x: 5.663000106811523 y:9.597999572753906 z:54.479000091552734
        - atom: O x: 6.453000068664551 y:9.491999626159668 z:53.529998779296875
        - atom: CB x: 7.515999794006348 y:9.8149995803833 z:56.21200180053711
        - atom: CG x: 8.607000350952148 y:10.362000465393066 z:55.303001403808594
        - atom: CD x: 9.99899959564209 y:9.871000289916992 z:55.709999084472656
        - atom: CE x: 10.60200023651123 y:10.678999900817871 z:56.86199951171875
        - atom: NZ x: 9.82699966430664 y:10.61400032043457 z:58.130001068115234
      - residue LEU has 8 atoms
        - atom: N x: 4.395999908447266 y:9.199000358581543 z:54.41299819946289
        - atom: CA x: 3.8239998817443848 y:8.581000328063965 z:53.22800064086914
        - atom: C x: 2.6070001125335693 y:9.369999885559082 z:52.75899887084961
        - atom: O x: 1.850000023841858 y:9.902000427246094 z:53.573001861572266
        - atom: CB x: 3.36299991607666 y:7.158999919891357 z:53.55099868774414
        - atom: CG x: 4.328999996185303 y:6.171999931335449 z:54.19900131225586
        - atom: CD1 x: 3.621999979019165 y:4.828999996185303 z:54.38100051879883
        - atom: CD2 x: 5.563000202178955 y:6.019000053405762 z:53.32899856567383
      - residue ASN has 8 atoms
        - atom: N x: 2.4019999504089355 y:9.430999755859375 z:51.45000076293945
        - atom: CA x: 1.2419999837875366 y:10.133999824523926 z:50.926998138427734
        - atom: C x: 0.014000000432133675 y:9.26099967956543 z:51.11600112915039
        - atom: O x: 0.12300000339746475 y:8.086999893188477 z:51.41600036621094
        - atom: CB x: 1.4190000295639038 y:10.456000328063965 z:49.446998596191406
        - atom: CG x: 1.8220000267028809 y:9.25100040435791 z:48.641998291015625
        - atom: OD1 x: 1.2480000257492065 y:8.178000450134277 z:48.77899932861328
        - atom: ND2 x: 2.812999963760376 y:9.425999641418457 z:47.790000915527344
      - residue HIS has 10 atoms
        - atom: N x: -1.1540000438690186 y:9.850000381469727 z:50.94499969482422
        - atom: CA x: -2.4070000648498535 y:9.142999649047852 z:51.106998443603516
        - atom: C x: -2.4030001163482666 y:7.800000190734863 z:50.391998291015625
        - atom: O x: -2.8350000381469727 y:6.7829999923706055 z:50.939998626708984
        - atom: CB x: -3.5369999408721924 y:10.003999710083008 z:50.566001892089844
        - atom: CG x: -4.88100004196167 y:9.364999771118164 z:50.6619987487793
        - atom: ND1 x: -5.572999954223633 y:9.265000343322754 z:51.8489990234375
        - atom: CD2 x: -5.666999816894531 y:8.79800033569336 z:49.720001220703125
        - atom: CE1 x: -6.730000019073486 y:8.668000221252441 z:51.6349983215332
        - atom: NE2 x: -6.811999797821045 y:8.37399959564209 z:50.35100173950195
      - residue HIS has 10 atoms
        - atom: N x: -1.8949999809265137 y:7.797999858856201 z:49.17100143432617
        - atom: CA x: -1.8609999418258667 y:6.583000183105469 z:48.375
        - atom: C x: -0.9599999785423279 y:5.51200008392334 z:48.986000061035156
        - atom: O x: -1.3209999799728394 y:4.3420000076293945 z:49.013999938964844
        - atom: CB x: -1.4359999895095825 y:6.927999973297119 z:46.933998107910156
        - atom: CG x: -1.406000018119812 y:5.757999897003174 z:45.99700164794922
        - atom: ND1 x: -1.434999942779541 y:5.908999919891357 z:44.62900161743164
        - atom: CD2 x: -1.2580000162124634 y:4.429999828338623 z:46.2239990234375
        - atom: CE1 x: -1.3009999990463257 y:4.728000164031982 z:44.05400085449219
        - atom: NE2 x: -1.190999984741211 y:3.815000057220459 z:45.000999450683594
      - residue GLN has 9 atoms
        - atom: N x: 0.20800000429153442 y:5.910999774932861 z:49.47100067138672
        - atom: CA x: 1.1390000581741333 y:4.968999862670898 z:50.07500076293945
        - atom: C x: 0.5680000185966492 y:4.394000053405762 z:51.38800048828125
        - atom: O x: 0.800000011920929 y:3.2219998836517334 z:51.69599914550781
        - atom: CB x: 2.499000072479248 y:5.65500020980835 z:50.30099868774414
        - atom: CG x: 3.200000047683716 y:6.076000213623047 z:49.00299835205078
        - atom: CD x: 4.383999824523926 y:7.015999794006348 z:49.22100067138672
        - atom: OE1 x: 4.260000228881836 y:8.043000221252441 z:49.88100051879883
        - atom: NE2 x: 5.531000137329102 y:6.669000148773193 z:48.65399932861328
      - residue ARG has 11 atoms
        - atom: N x: -0.18000000715255737 y:5.201000213623047 z:52.150001525878906
        - atom: CA x: -0.777999997138977 y:4.710000038146973 z:53.39099884033203
        - atom: C x: -1.7100000381469727 y:3.572999954223633 z:53.02399826049805
        - atom: O x: -1.562999963760376 y:2.4649999141693115 z:53.52199935913086
        - atom: CB x: -1.6130000352859497 y:5.7779998779296875 z:54.10200119018555
        - atom: CG x: -0.9010000228881836 y:6.5980000495910645 z:55.172000885009766
        - atom: CD x: -0.2150000035762787 y:7.790999889373779 z:54.56999969482422
        - atom: NE x: 0.1120000034570694 y:8.810999870300293 z:55.56100082397461
        - atom: CZ x: -0.7559999823570251 y:9.329000473022461 z:56.428001403808594
        - atom: NH1 x: -2.0209999084472656 y:8.916000366210938 z:56.444000244140625
        - atom: NH2 x: -0.3630000054836273 y:10.286999702453613 z:57.26100158691406
      - residue ILE has 8 atoms
        - atom: N x: -2.6760001182556152 y:3.8610000610351562 z:52.15399932861328
        - atom: CA x: -3.6410000324249268 y:2.8570001125335693 z:51.694000244140625
        - atom: C x: -2.88700008392334 y:1.61899995803833 z:51.20600128173828
        - atom: O x: -3.2730000019073486 y:0.48100000619888306 z:51.500999450683594
        - atom: CB x: -4.520999908447266 y:3.4000000953674316 z:50.507999420166016
        - atom: CG1 x: -5.324999809265137 y:4.625999927520752 z:50.95399856567383
        - atom: CG2 x: -5.440999984741211 y:2.302999973297119 z:49.98400115966797
        - atom: CD1 x: -6.333000183105469 y:4.361000061035156 z:52.060001373291016
      - residue GLY has 4 atoms
        - atom: N x: -1.8070000410079956 y:1.8609999418258667 z:50.465999603271484
        - atom: CA x: -0.996999979019165 y:0.7850000262260437 z:49.92599868774414
        - atom: C x: -0.5400000214576721 y:-0.16500000655651093 z:51.00400161743164
        - atom: O x: -0.7350000143051147 y:-1.371000051498413 z:50.88600158691406
      - residue LEU has 8 atoms
        - atom: N x: 0.05900000035762787 y:0.4000000059604645 z:52.053001403808594
        - atom: CA x: 0.5699999928474426 y:-0.34200000762939453 z:53.20199966430664
        - atom: C x: -0.5519999861717224 y:-1.0260000228881836 z:53.93899917602539
        - atom: O x: -0.4169999957084656 y:-2.1730000972747803 z:54.332000732421875
        - atom: CB x: 1.2879999876022339 y:0.6060000061988831 z:54.16699981689453
        - atom: CG x: 1.7599999904632568 y:0.08100000023841858 z:55.53300094604492
        - atom: CD1 x: 2.7009999752044678 y:-1.0989999771118164 z:55.36000061035156
        - atom: CD2 x: 2.4820001125335693 y:1.2120000123977661 z:56.27399826049805
      - residue LYS has 9 atoms
        - atom: N x: -1.6549999713897705 y:-0.3050000071525574 z:54.11899948120117
        - atom: CA x: -2.8510000705718994 y:-0.7960000038146973 z:54.805999755859375
        - atom: C x: -3.437999963760376 y:-2.068000078201294 z:54.21099853515625
        - atom: O x: -3.943000078201294 y:-2.9210000038146973 z:54.93199920654297
        - atom: CB x: -3.940000057220459 y:0.2750000059604645 z:54.79199981689453
        - atom: CG x: -5.296000003814697 y:-0.2150000035762787 z:55.270999908447266
        - atom: CD x: -6.254000186920166 y:0.9430000185966492 z:55.45000076293945
        - atom: CE x: -7.507999897003174 y:0.5070000290870667 z:56.176998138427734
        - atom: NZ x: -8.45300006866455 y:1.6299999952316284 z:56.4119987487793
      - residue TYR has 12 atoms
        - atom: N x: -3.3940000534057617 y:-2.177999973297119 z:52.891998291015625
        - atom: CA x: -3.928999900817871 y:-3.3459999561309814 z:52.2140007019043
        - atom: C x: -2.806999921798706 y:-4.0879998207092285 z:51.51499938964844
        - atom: O x: -3.015000104904175 y:-4.678999900817871 z:50.43899917602539
        - atom: CB x: -4.980999946594238 y:-2.921999931335449 z:51.1870002746582
        - atom: CG x: -6.118000030517578 y:-2.1530001163482666 z:51.79399871826172
        - atom: CD1 x: -6.923999786376953 y:-2.7249999046325684 z:52.77000045776367
        - atom: CD2 x: -6.373000144958496 y:-0.8399999737739563 z:51.41600036621094
        - atom: CE1 x: -7.953999996185303 y:-2.003000020980835 z:53.3650016784668
        - atom: CE2 x: -7.40500020980835 y:-0.10899999737739563 z:51.999000549316406
        - atom: CZ x: -8.187999725341797 y:-0.6949999928474426 z:52.97100067138672
        - atom: OH x: -9.218999862670898 y:0.01899999938905239 z:53.53499984741211
      - residue PHE has 11 atoms
        - atom: N x: -1.6200000047683716 y:-4.072000026702881 z:52.117000579833984
        - atom: CA x: -0.4959999918937683 y:-4.738999843597412 z:51.47700119018555
        - atom: C x: -0.7870000004768372 y:-6.201000213623047 z:51.15299987792969
        - atom: O x: -0.6729999780654907 y:-6.626999855041504 z:50.005001068115234
        - atom: CB x: 0.7450000047683716 y:-4.664000034332275 z:52.33300018310547
        - atom: CG x: 1.934000015258789 y:-5.28000020980835 z:51.691001892089844
        - atom: CD1 x: 2.6610000133514404 y:-4.579999923706055 z:50.74100112915039
        - atom: CD2 x: 2.321000099182129 y:-6.566999912261963 z:52.01900100708008
        - atom: CE1 x: 3.7679998874664307 y:-5.1479997634887695 z:50.12099838256836
        - atom: CE2 x: 3.427000045776367 y:-7.1579999923706055 z:51.409000396728516
        - atom: CZ x: 4.156000137329102 y:-6.446000099182129 z:50.45500183105469
      - residue GLY has 4 atoms
        - atom: N x: -1.159999966621399 y:-6.968999862670898 z:52.16699981689453
        - atom: CA x: -1.4630000591278076 y:-8.36299991607666 z:51.941001892089844
        - atom: C x: -2.6440000534057617 y:-8.527000427246094 z:51.00699996948242
        - atom: O x: -2.572000026702881 y:-9.300000190734863 z:50.05500030517578
      - residue ASP has 8 atoms
        - atom: N x: -3.7300000190734863 y:-7.806000232696533 z:51.2760009765625
        - atom: CA x: -4.914000034332275 y:-7.888999938964844 z:50.43600082397461
        - atom: C x: -4.5960001945495605 y:-7.710999965667725 z:48.95600128173828
        - atom: O x: -4.974999904632568 y:-8.550000190734863 z:48.137001037597656
        - atom: CB x: -5.949999809265137 y:-6.8480000495910645 z:50.856998443603516
        - atom: CG x: -6.870999813079834 y:-7.361999988555908 z:51.93000030517578
        - atom: OD1 x: -6.843999862670898 y:-8.590999603271484 z:52.15800094604492
        - atom: OD2 x: -7.624000072479248 y:-6.559999942779541 z:52.5369987487793
      - residue PHE has 11 atoms
        - atom: N x: -3.8889999389648438 y:-6.633999824523926 z:48.61899948120117
        - atom: CA x: -3.5399999618530273 y:-6.348999977111816 z:47.233001708984375
        - atom: C x: -2.683000087738037 y:-7.379000186920166 z:46.516998291015625
        - atom: O x: -2.6549999713897705 y:-7.396999835968018 z:45.290000915527344
        - atom: CB x: -2.8589999675750732 y:-4.974999904632568 z:47.108001708984375
        - atom: CG x: -3.7939999103546143 y:-3.812000036239624 z:47.305999755859375
        - atom: CD1 x: -5.133999824523926 y:-4.020999908447266 z:47.62699890136719
        - atom: CD2 x: -3.3239998817443848 y:-2.5139999389648438 z:47.233001708984375
        - atom: CE1 x: -5.98199987411499 y:-2.9639999866485596 z:47.88100051879883
        - atom: CE2 x: -4.168000221252441 y:-1.437999963760376 z:47.48699951171875
        - atom: CZ x: -5.502999782562256 y:-1.6649999618530273 z:47.814998626708984
      - residue GLU has 9 atoms
        - atom: N x: -1.9630000591278076 y:-8.22700023651123 z:47.244998931884766
        - atom: CA x: -1.1390000581741333 y:-9.21399974822998 z:46.55099868774414
        - atom: C x: -1.9110000133514404 y:-10.48900032043457 z:46.32899856567383
        - atom: O x: -1.409000039100647 y:-11.414999961853027 z:45.70899963378906
        - atom: CB x: 0.16899999976158142 y:-9.505000114440918 z:47.30400085449219
        - atom: CG x: 1.1510000228881836 y:-8.329999923706055 z:47.29899978637695
        - atom: CD x: 2.6040000915527344 y:-8.77299976348877 z:47.356998443603516
        - atom: OE1 x: 2.9189999103546143 y:-9.692000389099121 z:48.141998291015625
        - atom: OE2 x: 3.434000015258789 y:-8.196000099182129 z:46.624000549316406
      - residue LYS has 9 atoms
        - atom: N x: -3.138000011444092 y:-10.534000396728516 z:46.82699966430664
        - atom: CA x: -3.9719998836517334 y:-11.711000442504883 z:46.63999938964844
        - atom: C x: -4.692999839782715 y:-11.647000312805176 z:45.2859992980957
        - atom: O x: -5.2129998207092285 y:-10.595000267028809 z:44.89500045776367
        - atom: CB x: -5.033999919891357 y:-11.817000389099121 z:47.742000579833984
        - atom: CG x: -4.519999980926514 y:-12.019000053405762 z:49.15399932861328
        - atom: CD x: -5.681000232696533 y:-12.40999984741211 z:50.0629997253418
        - atom: CE x: -5.315000057220459 y:-12.395000457763672 z:51.53200149536133
        - atom: NZ x: -4.199999809265137 y:-13.324000358581543 z:51.86800003051758
      - residue ARG has 11 atoms
        - atom: N x: -4.708000183105469 y:-12.767999649047852 z:44.57099914550781
        - atom: CA x: -5.4120001792907715 y:-12.85200023651123 z:43.29800033569336
        - atom: C x: -6.906000137329102 y:-12.857999801635742 z:43.64899826049805
        - atom: O x: -7.281000137329102 y:-13.098999977111816 z:44.79600143432617
        - atom: CB x: -5.052000045776367 y:-14.151000022888184 z:42.57400131225586
        - atom: CG x: -3.5899999141693115 y:-14.277000427246094 z:42.189998626708984
        - atom: CD x: -3.253000020980835 y:-13.343000411987305 z:41.04800033569336
        - atom: NE x: -4.007999897003174 y:-13.678000450134277 z:39.84000015258789
        - atom: CZ x: -4.105000019073486 y:-12.894000053405762 z:38.768001556396484
        - atom: NH1 x: -3.496999979019165 y:-11.711999893188477 z:38.73899841308594
        - atom: NH2 x: -4.809000015258789 y:-13.298999786376953 z:37.71799850463867
      - residue ILE has 8 atoms
        - atom: N x: -7.75600004196167 y:-12.595000267028809 z:42.66600036621094
        - atom: CA x: -9.199000358581543 y:-12.581000328063965 z:42.89099884033203
        - atom: C x: -9.857999801635742 y:-13.762999534606934 z:42.17300033569336
        - atom: O x: -9.720000267028809 y:-13.904000282287598 z:40.957000732421875
        - atom: CB x: -9.817000389099121 y:-11.27400016784668 z:42.358001708984375
        - atom: CG1 x: -9.052000045776367 y:-10.076000213623047 z:42.92499923706055
        - atom: CG2 x: -11.300999641418457 y:-11.206000328063965 z:42.729000091552734
        - atom: CD1 x: -9.505000114440918 y:-8.73900032043457 z:42.39799880981445
      - residue PRO has 7 atoms
        - atom: N x: -10.585000038146973 y:-14.626999855041504 z:42.9119987487793
        - atom: CA x: -11.241999626159668 y:-15.781999588012695 z:42.277000427246094
        - atom: C x: -12.177000045776367 y:-15.265999794006348 z:41.198001861572266
        - atom: O x: -12.9399995803833 y:-14.333000183105469 z:41.44900131225586
        - atom: CB x: -12.015000343322754 y:-16.426000595092773 z:43.42599868774414
        - atom: CG x: -11.246999740600586 y:-15.991999626159668 z:44.65399932861328
        - atom: CD x: -10.90999984741211 y:-14.5600004196167 z:44.3489990234375
      - residue ARG has 11 atoms
        - atom: N x: -12.13700008392334 y:-15.86400032043457 z:40.007999420166016
        - atom: CA x: -12.998000144958496 y:-15.402000427246094 z:38.92300033569336
        - atom: C x: -14.454999923706055 y:-15.329000473022461 z:39.33000183105469
        - atom: O x: -15.230999946594238 y:-14.598999977111816 z:38.73400115966797
        - atom: CB x: -12.876999855041504 y:-16.285999298095703 z:37.683998107910156
        - atom: CG x: -13.494000434875488 y:-15.621000289916992 z:36.470001220703125
        - atom: CD x: -13.788999557495117 y:-16.57900047302246 z:35.345001220703125
        - atom: NE x: -14.845000267028809 y:-16.03700065612793 z:34.49399948120117
        - atom: CZ x: -14.718000411987305 y:-14.97599983215332 z:33.696998596191406
        - atom: NH1 x: -13.567000389099121 y:-14.322999954223633 z:33.61399841308594
        - atom: NH2 x: -15.767000198364258 y:-14.541999816894531 z:33.007999420166016
      - residue GLU has 9 atoms
        - atom: N x: -14.829000473022461 y:-16.084999084472656 z:40.34700012207031
        - atom: CA x: -16.200000762939453 y:-16.082000732421875 z:40.83100128173828
        - atom: C x: -16.530000686645508 y:-14.770999908447266 z:41.529998779296875
        - atom: O x: -17.562000274658203 y:-14.151000022888184 z:41.26499938964844
        - atom: CB x: -16.413999557495117 y:-17.25200080871582 z:41.79399871826172
        - atom: CG x: -17.667999267578125 y:-17.152000427246094 z:42.63999938964844
        - atom: CD x: -18.077999114990234 y:-18.496999740600586 z:43.21699905395508
        - atom: OE1 x: -18.999000549316406 y:-18.52400016784668 z:44.064998626708984
        - atom: OE2 x: -17.48699951171875 y:-19.530000686645508 z:42.816001892089844
      - residue GLU has 9 atoms
        - atom: N x: -15.652999877929688 y:-14.359000205993652 z:42.4370002746582
        - atom: CA x: -15.861000061035156 y:-13.123000144958496 z:43.167999267578125
        - atom: C x: -15.913000106811523 y:-11.949999809265137 z:42.1879997253418
        - atom: O x: -16.642000198364258 y:-10.979999542236328 z:42.409000396728516
        - atom: CB x: -14.75100040435791 y:-12.937999725341797 z:44.20800018310547
        - atom: CG x: -14.975000381469727 y:-13.76099967956543 z:45.46699905395508
        - atom: CD x: -13.857000350952148 y:-13.616000175476074 z:46.49100112915039
        - atom: OE1 x: -13.395000457763672 y:-12.477999687194824 z:46.71699905395508
        - atom: OE2 x: -13.449999809265137 y:-14.640999794006348 z:47.08100128173828
      - residue MET has 8 atoms
        - atom: N x: -15.138999938964844 y:-12.048999786376953 z:41.106998443603516
        - atom: CA x: -15.130000114440918 y:-11.010000228881836 z:40.0890007019043
        - atom: C x: -16.57699966430664 y:-10.881999969482422 z:39.64799880981445
        - atom: O x: -17.172000885009766 y:-9.8100004196167 z:39.71099853515625
        - atom: CB x: -14.267999649047852 y:-11.425999641418457 z:38.893001556396484
        - atom: CG x: -12.784000396728516 y:-11.329000473022461 z:39.141998291015625
        - atom: SD x: -12.277000427246094 y:-9.61400032043457 z:39.38199996948242
        - atom: CE x: -11.970999717712402 y:-9.13599967956543 z:37.689998626708984
      - residue LEU has 8 atoms
        - atom: N x: -17.142000198364258 y:-12.005999565124512 z:39.222999572753906
        - atom: CA x: -18.52199935913086 y:-12.043999671936035 z:38.777000427246094
        - atom: C x: -19.43400001525879 y:-11.295000076293945 z:39.74399948120117
        - atom: O x: -20.256000518798828 y:-10.489999771118164 z:39.3129997253418
        - atom: CB x: -18.979000091552734 y:-13.49899959564209 z:38.625999450683594
        - atom: CG x: -18.22599983215332 y:-14.336000442504883 z:37.57699966430664
        - atom: CD1 x: -18.56999969482422 y:-15.805999755859375 z:37.749000549316406
        - atom: CD2 x: -18.573999404907227 y:-13.864999771118164 z:36.16899871826172
      - residue GLN has 9 atoms
        - atom: N x: -19.2810001373291 y:-11.53499984741211 z:41.04499816894531
        - atom: CA x: -20.1299991607666 y:-10.86299991607666 z:42.040000915527344
        - atom: C x: -19.868999481201172 y:-9.359000205993652 z:42.04899978637695
        - atom: O x: -20.73900032043457 y:-8.557000160217285 z:42.40599822998047
        - atom: CB x: -19.88800048828125 y:-11.430999755859375 z:43.44499969482422
        - atom: CG x: -19.590999603271484 y:-12.925000190734863 z:43.465999603271484
        - atom: CD x: -19.812999725341797 y:-13.557999610900879 z:44.827999114990234
        - atom: OE1 x: -19.44499969482422 y:-14.71399974822998 z:45.05099868774414
        - atom: NE2 x: -20.426000595092773 y:-12.809000015258789 z:45.742000579833984
      - residue MET has 8 atoms
        - atom: N x: -18.6560001373291 y:-8.982999801635742 z:41.66299819946289
        - atom: CA x: -18.284000396728516 y:-7.578999996185303 z:41.612998962402344
        - atom: C x: -18.82900047302246 y:-7.03000020980835 z:40.29999923706055
        - atom: O x: -19.385000228881836 y:-5.929999828338623 z:40.25899887084961
        - atom: CB x: -16.759000778198242 y:-7.435999870300293 z:41.68299865722656
        - atom: CG x: -16.158000946044922 y:-7.941999912261963 z:42.99399948120117
        - atom: SD x: -14.380999565124512 y:-8.246999740600586 z:42.926998138427734
        - atom: CE x: -13.717000007629395 y:-6.666999816894531 z:43.327999114990234
      - residue GLN has 9 atoms
        - atom: N x: -18.690000534057617 y:-7.821000099182129 z:39.236000061035156
        - atom: CA x: -19.16900062561035 y:-7.436999797821045 z:37.9119987487793
        - atom: C x: -20.66699981689453 y:-7.296000003814697 z:37.957000732421875
        - atom: O x: -21.280000686645508 y:-6.793000221252441 z:37.0260009765625
        - atom: CB x: -18.819000244140625 y:-8.5 z:36.875999450683594
        - atom: CG x: -19.424999237060547 y:-8.256999969482422 z:35.5
        - atom: CD x: -19.215999603271484 y:-9.430999755859375 z:34.56100082397461
        - atom: OE1 x: -19.83799934387207 y:-10.493000030517578 z:34.7140007019043
        - atom: NE2 x: -18.32699966430664 y:-9.251999855041504 z:33.58399963378906
      - residue ASP has 8 atoms
        - atom: N x: -21.257999420166016 y:-7.749000072479248 z:39.04999923706055
        - atom: CA x: -22.69499969482422 y:-7.681000232696533 z:39.194000244140625
        - atom: C x: -23.049999237060547 y:-6.394999980926514 z:39.89699935913086
        - atom: O x: -23.94499969482422 y:-5.671999931335449 z:39.46900177001953
        - atom: CB x: -23.18600082397461 y:-8.876999855041504 z:40.00299835205078
        - atom: CG x: -24.58799934387207 y:-9.300999641418457 z:39.630001068115234
        - atom: OD1 x: -25.54599952697754 y:-8.54699993133545 z:39.91600036621094
        - atom: OD2 x: -24.722000122070312 y:-10.397000312805176 z:39.04600143432617
      - residue ILE has 8 atoms
        - atom: N x: -22.33099937438965 y:-6.107999801635742 z:40.97600173950195
        - atom: CA x: -22.56999969482422 y:-4.901000022888184 z:41.7599983215332
        - atom: C x: -22.198999404907227 y:-3.635999917984009 z:40.992000579833984
        - atom: O x: -22.82900047302246 y:-2.5940001010894775 z:41.16600036621094
        - atom: CB x: -21.783000946044922 y:-4.942999839782715 z:43.0989990234375
        - atom: CG1 x: -22.229999542236328 y:-6.1579999923706055 z:43.92100143432617
        - atom: CG2 x: -22.006999969482422 y:-3.6570000648498535 z:43.88999938964844
        - atom: CD1 x: -21.645999908447266 y:-6.208000183105469 z:45.327999114990234
      - residue VAL has 7 atoms
        - atom: N x: -21.18000030517578 y:-3.7290000915527344 z:40.14099884033203
        - atom: CA x: -20.750999450683594 y:-2.5759999752044678 z:39.361000061035156
        - atom: C x: -21.81100082397461 y:-2.3359999656677246 z:38.30500030517578
        - atom: O x: -22.53499984741211 y:-1.3489999771118164 z:38.35900115966797
        - atom: CB x: -19.393999099731445 y:-2.825000047683716 z:38.67300033569336
        - atom: CG1 x: -18.95199966430664 y:-1.5759999752044678 z:37.946998596191406
        - atom: CG2 x: -18.347000122070312 y:-3.2209999561309814 z:39.69900131225586
      - residue LEU has 8 atoms
        - atom: N x: -21.909000396728516 y:-3.263000011444092 z:37.358001708984375
        - atom: CA x: -22.89699935913086 y:-3.177999973297119 z:36.290000915527344
        - atom: C x: -24.26300048828125 y:-2.7330000400543213 z:36.8120002746582
        - atom: O x: -24.941999435424805 y:-1.906000018119812 z:36.19200134277344
        - atom: CB x: -23.040000915527344 y:-4.533999919891357 z:35.59600067138672
        - atom: CG x: -22.295000076293945 y:-4.75 z:34.27399826049805
        - atom: CD1 x: -20.80900001525879 y:-4.521999835968018 z:34.46500015258789
        - atom: CD2 x: -22.566999435424805 y:-6.160999774932861 z:33.75899887084961
      - residue ASN has 8 atoms
        - atom: N x: -24.6560001373291 y:-3.2720000743865967 z:37.96200180053711
        - atom: CA x: -25.947999954223633 y:-2.943000078201294 z:38.551998138427734
        - atom: C x: -26.011999130249023 y:-1.4980000257492065 z:39.018001556396484
        - atom: O x: -26.774999618530273 y:-0.6959999799728394 z:38.49100112915039
        - atom: CB x: -26.240999221801758 y:-3.865999937057495 z:39.736000061035156
        - atom: CG x: -27.707000732421875 y:-3.8570001125335693 z:40.130001068115234
        - atom: OD1 x: -28.28499984741211 y:-2.805999994277954 z:40.42100143432617
        - atom: ND2 x: -28.31800079345703 y:-5.035999774932861 z:40.14099884033203
      - residue GLU has 9 atoms
        - atom: N x: -25.208999633789062 y:-1.1749999523162842 z:40.02000045776367
        - atom: CA x: -25.179000854492188 y:0.16699999570846558 z:40.577999114990234
        - atom: C x: -25.06399917602539 y:1.25 z:39.516998291015625
        - atom: O x: -25.56100082397461 y:2.3570001125335693 z:39.70199966430664
        - atom: CB x: -24.020999908447266 y:0.2759999930858612 z:41.569000244140625
        - atom: CG x: -24.288000106811523 y:-0.4399999976158142 z:42.861000061035156
        - atom: CD x: -25.4689998626709 y:0.15700000524520874 z:43.57600021362305
        - atom: OE1 x: -25.375999450683594 y:1.3259999752044678 z:43.999000549316406
        - atom: OE2 x: -26.4950008392334 y:-0.5339999794960022 z:43.70399856567383
      - residue VAL has 7 atoms
        - atom: N x: -24.398000717163086 y:0.9309999942779541 z:38.41400146484375
        - atom: CA x: -24.229999542236328 y:1.8899999856948853 z:37.33399963378906
        - atom: C x: -25.618999481201172 y:2.247999906539917 z:36.79499816894531
        - atom: O x: -25.95599937438965 y:3.4240000247955322 z:36.630001068115234
        - atom: CB x: -23.381000518798828 y:1.2999999523162842 z:36.17900085449219
        - atom: CG1 x: -23.075000762939453 y:2.36899995803833 z:35.16899871826172
        - atom: CG2 x: -22.10099983215332 y:0.7269999980926514 z:36.702999114990234
      - residue LYS has 9 atoms
        - atom: N x: -26.413999557495117 y:1.215000033378601 z:36.52299880981445
        - atom: CA x: -27.770000457763672 y:1.378000020980835 z:36.016998291015625
        - atom: C x: -28.56100082397461 y:2.3529999256134033 z:36.87699890136719
        - atom: O x: -29.222999572753906 y:3.249000072479248 z:36.358001708984375
        - atom: CB x: -28.500999450683594 y:0.03500000014901161 z:36.00199890136719
        - atom: CG x: -29.937999725341797 y:0.13699999451637268 z:35.51100158691406
        - atom: CD x: -30.6560001373291 y:-1.2070000171661377 z:35.52299880981445
        - atom: CE x: -31.038000106811523 y:-1.6349999904632568 z:36.933998107910156
        - atom: NZ x: -31.767000198364258 y:-2.940999984741211 z:36.91899871826172
      - residue LYS has 9 atoms
        - atom: N x: -28.483999252319336 y:2.1700000762939453 z:38.189998626708984
        - atom: CA x: -29.195999145507812 y:3.01200008392334 z:39.145999908447266
        - atom: C x: -28.899999618530273 y:4.515999794006348 z:39.060001373291016
        - atom: O x: -29.618000030517578 y:5.326000213623047 z:39.63399887084961
        - atom: CB x: -28.916000366210938 y:2.5190000534057617 z:40.564998626708984
        - atom: CG x: -29.30299949645996 y:1.0679999589920044 z:40.792999267578125
        - atom: CD x: -29.030000686645508 y:0.6269999742507935 z:42.22800064086914
        - atom: CE x: -29.3700008392334 y:-0.847000002861023 z:42.40999984741211
        - atom: NZ x: -29.13800048828125 y:-1.3320000171661377 z:43.79899978637695
      - residue VAL has 7 atoms
        - atom: N x: -27.844999313354492 y:4.8979997634887695 z:38.35499954223633
        - atom: CA x: -27.518999099731445 y:6.308000087738037 z:38.22700119018555
        - atom: C x: -28.152000427246094 y:6.7729997634887695 z:36.92399978637695
        - atom: O x: -28.701000213623047 y:7.872000217437744 z:36.827999114990234
        - atom: CB x: -25.989999771118164 y:6.511000156402588 z:38.16600036621094
        - atom: CG1 x: -25.635000228881836 y:7.994999885559082 z:38.32899856567383
        - atom: CG2 x: -25.32699966430664 y:5.671000003814697 z:39.244998931884766
      - residue ASP has 8 atoms
        - atom: N x: -28.059999465942383 y:5.916999816894531 z:35.91699981689453
        - atom: CA x: -28.628000259399414 y:6.202000141143799 z:34.62099838256836
        - atom: C x: -28.538000106811523 y:4.939000129699707 z:33.79800033569336
        - atom: O x: -27.46500015258789 y:4.364999771118164 z:33.65299987792969
        - atom: CB x: -27.874000549316406 y:7.335000038146973 z:33.917999267578125
        - atom: CG x: -28.533000946044922 y:7.744999885559082 z:32.60300064086914
        - atom: OD1 x: -29.73699951171875 y:8.086999893188477 z:32.624000549316406
        - atom: OD2 x: -27.854000091552734 y:7.7210001945495605 z:31.55299949645996
      - residue SER has 6 atoms
        - atom: N x: -29.67799949645996 y:4.511000156402588 z:33.266998291015625
        - atom: CA x: -29.750999450683594 y:3.305000066757202 z:32.45500183105469
        - atom: C x: -29.03700065612793 y:3.424999952316284 z:31.115999221801758
        - atom: O x: -29.08099937438965 y:2.493000030517578 z:30.319000244140625
        - atom: CB x: -31.204999923706055 y:2.9260001182556152 z:32.183998107910156
        - atom: OG x: -31.709999084472656 y:3.6610000133514404 z:31.082000732421875
      - residue GLU has 9 atoms
        - atom: N x: -28.38800048828125 y:4.552000045776367 z:30.847999572753906
        - atom: CA x: -27.687999725341797 y:4.685999870300293 z:29.575000762939453
        - atom: C x: -26.202999114990234 y:4.35099983215332 z:29.645999908447266
        - atom: O x: -25.54199981689453 y:4.173999786376953 z:28.621999740600586
        - atom: CB x: -27.898000717163086 y:6.085999965667725 z:29.003999710083008
        - atom: CG x: -29.305999755859375 y:6.269999980926514 z:28.450000762939453
        - atom: CD x: -29.743999481201172 y:5.085999965667725 z:27.591999053955078
        - atom: OE1 x: -29.18400001525879 y:4.901000022888184 z:26.48900032043457
        - atom: OE2 x: -30.64299964904785 y:4.333000183105469 z:28.02899932861328
      - residue TYR has 12 atoms
        - atom: N x: -25.69300079345703 y:4.261000156402588 z:30.868000030517578
        - atom: CA x: -24.302000045776367 y:3.9110000133514404 z:31.118000030517578
        - atom: C x: -24.009000778198242 y:2.4860000610351562 z:30.6299991607666
        - atom: O x: -24.80500030517578 y:1.5779999494552612 z:30.854000091552734
        - atom: CB x: -24.033000946044922 y:3.9600000381469727 z:32.612998962402344
        - atom: CG x: -23.69300079345703 y:5.311999797821045 z:33.18600082397461
        - atom: CD1 x: -22.573999404907227 y:6.00600004196167 z:32.75400161743164
        - atom: CD2 x: -24.45400047302246 y:5.866000175476074 z:34.209999084472656
        - atom: CE1 x: -22.222999572753906 y:7.206999778747559 z:33.33100128173828
        - atom: CE2 x: -24.111000061035156 y:7.065999984741211 z:34.78499984741211
        - atom: CZ x: -22.993999481201172 y:7.724999904632568 z:34.340999603271484
        - atom: OH x: -22.635000228881836 y:8.914999961853027 z:34.90700149536133
      - residue ILE has 8 atoms
        - atom: N x: -22.875 y:2.2880001068115234 z:29.96299934387207
        - atom: CA x: -22.486000061035156 y:0.9539999961853027 z:29.506000518798828
        - atom: C x: -21.17099952697754 y:0.5669999718666077 z:30.18600082397461
        - atom: O x: -20.097000122070312 y:0.6959999799728394 z:29.594999313354492
        - atom: CB x: -22.257999420166016 y:0.8889999985694885 z:27.974000930786133
        - atom: CG1 x: -23.577999114990234 y:1.0160000324249268 z:27.23200035095215
        - atom: CG2 x: -21.613000869750977 y:-0.45100000500679016 z:27.584999084472656
        - atom: CD1 x: -23.41699981689453 y:0.8740000128746033 z:25.736000061035156
      - residue ALA has 5 atoms
        - atom: N x: -21.249000549316406 y:0.10000000149011612 z:31.42799949645996
        - atom: CA x: -20.040000915527344 y:-0.296999990940094 z:32.15399932861328
        - atom: C x: -19.613000869750977 y:-1.6979999542236328 z:31.74799919128418
        - atom: O x: -20.31399917602539 y:-2.6679999828338623 z:32.02799987792969
        - atom: CB x: -20.28700065612793 y:-0.24199999868869781 z:33.65700149536133
      - residue THR has 7 atoms
        - atom: N x: -18.457000732421875 y:-1.7899999618530273 z:31.097999572753906
        - atom: CA x: -17.916000366210938 y:-3.066999912261963 z:30.64299964904785
        - atom: C x: -16.632999420166016 y:-3.4679999351501465 z:31.371000289916992
        - atom: O x: -15.590999603271484 y:-2.819999933242798 z:31.200000762939453
        - atom: CB x: -17.61199951171875 y:-3.0190000534057617 z:29.134000778198242
        - atom: OG1 x: -18.81399917602539 y:-2.7090001106262207 z:28.420000076293945
        - atom: CG2 x: -17.062000274658203 y:-4.354000091552734 z:28.64299964904785
      - residue VAL has 7 atoms
        - atom: N x: -16.701000213623047 y:-4.531000137329102 z:32.178001403808594
        - atom: CA x: -15.51200008392334 y:-5.008999824523926 z:32.893001556396484
        - atom: C x: -14.501999855041504 y:-5.539999961853027 z:31.885000228881836
        - atom: O x: -14.866999626159668 y:-6.291999816894531 z:31.0
        - atom: CB x: -15.82800006866455 y:-6.168000221252441 z:33.861000061035156
        - atom: CG1 x: -14.53499984741211 y:-6.660999774932861 z:34.49399948120117
        - atom: CG2 x: -16.80299949645996 y:-5.7170000076293945 z:34.933998107910156
      - residue CYS has 6 atoms
        - atom: N x: -13.236000061035156 y:-5.158999919891357 z:32.01599884033203
        - atom: CA x: -12.208000183105469 y:-5.639999866485596 z:31.089000701904297
        - atom: C x: -10.972000122070312 y:-6.2220001220703125 z:31.773000717163086
        - atom: O x: -11.039999961853027 y:-6.798999786376953 z:32.85300064086914
        - atom: CB x: -11.751999855041504 y:-4.51800012588501 z:30.163000106811523
        - atom: SG x: -13.08899974822998 y:-3.6470000743865967 z:29.341999053955078
      - residue GLY has 4 atoms
        - atom: N x: -9.829999923706055 y:-6.051000118255615 z:31.124000549316406
        - atom: CA x: -8.604000091552734 y:-6.572999954223633 z:31.680999755859375
        - atom: C x: -8.550999641418457 y:-8.071999549865723 z:31.476999282836914
        - atom: O x: -9.340999603271484 y:-8.630000114440918 z:30.722000122070312
      - residue SER has 6 atoms
        - atom: N x: -7.61899995803833 y:-8.729999542236328 z:32.15399932861328
        - atom: CA x: -7.484000205993652 y:-10.166000366210938 z:32.025001525878906
        - atom: C x: -8.803000450134277 y:-10.85200023651123 z:32.362998962402344
        - atom: O x: -8.97700023651123 y:-12.031000137329102 z:32.077999114990234
        - atom: CB x: -6.353000164031982 y:-10.680999755859375 z:32.926998138427734
        - atom: OG x: -6.578000068664551 y:-10.366000175476074 z:34.28799819946289
      - residue PHE has 11 atoms
        - atom: N x: -9.734999656677246 y:-10.123000144958496 z:32.96799850463867
        - atom: CA x: -11.02400016784668 y:-10.720999717712402 z:33.28300094604492
        - atom: C x: -11.821999549865723 y:-10.930999755859375 z:32.000999450683594
        - atom: O x: -12.414999961853027 y:-11.984999656677246 z:31.797000885009766
        - atom: CB x: -11.848999977111816 y:-9.84000015258789 z:34.20500183105469
        - atom: CG x: -13.270000457763672 y:-10.277000427246094 z:34.305999755859375
        - atom: CD1 x: -13.663000106811523 y:-11.180000305175781 z:35.28200149536133
        - atom: CD2 x: -14.206999778747559 y:-9.845999717712402 z:33.369998931884766
        - atom: CE1 x: -14.968000411987305 y:-11.656000137329102 z:35.32699966430664
        - atom: CE2 x: -15.517999649047852 y:-10.312000274658203 z:33.39799880981445
        - atom: CZ x: -15.902999877929688 y:-11.220999717712402 z:34.37900161743164
      - residue ARG has 11 atoms
        - atom: N x: -11.862000465393066 y:-9.913000106811523 z:31.148000717163086
        - atom: CA x: -12.595000267028809 y:-10.017999649047852 z:29.895000457763672
        - atom: C x: -11.9350004196167 y:-11.093999862670898 z:29.05299949645996
        - atom: O x: -12.581999778747559 y:-11.767000198364258 z:28.249000549316406
        - atom: CB x: -12.574000358581543 y:-8.678999900817871 z:29.16200065612793
        - atom: CG x: -13.28499984741211 y:-8.682000160217285 z:27.829999923706055
        - atom: CD x: -14.185999870300293 y:-7.460000038146973 z:27.68899917602539
        - atom: NE x: -14.734000205993652 y:-7.388000011444092 z:26.347000122070312
        - atom: CZ x: -13.996999740600586 y:-7.210000038146973 z:25.257999420166016
        - atom: NH1 x: -12.6850004196167 y:-7.070000171661377 z:25.35300064086914
        - atom: NH2 x: -14.567999839782715 y:-7.215000152587891 z:24.062999725341797
      - residue ARG has 11 atoms
        - atom: N x: -10.635000228881836 y:-11.258999824523926 z:29.259000778198242
        - atom: CA x: -9.885000228881836 y:-12.258999824523926 z:28.534000396728516
        - atom: C x: -10.24899959564209 y:-13.630999565124512 z:29.086000442504883
        - atom: O x: -9.66100025177002 y:-14.633999824523926 z:28.714000701904297
        - atom: CB x: -8.387999534606934 y:-12.006999969482422 z:28.687999725341797
        - atom: CG x: -7.964000225067139 y:-10.605999946594238 z:28.301000595092773
        - atom: CD x: -6.538000106811523 y:-10.583000183105469 z:27.792999267578125
        - atom: NE x: -5.581999778747559 y:-11.0600004196167 z:28.784000396728516
        - atom: CZ x: -5.169000148773193 y:-10.347000122070312 z:29.82200050354004
        - atom: NH1 x: -5.623000144958496 y:-9.119000434875488 z:30.011999130249023
        - atom: NH2 x: -4.296000003814697 y:-10.855999946594238 z:30.66900062561035
      - residue GLY has 4 atoms
        - atom: N x: -11.241999626159668 y:-13.666000366210938 z:29.965999603271484
        - atom: CA x: -11.654000282287598 y:-14.925000190734863 z:30.55900001525879
        - atom: C x: -10.503999710083008 y:-15.541999816894531 z:31.332000732421875
        - atom: O x: -9.788000106811523 y:-16.39900016784668 z:30.81100082397461
      - residue ALA has 5 atoms
        - atom: N x: -10.319000244140625 y:-15.102999687194824 z:32.573001861572266
        - atom: CA x: -9.23900032043457 y:-15.609000205993652 z:33.4109992980957
        - atom: C x: -9.798999786376953 y:-16.110000610351562 z:34.7239990234375
        - atom: O x: -10.76099967956543 y:-15.543999671936035 z:35.250999450683594
        - atom: CB x: -8.211999893188477 y:-14.51099967956543 z:33.6619987487793
      - residue GLU has 9 atoms
        - atom: N x: -9.192999839782715 y:-17.165000915527344 z:35.25699996948242
        - atom: CA x: -9.666000366210938 y:-17.74799919128418 z:36.512001037597656
        - atom: C x: -9.555000305175781 y:-16.80900001525879 z:37.69599914550781
        - atom: O x: -10.270000457763672 y:-16.94700050354004 z:38.68600082397461
        - atom: CB x: -8.932000160217285 y:-19.05900001525879 z:36.80099868774414
        - atom: CG x: -9.420000076293945 y:-20.18199920654297 z:35.91999816894531
        - atom: CD x: -10.944999694824219 y:-20.224000930786133 z:35.84400177001953
        - atom: OE1 x: -11.60200023651123 y:-20.437999725341797 z:36.89699935913086
        - atom: OE2 x: -11.484999656677246 y:-20.034000396728516 z:34.72700119018555
      - residue SER has 6 atoms
        - atom: N x: -8.654999732971191 y:-15.845999717712402 z:37.58000183105469
        - atom: CA x: -8.458000183105469 y:-14.861000061035156 z:38.625999450683594
        - atom: C x: -7.815999984741211 y:-13.618000030517578 z:38.0099983215332
        - atom: O x: -7.223999977111816 y:-13.684000015258789 z:36.92599868774414
        - atom: CB x: -7.578000068664551 y:-15.440999984741211 z:39.744998931884766
        - atom: OG x: -6.326000213623047 y:-15.878999710083008 z:39.25
      - residue SER has 6 atoms
        - atom: N x: -7.935999870300293 y:-12.489999771118164 z:38.70100021362305
        - atom: CA x: -7.374000072479248 y:-11.253000259399414 z:38.196998596191406
        - atom: C x: -6.690999984741211 y:-10.42300033569336 z:39.26900100708008
        - atom: O x: -7.107999801635742 y:-10.406000137329102 z:40.42399978637695
        - atom: CB x: -8.47599983215332 y:-10.42199993133545 z:37.54199981689453
        - atom: OG x: -9.085000038146973 y:-11.130999565124512 z:36.481998443603516
      - residue GLY has 4 atoms
        - atom: N x: -5.633999824523926 y:-9.72700023651123 z:38.882999420166016
        - atom: CA x: -4.954999923706055 y:-8.890999794006348 z:39.84299850463867
        - atom: C x: -5.926000118255615 y:-7.854000091552734 z:40.37900161743164
        - atom: O x: -5.889999866485596 y:-7.50600004196167 z:41.551998138427734
      - residue ASP has 8 atoms
        - atom: N x: -6.810999870300293 y:-7.369999885559082 z:39.51900100708008
        - atom: CA x: -7.783999919891357 y:-6.349999904632568 z:39.9119987487793
        - atom: C x: -9.005000114440918 y:-6.341000080108643 z:38.992000579833984
        - atom: O x: -9.175000190734863 y:-7.230999946594238 z:38.16699981689453
        - atom: CB x: -7.130000114440918 y:-4.9670000076293945 z:39.8650016784668
        - atom: CG x: -6.76800012588501 y:-4.546000003814697 z:38.452999114990234
        - atom: OD1 x: -6.9720001220703125 y:-5.339000225067139 z:37.50899887084961
        - atom: OD2 x: -6.2779998779296875 y:-3.4170000553131104 z:38.27899932861328
      - residue MET has 8 atoms
        - atom: N x: -9.845999717712402 y:-5.321000099182129 z:39.1510009765625
        - atom: CA x: -11.045000076293945 y:-5.1479997634887695 z:38.334999084472656
        - atom: C x: -10.956000328063965 y:-3.8489999771118164 z:37.55500030517578
        - atom: O x: -10.967000007629395 y:-2.7790000438690186 z:38.13800048828125
        - atom: CB x: -12.298999786376953 y:-5.109000205993652 z:39.194000244140625
        - atom: CG x: -13.512999534606934 y:-4.709000110626221 z:38.38399887084961
        - atom: SD x: -15.081000328063965 y:-5.085999965667725 z:39.16600036621094
        - atom: CE x: -15.109999656677246 y:-6.809000015258789 z:38.875
      - residue ASP has 8 atoms
        - atom: N x: -10.873000144958496 y:-3.950000047683716 z:36.23500061035156
        - atom: CA x: -10.781000137329102 y:-2.7780001163482666 z:35.367000579833984
        - atom: C x: -12.133000373840332 y:-2.5320000648498535 z:34.70500183105469
        - atom: O x: -12.66100025177002 y:-3.4049999713897705 z:34.04100036621094
        - atom: CB x: -9.710000038146973 y:-3.0380001068115234 z:34.321998596191406
        - atom: CG x: -8.418999671936035 y:-3.5199999809265137 z:34.94300079345703
        - atom: OD1 x: -7.6579999923706055 y:-2.6649999618530273 z:35.45100021362305
        - atom: OD2 x: -8.175999641418457 y:-4.752999782562256 z:34.95899963378906
      - residue VAL has 7 atoms
        - atom: N x: -12.694000244140625 y:-1.3459999561309814 z:34.887001037597656
        - atom: CA x: -13.998000144958496 y:-1.0369999408721924 z:34.314998626708984
        - atom: C x: -13.968999862670898 y:0.0860000029206276 z:33.28300094604492
        - atom: O x: -13.496000289916992 y:1.1820000410079956 z:33.5629997253418
        - atom: CB x: -14.99899959564209 y:-0.6549999713897705 z:35.433998107910156
        - atom: CG1 x: -16.375 y:-0.4050000011920929 z:34.85599899291992
        - atom: CG2 x: -15.0649995803833 y:-1.7660000324249268 z:36.45800018310547
      - residue LEU has 8 atoms
        - atom: N x: -14.458000183105469 y:-0.19699999690055847 z:32.082000732421875
        - atom: CA x: -14.527999877929688 y:0.8050000071525574 z:31.0310001373291
        - atom: C x: -15.949999809265137 y:1.3270000219345093 z:31.106000900268555
        - atom: O x: -16.90399932861328 y:0.5569999814033508 z:31.158000946044922
        - atom: CB x: -14.281000137329102 y:0.19300000369548798 z:29.663999557495117
        - atom: CG x: -14.069000244140625 y:1.2020000219345093 z:28.530000686645508
        - atom: CD1 x: -12.979000091552734 y:2.184999942779541 z:28.922000885009766
        - atom: CD2 x: -13.649999618530273 y:0.48399999737739563 z:27.270000457763672
      - residue LEU has 8 atoms
        - atom: N x: -16.086999893188477 y:2.640000104904175 z:31.107999801635742
        - atom: CA x: -17.38800048828125 y:3.260999917984009 z:31.239999771118164
        - atom: C x: -17.714000701904297 y:4.26200008392334 z:30.121999740600586
        - atom: O x: -16.847000122070312 y:5.017000198364258 z:29.67799949645996
        - atom: CB x: -17.423999786376953 y:3.9570000171661377 z:32.59700012207031
        - atom: CG x: -18.70199966430664 y:4.685999870300293 z:32.948001861572266
        - atom: CD1 x: -19.889999389648438 y:3.7049999237060547 z:32.92599868774414
        - atom: CD2 x: -18.520000457763672 y:5.311999797821045 z:34.292999267578125
      - residue THR has 7 atoms
        - atom: N x: -18.966999053955078 y:4.270999908447266 z:29.67099952697754
        - atom: CA x: -19.382999420166016 y:5.206999778747559 z:28.621999740600586
        - atom: C x: -20.781999588012695 y:5.7170000076293945 z:28.87299919128418
        - atom: O x: -21.530000686645508 y:5.166999816894531 z:29.683000564575195
        - atom: CB x: -19.409000396728516 y:4.563000202178955 z:27.23900032043457
        - atom: OG1 x: -20.46500015258789 y:3.6029999256134033 z:27.19499969482422
        - atom: CG2 x: -18.097000122070312 y:3.871000051498413 z:26.937999725341797
      - residue HIS has 10 atoms
        - atom: N x: -21.13599967956543 y:6.7769999504089355 z:28.163999557495117
        - atom: CA x: -22.46500015258789 y:7.359000205993652 z:28.28700065612793
        - atom: C x: -22.768999099731445 y:8.1899995803833 z:27.04800033569336
        - atom: O x: -21.88599967956543 y:8.836999893188477 z:26.488000869750977
        - atom: CB x: -22.566999435424805 y:8.227999687194824 z:29.542999267578125
        - atom: CG x: -23.91200065612793 y:8.859999656677246 z:29.735000610351562
        - atom: ND1 x: -24.489999771118164 y:9.684000015258789 z:28.79199981689453
        - atom: CD2 x: -24.777999877929688 y:8.817000389099121 z:30.777000427246094
        - atom: CE1 x: -25.650999069213867 y:10.123000144958496 z:29.243999481201172
        - atom: NE2 x: -25.850000381469727 y:9.612000465393066 z:30.44700050354004
      - residue PRO has 7 atoms
        - atom: N x: -24.027999877929688 y:8.15999984741211 z:26.590999603271484
        - atom: CA x: -24.441999435424805 y:8.918999671936035 z:25.409000396728516
        - atom: C x: -24.042999267578125 y:10.402999877929688 z:25.429000854492188
        - atom: O x: -23.601999282836914 y:10.946000099182129 z:24.416000366210938
        - atom: CB x: -25.95199966430664 y:8.711999893188477 z:25.395999908447266
        - atom: CG x: -26.070999145507812 y:7.288000106811523 z:25.88599967956543
        - atom: CD x: -25.117000579833984 y:7.2789998054504395 z:27.059999465942383
      - residue SER has 6 atoms
        - atom: N x: -24.176000595092773 y:11.045000076293945 z:26.583999633789062
        - atom: CA x: -23.854000091552734 y:12.461999893188477 z:26.711000442504883
        - atom: C x: -22.368000030517578 y:12.763999938964844 z:26.673999786376953
        - atom: O x: -21.957000732421875 y:13.888999938964844 z:26.972999572753906
        - atom: CB x: -24.410999298095703 y:13.015000343322754 z:28.018999099731445
        - atom: OG x: -23.520000457763672 y:12.762999534606934 z:29.091999053955078
      - residue PHE has 11 atoms
        - atom: N x: -21.558000564575195 y:11.779999732971191 z:26.30699920654297
        - atom: CA x: -20.12299919128418 y:11.99899959564209 z:26.285999298095703
        - atom: C x: -19.398000717163086 y:11.35200023651123 z:25.132999420166016
        - atom: O x: -19.242000579833984 y:10.137999534606934 z:25.084999084472656
        - atom: CB x: -19.506000518798828 y:11.520999908447266 z:27.60099983215332
        - atom: CG x: -18.007999420166016 y:11.626999855041504 z:27.636999130249023
        - atom: CD1 x: -17.367000579833984 y:12.77299976348877 z:27.167999267578125
        - atom: CD2 x: -17.236000061035156 y:10.593999862670898 z:28.156999588012695
        - atom: CE1 x: -15.989999771118164 y:12.890000343322754 z:27.218000411987305
        - atom: CE2 x: -15.854999542236328 y:10.704000473022461 z:28.211000442504883
        - atom: CZ x: -15.229999542236328 y:11.857000350952148 z:27.739999771118164
      - residue THR has 7 atoms
        - atom: N x: -18.934999465942383 y:12.182999610900879 z:24.211000442504883
        - atom: CA x: -18.201000213623047 y:11.710000038146973 z:23.042999267578125
        - atom: C x: -17.07200050354004 y:12.701000213623047 z:22.77400016784668
        - atom: O x: -16.788000106811523 y:13.565999984741211 z:23.59600067138672
        - atom: CB x: -19.110000610351562 y:11.645999908447266 z:21.799999237060547
        - atom: OG1 x: -19.204999923706055 y:12.947999954223633 z:21.209999084472656
        - atom: CG2 x: -20.5049991607666 y:11.180000305175781 z:22.18400001525879
      - residue SER has 6 atoms
        - atom: N x: -16.42799949645996 y:12.579000473022461 z:21.625999450683594
        - atom: CA x: -15.345999717712402 y:13.48900032043457 z:21.288000106811523
        - atom: C x: -15.72700023651123 y:14.932999610900879 z:21.63599967956543
        - atom: O x: -15.057999610900879 y:15.576000213623047 z:22.45199966430664
        - atom: CB x: -15.020000457763672 y:13.368000030517578 z:19.798999786376953
        - atom: OG x: -14.71500015258789 y:12.024999618530273 z:19.464000701904297
      - residue GLU has 9 atoms
        - atom: N x: -16.80699920654297 y:15.42199993133545 z:21.023000717163086
        - atom: CA x: -17.32900047302246 y:16.783000946044922 z:21.238000869750977
        - atom: C x: -17.645000457763672 y:17.051000595092773 z:22.7189998626709
        - atom: O x: -16.93400001525879 y:17.798999786376953 z:23.395999908447266
        - atom: CB x: -18.590999603271484 y:16.97100067138672 z:20.389999389648438
        - atom: CG x: -19.5049991607666 y:15.744000434875488 z:20.41900062561035
        - atom: CD x: -20.75200080871582 y:15.880999565124512 z:19.555999755859375
        - atom: OE1 x: -20.6200008392334 y:16.08300018310547 z:18.32900047302246
        - atom: OE2 x: -21.8700008392334 y:15.776000022888184 z:20.10700035095215
      - residue SER has 6 atoms
        - atom: N x: -18.738000869750977 y:16.454999923706055 z:23.19099998474121
        - atom: CA x: -19.179000854492188 y:16.530000686645508 z:24.583999633789062
        - atom: C x: -19.48200035095215 y:17.86400032043457 z:25.290000915527344
        - atom: O x: -20.475000381469727 y:17.961999893188477 z:26.020999908447266
        - atom: CB x: -18.18199920654297 y:15.746000289916992 z:25.451000213623047
        - atom: OG x: -16.867000579833984 y:16.288999557495117 z:25.367000579833984
      - residue THR has 7 atoms
        - atom: N x: -18.636999130249023 y:18.87299919128418 z:25.0939998626709
        - atom: CA x: -18.801000595092773 y:20.159000396728516 z:25.781999588012695
        - atom: C x: -18.413999557495117 y:19.841999053955078 z:27.225000381469727
        - atom: O x: -18.558000564575195 y:20.67099952697754 z:28.12700080871582
        - atom: CB x: -20.27400016784668 y:20.67799949645996 z:25.78700065612793
        - atom: OG1 x: -20.80299949645996 y:20.674999237060547 z:24.45400047302246
        - atom: CG2 x: -20.33799934387207 y:22.104999542236328 z:26.34600067138672
      - residue LYS has 9 atoms
        - atom: N x: -17.930999755859375 y:18.615999221801758 z:27.42099952697754
        - atom: CA x: -17.509000778198242 y:18.101999282836914 z:28.725000381469727
        - atom: C x: -18.625 y:18.062000274658203 z:29.767000198364258
        - atom: O x: -19.027000427246094 y:19.090999603271484 z:30.31800079345703
        - atom: CB x: -16.312000274658203 y:18.898000717163086 z:29.25200080871582
        - atom: CG x: -14.979999542236328 y:18.506999969482422 z:28.608999252319336
        - atom: CD x: -14.986000061035156 y:18.663999557495117 z:27.079999923706055
        - atom: CE x: -13.618000030517578 y:18.32900047302246 z:26.48699951171875
        - atom: NZ x: -13.541999816894531 y:18.54800033569336 z:25.016000747680664
      - residue GLN has 9 atoms
        - atom: N x: -19.118999481201172 y:16.850000381469727 z:30.014999389648438
        - atom: CA x: -20.18400001525879 y:16.606000900268555 z:30.979000091552734
        - atom: C x: -19.53700065612793 y:16.427000045776367 z:32.35100173950195
        - atom: O x: -18.87299919128418 y:15.42199993133545 z:32.61600112915039
        - atom: CB x: -20.966999053955078 y:15.35099983215332 z:30.586000442504883
        - atom: CG x: -22.29400062561035 y:15.206999778747559 z:31.299999237060547
        - atom: CD x: -23.20400047302246 y:16.392000198364258 z:31.062000274658203
        - atom: OE1 x: -23.5310001373291 y:16.709999084472656 z:29.92300033569336
        - atom: NE2 x: -23.618000030517578 y:17.05500030517578 z:32.137001037597656
      - residue PRO has 7 atoms
        - atom: N x: -19.719999313354492 y:17.417999267578125 z:33.23699951171875
        - atom: CA x: -19.187000274658203 y:17.464000701904297 z:34.60200119018555
        - atom: C x: -19.802000045776367 y:16.465999603271484 z:35.58100128173828
        - atom: O x: -20.979000091552734 y:16.569000244140625 z:35.93000030517578
        - atom: CB x: -19.45400047302246 y:18.90399932861328 z:35.012001037597656
        - atom: CG x: -20.766000747680664 y:19.173999786376953 z:34.35300064086914
        - atom: CD x: -20.55299949645996 y:18.604999542236328 z:32.970001220703125
      - residue LYS has 9 atoms
        - atom: N x: -18.98699951171875 y:15.51099967956543 z:36.02000045776367
        - atom: CA x: -19.39900016784668 y:14.482000350952148 z:36.97200012207031
        - atom: C x: -20.075000762939453 y:13.255000114440918 z:36.362998962402344
        - atom: O x: -20.964000701904297 y:12.654999732971191 z:36.9739990234375
        - atom: CB x: -20.297000885009766 y:15.085000038146973 z:38.06100082397461
        - atom: CG x: -19.63599967956543 y:16.225000381469727 z:38.82099914550781
        - atom: CD x: -20.55299949645996 y:16.827999114990234 z:39.87300109863281
        - atom: CE x: -19.891000747680664 y:18.023000717163086 z:40.55099868774414
        - atom: NZ x: -20.739999771118164 y:18.586000442504883 z:41.63999938964844
      - residue LEU has 8 atoms
        - atom: N x: -19.663999557495117 y:12.876999855041504 z:35.15700149536133
        - atom: CA x: -20.231000900268555 y:11.685999870300293 z:34.54800033569336
        - atom: C x: -19.660999298095703 y:10.541000366210938 z:35.36899948120117
        - atom: O x: -20.357999801635742 y:9.57800006866455 z:35.69499969482422
        - atom: CB x: -19.77899932861328 y:11.529000282287598 z:33.09600067138672
        - atom: CG x: -20.839000701904297 y:11.605999946594238 z:31.996999740600586
        - atom: CD1 x: -20.340999603271484 y:10.803999900817871 z:30.812000274658203
        - atom: CD2 x: -22.187000274658203 y:11.057000160217285 z:32.479000091552734
      - residue LEU has 8 atoms
        - atom: N x: -18.3799991607666 y:10.666000366210938 z:35.709999084472656
        - atom: CA x: -17.700000762939453 y:9.656000137329102 z:36.494998931884766
        - atom: C x: -17.95599937438965 y:9.869999885559082 z:37.96799850463867
        - atom: O x: -18.058000564575195 y:8.918999671936035 z:38.729000091552734
        - atom: CB x: -16.20400047302246 y:9.694000244140625 z:36.222999572753906
        - atom: CG x: -15.364999771118164 y:8.619000434875488 z:36.91600036621094
        - atom: CD1 x: -15.930000305175781 y:7.230999946594238 z:36.617000579833984
        - atom: CD2 x: -13.913000106811523 y:8.743000030517578 z:36.44200134277344
      - residue HIS has 10 atoms
        - atom: N x: -18.06999969482422 y:11.121999740600586 z:38.37699890136719
        - atom: CA x: -18.312000274658203 y:11.401000022888184 z:39.779998779296875
        - atom: C x: -19.5310001373291 y:10.654999732971191 z:40.31700134277344
        - atom: O x: -19.44099998474121 y:9.95300006866455 z:41.316001892089844
        - atom: CB x: -18.496999740600586 y:12.901000022888184 z:40.000999450683594
        - atom: CG x: -18.812000274658203 y:13.258999824523926 z:41.41999816894531
        - atom: ND1 x: -17.89900016784668 y:13.11299991607666 z:42.44200134277344
        - atom: CD2 x: -19.959999084472656 y:13.682999610900879 z:41.99700164794922
        - atom: CE1 x: -18.474000930786133 y:13.425000190734863 z:43.59000015258789
        - atom: NE2 x: -19.725000381469727 y:13.77400016784668 z:43.347999572753906
      - residue GLN has 9 atoms
        - atom: N x: -20.66900062561035 y:10.812999725341797 z:39.64699935913086
        - atom: CA x: -21.92300033569336 y:10.175999641418457 z:40.055999755859375
        - atom: C x: -21.83099937438965 y:8.678000450134277 z:40.29800033569336
        - atom: O x: -22.37700080871582 y:8.17300033569336 z:41.268001556396484
        - atom: CB x: -23.016000747680664 y:10.432000160217285 z:39.018001556396484
        - atom: CG x: -23.368000030517578 y:11.890999794006348 z:38.82099914550781
        - atom: CD x: -24.46299934387207 y:12.07699966430664 z:37.78099822998047
        - atom: OE1 x: -25.597999572753906 y:11.62600040435791 z:37.9640007019043
        - atom: NE2 x: -24.124000549316406 y:12.73799991607666 z:36.67900085449219
      - residue VAL has 7 atoms
        - atom: N x: -21.155000686645508 y:7.968999862670898 z:39.409000396728516
        - atom: CA x: -21.006000518798828 y:6.53000020980835 z:39.54600143432617
        - atom: C x: -20.003000259399414 y:6.197000026702881 z:40.6510009765625
        - atom: O x: -20.218000411987305 y:5.28000020980835 z:41.4379997253418
        - atom: CB x: -20.562999725341797 y:5.888000011444092 z:38.20899963378906
        - atom: CG1 x: -20.05699920654297 y:4.473999977111816 z:38.441001892089844
        - atom: CG2 x: -21.73699951171875 y:5.868000030517578 z:37.24599838256836
      - residue VAL has 7 atoms
        - atom: N x: -18.913999557495117 y:6.947000026702881 z:40.720001220703125
        - atom: CA x: -17.933000564575195 y:6.690000057220459 z:41.75199890136719
        - atom: C x: -18.690000534057617 y:6.857999801635742 z:43.042999267578125
        - atom: O x: -18.660999298095703 y:6.008999824523926 z:43.92399978637695
        - atom: CB x: -16.781999588012695 y:7.709000110626221 z:41.72200012207031
        - atom: CG1 x: -15.850000381469727 y:7.456999778747559 z:42.880001068115234
        - atom: CG2 x: -16.020000457763672 y:7.6020002365112305 z:40.41999816894531
      - residue GLU has 9 atoms
        - atom: N x: -19.398000717163086 y:7.968999862670898 z:43.132999420166016
        - atom: CA x: -20.167999267578125 y:8.276000022888184 z:44.319000244140625
        - atom: C x: -21.114999771118164 y:7.140999794006348 z:44.65999984741211
        - atom: O x: -21.065000534057617 y:6.604000091552734 z:45.75699996948242
        - atom: CB x: -20.961000442504883 y:9.5600004196167 z:44.09700012207031
        - atom: CG x: -21.607999801635742 y:10.109999656677246 z:45.33399963378906
        - atom: CD x: -22.40399932861328 y:11.36299991607666 z:45.042999267578125
        - atom: OE1 x: -23.4689998626709 y:11.255999565124512 z:44.395999908447266
        - atom: OE2 x: -21.961999893188477 y:12.458000183105469 z:45.452999114990234
      - residue GLN has 9 atoms
        - atom: N x: -21.9689998626709 y:6.763000011444092 z:43.715999603271484
        - atom: CA x: -22.940000534057617 y:5.702000141143799 z:43.96500015258789
        - atom: C x: -22.292999267578125 y:4.389999866485596 z:44.44900131225586
        - atom: O x: -22.858999252319336 y:3.684000015258789 z:45.28799819946289
        - atom: CB x: -23.791000366210938 y:5.4720001220703125 z:42.70100021362305
        - atom: CG x: -24.867000579833984 y:4.372000217437744 z:42.79600143432617
        - atom: CD x: -26.01300048828125 y:4.7129998207092285 z:43.7400016784668
        - atom: OE1 x: -25.9689998626709 y:5.706999778747559 z:44.46099853515625
        - atom: NE2 x: -27.04400062561035 y:3.874000072479248 z:43.742000579833984
      - residue LEU has 8 atoms
        - atom: N x: -21.11199951171875 y:4.065000057220459 z:43.93299865722656
        - atom: CA x: -20.437000274658203 y:2.8420000076293945 z:44.3489990234375
        - atom: C x: -19.951000213623047 y:2.9660000801086426 z:45.7859992980957
        - atom: O x: -19.659000396728516 y:1.9639999866485596 z:46.42499923706055
        - atom: CB x: -19.267000198364258 y:2.5199999809265137 z:43.4109992980957
        - atom: CG x: -19.673999786376953 y:1.9570000171661377 z:42.04199981689453
        - atom: CD1 x: -18.472999572753906 y:1.777999997138977 z:41.165000915527344
        - atom: CD2 x: -20.384000778198242 y:0.628000020980835 z:42.23400115966797
      - residue GLN has 9 atoms
        - atom: N x: -19.868000030517578 y:4.198999881744385 z:46.28799819946289
        - atom: CA x: -19.44499969482422 y:4.461999893188477 z:47.66899871826172
        - atom: C x: -20.687999725341797 y:4.511000156402588 z:48.558998107910156
        - atom: O x: -20.60099983215332 y:4.388999938964844 z:49.7869987487793
        - atom: CB x: -18.71500015258789 y:5.809000015258789 z:47.7859992980957
        - atom: CG x: -17.40399932861328 y:5.919000148773193 z:47.03499984741211
        - atom: CD x: -16.65999984741211 y:7.2210001945495605 z:47.33300018310547
        - atom: OE1 x: -17.259000778198242 y:8.29800033569336 z:47.375999450683594
        - atom: NE2 x: -15.347000122070312 y:7.123000144958496 z:47.527000427246094
      - residue LYS has 9 atoms
        - atom: N x: -21.84000015258789 y:4.710000038146973 z:47.92300033569336
        - atom: CA x: -23.118000030517578 y:4.790999889373779 z:48.62099838256836
        - atom: C x: -23.485000610351562 y:3.427999973297119 z:49.20899963378906
        - atom: O x: -23.861000061035156 y:3.321000099182129 z:50.37699890136719
        - atom: CB x: -24.209999084472656 y:5.244999885559082 z:47.6510009765625
        - atom: CG x: -25.493000030517578 y:5.758999824523926 z:48.308998107910156
        - atom: CD x: -25.284000396728516 y:7.151000022888184 z:48.91600036621094
        - atom: CE x: -26.61400032043457 y:7.869999885559082 z:49.20199966430664
        - atom: NZ x: -27.492000579833984 y:7.140999794006348 z:50.17300033569336
      - residue VAL has 7 atoms
        - atom: N x: -23.381000518798828 y:2.38700008392334 z:48.391998291015625
        - atom: CA x: -23.690000534057617 y:1.0379999876022339 z:48.84199905395508
        - atom: C x: -22.56100082397461 y:0.5149999856948853 z:49.72800064086914
        - atom: O x: -22.729000091552734 y:-0.4690000116825104 z:50.45100021362305
        - atom: CB x: -23.85300064086914 y:0.07800000160932541 z:47.645999908447266
        - atom: CG1 x: -25.08300018310547 y:0.44999998807907104 z:46.845001220703125
        - atom: CG2 x: -22.618999481201172 y:0.13099999725818634 z:46.76300048828125
      - residue HIS has 10 atoms
        - atom: N x: -21.413999557495117 y:1.187999963760376 z:49.66400146484375
        - atom: CA x: -20.229000091552734 y:0.8109999895095825 z:50.428001403808594
        - atom: C x: -19.409000396728516 y:-0.27000001072883606 z:49.709999084472656
        - atom: O x: -18.84000015258789 y:-1.152999997138977 z:50.35200119018555
        - atom: CB x: -20.610000610351562 y:0.33399999141693115 z:51.8390007019043
        - atom: CG x: -21.040000915527344 y:1.437000036239624 z:52.7599983215332
        - atom: ND1 x: -22.143999099731445 y:1.3350000381469727 z:53.582000732421875
        - atom: CD2 x: -20.5 y:2.6549999713897705 z:53.0099983215332
        - atom: CE1 x: -22.266000747680664 y:2.440000057220459 z:54.297000885009766
        - atom: NE2 x: -21.281999588012695 y:3.257999897003174 z:53.96900177001953
      - residue PHE has 11 atoms
        - atom: N x: -19.360000610351562 y:-0.20000000298023224 z:48.37799835205078
        - atom: CA x: -18.570999145507812 y:-1.1480000019073486 z:47.59000015258789
        - atom: C x: -17.174999237060547 y:-0.5789999961853027 z:47.39500045776367
        - atom: O x: -16.20800018310547 y:-1.3270000219345093 z:47.3650016784668
        - atom: CB x: -19.187999725341797 y:-1.3940000534057617 z:46.220001220703125
        - atom: CG x: -18.344999313354492 y:-2.2720000743865967 z:45.32500076293945
        - atom: CD1 x: -18.054000854492188 y:-3.5820000171661377 z:45.685001373291016
        - atom: CD2 x: -17.84600067138672 y:-1.784999966621399 z:44.11899948120117
        - atom: CE1 x: -17.288999557495117 y:-4.38700008392334 z:44.86800003051758
        - atom: CE2 x: -17.076000213623047 y:-2.5869998931884766 z:43.29399871826172
        - atom: CZ x: -16.79800033569336 y:-3.8910000324249268 z:43.67100143432617
      - residue ILE has 8 atoms
        - atom: N x: -17.072999954223633 y:0.7419999837875366 z:47.24300003051758
        - atom: CA x: -15.77400016784668 y:1.3860000371932983 z:47.08300018310547
        - atom: C x: -15.430999755859375 y:1.9910000562667847 z:48.42300033569336
        - atom: O x: -16.05900001525879 y:2.953000068664551 z:48.85200119018555
        - atom: CB x: -15.774999618530273 y:2.503000020980835 z:45.97999954223633
        - atom: CG1 x: -15.883000373840332 y:1.871000051498413 z:44.58399963378906
        - atom: CG2 x: -14.479000091552734 y:3.2899999618530273 z:46.02199935913086
        - atom: CD1 x: -15.685999870300293 y:2.8510000705718994 z:43.44300079345703
      - residue THR has 7 atoms
        - atom: N x: -14.427000045776367 y:1.4140000343322754 z:49.073001861572266
        - atom: CA x: -13.984999656677246 y:1.8559999465942383 z:50.388999938964844
        - atom: C x: -12.88599967956543 y:2.9140000343322754 z:50.402000427246094
        - atom: O x: -12.743000030517578 y:3.63100004196167 z:51.39099884033203
        - atom: CB x: -13.479000091552734 y:0.6610000133514404 z:51.25299835205078
        - atom: OG1 x: -12.404000282287598 y:-0.0020000000949949026 z:50.58300018310547
        - atom: CG2 x: -14.581000328063965 y:-0.32600000500679016 z:51.51499938964844
      - residue ASP has 8 atoms
        - atom: N x: -12.095000267028809 y:3.01200008392334 z:49.3390007019043
        - atom: CA x: -11.015000343322754 y:4.000999927520752 z:49.31800079345703
        - atom: C x: -10.654000282287598 y:4.551000118255615 z:47.93299865722656
        - atom: O x: -10.78600025177002 y:3.868000030517578 z:46.915000915527344
        - atom: CB x: -9.744000434875488 y:3.4130001068115234 z:49.9630012512207
        - atom: CG x: -10.015000343322754 y:2.7699999809265137 z:51.31800079345703
        - atom: OD1 x: -10.675000190734863 y:1.7079999446868896 z:51.349998474121094
        - atom: OD2 x: -9.574000358581543 y:3.3239998817443848 z:52.35100173950195
      - residue THR has 7 atoms
        - atom: N x: -10.157999992370605 y:5.7870001792907715 z:47.93199920654297
        - atom: CA x: -9.746999740600586 y:6.508999824523926 z:46.73899841308594
        - atom: C x: -8.234999656677246 y:6.723999977111816 z:46.68000030517578
        - atom: O x: -7.664999961853027 y:7.307000160217285 z:47.59000015258789
        - atom: CB x: -10.407999992370605 y:7.89300012588501 z:46.715999603271484
        - atom: OG1 x: -11.79800033569336 y:7.748000144958496 z:46.40999984741211
        - atom: CG2 x: -9.73799991607666 y:8.803000450134277 z:45.6879997253418
      - residue LEU has 8 atoms
        - atom: N x: -7.583000183105469 y:6.265999794006348 z:45.612998962402344
        - atom: CA x: -6.146999835968018 y:6.489999771118164 z:45.47800064086914
        - atom: C x: -5.991000175476074 y:7.702000141143799 z:44.57099914550781
        - atom: O x: -5.010000228881836 y:8.442000389099121 z:44.667999267578125
        - atom: CB x: -5.427999973297119 y:5.298999786376953 z:44.83100128173828
        - atom: CG x: -5.5980000495910645 y:3.871999979019165 z:45.35599899291992
        - atom: CD1 x: -4.579999923706055 y:2.9730000495910645 z:44.696998596191406
        - atom: CD2 x: -5.414999961853027 y:3.8259999752044678 z:46.847999572753906
      - residue SER has 6 atoms
        - atom: N x: -6.9710001945495605 y:7.901000022888184 z:43.694000244140625
        - atom: CA x: -6.947999954223633 y:9.012999534606934 z:42.74399948120117
        - atom: C x: -8.258999824523926 y:9.112000465393066 z:41.98500061035156
        - atom: O x: -8.848999977111816 y:8.095000267028809 z:41.61399841308594
        - atom: CB x: -5.817999839782715 y:8.831999778747559 z:41.74100112915039
        - atom: OG x: -6.002999782562256 y:7.638999938964844 z:41.01300048828125
      - residue LYS has 9 atoms
        - atom: N x: -8.70300006866455 y:10.340999603271484 z:41.74800109863281
        - atom: CA x: -9.954000473022461 y:10.569999694824219 z:41.04100036621094
        - atom: C x: -9.918000221252441 y:11.857999801635742 z:40.21900177001953
        - atom: O x: -9.762999534606934 y:12.961999893188477 z:40.74599838256836
        - atom: CB x: -11.107999801635742 y:10.605999946594238 z:42.04499816894531
        - atom: CG x: -12.496000289916992 y:10.840999603271484 z:41.47100067138672
        - atom: CD x: -13.52299976348877 y:10.961000442504883 z:42.61000061035156
        - atom: CE x: -14.862000465393066 y:11.560999870300293 z:42.15599822998047
        - atom: NZ x: -14.739999771118164 y:12.946999549865723 z:41.57699966430664
      - residue GLY has 4 atoms
        - atom: N x: -10.03600025177002 y:11.694000244140625 z:38.90800094604492
        - atom: CA x: -10.041999816894531 y:12.824000358581543 z:38.00600051879883
        - atom: C x: -11.36400032043457 y:12.800000190734863 z:37.26900100708008
        - atom: O x: -12.270999908447266 y:12.064000129699707 z:37.66899871826172
      - residue GLU has 9 atoms
        - atom: N x: -11.475000381469727 y:13.581999778747559 z:36.19599914550781
        - atom: CA x: -12.708999633789062 y:13.637999534606934 z:35.41299819946289
        - atom: C x: -12.991000175476074 y:12.404999732971191 z:34.569000244140625
        - atom: O x: -14.145000457763672 y:12.163000106811523 z:34.23899841308594
        - atom: CB x: -12.729000091552734 y:14.871000289916992 z:34.49399948120117
        - atom: CG x: -12.994000434875488 y:16.202999114990234 z:35.20000076293945
        - atom: CD x: -14.388999938964844 y:16.284000396728516 z:35.803001403808594
        - atom: OE1 x: -14.821999549865723 y:15.300000190734863 z:36.452999114990234
        - atom: OE2 x: -15.04800033569336 y:17.33300018310547 z:35.64099884033203
      - residue THR has 7 atoms
        - atom: N x: -11.963000297546387 y:11.63700008392334 z:34.209999084472656
        - atom: CA x: -12.175000190734863 y:10.432999610900879 z:33.39699935913086
        - atom: C x: -11.51200008392334 y:9.157999992370605 z:33.95399856567383
        - atom: O x: -11.673999786376953 y:8.072999954223633 z:33.38600158691406
        - atom: CB x: -11.6850004196167 y:10.630000114440918 z:31.908000946044922
        - atom: OG1 x: -10.255999565124512 y:10.644000053405762 z:31.856000900268555
        - atom: CG2 x: -12.185999870300293 y:11.944999694824219 z:31.336999893188477
      - residue LYS has 9 atoms
        - atom: N x: -10.781000137329102 y:9.277000427246094 z:35.06399917602539
        - atom: CA x: -10.095999717712402 y:8.119999885559082 z:35.63800048828125
        - atom: C x: -10.126999855041504 y:8.034000396728516 z:37.154998779296875
        - atom: O x: -9.835000038146973 y:9.008000373840332 z:37.849998474121094
        - atom: CB x: -8.642999649047852 y:8.10099983215332 z:35.18199920654297
        - atom: CG x: -7.811999797821045 y:7.0980000495910645 z:35.92300033569336
        - atom: CD x: -6.353000164031982 y:7.2220001220703125 z:35.58100128173828
        - atom: CE x: -5.540999889373779 y:6.206999778747559 z:36.380001068115234
        - atom: NZ x: -4.105000019073486 y:6.232999801635742 z:36.0
      - residue PHE has 11 atoms
        - atom: N x: -10.454000473022461 y:6.8460001945495605 z:37.65800094604492
        - atom: CA x: -10.522000312805176 y:6.5879998207092285 z:39.090999603271484
        - atom: C x: -9.812000274658203 y:5.298999786376953 z:39.49700164794922
        - atom: O x: -10.163999557495117 y:4.2129998207092285 z:39.051998138427734
        - atom: CB x: -11.984000205993652 y:6.501999855041504 z:39.547000885009766
        - atom: CG x: -12.156000137329102 y:6.059999942779541 z:40.986000061035156
        - atom: CD1 x: -11.930999755859375 y:6.936999797821045 z:42.0359992980957
        - atom: CD2 x: -12.531000137329102 y:4.756999969482422 z:41.2859992980957
        - atom: CE1 x: -12.079000473022461 y:6.519000053405762 z:43.36600112915039
        - atom: CE2 x: -12.678999900817871 y:4.329999923706055 z:42.61800003051758
        - atom: CZ x: -12.45300006866455 y:5.210999965667725 z:43.652000427246094
      - residue MET has 8 atoms
        - atom: N x: -8.805999755859375 y:5.428999900817871 z:40.35100173950195
        - atom: CA x: -8.081999778747559 y:4.275000095367432 z:40.875
        - atom: C x: -8.491999626159668 y:4.190000057220459 z:42.34199905395508
        - atom: O x: -8.345999717712402 y:5.159999847412109 z:43.09000015258789
        - atom: CB x: -6.578999996185303 y:4.486000061035156 z:40.77000045776367
        - atom: CG x: -6.034999847412109 y:4.218999862670898 z:39.39500045776367
        - atom: SD x: -4.295000076293945 y:4.629000186920166 z:39.29399871826172
        - atom: CE x: -3.693000078201294 y:3.8350000381469727 z:40.74300003051758
      - residue GLY has 4 atoms
        - atom: N x: -9.01200008392334 y:3.0390000343322754 z:42.7599983215332
        - atom: CA x: -9.442999839782715 y:2.933000087738037 z:44.13600158691406
        - atom: C x: -9.482999801635742 y:1.5640000104904175 z:44.742000579833984
        - atom: O x: -8.850000381469727 y:0.6309999823570251 z:44.27000045776367
      - residue VAL has 7 atoms
        - atom: N x: -10.26200008392334 y:1.4559999704360962 z:45.80400085449219
        - atom: CA x: -10.385000228881836 y:0.21899999678134918 z:46.54199981689453
        - atom: C x: -11.847000122070312 y:-0.14499999582767487 z:46.7239990234375
        - atom: O x: -12.666000366210938 y:0.7099999785423279 z:47.07899856567383
        - atom: CB x: -9.720000267028809 y:0.36800000071525574 z:47.94599914550781
        - atom: CG1 x: -9.960000038146973 y:-0.8809999823570251 z:48.790000915527344
        - atom: CG2 x: -8.218000411987305 y:0.6430000066757202 z:47.7869987487793
      - residue CYS has 6 atoms
        - atom: N x: -12.168999671936035 y:-1.4140000343322754 z:46.46799850463867
        - atom: CA x: -13.529000282287598 y:-1.909000039100647 z:46.63399887084961
        - atom: C x: -13.513999938964844 y:-3.187000036239624 z:47.46699905395508
        - atom: O x: -12.456000328063965 y:-3.759000062942505 z:47.72200012207031
        - atom: CB x: -14.20300006866455 y:-2.1549999713897705 z:45.277000427246094
        - atom: SG x: -13.541000366210938 y:-3.48799991607666 z:44.275001525878906
      - residue GLN has 9 atoms
        - atom: N x: -14.690999984741211 y:-3.625999927520752 z:47.900001525878906
        - atom: CA x: -14.809000015258789 y:-4.818999767303467 z:48.72600173950195
        - atom: C x: -16.209999084472656 y:-5.434999942779541 z:48.64799880981445
        - atom: O x: -17.215999603271484 y:-4.756999969482422 z:48.869998931884766
        - atom: CB x: -14.467000007629395 y:-4.459000110626221 z:50.178001403808594
        - atom: CG x: -14.763999938964844 y:-5.531000137329102 z:51.202999114990234
        - atom: CD x: -14.333999633789062 y:-5.130000114440918 z:52.604000091552734
        - atom: OE1 x: -14.741000175476074 y:-4.0879998207092285 z:53.11800003051758
        - atom: NE2 x: -13.508000373840332 y:-5.961999893188477 z:53.231998443603516
      - residue LEU has 8 atoms
        - atom: N x: -16.267000198364258 y:-6.71999979019165 z:48.31399917602539
        - atom: CA x: -17.533000946044922 y:-7.429999828338623 z:48.22800064086914
        - atom: C x: -18.14900016784668 y:-7.479000091552734 z:49.61899948120117
        - atom: O x: -17.454999923706055 y:-7.729000091552734 z:50.595001220703125
        - atom: CB x: -17.297000885009766 y:-8.852999687194824 z:47.722999572753906
        - atom: CG x: -16.979000091552734 y:-9.00100040435791 z:46.236000061035156
        - atom: CD1 x: -16.43600082397461 y:-10.39799976348877 z:45.946998596191406
        - atom: CD2 x: -18.249000549316406 y:-8.720000267028809 z:45.43000030517578
      - residue PRO has 7 atoms
        - atom: N x: -19.459999084472656 y:-7.241000175476074 z:49.733001708984375
        - atom: CA x: -20.0939998626709 y:-7.28000020980835 z:51.053001403808594
        - atom: C x: -20.091999053955078 y:-8.692999839782715 z:51.62099838256836
        - atom: O x: -20.04400062561035 y:-9.668000221252441 z:50.87300109863281
        - atom: CB x: -21.49799919128418 y:-6.7829999923706055 z:50.763999938964844
        - atom: CG x: -21.75200080871582 y:-7.359000205993652 z:49.42300033569336
        - atom: CD x: -20.466999053955078 y:-7.035999774932861 z:48.683998107910156
      - residue SER has 6 atoms
        - atom: N x: -20.14299964904785 y:-8.800000190734863 z:52.944000244140625
        - atom: CA x: -20.150999069213867 y:-10.104999542236328 z:53.59000015258789
        - atom: C x: -21.516000747680664 y:-10.470999717712402 z:54.14400100708008
        - atom: O x: -22.22800064086914 y:-9.626999855041504 z:54.69300079345703
        - atom: CB x: -19.11400032043457 y:-10.157999992370605 z:54.71099853515625
        - atom: OG x: -17.80299949645996 y:-10.243000030517578 z:54.176998138427734
      - residue LYS has 9 atoms
        - atom: N x: -21.854999542236328 y:-11.748000144958496 z:53.99100112915039
        - atom: CA x: -23.124000549316406 y:-12.317000389099121 z:54.44300079345703
        - atom: C x: -23.631999969482422 y:-11.708000183105469 z:55.74700164794922
        - atom: O x: -24.525999069213867 y:-10.859999656677246 z:55.74100112915039
        - atom: CB x: -22.985000610351562 y:-13.836000442504883 z:54.61800003051758
        - atom: CG x: -22.371000289916992 y:-14.569000244140625 z:53.42399978637695
        - atom: CD x: -20.875999450683594 y:-14.298999786376953 z:53.28200149536133
        - atom: CE x: -20.301000595092773 y:-14.970999717712402 z:52.04600143432617
        - atom: NZ x: -18.827999114990234 y:-14.781999588012695 z:51.97600173950195
      - residue ASN has 8 atoms
        - atom: N x: -23.066999435424805 y:-12.161999702453613 z:56.861000061035156
        - atom: CA x: -23.440000534057617 y:-11.675999641418457 z:58.18600082397461
        - atom: C x: -22.19700050354004 y:-11.550000190734863 z:59.04600143432617
        - atom: O x: -21.503999710083008 y:-10.529999732971191 z:59.018001556396484
        - atom: CB x: -24.42300033569336 y:-12.637999534606934 z:58.86199951171875
        - atom: CG x: -25.77899932861328 y:-12.663999557495117 z:58.180999755859375
        - atom: OD1 x: -25.885000228881836 y:-12.98799991607666 z:56.99300003051758
        - atom: ND2 x: -26.826000213623047 y:-12.321999549865723 z:58.93000030517578
      - residue ASP has 8 atoms
        - atom: N x: -21.91200065612793 y:-12.593999862670898 z:59.8120002746582
        - atom: CA x: -20.743000030517578 y:-12.5649995803833 z:60.667999267578125
        - atom: C x: -19.663999557495117 y:-13.559000015258789 z:60.22200012207031
        - atom: O x: -19.101999282836914 y:-14.295999526977539 z:61.034000396728516
        - atom: CB x: -21.1560001373291 y:-12.817000389099121 z:62.12099838256836
        - atom: CG x: -20.41699981689453 y:-11.913000106811523 z:63.0989990234375
        - atom: OD1 x: -20.413000106811523 y:-10.680999755859375 z:62.880001068115234
        - atom: OD2 x: -19.844999313354492 y:-12.430999755859375 z:64.08399963378906
      - residue GLU has 9 atoms
        - atom: N x: -19.38800048828125 y:-13.57699966430664 z:58.917999267578125
        - atom: CA x: -18.354000091552734 y:-14.447999954223633 z:58.375
        - atom: C x: -17.06800079345703 y:-13.638999938964844 z:58.441001892089844
        - atom: O x: -16.729000091552734 y:-13.08899974822998 z:59.4900016784668
        - atom: CB x: -18.63800048828125 y:-14.824999809265137 z:56.91699981689453
        - atom: CG x: -19.93899917602539 y:-15.576000213623047 z:56.67300033569336
        - atom: CD x: -21.152000427246094 y:-14.701000213623047 z:56.88600158691406
        - atom: OE1 x: -21.05900001525879 y:-13.493000030517578 z:56.584999084472656
        - atom: OE2 x: -22.195999145507812 y:-15.218000411987305 z:57.3380012512207
      - residue LYS has 9 atoms
        - atom: N x: -16.361000061035156 y:-13.54699993133545 z:57.319000244140625
        - atom: CA x: -15.116000175476074 y:-12.793999671936035 z:57.284000396728516
        - atom: C x: -15.039999961853027 y:-11.869000434875488 z:56.07699966430664
        - atom: O x: -15.192000389099121 y:-12.310999870300293 z:54.941001892089844
        - atom: CB x: -13.92300033569336 y:-13.751999855041504 z:57.27399826049805
        - atom: CG x: -12.5600004196167 y:-13.060999870300293 z:57.27399826049805
        - atom: CD x: -11.418999671936035 y:-14.069999694824219 z:57.36899948120117
        - atom: CE x: -11.454000473022461 y:-15.064000129699707 z:56.21500015258789
        - atom: NZ x: -10.368000030517578 y:-16.07900047302246 z:56.319000244140625
      - residue GLU has 9 atoms
        - atom: N x: -14.805000305175781 y:-10.585000038146973 z:56.340999603271484
        - atom: CA x: -14.687000274658203 y:-9.57800006866455 z:55.292999267578125
        - atom: C x: -13.902999877929688 y:-10.180000305175781 z:54.125999450683594
        - atom: O x: -12.942000389099121 y:-10.918999671936035 z:54.34199905395508
        - atom: CB x: -13.907999992370605 y:-8.350000381469727 z:55.79999923706055
        - atom: CG x: -14.197999954223633 y:-7.88700008392334 z:57.22200012207031
        - atom: CD x: -13.293000221252441 y:-6.72599983215332 z:57.652000427246094
        - atom: OE1 x: -13.357000350952148 y:-5.650000095367432 z:57.01900100708008
        - atom: OE2 x: -12.512999534606934 y:-6.883999824523926 z:58.62099838256836
      - residue TYR has 12 atoms
        - atom: N x: -14.315999984741211 y:-9.883000373840332 z:52.895999908447266
        - atom: CA x: -13.588000297546387 y:-10.373000144958496 z:51.72700119018555
        - atom: C x: -12.331000328063965 y:-9.508000373840332 z:51.678001403808594
        - atom: O x: -12.291000366210938 y:-8.444000244140625 z:52.292999267578125
        - atom: CB x: -14.402000427246094 y:-10.159000396728516 z:50.44300079345703
        - atom: CG x: -15.472000122070312 y:-11.201000213623047 z:50.17599868774414
        - atom: CD1 x: -15.234999656677246 y:-12.276000022888184 z:49.31800079345703
        - atom: CD2 x: -16.729000091552734 y:-11.105999946594238 z:50.7760009765625
        - atom: CE1 x: -16.225000381469727 y:-13.22700023651123 z:49.064998626708984
        - atom: CE2 x: -17.722999572753906 y:-12.048999786376953 z:50.52899932861328
        - atom: CZ x: -17.465999603271484 y:-13.100000381469727 z:49.67599868774414
        - atom: OH x: -18.458999633789062 y:-14.013999938964844 z:49.433998107910156
      - residue PRO has 7 atoms
        - atom: N x: -11.282999992370605 y:-9.958999633789062 z:50.972999572753906
        - atom: CA x: -10.079999923706055 y:-9.125 z:50.917999267578125
        - atom: C x: -10.451000213623047 y:-7.831999778747559 z:50.20899963378906
        - atom: O x: -11.345000267028809 y:-7.835000038146973 z:49.35900115966797
        - atom: CB x: -9.114999771118164 y:-9.960000038146973 z:50.07699966430664
        - atom: CG x: -9.54699993133545 y:-11.354000091552734 z:50.3380012512207
        - atom: CD x: -11.050999641418457 y:-11.258999824523926 z:50.32500076293945
      - residue HIS has 10 atoms
        - atom: N x: -9.805000305175781 y:-6.724999904632568 z:50.560001373291016
        - atom: CA x: -10.095000267028809 y:-5.4710001945495605 z:49.867000579833984
        - atom: C x: -9.428000450134277 y:-5.605000019073486 z:48.49399948120117
        - atom: O x: -8.277999877929688 y:-6.047999858856201 z:48.395999908447266
        - atom: CB x: -9.512999534606934 y:-4.267000198364258 z:50.619998931884766
        - atom: CG x: -10.348999977111816 y:-3.796999931335449 z:51.77000045776367
        - atom: ND1 x: -10.534000396728516 y:-4.544000148773193 z:52.91400146484375
        - atom: CD2 x: -11.008000373840332 y:-2.631999969482422 z:51.97100067138672
        - atom: CE1 x: -11.263999938964844 y:-3.8559999465942383 z:53.77299880981445
        - atom: NE2 x: -11.564000129699707 y:-2.691999912261963 z:53.224998474121094
      - residue ARG has 11 atoms
        - atom: N x: -10.140999794006348 y:-5.234000205993652 z:47.4370002746582
        - atom: CA x: -9.592000007629395 y:-5.364999771118164 z:46.08599853515625
        - atom: C x: -9.380000114440918 y:-4.051000118255615 z:45.33399963378906
        - atom: O x: -10.031000137329102 y:-3.0390000343322754 z:45.611000061035156
        - atom: CB x: -10.51200008392334 y:-6.256999969482422 z:45.25899887084961
        - atom: CG x: -10.968999862670898 y:-7.511000156402588 z:45.96200180053711
        - atom: CD x: -9.836999893188477 y:-8.48799991607666 z:46.11199951171875
        - atom: NE x: -10.319000244140625 y:-9.800999641418457 z:46.51900100708008
        - atom: CZ x: -9.5600004196167 y:-10.888999938964844 z:46.54499816894531
        - atom: NH1 x: -8.28499984741211 y:-10.8100004196167 z:46.19200134277344
        - atom: NH2 x: -10.07699966430664 y:-12.057000160217285 z:46.902000427246094
      - residue ARG has 11 atoms
        - atom: N x: -8.461999893188477 y:-4.076000213623047 z:44.375
        - atom: CA x: -8.197999954223633 y:-2.8940000534057617 z:43.558998107910156
        - atom: C x: -9.196999549865723 y:-2.7960000038146973 z:42.402000427246094
        - atom: O x: -9.545999526977539 y:-3.7890000343322754 z:41.75600051879883
        - atom: CB x: -6.775000095367432 y:-2.9260001182556152 z:42.994998931884766
        - atom: CG x: -5.702000141143799 y:-2.631999969482422 z:44.012001037597656
        - atom: CD x: -5.521999835968018 y:-1.1480000019073486 z:44.24100112915039
        - atom: NE x: -4.9710001945495605 y:-0.4950000047683716 z:43.0629997253418
        - atom: CZ x: -5.703999996185303 y:0.11400000005960464 z:42.13800048828125
        - atom: NH1 x: -7.0279998779296875 y:0.16500000655651093 z:42.25899887084961
        - atom: NH2 x: -5.113999843597412 y:0.652999997138977 z:41.07899856567383
      - residue ILE has 8 atoms
        - atom: N x: -9.649999618530273 y:-1.5729999542236328 z:42.15399932861328
        - atom: CA x: -10.597000122070312 y:-1.2949999570846558 z:41.0880012512207
        - atom: C x: -10.175000190734863 y:-0.020999999716877937 z:40.34199905395508
        - atom: O x: -9.767999649047852 y:0.9660000205039978 z:40.95800018310547
        - atom: CB x: -12.017999649047852 y:-1.1380000114440918 z:41.68000030517578
        - atom: CG1 x: -13.008999824523926 y:-0.7609999775886536 z:40.59199905395508
        - atom: CG2 x: -12.031000137329102 y:-0.08799999952316284 z:42.75
        - atom: CD1 x: -14.376999855041504 y:-0.5450000166893005 z:41.137001037597656
      - residue ASP has 8 atoms
        - atom: N x: -10.21500015258789 y:-0.07400000095367432 z:39.01499938964844
        - atom: CA x: -9.883000373840332 y:1.069000005722046 z:38.1619987487793
        - atom: C x: -11.109000205993652 y:1.2790000438690186 z:37.2760009765625
        - atom: O x: -11.706999778747559 y:0.3100000023841858 z:36.80699920654297
        - atom: CB x: -8.668000221252441 y:0.7850000262260437 z:37.270999908447266
        - atom: CG x: -7.4070000648498535 y:0.503000020980835 z:38.064998626708984
        - atom: OD1 x: -7.235000133514404 y:1.093000054359436 z:39.1510009765625
        - atom: OD2 x: -6.578999996185303 y:-0.30000001192092896 z:37.5890007019043
      - residue ILE has 8 atoms
        - atom: N x: -11.487000465393066 y:2.5350000858306885 z:37.05500030517578
        - atom: CA x: -12.64799976348877 y:2.8480000495910645 z:36.23400115966797
        - atom: C x: -12.291999816894531 y:4.013000011444092 z:35.319000244140625
        - atom: O x: -11.878999710083008 y:5.072000026702881 z:35.79499816894531
        - atom: CB x: -13.845999717712402 y:3.256999969482422 z:37.12300109863281
        - atom: CG1 x: -14.107999801635742 y:2.1679999828338623 z:38.16699981689453
        - atom: CG2 x: -15.086999893188477 y:3.505000114440918 z:36.266998291015625
        - atom: CD1 x: -15.119000434875488 y:2.562000036239624 z:39.233001708984375
      - residue ARG has 11 atoms
        - atom: N x: -12.4399995803833 y:3.8239998817443848 z:34.01100158691406
        - atom: CA x: -12.133000373840332 y:4.89300012588501 z:33.064998626708984
        - atom: C x: -13.319999694824219 y:5.24399995803833 z:32.17399978637695
        - atom: O x: -13.930999755859375 y:4.36899995803833 z:31.548999786376953
        - atom: CB x: -10.928000450134277 y:4.513000011444092 z:32.202999114990234
        - atom: CG x: -9.746000289916992 y:4.109000205993652 z:33.055999755859375
        - atom: CD x: -8.42300033569336 y:4.166999816894531 z:32.321998596191406
        - atom: NE x: -7.381999969482422 y:3.446000099182129 z:33.055999755859375
        - atom: CZ x: -6.118000030517578 y:3.3529999256134033 z:32.65599822998047
        - atom: NH1 x: -5.738999843597412 y:3.947000026702881 z:31.527999877929688
        - atom: NH2 x: -5.239999771118164 y:2.6530001163482666 z:33.36800003051758
      - residue LEU has 8 atoms
        - atom: N x: -13.649999618530273 y:6.5329999923706055 z:32.150001525878906
        - atom: CA x: -14.743000030517578 y:7.039999961853027 z:31.347000122070312
        - atom: C x: -14.180999755859375 y:7.448999881744385 z:29.990999221801758
        - atom: O x: -13.451000213623047 y:8.435999870300293 z:29.905000686645508
        - atom: CB x: -15.355999946594238 y:8.258999824523926 z:32.018001556396484
        - atom: CG x: -16.48200035095215 y:8.942999839782715 z:31.2450008392334
        - atom: CD1 x: -17.711000442504883 y:8.062999725341797 z:31.25
        - atom: CD2 x: -16.80299949645996 y:10.270000457763672 z:31.878000259399414
      - residue ILE has 8 atoms
        - atom: N x: -14.506999969482422 y:6.693999767303467 z:28.940000534057617
        - atom: CA x: -14.029000282287598 y:7.00600004196167 z:27.59600067138672
        - atom: C x: -15.149999618530273 y:7.5229997634887695 z:26.711000442504883
        - atom: O x: -16.299999237060547 y:7.142000198364258 z:26.871999740600586
        - atom: CB x: -13.437999725341797 y:5.7779998779296875 z:26.885000228881836
        - atom: CG1 x: -14.513999938964844 y:4.703999996185303 z:26.7549991607666
        - atom: CG2 x: -12.199999809265137 y:5.271999835968018 z:27.624000549316406
        - atom: CD1 x: -14.071999549865723 y:3.513000011444092 z:25.937999725341797
      - residue PRO has 7 atoms
        - atom: N x: -14.821000099182129 y:8.404000282287598 z:25.766000747680664
        - atom: CA x: -15.810999870300293 y:8.979000091552734 z:24.83799934387207
        - atom: C x: -16.490999221801758 y:7.840000152587891 z:24.062999725341797
        - atom: O x: -15.810999870300293 y:6.901000022888184 z:23.624000549316406
        - atom: CB x: -14.961999893188477 y:9.873000144958496 z:23.937999725341797
        - atom: CG x: -13.824999809265137 y:10.289999961853027 z:24.843000411987305
        - atom: CD x: -13.48900032043457 y:8.99899959564209 z:25.56800079345703
      - residue LYS has 9 atoms
        - atom: N x: -17.80900001525879 y:7.921999931335449 z:23.8799991607666
        - atom: CA x: -18.554000854492188 y:6.8480000495910645 z:23.209999084472656
        - atom: C x: -18.02199935913086 y:6.297999858856201 z:21.886999130249023
        - atom: O x: -17.986000061035156 y:5.081999778747559 z:21.684999465942383
        - atom: CB x: -20.007999420166016 y:7.251999855041504 z:22.993000030517578
        - atom: CG x: -20.899999618530273 y:6.093999862670898 z:22.548999786376953
        - atom: CD x: -21.552000045776367 y:5.38100004196167 z:23.746000289916992
        - atom: CE x: -22.51300048828125 y:4.2829999923706055 z:23.280000686645508
        - atom: NZ x: -23.47800064086914 y:3.8610000610351562 z:24.336000442504883
      - residue ASP has 8 atoms
        - atom: N x: -17.625999450683594 y:7.181000232696533 z:20.983999252319336
        - atom: CA x: -17.1200008392334 y:6.754000186920166 z:19.68600082397461
        - atom: C x: -15.680000305175781 y:6.251999855041504 z:19.711999893188477
        - atom: O x: -15.003000259399414 y:6.2179999351501465 z:18.670000076293945
        - atom: CB x: -17.22599983215332 y:7.90500020980835 z:18.687000274658203
        - atom: CG x: -16.69099998474121 y:9.199000358581543 z:19.2450008392334
        - atom: OD1 x: -15.991000175476074 y:9.913999557495117 z:18.503999710083008
        - atom: OD2 x: -16.976999282836914 y:9.498000144958496 z:20.422000885009766
      - residue GLN has 9 atoms
        - atom: N x: -15.208000183105469 y:5.869999885559082 z:20.895000457763672
        - atom: CA x: -13.840999603271484 y:5.36899995803833 z:21.02899932861328
        - atom: C x: -13.864999771118164 y:4.067999839782715 z:21.81100082397461
        - atom: O x: -12.859999656677246 y:3.375 z:21.93899917602539
        - atom: CB x: -12.97700023651123 y:6.406000137329102 z:21.72800064086914
        - atom: CG x: -13.196000099182129 y:7.809000015258789 z:21.20599937438965
        - atom: CD x: -11.937000274658203 y:8.630999565124512 z:21.261999130249023
        - atom: OE1 x: -11.22599983215332 y:8.621999740600586 z:22.266000747680664
        - atom: NE2 x: -11.645999908447266 y:9.350000381469727 z:20.18199920654297
      - residue TYR has 12 atoms
        - atom: N x: -15.048999786376953 y:3.755000114440918 z:22.316999435424805
        - atom: CA x: -15.3100004196167 y:2.546999931335449 z:23.077999114990234
        - atom: C x: -14.543000221252441 y:1.3359999656677246 z:22.562999725341797
        - atom: O x: -13.607999801635742 y:0.8619999885559082 z:23.190000534057617
        - atom: CB x: -16.804000854492188 y:2.242000102996826 z:23.031999588012695
        - atom: CG x: -17.19499969482422 y:1.00600004196167 z:23.79199981689453
        - atom: CD1 x: -17.104999542236328 y:0.9660000205039978 z:25.180999755859375
        - atom: CD2 x: -17.6299991607666 y:-0.13699999451637268 z:23.121000289916992
        - atom: CE1 x: -17.437999725341797 y:-0.1850000023841858 z:25.889999389648438
        - atom: CE2 x: -17.964000701904297 y:-1.2970000505447388 z:23.815000534057617
        - atom: CZ x: -17.865999221801758 y:-1.319000005722046 z:25.20199966430664
        - atom: OH x: -18.17799949645996 y:-2.4670000076293945 z:25.902000427246094
      - residue TYR has 12 atoms
        - atom: N x: -14.942999839782715 y:0.8270000219345093 z:21.410999298095703
        - atom: CA x: -14.288000106811523 y:-0.3409999907016754 z:20.8700008392334
        - atom: C x: -12.777999877929688 y:-0.21400000154972076 z:20.922000885009766
        - atom: O x: -12.097000122070312 y:-1.1469999551773071 z:21.32200050354004
        - atom: CB x: -14.779999732971191 y:-0.5960000157356262 z:19.445999145507812
        - atom: CG x: -16.284000396728516 y:-0.7670000195503235 z:19.385000228881836
        - atom: CD1 x: -16.902000427246094 y:-1.9190000295639038 z:19.878999710083008
        - atom: CD2 x: -17.097999572753906 y:0.25699999928474426 z:18.899999618530273
        - atom: CE1 x: -18.301000595092773 y:-2.0450000762939453 z:19.89900016784668
        - atom: CE2 x: -18.493999481201172 y:0.1469999998807907 z:18.916000366210938
        - atom: CZ x: -19.089000701904297 y:-1.0019999742507935 z:19.420000076293945
        - atom: OH x: -20.4689998626709 y:-1.069000005722046 z:19.485000610351562
      - residue CYS has 6 atoms
        - atom: N x: -12.243000030517578 y:0.9359999895095825 z:20.545000076293945
        - atom: CA x: -10.789999961853027 y:1.1050000190734863 z:20.573999404907227
        - atom: C x: -10.241999626159668 y:1.0920000076293945 z:22.003999710083008
        - atom: O x: -9.145000457763672 y:0.6069999933242798 z:22.257999420166016
        - atom: CB x: -10.390999794006348 y:2.4019999504089355 z:19.875999450683594
        - atom: SG x: -9.300999641418457 y:2.1089999675750732 z:18.48900032043457
      - residue GLY has 4 atoms
        - atom: N x: -11.019000053405762 y:1.6349999904632568 z:22.93199920654297
        - atom: CA x: -10.604000091552734 y:1.6460000276565552 z:24.31800079345703
        - atom: C x: -10.835000038146973 y:0.289000004529953 z:24.96299934387207
        - atom: O x: -10.050999641418457 y:-0.16200000047683716 z:25.792999267578125
      - residue VAL has 7 atoms
        - atom: N x: -11.920000076293945 y:-0.36800000071525574 z:24.582000732421875
        - atom: CA x: -12.220999717712402 y:-1.6660000085830688 z:25.134000778198242
        - atom: C x: -11.131999969482422 y:-2.628000020980835 z:24.66900062561035
        - atom: O x: -10.866999626159668 y:-3.63700008392334 z:25.305999755859375
        - atom: CB x: -13.607000350952148 y:-2.1589999198913574 z:24.66699981689453
        - atom: CG1 x: -13.576000213623047 y:-2.502000093460083 z:23.184999465942383
        - atom: CG2 x: -14.036999702453613 y:-3.3519999980926514 z:25.479999542236328
      - residue LEU has 8 atoms
        - atom: N x: -10.487000465393066 y:-2.309999942779541 z:23.559999465942383
        - atom: CA x: -9.4399995803833 y:-3.1710000038146973 z:23.065000534057617
        - atom: C x: -8.232999801635742 y:-2.9670000076293945 z:23.94700050354004
        - atom: O x: -7.6620001792907715 y:-3.9210000038146973 z:24.485000610351562
        - atom: CB x: -9.074000358581543 y:-2.805999994277954 z:21.634000778198242
        - atom: CG x: -7.961999893188477 y:-3.6480000019073486 z:21.007999420166016
        - atom: CD1 x: -8.39900016784668 y:-5.107999801635742 z:20.95599937438965
        - atom: CD2 x: -7.644999980926514 y:-3.119999885559082 z:19.613000869750977
      - residue TYR has 12 atoms
        - atom: N x: -7.855000019073486 y:-1.7059999704360962 z:24.0939998626709
        - atom: CA x: -6.703000068664551 y:-1.3450000286102295 z:24.893999099731445
        - atom: C x: -6.7870001792907715 y:-1.8880000114440918 z:26.312999725341797
        - atom: O x: -5.877999782562256 y:-2.578000068664551 z:26.77199935913086
        - atom: CB x: -6.550000190734863 y:0.17399999499320984 z:24.950000762939453
        - atom: CG x: -5.408999919891357 y:0.6000000238418579 z:25.836000442504883
        - atom: CD1 x: -4.098999977111816 y:0.5410000085830688 z:25.382999420166016
        - atom: CD2 x: -5.636000156402588 y:0.9879999756813049 z:27.158000946044922
        - atom: CE1 x: -3.0409998893737793 y:0.8510000109672546 z:26.216999053955078
        - atom: CE2 x: -4.584000110626221 y:1.2960000038146973 z:28.003999710083008
        - atom: CZ x: -3.2880001068115234 y:1.222000002861023 z:27.525999069213867
        - atom: OH x: -2.2260000705718994 y:1.49399995803833 z:28.360000610351562
      - residue PHE has 11 atoms
        - atom: N x: -7.882999897003174 y:-1.565000057220459 z:26.993999481201172
        - atom: CA x: -8.121000289916992 y:-1.968999981880188 z:28.378000259399414
        - atom: C x: -8.307999610900879 y:-3.4790000915527344 z:28.600000381469727
        - atom: O x: -8.409000396728516 y:-3.937999963760376 z:29.736000061035156
        - atom: CB x: -9.335000038146973 y:-1.2009999752044678 z:28.913999557495117
        - atom: CG x: -9.093999862670898 y:-0.5210000276565552 z:30.23200035095215
        - atom: CD1 x: -7.830999851226807 y:-0.009999999776482582 z:30.555999755859375
        - atom: CD2 x: -10.133000373840332 y:-0.37299999594688416 z:31.152999877929688
        - atom: CE1 x: -7.607999801635742 y:0.6340000033378601 z:31.783000946044922
        - atom: CE2 x: -9.920999526977539 y:0.27399998903274536 z:32.38800048828125
        - atom: CZ x: -8.659000396728516 y:0.7749999761581421 z:32.70100021362305
      - residue THR has 7 atoms
        - atom: N x: -8.368000030517578 y:-4.252999782562256 z:27.52199935913086
        - atom: CA x: -8.527000427246094 y:-5.695000171661377 z:27.659000396728516
        - atom: C x: -7.127999782562256 y:-6.291999816894531 z:27.558000564575195
        - atom: O x: -6.834000110626221 y:-7.348999977111816 z:28.125
        - atom: CB x: -9.447999954223633 y:-6.2870001792907715 z:26.538000106811523
        - atom: OG1 x: -10.755999565124512 y:-5.709000110626221 z:26.632999420166016
        - atom: CG2 x: -9.590999603271484 y:-7.790999889373779 z:26.69499969482422
      - residue GLY has 4 atoms
        - atom: N x: -6.26200008392334 y:-5.583000183105469 z:26.841999053955078
        - atom: CA x: -4.89900016784668 y:-6.0329999923706055 z:26.658000946044922
        - atom: C x: -4.8379998207092285 y:-7.366000175476074 z:25.944000244140625
        - atom: O x: -5.651000022888184 y:-7.636000156402588 z:25.055999755859375
      - residue SER has 6 atoms
        - atom: N x: -3.8940000534057617 y:-8.215999603271484 z:26.344999313354492
        - atom: CA x: -2.950000047683716 y:-7.925000190734863 z:27.43899917602539
        - atom: C x: -1.9830000400543213 y:-6.807000160217285 z:27.10099983215332
        - atom: O x: -1.75600004196167 y:-6.502999782562256 z:25.93000030517578
        - atom: CB x: -2.1080000400543213 y:-9.154000282287598 z:27.775999069213867
        - atom: OG x: -1.0529999732971191 y:-9.291999816894531 z:26.840999603271484
      - residue ASP has 8 atoms
        - atom: N x: -1.3969999551773071 y:-6.228000164031982 z:28.145000457763672
        - atom: CA x: -0.42899999022483826 y:-5.145999908447266 z:28.013999938964844
        - atom: C x: 0.6370000243186951 y:-5.468999862670898 z:26.96299934387207
        - atom: O x: 0.9330000281333923 y:-4.64900016784668 z:26.097000122070312
        - atom: CB x: 0.22100000083446503 y:-4.900000095367432 z:29.3700008392334
        - atom: CG x: 0.7870000004768372 y:-6.170000076293945 z:29.974000930786133
        - atom: OD1 x: 1.9320000410079956 y:-6.541999816894531 z:29.61400032043457
        - atom: OD2 x: 0.07400000095367432 y:-6.804999828338623 z:30.790000915527344
      - residue ILE has 8 atoms
        - atom: N x: 1.215999960899353 y:-6.6620001792907715 z:27.04199981689453
        - atom: CA x: 2.2239999771118164 y:-7.057000160217285 z:26.06999969482422
        - atom: C x: 1.5240000486373901 y:-7.189000129699707 z:24.72800064086914
        - atom: O x: 2.115000009536743 y:-6.8979997634887695 z:23.695999145507812
        - atom: CB x: 2.88700008392334 y:-8.416000366210938 z:26.416000366210938
        - atom: CG1 x: 3.5199999809265137 y:-8.373000144958496 z:27.809999465942383
        - atom: CG2 x: 3.9570000171661377 y:-8.734999656677246 z:25.385000228881836
        - atom: CD1 x: 4.730000019073486 y:-7.460999965667725 z:27.913000106811523
      - residue PHE has 11 atoms
        - atom: N x: 0.27000001072883606 y:-7.638999938964844 z:24.740999221801758
        - atom: CA x: -0.4909999966621399 y:-7.76800012588501 z:23.500999450683594
        - atom: C x: -0.550000011920929 y:-6.389999866485596 z:22.841999053955078
        - atom: O x: -0.3019999861717224 y:-6.252999782562256 z:21.641000747680664
        - atom: CB x: -1.9140000343322754 y:-8.26200008392334 z:23.777000427246094
        - atom: CG x: -2.802999973297119 y:-8.269000053405762 z:22.55900001525879
        - atom: CD1 x: -4.051000118255615 y:-7.645999908447266 z:22.586000442504883
        - atom: CD2 x: -2.3959999084472656 y:-8.892999649047852 z:21.381999969482422
        - atom: CE1 x: -4.880000114440918 y:-7.64300012588501 z:21.461000442504883
        - atom: CE2 x: -3.2209999561309814 y:-8.895000457763672 z:20.25200080871582
        - atom: CZ x: -4.4629998207092285 y:-8.267000198364258 z:20.29599952697754
      - residue ASN has 8 atoms
        - atom: N x: -0.8730000257492065 y:-5.379000186920166 z:23.64900016784668
        - atom: CA x: -0.9649999737739563 y:-3.994999885559082 z:23.198999404907227
        - atom: C x: 0.36899998784065247 y:-3.4709999561309814 z:22.68199920654297
        - atom: O x: 0.4090000092983246 y:-2.625 z:21.791000366210938
        - atom: CB x: -1.4759999513626099 y:-3.121000051498413 z:24.334999084472656
        - atom: CG x: -2.9230000972747803 y:-3.3919999599456787 z:24.648000717163086
        - atom: OD1 x: -3.4649999141693115 y:-4.428999900817871 z:24.25200080871582
        - atom: ND2 x: -3.565000057220459 y:-2.4709999561309814 z:25.361000061035156
      - residue LYS has 9 atoms
        - atom: N x: 1.4589999914169312 y:-3.9660000801086426 z:23.25200080871582
        - atom: CA x: 2.7829999923706055 y:-3.575000047683716 z:22.798999786376953
        - atom: C x: 2.8970000743865967 y:-4.184000015258789 z:21.39900016784668
        - atom: O x: 3.390000104904175 y:-3.553999900817871 z:20.46500015258789
        - atom: CB x: 3.865000009536743 y:-4.192999839782715 z:23.691999435424805
        - atom: CG x: 4.803999900817871 y:-3.2190001010894775 z:24.374000549316406
        - atom: CD x: 4.2220001220703125 y:-2.7219998836517334 z:25.68199920654297
        - atom: CE x: 5.249000072479248 y:-1.906999945640564 z:26.447999954223633
        - atom: NZ x: 4.71999979019165 y:-1.440000057220459 z:27.759000778198242
      - residue ASN has 8 atoms
        - atom: N x: 2.4240000247955322 y:-5.421000003814697 z:21.270999908447266
        - atom: CA x: 2.4730000495910645 y:-6.144999980926514 z:20.006000518798828
        - atom: C x: 1.680999994277954 y:-5.458000183105469 z:18.91900062561035
        - atom: O x: 2.183000087738037 y:-5.236999988555908 z:17.82200050354004
        - atom: CB x: 1.9279999732971191 y:-7.566999912261963 z:20.170000076293945
        - atom: CG x: 2.819000005722046 y:-8.437000274658203 z:21.020999908447266
        - atom: OD1 x: 4.0329999923706055 y:-8.473999977111816 z:20.822999954223633
        - atom: ND2 x: 2.2230000495910645 y:-9.152000427246094 z:21.969999313354492
      - residue MET has 8 atoms
        - atom: N x: 0.43299999833106995 y:-5.135000228881836 z:19.23699951171875
        - atom: CA x: -0.46299999952316284 y:-4.486000061035156 z:18.29400062561035
        - atom: C x: -0.013000000268220901 y:-3.0759999752044678 z:17.910999298095703
        - atom: O x: 0.13500000536441803 y:-2.7690000534057617 z:16.731000900268555
        - atom: CB x: -1.8730000257492065 y:-4.451000213623047 z:18.875
        - atom: CG x: -2.9140000343322754 y:-3.936000108718872 z:17.91699981689453
        - atom: SD x: -4.511000156402588 y:-3.989000082015991 z:18.68199920654297
        - atom: CE x: -5.236000061035156 y:-5.382999897003174 z:17.812000274658203
      - residue ARG has 11 atoms
        - atom: N x: 0.20499999821186066 y:-2.2179999351501465 z:18.899999618530273
        - atom: CA x: 0.6489999890327454 y:-0.8560000061988831 z:18.618000030517578
        - atom: C x: 2.0329999923706055 y:-0.8849999904632568 z:17.986000061035156
        - atom: O x: 2.75600004196167 y:0.10899999737739563 z:18.027000427246094
        - atom: CB x: 0.7039999961853027 y:-0.02199999988079071 z:19.905000686645508
        - atom: CG x: -0.6389999985694885 y:0.16200000047683716 z:20.607999801635742
        - atom: CD x: -0.546999990940094 y:1.11899995803833 z:21.801000595092773
        - atom: NE x: 0.36800000071525574 y:0.6430000066757202 z:22.839000701904297
        - atom: CZ x: 1.690000057220459 y:0.8040000200271606 z:22.823999404907227
        - atom: NH1 x: 2.2869999408721924 y:1.440999984741211 z:21.822999954223633
        - atom: NH2 x: 2.4210000038146973 y:0.3109999895095825 z:23.812000274658203
      - residue ALA has 5 atoms
        - atom: N x: 2.3959999084472656 y:-2.0299999713897705 z:17.41200065612793
        - atom: CA x: 3.694999933242798 y:-2.2079999446868896 z:16.777000427246094
        - atom: C x: 3.558000087738037 y:-2.7639999389648438 z:15.357999801635742
        - atom: O x: 4.267000198364258 y:-2.3389999866485596 z:14.446999549865723
        - atom: CB x: 4.560999870300293 y:-3.131999969482422 z:17.625
      - residue HIS has 10 atoms
        - atom: N x: 2.6530001163482666 y:-3.7170000076293945 z:15.168000221252441
        - atom: CA x: 2.447000026702881 y:-4.2870001792907715 z:13.842000007629395
        - atom: C x: 1.50600004196167 y:-3.38100004196167 z:13.050000190734863
        - atom: O x: 1.3990000486373901 y:-3.496000051498413 z:11.829999923706055
        - atom: CB x: 1.8489999771118164 y:-5.692999839782715 z:13.930999755859375
        - atom: CG x: 2.2960000038146973 y:-6.5980000495910645 z:12.826000213623047
        - atom: ND1 x: 3.5880000591278076 y:-7.076000213623047 z:12.737000465393066
        - atom: CD2 x: 1.6419999599456787 y:-7.076000213623047 z:11.741000175476074
        - atom: CE1 x: 3.7090001106262207 y:-7.809999942779541 z:11.645000457763672
        - atom: NE2 x: 2.5429999828338623 y:-7.827000141143799 z:11.02299976348877
      - residue ALA has 5 atoms
        - atom: N x: 0.828000009059906 y:-2.4809999465942383 z:13.76200008392334
        - atom: CA x: -0.10000000149011612 y:-1.5369999408721924 z:13.149999618530273
        - atom: C x: 0.6909999847412109 y:-0.40799999237060547 z:12.517999649047852
        - atom: O x: 0.12399999797344208 y:0.5239999890327454 z:11.958000183105469
        - atom: CB x: -1.0499999523162842 y:-0.9750000238418579 z:14.199999809265137
      - residue LEU has 8 atoms
        - atom: N x: 2.009999990463257 y:-0.4959999918937683 z:12.625
        - atom: CA x: 2.8910000324249268 y:0.5099999904632568 z:12.059000015258789
        - atom: C x: 3.50600004196167 y:-0.03500000014901161 z:10.78499984741211
        - atom: O x: 3.7899999618530273 y:0.7179999947547913 z:9.859999656677246
        - atom: CB x: 3.9809999465942383 y:0.875 z:13.062000274658203
        - atom: CG x: 3.4670000076293945 y:1.5980000495910645 z:14.305000305175781
        - atom: CD1 x: 4.455999851226807 y:1.4429999589920044 z:15.440999984741211
        - atom: CD2 x: 3.243000030517578 y:3.062999963760376 z:13.977999687194824
      - residue GLU has 9 atoms
        - atom: N x: 3.7119998931884766 y:-1.3480000495910645 z:10.744999885559082
        - atom: CA x: 4.270999908447266 y:-2.0 z:9.562999725341797
        - atom: C x: 3.1630001068115234 y:-2.0859999656677246 z:8.519000053405762
        - atom: O x: 3.4089999198913574 y:-2.381999969482422 z:7.3460001945495605
        - atom: CB x: 4.775000095367432 y:-3.4110000133514404 z:9.897000312805176
        - atom: CG x: 6.122000217437744 y:-3.4679999351501465 z:10.611000061035156
        - atom: CD x: 6.538000106811523 y:-4.894000053405762 z:10.965999603271484
        - atom: OE1 x: 5.827000141143799 y:-5.545000076293945 z:11.767999649047852
        - atom: OE2 x: 7.573999881744385 y:-5.364999771118164 z:10.442000389099121
      - residue LYS has 9 atoms
        - atom: N x: 1.937000036239624 y:-1.8250000476837158 z:8.96399974822998
        - atom: CA x: 0.7760000228881836 y:-1.8489999771118164 z:8.09000015258789
        - atom: C x: 0.4650000035762787 y:-0.4359999895095825 z:7.625
        - atom: O x: -0.1469999998807907 y:-0.23800000548362732 z:6.577000141143799
        - atom: CB x: -0.42500001192092896 y:-2.430999994277954 z:8.829000473022461
        - atom: CG x: -0.34700000286102295 y:-3.931999921798706 z:9.03600025177002
        - atom: CD x: -0.3109999895095825 y:-4.669000148773193 z:7.701000213623047
        - atom: CE x: -0.36899998784065247 y:-6.182000160217285 z:7.88100004196167
        - atom: NZ x: -0.4009999930858612 y:-6.886000156402588 z:6.570000171661377
      - residue GLY has 4 atoms
        - atom: N x: 0.8970000147819519 y:0.5450000166893005 z:8.40999984741211
        - atom: CA x: 0.6600000262260437 y:1.930999994277954 z:8.053999900817871
        - atom: C x: -0.44699999690055847 y:2.5869998931884766 z:8.862000465393066
        - atom: O x: -1.2719999551773071 y:3.318000078201294 z:8.3100004196167
      - residue PHE has 11 atoms
        - atom: N x: -0.4729999899864197 y:2.3239998817443848 z:10.166999816894531
        - atom: CA x: -1.4789999723434448 y:2.8940000534057617 z:11.060999870300293
        - atom: C x: -0.8289999961853027 y:3.25 z:12.390000343322754
        - atom: O x: 0.3659999966621399 y:3.0260000228881836 z:12.576000213623047
        - atom: CB x: -2.614000082015991 y:1.8949999809265137 z:11.293999671936035
        - atom: CG x: -3.365000009536743 y:1.534999966621399 z:10.04699993133545
        - atom: CD1 x: -2.7880001068115234 y:0.7170000076293945 z:9.079999923706055
        - atom: CD2 x: -4.638999938964844 y:2.0510001182556152 z:9.812999725341797
        - atom: CE1 x: -3.4639999866485596 y:0.42100000381469727 z:7.896999835968018
        - atom: CE2 x: -5.323999881744385 y:1.7610000371932983 z:8.633999824523926
        - atom: CZ x: -4.734000205993652 y:0.9449999928474426 z:7.675000190734863
      - residue THR has 7 atoms
        - atom: N x: -1.6059999465942383 y:3.812999963760376 z:13.309000015258789
        - atom: CA x: -1.0820000171661377 y:4.171000003814697 z:14.621000289916992
        - atom: C x: -2.1449999809265137 y:4.130000114440918 z:15.713000297546387
        - atom: O x: -2.8350000381469727 y:5.118000030517578 z:15.982999801635742
        - atom: CB x: -0.4440000057220459 y:5.560999870300293 z:14.616999626159668
        - atom: OG1 x: -0.1979999989271164 y:5.96999979019165 z:15.970999717712402
        - atom: CG2 x: -1.3569999933242798 y:6.568999767303467 z:13.937999725341797
      - residue ILE has 8 atoms
        - atom: N x: -2.260999917984009 y:2.9660000801086426 z:16.34000015258789
        - atom: CA x: -3.2179999351501465 y:2.749000072479248 z:17.410999298095703
        - atom: C x: -2.7730000019073486 y:3.4049999713897705 z:18.715999603271484
        - atom: O x: -1.5839999914169312 y:3.5250000953674316 z:18.99799919128418
        - atom: CB x: -3.384000062942505 y:1.25 z:17.70800018310547
        - atom: CG1 x: -3.8320000171661377 y:0.5090000033378601 z:16.45400047302246
        - atom: CG2 x: -4.36899995803833 y:1.0549999475479126 z:18.841999053955078
        - atom: CD1 x: -3.9230000972747803 y:-0.9929999709129333 z:16.635000228881836
      - residue ASN has 8 atoms
        - atom: N x: -3.750999927520752 y:3.8329999446868896 z:19.49799919128418
        - atom: CA x: -3.5160000324249268 y:4.416999816894531 z:20.804000854492188
        - atom: C x: -4.771999835968018 y:3.9769999980926514 z:21.53499984741211
        - atom: O x: -5.671000003814697 y:3.4179999828338623 z:20.91699981689453
        - atom: CB x: -3.364000082015991 y:5.951000213623047 z:20.72800064086914
        - atom: CG x: -4.677000045776367 y:6.679999828338623 z:20.570999145507812
        - atom: OD1 x: -5.383999824523926 y:6.507999897003174 z:19.586000442504883
        - atom: ND2 x: -5.002999782562256 y:7.520999908447266 z:21.547000885009766
      - residue GLU has 9 atoms
        - atom: N x: -4.8480000495910645 y:4.176000118255615 z:22.83799934387207
        - atom: CA x: -6.034999847412109 y:3.7279999256134033 z:23.54800033569336
        - atom: C x: -7.315999984741211 y:4.426000118255615 z:23.10700035095215
        - atom: O x: -8.413999557495117 y:4.002999782562256 z:23.4689998626709
        - atom: CB x: -5.839000225067139 y:3.9059998989105225 z:25.049999237060547
        - atom: CG x: -5.285999774932861 y:5.250999927520752 z:25.452999114990234
        - atom: CD x: -5.427000045776367 y:5.492000102996826 z:26.93899917602539
        - atom: OE1 x: -6.584000110626221 y:5.568999767303467 z:27.41699981689453
        - atom: OE2 x: -4.386000156402588 y:5.5960001945495605 z:27.628999710083008
      - residue TYR has 12 atoms
        - atom: N x: -7.186999797821045 y:5.4730000495910645 z:22.301000595092773
        - atom: CA x: -8.359000205993652 y:6.21999979019165 z:21.871999740600586
        - atom: C x: -8.829000473022461 y:6.129000186920166 z:20.430999755859375
        - atom: O x: -10.012999534606934 y:6.314000129699707 z:20.163000106811523
        - atom: CB x: -8.189000129699707 y:7.686999797821045 z:22.2549991607666
        - atom: CG x: -8.407999992370605 y:7.910999774932861 z:23.726999282836914
        - atom: CD1 x: -9.579999923706055 y:7.461999893188477 z:24.343000411987305
        - atom: CD2 x: -7.442999839782715 y:8.538999557495117 z:24.511999130249023
        - atom: CE1 x: -9.788999557495117 y:7.626999855041504 z:25.70400047302246
        - atom: CE2 x: -7.639999866485596 y:8.711000442504883 z:25.878999710083008
        - atom: CZ x: -8.817999839782715 y:8.24899959564209 z:26.469999313354492
        - atom: OH x: -9.015999794006348 y:8.385000228881836 z:27.82900047302246
      - residue THR has 7 atoms
        - atom: N x: -7.926000118255615 y:5.84499979019165 z:19.503999710083008
        - atom: CA x: -8.315999984741211 y:5.76200008392334 z:18.10300064086914
        - atom: C x: -7.355000019073486 y:4.928999900817871 z:17.274999618530273
        - atom: O x: -6.382999897003174 y:4.380000114440918 z:17.781999588012695
        - atom: CB x: -8.359000205993652 y:7.159999847412109 z:17.450000762939453
        - atom: OG1 x: -7.072000026702881 y:7.771999835968018 z:17.58099937438965
        - atom: CG2 x: -9.40999984741211 y:8.045999526977539 z:18.10300064086914
      - residue ILE has 8 atoms
        - atom: N x: -7.651000022888184 y:4.840000152587891 z:15.984999656677246
        - atom: CA x: -6.809999942779541 y:4.129000186920166 z:15.03600025177002
        - atom: C x: -6.605000019073486 y:5.14300012588501 z:13.92300033569336
        - atom: O x: -7.561999797821045 y:5.546000003814697 z:13.265999794006348
        - atom: CB x: -7.505000114440918 y:2.8489999771118164 z:14.496000289916992
        - atom: CG1 x: -6.677000045776367 y:2.243000030517578 z:13.366000175476074
        - atom: CG2 x: -8.907999992370605 y:3.1640000343322754 z:14.024999618530273
        - atom: CD1 x: -5.2870001792907715 y:1.8519999980926514 z:13.770000457763672
      - residue ARG has 11 atoms
        - atom: N x: -5.361999988555908 y:5.576000213623047 z:13.73900032043457
        - atom: CA x: -5.0320000648498535 y:6.578000068664551 z:12.72599983215332
        - atom: C x: -4.03000020980835 y:6.0970001220703125 z:11.682000160217285
        - atom: O x: -3.0840001106262207 y:5.367000102996826 z:11.996000289916992
        - atom: CB x: -4.446000099182129 y:7.829999923706055 z:13.387999534606934
        - atom: CG x: -5.349999904632568 y:8.541000366210938 z:14.371999740600586
        - atom: CD x: -4.564000129699707 y:9.571000099182129 z:15.16100025177002
        - atom: NE x: -5.436999797821045 y:10.416000366210938 z:15.961999893188477
        - atom: CZ x: -6.255000114440918 y:11.333999633789062 z:15.456000328063965
        - atom: NH1 x: -6.309000015258789 y:11.53499984741211 z:14.142999649047852
        - atom: NH2 x: -7.034999847412109 y:12.043000221252441 z:16.260000228881836
      - residue PRO has 7 atoms
        - atom: N x: -4.21999979019165 y:6.513000011444092 z:10.418999671936035
        - atom: CA x: -3.3289999961853027 y:6.136000156402588 z:9.314000129699707
        - atom: C x: -2.0810000896453857 y:7.013000011444092 z:9.279999732971191
        - atom: O x: -2.1059999465942383 y:8.13700008392334 z:9.77299976348877
        - atom: CB x: -4.203000068664551 y:6.354000091552734 z:8.08899974822998
        - atom: CG x: -5.043000221252441 y:7.53000020980835 z:8.503999710083008
        - atom: CD x: -5.443999767303467 y:7.158999919891357 z:9.90999984741211
      - residue LEU has 8 atoms
        - atom: N x: -0.9909999966621399 y:6.5 z:8.71500015258789
        - atom: CA x: 0.23899999260902405 y:7.2820000648498535 z:8.612000465393066
        - atom: C x: 0.4749999940395355 y:7.710999965667725 z:7.160999774932861
        - atom: O x: 0.6140000224113464 y:6.875999927520752 z:6.260000228881836
        - atom: CB x: 1.4550000429153442 y:6.493000030517578 z:9.128000259399414
        - atom: CG x: 1.6330000162124634 y:6.239999771118164 z:10.633000373840332
        - atom: CD1 x: 3.072000026702881 y:5.822000026702881 z:10.888999938964844
        - atom: CD2 x: 1.3270000219345093 y:7.493000030517578 z:11.430999755859375
      - residue GLY has 4 atoms
        - atom: N x: 0.5199999809265137 y:9.02400016784668 z:6.947000026702881
        - atom: CA x: 0.7110000252723694 y:9.560999870300293 z:5.611999988555908
        - atom: C x: 2.055000066757202 y:9.293999671936035 z:4.956999778747559
        - atom: O x: 2.5769999027252197 y:8.173999786376953 z:5.01200008392334
      - residue VAL has 5 atoms
        - atom: N x: 2.6010000705718994 y:10.335000038146973 z:4.326000213623047
        - atom: CA x: 3.885999917984009 y:10.26200008392334 z:3.632999897003174
        - atom: C x: 5.041999816894531 y:10.295999526977539 z:4.625999927520752
        - atom: O x: 5.809000015258789 y:9.336999893188477 z:4.73799991607666
        - atom: CB x: 4.046000003814697 y:11.435999870300293 z:2.6449999809265137
      - residue THR has 7 atoms
        - atom: N x: 5.1620001792907715 y:11.411999702453613 z:5.3379998207092285
        - atom: CA x: 6.205999851226807 y:11.58899974822998 z:6.3429999351501465
        - atom: C x: 5.745999813079834 y:10.847000122070312 z:7.5879998207092285
        - atom: O x: 6.538000106811523 y:10.524999618530273 z:8.479999542236328
        - atom: CB x: 6.401000022888184 y:13.09000015258789 z:6.693999767303467
        - atom: OG1 x: 7.418000221252441 y:13.229000091552734 z:7.696000099182129
        - atom: CG2 x: 5.10099983215332 y:13.690999984741211 z:7.216000080108643
      - residue GLY has 4 atoms
        - atom: N x: 4.451000213623047 y:10.559000015258789 z:7.620999813079834
        - atom: CA x: 3.871999979019165 y:9.878999710083008 z:8.756999969482422
        - atom: C x: 3.1549999713897705 y:10.939000129699707 z:9.560999870300293
        - atom: O x: 3.7009999752044678 y:11.47599983215332 z:10.526000022888184
      - residue VAL has 7 atoms
        - atom: N x: 1.9320000410079956 y:11.253999710083008 z:9.142000198364258
        - atom: CA x: 1.121000051498413 y:12.267000198364258 z:9.810999870300293
        - atom: C x: -0.13600000739097595 y:11.644000053405762 z:10.413000106811523
        - atom: O x: -0.7139999866485596 y:10.715999603271484 z:9.848999977111816
        - atom: CB x: 0.6930000185966492 y:13.37600040435791 z:8.821000099182129
        - atom: CG1 x: 0.11800000071525574 y:14.564000129699707 z:9.583999633789062
        - atom: CG2 x: 1.8819999694824219 y:13.795000076293945 z:7.960999965667725
      - residue ALA has 5 atoms
        - atom: N x: -0.5550000071525574 y:12.157999992370605 z:11.562000274658203
        - atom: CA x: -1.746000051498413 y:11.645999908447266 z:12.223999977111816
        - atom: C x: -2.989000082015991 y:11.880000114440918 z:11.366999626159668
        - atom: O x: -3.7219998836517334 y:12.854999542236328 z:11.567999839782715
        - atom: CB x: -1.9160000085830688 y:12.317000389099121 z:13.588000297546387
      - residue GLY has 4 atoms
        - atom: N x: -3.2219998836517334 y:10.994000434875488 z:10.402999877929688
        - atom: CA x: -4.394999980926514 y:11.140999794006348 z:9.5649995803833
        - atom: C x: -5.603000164031982 y:11.170000076293945 z:10.477999687194824
        - atom: O x: -5.493000030517578 y:10.807000160217285 z:11.645999908447266
      - residue GLU has 9 atoms
        - atom: N x: -6.754000186920166 y:11.597999572753906 z:9.97599983215332
        - atom: CA x: -7.928999900817871 y:11.63700008392334 z:10.82699966430664
        - atom: C x: -8.236000061035156 y:10.243000030517578 z:11.357999801635742
        - atom: O x: -7.811999797821045 y:9.243000030517578 z:10.781999588012695
        - atom: CB x: -9.128000259399414 y:12.204000473022461 z:10.067999839782715
        - atom: CG x: -8.973999977111816 y:13.675999641418457 z:9.729000091552734
        - atom: CD x: -8.668999671936035 y:14.520999908447266 z:10.954000473022461
        - atom: OE1 x: -9.545999526977539 y:14.63599967956543 z:11.836999893188477
        - atom: OE2 x: -7.546000003814697 y:15.064000129699707 z:11.038999557495117
      - residue PRO has 7 atoms
        - atom: N x: -8.956999778747559 y:10.168000221252441 z:12.486000061035156
        - atom: CA x: -9.35099983215332 y:8.928999900817871 z:13.156000137329102
        - atom: C x: -10.333999633789062 y:8.079000473022461 z:12.36299991607666
        - atom: O x: -11.458999633789062 y:8.48799991607666 z:12.119999885559082
        - atom: CB x: -9.963000297546387 y:9.427000045776367 z:14.458000183105469
        - atom: CG x: -9.27299976348877 y:10.722000122070312 z:14.6899995803833
        - atom: CD x: -9.281999588012695 y:11.329000473022461 z:13.32800006866455
      - residue LEU has 8 atoms
        - atom: N x: -9.914999961853027 y:6.882999897003174 z:11.980999946594238
        - atom: CA x: -10.781000137329102 y:5.994999885559082 z:11.220000267028809
        - atom: C x: -12.0 y:5.538000106811523 z:12.052000045776367
        - atom: O x: -11.925000190734863 y:5.4029998779296875 z:13.284000396728516
        - atom: CB x: -9.970000267028809 y:4.785999774932861 z:10.727999687194824
        - atom: CG x: -8.637999534606934 y:5.125 z:10.034000396728516
        - atom: CD1 x: -7.88100004196167 y:3.8529999256134033 z:9.711999893188477
        - atom: CD2 x: -8.88599967956543 y:5.926000118255615 z:8.770999908447266
      - residue PRO has 7 atoms
        - atom: N x: -13.142999649047852 y:5.301000118255615 z:11.381999969482422
        - atom: CA x: -14.369999885559082 y:4.864999771118164 z:12.055999755859375
        - atom: C x: -14.175000190734863 y:3.4600000381469727 z:12.61299991607666
        - atom: O x: -13.482000350952148 y:2.6470000743865967 z:12.015000343322754
        - atom: CB x: -15.402999877929688 y:4.925000190734863 z:10.942999839782715
        - atom: CG x: -14.595000267028809 y:4.534999847412109 z:9.737000465393066
        - atom: CD x: -13.314000129699707 y:5.303999900817871 z:9.918000221252441
      - residue VAL has 7 atoms
        - atom: N x: -14.791000366210938 y:3.1710000038146973 z:13.751999855041504
        - atom: CA x: -14.619999885559082 y:1.871999979019165 z:14.383999824523926
        - atom: C x: -15.878000259399414 y:1.4279999732971191 z:15.11400032043457
        - atom: O x: -16.320999145507812 y:2.0989999771118164 z:16.045000076293945
        - atom: CB x: -13.45199966430664 y:1.9279999732971191 z:15.414999961853027
        - atom: CG1 x: -13.395000457763672 y:0.6629999876022339 z:16.229000091552734
        - atom: CG2 x: -12.142000198364258 y:2.13700008392334 z:14.706000328063965
      - residue ASP has 8 atoms
        - atom: N x: -16.44499969482422 y:0.29499998688697815 z:14.708000183105469
        - atom: CA x: -17.641000747680664 y:-0.2070000022649765 z:15.37600040435791
        - atom: C x: -17.44300079345703 y:-1.562000036239624 z:16.04199981689453
        - atom: O x: -18.38599967956543 y:-2.1410000324249268 z:16.584999084472656
        - atom: CB x: -18.812000274658203 y:-0.27399998903274536 z:14.397000312805176
        - atom: CG x: -19.378000259399414 y:1.090999960899353 z:14.090999603271484
        - atom: OD1 x: -19.974000930786133 y:1.7089999914169312 z:15.01099967956543
        - atom: OD2 x: -19.208999633789062 y:1.5449999570846558 z:12.937000274658203
      - residue SER has 6 atoms
        - atom: N x: -16.21299934387207 y:-2.056999921798706 z:16.011999130249023
        - atom: CA x: -15.904000282287598 y:-3.3350000381469727 z:16.624000549316406
        - atom: C x: -14.416999816894531 y:-3.440999984741211 z:16.860000610351562
        - atom: O x: -13.630000114440918 y:-2.6700000762939453 z:16.297000885009766
        - atom: CB x: -16.336000442504883 y:-4.482999801635742 z:15.71399974822998
        - atom: OG x: -15.477999687194824 y:-4.5929999351501465 z:14.583999633789062
      - residue GLU has 9 atoms
        - atom: N x: -14.02299976348877 y:-4.389999866485596 z:17.70199966430664
        - atom: CA x: -12.605999946594238 y:-4.583000183105469 z:17.94700050354004
        - atom: C x: -12.114999771118164 y:-5.175000190734863 z:16.631000518798828
        - atom: O x: -11.086999893188477 y:-4.754000186920166 z:16.094999313354492
        - atom: CB x: -12.359999656677246 y:-5.572000026702881 z:19.093000411987305
        - atom: CG x: -12.958000183105469 y:-5.177999973297119 z:20.433000564575195
        - atom: CD x: -12.744000434875488 y:-6.241000175476074 z:21.503000259399414
        - atom: OE1 x: -11.678000450134277 y:-6.239999771118164 z:22.149999618530273
        - atom: OE2 x: -13.63700008392334 y:-7.091000080108643 z:21.690000534057617
      - residue LYS has 9 atoms
        - atom: N x: -12.881999969482422 y:-6.133999824523926 z:16.10300064086914
        - atom: CA x: -12.550999641418457 y:-6.808000087738037 z:14.845000267028809
        - atom: C x: -12.190999984741211 y:-5.770999908447266 z:13.795000076293945
        - atom: O x: -11.251999855041504 y:-5.955999851226807 z:13.017000198364258
        - atom: CB x: -13.72700023651123 y:-7.6579999923706055 z:14.350000381469727
        - atom: CG x: -13.319999694824219 y:-8.717000007629395 z:13.312999725341797
        - atom: CD x: -14.470999717712402 y:-9.666000366210938 z:12.951000213623047
        - atom: CE x: -13.95300006866455 y:-10.96500015258789 z:12.319999694824219
        - atom: NZ x: -13.071999549865723 y:-10.746999740600586 z:11.128999710083008
      - residue ASP has 8 atoms
        - atom: N x: -12.949999809265137 y:-4.681000232696533 z:13.784000396728516
        - atom: CA x: -12.708999633789062 y:-3.5869998931884766 z:12.864999771118164
        - atom: C x: -11.27299976348877 y:-3.0889999866485596 z:12.994000434875488
        - atom: O x: -10.62399959564209 y:-2.819999933242798 z:11.98799991607666
        - atom: CB x: -13.6850004196167 y:-2.4489998817443848 z:13.14900016784668
        - atom: CG x: -15.019000053405762 y:-2.638000011444092 z:12.45199966430664
        - atom: OD1 x: -15.416999816894531 y:-3.799999952316284 z:12.22700023651123
        - atom: OD2 x: -15.673999786376953 y:-1.6230000257492065 z:12.137999534606934
      - residue ILE has 8 atoms
        - atom: N x: -10.767000198364258 y:-2.9700000286102295 z:14.220000267028809
        - atom: CA x: -9.394000053405762 y:-2.506999969482422 z:14.414999961853027
        - atom: C x: -8.388999938964844 y:-3.507999897003174 z:13.859999656677246
        - atom: O x: -7.361000061035156 y:-3.1089999675750732 z:13.307999610900879
        - atom: CB x: -9.074000358581543 y:-2.252000093460083 z:15.904000282287598
        - atom: CG1 x: -9.920999526977539 y:-1.0920000076293945 z:16.42300033569336
        - atom: CG2 x: -7.604000091552734 y:-1.9160000085830688 z:16.07200050354004
        - atom: CD1 x: -9.934000015258789 y:-0.9750000238418579 z:17.92300033569336
      - residue PHE has 11 atoms
        - atom: N x: -8.67199993133545 y:-4.802999973297119 z:13.996999740600586
        - atom: CA x: -7.755000114440918 y:-5.816999912261963 z:13.468000411987305
        - atom: C x: -7.697000026702881 y:-5.741000175476074 z:11.954000473022461
        - atom: O x: -6.613999843597412 y:-5.801000118255615 z:11.366000175476074
        - atom: CB x: -8.1850004196167 y:-7.229000091552734 z:13.838000297546387
        - atom: CG x: -8.031000137329102 y:-7.553999900817871 z:15.281000137329102
        - atom: CD1 x: -8.97599983215332 y:-7.142000198364258 z:16.200000762939453
        - atom: CD2 x: -6.9629998207092285 y:-8.329000473022461 z:15.71399974822998
        - atom: CE1 x: -8.86400032043457 y:-7.50600004196167 z:17.531999588012695
        - atom: CE2 x: -6.8420000076293945 y:-8.699000358581543 z:17.04400062561035
        - atom: CZ x: -7.793000221252441 y:-8.289999961853027 z:17.95400047302246
      - residue ASP has 8 atoms
        - atom: N x: -8.868000030517578 y:-5.627999782562256 z:11.32800006866455
        - atom: CA x: -8.956000328063965 y:-5.539999961853027 z:9.875
        - atom: C x: -7.9770002365112305 y:-4.494999885559082 z:9.343000411987305
        - atom: O x: -7.117000102996826 y:-4.798999786376953 z:8.513999938964844
        - atom: CB x: -10.378999710083008 y:-5.177999973297119 z:9.451000213623047
        - atom: CG x: -11.38599967956543 y:-6.243000030517578 z:9.824000358581543
        - atom: OD1 x: -11.04800033569336 y:-7.438000202178955 z:9.717000007629395
        - atom: OD2 x: -12.520000457763672 y:-5.888000011444092 z:10.206999778747559
      - residue TYR has 12 atoms
        - atom: N x: -8.109999656677246 y:-3.2669999599456787 z:9.835000038146973
        - atom: CA x: -7.236000061035156 y:-2.171999931335449 z:9.430000305175781
        - atom: C x: -5.750999927520752 y:-2.553999900817871 z:9.388999938964844
        - atom: O x: -5.015999794006348 y:-2.0889999866485596 z:8.51200008392334
        - atom: CB x: -7.4120001792907715 y:-0.9829999804496765 z:10.37600040435791
        - atom: CG x: -8.711999893188477 y:-0.2290000021457672 z:10.222999572753906
        - atom: CD1 x: -8.961999893188477 y:0.5600000023841858 z:9.097999572753906
        - atom: CD2 x: -9.673999786376953 y:-0.26100000739097595 z:11.227999687194824
        - atom: CE1 x: -10.13700008392334 y:1.3040000200271606 z:8.98799991607666
        - atom: CE2 x: -10.85200023651123 y:0.4740000069141388 z:11.125
        - atom: CZ x: -11.074000358581543 y:1.253999948501587 z:10.008000373840332
        - atom: OH x: -12.22599983215332 y:1.99399995803833 z:9.934000015258789
      - residue ILE has 8 atoms
        - atom: N x: -5.306000232696533 y:-3.385999917984009 z:10.331999778747559
        - atom: CA x: -3.9000000953674316 y:-3.7909998893737793 z:10.378999710083008
        - atom: C x: -3.6470000743865967 y:-5.202000141143799 z:9.848999977111816
        - atom: O x: -2.5460000038146973 y:-5.744999885559082 z:9.998000144958496
        - atom: CB x: -3.3369998931884766 y:-3.7060000896453857 z:11.810999870300293
        - atom: CG1 x: -4.114999771118164 y:-4.64900016784668 z:12.734999656677246
        - atom: CG2 x: -3.4070000648498535 y:-2.2730000019073486 z:12.29800033569336
        - atom: CD1 x: -3.5190000534057617 y:-4.806000232696533 z:14.109000205993652
      - residue GLN has 9 atoms
        - atom: N x: -4.672999858856201 y:-5.791999816894531 z:9.23799991607666
        - atom: CA x: -4.566999912261963 y:-7.129000186920166 z:8.661999702453613
        - atom: C x: -3.9079999923706055 y:-8.130999565124512 z:9.602999687194824
        - atom: O x: -2.7799999713897705 y:-8.581999778747559 z:9.387999534606934
        - atom: CB x: -3.802999973297119 y:-7.051000118255615 z:7.3420000076293945
        - atom: CG x: -4.520999908447266 y:-6.198999881744385 z:6.308000087738037
        - atom: CD x: -3.6029999256134033 y:-5.708000183105469 z:5.218999862670898
        - atom: OE1 x: -2.9730000495910645 y:-6.502999782562256 z:4.520999908447266
        - atom: NE2 x: -3.515000104904175 y:-4.388000011444092 z:5.065999984741211
      - residue TRP has 14 atoms
        - atom: N x: -4.6479997634887695 y:-8.468000411987305 z:10.651000022888184
        - atom: CA x: -4.2129998207092285 y:-9.406999588012695 z:11.666000366210938
        - atom: C x: -5.4029998779296875 y:-10.319000244140625 z:11.925000190734863
        - atom: O x: -6.546999931335449 y:-9.857000350952148 z:11.963000297546387
        - atom: CB x: -3.867000102996826 y:-8.654000282287598 z:12.949999809265137
        - atom: CG x: -2.4119999408721924 y:-8.647000312805176 z:13.345000267028809
        - atom: CD1 x: -1.3270000219345093 y:-8.75100040435791 z:12.519000053405762
        - atom: CD2 x: -1.8910000324249268 y:-8.4350004196167 z:14.666000366210938
        - atom: NE1 x: -0.164000004529953 y:-8.61299991607666 z:13.244999885559082
        - atom: CE2 x: -0.4819999933242798 y:-8.416000366210938 z:14.562999725341797
        - atom: CE3 x: -2.4809999465942383 y:-8.253999710083008 z:15.925999641418457
        - atom: CZ2 x: 0.34700000286102295 y:-8.222999572753906 z:15.670999526977539
        - atom: CZ3 x: -1.6579999923706055 y:-8.062000274658203 z:17.027000427246094
        - atom: CH2 x: -0.257999986410141 y:-8.04800033569336 z:16.891000747680664
      - residue LYS has 9 atoms
        - atom: N x: -5.131999969482422 y:-11.611000061035156 z:12.079999923706055
        - atom: CA x: -6.172999858856201 y:-12.593999862670898 z:12.36400032043457
        - atom: C x: -6.895999908447266 y:-12.119000434875488 z:13.630999565124512
        - atom: O x: -6.25 y:-11.840999603271484 z:14.640000343322754
        - atom: CB x: -5.515999794006348 y:-13.961000442504883 z:12.612000465393066
        - atom: CG x: -6.453999996185303 y:-15.081999778747559 z:13.057999610900879
        - atom: CD x: -5.710000038146973 y:-16.18600082397461 z:13.833000183105469
        - atom: CE x: -4.585000038146973 y:-16.8439998626709 z:13.029000282287598
        - atom: NZ x: -3.36299991607666 y:-15.994999885559082 z:12.892999649047852
      - residue TYR has 12 atoms
        - atom: N x: -8.222000122070312 y:-12.010000228881836 z:13.583000183105469
        - atom: CA x: -8.960000038146973 y:-11.565999984741211 z:14.760000228881836
        - atom: C x: -8.760000228881836 y:-12.576000213623047 z:15.869999885559082
        - atom: O x: -8.963000297546387 y:-13.774999618530273 z:15.677000045776367
        - atom: CB x: -10.458000183105469 y:-11.418999671936035 z:14.470000267028809
        - atom: CG x: -11.286999702453613 y:-11.11299991607666 z:15.708000183105469
        - atom: CD1 x: -10.930999755859375 y:-10.07800006866455 z:16.576000213623047
        - atom: CD2 x: -12.423999786376953 y:-11.857999801635742 z:16.016000747680664
        - atom: CE1 x: -11.687000274658203 y:-9.791999816894531 z:17.722999572753906
        - atom: CE2 x: -13.187000274658203 y:-11.57800006866455 z:17.160999298095703
        - atom: CZ x: -12.8100004196167 y:-10.543999671936035 z:18.007999420166016
        - atom: OH x: -13.557000160217285 y:-10.265999794006348 z:19.131999969482422
      - residue ARG has 11 atoms
        - atom: N x: -8.35099983215332 y:-12.07800006866455 z:17.030000686645508
        - atom: CA x: -8.109999656677246 y:-12.918000221252441 z:18.19099998474121
        - atom: C x: -9.045999526977539 y:-12.545000076293945 z:19.327999114990234
        - atom: O x: -9.180000305175781 y:-11.371999740600586 z:19.68600082397461
        - atom: CB x: -6.64300012588501 y:-12.793999671936035 z:18.628999710083008
        - atom: CG x: -5.697000026702881 y:-13.623000144958496 z:17.770999908447266
        - atom: CD x: -4.306000232696533 y:-13.03600025177002 z:17.694000244140625
        - atom: NE x: -3.683000087738037 y:-12.902999877929688 z:19.003999710083008
        - atom: CZ x: -2.4519999027252197 y:-12.432999610900879 z:19.19300079345703
        - atom: NH1 x: -1.718999981880188 y:-12.057999610900879 z:18.14900016784668
        - atom: NH2 x: -1.9579999446868896 y:-12.322999954223633 z:20.422000885009766
      - residue GLU has 9 atoms
        - atom: N x: -9.708999633789062 y:-13.553999900817871 z:19.881999969482422
        - atom: CA x: -10.630000114440918 y:-13.32800006866455 z:20.979999542236328
        - atom: C x: -9.880999565124512 y:-12.907999992370605 z:22.240999221801758
        - atom: O x: -8.704000473022461 y:-13.222000122070312 z:22.416000366210938
        - atom: CB x: -11.458000183105469 y:-14.58899974822998 z:21.243000030517578
        - atom: CG x: -12.715999603271484 y:-14.678000450134277 z:20.395999908447266
        - atom: CD x: -13.70300006866455 y:-13.559000015258789 z:20.702999114990234
        - atom: OE1 x: -14.116000175476074 y:-13.442999839782715 z:21.875999450683594
        - atom: OE2 x: -14.069000244140625 y:-12.795999526977539 z:19.7810001373291
      - residue PRO has 7 atoms
        - atom: N x: -10.557000160217285 y:-12.173999786376953 z:23.131999969482422
        - atom: CA x: -9.939000129699707 y:-11.720000267028809 z:24.371000289916992
        - atom: C x: -9.152999877929688 y:-12.814000129699707 z:25.082000732421875
        - atom: O x: -8.093999862670898 y:-12.553000450134277 z:25.649999618530273
        - atom: CB x: -11.133000373840332 y:-11.241999626159668 z:25.18000030517578
        - atom: CG x: -11.991999626159668 y:-10.654999732971191 z:24.128000259399414
        - atom: CD x: -11.949000358581543 y:-11.706999778747559 z:23.049999237060547
      - residue LYS has 9 atoms
        - atom: N x: -9.663999557495117 y:-14.041000366210938 z:25.042999267578125
        - atom: CA x: -8.987000465393066 y:-15.14900016784668 z:25.709999084472656
        - atom: C x: -7.636000156402588 y:-15.522000312805176 z:25.11199951171875
        - atom: O x: -6.769999980926514 y:-16.047000885009766 z:25.81800079345703
        - atom: CB x: -9.890999794006348 y:-16.393999099731445 z:25.76099967956543
        - atom: CG x: -10.576000213623047 y:-16.767000198364258 z:24.45599937438965
        - atom: CD x: -11.342000007629395 y:-18.08099937438965 z:24.591999053955078
        - atom: CE x: -12.46399974822998 y:-18.19700050354004 z:23.55500030517578
        - atom: NZ x: -11.987000465393066 y:-18.033000946044922 z:22.152999877929688
      - residue ASP has 8 atoms
        - atom: N x: -7.442999839782715 y:-15.236000061035156 z:23.82699966430664
        - atom: CA x: -6.190999984741211 y:-15.576000213623047 z:23.158000946044922
        - atom: C x: -5.249000072479248 y:-14.38599967956543 z:23.02199935913086
        - atom: O x: -4.289000034332275 y:-14.437000274658203 z:22.250999450683594
        - atom: CB x: -6.478000164031982 y:-16.13599967956543 z:21.766000747680664
        - atom: CG x: -7.806000232696533 y:-16.85700035095215 z:21.69099998474121
        - atom: OD1 x: -7.918000221252441 y:-17.975000381469727 z:22.240999221801758
        - atom: OD2 x: -8.744000434875488 y:-16.29400062561035 z:21.08300018310547
      - residue ARG has 11 atoms
        - atom: N x: -5.5269999504089355 y:-13.3100004196167 z:23.753000259399414
        - atom: CA x: -4.684999942779541 y:-12.119999885559082 z:23.701000213623047
        - atom: C x: -3.753000020980835 y:-12.059000015258789 z:24.905000686645508
        - atom: O x: -2.9630000591278076 y:-11.131999969482422 z:25.038000106811523
        - atom: CB x: -5.535999774932861 y:-10.854000091552734 z:23.65399932861328
        - atom: CG x: -6.466000080108643 y:-10.753000259399414 z:22.45599937438965
        - atom: CD x: -7.349999904632568 y:-9.517000198364258 z:22.576000213623047
        - atom: NE x: -8.53499984741211 y:-9.595999717712402 z:21.73699951171875
        - atom: CZ x: -9.552000045776367 y:-8.748000144958496 z:21.80900001525879
        - atom: NH1 x: -9.529999732971191 y:-7.751999855041504 z:22.68600082397461
        - atom: NH2 x: -10.593000411987305 y:-8.897000312805176 z:21.003000259399414
      - residue SER has 6 atoms
        - atom: N x: -3.8580000400543213 y:-13.041000366210938 z:25.791000366210938
        - atom: CA x: -2.989000082015991 y:-13.07699966430664 z:26.95599937438965
        - atom: C x: -1.5839999914169312 y:-13.416000366210938 z:26.474000930786133
        - atom: O x: -1.284999966621399 y:-14.574000358581543 z:26.16699981689453
        - atom: CB x: -3.4690001010894775 y:-14.126999855041504 z:27.961000442504883
        - atom: OG x: -4.433000087738037 y:-13.57800006866455 z:28.847000122070312
      - residue GLU has 10 atoms
        - atom: N x: -0.7360000014305115 y:-12.394000053405762 z:26.395999908447266
        - atom: CA x: 0.6309999823570251 y:-12.565999984741211 z:25.93899917602539
        - atom: C x: 1.6269999742507935 y:-11.968999862670898 z:26.92799949645996
        - atom: O x: 2.7279999256134033 y:-12.541000366210938 z:27.077999114990234
        - atom: CB x: 0.7960000038146973 y:-11.9399995803833 z:24.552000045776367
        - atom: CG x: -0.11400000005960464 y:-12.574999809265137 z:23.51099967956543
        - atom: CD x: 0.17499999701976776 y:-12.116999626159668 z:22.09000015258789
        - atom: OE1 x: 0.09000000357627869 y:-10.902999877929688 z:21.815000534057617
        - atom: OE2 x: 0.4819999933242798 y:-12.97700023651123 z:21.23900032043457
        - atom: OXT x: 1.3029999732971191 y:-10.935999870300293 z:27.54400062561035
      - residue MN has 1 atoms
        - atom: MN x: -6.214000225067139 y:-5.52400016784668 z:35.61399841308594
      - residue MN has 1 atoms
        - atom: MN x: -6.142000198364258 y:-2.124000072479248 z:36.37300109863281
      - residue MN has 1 atoms
        - atom: MN x: 13.84000015258789 y:-1.5140000581741333 z:61.231998443603516
      - residue MN has 1 atoms
        - atom: MN x: 8.105999946594238 y:-25.408000946044922 z:15.770000457763672
      - residue NA has 1 atoms
        - atom: NA x: 4.251999855041504 y:-0.11299999803304672 z:43.87799835205078
      - residue NA has 1 atoms
        - atom: NA x: 16.698999404907227 y:-13.654000282287598 z:18.052000045776367
      - residue F2A has 30 atoms
        - atom: PA x: -3.8420000076293945 y:-3.880000114440918 z:34.38800048828125
        - atom: O1A x: -5.063000202178955 y:-3.622999906539917 z:35.20000076293945
        - atom: O2A x: -2.5329999923706055 y:-3.359999895095825 z:34.85300064086914
        - atom: C3A x: -3.6730000972747803 y:-5.749000072479248 z:34.435001373291016
        - atom: O5' x: -4.066999912261963 y:-3.2890000343322754 z:32.92499923706055
        - atom: PB x: -4.76800012588501 y:-7.072999954223633 z:33.6879997253418
        - atom: O1B x: -4.315000057220459 y:-7.23199987411499 z:32.28099822998047
        - atom: O2B x: -6.175000190734863 y:-6.676000118255615 z:33.970001220703125
        - atom: O3B x: -4.465000152587891 y:-8.342000007629395 z:34.42300033569336
        - atom: PG x: -4.432000160217285 y:-8.357000350952148 z:35.915000915527344
        - atom: O1G x: -2.990999937057495 y:-8.444000244140625 z:36.2599983215332
        - atom: O2G x: -5.375 y:-9.385000228881836 z:36.42900085449219
        - atom: O3G x: -4.946000099182129 y:-7.052999973297119 z:36.409000396728516
        - atom: C5' x: -5.205999851226807 y:-3.6419999599456787 z:32.145999908447266
        - atom: C4' x: -4.960000038146973 y:-3.3380000591278076 z:30.687000274658203
        - atom: O4' x: -4.2230000495910645 y:-2.0969998836517334 z:30.54800033569336
        - atom: C1' x: -3.4019999504089355 y:-2.1610000133514404 z:29.38800048828125
        - atom: N9 x: -2.00600004196167 y:-1.9320000410079956 z:29.775999069213867
        - atom: C4 x: -1.0019999742507935 y:-1.4759999513626099 z:28.95199966430664
        - atom: N3 x: -1.1009999513626099 y:-1.1349999904632568 z:27.658000946044922
        - atom: C2 x: 0.08100000023841858 y:-0.7540000081062317 z:27.180999755859375
        - atom: N1 x: 1.2619999647140503 y:-0.6800000071525574 z:27.80299949645996
        - atom: C6 x: 1.3289999961853027 y:-1.0219999551773071 z:29.106000900268555
        - atom: N6 x: 2.506999969482422 y:-0.9359999895095825 z:29.729999542236328
        - atom: C5 x: 0.14499999582767487 y:-1.4479999542236328 z:29.731000900268555
        - atom: N7 x: -0.12700000405311584 y:-1.8680000305175781 z:31.024999618530273
        - atom: C8 x: -1.4129999876022339 y:-2.138000011444092 z:31.003999710083008
        - atom: C2' x: -3.621999979019165 y:-3.5390000343322754 z:28.760000228881836
        - atom: C3' x: -4.086999893188477 y:-4.3429999351501465 z:29.964000701904297
        - atom: O3' x: -4.868000030517578 y:-5.460000038146973 z:29.570999145507812
      - residue HOH has 1 atoms
        - atom: O x: -2.4089999198913574 y:8.484999656677246 z:43.20899963378906
      - residue HOH has 1 atoms
        - atom: O x: -0.14300000667572021 y:-1.7710000276565552 z:48.332000732421875
      - residue HOH has 1 atoms
        - atom: O x: -16.437999725341797 y:-4.840000152587891 z:18.80699920654297
      - residue HOH has 1 atoms
        - atom: O x: 16.079999923706055 y:1.4079999923706055 z:30.270999908447266
      - residue HOH has 1 atoms
        - atom: O x: 21.016000747680664 y:-1.5190000534057617 z:33.81999969482422
      - residue HOH has 1 atoms
        - atom: O x: -6.730999946594238 y:0.6259999871253967 z:20.711999893188477
      - residue HOH has 1 atoms
        - atom: O x: 20.124000549316406 y:-7.186999797821045 z:32.66400146484375
      - residue HOH has 1 atoms
        - atom: O x: -12.125 y:5.327000141143799 z:17.954999923706055
      - residue HOH has 1 atoms
        - atom: O x: -13.345999717712402 y:10.083999633789062 z:45.89799880981445
      - residue HOH has 1 atoms
        - atom: O x: -8.428000450134277 y:6.59499979019165 z:30.35300064086914
      - residue HOH has 1 atoms
        - atom: O x: -18.88599967956543 y:7.940000057220459 z:27.29599952697754
      - residue HOH has 1 atoms
        - atom: O x: -12.711000442504883 y:-14.880000114440918 z:25.305999755859375
      - residue HOH has 1 atoms
        - atom: O x: 13.637999534606934 y:-8.12399959564209 z:24.416000366210938
      - residue HOH has 1 atoms
        - atom: O x: -4.113999843597412 y:-2.135999917984009 z:36.98699951171875
      - residue HOH has 1 atoms
        - atom: O x: 12.25 y:-8.463000297546387 z:47.82099914550781
      - residue HOH has 1 atoms
        - atom: O x: 13.711000442504883 y:2.4779999256134033 z:60.03499984741211
      - residue HOH has 1 atoms
        - atom: O x: 13.440999984741211 y:-24.489999771118164 z:30.077999114990234
      - residue HOH has 1 atoms
        - atom: O x: -1.406000018119812 y:-12.001999855041504 z:50.17599868774414
      - residue HOH has 1 atoms
        - atom: O x: -18.986000061035156 y:-14.868000030517578 z:32.553001403808594
      - residue HOH has 1 atoms
        - atom: O x: -10.734000205993652 y:-14.918000221252441 z:48.27399826049805
      - residue HOH has 1 atoms
        - atom: O x: 11.635000228881836 y:-24.492000579833984 z:31.9689998626709
      - residue HOH has 1 atoms
        - atom: O x: 3.058000087738037 y:-2.069999933242798 z:43.28900146484375
      - residue HOH has 1 atoms
        - atom: O x: 1.7419999837875366 y:-11.512999534606934 z:49.70600128173828
      - residue HOH has 1 atoms
        - atom: O x: -25.611000061035156 y:13.20199966430664 z:33.939998626708984
      - residue HOH has 1 atoms
        - atom: O x: -29.035999298095703 y:5.309000015258789 z:24.209999084472656
      - residue HOH has 1 atoms
        - atom: O x: 0.3100000023841858 y:-5.184999942779541 z:48.196998596191406
      - residue HOH has 1 atoms
        - atom: O x: -13.279000282287598 y:3.0230000019073486 z:18.819000244140625
      - residue HOH has 1 atoms
        - atom: O x: -23.634000778198242 y:-16.91900062561035 z:58.840999603271484
      - residue HOH has 1 atoms
        - atom: O x: -2.9119999408721924 y:-6.1479997634887695 z:54.277000427246094
      - residue HOH has 1 atoms
        - atom: O x: -1.1610000133514404 y:10.043000221252441 z:47.38800048828125
      - residue HOH has 1 atoms
        - atom: O x: 29.593000411987305 y:-14.854999542236328 z:40.95399856567383
      - residue HOH has 1 atoms
        - atom: O x: -12.48900032043457 y:5.578999996185303 z:53.430999755859375
      - residue HOH has 1 atoms
        - atom: O x: 12.057000160217285 y:2.822999954223633 z:36.19300079345703
      - residue HOH has 1 atoms
        - atom: O x: 27.393999099731445 y:-13.095000267028809 z:37.10499954223633
      - residue HOH has 1 atoms
        - atom: O x: -28.520000457763672 y:9.92199993133545 z:38.66999816894531
      - residue HOH has 1 atoms
        - atom: O x: -5.872000217437744 y:10.038999557495117 z:19.493999481201172
      - residue HOH has 1 atoms
        - atom: O x: 25.288000106811523 y:-19.02199935913086 z:24.20199966430664
      - residue HOH has 1 atoms
        - atom: O x: -3.128999948501587 y:-4.6519999504089355 z:39.78499984741211
      - residue HOH has 1 atoms
        - atom: O x: -15.873000144958496 y:-9.145000457763672 z:20.726999282836914
      - residue HOH has 1 atoms
        - atom: O x: -5.986999988555908 y:-5.311999797821045 z:55.07600021362305
      - residue HOH has 1 atoms
        - atom: O x: -22.631999969482422 y:-11.35200023651123 z:32.91999816894531
      - residue HOH has 1 atoms
        - atom: O x: 15.930000305175781 y:-11.468000411987305 z:48.625
      - residue HOH has 1 atoms
        - atom: O x: 10.845999717712402 y:10.20199966430664 z:45.08700180053711
      - residue HOH has 1 atoms
        - atom: O x: -1.7580000162124634 y:-6.790999889373779 z:39.04999923706055
      - residue HOH has 1 atoms
        - atom: O x: 0.8429999947547913 y:1.375 z:59.32500076293945
      - residue HOH has 1 atoms
        - atom: O x: -23.67099952697754 y:9.42199993133545 z:51.630001068115234
      - residue HOH has 1 atoms
        - atom: O x: -7.863999843597412 y:-7.434000015258789 z:35.81700134277344
      - residue HOH has 1 atoms
        - atom: O x: -14.73900032043457 y:-2.5480000972747803 z:57.404998779296875
      - residue HOH has 1 atoms
        - atom: O x: -12.61299991607666 y:-3.4010000228881836 z:56.3650016784668
      - residue HOH has 1 atoms
        - atom: O x: -12.157999992370605 y:14.347999572753906 z:9.017999649047852
      - residue HOH has 1 atoms
        - atom: O x: -10.178999900817871 y:16.46299934387207 z:7.783999919891357
      - residue HOH has 1 atoms
        - atom: O x: -26.187999725341797 y:1.3630000352859497 z:32.53200149536133
      - residue HOH has 1 atoms
        - atom: O x: -19.97100067138672 y:13.097999572753906 z:46.61899948120117
      - residue HOH has 1 atoms
        - atom: O x: 24.52400016784668 y:-18.415000915527344 z:41.80699920654297
      - residue HOH has 1 atoms
        - atom: O x: -18.277999877929688 y:-7.002999782562256 z:31.499000549316406
      - residue HOH has 1 atoms
        - atom: O x: -17.966999053955078 y:-11.64799976348877 z:31.121000289916992
      - residue HOH has 1 atoms
        - atom: O x: 19.69499969482422 y:-9.303000450134277 z:57.77000045776367
      - residue HOH has 1 atoms
        - atom: O x: 20.47800064086914 y:-7.195000171661377 z:55.983001708984375
      - residue HOH has 1 atoms
        - atom: O x: -20.400999069213867 y:-4.622000217437744 z:26.72800064086914
      - residue HOH has 1 atoms
        - atom: O x: -23.23699951171875 y:-3.7679998874664307 z:26.531999588012695
      - residue HOH has 1 atoms
        - atom: O x: -21.20199966430664 y:0.3619999885559082 z:21.589000701904297
      - residue HOH has 1 atoms
        - atom: O x: -1.5870000123977661 y:-0.9639999866485596 z:42.207000732421875
      - residue HOH has 1 atoms
        - atom: O x: -24.679000854492188 y:-1.2269999980926514 z:32.99100112915039
      - residue HOH has 1 atoms
        - atom: O x: -27.02199935913086 y:10.708000183105469 z:33.94599914550781
      - residue HOH has 1 atoms
        - atom: O x: 11.821000099182129 y:-2.0350000858306885 z:62.28200149536133
      - residue HOH has 1 atoms
        - atom: O x: 13.04800033569336 y:-3.318000078201294 z:60.446998596191406
      - residue HOH has 1 atoms
        - atom: O x: -16.23699951171875 y:-0.24300000071525574 z:10.319000244140625
      - residue HOH has 1 atoms
        - atom: O x: -18.378000259399414 y:4.208000183105469 z:55.77299880981445
      - residue HOH has 1 atoms
        - atom: O x: -17.55299949645996 y:3.2249999046325684 z:51.25199890136719
      - residue HOH has 1 atoms
        - atom: O x: 9.491000175476074 y:-6.734000205993652 z:43.38999938964844
      - residue HOH has 1 atoms
        - atom: O x: 23.27199935913086 y:-28.881000518798828 z:39.137001037597656
      - residue HOH has 1 atoms
        - atom: O x: -13.192999839782715 y:17.964000701904297 z:19.21299934387207
      - residue HOH has 1 atoms
        - atom: O x: 21.905000686645508 y:-4.89900016784668 z:35.422000885009766
      - residue HOH has 1 atoms
        - atom: O x: 2.9800000190734863 y:-5.75 z:44.49599838256836
      - residue HOH has 1 atoms
        - atom: O x: 4.548999786376953 y:-9.392000198364258 z:42.6619987487793
      - residue HOH has 1 atoms
        - atom: O x: 4.017000198364258 y:-12.059000015258789 z:46.9379997253418
      - residue HOH has 1 atoms
        - atom: O x: 6.761000156402588 y:-12.234000205993652 z:47.72800064086914
      - residue HOH has 1 atoms
        - atom: O x: 5.676000118255615 y:-16.034000396728516 z:45.32099914550781
      - residue HOH has 1 atoms
        - atom: O x: -7.611999988555908 y:-15.508000373840332 z:46.83700180053711
      - residue HOH has 1 atoms
        - atom: O x: 10.524999618530273 y:-10.456999778747559 z:40.52899932861328
      - residue HOH has 1 atoms
        - atom: O x: 6.034999847412109 y:-0.2840000092983246 z:30.01300048828125
      - residue HOH has 1 atoms
        - atom: O x: 7.501999855041504 y:-17.215999603271484 z:20.152000427246094
      - residue HOH has 1 atoms
        - atom: O x: 7.015999794006348 y:-19.85099983215332 z:17.801000595092773
      - residue HOH has 1 atoms
        - atom: O x: 10.140999794006348 y:-20.489999771118164 z:16.503999710083008
      - residue HOH has 1 atoms
        - atom: O x: -28.062999725341797 y:-9.74899959564209 z:39.11600112915039
      - residue HOH has 1 atoms
        - atom: O x: -13.135000228881836 y:6.835000038146973 z:48.64500045776367
      - residue HOH has 1 atoms
        - atom: O x: -12.461000442504883 y:13.706000328063965 z:21.788999557495117
      - residue HOH has 1 atoms
        - atom: O x: -21.52199935913086 y:-11.213000297546387 z:47.9640007019043
      - residue HOH has 1 atoms
        - atom: O x: -22.802000045776367 y:-13.795999526977539 z:49.27899932861328
      - residue HOH has 1 atoms
        - atom: O x: 17.39699935913086 y:-18.308000564575195 z:38.902000427246094
      - residue HOH has 1 atoms
        - atom: O x: 13.23799991607666 y:-16.785999298095703 z:38.619998931884766
      - residue HOH has 1 atoms
        - atom: O x: 11.210000038146973 y:-8.220000267028809 z:18.395999908447266
      - residue HOH has 1 atoms
        - atom: O x: -1.9579999446868896 y:10.479000091552734 z:54.09700012207031
      - residue HOH has 1 atoms
        - atom: O x: 18.85700035095215 y:-12.720999717712402 z:17.263999938964844

Once we have the coordinates of an atom we can compute distances between atoms or angles. We can also align two structures rototranslating the two to minimize their distance. We will not cover this and many other features that are provided by Biopython, such as Pyhlogentic analysis tools, interface towards pathways in KEGG, clustering, etc. If you are interested can find all the features available in the Biopython tutorial.

Exercises

1. Write a python script that retrieves all the information present in SRA regarding PacBio sequencing performed on E.coli strain K12 (query term is “E.coli K12 wgs PacBio”). Print the number of results and for each id report the title, the accession id, the total number of spots and total number of bases sequenced.

Sample output:

Entries found: 10
Results for id: 6705337
 - acc="SRR8154667"
 - total_spots="163482"
 - total_bases="1561717136"
Results for id: 6705336
 - acc="SRR8154668"
 - total_spots="163482"
 - total_bases="897324802"
Results for id: 6705335
 - acc="SRR8154669"
 - total_spots="163482"
 - total_bases="1570240924"

 ...
 ...

Show/Hide Solution

%reset -s -f

from Bio import Entrez

Entrez.email = "my_email"
handle = Entrez.esearch(db="sra", term="E.coli K12 wgs PacBio", retmax = 100)
res = Entrez.read(handle)
#uncomment to see all fields:
#for el in res.keys():
#    print(el , " : ", res[el])
print("Entries found: {}".format(res["Count"]))


for ids in res["IdList"]:
    print("Results for id:", ids)
    handle = Entrez.esummary(db="sra",  id = ids)
    res = Entrez.read(handle)
    #uncomment to see all info
    #print(res)
    for r in res:
        info = r['ExpXml']
        #print(info)
        runs = r['Runs']
        #some text parsing to do:
        title = info.split("Title>")
        #print(title)
        print(title[1][:-2])
        #print(runs)
        r = runs.split(" ")
        #print(r)
        print(" - {}\n - {}\n - {}".format(r[1],
                                           r[2],
                                           r[3]))

Entries found: 10
Results for id: 6705337
PacBio RSII sequencing of E. coli K12
 - acc="SRR8154667"
 - total_spots="163482"
 - total_bases="1561717136"
Results for id: 6705336
PacBio RSII sequencing of E. coli K12
 - acc="SRR8154668"
 - total_spots="163482"
 - total_bases="897324802"
Results for id: 6705335
PacBio RSII sequencing of E. coli K12
 - acc="SRR8154669"
 - total_spots="163482"
 - total_bases="1570240924"
Results for id: 6705329
PacBio RSII sequencing of E. coli K12
 - acc="SRR8154675"
 - total_spots="163482"
 - total_bases="1765639407"
Results for id: 357838
E. coli K12 PacBio RS C2 CCS sequencing
 - acc="SRR801672"
 - total_spots="81741"
 - total_bases="247537688"
Results for id: 357018
E. coli K12 MG1655 PacBio RS C2 Sequencing
 - acc="SRR797943"
 - total_spots="81741"
 - total_bases="207734764"
Results for id: 357016
E. Coli K12 454 Sequencing To Use For PacBio RS Correction
 - acc="SRR797242"
 - total_spots="1385764"
 - total_bases="720878709"
Results for id: 285699
WGA E. coli genome DNA sequenced by C2 chemistry (Null)
 - acc="SRR631042"
 - total_spots="81741"
 - total_bases="174897723"
Results for id: 285698
Native E. coli genome DNA sequenced by C2 chemistry
 - acc="SRR631040"
 - total_spots="81741"
 - total_bases="109074629"
Results for id: 285697
WGA E. coli genome DNA sequenced by FCR chemistry
 - acc="SRR644306"
 - total_spots="60667"
 - total_bases="26862325"

2. Write a python function that reads all the entries of a blast alignment file in .xml format (like blast_res_apple.xml and outputs all the HSPs (see example below) having bitscore > B, alignment length > A and minimum percentage of identity > I, where B, A and I are input thresholds. Hint: implement a filtering function: filterHSPs(align, minBitscore = 0, minAlignLen = 0, minPercIdent = 0.1).

Alignments of MDC020656.85
    MDC020656.85: 1939-2593
    gi|125995253|dbj|AB270792.1|: 201263-201917
    Score:820.917 AlignLen:579 Id/Len:0.8812785388127854
    MDC020656.85: 1446-1935
    gi|125995253|dbj|AB270792.1|: 306490-306017
    Score:582.873 AlignLen:428 Id/Len:0.8629032258064516
    ....
    ....

that is reporting the HSP with query start-end position, subject start-end position, score, alignment length and number of identities / alignment length.

Show/Hide Solution

%reset -s -f

from Bio.Blast import NCBIXML


def filterHSPs(align, minBitscore = 0, minAlignLen = 0, minPercIdent = 0.1):
    ret = []

    for h in align.hsps:
            b = h.bits
            i = h.identities
            al = h.align_length
            toOut = ((b > minBitscore) and
                    (al > minAlignLen) and
                    (i/al > minPercIdent))



            if(toOut):
                qs = h.query_start
                ss = h.sbjct_start
                qe = h.query_end
                se = h.sbjct_end
                ret.append([qs,qe, ss,se, b, i, al])

    return ret

result_handle = open("file_samples/blast_res_apple.xml")


for res in NCBIXML.parse(result_handle):
    print("Alignments of {}".format(res.query))
    for align in res.alignments:
        filtered = filterHSPs(align, 300, 50, 0.8)
        if(len(filtered) > 0):
            for h in filtered:
                title = align.title.split( )[0]
                print("\t{}: {}-{}".format(res.query,h[0],h[1]))
                print("\t{}: {}-{}".format(title,h[2],h[3]))
                print("\tScore:{} AlignLen:{} Id/Len:{}".format(
                                                                h[4],
                                                                h[5],
                                                                h[5]/h[6]
                                                               ))





result_handle.close()

Alignments of MDC020656.85
        MDC020656.85: 1939-2593
        gi|125995253|dbj|AB270792.1|: 201263-201917
        Score:820.917 AlignLen:579 Id/Len:0.8812785388127854
        MDC020656.85: 1446-1935
        gi|125995253|dbj|AB270792.1|: 306490-306017
        Score:582.873 AlignLen:428 Id/Len:0.8629032258064516
        MDC020656.85: 1447-1935
        gi|125995253|dbj|AB270792.1|: 202375-202869
        Score:543.199 AlignLen:424 Id/Len:0.848
        MDC020656.85: 1031-1475
        gi|125995253|dbj|AB270792.1|: 201861-202300
        Score:417.864 AlignLen:370 Id/Len:0.8078602620087336
Alignments of MDC001115.177
        MDC001115.177: 93-1292
        gi|125995253|dbj|AB270792.1|: 116873-118061
        Score:1196.92 AlignLen:1007 Id/Len:0.8186991869918699
        MDC001115.177: 2777-3118
        gi|125995253|dbj|AB270792.1|: 124753-125093
        Score:419.668 AlignLen:301 Id/Len:0.8775510204081632
Alignments of MDC013284.379
        MDC013284.379: 821-1195
        gi|1632177573|ref|XM_008340665.3|: 1263-1637
        Score:677.55 AlignLen:375 Id/Len:1.0
        MDC013284.379: 450-723
        gi|1632177573|ref|XM_008340665.3|: 994-1267
        Score:495.409 AlignLen:274 Id/Len:1.0
        MDC013284.379: 96-348
        gi|1632177573|ref|XM_008340665.3|: 746-998
        Score:457.539 AlignLen:253 Id/Len:1.0
        MDC013284.379: 823-1121
        gi|1632246347|ref|XM_029093378.1|: 1290-1588
        Score:450.325 AlignLen:279 Id/Len:0.9331103678929766
        MDC013284.379: 456-723
        gi|1632246347|ref|XM_029093378.1|: 1025-1292
        Score:398.929 AlignLen:249 Id/Len:0.9291044776119403
        MDC013284.379: 96-358
        gi|1632246347|ref|XM_029093378.1|: 759-1021
        Score:376.387 AlignLen:241 Id/Len:0.9163498098859315
        MDC013284.379: 3264-3519
        gi|1632172110|ref|XM_029088641.1|: 3-257
        Score:442.21 AlignLen:252 Id/Len:0.984375
        MDC013284.379: 4187-4398
        gi|1632172110|ref|XM_029088641.1|: 255-466
        Score:383.6 AlignLen:212 Id/Len:1.0
        MDC013284.379: 4477-4657
        gi|1632172110|ref|XM_029088641.1|: 463-643
        Score:327.696 AlignLen:181 Id/Len:1.0
        MDC013284.379: 4187-4398
        gi|1632172108|ref|XM_029088637.1|: 205-416
        Score:383.6 AlignLen:212 Id/Len:1.0
        MDC013284.379: 3312-3519
        gi|1632172108|ref|XM_029088637.1|: 1-207
        Score:355.648 AlignLen:204 Id/Len:0.9807692307692307
        MDC013284.379: 4477-4657
        gi|1632172108|ref|XM_029088637.1|: 413-593
        Score:327.696 AlignLen:181 Id/Len:1.0
        MDC013284.379: 4180-4398
        gi|1632172509|ref|XM_029089075.1|: 346-564
        Score:342.123 AlignLen:207 Id/Len:0.9452054794520548
        MDC013284.379: 4477-4657
        gi|1632172509|ref|XM_029089075.1|: 561-741
        Score:309.662 AlignLen:177 Id/Len:0.9779005524861878
        MDC013284.379: 4180-4398
        gi|1632172507|ref|XM_029089065.1|: 366-584
        Score:342.123 AlignLen:207 Id/Len:0.9452054794520548
        MDC013284.379: 4477-4657
        gi|1632172507|ref|XM_029089065.1|: 581-761
        Score:309.662 AlignLen:177 Id/Len:0.9779005524861878
        MDC013284.379: 4188-4398
        gi|1632172505|ref|XM_029089057.1|: 252-462
        Score:341.221 AlignLen:202 Id/Len:0.957345971563981
        MDC013284.379: 4477-4657
        gi|1632172505|ref|XM_029089057.1|: 459-639
        Score:309.662 AlignLen:177 Id/Len:0.9779005524861878
Alignments of MDC018185.243
        MDC018185.243: 19988-22671
        gi|1330174482|gb|KF530876.2|: 292955-295629
        Score:3686.47 AlignLen:2431 Id/Len:0.9043898809523809
        MDC018185.243: 20998-22671
        gi|1330174482|gb|KF530876.2|: 66778-65106
        Score:2140.08 AlignLen:1479 Id/Len:0.8835125448028673
        MDC018185.243: 19983-21003
        gi|1330174482|gb|KF530876.2|: 69724-68700
        Score:1150.03 AlignLen:873 Id/Len:0.8508771929824561
        MDC018185.243: 19988-20502
        gi|1330174482|gb|KF530876.2|: 301521-302035
        Score:710.01 AlignLen:465 Id/Len:0.9029126213592233
        MDC018185.243: 19988-20502
        gi|1330174482|gb|KF530876.2|: 138308-138818
        Score:704.6 AlignLen:465 Id/Len:0.9029126213592233
        MDC018185.243: 19988-20502
        gi|1330174482|gb|KF530876.2|: 55834-55319
        Score:672.139 AlignLen:458 Id/Len:0.8875968992248062
        MDC018185.243: 20211-20452
        gi|1330174482|gb|KF530876.2|: 147775-147534
        Score:370.977 AlignLen:227 Id/Len:0.9380165289256198
        MDC018185.243: 20211-20452
        gi|1330174482|gb|KF530876.2|: 342492-342251
        Score:370.977 AlignLen:227 Id/Len:0.9380165289256198
        MDC018185.243: 19988-22671
        gi|530721664|gb|KF530875.1|: 284755-287429
        Score:3686.47 AlignLen:2431 Id/Len:0.9043898809523809
        MDC018185.243: 20998-22671
        gi|530721664|gb|KF530875.1|: 66778-65106
        Score:2140.08 AlignLen:1479 Id/Len:0.8835125448028673
        MDC018185.243: 19983-21003
        gi|530721664|gb|KF530875.1|: 69724-68700
        Score:1150.03 AlignLen:873 Id/Len:0.8508771929824561
        MDC018185.243: 19988-20502
        gi|530721664|gb|KF530875.1|: 293321-293835
        Score:710.01 AlignLen:465 Id/Len:0.9029126213592233
        MDC018185.243: 19988-20502
        gi|530721664|gb|KF530875.1|: 138308-138818
        Score:706.404 AlignLen:465 Id/Len:0.9029126213592233
        MDC018185.243: 19988-20502
        gi|530721664|gb|KF530875.1|: 55834-55319
        Score:672.139 AlignLen:458 Id/Len:0.8875968992248062
        MDC018185.243: 20211-20452
        gi|530721664|gb|KF530875.1|: 147775-147534
        Score:372.78 AlignLen:227 Id/Len:0.9380165289256198
        MDC018185.243: 20211-20452
        gi|530721664|gb|KF530875.1|: 334292-334051
        Score:370.977 AlignLen:227 Id/Len:0.9380165289256198
        MDC018185.243: 19988-22671
        gi|1183577511|dbj|LC050646.1|: 76338-79012
        Score:3686.47 AlignLen:2431 Id/Len:0.9043898809523809
        MDC018185.243: 19988-20502
        gi|1183577511|dbj|LC050646.1|: 84903-85417
        Score:710.01 AlignLen:465 Id/Len:0.9029126213592233
        MDC018185.243: 20211-20452
        gi|1183577511|dbj|LC050646.1|: 125887-125646
        Score:370.977 AlignLen:227 Id/Len:0.9380165289256198
        MDC018185.243: 19988-22671
        gi|1183577509|dbj|LC050645.1|: 58043-60717
        Score:3686.47 AlignLen:2431 Id/Len:0.9043898809523809
        MDC018185.243: 19988-20502
        gi|1183577509|dbj|LC050645.1|: 66608-67122
        Score:710.01 AlignLen:465 Id/Len:0.9029126213592233
        MDC018185.243: 20211-20452
        gi|1183577509|dbj|LC050645.1|: 107592-107351
        Score:370.977 AlignLen:227 Id/Len:0.9380165289256198
        MDC018185.243: 19988-22671
        gi|571026231|emb|HF968765.1|: 83128-85802
        Score:3686.47 AlignLen:2431 Id/Len:0.9043898809523809
        MDC018185.243: 19988-20502
        gi|571026231|emb|HF968765.1|: 91693-92207
        Score:710.01 AlignLen:465 Id/Len:0.9029126213592233
        MDC018185.243: 20211-20452
        gi|571026231|emb|HF968765.1|: 132677-132436
        Score:370.977 AlignLen:227 Id/Len:0.9380165289256198
        MDC018185.243: 19988-22671
        gi|571026244|emb|HF968766.1|: 27097-29772
        Score:3663.03 AlignLen:2425 Id/Len:0.9021577380952381
        MDC018185.243: 19988-20502
        gi|571026244|emb|HF968766.1|: 35546-36060
        Score:710.01 AlignLen:465 Id/Len:0.9029126213592233
        MDC018185.243: 20211-20452
        gi|571026244|emb|HF968766.1|: 48521-48779
        Score:340.32 AlignLen:228 Id/Len:0.8803088803088803
        MDC018185.243: 19987-22187
        gi|125995253|dbj|AB270792.1|: 219104-221312
        Score:2290.66 AlignLen:1843 Id/Len:0.8324299909665763
        MDC018185.243: 19988-20502
        gi|125995253|dbj|AB270792.1|: 304541-304027
        Score:691.977 AlignLen:461 Id/Len:0.8951456310679612
        MDC018185.243: 19988-20502
        gi|125995253|dbj|AB270792.1|: 231533-232049
        Score:679.353 AlignLen:461 Id/Len:0.8916827852998066
        MDC018185.243: 20211-20502
        gi|125995253|dbj|AB270792.1|: 33979-34270
        Score:425.078 AlignLen:269 Id/Len:0.9212328767123288
        MDC018185.243: 20211-20452
        gi|125995253|dbj|AB270792.1|: 46757-46998
        Score:375.485 AlignLen:228 Id/Len:0.9421487603305785
        MDC018185.243: 10123-11112
        gi|1632238753|ref|XM_008392551.3|: 990-1
        Score:1786.62 AlignLen:990 Id/Len:1.0
        MDC018185.243: 7120-7915
        gi|1632238753|ref|XM_008392551.3|: 829-30
        Score:1171.67 AlignLen:746 Id/Len:0.9255583126550868
        MDC018185.243: 6844-7250
        gi|1632238753|ref|XM_008392551.3|: 990-577
        Score:551.314 AlignLen:373 Id/Len:0.894484412470024
        MDC018185.243: 10284-11129
        gi|1632247443|ref|XM_008389659.3|: 835-1
        Score:1227.58 AlignLen:782 Id/Len:0.9210836277974087
        MDC018185.243: 7034-7920
        gi|1632247443|ref|XM_008389659.3|: 921-43
        Score:1176.18 AlignLen:799 Id/Len:0.8907469342251951
        MDC018185.243: 10322-10536
        gi|1632247443|ref|XM_008389659.3|: 921-707
        Score:312.367 AlignLen:198 Id/Len:0.9209302325581395
        MDC018185.243: 19987-20963
        gi|117938437|gb|DQ886413.1|: 981-1
        Score:1098.64 AlignLen:833 Id/Len:0.8491335372069317
        MDC018185.243: 10413-11185
        gi|1632262963|ref|XM_008363755.3|: 769-2
        Score:946.252 AlignLen:680 Id/Len:0.8706786171574904
        MDC018185.243: 7251-7918
        gi|1632262963|ref|XM_008363755.3|: 770-104
        Score:801.08 AlignLen:586 Id/Len:0.8643067846607669
        MDC018185.243: 6277-6753
        gi|1632238751|ref|XM_008392549.3|: 527-1003
        Score:861.493 AlignLen:477 Id/Len:1.0
        MDC018185.243: 9579-10031
        gi|1632238751|ref|XM_008392549.3|: 543-1003
        Score:736.159 AlignLen:440 Id/Len:0.9544468546637744
        MDC018185.243: 4598-4897
        gi|1632238751|ref|XM_008392549.3|: 1-300
        Score:539.592 AlignLen:299 Id/Len:0.9966666666666667
        MDC018185.243: 19987-20502
        gi|313184264|emb|FN823234.1|: 66377-65862
        Score:734.356 AlignLen:471 Id/Len:0.9127906976744186
        MDC018185.243: 19990-20505
        gi|313184264|emb|FN823234.1|: 64635-65166
        Score:699.19 AlignLen:472 Id/Len:0.8838951310861424
        MDC018185.243: 19988-20502
        gi|114199045|gb|DQ886019.1|: 1826-2338
        Score:711.814 AlignLen:466 Id/Len:0.9048543689320389
        MDC018185.243: 19988-20502
        gi|114199049|gb|DQ886021.1|: 1342-1870
        Score:698.288 AlignLen:469 Id/Len:0.8865784499054821
        MDC018185.243: 3417-3881
        gi|1632263306|ref|XM_029096579.1|: 468-9
        Score:628.859 AlignLen:420 Id/Len:0.8993576017130621
        MDC018185.243: 19987-20453
        gi|1227417682|gb|KX822762.1|: 468-1
        Score:617.137 AlignLen:417 Id/Len:0.8910256410256411
        MDC018185.243: 12968-13397
        gi|1632255190|ref|XR_003769783.1|: 3194-2754
        Score:499.016 AlignLen:379 Id/Len:0.8574660633484162
        MDC018185.243: 17934-18409
        gi|1632228214|ref|XR_003766910.1|: 1322-1795
        Score:426.881 AlignLen:387 Id/Len:0.80625
        MDC018185.243: 20211-20452
        gi|313184297|emb|FN823235.1|: 121925-122166
        Score:379.994 AlignLen:229 Id/Len:0.9462809917355371
        MDC018185.243: 20211-20452
        gi|313184297|emb|FN823235.1|: 5080-5321
        Score:352.943 AlignLen:223 Id/Len:0.9214876033057852
        MDC018185.243: 20211-20452
        gi|339431357|gb|HQ445899.1|: 69560-69801
        Score:370.977 AlignLen:227 Id/Len:0.9380165289256198
        MDC018185.243: 20211-20452
        gi|86438843|emb|AM167520.1|: 28866-29107
        Score:370.977 AlignLen:227 Id/Len:0.9380165289256198
        MDC018185.243: 20211-20452
        gi|86438843|emb|AM167520.1|: 38530-38289
        Score:370.977 AlignLen:227 Id/Len:0.9380165289256198
        MDC018185.243: 18146-18425
        gi|1632218186|ref|XR_003776530.1|: 344-624
        Score:348.435 AlignLen:246 Id/Len:0.8754448398576512
        MDC018185.243: 18131-18425
        gi|1632219812|ref|XR_003776654.1|: 430-723
        Score:336.713 AlignLen:254 Id/Len:0.8581081081081081
        MDC018185.243: 18131-18425
        gi|1632219810|ref|XR_003776652.1|: 659-952
        Score:336.713 AlignLen:254 Id/Len:0.8581081081081081
        MDC018185.243: 20211-20452
        gi|541903978|gb|KF055410.1|: 30953-31211
        Score:335.811 AlignLen:227 Id/Len:0.8764478764478765
        MDC018185.243: 1035-1376
        gi|1632268443|ref|XR_001790922.2|: 431-84
        Score:324.089 AlignLen:286 Id/Len:0.8125
        MDC018185.243: 1035-1342
        gi|1632198832|ref|XR_003774309.1|: 355-49
        Score:317.778 AlignLen:258 Id/Len:0.8349514563106796
        MDC018185.243: 18130-18436
        gi|1632207113|ref|XR_003775191.1|: 469-777
        Score:306.957 AlignLen:255 Id/Len:0.8225806451612904
Alignments of MDC018185.241
        MDC018185.241: 1952-3265
        gi|1632261394|ref|XM_008342019.3|: 1314-1
        Score:2350.17 AlignLen:1311 Id/Len:0.996958174904943
        MDC018185.241: 1952-3399
        gi|1632240204|ref|XM_008391913.3|: 1448-22
        Score:1505.3 AlignLen:1236 Id/Len:0.8218085106382979
        MDC018185.241: 10688-11460
        gi|1632257016|ref|XM_017323798.2|: 929-160
        Score:1330.37 AlignLen:759 Id/Len:0.981888745148771
        MDC018185.241: 9977-10496
        gi|1632257016|ref|XM_017323798.2|: 1421-902
        Score:928.218 AlignLen:516 Id/Len:0.9923076923076923
        MDC018185.241: 10688-11454
        gi|1632257020|ref|XM_029095849.1|: 907-144
        Score:1319.55 AlignLen:753 Id/Len:0.9817470664928292
        MDC018185.241: 9977-10496
        gi|1632257020|ref|XM_029095849.1|: 1399-880
        Score:928.218 AlignLen:516 Id/Len:0.9923076923076923
        MDC018185.241: 10688-11409
        gi|1632257018|ref|XM_008342020.3|: 878-160
        Score:1241.1 AlignLen:709 Id/Len:0.981994459833795
        MDC018185.241: 9977-10496
        gi|1632257018|ref|XM_008342020.3|: 1370-851
        Score:928.218 AlignLen:516 Id/Len:0.9923076923076923
        MDC018185.241: 10686-11459
        gi|1632240978|ref|XM_008391689.3|: 886-123
        Score:936.333 AlignLen:674 Id/Len:0.8696774193548387
        MDC018185.241: 10214-10496
        gi|1632240978|ref|XM_008391689.3|: 1128-857
        Score:330.401 AlignLen:243 Id/Len:0.8526315789473684
        MDC018185.241: 22418-23085
        gi|1632220941|ref|XR_003776790.1|: 723-22
        Score:807.392 AlignLen:598 Id/Len:0.844632768361582
        MDC018185.241: 18138-18558
        gi|1632263230|ref|XM_008342179.2|: 351-771
        Score:746.078 AlignLen:417 Id/Len:0.9904988123515439
        MDC018185.241: 5323-5766
        gi|1632233144|ref|XR_003767438.1|: 458-902
        Score:630.662 AlignLen:408 Id/Len:0.912751677852349
        MDC018185.241: 12707-13182
        gi|1632266554|ref|XM_017328275.2|: 4-475
        Score:618.94 AlignLen:426 Id/Len:0.8930817610062893
        MDC018185.241: 12979-13399
        gi|1632238051|ref|XM_008391090.3|: 166-581
        Score:426.881 AlignLen:350 Id/Len:0.8293838862559242
        MDC018185.241: 21727-22114
        gi|1632209355|ref|XR_003775372.1|: 1708-1317
        Score:414.258 AlignLen:331 Id/Len:0.8275
        MDC018185.241: 5340-5765
        gi|1632267776|ref|XR_003770870.1|: 1717-1294
        Score:396.224 AlignLen:355 Id/Len:0.8179723502304147

3. Write a python function retrieve_sequences(search_term, number, outfile) that retrieves the first number of sequences from NCBI’s “nucleotide” database having a search term term (hint: use term and retmax parameters of Entrez.esearch) and stores them in a fasta file outfile (hint: use SeqIO.write). Test your code retrieving the first 5 entries having search term “starch AND Malus Domestica [Organism]”

Show/Hide Solution

%reset -s -f

from Bio import Entrez
from Bio import SeqIO

def retrieve_sequences(search_term, number, filename):
    Entrez.email = "my_email"
    handle = Entrez.esearch(db="nucleotide",
                            term=search_term,
                            retmax=5)
    res = Entrez.read(handle)
    records = []
    for el in res["IdList"]:
        handle = Entrez.efetch(db="nucleotide",
                               id=el,
                               rettype = "gb",
                               retmode="text")
        my_seq = SeqIO.read(handle, format = "genbank")
        records.append(my_seq)
    N = SeqIO.write(records, filename, "fasta")
    print("Search term was: ", search_term)
    print("{} sequences written to {}".format(N,filename))

s_term = "starch AND Malus Domestica [Organism]"
retrieve_sequences(s_term, 5, "file_samples/starch_sequences.fasta")

Search term was:  starch AND Malus Domestica [Organism]
5 sequences written to file_samples/starch_sequences.fasta

4. Write a python function that aligns the sequences in the file created in exercise 3. (here you can find mine) against the NCBI nr database limiting the hits to the Malus Domestica organism (parameter entrez_query=‘“Malus Domestica” [Organism]’ in qblast)and prints to screen the following info for each hsp:
   1. The title;
   2. Score and e-value;
   3. The number of alignments on the same subject, the number of identities and positives and the alignment length;
   4. The number of mismatches and the list of their positions (hint: you can use the match string and look for ” “).

Show/Hide Solution

from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML

fasta_string = open("file_samples/starch_sequences.fasta").read()

res_handle = NCBIWWW.qblast("blastn", "nt", fasta_string,
                            entrez_query='"Malus Domestica" [Organism]'
                           )

for align in NCBIXML.parse(res_handle):

    for a in align.alignments:
            print("Align Title:{}".format(a.title))

            for h in a.hsps:
                s = h.score
                e = h.expect
                n = h.num_alignments
                i = h.identities
                p = h.positives
                m = h.match
                al = h.align_length
                misM = [str(x) for x in range(len(m)) if m[x] == " "]
                print("Score: {} E-val: {}".format(s,e))
                print("N.aligns:{} Ident:{} Pos.:{} Align len:{}".format(
                    n,i,p,al))
                if(len(misM)):
                    print("Num mismatches:",len(misM))
                    print("Mismatch pos:", ",".join(misM))
                else:
                    print("No mismatches")
                print("")


res_handle.close()

Align Title:gi|1040975204|ref|NM_001328845.1| Malus domestica glucose-1-phosphate adenylyltransferase small subunit, chloroplastic/amyloplastic (LOC103421714), mRNA >gi|295684200|gb|GU983663.1| Malus x domestica ADP glucose pyrophosphorylase small subunit 1-like protein mRNA, complete cds
Score: 3630.0 E-val: 0.0
N.aligns:None Ident:1815 Pos.:1815 Align len:1815
No mismatches

Align Title:gi|1632214376|ref|XM_029108108.1| PREDICTED: Malus domestica glucose-1-phosphate adenylyltransferase small subunit, chloroplastic/amyloplastic (LOC103421714), mRNA
Score: 3390.0 E-val: 0.0
N.aligns:None Ident:1767 Pos.:1767 Align len:1815
Num mismatches: 48
Mismatch pos: 8,16,17,18,19,21,28,31,47,51,56,58,71,72,74,91,104,106,110,128,134,162,167,180,187,190,191,198,221,227,230,254,302,338,341,428,431,521,602,641,662,665,688,701,758,914,1531,1811

Align Title:gi|1632265869|ref|XM_008344054.3| PREDICTED: Malus domestica glucose-1-phosphate adenylyltransferase small subunit, chloroplastic/amyloplastic (LOC103405088), transcript variant X1, mRNA
Score: 3290.0 E-val: 0.0
N.aligns:None Ident:1749 Pos.:1749 Align len:1818
Num mismatches: 69
Mismatch pos: 824,860,867,942,1031,1044,1122,1157,1190,1277,1295,1367,1371,1376,1382,1388,1394,1412,1445,1457,1477,1583,1584,1585,1589,1610,1614,1615,1617,1622,1632,1633,1649,1650,1651,1652,1653,1654,1655,1656,1657,1658,1659,1660,1661,1663,1670,1671,1681,1683,1686,1696,1709,1713,1719,1733,1745,1749,1762,1763,1764,1765,1766,1774,1775,1788,1790,1804,1814

Align Title:gi|1632265871|ref|XR_003770676.1| PREDICTED: Malus domestica glucose-1-phosphate adenylyltransferase small subunit, chloroplastic/amyloplastic (LOC103405088), transcript variant X2, misc_RNA
Score: 2455.0 E-val: 0.0
N.aligns:None Ident:1241 Pos.:1241 Align len:1250
Num mismatches: 9
Mismatch pos: 824,860,867,942,1031,1044,1122,1157,1190

Score: 843.0 E-val: 0.0
N.aligns:None Ident:512 Pos.:512 Align len:572
Num mismatches: 60
Mismatch pos: 31,49,121,125,130,136,142,148,166,199,211,231,337,338,339,343,364,368,369,371,376,386,387,403,404,405,406,407,408,409,410,411,412,413,414,415,417,424,425,435,437,440,450,463,467,473,487,499,503,516,517,518,519,520,528,529,542,544,558,568

Align Title:gi|1632255889|ref|XM_008342710.3| PREDICTED: Malus domestica glucose-1-phosphate adenylyltransferase large subunit 3, chloroplastic/amyloplastic (LOC103403858), mRNA
Score: 140.0 E-val: 9.46061e-28
N.aligns:None Ident:423 Pos.:423 Align len:651
Num mismatches: 228
Mismatch pos: 2,5,11,14,20,26,27,34,39,41,49,56,59,72,74,75,76,84,85,86,98,102,108,110,116,120,128,129,130,131,132,134,135,136,140,141,143,147,149,152,155,164,167,170,173,179,180,182,185,186,191,192,194,200,201,202,203,204,205,207,208,211,212,215,216,217,220,222,223,224,225,226,227,230,233,235,239,248,251,254,255,256,257,260,262,263,267,268,269,273,274,275,276,277,278,280,281,283,284,290,299,302,311,312,314,317,319,321,322,323,327,329,332,338,342,343,344,345,346,350,352,353,354,356,357,358,362,363,365,366,369,374,375,377,380,393,395,404,405,406,408,410,412,413,414,419,420,421,422,428,429,431,433,436,437,440,443,446,449,450,452,453,456,457,459,464,473,475,476,479,482,483,485,487,495,506,509,510,512,513,515,522,524,525,527,529,531,533,534,537,540,543,552,555,556,558,561,564,567,571,572,573,576,582,585,586,588,594,598,599,600,602,603,607,608,613,614,616,620,621,624,627,633,634,635,642,643,645

Score: 42.0 E-val: 0.3771
N.aligns:None Ident:33 Pos.:33 Align len:41
Num mismatches: 8
Mismatch pos: 8,10,11,12,16,17,29,35

Align Title:gi|1632239043|ref|XM_029091606.1| PREDICTED: Malus domestica glucose-1-phosphate adenylyltransferase large subunit 3, chloroplastic/amyloplastic (LOC103453087), mRNA
Score: 127.0 E-val: 5.9703e-24
N.aligns:None Ident:131 Pos.:131 Align len:176
Num mismatches: 45
Mismatch pos: 2,5,11,14,23,26,27,34,39,41,49,56,59,72,74,79,81,82,83,95,99,101,105,107,113,117,125,126,127,128,129,131,132,133,137,138,140,144,146,149,152,161,164,167,170

Score: 68.0 E-val: 3.305e-08
N.aligns:None Ident:237 Pos.:237 Align len:366
Num mismatches: 129
Mismatch pos: 5,14,17,26,34,36,37,38,42,44,53,57,58,59,60,61,65,67,68,69,71,74,75,78,80,81,84,89,90,92,95,108,110,119,120,121,123,125,127,128,129,134,135,136,137,140,143,144,146,148,149,151,152,158,161,164,165,167,168,171,172,174,176,179,188,190,191,194,197,198,200,202,203,206,210,221,224,225,227,228,237,239,240,242,244,246,248,249,252,255,258,264,267,270,271,273,276,279,282,286,287,288,291,297,300,301,303,309,313,314,315,317,318,322,323,328,329,330,331,335,336,339,342,348,349,350,357,358,360

Align Title:gi|1632170348|ref|XM_029108064.1| PREDICTED: Malus domestica inactive glucose-1-phosphate adenylyltransferase small subunit 2, chloroplastic-like (LOC103446459), mRNA
Score: 114.0 E-val: 1.07946e-20
N.aligns:None Ident:244 Pos.:244 Align len:368
Num mismatches: 124
Mismatch pos: 6,15,18,22,23,24,25,26,27,30,33,36,40,42,44,52,54,55,56,58,60,63,66,68,69,72,75,78,81,84,87,88,93,100,101,105,111,112,114,120,121,124,126,127,128,129,131,132,134,139,140,141,142,143,144,145,146,147,148,154,164,166,169,170,175,178,179,181,192,193,197,198,200,201,202,214,217,220,226,233,234,235,237,238,239,245,248,250,253,259,260,266,267,269,270,273,282,286,291,292,294,298,300,303,306,315,316,321,322,324,327,328,333,336,337,342,344,345,348,351,357,360,361,363

Score: 84.0 E-val: 1.50047e-12
N.aligns:None Ident:90 Pos.:90 Align len:122
Num mismatches: 32
Mismatch pos: 8,12,13,14,23,29,32,35,37,38,41,47,48,52,66,67,68,70,77,80,86,89,90,92,93,95,97,98,102,104,114,116

Align Title:gi|1632253863|ref|XM_008389820.3| PREDICTED: Malus domestica glucose-1-phosphate adenylyltransferase large subunit, chloroplastic/amyloplastic-like (LOC103450465), mRNA
Score: 105.0 E-val: 5.59172e-18
N.aligns:None Ident:497 Pos.:497 Align len:786
Num mismatches: 289
Mismatch pos: 4,5,9,11,14,20,23,29,30,32,37,38,39,40,41,53,63,65,68,75,77,83,84,85,87,89,90,91,92,98,100,101,102,104,105,107,110,113,115,116,119,122,123,124,128,137,140,144,150,155,156,157,158,160,162,163,165,166,169,173,176,177,180,181,183,184,185,186,189,192,198,205,207,214,215,219,221,222,225,227,232,234,235,236,238,239,240,241,242,243,249,252,255,258,261,267,270,273,276,278,279,280,282,286,288,297,298,299,300,301,302,304,309,310,311,316,317,319,321,322,324,325,328,330,331,333,334,336,339,346,348,364,365,367,369,375,379,380,381,386,387,390,393,394,399,405,408,411,412,414,415,416,418,420,432,434,435,438,441,442,444,446,447,449,450,453,454,456,462,465,468,469,471,472,473,474,477,478,480,483,486,487,489,498,504,510,511,512,513,514,516,519,520,525,529,531,537,540,544,546,547,552,556,557,562,563,565,569,570,571,573,576,579,580,592,593,594,595,602,604,610,611,613,616,618,619,620,626,628,629,631,632,634,638,640,641,643,644,645,646,648,649,651,656,657,659,660,661,670,673,674,675,676,679,680,689,690,691,692,695,698,699,700,702,703,705,706,707,708,709,711,712,715,718,721,727,729,730,731,735,745,754,757,758,760,761,764,771,773

Align Title:gi|1632247379|ref|XM_008338947.3| PREDICTED: Malus domestica inactive glucose-1-phosphate adenylyltransferase small subunit 2, chloroplastic-like (LOC103400295), mRNA
Score: 104.0 E-val: 5.59172e-18
N.aligns:None Ident:233 Pos.:233 Align len:354
Num mismatches: 121
Mismatch pos: 6,15,18,22,23,24,25,26,27,30,33,36,40,42,44,52,54,55,56,58,60,63,68,69,72,75,79,81,84,87,88,93,100,101,105,111,112,114,120,121,124,126,127,128,129,130,131,132,134,139,140,141,142,143,144,150,160,163,165,166,171,174,175,177,186,188,189,193,194,197,198,210,213,216,222,229,230,231,233,234,235,241,244,246,249,253,255,256,257,258,262,263,264,267,276,280,282,285,286,288,292,294,297,300,309,310,315,316,318,321,322,323,325,330,331,336,338,341,342,345,351

Score: 70.0 E-val: 9.46897e-09
N.aligns:None Ident:86 Pos.:86 Align len:120
Num mismatches: 34
Mismatch pos: 6,10,11,12,21,27,30,33,35,36,39,40,42,45,46,50,64,65,66,68,75,78,84,87,90,91,93,95,96,100,102,105,112,114

Align Title:gi|1632219716|ref|XM_008379059.3| PREDICTED: Malus domestica glucose-1-phosphate adenylyltransferase large subunit 1-like (LOC103440384), transcript variant X2, mRNA
Score: 102.0 E-val: 1.9517e-17
N.aligns:None Ident:345 Pos.:345 Align len:528
Num mismatches: 183
Mismatch pos: 4,5,8,11,14,18,20,25,27,28,33,38,41,44,47,51,53,56,59,63,74,75,77,78,79,80,86,88,89,92,98,104,110,116,128,129,132,137,138,140,144,145,147,149,153,154,155,159,160,162,165,166,167,168,169,170,173,176,182,188,191,194,198,199,200,203,205,208,209,210,212,216,218,219,220,221,222,223,224,233,236,239,242,245,251,257,260,262,263,264,266,270,272,280,281,282,283,284,285,288,292,293,294,295,301,306,308,309,312,315,317,318,323,330,332,336,338,344,348,349,351,353,357,359,363,364,365,369,370,371,374,376,377,378,383,386,389,392,393,395,396,398,401,402,404,406,408,409,413,417,419,420,423,426,427,429,431,432,434,438,442,450,453,454,456,462,465,466,469,472,473,484,490,491,501,502,504,507,513,517,519,521,522

Score: 59.0 E-val: 1.71203e-05
N.aligns:None Ident:133 Pos.:133 Align len:202
Num mismatches: 69
Mismatch pos: 2,10,13,19,22,23,25,31,32,37,39,40,41,42,43,46,49,50,51,54,56,58,61,63,64,67,73,82,84,85,89,91,92,94,98,102,103,104,105,124,125,127,130,133,134,136,137,139,142,144,148,149,151,154,156,157,160,161,162,166,177,178,181,182,183,185,186,195,198

Align Title:gi|1632219715|ref|XM_008379058.3| PREDICTED: Malus domestica glucose-1-phosphate adenylyltransferase large subunit 1-like (LOC103440384), transcript variant X1, mRNA
Score: 102.0 E-val: 1.9517e-17
N.aligns:None Ident:345 Pos.:345 Align len:528
Num mismatches: 183
Mismatch pos: 4,5,8,11,14,18,20,25,27,28,33,38,41,44,47,51,53,56,59,63,74,75,77,78,79,80,86,88,89,92,98,104,110,116,128,129,132,137,138,140,144,145,147,149,153,154,155,159,160,162,165,166,167,168,169,170,173,176,182,188,191,194,198,199,200,203,205,208,209,210,212,216,218,219,220,221,222,223,224,233,236,239,242,245,251,257,260,262,263,264,266,270,272,280,281,282,283,284,285,288,292,293,294,295,301,306,308,309,312,315,317,318,323,330,332,336,338,344,348,349,351,353,357,359,363,364,365,369,370,371,374,376,377,378,383,386,389,392,393,395,396,398,401,402,404,406,408,409,413,417,419,420,423,426,427,429,431,432,434,438,442,450,453,454,456,462,465,466,469,472,473,484,490,491,501,502,504,507,513,517,519,521,522

Score: 59.0 E-val: 1.71203e-05
N.aligns:None Ident:133 Pos.:133 Align len:202
Num mismatches: 69
Mismatch pos: 2,10,13,19,22,23,25,31,32,37,39,40,41,42,43,46,49,50,51,54,56,58,61,63,64,67,73,82,84,85,89,91,92,94,98,102,103,104,105,124,125,127,130,133,134,136,137,139,142,144,148,149,151,154,156,157,160,161,162,166,177,178,181,182,183,185,186,195,198

Align Title:gi|1632207701|ref|XM_029106623.1| PREDICTED: Malus domestica glucose-1-phosphate adenylyltransferase large subunit, chloroplastic/amyloplastic-like (LOC114826430), transcript variant X2, mRNA
Score: 98.0 E-val: 2.37766e-16
N.aligns:None Ident:519 Pos.:519 Align len:823
Num mismatches: 304
Mismatch pos: 7,10,13,16,19,20,22,25,27,28,31,32,34,39,40,44,46,49,55,58,64,65,67,72,73,74,75,76,88,98,100,103,110,112,118,119,120,122,124,125,126,127,133,135,136,137,139,140,142,145,148,150,151,154,157,158,159,163,172,175,179,185,191,192,193,195,197,198,200,201,204,208,211,212,215,216,218,219,220,221,224,227,233,240,242,249,250,251,252,253,254,255,258,262,265,267,271,275,276,277,278,280,281,287,290,293,296,299,305,308,311,314,316,317,318,320,324,326,329,335,336,337,338,339,340,342,347,348,349,355,357,360,362,363,364,366,368,371,372,374,377,384,386,389,402,403,405,407,413,417,418,419,424,425,428,431,432,437,443,446,449,450,452,453,454,456,458,470,472,473,476,479,480,482,484,485,487,488,491,492,494,500,503,506,507,509,510,511,512,515,516,518,521,524,525,527,536,542,548,550,551,552,554,557,558,563,567,569,575,578,582,584,585,590,594,595,600,601,603,604,605,610,611,612,614,615,616,617,629,630,631,632,639,641,647,648,650,653,655,656,657,663,665,666,669,671,675,677,678,680,681,682,683,685,686,688,693,694,696,697,698,707,710,711,712,713,716,717,726,727,728,729,732,735,736,737,739,740,742,743,744,745,746,748,749,752,755,758,761,764,766,767,768,772,782,791,794,795,797,798,801,808,809,810

Align Title:gi|1632207699|ref|XM_029106622.1| PREDICTED: Malus domestica glucose-1-phosphate adenylyltransferase large subunit, chloroplastic/amyloplastic-like (LOC114826430), transcript variant X1, mRNA
Score: 98.0 E-val: 2.37766e-16
N.aligns:None Ident:519 Pos.:519 Align len:823
Num mismatches: 304
Mismatch pos: 7,10,13,16,19,20,22,25,27,28,31,32,34,39,40,44,46,49,55,58,64,65,67,72,73,74,75,76,88,98,100,103,110,112,118,119,120,122,124,125,126,127,133,135,136,137,139,140,142,145,148,150,151,154,157,158,159,163,172,175,179,185,191,192,193,195,197,198,200,201,204,208,211,212,215,216,218,219,220,221,224,227,233,240,242,249,250,251,252,253,254,255,258,262,265,267,271,275,276,277,278,280,281,287,290,293,296,299,305,308,311,314,316,317,318,320,324,326,329,335,336,337,338,339,340,342,347,348,349,355,357,360,362,363,364,366,368,371,372,374,377,384,386,389,402,403,405,407,413,417,418,419,424,425,428,431,432,437,443,446,449,450,452,453,454,456,458,470,472,473,476,479,480,482,484,485,487,488,491,492,494,500,503,506,507,509,510,511,512,515,516,518,521,524,525,527,536,542,548,550,551,552,554,557,558,563,567,569,575,578,582,584,585,590,594,595,600,601,603,604,605,610,611,612,614,615,616,617,629,630,631,632,639,641,647,648,650,653,655,656,657,663,665,666,669,671,675,677,678,680,681,682,683,685,686,688,693,694,696,697,698,707,710,711,712,713,716,717,726,727,728,729,732,735,736,737,739,740,742,743,744,745,746,748,749,752,755,758,761,764,766,767,768,772,782,791,794,795,797,798,801,808,809,810

Align Title:gi|1632193374|ref|XM_029103016.1| PREDICTED: Malus domestica putative cyclin-B3-1 (LOC103409736), transcript variant X1, mRNA
Score: 50.0 E-val: 0.00254088
N.aligns:None Ident:41 Pos.:41 Align len:51
Num mismatches: 10
Mismatch pos: 7,8,9,22,23,28,32,34,43,48

Align Title:gi|1632236059|ref|XM_008390912.3| PREDICTED: Malus domestica cyclin-J18 (LOC103451508), mRNA
Score: 44.0 E-val: 0.108041
N.aligns:None Ident:50 Pos.:50 Align len:65
Num mismatches: 15
Mismatch pos: 11,12,13,20,23,27,29,31,37,39,46,47,49,54,55

Align Title:gi|1632255893|ref|XM_029095576.1| PREDICTED: Malus domestica DEAD-box ATP-dependent RNA helicase 58, chloroplastic (LOC103416842), transcript variant X2, mRNA
Score: 43.0 E-val: 0.3771
N.aligns:None Ident:35 Pos.:35 Align len:44
Num mismatches: 9
Mismatch pos: 2,11,13,14,15,19,20,32,38

Score: 39.0 E-val: 4.59402
N.aligns:None Ident:30 Pos.:30 Align len:37
Num mismatches: 7
Mismatch pos: 2,7,8,10,13,26,28

Align Title:gi|1632255891|ref|XM_029095575.1| PREDICTED: Malus domestica DEAD-box ATP-dependent RNA helicase 58, chloroplastic (LOC103416842), transcript variant X1, mRNA
Score: 43.0 E-val: 0.3771
N.aligns:None Ident:35 Pos.:35 Align len:44
Num mismatches: 9
Mismatch pos: 2,11,13,14,15,19,20,32,38

Align Title:gi|1632189520|ref|XM_029102026.1| PREDICTED: Malus domestica glucose-1-phosphate adenylyltransferase large subunit 1-like (LOC103448413), transcript variant X2, mRNA
Score: 43.0 E-val: 0.3771
N.aligns:None Ident:132 Pos.:132 Align len:203
Num mismatches: 71
Mismatch pos: 2,10,17,19,22,23,25,28,31,32,37,39,40,41,42,43,45,49,50,51,56,58,62,65,68,74,77,83,85,86,90,92,93,95,103,104,105,106,107,113,125,126,127,128,131,134,135,137,138,140,145,149,150,152,155,157,158,161,162,163,164,167,178,179,182,183,184,186,187,196,199

Align Title:gi|1632189519|ref|XM_008387677.3| PREDICTED: Malus domestica glucose-1-phosphate adenylyltransferase large subunit 1-like (LOC103448413), transcript variant X1, mRNA
Score: 43.0 E-val: 0.3771
N.aligns:None Ident:132 Pos.:132 Align len:203
Num mismatches: 71
Mismatch pos: 2,10,17,19,22,23,25,28,31,32,37,39,40,41,42,43,45,49,50,51,56,58,62,65,68,74,77,83,85,86,90,92,93,95,103,104,105,106,107,113,125,126,127,128,131,134,135,137,138,140,145,149,150,152,155,157,158,161,162,163,164,167,178,179,182,183,184,186,187,196,199

Align Title:gi|1632212049|ref|XM_029107614.1| PREDICTED: Malus domestica probable alpha-mannosidase At5g13980 (LOC103442701), mRNA
Score: 42.0 E-val: 0.3771
N.aligns:None Ident:27 Pos.:27 Align len:31
Num mismatches: 4
Mismatch pos: 3,15,17,26

Align Title:gi|1632171654|ref|XM_008388982.3| PREDICTED: Malus domestica protein phosphatase 1 regulatory inhibitor subunit PPP1R7 homolog (LOC103449645), transcript variant X2, mRNA
Score: 42.0 E-val: 0.3771
N.aligns:None Ident:24 Pos.:24 Align len:26
Num mismatches: 2
Mismatch pos: 11,12

Align Title:gi|1632171652|ref|XM_008388975.3| PREDICTED: Malus domestica protein phosphatase 1 regulatory inhibitor subunit PPP1R7 homolog (LOC103449645), transcript variant X1, mRNA
Score: 42.0 E-val: 0.3771
N.aligns:None Ident:24 Pos.:24 Align len:26
Num mismatches: 2
Mismatch pos: 11,12

Align Title:gi|1632245134|ref|XM_008362507.2| PREDICTED: Malus domestica trihelix transcription factor GTL1-like (LOC103424425), transcript variant X2, mRNA
Score: 40.0 E-val: 1.31621
N.aligns:None Ident:29 Pos.:29 Align len:35
Num mismatches: 6
Mismatch pos: 2,9,11,12,20,23

Align Title:gi|1632245132|ref|XM_008362506.2| PREDICTED: Malus domestica trihelix transcription factor GTL1-like (LOC103424425), transcript variant X1, mRNA
Score: 40.0 E-val: 1.31621
N.aligns:None Ident:29 Pos.:29 Align len:35
Num mismatches: 6
Mismatch pos: 2,9,11,12,20,23

Align Title:gi|1632251859|ref|XM_029094697.1| PREDICTED: Malus domestica ankyrin repeat-containing protein BDA1-like (LOC103400846), mRNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 14

Align Title:gi|1632226737|ref|XM_008387075.3| PREDICTED: Malus domestica beta-galactosidase 8-like (LOC103447870), mRNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:29 Pos.:29 Align len:34
Num mismatches: 5
Mismatch pos: 3,8,26,27,28

Align Title:gi|1632215401|ref|XM_008362221.3| PREDICTED: Malus domestica dentin sialophosphoprotein (LOC103424144), mRNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:27 Pos.:27 Align len:32
Num mismatches: 5
Mismatch pos: 4,6,9,23,26

Align Title:gi|1632209843|ref|XR_003775517.1| PREDICTED: Malus domestica uncharacterized LOC108170672 (LOC108170672), transcript variant X42, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 5

Align Title:gi|1632209842|ref|XR_003775516.1| PREDICTED: Malus domestica uncharacterized LOC108170672 (LOC108170672), transcript variant X41, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 5

Align Title:gi|1632209839|ref|XR_003775513.1| PREDICTED: Malus domestica uncharacterized LOC108170672 (LOC108170672), transcript variant X38, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 5

Align Title:gi|1632209837|ref|XR_003775511.1| PREDICTED: Malus domestica uncharacterized LOC108170672 (LOC108170672), transcript variant X36, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 5

Align Title:gi|1632209835|ref|XR_003775509.1| PREDICTED: Malus domestica uncharacterized LOC108170672 (LOC108170672), transcript variant X34, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 5

Align Title:gi|1632209834|ref|XR_003775508.1| PREDICTED: Malus domestica uncharacterized LOC108170672 (LOC108170672), transcript variant X33, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 5

Align Title:gi|1632209833|ref|XR_003775507.1| PREDICTED: Malus domestica uncharacterized LOC108170672 (LOC108170672), transcript variant X32, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 5

Align Title:gi|1632209832|ref|XR_003775506.1| PREDICTED: Malus domestica uncharacterized LOC108170672 (LOC108170672), transcript variant X31, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 5

Align Title:gi|1632209831|ref|XR_003775505.1| PREDICTED: Malus domestica uncharacterized LOC108170672 (LOC108170672), transcript variant X30, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 5

Align Title:gi|1632209828|ref|XR_003775504.1| PREDICTED: Malus domestica uncharacterized LOC108170672 (LOC108170672), transcript variant X28, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 5

Align Title:gi|1632209820|ref|XM_029107091.1| PREDICTED: Malus domestica uncharacterized LOC108170672 (LOC108170672), transcript variant X24, mRNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 5

Align Title:gi|1632209819|ref|XR_003775503.1| PREDICTED: Malus domestica uncharacterized LOC108170672 (LOC108170672), transcript variant X23, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 5

Align Title:gi|1632209818|ref|XR_003775502.1| PREDICTED: Malus domestica uncharacterized LOC108170672 (LOC108170672), transcript variant X22, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 5

Align Title:gi|1632209811|ref|XR_003775497.1| PREDICTED: Malus domestica uncharacterized LOC108170672 (LOC108170672), transcript variant X16, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 5

Align Title:gi|1632209810|ref|XR_003775496.1| PREDICTED: Malus domestica uncharacterized LOC108170672 (LOC108170672), transcript variant X15, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 5

Align Title:gi|1632209806|ref|XR_003775492.1| PREDICTED: Malus domestica uncharacterized LOC108170672 (LOC108170672), transcript variant X11, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 5

Align Title:gi|1632257928|ref|XR_524259.3| PREDICTED: Malus domestica protein transport protein Sec61 subunit gamma (LOC103403987), transcript variant X2, misc_RNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:24 Pos.:24 Align len:26
Num mismatches: 2
Mismatch pos: 7,9

Align Title:gi|1632243939|ref|XR_003768479.1| PREDICTED: Malus domestica serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform-like (LOC103455205), transcript variant X6, misc_RNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:27 Pos.:27 Align len:31
Num mismatches: 4
Mismatch pos: 6,9,13,19

Align Title:gi|1632243938|ref|XR_003768478.1| PREDICTED: Malus domestica serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform-like (LOC103455205), transcript variant X5, misc_RNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:27 Pos.:27 Align len:31
Num mismatches: 4
Mismatch pos: 6,9,13,19

Align Title:gi|1632243936|ref|XM_008394794.3| PREDICTED: Malus domestica serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform-like (LOC103455205), transcript variant X4, mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:27 Pos.:27 Align len:31
Num mismatches: 4
Mismatch pos: 6,9,13,19

Align Title:gi|1632243934|ref|XM_008394793.3| PREDICTED: Malus domestica serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform-like (LOC103455205), transcript variant X3, mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:27 Pos.:27 Align len:31
Num mismatches: 4
Mismatch pos: 6,9,13,19

Align Title:gi|1632243932|ref|XM_008394792.3| PREDICTED: Malus domestica serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform-like (LOC103455205), transcript variant X2, mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:27 Pos.:27 Align len:31
Num mismatches: 4
Mismatch pos: 6,9,13,19

Align Title:gi|1632243930|ref|XM_008394791.3| PREDICTED: Malus domestica serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform-like (LOC103455205), transcript variant X1, mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:27 Pos.:27 Align len:31
Num mismatches: 4
Mismatch pos: 6,9,13,19

Align Title:gi|658309847|ref|NM_001293907.1| Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic-like (LOC103439436), mRNA >gi|182636945|gb|EU586116.1| Malus x domestica granule bound starch synthase Ib precursor (GBSSIb) mRNA, complete cds
Score: 3696.0 E-val: 0.0
N.aligns:None Ident:1848 Pos.:1848 Align len:1848
No mismatches

Align Title:gi|1632200625|ref|XM_029104747.1| PREDICTED: Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic-like (LOC103439436), transcript variant X2, mRNA
Score: 3687.0 E-val: 0.0
N.aligns:None Ident:1847 Pos.:1847 Align len:1848
Num mismatches: 1
Mismatch pos: 1743

Align Title:gi|1632200623|ref|XM_008378000.3| PREDICTED: Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic-like (LOC103439436), transcript variant X1, mRNA
Score: 3687.0 E-val: 0.0
N.aligns:None Ident:1847 Pos.:1847 Align len:1848
Num mismatches: 1
Mismatch pos: 1743

Align Title:gi|1632200627|ref|XM_029104748.1| PREDICTED: Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic-like (LOC103439436), transcript variant X3, mRNA
Score: 3646.0 E-val: 0.0
N.aligns:None Ident:1838 Pos.:1838 Align len:1848
Num mismatches: 10
Mismatch pos: 1732,1733,1734,1735,1736,1737,1739,1740,1741,1743

Align Title:gi|357528265|gb|JN187083.1| Malus x domestica granule-bound starch synthase GBSS4 pseudogene, complete sequence
Score: 1457.0 E-val: 0.0
N.aligns:None Ident:774 Pos.:774 Align len:804
Num mismatches: 30
Mismatch pos: 34,35,145,213,218,270,271,272,273,332,334,340,401,403,407,410,421,527,538,560,597,689,705,731,747,748,789,791,793,795

Align Title:gi|1632245385|ref|XM_008394428.2| PREDICTED: Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic (LOC103454831), transcript variant X2, mRNA
Score: 1310.0 E-val: 0.0
N.aligns:None Ident:1226 Pos.:1226 Align len:1604
Num mismatches: 378
Mismatch pos: 6,12,14,18,24,27,34,39,40,42,45,60,72,93,111,114,123,126,129,136,138,144,147,150,162,174,177,179,180,183,184,193,195,196,201,204,206,209,210,211,212,213,219,225,228,231,246,261,264,278,282,285,288,290,291,300,308,318,324,328,329,330,333,338,339,344,354,358,361,363,370,372,373,375,384,388,390,392,393,402,408,412,414,422,429,432,435,441,447,450,459,463,468,471,486,489,495,502,504,510,513,519,522,525,528,531,535,537,539,540,543,546,549,551,552,561,570,579,589,591,592,598,599,602,605,606,609,614,618,624,626,627,629,630,632,636,638,641,644,647,668,671,674,677,680,683,692,701,704,710,711,713,716,719,724,725,728,729,731,737,745,752,753,768,769,772,773,776,782,785,800,801,806,809,810,812,813,815,818,819,820,821,824,827,843,845,848,851,860,862,863,866,875,876,877,879,880,882,883,894,895,896,897,905,906,907,908,923,924,929,932,935,938,950,953,954,959,962,965,968,969,980,983,986,995,1001,1004,1013,1016,1022,1028,1029,1037,1040,1041,1043,1044,1046,1050,1053,1054,1055,1056,1058,1062,1064,1067,1073,1082,1088,1091,1098,1099,1100,1108,1113,1115,1121,1124,1128,1129,1130,1131,1136,1139,1141,1145,1148,1149,1150,1155,1157,1160,1173,1175,1178,1192,1193,1195,1196,1199,1200,1208,1217,1223,1232,1235,1238,1241,1247,1256,1259,1263,1265,1274,1280,1289,1295,1298,1301,1302,1304,1307,1316,1325,1328,1340,1349,1355,1358,1364,1367,1369,1370,1381,1382,1389,1390,1391,1400,1403,1406,1411,1418,1419,1421,1423,1426,1430,1433,1439,1442,1445,1447,1454,1457,1458,1459,1460,1472,1481,1493,1497,1499,1502,1503,1505,1511,1512,1514,1515,1521,1526,1527,1531,1532,1535,1537,1538,1539,1540,1543,1549,1550,1553,1554,1559,1562,1565,1568,1574,1577,1580,1583,1593,1595,1598,1601

Align Title:gi|1632245384|ref|XM_008394427.3| PREDICTED: Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic (LOC103454831), transcript variant X1, mRNA
Score: 1310.0 E-val: 0.0
N.aligns:None Ident:1226 Pos.:1226 Align len:1604
Num mismatches: 378
Mismatch pos: 6,12,14,18,24,27,34,39,40,42,45,60,72,93,111,114,123,126,129,136,138,144,147,150,162,174,177,179,180,183,184,193,195,196,201,204,206,209,210,211,212,213,219,225,228,231,246,261,264,278,282,285,288,290,291,300,308,318,324,328,329,330,333,338,339,344,354,358,361,363,370,372,373,375,384,388,390,392,393,402,408,412,414,422,429,432,435,441,447,450,459,463,468,471,486,489,495,502,504,510,513,519,522,525,528,531,535,537,539,540,543,546,549,551,552,561,570,579,589,591,592,598,599,602,605,606,609,614,618,624,626,627,629,630,632,636,638,641,644,647,668,671,674,677,680,683,692,701,704,710,711,713,716,719,724,725,728,729,731,737,745,752,753,768,769,772,773,776,782,785,800,801,806,809,810,812,813,815,818,819,820,821,824,827,843,845,848,851,860,862,863,866,875,876,877,879,880,882,883,894,895,896,897,905,906,907,908,923,924,929,932,935,938,950,953,954,959,962,965,968,969,980,983,986,995,1001,1004,1013,1016,1022,1028,1029,1037,1040,1041,1043,1044,1046,1050,1053,1054,1055,1056,1058,1062,1064,1067,1073,1082,1088,1091,1098,1099,1100,1108,1113,1115,1121,1124,1128,1129,1130,1131,1136,1139,1141,1145,1148,1149,1150,1155,1157,1160,1173,1175,1178,1192,1193,1195,1196,1199,1200,1208,1217,1223,1232,1235,1238,1241,1247,1256,1259,1263,1265,1274,1280,1289,1295,1298,1301,1302,1304,1307,1316,1325,1328,1340,1349,1355,1358,1364,1367,1369,1370,1381,1382,1389,1390,1391,1400,1403,1406,1411,1418,1419,1421,1423,1426,1430,1433,1439,1442,1445,1447,1454,1457,1458,1459,1460,1472,1481,1493,1497,1499,1502,1503,1505,1511,1512,1514,1515,1521,1526,1527,1531,1532,1535,1537,1538,1539,1540,1543,1549,1550,1553,1554,1559,1562,1565,1568,1574,1577,1580,1583,1593,1595,1598,1601

Align Title:gi|1632195925|ref|XM_008375918.3| PREDICTED: Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic-like (LOC103437450), transcript variant X2, mRNA
Score: 1253.0 E-val: 0.0
N.aligns:None Ident:1214 Pos.:1214 Align len:1605
Num mismatches: 391
Mismatch pos: 5,11,17,23,26,33,38,39,44,59,71,92,95,104,110,113,116,122,125,128,134,135,137,143,146,149,152,161,173,176,177,178,179,182,183,184,192,194,195,200,203,205,208,209,210,211,212,218,224,227,230,245,260,263,276,281,284,287,299,305,307,317,323,327,328,329,330,332,337,338,341,343,346,353,356,357,360,362,369,371,374,383,387,389,391,392,401,404,407,410,411,413,414,421,428,431,446,449,452,458,467,470,480,485,488,494,501,503,507,512,518,521,524,527,530,536,538,539,542,545,548,550,551,560,569,578,588,592,593,594,596,602,603,611,612,615,621,623,624,626,627,629,633,635,638,641,644,653,657,660,668,671,674,677,680,689,698,701,707,708,710,716,721,725,726,728,734,750,752,765,766,769,770,773,779,782,788,797,798,803,807,809,810,812,815,816,817,818,821,824,825,842,845,848,857,859,860,869,870,872,873,874,876,877,879,891,892,894,902,903,904,905,918,920,926,929,932,935,947,950,953,956,959,962,965,966,974,977,978,980,983,992,998,1001,1019,1025,1026,1034,1037,1038,1040,1041,1043,1047,1049,1050,1051,1056,1058,1060,1061,1062,1064,1067,1070,1074,1079,1082,1085,1091,1095,1096,1097,1098,1105,1110,1112,1113,1121,1124,1126,1127,1128,1133,1136,1138,1139,1142,1145,1146,1147,1152,1154,1157,1171,1172,1173,1175,1181,1189,1190,1192,1193,1196,1197,1212,1214,1229,1232,1235,1244,1256,1260,1262,1271,1277,1278,1286,1292,1295,1298,1299,1301,1304,1313,1322,1325,1337,1345,1346,1352,1355,1361,1364,1365,1366,1367,1378,1379,1386,1387,1388,1400,1403,1408,1409,1415,1416,1418,1420,1423,1430,1436,1439,1442,1444,1451,1454,1455,1456,1457,1460,1469,1478,1490,1494,1496,1499,1500,1502,1508,1509,1511,1512,1518,1523,1524,1528,1529,1532,1535,1536,1537,1540,1542,1546,1547,1549,1550,1551,1556,1559,1562,1565,1571,1577,1580,1592,1595,1598,1601

Score: 40.0 E-val: 1.31621
N.aligns:None Ident:26 Pos.:26 Align len:30
Num mismatches: 4
Mismatch pos: 2,17,19,23

Align Title:gi|1632195924|ref|XM_008375917.3| PREDICTED: Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic-like (LOC103437450), transcript variant X1, mRNA
Score: 1253.0 E-val: 0.0
N.aligns:None Ident:1214 Pos.:1214 Align len:1605
Num mismatches: 391
Mismatch pos: 5,11,17,23,26,33,38,39,44,59,71,92,95,104,110,113,116,122,125,128,134,135,137,143,146,149,152,161,173,176,177,178,179,182,183,184,192,194,195,200,203,205,208,209,210,211,212,218,224,227,230,245,260,263,276,281,284,287,299,305,307,317,323,327,328,329,330,332,337,338,341,343,346,353,356,357,360,362,369,371,374,383,387,389,391,392,401,404,407,410,411,413,414,421,428,431,446,449,452,458,467,470,480,485,488,494,501,503,507,512,518,521,524,527,530,536,538,539,542,545,548,550,551,560,569,578,588,592,593,594,596,602,603,611,612,615,621,623,624,626,627,629,633,635,638,641,644,653,657,660,668,671,674,677,680,689,698,701,707,708,710,716,721,725,726,728,734,750,752,765,766,769,770,773,779,782,788,797,798,803,807,809,810,812,815,816,817,818,821,824,825,842,845,848,857,859,860,869,870,872,873,874,876,877,879,891,892,894,902,903,904,905,918,920,926,929,932,935,947,950,953,956,959,962,965,966,974,977,978,980,983,992,998,1001,1019,1025,1026,1034,1037,1038,1040,1041,1043,1047,1049,1050,1051,1056,1058,1060,1061,1062,1064,1067,1070,1074,1079,1082,1085,1091,1095,1096,1097,1098,1105,1110,1112,1113,1121,1124,1126,1127,1128,1133,1136,1138,1139,1142,1145,1146,1147,1152,1154,1157,1171,1172,1173,1175,1181,1189,1190,1192,1193,1196,1197,1212,1214,1229,1232,1235,1244,1256,1260,1262,1271,1277,1278,1286,1292,1295,1298,1299,1301,1304,1313,1322,1325,1337,1345,1346,1352,1355,1361,1364,1365,1366,1367,1378,1379,1386,1387,1388,1400,1403,1408,1409,1415,1416,1418,1420,1423,1430,1436,1439,1442,1444,1451,1454,1455,1456,1457,1460,1469,1478,1490,1494,1496,1499,1500,1502,1508,1509,1511,1512,1518,1523,1524,1528,1529,1532,1535,1536,1537,1540,1542,1546,1547,1549,1550,1551,1556,1559,1562,1565,1571,1577,1580,1592,1595,1598,1601

Score: 40.0 E-val: 1.31621
N.aligns:None Ident:26 Pos.:26 Align len:30
Num mismatches: 4
Mismatch pos: 2,17,19,23

Align Title:gi|658309783|ref|NM_001293995.1| Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic-like (LOC103437450), mRNA >gi|182636943|gb|EU586115.1| Malus x domestica granule bound starch synthase Ia precursor (GBSSIa) mRNA, complete cds
Score: 1253.0 E-val: 0.0
N.aligns:None Ident:1214 Pos.:1214 Align len:1605
Num mismatches: 391
Mismatch pos: 5,11,17,23,26,33,38,39,44,59,71,92,95,104,110,113,116,122,125,128,134,135,137,143,146,149,152,161,173,176,177,178,179,182,183,184,192,194,195,200,203,205,208,209,210,211,212,218,224,227,230,245,260,263,276,281,284,287,299,305,307,317,323,327,328,329,330,332,337,338,341,343,346,353,356,357,360,362,369,371,374,383,387,389,391,392,401,404,407,410,411,413,414,421,428,431,446,449,452,458,467,470,480,485,488,494,501,503,507,512,518,521,524,527,530,536,538,539,542,545,548,550,551,560,569,578,588,592,593,594,596,602,603,611,612,615,621,623,624,626,627,629,633,635,638,641,644,653,657,660,668,671,674,677,680,689,698,701,707,708,710,716,721,725,726,728,734,750,752,765,766,769,770,773,779,782,788,797,798,803,807,809,810,812,815,816,817,818,821,824,825,842,845,848,857,859,860,869,870,872,873,874,876,877,879,891,892,894,902,903,904,905,918,920,926,929,932,935,947,950,953,956,959,962,965,966,974,977,978,980,983,992,998,1001,1019,1025,1026,1034,1037,1038,1040,1041,1043,1047,1049,1050,1051,1056,1058,1060,1061,1062,1064,1067,1070,1074,1079,1082,1085,1091,1095,1096,1097,1098,1105,1110,1112,1113,1121,1124,1126,1127,1128,1133,1136,1138,1139,1142,1145,1146,1147,1152,1154,1157,1171,1172,1173,1175,1181,1189,1190,1192,1193,1196,1197,1212,1214,1229,1232,1235,1244,1256,1260,1262,1271,1277,1278,1286,1292,1295,1298,1299,1301,1304,1313,1322,1325,1337,1345,1346,1352,1355,1361,1364,1365,1366,1367,1378,1379,1386,1387,1388,1400,1403,1408,1409,1415,1416,1418,1420,1423,1430,1436,1439,1442,1444,1451,1454,1455,1456,1457,1460,1469,1478,1490,1494,1496,1499,1500,1502,1508,1509,1511,1512,1518,1523,1524,1528,1529,1532,1535,1536,1537,1540,1542,1546,1547,1549,1550,1551,1556,1559,1562,1565,1571,1577,1580,1592,1595,1598,1601

Score: 40.0 E-val: 1.31621
N.aligns:None Ident:26 Pos.:26 Align len:30
Num mismatches: 4
Mismatch pos: 2,17,19,23

Align Title:gi|357528261|gb|JN187081.1| Malus x domestica granule-bound starch synthase GBSS2 gene, complete cds
Score: 717.0 E-val: 0.0
N.aligns:None Ident:360 Pos.:360 Align len:361
Num mismatches: 1
Mismatch pos: 358

Score: 495.0 E-val: 7.73152e-124
N.aligns:None Ident:249 Pos.:249 Align len:250
Num mismatches: 1
Mismatch pos: 2

Score: 430.0 E-val: 1.81989e-106
N.aligns:None Ident:215 Pos.:215 Align len:215
No mismatches

Score: 389.0 E-val: 4.57377e-95
N.aligns:None Ident:199 Pos.:199 Align len:201
Num mismatches: 2
Mismatch pos: 5,6

Score: 356.0 E-val: 2.21904e-86
N.aligns:None Ident:178 Pos.:178 Align len:178
No mismatches

Score: 260.0 E-val: 2.53415e-60
N.aligns:None Ident:130 Pos.:130 Align len:130
No mismatches

Score: 238.0 E-val: 2.37346e-54
N.aligns:None Ident:119 Pos.:119 Align len:119
No mismatches

Score: 209.0 E-val: 3.29916e-46
N.aligns:None Ident:106 Pos.:106 Align len:107
Num mismatches: 1
Mismatch pos: 103

Score: 188.0 E-val: 8.85288e-41
N.aligns:None Ident:94 Pos.:94 Align len:94
No mismatches

Score: 174.0 E-val: 5.58678e-37
N.aligns:None Ident:87 Pos.:87 Align len:87
No mismatches

Score: 162.0 E-val: 1.01011e-33
N.aligns:None Ident:81 Pos.:81 Align len:81
No mismatches

Score: 134.0 E-val: 4.02275e-26
N.aligns:None Ident:67 Pos.:67 Align len:67
No mismatches

Align Title:gi|357528259|gb|JN187080.1| Malus x domestica granule-bound starch synthase GBSS1 gene, complete cds
Score: 196.0 E-val: 5.96503e-43
N.aligns:None Ident:188 Pos.:188 Align len:248
Num mismatches: 60
Mismatch pos: 2,5,13,16,19,22,25,34,43,46,52,53,55,61,66,70,71,73,79,95,97,110,111,114,115,118,124,127,133,142,143,148,152,154,155,157,160,161,162,163,166,169,170,187,190,193,202,204,205,214,215,217,218,219,221,222,224,236,237,239

Score: 150.0 E-val: 1.82633e-30
N.aligns:None Ident:96 Pos.:96 Align len:110
Num mismatches: 14
Mismatch pos: 5,11,17,23,26,33,38,39,44,59,71,92,95,104

Score: 148.0 E-val: 6.37451e-30
N.aligns:None Ident:146 Pos.:146 Align len:194
Num mismatches: 48
Mismatch pos: 2,5,11,15,16,17,18,25,30,32,33,41,44,46,47,48,53,56,58,59,62,65,66,67,72,74,77,91,92,93,95,101,109,110,112,113,116,117,132,134,149,152,155,164,176,180,182,191

Score: 132.0 E-val: 1.40408e-25
N.aligns:None Ident:105 Pos.:105 Align len:131
Num mismatches: 26
Mismatch pos: 12,14,20,23,26,29,41,44,47,50,53,56,59,60,68,71,72,74,77,86,92,95,113,119,120,128

Score: 111.0 E-val: 1.31505e-19
N.aligns:None Ident:72 Pos.:72 Align len:83
Num mismatches: 11
Mismatch pos: 5,11,14,17,32,47,50,63,68,71,74

Score: 107.0 E-val: 1.60205e-18
N.aligns:None Ident:94 Pos.:94 Align len:121
Num mismatches: 27
Mismatch pos: 10,11,18,19,20,32,35,40,41,47,48,50,52,55,62,68,71,74,76,83,86,87,88,89,92,101,110

Score: 89.0 E-val: 1.23166e-13
N.aligns:None Ident:70 Pos.:70 Align len:87
Num mismatches: 17
Mismatch pos: 5,6,14,20,23,26,27,29,32,41,50,53,65,73,74,80,83

Score: 77.0 E-val: 2.22689e-10
N.aligns:None Ident:73 Pos.:73 Align len:96
Num mismatches: 23
Mismatch pos: 11,17,19,29,35,39,40,41,42,44,49,50,53,55,58,65,68,69,72,74,81,83,86

Score: 61.0 E-val: 4.90505e-06
N.aligns:None Ident:53 Pos.:53 Align len:68
Num mismatches: 15
Mismatch pos: 5,9,11,13,14,23,26,29,32,33,35,36,43,50,53

Score: 60.0 E-val: 4.90505e-06
N.aligns:None Ident:51 Pos.:51 Align len:65
Num mismatches: 14
Mismatch pos: 2,5,11,14,17,23,24,26,32,35,38,41,50,62

Score: 53.0 E-val: 0.000727974
N.aligns:None Ident:82 Pos.:82 Align len:119
Num mismatches: 37
Mismatch pos: 4,8,10,13,14,16,22,23,25,26,32,37,38,42,43,46,49,50,51,54,56,60,61,63,64,65,70,73,76,79,85,91,94,106,109,112,115

Score: 40.0 E-val: 1.31621
N.aligns:None Ident:26 Pos.:26 Align len:30
Num mismatches: 4
Mismatch pos: 2,17,19,23

Align Title:gi|357528263|gb|JN187082.1| Malus x domestica granule-bound starch synthase GBSS3 gene, complete cds
Score: 181.0 E-val: 1.31388e-38
N.aligns:None Ident:185 Pos.:185 Align len:248
Num mismatches: 63
Mismatch pos: 10,13,16,19,22,25,34,43,46,52,53,55,58,61,66,67,70,71,73,79,87,94,95,110,111,114,115,118,124,127,142,143,148,151,152,154,155,157,160,161,162,163,166,169,185,187,190,193,202,204,205,208,217,218,219,221,222,224,225,236,237,238,239

Score: 158.0 E-val: 1.23057e-32
N.aligns:None Ident:148 Pos.:148 Align len:194
Num mismatches: 46
Mismatch pos: 5,8,15,16,17,25,30,32,38,41,45,46,47,48,53,56,58,62,65,66,67,72,74,77,90,92,95,109,110,112,113,116,117,125,134,140,149,152,155,158,164,173,176,180,182,191

Score: 152.0 E-val: 5.23252e-31
N.aligns:None Ident:97 Pos.:97 Align len:111
Num mismatches: 14
Mismatch pos: 6,12,14,18,24,27,34,39,40,42,45,60,72,93

Score: 137.0 E-val: 1.15254e-26
N.aligns:None Ident:131 Pos.:131 Align len:172
Num mismatches: 41
Mismatch pos: 13,14,19,22,25,28,40,43,44,49,52,55,58,59,70,73,76,85,91,94,103,106,112,118,119,127,130,131,133,134,136,140,143,144,145,146,148,152,154,157,163

Score: 107.0 E-val: 1.60205e-18
N.aligns:None Ident:94 Pos.:94 Align len:121
Num mismatches: 27
Mismatch pos: 10,11,18,19,20,29,32,35,40,47,48,50,52,55,59,62,68,71,74,76,83,86,87,88,89,101,110

Score: 99.0 E-val: 2.37766e-16
N.aligns:None Ident:72 Pos.:72 Align len:87
Num mismatches: 15
Mismatch pos: 5,14,20,23,26,27,29,32,41,50,53,65,74,80,83

Score: 98.0 E-val: 2.37766e-16
N.aligns:None Ident:64 Pos.:64 Align len:74
Num mismatches: 10
Mismatch pos: 5,11,14,17,32,47,50,64,68,71

Score: 97.0 E-val: 8.29884e-16
N.aligns:None Ident:77 Pos.:77 Align len:96
Num mismatches: 19
Mismatch pos: 11,19,29,35,39,40,41,44,49,50,55,65,69,72,74,81,83,84,86

Score: 90.0 E-val: 3.52876e-14
N.aligns:None Ident:72 Pos.:72 Align len:90
Num mismatches: 18
Mismatch pos: 2,5,14,18,23,26,41,44,50,57,59,65,68,74,77,80,83,86

Score: 89.0 E-val: 1.23166e-13
N.aligns:None Ident:85 Pos.:85 Align len:110
Num mismatches: 25
Mismatch pos: 8,17,26,36,38,39,45,46,49,52,53,56,61,65,71,73,74,76,77,79,83,85,88,91,94

Score: 82.0 E-val: 5.23714e-12
N.aligns:None Ident:65 Pos.:65 Align len:81
Num mismatches: 16
Mismatch pos: 2,11,14,17,24,26,32,35,38,50,62,65,67,68,71,72

Align Title:gi|1632212983|ref|XM_008367179.3| PREDICTED: Malus domestica granule-bound starch synthase 2, chloroplastic/amyloplastic-like (LOC103429037), mRNA
Score: 54.0 E-val: 0.000208568
N.aligns:None Ident:49 Pos.:49 Align len:63
Num mismatches: 14
Mismatch pos: 4,7,10,28,31,32,34,44,45,46,49,50,51,60

Align Title:gi|1632163374|ref|XM_029098420.1| PREDICTED: Malus domestica granule-bound starch synthase 2, chloroplastic/amyloplastic (LOC103404446), mRNA
Score: 54.0 E-val: 0.000208568
N.aligns:None Ident:49 Pos.:49 Align len:63
Num mismatches: 14
Mismatch pos: 4,7,10,28,31,32,34,44,45,46,48,50,51,60

Align Title:gi|1632223611|ref|XM_029087607.1| PREDICTED: Malus domestica starch synthase 3, chloroplastic/amyloplastic-like (LOC103429752), partial mRNA
Score: 46.0 E-val: 0.0309542
N.aligns:None Ident:41 Pos.:41 Align len:53
Num mismatches: 12
Mismatch pos: 2,14,17,23,24,25,26,28,29,32,41,49

Align Title:gi|1632194644|ref|XM_029103312.1| PREDICTED: Malus domestica starch synthase 3, chloroplastic/amyloplastic (LOC103434594), mRNA
Score: 44.0 E-val: 0.108041
N.aligns:None Ident:55 Pos.:55 Align len:77
Num mismatches: 22
Mismatch pos: 2,6,8,12,17,18,19,20,23,26,38,41,47,48,49,50,52,53,56,62,65,73

Align Title:gi|1632206082|ref|XM_008358830.3| PREDICTED: Malus domestica starch synthase 1, chloroplastic/amyloplastic (LOC103420788), transcript variant X2, mRNA
Score: 42.0 E-val: 0.3771
N.aligns:None Ident:42 Pos.:42 Align len:56
Num mismatches: 14
Mismatch pos: 5,11,17,20,22,23,26,27,30,32,35,39,41,53

Align Title:gi|1632206081|ref|XM_008358828.3| PREDICTED: Malus domestica starch synthase 1, chloroplastic/amyloplastic (LOC103420788), transcript variant X1, mRNA
Score: 42.0 E-val: 0.3771
N.aligns:None Ident:42 Pos.:42 Align len:56
Num mismatches: 14
Mismatch pos: 5,11,17,20,22,23,26,27,30,32,35,39,41,53

Align Title:gi|1632224947|ref|XM_029087990.1| PREDICTED: Malus domestica sufE-like protein 1, chloroplastic/mitochondrial (LOC103419427), mRNA
Score: 41.0 E-val: 1.31621
N.aligns:None Ident:22 Pos.:22 Align len:23
Num mismatches: 1
Mismatch pos: 18

Align Title:gi|1632263211|ref|XM_029096539.1| PREDICTED: Malus domestica vinorine synthase-like (LOC103431869), mRNA
Score: 40.0 E-val: 1.31621
N.aligns:None Ident:23 Pos.:23 Align len:25
Num mismatches: 2
Mismatch pos: 6,10

Align Title:gi|1632254475|ref|XR_003769651.1| PREDICTED: Malus domestica neuroguidin-like (LOC103425272), transcript variant X5, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 8

Align Title:gi|1632254473|ref|XR_003769649.1| PREDICTED: Malus domestica neuroguidin-like (LOC103425272), transcript variant X3, misc_RNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 8

Align Title:gi|1632195180|ref|XM_029103459.1| PREDICTED: Malus domestica uncharacterized LOC114825112 (LOC114825112), mRNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:23 Pos.:23 Align len:24
Num mismatches: 1
Mismatch pos: 9

Align Title:gi|1632266859|ref|XM_008343789.3| PREDICTED: Malus domestica probable beta-1,3-galactosyltransferase 2 (LOC103404820), transcript variant X2, mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:25 Pos.:25 Align len:29
Num mismatches: 4
Mismatch pos: 4,6,10,14

Align Title:gi|1632266858|ref|XM_008343788.3| PREDICTED: Malus domestica probable beta-1,3-galactosyltransferase 2 (LOC103404820), transcript variant X1, mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:25 Pos.:25 Align len:29
Num mismatches: 4
Mismatch pos: 4,6,10,14

Align Title:gi|1632242149|ref|XM_008395235.3| PREDICTED: Malus domestica UV-B-induced protein At3g17800, chloroplastic-like (LOC103455652), transcript variant X2, mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:28 Pos.:28 Align len:34
Num mismatches: 6
Mismatch pos: 2,7,8,25,26,31

Align Title:gi|1632242147|ref|XM_008395234.3| PREDICTED: Malus domestica UV-B-induced protein At3g17800, chloroplastic-like (LOC103455652), transcript variant X1, mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:28 Pos.:28 Align len:34
Num mismatches: 6
Mismatch pos: 2,7,8,25,26,31

Align Title:gi|1632237734|ref|XM_008392593.3| PREDICTED: Malus domestica mediator of RNA polymerase II transcription subunit 33A-like (LOC103453060), mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 8,9

Align Title:gi|1632203209|ref|XM_029105544.1| PREDICTED: Malus domestica lysine-specific demethylase JMJ25-like (LOC103410099), transcript variant X2, mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 11,13

Align Title:gi|1632203207|ref|XM_029105543.1| PREDICTED: Malus domestica lysine-specific demethylase JMJ25-like (LOC103410099), transcript variant X1, mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 11,13

Align Title:gi|1632182079|ref|XR_003772270.1| PREDICTED: Malus domestica uncharacterized LOC108172495 (LOC108172495), ncRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:27 Pos.:27 Align len:31
Num mismatches: 4
Mismatch pos: 5,8,23,27

Align Title:gi|1632195925|ref|XM_008375918.3| PREDICTED: Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic-like (LOC103437450), transcript variant X2, mRNA
Score: 3690.0 E-val: 0.0
N.aligns:None Ident:1845 Pos.:1845 Align len:1845
No mismatches

Align Title:gi|1632195924|ref|XM_008375917.3| PREDICTED: Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic-like (LOC103437450), transcript variant X1, mRNA
Score: 3690.0 E-val: 0.0
N.aligns:None Ident:1845 Pos.:1845 Align len:1845
No mismatches

Align Title:gi|658309783|ref|NM_001293995.1| Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic-like (LOC103437450), mRNA >gi|182636943|gb|EU586115.1| Malus x domestica granule bound starch synthase Ia precursor (GBSSIa) mRNA, complete cds
Score: 3690.0 E-val: 0.0
N.aligns:None Ident:1845 Pos.:1845 Align len:1845
No mismatches

Align Title:gi|1632245385|ref|XM_008394428.2| PREDICTED: Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic (LOC103454831), transcript variant X2, mRNA
Score: 2961.0 E-val: 0.0
N.aligns:None Ident:1698 Pos.:1698 Align len:1843
Num mismatches: 145
Mismatch pos: 9,15,20,23,29,37,48,59,68,70,122,140,163,169,171,176,187,213,215,229,239,253,257,281,311,335,344,356,374,392,417,424,516,517,529,530,539,545,569,570,581,586,596,612,644,650,654,674,680,692,702,720,747,749,774,788,830,831,832,839,846,852,863,893,897,900,905,908,950,953,956,962,974,982,989,992,1028,1046,1065,1080,1082,1103,1109,1110,1120,1133,1142,1145,1158,1161,1191,1193,1214,1218,1250,1253,1280,1289,1292,1302,1307,1314,1322,1328,1331,1338,1353,1358,1364,1365,1376,1379,1410,1411,1413,1421,1433,1445,1452,1460,1478,1493,1496,1518,1541,1577,1585,1605,1626,1637,1649,1656,1667,1679,1700,1736,1764,1774,1782,1789,1799,1811,1814,1820,1830

Align Title:gi|1632245384|ref|XM_008394427.3| PREDICTED: Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic (LOC103454831), transcript variant X1, mRNA
Score: 2961.0 E-val: 0.0
N.aligns:None Ident:1698 Pos.:1698 Align len:1843
Num mismatches: 145
Mismatch pos: 9,15,20,23,29,37,48,59,68,70,122,140,163,169,171,176,187,213,215,229,239,253,257,281,311,335,344,356,374,392,417,424,516,517,529,530,539,545,569,570,581,586,596,612,644,650,654,674,680,692,702,720,747,749,774,788,830,831,832,839,846,852,863,893,897,900,905,908,950,953,956,962,974,982,989,992,1028,1046,1065,1080,1082,1103,1109,1110,1120,1133,1142,1145,1158,1161,1191,1193,1214,1218,1250,1253,1280,1289,1292,1302,1307,1314,1322,1328,1331,1338,1353,1358,1364,1365,1376,1379,1410,1411,1413,1421,1433,1445,1452,1460,1478,1493,1496,1518,1541,1577,1585,1605,1626,1637,1649,1656,1667,1679,1700,1736,1764,1774,1782,1789,1799,1811,1814,1820,1830

Align Title:gi|658309847|ref|NM_001293907.1| Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic-like (LOC103439436), mRNA >gi|182636945|gb|EU586116.1| Malus x domestica granule bound starch synthase Ib precursor (GBSSIb) mRNA, complete cds
Score: 1253.0 E-val: 0.0
N.aligns:None Ident:1214 Pos.:1214 Align len:1605
Num mismatches: 391
Mismatch pos: 5,11,17,23,26,33,38,39,44,59,71,92,95,104,110,113,116,122,125,128,134,135,137,143,146,149,152,161,173,176,177,178,179,182,183,184,192,194,195,200,203,205,208,209,210,211,212,218,224,227,230,245,260,263,276,281,284,287,299,305,307,317,323,327,328,329,330,332,337,338,341,343,346,353,356,357,360,362,369,371,374,383,387,389,391,392,401,404,407,410,411,413,414,421,428,431,446,449,452,458,467,470,480,485,488,494,501,503,507,512,518,521,524,527,530,536,538,539,542,545,548,550,551,560,569,578,588,592,593,594,596,602,603,611,612,615,621,623,624,626,627,629,633,635,638,641,644,653,657,660,668,671,674,677,680,689,698,701,707,708,710,716,721,725,726,728,734,750,752,765,766,769,770,773,779,782,788,797,798,803,807,809,810,812,815,816,817,818,821,824,825,842,845,848,857,859,860,869,870,872,873,874,876,877,879,891,892,894,902,903,904,905,918,920,926,929,932,935,947,950,953,956,959,962,965,966,974,977,978,980,983,992,998,1001,1019,1025,1026,1034,1037,1038,1040,1041,1043,1047,1049,1050,1051,1056,1058,1060,1061,1062,1064,1067,1070,1074,1079,1082,1085,1091,1095,1096,1097,1098,1105,1110,1112,1113,1121,1124,1126,1127,1128,1133,1136,1138,1139,1142,1145,1146,1147,1152,1154,1157,1171,1172,1173,1175,1181,1189,1190,1192,1193,1196,1197,1212,1214,1229,1232,1235,1244,1256,1260,1262,1271,1277,1278,1286,1292,1295,1298,1299,1301,1304,1313,1322,1325,1337,1345,1346,1352,1355,1361,1364,1365,1366,1367,1378,1379,1386,1387,1388,1400,1403,1408,1409,1415,1416,1418,1420,1423,1430,1436,1439,1442,1444,1451,1454,1455,1456,1457,1460,1469,1478,1490,1494,1496,1499,1500,1502,1508,1509,1511,1512,1518,1523,1524,1528,1529,1532,1535,1536,1537,1540,1542,1546,1547,1549,1550,1551,1556,1559,1562,1565,1571,1577,1580,1592,1595,1598,1601

Score: 40.0 E-val: 1.31621
N.aligns:None Ident:26 Pos.:26 Align len:30
Num mismatches: 4
Mismatch pos: 2,17,19,23

Align Title:gi|1632200625|ref|XM_029104747.1| PREDICTED: Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic-like (LOC103439436), transcript variant X2, mRNA
Score: 1249.0 E-val: 0.0
N.aligns:None Ident:1214 Pos.:1214 Align len:1605
Num mismatches: 391
Mismatch pos: 5,11,17,23,26,33,38,39,44,59,71,92,95,104,110,113,116,122,125,128,134,135,137,143,146,149,152,161,173,176,177,178,179,182,183,184,192,194,195,200,203,205,208,209,210,211,212,218,224,227,230,245,260,263,276,281,284,287,299,305,307,317,323,327,328,329,330,332,337,338,341,343,346,353,356,357,360,362,369,371,374,383,387,389,391,392,401,404,407,410,411,413,414,421,428,431,446,449,452,458,467,470,480,485,488,494,501,503,507,512,518,521,524,527,530,536,538,539,542,545,548,550,551,560,569,578,588,592,593,594,596,602,603,611,612,615,621,623,624,626,627,629,633,635,638,641,644,653,657,660,668,671,674,677,680,689,698,701,707,708,710,716,721,725,726,728,734,750,752,765,766,769,770,773,779,782,788,797,798,803,807,809,810,812,815,816,817,818,821,824,825,842,845,848,857,859,860,869,870,872,873,874,876,877,879,891,892,894,902,903,904,905,918,920,926,929,932,935,947,950,953,956,959,962,965,966,974,977,978,980,983,992,998,1001,1019,1025,1026,1034,1037,1038,1040,1041,1043,1047,1049,1050,1051,1056,1058,1060,1061,1062,1064,1067,1070,1074,1079,1082,1085,1091,1095,1096,1097,1098,1105,1110,1112,1113,1121,1124,1126,1127,1128,1133,1136,1138,1139,1142,1145,1146,1147,1152,1154,1157,1171,1172,1173,1175,1181,1189,1190,1192,1193,1196,1197,1212,1214,1229,1232,1235,1244,1256,1260,1262,1271,1277,1278,1286,1292,1295,1298,1299,1301,1304,1313,1322,1325,1337,1345,1346,1352,1355,1361,1364,1365,1366,1367,1378,1379,1386,1387,1388,1400,1403,1408,1409,1415,1416,1418,1420,1423,1430,1436,1439,1442,1444,1451,1454,1455,1456,1457,1460,1469,1478,1490,1494,1496,1497,1500,1502,1508,1509,1511,1512,1518,1523,1524,1528,1529,1532,1535,1536,1537,1540,1542,1546,1547,1549,1550,1551,1556,1559,1562,1565,1571,1577,1580,1592,1595,1598,1601

Score: 40.0 E-val: 1.31621
N.aligns:None Ident:26 Pos.:26 Align len:30
Num mismatches: 4
Mismatch pos: 2,17,19,23

Align Title:gi|1632200623|ref|XM_008378000.3| PREDICTED: Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic-like (LOC103439436), transcript variant X1, mRNA
Score: 1249.0 E-val: 0.0
N.aligns:None Ident:1214 Pos.:1214 Align len:1605
Num mismatches: 391
Mismatch pos: 5,11,17,23,26,33,38,39,44,59,71,92,95,104,110,113,116,122,125,128,134,135,137,143,146,149,152,161,173,176,177,178,179,182,183,184,192,194,195,200,203,205,208,209,210,211,212,218,224,227,230,245,260,263,276,281,284,287,299,305,307,317,323,327,328,329,330,332,337,338,341,343,346,353,356,357,360,362,369,371,374,383,387,389,391,392,401,404,407,410,411,413,414,421,428,431,446,449,452,458,467,470,480,485,488,494,501,503,507,512,518,521,524,527,530,536,538,539,542,545,548,550,551,560,569,578,588,592,593,594,596,602,603,611,612,615,621,623,624,626,627,629,633,635,638,641,644,653,657,660,668,671,674,677,680,689,698,701,707,708,710,716,721,725,726,728,734,750,752,765,766,769,770,773,779,782,788,797,798,803,807,809,810,812,815,816,817,818,821,824,825,842,845,848,857,859,860,869,870,872,873,874,876,877,879,891,892,894,902,903,904,905,918,920,926,929,932,935,947,950,953,956,959,962,965,966,974,977,978,980,983,992,998,1001,1019,1025,1026,1034,1037,1038,1040,1041,1043,1047,1049,1050,1051,1056,1058,1060,1061,1062,1064,1067,1070,1074,1079,1082,1085,1091,1095,1096,1097,1098,1105,1110,1112,1113,1121,1124,1126,1127,1128,1133,1136,1138,1139,1142,1145,1146,1147,1152,1154,1157,1171,1172,1173,1175,1181,1189,1190,1192,1193,1196,1197,1212,1214,1229,1232,1235,1244,1256,1260,1262,1271,1277,1278,1286,1292,1295,1298,1299,1301,1304,1313,1322,1325,1337,1345,1346,1352,1355,1361,1364,1365,1366,1367,1378,1379,1386,1387,1388,1400,1403,1408,1409,1415,1416,1418,1420,1423,1430,1436,1439,1442,1444,1451,1454,1455,1456,1457,1460,1469,1478,1490,1494,1496,1497,1500,1502,1508,1509,1511,1512,1518,1523,1524,1528,1529,1532,1535,1536,1537,1540,1542,1546,1547,1549,1550,1551,1556,1559,1562,1565,1571,1577,1580,1592,1595,1598,1601

Score: 40.0 E-val: 1.31621
N.aligns:None Ident:26 Pos.:26 Align len:30
Num mismatches: 4
Mismatch pos: 2,17,19,23

Align Title:gi|1632200627|ref|XM_029104748.1| PREDICTED: Malus domestica granule-bound starch synthase 1, chloroplastic/amyloplastic-like (LOC103439436), transcript variant X3, mRNA
Score: 1235.0 E-val: 0.0
N.aligns:None Ident:1213 Pos.:1213 Align len:1608
Num mismatches: 395
Mismatch pos: 5,11,17,23,26,33,38,39,44,59,71,92,95,104,110,113,116,122,125,128,134,135,137,143,146,149,152,161,173,176,177,178,179,182,183,184,192,194,195,200,203,205,208,209,210,211,212,218,224,227,230,245,260,263,276,281,284,287,299,305,307,317,323,327,328,329,330,332,337,338,341,343,346,353,356,357,360,362,369,371,374,383,387,389,391,392,401,404,407,410,411,413,414,421,428,431,446,449,452,458,467,470,480,485,488,494,501,503,507,512,518,521,524,527,530,536,538,539,542,545,548,550,551,560,569,578,588,592,593,594,596,602,603,611,612,615,621,623,624,626,627,629,633,635,638,641,644,653,657,660,668,671,674,677,680,689,698,701,707,708,710,716,721,725,726,728,734,750,752,765,766,769,770,773,779,782,788,797,798,803,807,809,810,812,815,816,817,818,821,824,825,842,845,848,857,859,860,869,870,872,873,874,876,877,879,891,892,894,902,903,904,905,918,920,926,929,932,935,947,950,953,956,959,962,965,966,974,977,978,980,983,992,998,1001,1019,1025,1026,1034,1037,1038,1040,1041,1043,1047,1049,1050,1051,1056,1058,1060,1061,1062,1064,1067,1070,1074,1079,1082,1085,1091,1095,1096,1097,1098,1105,1110,1112,1113,1121,1124,1126,1127,1128,1133,1136,1138,1139,1142,1145,1146,1147,1152,1154,1157,1171,1172,1173,1175,1181,1189,1190,1192,1193,1196,1197,1212,1214,1229,1232,1235,1244,1256,1260,1262,1271,1277,1278,1286,1292,1295,1298,1299,1301,1304,1313,1322,1325,1337,1345,1346,1352,1355,1361,1364,1365,1366,1367,1378,1379,1386,1387,1388,1400,1403,1408,1409,1415,1416,1418,1420,1423,1430,1436,1439,1442,1444,1451,1454,1455,1456,1457,1460,1469,1478,1489,1491,1492,1493,1494,1496,1500,1501,1502,1505,1511,1512,1514,1515,1521,1526,1527,1531,1532,1535,1538,1539,1540,1543,1545,1549,1550,1552,1553,1554,1559,1562,1565,1568,1574,1580,1583,1595,1598,1601,1604

Score: 40.0 E-val: 1.31621
N.aligns:None Ident:26 Pos.:26 Align len:30
Num mismatches: 4
Mismatch pos: 2,17,19,23

Align Title:gi|357528259|gb|JN187080.1| Malus x domestica granule-bound starch synthase GBSS1 gene, complete cds
Score: 705.0 E-val: 0.0
N.aligns:None Ident:354 Pos.:354 Align len:355
Num mismatches: 1
Mismatch pos: 352

Score: 494.0 E-val: 7.73152e-124
N.aligns:None Ident:247 Pos.:247 Align len:247
No mismatches

Score: 388.0 E-val: 4.57377e-95
N.aligns:None Ident:194 Pos.:194 Align len:194
No mismatches

Score: 363.0 E-val: 5.21867e-88
N.aligns:None Ident:183 Pos.:183 Align len:184
Num mismatches: 1
Mismatch pos: 181

Score: 260.0 E-val: 2.53415e-60
N.aligns:None Ident:130 Pos.:130 Align len:130
No mismatches

Score: 238.0 E-val: 2.37346e-54
N.aligns:None Ident:119 Pos.:119 Align len:119
No mismatches

Score: 229.0 E-val: 1.22948e-51
N.aligns:None Ident:116 Pos.:116 Align len:117
Num mismatches: 1
Mismatch pos: 113

Score: 212.0 E-val: 2.70812e-47
N.aligns:None Ident:106 Pos.:106 Align len:106
No mismatches

Score: 208.0 E-val: 3.29916e-46
N.aligns:None Ident:104 Pos.:104 Align len:104
No mismatches

Score: 193.0 E-val: 7.26689e-42
N.aligns:None Ident:98 Pos.:98 Align len:99
Num mismatches: 1
Mismatch pos: 2

Score: 176.0 E-val: 1.60064e-37
N.aligns:None Ident:88 Pos.:88 Align len:88
No mismatches

Score: 165.0 E-val: 2.89402e-34
N.aligns:None Ident:84 Pos.:84 Align len:85
Num mismatches: 1
Mismatch pos: 82

Score: 140.0 E-val: 9.46061e-28
N.aligns:None Ident:70 Pos.:70 Align len:70
No mismatches

Align Title:gi|357528265|gb|JN187083.1| Malus x domestica granule-bound starch synthase GBSS4 pseudogene, complete sequence
Score: 603.0 E-val: 3.74445e-153
N.aligns:None Ident:582 Pos.:582 Align len:765
Num mismatches: 183
Mismatch pos: 5,11,17,23,26,33,38,39,44,59,71,92,95,110,113,116,122,125,128,134,135,137,143,146,149,152,161,172,173,177,178,182,183,186,194,196,197,202,205,207,210,211,212,213,214,220,226,229,232,233,234,235,236,251,266,269,282,287,290,295,301,305,311,313,323,329,333,334,335,336,338,343,344,347,349,352,359,363,364,366,368,371,375,377,380,382,389,393,395,397,398,407,410,413,416,417,419,420,427,434,437,452,455,458,464,473,476,486,488,491,494,499,500,507,509,513,518,521,524,527,530,533,536,542,544,545,548,551,554,556,557,558,566,575,584,594,598,599,600,602,608,609,617,618,621,627,629,630,632,633,635,639,641,644,647,650,659,663,674,677,680,683,686,692,695,704,707,708,709,713,714,716,722,727,731,732,734,740,750,752,754,756,758

Align Title:gi|357528263|gb|JN187082.1| Malus x domestica granule-bound starch synthase GBSS3 gene, complete cds
Score: 570.0 E-val: 1.81668e-144
N.aligns:None Ident:327 Pos.:327 Align len:355
Num mismatches: 28
Mismatch pos: 9,15,20,23,29,37,48,59,68,70,122,140,163,169,171,176,187,213,215,229,239,253,257,281,311,335,344,352

Score: 384.0 E-val: 5.572e-94
N.aligns:None Ident:225 Pos.:225 Align len:247
Num mismatches: 22
Mismatch pos: 2,5,10,13,55,58,61,67,79,87,94,97,133,151,170,185,187,208,214,215,225,238

Score: 283.0 E-val: 2.70573e-66
N.aligns:None Ident:173 Pos.:173 Align len:194
Num mismatches: 21
Mismatch pos: 2,8,11,18,33,38,44,45,56,59,90,91,93,101,113,125,132,140,158,173,176

Score: 279.0 E-val: 3.29625e-65
N.aligns:None Ident:162 Pos.:162 Align len:177
Num mismatches: 15
Mismatch pos: 11,14,44,46,67,71,103,106,133,142,145,155,160,167,174

Score: 220.0 E-val: 1.82472e-49
N.aligns:None Ident:122 Pos.:122 Align len:130
Num mismatches: 8
Mismatch pos: 6,27,38,50,57,68,80,101

Score: 188.0 E-val: 8.85288e-41
N.aligns:None Ident:97 Pos.:97 Align len:99
Num mismatches: 2
Mismatch pos: 86,87

Score: 184.0 E-val: 1.0785e-39
N.aligns:None Ident:107 Pos.:107 Align len:117
Num mismatches: 10
Mismatch pos: 10,38,48,56,63,73,85,88,94,104

Score: 182.0 E-val: 3.76434e-39
N.aligns:None Ident:106 Pos.:106 Align len:116
Num mismatches: 10
Mismatch pos: 4,46,47,48,55,62,68,79,109,113

Score: 178.0 E-val: 4.58591e-38
N.aligns:None Ident:98 Pos.:98 Align len:104
Num mismatches: 6
Mismatch pos: 8,18,36,63,65,90

Score: 156.0 E-val: 4.29511e-32
N.aligns:None Ident:84 Pos.:84 Align len:88
Num mismatches: 4
Mismatch pos: 7,30,66,74

Score: 152.0 E-val: 5.23252e-31
N.aligns:None Ident:88 Pos.:88 Align len:96
Num mismatches: 8
Mismatch pos: 12,18,42,43,54,59,69,85

Score: 140.0 E-val: 9.46061e-28
N.aligns:None Ident:79 Pos.:79 Align len:85
Num mismatches: 6
Mismatch pos: 6,24,42,67,74,82

Score: 115.0 E-val: 1.07946e-20
N.aligns:None Ident:65 Pos.:65 Align len:70
Num mismatches: 5
Mismatch pos: 26,32,36,56,62

Align Title:gi|357528261|gb|JN187081.1| Malus x domestica granule-bound starch synthase GBSS2 gene, complete cds
Score: 194.0 E-val: 2.082e-42
N.aligns:None Ident:187 Pos.:187 Align len:247
Num mismatches: 60
Mismatch pos: 2,5,13,16,19,22,25,34,43,46,52,53,55,61,66,70,71,73,79,95,97,110,111,114,115,118,124,127,133,142,143,148,152,154,155,157,160,161,162,163,166,169,170,187,190,193,202,204,205,214,215,217,218,219,221,222,224,236,237,239

Score: 150.0 E-val: 1.82633e-30
N.aligns:None Ident:96 Pos.:96 Align len:110
Num mismatches: 14
Mismatch pos: 5,11,17,23,26,33,38,39,44,59,71,92,95,104

Score: 148.0 E-val: 6.37451e-30
N.aligns:None Ident:146 Pos.:146 Align len:194
Num mismatches: 48
Mismatch pos: 2,5,11,15,16,17,18,25,30,32,33,41,44,46,47,48,53,56,58,59,62,65,66,67,72,74,77,91,92,93,95,101,109,110,112,113,116,117,132,134,149,152,155,164,176,180,182,191

Score: 132.0 E-val: 1.40408e-25
N.aligns:None Ident:105 Pos.:105 Align len:131
Num mismatches: 26
Mismatch pos: 12,14,20,23,26,29,41,44,47,50,53,56,59,60,68,71,72,74,77,86,92,95,113,119,120,128

Score: 108.0 E-val: 4.58996e-19
N.aligns:None Ident:72 Pos.:72 Align len:84
Num mismatches: 12
Mismatch pos: 5,11,14,17,32,47,50,63,68,71,74,80

Score: 107.0 E-val: 1.60205e-18
N.aligns:None Ident:94 Pos.:94 Align len:121
Num mismatches: 27
Mismatch pos: 10,11,18,19,20,32,35,40,41,47,48,50,52,55,62,68,71,74,76,83,86,87,88,89,92,101,110

Score: 91.0 E-val: 3.52876e-14
N.aligns:None Ident:71 Pos.:71 Align len:88
Num mismatches: 17
Mismatch pos: 6,7,15,21,24,27,28,30,33,42,51,54,66,74,75,81,84

Score: 73.0 E-val: 2.71291e-09
N.aligns:None Ident:71 Pos.:71 Align len:94
Num mismatches: 23
Mismatch pos: 11,17,19,29,35,39,40,41,42,44,49,50,53,55,58,65,68,69,72,74,81,83,86

Score: 62.0 E-val: 1.40532e-06
N.aligns:None Ident:52 Pos.:52 Align len:66
Num mismatches: 14
Mismatch pos: 3,6,12,15,18,24,25,27,33,36,39,42,51,63

Score: 61.0 E-val: 4.90505e-06
N.aligns:None Ident:53 Pos.:53 Align len:68
Num mismatches: 15
Mismatch pos: 4,8,10,12,13,22,25,28,31,32,34,35,42,49,52

Score: 53.0 E-val: 0.000727974
N.aligns:None Ident:82 Pos.:82 Align len:119
Num mismatches: 37
Mismatch pos: 4,8,10,13,14,16,22,23,25,26,32,37,38,42,43,46,49,50,51,54,56,60,61,63,64,65,70,73,76,79,85,91,94,106,109,112,115

Score: 40.0 E-val: 1.31621
N.aligns:None Ident:26 Pos.:26 Align len:30
Num mismatches: 4
Mismatch pos: 2,17,19,23

Align Title:gi|1632215725|ref|XM_029108378.1| PREDICTED: Malus domestica NEDD8-specific protease 1-like (LOC114827019), mRNA
Score: 79.0 E-val: 6.38014e-11
N.aligns:None Ident:53 Pos.:53 Align len:62
Num mismatches: 9
Mismatch pos: 2,11,26,28,29,36,45,50,58

Align Title:gi|1632206082|ref|XM_008358830.3| PREDICTED: Malus domestica starch synthase 1, chloroplastic/amyloplastic (LOC103420788), transcript variant X2, mRNA
Score: 56.0 E-val: 5.97557e-05
N.aligns:None Ident:49 Pos.:49 Align len:63
Num mismatches: 14
Mismatch pos: 5,8,14,17,20,22,26,27,30,32,50,53,56,59

Align Title:gi|1632206081|ref|XM_008358828.3| PREDICTED: Malus domestica starch synthase 1, chloroplastic/amyloplastic (LOC103420788), transcript variant X1, mRNA
Score: 56.0 E-val: 5.97557e-05
N.aligns:None Ident:49 Pos.:49 Align len:63
Num mismatches: 14
Mismatch pos: 5,8,14,17,20,22,26,27,30,32,50,53,56,59

Align Title:gi|1632223611|ref|XM_029087607.1| PREDICTED: Malus domestica starch synthase 3, chloroplastic/amyloplastic-like (LOC103429752), partial mRNA
Score: 53.0 E-val: 0.000727974
N.aligns:None Ident:76 Pos.:76 Align len:109
Num mismatches: 33
Mismatch pos: 4,15,18,19,21,24,25,26,27,29,30,33,36,39,50,51,54,55,57,58,59,60,75,76,78,79,81,91,92,93,94,95,102

Align Title:gi|1632169330|ref|XM_008382548.3| PREDICTED: Malus domestica starch synthase 1, chloroplastic/amyloplastic (LOC103443655), mRNA
Score: 51.0 E-val: 0.00254088
N.aligns:None Ident:48 Pos.:48 Align len:63
Num mismatches: 15
Mismatch pos: 2,8,11,14,17,20,22,26,30,32,44,50,53,56,59

Align Title:gi|1284883255|gb|KY524597.1| Malus domestica AT1G02020 mRNA, partial sequence
Score: 51.0 E-val: 0.00254088
N.aligns:None Ident:48 Pos.:48 Align len:63
Num mismatches: 15
Mismatch pos: 2,8,11,14,17,20,22,26,30,32,44,50,53,56,59

Align Title:gi|1632194644|ref|XM_029103312.1| PREDICTED: Malus domestica starch synthase 3, chloroplastic/amyloplastic (LOC103434594), mRNA
Score: 48.0 E-val: 0.00886854
N.aligns:None Ident:75 Pos.:75 Align len:109
Num mismatches: 34
Mismatch pos: 4,15,18,19,21,24,25,26,27,29,30,33,36,39,50,51,54,55,57,58,59,60,75,76,78,79,81,91,92,93,94,95,99,102

Align Title:gi|1632261657|ref|XM_029096170.1| PREDICTED: Malus domestica chromatin structure-remodeling complex protein SYD-like (LOC103431977), transcript variant X2, mRNA
Score: 41.0 E-val: 1.31621
N.aligns:None Ident:25 Pos.:25 Align len:28
Num mismatches: 3
Mismatch pos: 4,5,7

Align Title:gi|1632261655|ref|XM_029096169.1| PREDICTED: Malus domestica chromatin structure-remodeling complex protein SYD-like (LOC103431977), transcript variant X1, mRNA
Score: 41.0 E-val: 1.31621
N.aligns:None Ident:25 Pos.:25 Align len:28
Num mismatches: 3
Mismatch pos: 4,5,7

Align Title:gi|1632241173|ref|XM_029092074.1| PREDICTED: Malus domestica cytochrome b561 and DOMON domain-containing protein At3g61750-like (LOC103404475), transcript variant X3, mRNA
Score: 41.0 E-val: 1.31621
N.aligns:None Ident:25 Pos.:25 Align len:28
Num mismatches: 3
Mismatch pos: 18,19,21

Align Title:gi|1632241171|ref|XM_029092073.1| PREDICTED: Malus domestica cytochrome b561 and DOMON domain-containing protein At3g61750-like (LOC103404475), transcript variant X2, mRNA
Score: 41.0 E-val: 1.31621
N.aligns:None Ident:25 Pos.:25 Align len:28
Num mismatches: 3
Mismatch pos: 18,19,21

Align Title:gi|1632241169|ref|XM_008343395.2| PREDICTED: Malus domestica cytochrome b561 and DOMON domain-containing protein At3g61750-like (LOC103404475), transcript variant X1, mRNA
Score: 41.0 E-val: 1.31621
N.aligns:None Ident:25 Pos.:25 Align len:28
Num mismatches: 3
Mismatch pos: 18,19,21

Align Title:gi|1632238354|ref|XM_008392532.3| PREDICTED: Malus domestica chromatin structure-remodeling complex protein SYD-like (LOC103453001), transcript variant X4, mRNA
Score: 41.0 E-val: 1.31621
N.aligns:None Ident:25 Pos.:25 Align len:28
Num mismatches: 3
Mismatch pos: 4,5,7

Align Title:gi|1632238350|ref|XM_008392530.3| PREDICTED: Malus domestica chromatin structure-remodeling complex protein SYD-like (LOC103453001), transcript variant X2, mRNA
Score: 41.0 E-val: 1.31621
N.aligns:None Ident:25 Pos.:25 Align len:28
Num mismatches: 3
Mismatch pos: 4,5,7

Align Title:gi|1632238348|ref|XM_008392529.3| PREDICTED: Malus domestica chromatin structure-remodeling complex protein SYD-like (LOC103453001), transcript variant X1, mRNA
Score: 41.0 E-val: 1.31621
N.aligns:None Ident:25 Pos.:25 Align len:28
Num mismatches: 3
Mismatch pos: 4,5,7

Align Title:gi|1632193684|ref|XM_008373360.3| PREDICTED: Malus domestica LRR receptor-like serine/threonine-protein kinase FLS2 (LOC103434977), mRNA
Score: 41.0 E-val: 1.31621
N.aligns:None Ident:30 Pos.:30 Align len:36
Num mismatches: 6
Mismatch pos: 7,11,16,17,18,19

Align Title:gi|1632166542|ref|XM_029091540.1| PREDICTED: Malus domestica plant UBX domain-containing protein 9-like (LOC103406662), transcript variant X5, mRNA
Score: 41.0 E-val: 1.31621
N.aligns:None Ident:32 Pos.:32 Align len:37
Num mismatches: 5
Mismatch pos: 7,11,15,20,32

Align Title:gi|1632166540|ref|XM_029091520.1| PREDICTED: Malus domestica plant UBX domain-containing protein 9-like (LOC103406662), transcript variant X4, mRNA
Score: 41.0 E-val: 1.31621
N.aligns:None Ident:32 Pos.:32 Align len:37
Num mismatches: 5
Mismatch pos: 7,11,15,20,32

Align Title:gi|1632166538|ref|XM_029091488.1| PREDICTED: Malus domestica plant UBX domain-containing protein 9-like (LOC103406662), transcript variant X3, mRNA
Score: 41.0 E-val: 1.31621
N.aligns:None Ident:32 Pos.:32 Align len:37
Num mismatches: 5
Mismatch pos: 7,11,15,20,32

Align Title:gi|1632166536|ref|XM_008345648.3| PREDICTED: Malus domestica plant UBX domain-containing protein 9-like (LOC103406662), transcript variant X2, mRNA
Score: 41.0 E-val: 1.31621
N.aligns:None Ident:32 Pos.:32 Align len:37
Num mismatches: 5
Mismatch pos: 7,11,15,20,32

Align Title:gi|1632166534|ref|XM_029091435.1| PREDICTED: Malus domestica plant UBX domain-containing protein 9-like (LOC103406662), transcript variant X1, mRNA
Score: 41.0 E-val: 1.31621
N.aligns:None Ident:32 Pos.:32 Align len:37
Num mismatches: 5
Mismatch pos: 7,11,15,20,32

Align Title:gi|1632192461|ref|XR_003773535.1| PREDICTED: Malus domestica uncharacterized LOC114824934 (LOC114824934), transcript variant X3, ncRNA
Score: 40.0 E-val: 1.31621
N.aligns:None Ident:23 Pos.:23 Align len:25
Num mismatches: 2
Mismatch pos: 18,19

Align Title:gi|1632170586|ref|XM_029108527.1| PREDICTED: Malus domestica glycerophosphodiester phosphodiesterase GDPDL7-like (LOC103406697), transcript variant X3, mRNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 11

Align Title:gi|1632170584|ref|XM_008345687.2| PREDICTED: Malus domestica glycerophosphodiester phosphodiesterase GDPDL7-like (LOC103406697), transcript variant X2, mRNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 11

Align Title:gi|1632170582|ref|XM_008345686.2| PREDICTED: Malus domestica glycerophosphodiester phosphodiesterase GDPDL7-like (LOC103406697), transcript variant X1, mRNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:21 Pos.:21 Align len:22
Num mismatches: 1
Mismatch pos: 11

Align Title:gi|1632214967|ref|XM_008382221.3| PREDICTED: Malus domestica uncharacterized LOC103443388 (LOC103443388), mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:27 Pos.:27 Align len:31
Num mismatches: 4
Mismatch pos: 11,15,21,24

Align Title:gi|1632213490|ref|XM_008381298.3| PREDICTED: Malus domestica uncharacterized LOC103442502 (LOC103442502), transcript variant X2, mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 11,21

Align Title:gi|1632213488|ref|XM_008381297.3| PREDICTED: Malus domestica uncharacterized LOC103442502 (LOC103442502), transcript variant X1, mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 11,21

Align Title:gi|1632192404|ref|XR_003773527.1| PREDICTED: Malus domestica uncharacterized LOC114824931 (LOC114824931), ncRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 18,19

Align Title:gi|1632168202|ref|XM_008375822.3| PREDICTED: Malus domestica dual specificity tyrosine-phosphorylation-regulated kinase 2-like (LOC103437351), transcript variant X2, mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 11,17

Align Title:gi|1632168200|ref|XM_017333399.2| PREDICTED: Malus domestica dual specificity tyrosine-phosphorylation-regulated kinase 2-like (LOC103437351), transcript variant X1, mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 11,17

Align Title:gi|658309773|ref|NM_001293931.1| Malus domestica probable alpha-amylase 2 (LOC103440221), mRNA >gi|7532798|gb|AF153828.1|AF153828 Malus domestica alpha-amylase mRNA, complete cds
Score: 3172.0 E-val: 0.0
N.aligns:None Ident:1586 Pos.:1586 Align len:1586
No mismatches

Align Title:gi|1632206575|ref|XM_008378889.3| PREDICTED: Malus domestica probable alpha-amylase 2 (LOC103440221), transcript variant X3, mRNA
Score: 3063.0 E-val: 0.0
N.aligns:None Ident:1559 Pos.:1559 Align len:1576
Num mismatches: 17
Mismatch pos: 318,384,440,462,463,572,655,738,759,946,952,1144,1171,1213,1335,1380,1573

Align Title:gi|1632206574|ref|XM_008378890.3| PREDICTED: Malus domestica probable alpha-amylase 2 (LOC103440221), transcript variant X2, mRNA
Score: 3063.0 E-val: 0.0
N.aligns:None Ident:1559 Pos.:1559 Align len:1576
Num mismatches: 17
Mismatch pos: 318,384,440,462,463,572,655,738,759,946,952,1144,1171,1213,1335,1380,1573

Align Title:gi|1632206573|ref|XM_008378891.3| PREDICTED: Malus domestica probable alpha-amylase 2 (LOC103440221), transcript variant X1, mRNA
Score: 3063.0 E-val: 0.0
N.aligns:None Ident:1559 Pos.:1559 Align len:1576
Num mismatches: 17
Mismatch pos: 318,384,440,462,463,572,655,738,759,946,952,1144,1171,1213,1335,1380,1573

Align Title:gi|1632252077|ref|XM_029094733.1| PREDICTED: Malus domestica probable alpha-amylase 2 (LOC103413819), mRNA
Score: 1948.0 E-val: 0.0
N.aligns:None Ident:1203 Pos.:1203 Align len:1339
Num mismatches: 136
Mismatch pos: 10,39,50,51,53,54,55,58,87,103,130,165,166,167,168,170,184,188,197,201,229,230,231,233,236,240,245,256,258,265,266,267,268,269,270,271,272,273,274,276,277,281,282,283,286,289,290,291,292,293,294,295,299,306,318,323,327,338,341,342,343,344,346,354,372,373,390,393,407,420,421,426,437,443,457,458,462,463,476,484,486,487,516,520,526,567,596,661,679,727,739,744,762,783,808,835,862,914,917,931,934,935,938,946,952,970,976,998,1022,1035,1036,1075,1087,1159,1168,1177,1183,1195,1198,1211,1213,1237,1250,1274,1276,1279,1282,1306,1315,1316,1317,1318,1319,1325,1329,1336

Score: 41.0 E-val: 1.31621
N.aligns:None Ident:30 Pos.:30 Align len:35
Num mismatches: 5
Mismatch pos: 15,18,23,26,28

Align Title:gi|60652322|gb|AY939872.1| Malus x domestica cytosolic alpha-amylase (AMY9) gene, complete cds
Score: 391.0 E-val: 1.31041e-95
N.aligns:None Ident:220 Pos.:220 Align len:235
Num mismatches: 15
Mismatch pos: 27,48,58,62,75,114,128,141,142,158,183,184,206,207,228

Score: 334.0 E-val: 2.07832e-80
N.aligns:None Ident:202 Pos.:202 Align len:225
Num mismatches: 23
Mismatch pos: 45,54,63,69,81,84,97,99,123,136,160,162,165,168,192,201,202,203,204,205,211,215,222

Score: 270.0 E-val: 4.89207e-63
N.aligns:None Ident:144 Pos.:144 Align len:150
Num mismatches: 6
Mismatch pos: 8,12,18,59,88,147

Score: 241.0 E-val: 6.80008e-55
N.aligns:None Ident:128 Pos.:128 Align len:133
Num mismatches: 5
Mismatch pos: 53,101,104,113,125

Score: 199.0 E-val: 1.70901e-43
N.aligns:None Ident:110 Pos.:110 Align len:117
Num mismatches: 7
Mismatch pos: 7,25,73,85,90,108,114

Score: 199.0 E-val: 1.70901e-43
N.aligns:None Ident:116 Pos.:116 Align len:127
Num mismatches: 11
Mismatch pos: 8,60,63,77,80,81,84,92,98,116,122

Score: 177.0 E-val: 1.60064e-37
N.aligns:None Ident:96 Pos.:96 Align len:101
Num mismatches: 5
Mismatch pos: 8,21,22,61,73

Score: 169.0 E-val: 2.37556e-35
N.aligns:None Ident:89 Pos.:89 Align len:92
Num mismatches: 3
Mismatch pos: 17,42,69

Score: 90.0 E-val: 3.52876e-14
N.aligns:None Ident:48 Pos.:48 Align len:50
Num mismatches: 2
Mismatch pos: 10,39

Score: 77.0 E-val: 2.22689e-10
N.aligns:None Ident:40 Pos.:40 Align len:41
Num mismatches: 1
Mismatch pos: 22

Score: 72.0 E-val: 2.71291e-09
N.aligns:None Ident:38 Pos.:38 Align len:40
Num mismatches: 2
Mismatch pos: 8,35

Score: 67.0 E-val: 1.15356e-07
N.aligns:None Ident:35 Pos.:35 Align len:36
Num mismatches: 1
Mismatch pos: 25

Align Title:gi|1632268526|ref|XM_008359555.3| PREDICTED: Malus domestica uncharacterized LOC103421513 (LOC103421513), mRNA
Score: 172.0 E-val: 1.94998e-36
N.aligns:None Ident:377 Pos.:377 Align len:563
Num mismatches: 186
Mismatch pos: 6,8,9,17,18,20,21,24,37,38,39,40,42,43,44,45,48,51,52,57,60,63,65,70,71,77,78,79,81,87,90,92,94,97,106,108,110,111,113,114,118,123,128,132,135,137,143,144,146,147,153,159,162,170,171,172,174,175,176,177,180,181,182,183,187,190,195,198,207,208,209,214,216,217,219,220,222,225,228,229,231,232,233,235,238,239,245,246,253,254,255,259,261,264,266,267,270,273,287,294,295,296,298,301,302,305,306,311,317,318,320,323,326,335,338,341,342,343,344,347,348,351,353,354,355,356,361,362,366,368,369,371,372,373,374,377,380,386,389,393,395,398,401,402,404,416,422,423,431,434,435,437,440,446,449,455,461,466,467,476,479,482,483,484,486,489,491,492,496,498,503,507,515,518,521,524,527,532,536,537,538,539,540,548,551,557

Align Title:gi|1632213193|ref|XM_008359554.3| PREDICTED: Malus domestica uncharacterized LOC103421512 (LOC103421512), mRNA
Score: 164.0 E-val: 2.89402e-34
N.aligns:None Ident:375 Pos.:375 Align len:561
Num mismatches: 186
Mismatch pos: 6,8,9,17,20,21,24,37,38,39,40,42,43,44,45,51,52,57,63,65,70,74,76,77,79,85,88,92,95,104,106,108,109,111,112,115,116,124,126,130,133,135,136,139,141,142,144,145,151,157,160,168,169,170,172,173,174,175,178,179,180,181,185,188,193,196,205,206,207,211,212,214,217,218,219,221,223,224,230,231,232,233,234,237,238,244,245,252,253,254,258,260,263,265,269,272,286,293,295,298,299,301,303,304,306,309,315,316,318,324,333,336,339,340,341,342,345,346,349,351,352,353,354,359,360,364,366,369,370,371,372,375,378,381,384,387,390,391,393,396,399,400,402,414,420,421,429,432,433,435,438,444,447,453,459,464,468,474,477,480,481,482,484,487,489,490,494,495,496,501,505,507,513,516,519,522,525,530,534,535,536,537,538,546,549,555

Align Title:gi|1632235994|ref|XM_029090866.1| PREDICTED: Malus domestica alpha-amylase 3, chloroplastic-like (AMY10), transcript variant X1, mRNA
Score: 122.0 E-val: 7.27331e-23
N.aligns:None Ident:129 Pos.:129 Align len:173
Num mismatches: 44
Mismatch pos: 5,11,17,20,21,35,41,42,50,54,59,62,71,77,80,85,93,94,95,98,101,103,104,107,108,110,111,112,113,117,119,122,125,126,134,135,137,140,143,146,151,155,167,170

Align Title:gi|658309971|ref|NM_001294091.1| Malus domestica alpha-amylase 3, chloroplastic-like (AMY10), mRNA >gi|60652316|gb|AY939869.1| Malus x domestica plastid alpha-amylase (AMY10) mRNA, complete cds; nuclear gene for plastid product
Score: 122.0 E-val: 7.27331e-23
N.aligns:None Ident:129 Pos.:129 Align len:173
Num mismatches: 44
Mismatch pos: 5,11,17,20,21,35,41,42,50,54,59,62,71,77,80,85,93,94,95,98,101,103,104,107,108,110,111,112,113,117,119,122,125,126,134,135,137,140,143,146,151,155,167,170

Align Title:gi|1632262880|ref|XM_008341710.3| PREDICTED: Malus domestica alpha-amylase 3, chloroplastic-like (LOC103402925), mRNA
Score: 115.0 E-val: 1.07946e-20
N.aligns:None Ident:130 Pos.:130 Align len:175
Num mismatches: 45
Mismatch pos: 5,11,17,20,21,35,41,42,50,54,59,62,71,77,80,85,93,94,95,98,101,102,107,108,110,112,113,114,115,119,121,124,127,128,130,136,137,139,142,145,148,153,157,169,172

Align Title:gi|1632174389|ref|XM_029092045.1| PREDICTED: Malus domestica uncharacterized LOC114820820 (LOC114820820), mRNA
Score: 101.0 E-val: 6.8121e-17
N.aligns:None Ident:61 Pos.:61 Align len:68
Num mismatches: 7
Mismatch pos: 21,26,27,34,47,51,65

Align Title:gi|1632189813|ref|XM_008374926.3| PREDICTED: Malus domestica alpha-amylase (LOC103436492), mRNA
Score: 77.0 E-val: 2.22689e-10
N.aligns:None Ident:104 Pos.:104 Align len:145
Num mismatches: 41
Mismatch pos: 3,6,10,18,33,36,39,41,42,46,52,55,58,59,62,65,67,68,70,74,79,82,83,91,94,97,100,103,109,112,113,116,118,121,124,127,130,132,135,136,139

Align Title:gi|1632189811|ref|XM_008374925.3| PREDICTED: Malus domestica alpha-amylase-like (LOC103436491), mRNA
Score: 73.0 E-val: 2.71291e-09
N.aligns:None Ident:101 Pos.:101 Align len:144
Num mismatches: 43
Mismatch pos: 3,6,10,12,15,18,33,36,39,40,41,43,44,45,51,54,57,58,60,61,64,66,67,69,73,78,81,82,84,90,96,99,105,108,112,115,117,120,123,129,134,135,138

Align Title:gi|60652318|gb|AY939870.1| Malus x domestica secreted alpha-amylase (AMY2) mRNA, partial cds
Score: 71.0 E-val: 9.46897e-09
N.aligns:None Ident:83 Pos.:83 Align len:112
Num mismatches: 29
Mismatch pos: 3,6,10,18,33,36,39,41,42,46,52,55,58,59,62,65,67,68,70,74,79,82,83,91,94,97,100,103,109

Align Title:gi|1632211733|ref|XR_003775807.1| PREDICTED: Malus domestica uncharacterized LOC103424175 (LOC103424175), transcript variant X2, ncRNA
Score: 68.0 E-val: 3.305e-08
N.aligns:None Ident:37 Pos.:37 Align len:39
Num mismatches: 2
Mismatch pos: 7,34

Align Title:gi|1632211732|ref|XR_003775806.1| PREDICTED: Malus domestica uncharacterized LOC103424175 (LOC103424175), transcript variant X1, ncRNA
Score: 68.0 E-val: 3.305e-08
N.aligns:None Ident:37 Pos.:37 Align len:39
Num mismatches: 2
Mismatch pos: 7,34

Align Title:gi|1632223006|ref|XM_008360451.3| PREDICTED: Malus domestica protein DEHYDRATION-INDUCED 19-like (LOC103422385), transcript variant X2, mRNA
Score: 43.0 E-val: 0.3771
N.aligns:None Ident:34 Pos.:34 Align len:40
Num mismatches: 6
Mismatch pos: 14,15,16,20,28,34

Align Title:gi|1632223005|ref|XM_008360449.3| PREDICTED: Malus domestica protein DEHYDRATION-INDUCED 19-like (LOC103422385), transcript variant X1, mRNA
Score: 43.0 E-val: 0.3771
N.aligns:None Ident:34 Pos.:34 Align len:40
Num mismatches: 6
Mismatch pos: 14,15,16,20,28,34

Align Title:gi|1632171122|ref|XR_528151.3| PREDICTED: Malus domestica uncharacterized LOC103426622 (LOC103426622), ncRNA
Score: 43.0 E-val: 0.3771
N.aligns:None Ident:26 Pos.:26 Align len:29
Num mismatches: 3
Mismatch pos: 8,21,23

Align Title:gi|1632215018|ref|XM_008382491.3| PREDICTED: Malus domestica uncharacterized protein C630.12 (LOC103443613), transcript variant X2, mRNA
Score: 40.0 E-val: 1.31621
N.aligns:None Ident:25 Pos.:25 Align len:27
Num mismatches: 2
Mismatch pos: 15,19

Align Title:gi|1632215017|ref|XM_008382490.3| PREDICTED: Malus domestica uncharacterized protein C630.12 (LOC103443613), transcript variant X1, mRNA
Score: 40.0 E-val: 1.31621
N.aligns:None Ident:25 Pos.:25 Align len:27
Num mismatches: 2
Mismatch pos: 15,19

Align Title:gi|1632200206|ref|XM_008350248.3| PREDICTED: Malus domestica probable LRR receptor-like serine/threonine-protein kinase At1g63430 (LOC103411618), mRNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:27 Pos.:27 Align len:32
Num mismatches: 5
Mismatch pos: 4,9,12,16,18

Align Title:gi|1632245259|ref|XM_029093131.1| PREDICTED: Malus domestica dynamin-related protein 4C-like (LOC114821184), mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:36 Pos.:36 Align len:45
Num mismatches: 9
Mismatch pos: 5,9,10,13,17,18,30,35,40

Align Title:gi|1632226752|ref|XM_029088520.1| PREDICTED: Malus domestica serine/threonine-protein kinase GRIK2 (LOC103401466), transcript variant X2, mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:28 Pos.:28 Align len:34
Num mismatches: 6
Mismatch pos: 4,6,9,24,26,27

Align Title:gi|1632226750|ref|XM_029088519.1| PREDICTED: Malus domestica serine/threonine-protein kinase GRIK2 (LOC103401466), transcript variant X1, mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:28 Pos.:28 Align len:34
Num mismatches: 6
Mismatch pos: 4,6,9,24,26,27

Align Title:gi|1632255559|ref|XM_029095487.1| PREDICTED: Malus domestica probable starch synthase 4, chloroplastic/amyloplastic (LOC103446268), transcript variant X2, mRNA
Score: 4494.0 E-val: 0.0
N.aligns:None Ident:2247 Pos.:2247 Align len:2247
No mismatches

Align Title:gi|1632255557|ref|XM_029095486.1| PREDICTED: Malus domestica probable starch synthase 4, chloroplastic/amyloplastic (LOC103446268), transcript variant X1, mRNA
Score: 4467.0 E-val: 0.0
N.aligns:None Ident:2247 Pos.:2247 Align len:2258
Num mismatches: 11
Mismatch pos: 240,241,242,243,244,245,246,247,248,249,250

Align Title:gi|1632166473|ref|XM_029090068.1| PREDICTED: Malus domestica probable starch synthase 4, chloroplastic/amyloplastic (LOC103426542), mRNA
Score: 4116.0 E-val: 0.0
N.aligns:None Ident:2176 Pos.:2176 Align len:2252
Num mismatches: 76
Mismatch pos: 10,18,19,24,25,29,88,141,142,143,154,167,170,197,230,231,232,233,234,235,236,237,238,239,240,255,256,357,394,429,503,540,552,591,619,654,675,731,745,765,804,807,808,831,844,858,918,1135,1158,1267,1282,1296,1359,1395,1531,1548,1549,1565,1596,1692,1733,1760,1839,1864,1961,2034,2056,2057,2145,2148,2172,2173,2174,2182,2219,2240

Align Title:gi|1632178903|ref|XM_008355920.3| PREDICTED: Malus domestica probable protein phosphatase 2C 6 (LOC103417757), mRNA
Score: 42.0 E-val: 0.3771
N.aligns:None Ident:35 Pos.:35 Align len:43
Num mismatches: 8
Mismatch pos: 13,14,15,16,17,19,32,34

Align Title:gi|1632162884|ref|XM_008377756.3| PREDICTED: Malus domestica mitogen-activated protein kinase homolog MMK2-like (LOC103439212), mRNA
Score: 42.0 E-val: 0.3771
N.aligns:None Ident:27 Pos.:27 Align len:31
Num mismatches: 4
Mismatch pos: 4,6,19,28

Align Title:gi|1632223925|ref|XM_029087690.1| PREDICTED: Malus domestica two-pore potassium channel 1-like (LOC103434415), mRNA
Score: 41.0 E-val: 1.31621
N.aligns:None Ident:25 Pos.:25 Align len:28
Num mismatches: 3
Mismatch pos: 2,16,20

Align Title:gi|1632205457|ref|XM_008378146.3| PREDICTED: Malus domestica oleosin 1-like (LOC103439585), mRNA
Score: 40.0 E-val: 1.31621
N.aligns:None Ident:29 Pos.:29 Align len:35
Num mismatches: 6
Mismatch pos: 2,5,20,22,29,31

Align Title:gi|1632186274|ref|XM_008365690.3| PREDICTED: Malus domestica uncharacterized LOC103427620 (LOC103427620), transcript variant X2, mRNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:30 Pos.:30 Align len:37
Num mismatches: 7
Mismatch pos: 12,17,18,20,23,29,34

Align Title:gi|1632186272|ref|XM_008365689.3| PREDICTED: Malus domestica uncharacterized LOC103427620 (LOC103427620), transcript variant X1, mRNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:30 Pos.:30 Align len:37
Num mismatches: 7
Mismatch pos: 12,17,18,20,23,29,34

Align Title:gi|1632183600|ref|XM_029100637.1| PREDICTED: Malus domestica uncharacterized LOC114824207 (LOC114824207), mRNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:41 Pos.:41 Align len:53
Num mismatches: 12
Mismatch pos: 2,8,10,11,13,17,31,32,35,36,42,45

Align Title:gi|1632167864|ref|XM_008389523.3| PREDICTED: Malus domestica heat shock cognate 70 kDa protein-like (LOC103450210), mRNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:27 Pos.:27 Align len:31
Num mismatches: 4
Mismatch pos: 5,7,19,20

Align Title:gi|1632167856|ref|XM_008364489.3| PREDICTED: Malus domestica heat shock cognate 70 kDa protein-like (LOC103426395), mRNA
Score: 39.0 E-val: 4.59402
N.aligns:None Ident:27 Pos.:27 Align len:31
Num mismatches: 4
Mismatch pos: 5,7,19,20

Align Title:gi|1632268257|ref|XR_003770907.1| PREDICTED: Malus domestica uncharacterized LOC108170119 (LOC108170119), ncRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 3,7

Align Title:gi|1632255849|ref|XM_008342676.3| PREDICTED: Malus domestica uncharacterized LOC103403829 (LOC103403829), mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:24 Pos.:24 Align len:26
Num mismatches: 2
Mismatch pos: 3,18

Align Title:gi|1632229560|ref|XM_008388384.3| PREDICTED: Malus domestica rho GTPase-activating protein 2 (LOC103449102), mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 2,21

Align Title:gi|1632219772|ref|XM_008379093.3| PREDICTED: Malus domestica probable receptor-like serine/threonine-protein kinase At4g34500 (LOC103440412), mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:25 Pos.:25 Align len:29
Num mismatches: 4
Mismatch pos: 12,16,22,23

Align Title:gi|1632200352|ref|XM_029104682.1| PREDICTED: Malus domestica ubiquitin-conjugating enzyme E2-23 kDa-like (LOC114825653), mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:19 Pos.:19 Align len:19
No mismatches

Align Title:gi|1632187865|ref|XR_003772816.1| PREDICTED: Malus domestica uncharacterized LOC103408678 (LOC103408678), transcript variant X14, ncRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 11,17

Align Title:gi|1632187864|ref|XR_003772815.1| PREDICTED: Malus domestica uncharacterized LOC103408678 (LOC103408678), transcript variant X13, ncRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 11,17

Align Title:gi|1632187863|ref|XR_003772814.1| PREDICTED: Malus domestica uncharacterized LOC103408678 (LOC103408678), transcript variant X12, ncRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 11,17

Align Title:gi|1632187861|ref|XR_003772812.1| PREDICTED: Malus domestica uncharacterized LOC103408678 (LOC103408678), transcript variant X10, ncRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 11,17

Align Title:gi|1632187860|ref|XR_003772811.1| PREDICTED: Malus domestica uncharacterized LOC103408678 (LOC103408678), transcript variant X9, ncRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 11,17

Align Title:gi|1632187859|ref|XR_003772810.1| PREDICTED: Malus domestica uncharacterized LOC103408678 (LOC103408678), transcript variant X8, ncRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 11,17

Align Title:gi|1632187857|ref|XR_003772808.1| PREDICTED: Malus domestica uncharacterized LOC103408678 (LOC103408678), transcript variant X6, ncRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 11,17

Align Title:gi|1632187855|ref|XR_003772806.1| PREDICTED: Malus domestica uncharacterized LOC103408678 (LOC103408678), transcript variant X4, ncRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 11,17

Align Title:gi|1632187854|ref|XR_003772805.1| PREDICTED: Malus domestica uncharacterized LOC103408678 (LOC103408678), transcript variant X3, ncRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 11,17

Align Title:gi|1632187852|ref|XR_003772803.1| PREDICTED: Malus domestica uncharacterized LOC103408678 (LOC103408678), transcript variant X1, ncRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 11,17

Align Title:gi|1632170394|ref|XM_008385860.3| PREDICTED: Malus domestica acyl-coenzyme A thioesterase 9, mitochondrial-like (LOC103446727), mRNA
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:22 Pos.:22 Align len:24
Num mismatches: 2
Mismatch pos: 3,19

Align Title:gi|1284951105|gb|KY538526.1| Malus domestica AT1G08610 mRNA, partial sequence
Score: 38.0 E-val: 4.59402
N.aligns:None Ident:25 Pos.:25 Align len:29
Num mismatches: 4
Mismatch pos: 12,16,22,23

5. Write a python function getPublicationInfo(title_term,other_term) that retrieves the first 20 pubmed publications having the title_term in the title and other_term somewhere else in the text (hint use: “Title” and “[Other Term]” as esearch parameter term). For each publication print:
   1. the title
   2. authors
   3. journal
   4. year of publication (hint: get and split properly the “PubDate” entry)
   5. a link to the pubmed entry (hint: it is the string “https://www.ncbi.nlm.nih.gov/pubmed/” followed by the pubmed id (“eid” entry of the dictionary “ArticleIds”). es: https://www.ncbi.nlm.nih.gov/pubmed/26919684

Hint: to see how to combine search terms test them here: https://www.ncbi.nlm.nih.gov/pubmed/advanced.

Test your code calling getPublicationInfo("apple","drought")

Show/Hide Solution

from Bio import Entrez

def getPublicationInfo(title_term,other_term):
    Entrez.email = "my_email"
    s_term = title_term + " [Title] AND " + other_term + " [Other Term]"
    handle = Entrez.esearch(db="pubmed", term=s_term)
    res = Entrez.read(handle)
#uncomment to see all info
#    for el in res.keys():
#        print(el , " : ", res[el])
#
#    print("")
    for ids in res["IdList"]:
        handle = Entrez.esummary(db="pubmed",  id = ids)
        res = Entrez.read(handle)
        #uncomment to see all info
        #print(res)
        for r in res:
            print(r["Title"])
            print(",".join(r["AuthorList"]))
            print(r["Source"])
            print(r["PubDate"].split()[0])
            print("https://www.ncbi.nlm.nih.gov/pubmed/" + r["ArticleIds"]["eid"])
            print("")

getPublicationInfo("apple","drought")

[Effects of PGPR inoculation on photosynthesis and physiological-ecological characteristics of apple seedlings under drought stress].
Xu XD,Zhang C,Qin C,Su YY,Zhou J,Zhang H,Zhang LX
Ying Yong Sheng Tai Xue Bao
2019
https://www.ncbi.nlm.nih.gov/pubmed/31621237

The ERF transcription factor MdERF38 promotes drought stress-induced anthocyanin biosynthesis in apple.
An JP,Zhang XW,Bi SQ,You CX,Wang XF,Hao YJ
Plant J
2019
https://www.ncbi.nlm.nih.gov/pubmed/31571281

MdGRF11, an apple 14-3-3 protein, acts as a positive regulator of drought and salt tolerance.
Ren YR,Yang YY,Zhang R,You CX,Zhao Q,Hao YJ
Plant Sci
2019
https://www.ncbi.nlm.nih.gov/pubmed/31521216

Response of sugar metabolism in apple leaves subjected to short-term drought stress.
Yang J,Zhang J,Li C,Zhang Z,Ma F,Li M
Plant Physiol Biochem
2019
https://www.ncbi.nlm.nih.gov/pubmed/31170640

An apple (Malus domestica) NAC transcription factor enhances drought tolerance in transgenic apple plants.
Jia D,Jiang Q,van Nocker S,Gong X,Ma F
Plant Physiol Biochem
2019
https://www.ncbi.nlm.nih.gov/pubmed/31015089

Impact of foliar fertilization on apple and pear trees in reconciling productivity and alleviation of environmental concerns under arid conditions.
Zargar M,Tumanyan A,Ivanenko E,Dronik A,Tyutyuma N,Pakina E
Commun Integr Biol
2019
https://www.ncbi.nlm.nih.gov/pubmed/30891112

Apple AP2/EREBP transcription factor MdSHINE2 confers drought resistance by regulating wax biosynthesis.
Zhang YL,Zhang CL,Wang GL,Wang YX,Qi CH,You CX,Li YY,Hao YJ
Planta
2019
https://www.ncbi.nlm.nih.gov/pubmed/30826884

Overexpression of the RNA binding protein MhYTP1 in transgenic apple enhances drought tolerance and WUE by improving ABA level under drought condition.
Guo T,Wang N,Xue Y,Guan Q,van Nocker S,Liu C,Ma F
Plant Sci
2019
https://www.ncbi.nlm.nih.gov/pubmed/30824018

Does fertilization explain the extraordinary hydraulic behaviour of apple trees?
Beikircher B,Losso A,Gemassmer M,Jansen S,Mayr S
J Exp Bot
2019
https://www.ncbi.nlm.nih.gov/pubmed/30793193

Neoformation and summer arrest are common sources of tree plasticity in response to water stress of apple cultivars.
Chen D,Pallas B,Martinez S,Wang Y,Costes E
Ann Bot
2019
https://www.ncbi.nlm.nih.gov/pubmed/30596816

An apple transcription factor, MdDREB76, confers salt and drought tolerance in transgenic tobacco by activating the expression of stress-responsive genes.
Sharma V,Goel P,Kumar S,Singh AK
Plant Cell Rep
2019
https://www.ncbi.nlm.nih.gov/pubmed/30511183

Comprehensive genomic analysis of the TYROSINE AMINOTRANSFERASE (TAT) genes in apple (Malus domestica) allows the identification of MdTAT2 conferring tolerance to drought and osmotic stresses in plants.
Wang H,Dong Q,Duan D,Zhao S,Li M,van Nocker S,Ma F,Mao K
Plant Physiol Biochem
2018
https://www.ncbi.nlm.nih.gov/pubmed/30391815

Genome-wide analyses of genes encoding FK506-binding proteins reveal their involvement in abiotic stress responses in apple.
Dong Q,Mao K,Duan D,Zhao S,Wang Y,Wang Q,Huang D,Li C,Liu C,Gong X,Ma F
BMC Genomics
2018
https://www.ncbi.nlm.nih.gov/pubmed/30253753

Genome-Wide Analysis and Cloning of the Apple Stress-Associated Protein Gene Family Reveals MdSAP15, Which Confers Tolerance to Drought and Osmotic Stresses in Transgenic Arabidopsis.
Dong Q,Duan D,Zhao S,Xu B,Luo J,Wang Q,Huang D,Liu C,Li C,Gong X,Mao K,Ma F
Int J Mol Sci
2018
https://www.ncbi.nlm.nih.gov/pubmed/30134640

An apple sucrose transporter MdSUT2.2 is a phosphorylation target for protein kinase MdCIPK22 in response to drought.
Ma QJ,Sun MH,Lu J,Kang H,You CX,Hao YJ
Plant Biotechnol J
2019
https://www.ncbi.nlm.nih.gov/pubmed/30133123

Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress.
Wang H,Zhao S,Mao K,Dong Q,Liang B,Li C,Wei Z,Li M,Ma F
BMC Plant Biol
2018
https://www.ncbi.nlm.nih.gov/pubmed/29940853

Significant and unique changes in phosphorylation levels of four phosphoproteins in two apple rootstock genotypes under drought stress.
Ren J,Mao J,Zuo C,Calderón-Urrea A,Dawuda MM,Zhao X,Li X,Chen B
Mol Genet Genomics
2017
https://www.ncbi.nlm.nih.gov/pubmed/28710562

Improvement of drought tolerance by overexpressing MdATG18a is mediated by modified antioxidant system and activated autophagy in transgenic apple.
Sun X,Wang P,Jia X,Huo L,Che R,Ma F
Plant Biotechnol J
2018
https://www.ncbi.nlm.nih.gov/pubmed/28703378

Genome Wide Identification and Characterization of Apple bHLH Transcription Factors and Expression Analysis in Response to Drought and Salt Stress.
Mao K,Dong Q,Li C,Liu C,Ma F
Front Plant Sci
2017
https://www.ncbi.nlm.nih.gov/pubmed/28443104

Comprehensive Genomic Identification and Expression Analysis of the Phosphate Transporter (PHT) Gene Family in Apple.
Sun T,Li M,Shao Y,Yu L,Ma F
Front Plant Sci
2017
https://www.ncbi.nlm.nih.gov/pubmed/28424713

6. Write some python code to retrieve the structure of two forms of the aspartate transcarbamoylase (PDB ids: 4FYW and 1D09). If you are interested, read more about the Aspartate Transcarbamoylase here. Write a function that gets the .cif file name and prints:
   1. the number of chains, residues and atoms present in the file;
   2. a histogram of the residues (plotting it with matplotlib) that are not water (encoded as “HOH”);
   3. a link to an online tool to visualize the 3D structure. The link will be “http://www.rcsb.org/pdb/ngl/ngl.do?pdbid=” followed by the PDB id of the protein (e.g. 1d09).

Show/Hide Solution

from Bio.PDB import *
import matplotlib.pyplot as plt

def printCifInfo(filename):

    parser = MMCIFParser(QUIET=True) #To disable warnings
    id = filename.split("/")[1].split(".")[0]

    structure = parser.get_structure(id, filename)
    chains = structure.get_chains()
    residues = structure.get_residues()

    atoms = structure.get_atoms()
    res_histo = {}
    resCnt = 0 #need this because while reading the residues
               #I am pulling stuff out of the iterator
    for res in residues:
        rname = res.get_resname()
        if(rname != "HOH"):
            if( rname not in res_histo):
                res_histo[rname] = 1
            else:
                res_histo[rname] += 1
        resCnt += 1
    plt.figure(figsize=(15,5))
    plt.bar(res_histo.keys(), res_histo.values())
    plt.show()
    print("Number of chains: {}".format(len(list(chains))))
    print("Number of residues: {}".format(resCnt))
    print("Number of atoms: {}".format(len(list(atoms))))
    print("http://www.rcsb.org/pdb/ngl/ngl.do?pdbid=" + id)

pdbl = PDBList()
structures = ["1D09", "4FYW"]
el = pdbl.download_pdb_files(structures, file_format = "mmCif", pdir = "file_samples/")

printCifInfo("file_samples/1d09.cif")
printCifInfo("file_samples/4fyw.cif")

Structure exists: 'file_samples/1d09.cif'
Structure exists: 'file_samples/4fyw.cif'

Number of chains: 4
Number of residues: 1547
Number of atoms: 7883
http://www.rcsb.org/pdb/ngl/ngl.do?pdbid=1d09

Number of chains: 4
Number of residues: 1483
Number of atoms: 7714
http://www.rcsb.org/pdb/ngl/ngl.do?pdbid=4fyw

Midterm test simulation

Before you start

Please write one single python script.

IMPORTANT: Add your name and ID (matricola) on top of each .py file!

Problem 1

Given a text string \(S\) (possibly on several lines), write a python function that takes the string \(S\) and a second string \(S_1\) (note: assumed to be shorter than S) in inpu and returns a list with all positions at which \(S_1\) starts in \(S\). If no such positions exist a warning message should be printed.

Ex.

S = """TGAATACATATTATTCCGC
GTCCTACCAAAAAATATACATAGATAT
GATACTAGGGGACCGGTTCCGGGATGATGAT"""

print(findPositions(S, "TGA"))
print(findPositions(S, "GAT"))
print(findPositions(S, "none"))

should return:

String 'TGA' found at the following positions:
[0, 45, 70, 73]

String 'GAT' found at the following positions:
[41, 46, 68, 71, 74]

Warning: string 'none' not found. Returning None
None

Problem 2

The .tsv file gene_models.tsv is a compact representation of the gene models on the genome having sequence specified in sequences.fasta. The first few lines are reported below:

Chr     feature start   end     ID
Chr05   gene    50988   51101   gene:MD05G1000100
Chr05   ncRNA   50988   51101   ncRNA:MD05G1000100
Chr05   gene    83210   83329   gene:MD05G1000200
Chr05   ncRNA   83210   83329   ncRNA:MD05G1000200
Chr05   gene    87650   91333   gene:MD05G1000300
Chr05   mRNA    87650   91333   mRNA:MD05G1000300
Chr05   CDS     87650   87727   CDS:MD05G1000300.8

as the header (first line) describes, the first column is the chromosome containing the feature (that can be gene, ncRNA, exon, CDS, …), the third and fourth columns are the start and end position of the feature on the chromosome and the fifth row is the identifier of the feature ID. Note that, unlike python strings, features in ``gene_models`` start from coordinate 1 instead of 0.

The file sequences.fasta stores sequence information in .fasta format. A mock entry is the following:

>Chr01
AGGCCTAGGTCTTCCAGAGTCGCTTTTTCCAGCTCCAGACCGATCTCTTCAG
AGGCCAATCGCCAGTTTACCACATACACCCAGACCGATCTCTTCAG

where the first line is the identifier of the read and starts with a “>”. The sequence follows the line with the identifier and can be on multiple lines.

Implement the following python functions:

1. computeGeneStats(filename): gets the filename of a .tsv file as explained above, stores its content in a suitable data structure of your choice (hint: pandas might help here), counts (and prints) the number of features of type gene, printing the minimum, maximum and average gene length in the whole file. The function should also produce a bar plot of the number of genes per chromosome.

Note: The function should return the data structure containing all the data.

Calling:

fn = "gene_models.tsv"
seqFile = "sequences.fasta"
GenesDF = computeGeneStats(fn)

should give:

29136 genes present
Avg gene length: 2724.71
Min gene length: 45
Max gene length: 53052

2. printSequence(geneInfo, geneID, sequenceFile): gets the geneInfo data structure created by computeGeneStats, a gene identifier geneID and the filename of a fasta formatted file sequenceFile and if geneID is present in geneInfo it prints its length and a fasta-formatted string reporting the sequence of the gene Note that chromosome, start and end position are saved in geneInfo. If the chromosome is not in the sequenceFile or geneID is not in geneInfo the function should display a corresponding message (see examples below). Optional: add a parameter outFile with default value None, that if set (it will contain the path to an output file) makes the function write the fasta entries to file outFile rather than to the screen.

Hint: you can use biophtyon to read a fasta file.

For example, assuming an entry:

ChrX   gene   3   7   gene:geneid1

in geneInfo and a sequence:

>ChrX
GATTACATAACACACTACA

in sequenceFile, calling printSequence(geneInfo,"geneid1",sequenceFile) should print:

Gene geneid1 is in ChrX and has length 5
>geneid1:ChrX:3_7
TTACA

Given GenesDF as returned by computeGeneStats, calling:

printSequence(GenesDF,"MD05G1000100",seqFile)
print("")
printSequence(GenesDF,"MD03G1000400",seqFile)
print("")
printSequence(GenesDF,"MD08G1000100",seqFile)
print("")
printSequence(GenesDF,"MD08G100019191",seqFile)

should give:

Gene MD05G1000100 is in Chr05 and has length 114
>MD05G1000100:Chr05:50988_51101
CGCCCAAGGGAGTGGATCCTGTAAGCCTTATATGTATATTCCCATCTCTACCTAGCACGAGGCCTTTTGGGAGCTCATTGGCTTCGGGTTATTGTCACATCCCGACCCGAGCCC

Gene MD03G1000400 is in Chr03 and has length 189
>MD03G1000400:Chr03:21801_21989
CGTATTATAGGAATTCTTCTTCCATTGAAAGGATGGATTGAAAGGATGGATGGCATGTTGTCTATACCTCTCGTCATTAGGATGTACAATAATGGCAGTATCACCGAGCATAGTTTCCACTCTAGTGGTGGCCACCATAATCTCACCAAAGTCTTCCTCTAGAGTATAAGCAAATGAAGTTAACATGCC

Gene MD08G1000100 is in Chr08 and has length 5384
Chr08 is not present in the sequence file.

GeneID MD08G100019191 is not present in the input file.
Gene MD05G1000100 is in Chr05 and has length 114

3. (Optional) Modify the function computeGeneStats(filename) to make it also plot a boxplot of the gene lengths per chromosome.

Expected output:

Available material for exams

The course notes can be used as the slides of the theory and practicals. Documents on the libraries are here:

• matplotlib
• numpy
• pandas
• biopython

You can download all of them here: archive

Download the data

Create a “qcbsciprolab-2019-31-10-NAME-SURNAME-ID” folder on the desktop. Download the following data to the folder that you just created.

The gene models .tsv file: gene_models.tsv and the fasta file with the sequences: sequences.fasta. Note that the files are gzipped, so before using them gunzip them in a terminal with:

gunzip sequences.fasta.gz
gunzip gene_models.tsv.gz

A possible solution:

Problem 1

%reset -s -f


def findPositions(S, S1):
    s1len = len(S1)
    S = S.replace("\n","")
    ret = [x for x in range(0,len(S)) if S[x:x+s1len] == S1]
    if len(ret) > 0:
        print("\nString '{}' found at the following positions:".format(S1))
        return ret
    else:
        print("\nWarning: string '{}' not found. Returning None".format(S1,S))



S = """TGAATACATATTATTCCGC
GTCCTACCAAAAAATATACATAGATAT
GATACTAGGGGACCGGTTCCGGGATGATGAT"""

print(findPositions(S, "TGA"))
print(findPositions(S, "GAT"))
print(findPositions(S, "none"))

String 'TGA' found at the following positions:
[0, 45, 70, 73]

String 'GAT' found at the following positions:
[41, 46, 68, 71, 74]

Warning: string 'none' not found. Returning None
None

Problem 2

%reset -s -f
"""exercise.py"""

import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
from Bio import SeqIO


def computeGeneStats(filename):
    geneInfo = pd.read_csv(filename, sep="\t", header = 0)
    genes = geneInfo[ geneInfo["feature"] == "gene"]
    #print(genes.head())
    print("{} genes present".format(genes.shape[0]))
    #print(genes.head())
    avg = np.mean(genes["end"] - genes["start"] + 1)
    m = np.min(genes["end"] - genes["start"] + 1 )
    M = np.max(genes["end"] - genes["start"] + 1 )
    print("Avg gene length: {:.2f}\nMin gene length: {}\nMax gene length: {}".format(avg, m, M))

    grpd = genes.groupby(["Chr"])
    agg = grpd.aggregate(pd.DataFrame.count)["feature"]
    agg.plot(kind = 'bar')
    plt.title("Gene count by Chr")
    plt.ylabel("# Genes")
    plt.xlabel("Chr")
    plt.show()

    bpdata = {}
    for i, g in grpd:
        if(i not in bpdata):
            bpdata[i] = []
        bpdata[i] = g["end"] - g["start"] + 1

    pdData = pd.DataFrame(bpdata)
    pdData.plot(kind='box')
    plt.title("Gene Lengths Boxplot")
    plt.ylabel("Gene length")
    plt.xlabel("Chr")
    plt.show()

    return geneInfo

def printSequence(geneInfo, geneID, sequenceFile, outFile = None):
        gn = "gene:" + geneID
        gene = geneInfo[geneInfo["ID"] == gn]
        of = None
        if outFile != None:
            of = open(outFile, "w")

        if len(gene) > 0:
            seqDict = SeqIO.to_dict(SeqIO.parse(sequenceFile, "fasta"))
            chr = gene.iloc[0]["Chr"]
            start = gene.iloc[0]["start"]
            end = gene.iloc[0]["end"]
            print("Gene {} is in {} and has length {}".format(geneID,chr, end-start + 1))
            if chr in seqDict:
                s = seqDict[chr].seq[start-1:end ]
                if outFile != None:
                    of.write(">"+geneID + ":" + chr +":" + str(start) + "_" + str(end)+"\n")
                    of.write(str(s)+"\n")
                else:
                    print(">"+geneID + ":" + chr +":" + str(start) + "_" + str(end))
                    print(str(s))
            else:
                print(chr, "is not present in the sequence file.")

        else:
            print("GeneID {} is not present in the input file.".format(geneID))

        if outFile != None:
            of.close()



fn = "./midterm_sim/gene_models.tsv"
seqFile = "./midterm_sim/sequences.fasta"

GenesDF = computeGeneStats(fn)
printSequence(GenesDF,"MD05G1000100",seqFile)
print("")
printSequence(GenesDF,"MD03G1000400",seqFile)
print("")
printSequence(GenesDF,"MD08G1000100",seqFile)
print("")
printSequence(GenesDF,"MD08G100019191",seqFile)

printSequence(GenesDF,"MD05G1000100",seqFile, "MD05G1000100.fasta")

29136 genes present
Avg gene length: 2724.71
Min gene length: 45
Max gene length: 53052

Gene MD05G1000100 is in Chr05 and has length 114
>MD05G1000100:Chr05:50988_51101
CGCCCAAGGGAGTGGATCCTGTAAGCCTTATATGTATATTCCCATCTCTACCTAGCACGAGGCCTTTTGGGAGCTCATTGGCTTCGGGTTATTGTCACATCCCGACCCGAGCCC

Gene MD03G1000400 is in Chr03 and has length 189
>MD03G1000400:Chr03:21801_21989
CGTATTATAGGAATTCTTCTTCCATTGAAAGGATGGATTGAAAGGATGGATGGCATGTTGTCTATACCTCTCGTCATTAGGATGTACAATAATGGCAGTATCACCGAGCATAGTTTCCACTCTAGTGGTGGCCACCATAATCTCACCAAAGTCTTCCTCTAGAGTATAAGCAAATGAAGTTAACATGCC

Gene MD08G1000100 is in Chr08 and has length 5384
Chr08 is not present in the sequence file.

GeneID MD08G100019191 is not present in the input file.
Gene MD05G1000100 is in Chr05 and has length 114

Index