{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# COMP 204 Lecture 27\n",
    "# Handling Sequence with BioPython\n",
    "## Yue Li\n",
    "#### based on materials from Mathieu Blanchette"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Edit directly on the notebook"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2\n",
      "Hello world\n"
     ]
    }
   ],
   "source": [
    "x=2\n",
    "print(x)\n",
    "print(\"Hello world\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# BioPython\n",
    "\n",
    "BioPython is a very popular third party Python package for handling biological data.\n",
    "\n",
    "In order to install:\n",
    "\n",
    "```\n",
    "conda install biopython\n",
    "```\n",
    "\n",
    "BioPython has three major functionalities:\n",
    "\n",
    "* Sequence Handling\n",
    "* 3D Structure\n",
    "* Population Genetics\n",
    "\n",
    "We'll focus on sequence handling in this lecture.\n",
    "\n",
    "Some useful references: [tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html), [website](http://biopython.org/), [wiki](http://biopython.org/wiki/Category%3AWiki_Documentation) (most of my examples are coming from these sources).\n",
    " \n",
    "# `BioPython.Seq`\n",
    "\n",
    "The main object we'll be dealing with are sequences. This is handled by the `Seq` class.\n",
    "\n",
    "As we know, we can have DNA, RNA, and Protein sequences.\n",
    "\n",
    "BioPython helps us cleanly distinguish and do different things with different kinds of sequences."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'Bio.Seq.Seq'>\n",
      "CCCGGAGAGA\n"
     ]
    }
   ],
   "source": [
    "#let's make a generic sequence\n",
    "\n",
    "from Bio.Seq import Seq # Seq is a class defined in Bio.Seq file\n",
    "\n",
    "my_seq = Seq(\"CCCGGAGAGA\")\n",
    "print(type(my_seq))\n",
    "#let's see what attributes this object has\n",
    "print(my_seq)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "It seems like there is a lot we can do with this object.\n",
    "\n",
    "The problem is at this point Python doesn't know what kind of sequence this is (DNA, RNA, Protein).\n",
    "\n",
    "We have to specify what kind of \"Alphabet\" the sequence belongs to."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Alphabet()\n"
     ]
    }
   ],
   "source": [
    "#right now it has just a generic alphabet\n",
    "print(my_seq.alphabet)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "DNAAlphabet()\n",
      "RNAAlphabet()\n",
      "ProteinAlphabet()\n"
     ]
    }
   ],
   "source": [
    "from Bio.Alphabet import generic_dna, generic_protein, generic_rna\n",
    "\n",
    "my_dna = Seq(\"CCCGGAGAG\", generic_dna)\n",
    "my_rna = Seq(\"ACCCGUUGU\", generic_rna)\n",
    "my_protein = Seq(\"AKKKGGGUUULL\", generic_protein)\n",
    "\n",
    "print(my_dna.alphabet)\n",
    "print(my_rna.alphabet)\n",
    "print(my_protein.alphabet)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Biopython will now know the difference for example between a DNA base `A` for adenine and the protein residue `A` for alanine.\n",
    "\n",
    "Now we can do some cool things.\n",
    "\n",
    "We can perform the main actions of the central dogma: transcribe and translate."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG\n",
      "MAIVMGR*KGAR*\n"
     ]
    }
   ],
   "source": [
    "my_gene = Seq(\"ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG\", generic_dna)\n",
    "\n",
    "#get the mRNA\n",
    "my_transcript = my_gene.transcribe()\n",
    "print(my_transcript)\n",
    "\n",
    "#get the protein from the mRNA\n",
    "my_protein = my_transcript.translate()\n",
    "print(my_protein)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "As you can see, we got some STOP codons represented as `*` and translation continued.\n",
    "\n",
    "We can get translation to actually stop when it encounters a STOP codon."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "MAIVMGR\n"
     ]
    }
   ],
   "source": [
    "myprot = my_transcript.translate(to_stop=True)\n",
    "print(myprot)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### General sequence methods\n",
    "\n",
    "There are some convenient operations for dealing with sequences."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can concatenate sequences if they are of matching type."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "AAACGGAGGAGAT\n"
     ]
    }
   ],
   "source": [
    "seq1 = Seq(\"AAACGGA\", generic_dna)\n",
    "seq2 = Seq(\"GGAGAT\", generic_dna)\n",
    "\n",
    "print(seq1 + seq2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can also index and slice as though we had strings."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "AAT\n"
     ]
    }
   ],
   "source": [
    "print(seq1[:2] + seq2[-1])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`Seq` objects are immutable, just like strings."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "ename": "TypeError",
     "evalue": "'Seq' object does not support item assignment",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-21-63a2f93c4add>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mseq1\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m2\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"G\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;31mTypeError\u001b[0m: 'Seq' object does not support item assignment"
     ]
    }
   ],
   "source": [
    "seq1[2] = \"G\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "There is another type of object called a `MutableSeq`. If we want to support mutability we can convert a `Seq` object to a `MutableSeq` object quite easily."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "MutableSeq('AAACGGA', DNAAlphabet())"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mut_seq = seq1.tomutable()\n",
    "mut_seq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GAACGGA\n"
     ]
    }
   ],
   "source": [
    "mut_seq[0] = \"G\"\n",
    "print(mut_seq)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can also do searching inside sequences."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "3\n",
      "2\n"
     ]
    }
   ],
   "source": [
    "myseq = Seq(\"CCAGAAACCCGGAA\", generic_dna)\n",
    "\n",
    "#find the first occurence of the pattern\n",
    "print(myseq.find(\"GAA\"))\n",
    "\n",
    "#find the number of non-overlapping occurrences of a pattern\n",
    "print(myseq.count(\"GAA\"))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Class Inheritance from Existing Class\n",
    "\n",
    "We can write new classes that extend any existing class, including those defined in BioPython.\n",
    "\n",
    "Example: Define the MySeq class that extends the Seq class to add:\n",
    "\n",
    "1. a list of confidence values (between 0 and 1) associated to each character in the sequence\n",
    "2. an average_confidence() method that computes the average confidence values for the sequence\n",
    "3. a gc_content() method that computes the fraction of bases that are either G or C"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 89,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GC content =  0.4\n",
      "Average confidence value =  0.8\n"
     ]
    }
   ],
   "source": [
    "from Bio.Seq import Seq\n",
    "\n",
    "class MySeq(Seq):\n",
    "    def __init__(self, seq, conf):\n",
    "        Seq.__init__(self, seq)\n",
    "        self.confidence = conf  # confidence values\n",
    "\n",
    "    # Seq doesn't compute GC content so \n",
    "    # we'll add that functionality\n",
    "    def gc_content(self):\n",
    "        return len([b for b in self if b in \"GC\"]) / len(self)\n",
    "    \n",
    "    def avg_confidence(self):\n",
    "        return sum(self.confidence)/len(self.confidence)\n",
    "\n",
    "seq1 = Seq(\"ACGTATG\")\n",
    "seq2 = MySeq(\"AAACG\",[0.9, 0.8, 0.5, 1, 0.8]) \n",
    "print(\"GC content = \",seq2.gc_content())\n",
    "print(\"Average confidence value = \", seq2.avg_confidence())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Sequence alignment\n",
    "\n",
    "Say you isolated some piece of DNA in the lab and obtained its sequence.\n",
    "\n",
    "You now want to find out which organism that sequence belongs to.\n",
    "\n",
    "You ask a biologist and they tell you to just \"BLAST it\". (recalled Lecture 14 miniBlast program)\n",
    "\n",
    "As you may know already, this is essentially the same as \"Google it\" for biologists.\n",
    "\n",
    "BLAST is an alignment algorithm that searches for your sequence of interest in a huge database of sequences whose origins are known.\n",
    "\n",
    "If you didn't know BioPython, you would take your sequence `CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC` \n",
    "and go to the [NCBI BLAST web server](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) and click on buttons like a monkey.\n",
    "\n",
    "Thanks to BioPython we can do this programatically!\n",
    "\n",
    "The `qblast` ('q' stands for query) method from the `Bio.Blast.NCBIWWW` module essentially sends our sequence to the BLAST web server.\n",
    "\n",
    "Here we are using the \"nucleotice BLAST\" algorithm so we say `blastn` and we are using it on the database of all nucleotide sequences, called `nt`.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "metadata": {},
   "outputs": [],
   "source": [
    "from Bio.Blast import NCBIWWW\n",
    "s = Seq(\"CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC\", generic_dna)\n",
    "result_handle = NCBIWWW.qblast(\"blastn\", \"nt\", s)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We wait a few seconds and get a `result_handle` which is like a temporary open file that we can read from.\n",
    "\n",
    "The format of this file is in XML so not easy to read, thankfully BioPython has an XML parser that extracts all the information for us."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "metadata": {},
   "outputs": [],
   "source": [
    "from Bio.Blast import NCBIXML\n",
    "blast_records = NCBIXML.parse(result_handle)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We get an \"iterator\" of BLAST record objects, or \"search results\". We can now loop over each of our search results and print some information.\n",
    "\n",
    "Here I am looping over all the results which each have an attribute `alignments` which are the alignments of our query sequence to some organism in the database.\n",
    "\n",
    "The `alignment` attribute itself has other attributes like the `query` sequence, the `length` and `title` of the matching organism.."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "****Alignment****\n",
      "sequence: gi|1539444317|emb|LR134163.1| Yersinia pseudotuberculosis strain NCTC10217 genome assembly, chromosome: 1\n",
      "length: 4687913\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1539444317|emb|LR134163.1| Yersinia pseudotuberculosis strain NCTC10217 genome assembly, chromosome: 1\n",
      "length: 4687913\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1539444317|emb|LR134163.1| Yersinia pseudotuberculosis strain NCTC10217 genome assembly, chromosome: 1\n",
      "length: 4687913\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1539444317|emb|LR134163.1| Yersinia pseudotuberculosis strain NCTC10217 genome assembly, chromosome: 1\n",
      "length: 4687913\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1539444317|emb|LR134163.1| Yersinia pseudotuberculosis strain NCTC10217 genome assembly, chromosome: 1\n",
      "length: 4687913\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1539444317|emb|LR134163.1| Yersinia pseudotuberculosis strain NCTC10217 genome assembly, chromosome: 1\n",
      "length: 4687913\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1539428816|emb|LR134160.1| Yersinia pseudotuberculosis strain NCTC8480 genome assembly, chromosome: 1\n",
      "length: 4678752\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1539428816|emb|LR134160.1| Yersinia pseudotuberculosis strain NCTC8480 genome assembly, chromosome: 1\n",
      "length: 4678752\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1539428816|emb|LR134160.1| Yersinia pseudotuberculosis strain NCTC8480 genome assembly, chromosome: 1\n",
      "length: 4678752\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1539428816|emb|LR134160.1| Yersinia pseudotuberculosis strain NCTC8480 genome assembly, chromosome: 1\n",
      "length: 4678752\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1539428816|emb|LR134160.1| Yersinia pseudotuberculosis strain NCTC8480 genome assembly, chromosome: 1\n",
      "length: 4678752\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1539428816|emb|LR134160.1| Yersinia pseudotuberculosis strain NCTC8480 genome assembly, chromosome: 1\n",
      "length: 4678752\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1519328943|gb|CP032566.1| Yersinia pseudotuberculosis strain IP2666pIB1 chromosome, complete genome\n",
      "length: 4614856\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1519328943|gb|CP032566.1| Yersinia pseudotuberculosis strain IP2666pIB1 chromosome, complete genome\n",
      "length: 4614856\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1519328943|gb|CP032566.1| Yersinia pseudotuberculosis strain IP2666pIB1 chromosome, complete genome\n",
      "length: 4614856\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1519328943|gb|CP032566.1| Yersinia pseudotuberculosis strain IP2666pIB1 chromosome, complete genome\n",
      "length: 4614856\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1519328943|gb|CP032566.1| Yersinia pseudotuberculosis strain IP2666pIB1 chromosome, complete genome\n",
      "length: 4614856\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1519328943|gb|CP032566.1| Yersinia pseudotuberculosis strain IP2666pIB1 chromosome, complete genome\n",
      "length: 4614856\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1518099716|gb|CP033699.1| Yersinia pestis strain FDAARGOS_601 chromosome, complete genome\n",
      "length: 4708493\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1518099716|gb|CP033699.1| Yersinia pestis strain FDAARGOS_601 chromosome, complete genome\n",
      "length: 4708493\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518099716|gb|CP033699.1| Yersinia pestis strain FDAARGOS_601 chromosome, complete genome\n",
      "length: 4708493\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518099716|gb|CP033699.1| Yersinia pestis strain FDAARGOS_601 chromosome, complete genome\n",
      "length: 4708493\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518099716|gb|CP033699.1| Yersinia pestis strain FDAARGOS_601 chromosome, complete genome\n",
      "length: 4708493\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1518095292|gb|CP033690.1| Yersinia pestis strain FDAARGOS_603 chromosome, complete genome\n",
      "length: 4636496\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1518095292|gb|CP033690.1| Yersinia pestis strain FDAARGOS_603 chromosome, complete genome\n",
      "length: 4636496\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518095292|gb|CP033690.1| Yersinia pestis strain FDAARGOS_603 chromosome, complete genome\n",
      "length: 4636496\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518095292|gb|CP033690.1| Yersinia pestis strain FDAARGOS_603 chromosome, complete genome\n",
      "length: 4636496\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518095292|gb|CP033690.1| Yersinia pestis strain FDAARGOS_603 chromosome, complete genome\n",
      "length: 4636496\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518095292|gb|CP033690.1| Yersinia pestis strain FDAARGOS_603 chromosome, complete genome\n",
      "length: 4636496\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1518090908|gb|CP033715.1| Yersinia pseudotuberculosis strain FDAARGOS_580 chromosome, complete genome\n",
      "length: 4910698\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1518090908|gb|CP033715.1| Yersinia pseudotuberculosis strain FDAARGOS_580 chromosome, complete genome\n",
      "length: 4910698\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518090908|gb|CP033715.1| Yersinia pseudotuberculosis strain FDAARGOS_580 chromosome, complete genome\n",
      "length: 4910698\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518090908|gb|CP033715.1| Yersinia pseudotuberculosis strain FDAARGOS_580 chromosome, complete genome\n",
      "length: 4910698\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518090908|gb|CP033715.1| Yersinia pseudotuberculosis strain FDAARGOS_580 chromosome, complete genome\n",
      "length: 4910698\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518090908|gb|CP033715.1| Yersinia pseudotuberculosis strain FDAARGOS_580 chromosome, complete genome\n",
      "length: 4910698\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1518086572|gb|CP033717.1| Yersinia pseudotuberculosis strain FDAARGOS_579 chromosome, complete genome\n",
      "length: 4614836\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1518086572|gb|CP033717.1| Yersinia pseudotuberculosis strain FDAARGOS_579 chromosome, complete genome\n",
      "length: 4614836\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518086572|gb|CP033717.1| Yersinia pseudotuberculosis strain FDAARGOS_579 chromosome, complete genome\n",
      "length: 4614836\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518086572|gb|CP033717.1| Yersinia pseudotuberculosis strain FDAARGOS_579 chromosome, complete genome\n",
      "length: 4614836\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518086572|gb|CP033717.1| Yersinia pseudotuberculosis strain FDAARGOS_579 chromosome, complete genome\n",
      "length: 4614836\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518086572|gb|CP033717.1| Yersinia pseudotuberculosis strain FDAARGOS_579 chromosome, complete genome\n",
      "length: 4614836\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1518082118|gb|CP033707.1| Yersinia pseudotuberculosis strain FDAARGOS_584 chromosome, complete genome\n",
      "length: 4689430\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1518082118|gb|CP033707.1| Yersinia pseudotuberculosis strain FDAARGOS_584 chromosome, complete genome\n",
      "length: 4689430\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518082118|gb|CP033707.1| Yersinia pseudotuberculosis strain FDAARGOS_584 chromosome, complete genome\n",
      "length: 4689430\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518082118|gb|CP033707.1| Yersinia pseudotuberculosis strain FDAARGOS_584 chromosome, complete genome\n",
      "length: 4689430\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518082118|gb|CP033707.1| Yersinia pseudotuberculosis strain FDAARGOS_584 chromosome, complete genome\n",
      "length: 4689430\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518082118|gb|CP033707.1| Yersinia pseudotuberculosis strain FDAARGOS_584 chromosome, complete genome\n",
      "length: 4689430\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1518077928|gb|CP033711.1| Yersinia pseudotuberculosis strain FDAARGOS_582 chromosome, complete genome\n",
      "length: 4762645\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1518077928|gb|CP033711.1| Yersinia pseudotuberculosis strain FDAARGOS_582 chromosome, complete genome\n",
      "length: 4762645\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518077928|gb|CP033711.1| Yersinia pseudotuberculosis strain FDAARGOS_582 chromosome, complete genome\n",
      "length: 4762645\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518077928|gb|CP033711.1| Yersinia pseudotuberculosis strain FDAARGOS_582 chromosome, complete genome\n",
      "length: 4762645\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518077928|gb|CP033711.1| Yersinia pseudotuberculosis strain FDAARGOS_582 chromosome, complete genome\n",
      "length: 4762645\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518077928|gb|CP033711.1| Yersinia pseudotuberculosis strain FDAARGOS_582 chromosome, complete genome\n",
      "length: 4762645\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1518073792|gb|CP033696.1| Yersinia pestis strain FDAARGOS_602 chromosome, complete genome\n",
      "length: 4607325\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1518073792|gb|CP033696.1| Yersinia pestis strain FDAARGOS_602 chromosome, complete genome\n",
      "length: 4607325\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518073792|gb|CP033696.1| Yersinia pestis strain FDAARGOS_602 chromosome, complete genome\n",
      "length: 4607325\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518073792|gb|CP033696.1| Yersinia pestis strain FDAARGOS_602 chromosome, complete genome\n",
      "length: 4607325\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518073792|gb|CP033696.1| Yersinia pestis strain FDAARGOS_602 chromosome, complete genome\n",
      "length: 4607325\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1518069154|gb|CP033713.1| Yersinia pseudotuberculosis strain FDAARGOS_581 chromosome, complete genome\n",
      "length: 5026929\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1518069154|gb|CP033713.1| Yersinia pseudotuberculosis strain FDAARGOS_581 chromosome, complete genome\n",
      "length: 5026929\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518069154|gb|CP033713.1| Yersinia pseudotuberculosis strain FDAARGOS_581 chromosome, complete genome\n",
      "length: 5026929\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518069154|gb|CP033713.1| Yersinia pseudotuberculosis strain FDAARGOS_581 chromosome, complete genome\n",
      "length: 5026929\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518069154|gb|CP033713.1| Yersinia pseudotuberculosis strain FDAARGOS_581 chromosome, complete genome\n",
      "length: 5026929\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518069154|gb|CP033713.1| Yersinia pseudotuberculosis strain FDAARGOS_581 chromosome, complete genome\n",
      "length: 5026929\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1518063815|gb|CP033709.1| Yersinia pseudotuberculosis strain FDAARGOS_583 chromosome, complete genome\n",
      "length: 4582218\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1518063815|gb|CP033709.1| Yersinia pseudotuberculosis strain FDAARGOS_583 chromosome, complete genome\n",
      "length: 4582218\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518063815|gb|CP033709.1| Yersinia pseudotuberculosis strain FDAARGOS_583 chromosome, complete genome\n",
      "length: 4582218\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518063815|gb|CP033709.1| Yersinia pseudotuberculosis strain FDAARGOS_583 chromosome, complete genome\n",
      "length: 4582218\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518063815|gb|CP033709.1| Yersinia pseudotuberculosis strain FDAARGOS_583 chromosome, complete genome\n",
      "length: 4582218\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1518063815|gb|CP033709.1| Yersinia pseudotuberculosis strain FDAARGOS_583 chromosome, complete genome\n",
      "length: 4582218\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1475399133|gb|CP031780.1| Yersinia pseudotuberculosis strain FDAARGOS_342 chromosome, complete genome\n",
      "length: 4905554\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1475399133|gb|CP031780.1| Yersinia pseudotuberculosis strain FDAARGOS_342 chromosome, complete genome\n",
      "length: 4905554\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1475399133|gb|CP031780.1| Yersinia pseudotuberculosis strain FDAARGOS_342 chromosome, complete genome\n",
      "length: 4905554\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1475399133|gb|CP031780.1| Yersinia pseudotuberculosis strain FDAARGOS_342 chromosome, complete genome\n",
      "length: 4905554\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1475399133|gb|CP031780.1| Yersinia pseudotuberculosis strain FDAARGOS_342 chromosome, complete genome\n",
      "length: 4905554\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1540021585|emb|LR134373.1| Yersinia pseudotuberculosis strain NCTC10275 genome assembly, chromosome: 1\n",
      "length: 4610200\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1540021585|emb|LR134373.1| Yersinia pseudotuberculosis strain NCTC10275 genome assembly, chromosome: 1\n",
      "length: 4610200\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1540021585|emb|LR134373.1| Yersinia pseudotuberculosis strain NCTC10275 genome assembly, chromosome: 1\n",
      "length: 4610200\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1540021585|emb|LR134373.1| Yersinia pseudotuberculosis strain NCTC10275 genome assembly, chromosome: 1\n",
      "length: 4610200\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1540021585|emb|LR134373.1| Yersinia pseudotuberculosis strain NCTC10275 genome assembly, chromosome: 1\n",
      "length: 4610200\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1540021585|emb|LR134373.1| Yersinia pseudotuberculosis strain NCTC10275 genome assembly, chromosome: 1\n",
      "length: 4610200\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1539808143|emb|LR134306.1| Yersinia pseudotuberculosis strain NCTC3571 genome assembly, chromosome: 1\n",
      "length: 4938759\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1539808143|emb|LR134306.1| Yersinia pseudotuberculosis strain NCTC3571 genome assembly, chromosome: 1\n",
      "length: 4938759\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1539808143|emb|LR134306.1| Yersinia pseudotuberculosis strain NCTC3571 genome assembly, chromosome: 1\n",
      "length: 4938759\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1539808143|emb|LR134306.1| Yersinia pseudotuberculosis strain NCTC3571 genome assembly, chromosome: 1\n",
      "length: 4938759\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1539808143|emb|LR134306.1| Yersinia pseudotuberculosis strain NCTC3571 genome assembly, chromosome: 1\n",
      "length: 4938759\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1539808143|emb|LR134306.1| Yersinia pseudotuberculosis strain NCTC3571 genome assembly, chromosome: 1\n",
      "length: 4938759\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1148994967|gb|CP019708.1| Yersinia pestis strain 195/P, complete genome\n",
      "length: 4655691\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1148994967|gb|CP019708.1| Yersinia pestis strain 195/P, complete genome\n",
      "length: 4655691\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1148994967|gb|CP019708.1| Yersinia pestis strain 195/P, complete genome\n",
      "length: 4655691\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1148994967|gb|CP019708.1| Yersinia pestis strain 195/P, complete genome\n",
      "length: 4655691\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1148994967|gb|CP019708.1| Yersinia pestis strain 195/P, complete genome\n",
      "length: 4655691\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1148994967|gb|CP019708.1| Yersinia pestis strain 195/P, complete genome\n",
      "length: 4655691\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1126835759|emb|LT596221.1| Yersinia pseudotuberculosis isolate NZYP4713 genome assembly, chromosome: 1\n",
      "length: 4724276\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1126835759|emb|LT596221.1| Yersinia pseudotuberculosis isolate NZYP4713 genome assembly, chromosome: 1\n",
      "length: 4724276\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1126835759|emb|LT596221.1| Yersinia pseudotuberculosis isolate NZYP4713 genome assembly, chromosome: 1\n",
      "length: 4724276\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1126835759|emb|LT596221.1| Yersinia pseudotuberculosis isolate NZYP4713 genome assembly, chromosome: 1\n",
      "length: 4724276\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1126835759|emb|LT596221.1| Yersinia pseudotuberculosis isolate NZYP4713 genome assembly, chromosome: 1\n",
      "length: 4724276\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1126835759|emb|LT596221.1| Yersinia pseudotuberculosis isolate NZYP4713 genome assembly, chromosome: 1\n",
      "length: 4724276\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|1046912481|gb|CP016273.1| Yersinia pestis strain Cadman chromosome, complete genome\n",
      "length: 4602429\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|1046912481|gb|CP016273.1| Yersinia pestis strain Cadman chromosome, complete genome\n",
      "length: 4602429\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1046912481|gb|CP016273.1| Yersinia pestis strain Cadman chromosome, complete genome\n",
      "length: 4602429\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1046912481|gb|CP016273.1| Yersinia pestis strain Cadman chromosome, complete genome\n",
      "length: 4602429\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1046912481|gb|CP016273.1| Yersinia pestis strain Cadman chromosome, complete genome\n",
      "length: 4602429\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|1046912481|gb|CP016273.1| Yersinia pestis strain Cadman chromosome, complete genome\n",
      "length: 4602429\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|908262105|gb|CP006794.1| Yersinia pestis 1045 sequence\n",
      "length: 4502257\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|908262105|gb|CP006794.1| Yersinia pestis 1045 sequence\n",
      "length: 4502257\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908262105|gb|CP006794.1| Yersinia pestis 1045 sequence\n",
      "length: 4502257\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908262105|gb|CP006794.1| Yersinia pestis 1045 sequence\n",
      "length: 4502257\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|908258101|gb|CP006754.1| Yersinia pestis 3067, complete genome\n",
      "length: 4526841\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|908258101|gb|CP006754.1| Yersinia pestis 3067, complete genome\n",
      "length: 4526841\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908258101|gb|CP006754.1| Yersinia pestis 3067, complete genome\n",
      "length: 4526841\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908258101|gb|CP006754.1| Yersinia pestis 3067, complete genome\n",
      "length: 4526841\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908258101|gb|CP006754.1| Yersinia pestis 3067, complete genome\n",
      "length: 4526841\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|908253871|gb|CP006751.1| Yersinia pestis 3770, complete genome\n",
      "length: 4523206\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|908253871|gb|CP006751.1| Yersinia pestis 3770, complete genome\n",
      "length: 4523206\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908253871|gb|CP006751.1| Yersinia pestis 3770, complete genome\n",
      "length: 4523206\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|908249689|gb|CP006748.1| Yersinia pestis 8787, complete genome\n",
      "length: 4467447\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|908249689|gb|CP006748.1| Yersinia pestis 8787, complete genome\n",
      "length: 4467447\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908249689|gb|CP006748.1| Yersinia pestis 8787, complete genome\n",
      "length: 4467447\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908249689|gb|CP006748.1| Yersinia pestis 8787, complete genome\n",
      "length: 4467447\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908249689|gb|CP006748.1| Yersinia pestis 8787, complete genome\n",
      "length: 4467447\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908249689|gb|CP006748.1| Yersinia pestis 8787, complete genome\n",
      "length: 4467447\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908249689|gb|CP006748.1| Yersinia pestis 8787, complete genome\n",
      "length: 4467447\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|908245216|gb|CP006806.1| Yersinia pestis 790 genome\n",
      "length: 4629525\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|908245216|gb|CP006806.1| Yersinia pestis 790 genome\n",
      "length: 4629525\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908245216|gb|CP006806.1| Yersinia pestis 790 genome\n",
      "length: 4629525\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908245216|gb|CP006806.1| Yersinia pestis 790 genome\n",
      "length: 4629525\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|908241204|gb|CP006758.1| Yersinia pestis 1522, complete genome\n",
      "length: 4530125\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|908241204|gb|CP006758.1| Yersinia pestis 1522, complete genome\n",
      "length: 4530125\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908241204|gb|CP006758.1| Yersinia pestis 1522, complete genome\n",
      "length: 4530125\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|908236972|gb|CP006762.1| Yersinia pestis 1413, complete genome\n",
      "length: 4528383\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|908236972|gb|CP006762.1| Yersinia pestis 1413, complete genome\n",
      "length: 4528383\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908236972|gb|CP006762.1| Yersinia pestis 1413, complete genome\n",
      "length: 4528383\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|908221924|gb|CP006792.1| Yersinia pestis 2944, complete genome\n",
      "length: 4491639\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|908221924|gb|CP006792.1| Yersinia pestis 2944, complete genome\n",
      "length: 4491639\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908221924|gb|CP006792.1| Yersinia pestis 2944, complete genome\n",
      "length: 4491639\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908221924|gb|CP006792.1| Yersinia pestis 2944, complete genome\n",
      "length: 4491639\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908221924|gb|CP006792.1| Yersinia pestis 2944, complete genome\n",
      "length: 4491639\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|908217725|gb|CP006783.1| Yersinia pestis 1412, complete genome\n",
      "length: 4524943\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|908217725|gb|CP006783.1| Yersinia pestis 1412, complete genome\n",
      "length: 4524943\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908217725|gb|CP006783.1| Yersinia pestis 1412, complete genome\n",
      "length: 4524943\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908217725|gb|CP006783.1| Yersinia pestis 1412, complete genome\n",
      "length: 4524943\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|908217725|gb|CP006783.1| Yersinia pestis 1412, complete genome\n",
      "length: 4524943\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|805411710|gb|CP009836.1| Yersinia pestis strain KIM5, complete genome\n",
      "length: 4605437\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|805411710|gb|CP009836.1| Yersinia pestis strain KIM5, complete genome\n",
      "length: 4605437\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|805411710|gb|CP009836.1| Yersinia pestis strain KIM5, complete genome\n",
      "length: 4605437\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|805411710|gb|CP009836.1| Yersinia pestis strain KIM5, complete genome\n",
      "length: 4605437\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|805411710|gb|CP009836.1| Yersinia pestis strain KIM5, complete genome\n",
      "length: 4605437\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|805411710|gb|CP009836.1| Yersinia pestis strain KIM5, complete genome\n",
      "length: 4605437\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755462371|gb|CP010293.1| Yersinia pestis strain Nairobi genome\n",
      "length: 4563069\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755462371|gb|CP010293.1| Yersinia pestis strain Nairobi genome\n",
      "length: 4563069\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755462371|gb|CP010293.1| Yersinia pestis strain Nairobi genome\n",
      "length: 4563069\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755462371|gb|CP010293.1| Yersinia pestis strain Nairobi genome\n",
      "length: 4563069\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755462371|gb|CP010293.1| Yersinia pestis strain Nairobi genome\n",
      "length: 4563069\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755457955|gb|CP010247.1| Yersinia pestis Pestoides G, complete genome\n",
      "length: 4529728\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755457955|gb|CP010247.1| Yersinia pestis Pestoides G, complete genome\n",
      "length: 4529728\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755457955|gb|CP010247.1| Yersinia pestis Pestoides G, complete genome\n",
      "length: 4529728\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755457955|gb|CP010247.1| Yersinia pestis Pestoides G, complete genome\n",
      "length: 4529728\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755457955|gb|CP010247.1| Yersinia pestis Pestoides G, complete genome\n",
      "length: 4529728\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755451319|gb|CP010067.1| Yersinia pseudotuberculosis str. PA3606, complete genome\n",
      "length: 4742580\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755451319|gb|CP010067.1| Yersinia pseudotuberculosis str. PA3606, complete genome\n",
      "length: 4742580\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755451319|gb|CP010067.1| Yersinia pseudotuberculosis str. PA3606, complete genome\n",
      "length: 4742580\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755451319|gb|CP010067.1| Yersinia pseudotuberculosis str. PA3606, complete genome\n",
      "length: 4742580\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755451319|gb|CP010067.1| Yersinia pseudotuberculosis str. PA3606, complete genome\n",
      "length: 4742580\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755451319|gb|CP010067.1| Yersinia pseudotuberculosis str. PA3606, complete genome\n",
      "length: 4742580\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755446508|gb|CP010023.1| Yersinia pestis str. Pestoides B, complete genome\n",
      "length: 4607660\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755446508|gb|CP010023.1| Yersinia pestis str. Pestoides B, complete genome\n",
      "length: 4607660\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755446508|gb|CP010023.1| Yersinia pestis str. Pestoides B, complete genome\n",
      "length: 4607660\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755446508|gb|CP010023.1| Yersinia pestis str. Pestoides B, complete genome\n",
      "length: 4607660\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755446508|gb|CP010023.1| Yersinia pestis str. Pestoides B, complete genome\n",
      "length: 4607660\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755442302|gb|CP009991.1| Yersinia pestis strain Nicholisk 41, complete genome\n",
      "length: 4523033\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755442302|gb|CP009991.1| Yersinia pestis strain Nicholisk 41, complete genome\n",
      "length: 4523033\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755442302|gb|CP009991.1| Yersinia pestis strain Nicholisk 41, complete genome\n",
      "length: 4523033\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755442302|gb|CP009991.1| Yersinia pestis strain Nicholisk 41, complete genome\n",
      "length: 4523033\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755442302|gb|CP009991.1| Yersinia pestis strain Nicholisk 41, complete genome\n",
      "length: 4523033\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755442302|gb|CP009991.1| Yersinia pestis strain Nicholisk 41, complete genome\n",
      "length: 4523033\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755438001|gb|CP009996.1| Yersinia pestis strain Java9, complete genome\n",
      "length: 4672688\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755438001|gb|CP009996.1| Yersinia pestis strain Java9, complete genome\n",
      "length: 4672688\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755438001|gb|CP009996.1| Yersinia pestis strain Java9, complete genome\n",
      "length: 4672688\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755438001|gb|CP009996.1| Yersinia pestis strain Java9, complete genome\n",
      "length: 4672688\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755438001|gb|CP009996.1| Yersinia pestis strain Java9, complete genome\n",
      "length: 4672688\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755438001|gb|CP009996.1| Yersinia pestis strain Java9, complete genome\n",
      "length: 4672688\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755429805|gb|CP009973.1| Yersinia pestis CO92, complete genome\n",
      "length: 4556337\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755429805|gb|CP009973.1| Yersinia pestis CO92, complete genome\n",
      "length: 4556337\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755429805|gb|CP009973.1| Yersinia pestis CO92, complete genome\n",
      "length: 4556337\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755429805|gb|CP009973.1| Yersinia pestis CO92, complete genome\n",
      "length: 4556337\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755429805|gb|CP009973.1| Yersinia pestis CO92, complete genome\n",
      "length: 4556337\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755429805|gb|CP009973.1| Yersinia pestis CO92, complete genome\n",
      "length: 4556337\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755425406|gb|CP009935.1| Yersinia pestis Angola, complete genome\n",
      "length: 4501786\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755425406|gb|CP009935.1| Yersinia pestis Angola, complete genome\n",
      "length: 4501786\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755425406|gb|CP009935.1| Yersinia pestis Angola, complete genome\n",
      "length: 4501786\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755425406|gb|CP009935.1| Yersinia pestis Angola, complete genome\n",
      "length: 4501786\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755425406|gb|CP009935.1| Yersinia pestis Angola, complete genome\n",
      "length: 4501786\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755421135|gb|CP009906.1| Yersinia pestis Antiqua, complete genome\n",
      "length: 4708024\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755421135|gb|CP009906.1| Yersinia pestis Antiqua, complete genome\n",
      "length: 4708024\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755421135|gb|CP009906.1| Yersinia pestis Antiqua, complete genome\n",
      "length: 4708024\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755421135|gb|CP009906.1| Yersinia pestis Antiqua, complete genome\n",
      "length: 4708024\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755421135|gb|CP009906.1| Yersinia pestis Antiqua, complete genome\n",
      "length: 4708024\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755416828|gb|CP009844.1| Yersinia pestis strain Dodson, complete genome\n",
      "length: 4654228\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755416828|gb|CP009844.1| Yersinia pestis strain Dodson, complete genome\n",
      "length: 4654228\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755416828|gb|CP009844.1| Yersinia pestis strain Dodson, complete genome\n",
      "length: 4654228\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755416828|gb|CP009844.1| Yersinia pestis strain Dodson, complete genome\n",
      "length: 4654228\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755416828|gb|CP009844.1| Yersinia pestis strain Dodson, complete genome\n",
      "length: 4654228\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755416828|gb|CP009844.1| Yersinia pestis strain Dodson, complete genome\n",
      "length: 4654228\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755404263|gb|CP009840.1| Yersinia pestis A1122, complete genome\n",
      "length: 4569625\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755404263|gb|CP009840.1| Yersinia pestis A1122, complete genome\n",
      "length: 4569625\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755404263|gb|CP009840.1| Yersinia pestis A1122, complete genome\n",
      "length: 4569625\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755404263|gb|CP009840.1| Yersinia pestis A1122, complete genome\n",
      "length: 4569625\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755404263|gb|CP009840.1| Yersinia pestis A1122, complete genome\n",
      "length: 4569625\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755404263|gb|CP009840.1| Yersinia pestis A1122, complete genome\n",
      "length: 4569625\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755395814|gb|CP009785.1| Yersinia pestis strain El Dorado, complete genome\n",
      "length: 4662886\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755395814|gb|CP009785.1| Yersinia pestis strain El Dorado, complete genome\n",
      "length: 4662886\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755395814|gb|CP009785.1| Yersinia pestis strain El Dorado, complete genome\n",
      "length: 4662886\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755395814|gb|CP009785.1| Yersinia pestis strain El Dorado, complete genome\n",
      "length: 4662886\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755395814|gb|CP009785.1| Yersinia pestis strain El Dorado, complete genome\n",
      "length: 4662886\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755395814|gb|CP009785.1| Yersinia pestis strain El Dorado, complete genome\n",
      "length: 4662886\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755387769|gb|CP009786.1| Yersinia pseudotuberculosis strain 1, complete genome\n",
      "length: 4728337\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755387769|gb|CP009786.1| Yersinia pseudotuberculosis strain 1, complete genome\n",
      "length: 4728337\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755387769|gb|CP009786.1| Yersinia pseudotuberculosis strain 1, complete genome\n",
      "length: 4728337\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755387769|gb|CP009786.1| Yersinia pseudotuberculosis strain 1, complete genome\n",
      "length: 4728337\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755387769|gb|CP009786.1| Yersinia pseudotuberculosis strain 1, complete genome\n",
      "length: 4728337\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755387769|gb|CP009786.1| Yersinia pseudotuberculosis strain 1, complete genome\n",
      "length: 4728337\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755383756|gb|CP009780.1| Yersinia pseudotuberculosis PB1/+, complete genome\n",
      "length: 4695575\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755383756|gb|CP009780.1| Yersinia pseudotuberculosis PB1/+, complete genome\n",
      "length: 4695575\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755383756|gb|CP009780.1| Yersinia pseudotuberculosis PB1/+, complete genome\n",
      "length: 4695575\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755383756|gb|CP009780.1| Yersinia pseudotuberculosis PB1/+, complete genome\n",
      "length: 4695575\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755383756|gb|CP009780.1| Yersinia pseudotuberculosis PB1/+, complete genome\n",
      "length: 4695575\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755383756|gb|CP009780.1| Yersinia pseudotuberculosis PB1/+, complete genome\n",
      "length: 4695575\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755375669|gb|CP009792.1| Yersinia pseudotuberculosis YPIII, complete genome\n",
      "length: 4689436\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755375669|gb|CP009792.1| Yersinia pseudotuberculosis YPIII, complete genome\n",
      "length: 4689436\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755375669|gb|CP009792.1| Yersinia pseudotuberculosis YPIII, complete genome\n",
      "length: 4689436\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755375669|gb|CP009792.1| Yersinia pseudotuberculosis YPIII, complete genome\n",
      "length: 4689436\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755375669|gb|CP009792.1| Yersinia pseudotuberculosis YPIII, complete genome\n",
      "length: 4689436\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755375669|gb|CP009792.1| Yersinia pseudotuberculosis YPIII, complete genome\n",
      "length: 4689436\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755371660|gb|CP009759.1| Yersinia pseudotuberculosis strain EP2/+, complete genome\n",
      "length: 4706165\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755371660|gb|CP009759.1| Yersinia pseudotuberculosis strain EP2/+, complete genome\n",
      "length: 4706165\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755371660|gb|CP009759.1| Yersinia pseudotuberculosis strain EP2/+, complete genome\n",
      "length: 4706165\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755371660|gb|CP009759.1| Yersinia pseudotuberculosis strain EP2/+, complete genome\n",
      "length: 4706165\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755371660|gb|CP009759.1| Yersinia pseudotuberculosis strain EP2/+, complete genome\n",
      "length: 4706165\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755371660|gb|CP009759.1| Yersinia pseudotuberculosis strain EP2/+, complete genome\n",
      "length: 4706165\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755367513|gb|CP009757.1| Yersinia pseudotuberculosis strain MD67, complete genome\n",
      "length: 4729753\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755367513|gb|CP009757.1| Yersinia pseudotuberculosis strain MD67, complete genome\n",
      "length: 4729753\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755367513|gb|CP009757.1| Yersinia pseudotuberculosis strain MD67, complete genome\n",
      "length: 4729753\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755367513|gb|CP009757.1| Yersinia pseudotuberculosis strain MD67, complete genome\n",
      "length: 4729753\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755367513|gb|CP009757.1| Yersinia pseudotuberculosis strain MD67, complete genome\n",
      "length: 4729753\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755367513|gb|CP009757.1| Yersinia pseudotuberculosis strain MD67, complete genome\n",
      "length: 4729753\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755363594|gb|CP009715.1| Yersinia pestis Pestoides F, complete genome\n",
      "length: 4519828\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755363594|gb|CP009715.1| Yersinia pestis Pestoides F, complete genome\n",
      "length: 4519828\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755363594|gb|CP009715.1| Yersinia pestis Pestoides F, complete genome\n",
      "length: 4519828\n",
      "e value: 0.0786671\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755363594|gb|CP009715.1| Yersinia pestis Pestoides F, complete genome\n",
      "length: 4519828\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755363594|gb|CP009715.1| Yersinia pestis Pestoides F, complete genome\n",
      "length: 4519828\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755359298|gb|CP009712.1| Yersinia pseudotuberculosis IP 32953, complete genome\n",
      "length: 4743972\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755359298|gb|CP009712.1| Yersinia pseudotuberculosis IP 32953, complete genome\n",
      "length: 4743972\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755359298|gb|CP009712.1| Yersinia pseudotuberculosis IP 32953, complete genome\n",
      "length: 4743972\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755359298|gb|CP009712.1| Yersinia pseudotuberculosis IP 32953, complete genome\n",
      "length: 4743972\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755359298|gb|CP009712.1| Yersinia pseudotuberculosis IP 32953, complete genome\n",
      "length: 4743972\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755359298|gb|CP009712.1| Yersinia pseudotuberculosis IP 32953, complete genome\n",
      "length: 4743972\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755355075|gb|CP009723.1| Yersinia pestis strain Shasta, complete genome\n",
      "length: 4659530\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755355075|gb|CP009723.1| Yersinia pestis strain Shasta, complete genome\n",
      "length: 4659530\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755355075|gb|CP009723.1| Yersinia pestis strain Shasta, complete genome\n",
      "length: 4659530\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755355075|gb|CP009723.1| Yersinia pestis strain Shasta, complete genome\n",
      "length: 4659530\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755355075|gb|CP009723.1| Yersinia pestis strain Shasta, complete genome\n",
      "length: 4659530\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755355075|gb|CP009723.1| Yersinia pestis strain Shasta, complete genome\n",
      "length: 4659530\n",
      "e value: 3.34501\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "||||||| |||||||||||||||||...\n",
      "CTCTCCCGGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755340697|gb|CP009704.1| Yersinia pestis strain Harbin35, complete genome\n",
      "length: 4531804\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755340697|gb|CP009704.1| Yersinia pestis strain Harbin35, complete genome\n",
      "length: 4531804\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755340697|gb|CP009704.1| Yersinia pestis strain Harbin35, complete genome\n",
      "length: 4531804\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755340697|gb|CP009704.1| Yersinia pestis strain Harbin35, complete genome\n",
      "length: 4531804\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n",
      "****Alignment****\n",
      "sequence: gi|755292271|gb|CP009492.1| Yersinia pestis strain PBM19, complete genome\n",
      "length: 4685423\n",
      "e value: 2.92906e-26\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGAC...\n",
      "****Alignment****\n",
      "sequence: gi|755292271|gb|CP009492.1| Yersinia pestis strain PBM19, complete genome\n",
      "length: 4685423\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755292271|gb|CP009492.1| Yersinia pestis strain PBM19, complete genome\n",
      "length: 4685423\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755292271|gb|CP009492.1| Yersinia pestis strain PBM19, complete genome\n",
      "length: 4685423\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755292271|gb|CP009492.1| Yersinia pestis strain PBM19, complete genome\n",
      "length: 4685423\n",
      "e value: 0.0786671\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "|||||||||||||||||||||||||...\n",
      "CTCTCCCAGCTGAGCTATAGCCCCA...\n",
      "****Alignment****\n",
      "sequence: gi|755292271|gb|CP009492.1| Yersinia pestis strain PBM19, complete genome\n",
      "length: 4685423\n",
      "e value: 0.958361\n",
      "AATCGTGTGAACGGGGCGCATGATAT...\n",
      "||||||||||||||||||||| ||||...\n",
      "AATCGTGTGAACGGGGCGCATCATAT...\n"
     ]
    }
   ],
   "source": [
    "for b in blast_records:\n",
    "    for alignment in b.alignments:\n",
    "        for hsp in alignment.hsps:\n",
    "            print('****Alignment****')\n",
    "            print('sequence:', alignment.title)\n",
    "            print('length:', alignment.length)\n",
    "            print('e value:', hsp.expect)\n",
    "            print(hsp.query[0:75] + '...')\n",
    "            print(hsp.match[0:75] + '...')\n",
    "            print(hsp.sbjct[0:75] + '...')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# `SeqRecord` and `SeqIO`\n",
    "\n",
    "Often, sequences have some additional information associated to them. \n",
    "\n",
    "A good example was the BLAST exercise which gave us sequences associated to specific organisms, and genomic locations.\n",
    "\n",
    "Ideally we would want to be able to keep this information along with our `Seq` if we have it.\n",
    "\n",
    "BioPython lets us do this with the `SeqRecord` and `SeqIO` classes.\n",
    "\n",
    "\n",
    "## Parsing with `SeqIO`\n",
    "\n",
    "The `SeqIO` class which stands for Sequence Input/Output lets us read and write from various sequence annotation file formats which are common in biological databases.\n",
    "\n",
    "I went to the [GenBank](https://www.ncbi.nlm.nih.gov/genbank/) sequence database and looked for some sequence related to the Bubonic Plague (Yersinia Pestis bacteria) [here](https://www.ncbi.nlm.nih.gov/nuccore/NZ_ADRZ01000932.1?report=fasta).\n",
    "\n",
    "\n",
    "\n",
    "We get a `fasta` file which is very common for sequence annotations so BioPython can parse it for us automatically.\n",
    "\n",
    "The annotation for a FASTA sequence is typically held in the header:\n",
    "\n",
    "```\n",
    ">NZ_ADRZ01000932.1 Yersinia pestis biovar Antiqua str. E1979001 Contig_E1979001_19275, whole genome shotgun sequence\n",
    "```\n",
    "\n",
    "The `SeqIO.parse` takes a path to a file and a format, in this case \"fasta\" and produces an iteratror over each entry in the fasta file.\n",
    "\n",
    "Each item produced by the iterator is a `SeqRecords` object.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ID: NZ_ADRZ01000932.1\n",
      "Name: NZ_ADRZ01000932.1\n",
      "Description: NZ_ADRZ01000932.1 Yersinia pestis biovar Antiqua str. E1979001 Contig_E1979001_19275, whole genome shotgun sequence\n",
      "Number of features: 0\n",
      "Seq('CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGG...AGC', SingleLetterAlphabet())\n"
     ]
    }
   ],
   "source": [
    "from Bio import SeqIO\n",
    "\n",
    "record = SeqIO.read(\"plague.fa\", \"fasta\")\n",
    "print(record)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The `SeqRecords` object has some useful attributes.\n",
    "\n",
    "The object contains a `Seq` object witih the sequence info."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 76,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGGGCGCATGATATGAGACCCCCGAAACTGTGTCAACGGCTAAATCGATTTCTCGTGTTAAGCGCTGAAAAAGCGGCCAAATCAGCCTGCAAATAACATAATAAGTGGAATGATGTTCACAAATTTGTTGTCACACCGCTGCTGTTATCAAATATAATAAATATCCTCCGGCATAGC\n"
     ]
    }
   ],
   "source": [
    "print(record.seq)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 77,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ID: NZ_ADRZ01000932.1\n",
      "Name: NZ_ADRZ01000932.1\n",
      "Description: NZ_ADRZ01000932.1 Yersinia pestis biovar Antiqua str. E1979001 Contig_E1979001_19275, whole genome shotgun sequence\n",
      "Number of features: 0\n",
      "Seq('CTCTCCCAGCTGAGCTATAGCCCCAATGCGCACATAATAAATCGTGTGAACGGG...AGC', SingleLetterAlphabet())\n"
     ]
    }
   ],
   "source": [
    "print(record)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 78,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NZ_ADRZ01000932.1\n"
     ]
    }
   ],
   "source": [
    "print(record.id)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NZ_ADRZ01000932.1 Yersinia pestis biovar Antiqua str. E1979001 Contig_E1979001_19275, whole genome shotgun sequence\n"
     ]
    }
   ],
   "source": [
    "print(record.description)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can also create our own `SeqRecord` objects."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ID: YP_025292.1\n",
      "Name: HokC\n",
      "Description: toxic membrane protein, small\n",
      "Number of features: 0\n",
      "Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF', IUPACProtein())\n"
     ]
    }
   ],
   "source": [
    "from Bio.Seq import Seq\n",
    "from Bio.SeqRecord import SeqRecord\n",
    "from Bio.Alphabet import IUPAC\n",
    "record = SeqRecord(Seq(\"MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF\",\n",
    "                       IUPAC.protein),\n",
    "                   id=\"YP_025292.1\", name=\"HokC\",\n",
    "                   description=\"toxic membrane protein, small\")\n",
    "print(record)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Then we can write it to FASTA format."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 81,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'>YP_025292.1 toxic membrane protein, small\\nMKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF\\n'"
      ]
     },
     "execution_count": 81,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record.format(\"fasta\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "And then store it in a file. \n",
    "\n",
    "So now we know how to read sequence information, as well as produce our own sequence records and store them."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 82,
   "metadata": {},
   "outputs": [],
   "source": [
    "f = open(\"myfasta.fa\", \"w\")\n",
    "f.write(record.format(\"fasta\"))\n",
    "f.close()    "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Making Multiple Sequence Alignments and Phylogenetic Trees\n",
    "\n",
    "Another thing biologists like to do is align (essentially, compare) sequences.\n",
    "\n",
    "We have seen multiple sequence alignment problem in our Assignment 2.\n",
    "\n",
    "Basically, we first align any pair of sequences and evaluate how they differ from each other based on the similarity score (i.e., similarity score = match scores + gap penalties + mismatch panalties).\n",
    "\n",
    "The similarity scores imply sequence phylogeny. \n",
    "\n",
    "We first compute a tree derived from the similarity between species in terms of their given sequences).\n",
    "\n",
    "We then predict how evolution took place to explain a particular set of observed sequences.\n",
    "\n",
    "\n",
    "\n",
    "### Step 1: Obtain some sequences and align them\n",
    "\n",
    "Use the fasta file p53.fa found here: https://www.cs.mcgill.ca/~yueli/teaching/COMP204_Winter2019/Lectures/27/p53.fa\n",
    "and use the ClustalW tool https://www.ebi.ac.uk/Tools/msa/clustalw2/\n",
    "to produce a multiple sequence alignment. The result is here: https://www.cs.mcgill.ca/~yueli/teaching/COMP204_Winter2019/Lectures/27/p53.aln"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "First install ClustalW by the following commandline in the Anaconda Prompt\n",
    "\n",
    "```\n",
    "conda install -c bioconda clustalw\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "### Step 2: Align the sequences"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 83,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "\n",
      " CLUSTAL 2.1 Multiple Sequence Alignments\n",
      "\n",
      "\n",
      "Sequence format is Pearson\n",
      "Sequence 1: human         70 bp\n",
      "Sequence 2: baboon        70 bp\n",
      "Sequence 3: mouse         70 bp\n",
      "Sequence 4: rat           70 bp\n",
      "Sequence 5: cow           70 bp\n",
      "Sequence 6: cat           67 bp\n",
      "Sequence 7: dog           67 bp\n",
      "Start of Pairwise alignments\n",
      "Aligning...\n",
      "\n",
      "Sequences (1:2) Aligned. Score:  98\n",
      "Sequences (1:3) Aligned. Score:  78\n",
      "Sequences (1:4) Aligned. Score:  77\n",
      "Sequences (1:5) Aligned. Score:  85\n",
      "Sequences (1:6) Aligned. Score:  82\n",
      "Sequences (1:7) Aligned. Score:  86\n",
      "Sequences (2:3) Aligned. Score:  77\n",
      "Sequences (2:4) Aligned. Score:  75\n",
      "Sequences (2:5) Aligned. Score:  84\n",
      "Sequences (2:6) Aligned. Score:  80\n",
      "Sequences (2:7) Aligned. Score:  85\n",
      "Sequences (3:4) Aligned. Score:  90\n",
      "Sequences (3:5) Aligned. Score:  74\n",
      "Sequences (3:6) Aligned. Score:  76\n",
      "Sequences (3:7) Aligned. Score:  80\n",
      "Sequences (4:5) Aligned. Score:  65\n",
      "Sequences (4:6) Aligned. Score:  74\n",
      "Sequences (4:7) Aligned. Score:  77\n",
      "Sequences (5:6) Aligned. Score:  74\n",
      "Sequences (5:7) Aligned. Score:  83\n",
      "Sequences (6:7) Aligned. Score:  86\n",
      "Guide tree file created:   [p53.dnd]\n",
      "\n",
      "There are 6 groups\n",
      "Start of Multiple Alignment\n",
      "\n",
      "Aligning...\n",
      "Group 1: Sequences:   2      Score:1320\n",
      "Group 2: Sequences:   3      Score:1209\n",
      "Group 3: Sequences:   2      Score:1168\n",
      "Group 4: Sequences:   5      Score:1050\n",
      "Group 5: Sequences:   2      Score:1225\n",
      "Group 6: Sequences:   7      Score:1075\n",
      "Alignment Score 8424\n",
      "\n",
      "CLUSTAL-Alignment file created  [p53.aln]\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "from Bio.Align.Applications import ClustalwCommandline\n",
    "in_file = \"p53.fa\"\n",
    "out_file = \"p53.aln\"\n",
    "cline = ClustalwCommandline(\"clustalw\", infile=in_file, outfile=out_file)\n",
    "stdout, stderr = cline()\n",
    "print(stdout)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now that we have `SeqRecord` objects we can align them.\n",
    "\n",
    "To do so, we need to put them in a `fasta` file.\n",
    "\n",
    "### Step 3: Load the resulting alignment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 84,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SingleLetterAlphabet() alignment with 7 rows and 70 columns\n",
      "CTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCAT...CCT human\n",
      "CTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCAT...CCT baboon\n",
      "CTCATAGGGCACCACCACACTGTGTCTAAAGGTGTTCCGGTCGT...CCT cow\n",
      "CTCGTAGGGCACCACGACGCTATGTCGGA---TGTTTCTGTCGT...CCT cat\n",
      "CTCATAAGGCACCACCACACTGTGTCGAA---TGTTTCTGTCGT...CCT dog\n",
      "CTCATAAGGTACCACCACGCTGTGGCGAAAAGTCTGCCTGTCTT...CCT mouse\n",
      "CTCATACGGTACCACCACGCTGTGCCGAAAAGTCTGCCTGTCGT...CCT rat\n"
     ]
    }
   ],
   "source": [
    "#open the alignmnent file\n",
    "from Bio import AlignIO\n",
    "aln = open(\"p53.aln\", \"r\") #use AlignIO to read the alignment file in 'clustal' format\n",
    "alignment = AlignIO.read(aln, \"clustal\")\n",
    "\n",
    "print(alignment)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 85,
   "metadata": {},
   "outputs": [],
   "source": [
    "#write our sequences to fasta format\n",
    "with open(\"seqs.fasta\", \"w\") as f:\n",
    "    SeqIO.write(seq_records, f, \"fasta\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can parse the alignment with the `AlignIO` module from BioPython.\n",
    "\n",
    "I won't go into detail on this module but it has a lot of useful funcionality for dealing with sequence alignments.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Step 4: Use the alignment to obtain a \"distance\" between all pairs of sequences\n",
    "\n",
    "Using the parsed alignment, we can get the distance (or difference) between all the sequences.\n",
    "\n",
    "This just tells us, for each pair of sequences, how different they are."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 86,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "human\t0\n",
      "baboon\t0.014285714285714235\t0\n",
      "cow\t0.1428571428571429\t0.15714285714285714\t0\n",
      "cat\t0.2142857142857143\t0.22857142857142854\t0.2857142857142857\t0\n",
      "dog\t0.17142857142857137\t0.18571428571428572\t0.19999999999999996\t0.12857142857142856\t0\n",
      "mouse\t0.2142857142857143\t0.22857142857142854\t0.2571428571428571\t0.27142857142857146\t0.22857142857142854\t0\n",
      "rat\t0.22857142857142854\t0.24285714285714288\t0.2571428571428571\t0.2857142857142857\t0.2571428571428571\t0.09999999999999998\t0\n",
      "\thuman\tbaboon\tcow\tcat\tdog\tmouse\trat\n"
     ]
    }
   ],
   "source": [
    "from Bio.Phylo.TreeConstruction import DistanceCalculator\n",
    "\n",
    "#calculate the distance matrix\n",
    "calculator = DistanceCalculator('identity')\n",
    "#adds distance matrix to the calculator object and returns it\n",
    "dm = calculator.get_distance(alignment)\n",
    "print(dm)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Step 5: Construct a tree from the set of distances\n",
    "\n",
    "And finally, we can construct a phylogenetic tree from the pairwise distances between all the sequences."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 87,
   "metadata": {},
   "outputs": [],
   "source": [
    "from Bio.Phylo.TreeConstruction import DistanceTreeConstructor\n",
    "\n",
    "#initialize a DistanceTreeConstructor object based on our distance calculator object\n",
    "constructor = DistanceTreeConstructor(calculator)\n",
    "\n",
    "#build the tree\n",
    "upgma_tree = constructor.build_tree(alignment)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "And let's use the `Phylo` module to visualize the result!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 88,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "from Bio import Phylo\n",
    "import pylab\n",
    "#draw the tree\n",
    "Phylo.draw(upgma_tree)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.2"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}