corona.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Corona Genome Analysis"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Let's start by retreiving the complete genome of Coronavirus. The records are extracted from the wuhan region. Source: https://www.ncbi.nlm.nih.gov/nuccore/NC_045512\n",
    "\n",
    ">Orthocoronavirinae, in the family Coronaviridae, order Nidovirales, and realm Riboviria. They are enveloped viruses with a positive-sense single-stranded RNA genome and a nucleocapsid of helical symmetry. This is wrapped in a icosahedral protein shell. The genome size of coronaviruses ranges from approximately 26 to 32 kilobases, one of the largest among RNA viruses. They have characteristic club-shaped spikes that project from their surface, which in electron micrographs create an image reminiscent of the solar corona, from which their name derives.\n",
    "\n",
    "<img src=\"./images_copy/wiki.png\" width=\"480\">\n",
    "\n",
    "> **Basic Information:** Coronavirus is a single stranded RNA-virus (DNA is double stranded). RNA polymers are made up of nucleotides. These nucleotides have three parts: 1) a five carbon Ribose sugar, 2) a phosphate molecule and 3) one of four nitrogenous bases: adenine(a), guanine(g), cytosine(c) or uracil(u) / thymine(t). \n",
    "\n",
    "> Thymine is found in DNA and Uracil in RNA. But for following analysis, you can consider (u) and (t) to be analogous. \n",
    "\n",
    "\n",
    "<img src=\"./images_copy/parts-of-nucleotide.jpg\" width=\"480\">"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "corona = \"\"\"\n",
    "        1 attaaaggtt tataccttcc caggtaacaa accaaccaac tttcgatctc ttgtagatct\n",
    "       61 gttctctaaa cgaactttaa aatctgtgtg gctgtcactc ggctgcatgc ttagtgcact\n",
    "      121 cacgcagtat aattaataac taattactgt cgttgacagg acacgagtaa ctcgtctatc\n",
    "      181 ttctgcaggc tgcttacggt ttcgtccgtg ttgcagccga tcatcagcac atctaggttt\n",
    "      241 cgtccgggtg tgaccgaaag gtaagatgga gagccttgtc cctggtttca acgagaaaac\n",
    "      301 acacgtccaa ctcagtttgc ctgttttaca ggttcgcgac gtgctcgtac gtggctttgg\n",
    "      361 agactccgtg gaggaggtct tatcagaggc acgtcaacat cttaaagatg gcacttgtgg\n",
    "      421 cttagtagaa gttgaaaaag gcgttttgcc tcaacttgaa cagccctatg tgttcatcaa\n",
    "      481 acgttcggat gctcgaactg cacctcatgg tcatgttatg gttgagctgg tagcagaact\n",
    "      541 cgaaggcatt cagtacggtc gtagtggtga gacacttggt gtccttgtcc ctcatgtggg\n",
    "      601 cgaaatacca gtggcttacc gcaaggttct tcttcgtaag aacggtaata aaggagctgg\n",
    "      661 tggccatagt tacggcgccg atctaaagtc atttgactta ggcgacgagc ttggcactga\n",
    "      721 tccttatgaa gattttcaag aaaactggaa cactaaacat agcagtggtg ttacccgtga\n",
    "      781 actcatgcgt gagcttaacg gaggggcata cactcgctat gtcgataaca acttctgtgg\n",
    "      841 ccctgatggc taccctcttg agtgcattaa agaccttcta gcacgtgctg gtaaagcttc\n",
    "      901 atgcactttg tccgaacaac tggactttat tgacactaag aggggtgtat actgctgccg\n",
    "      961 tgaacatgag catgaaattg cttggtacac ggaacgttct gaaaagagct atgaattgca\n",
    "     1021 gacacctttt gaaattaaat tggcaaagaa atttgacacc ttcaatgggg aatgtccaaa\n",
    "     1081 ttttgtattt cccttaaatt ccataatcaa gactattcaa ccaagggttg aaaagaaaaa\n",
    "     1141 gcttgatggc tttatgggta gaattcgatc tgtctatcca gttgcgtcac caaatgaatg\n",
    "     1201 caaccaaatg tgcctttcaa ctctcatgaa gtgtgatcat tgtggtgaaa cttcatggca\n",
    "     1261 gacgggcgat tttgttaaag ccacttgcga attttgtggc actgagaatt tgactaaaga\n",
    "     1321 aggtgccact acttgtggtt acttacccca aaatgctgtt gttaaaattt attgtccagc\n",
    "     1381 atgtcacaat tcagaagtag gacctgagca tagtcttgcc gaataccata atgaatctgg\n",
    "     1441 cttgaaaacc attcttcgta agggtggtcg cactattgcc tttggaggct gtgtgttctc\n",
    "     1501 ttatgttggt tgccataaca agtgtgccta ttgggttcca cgtgctagcg ctaacatagg\n",
    "     1561 ttgtaaccat acaggtgttg ttggagaagg ttccgaaggt cttaatgaca accttcttga\n",
    "     1621 aatactccaa aaagagaaag tcaacatcaa tattgttggt gactttaaac ttaatgaaga\n",
    "     1681 gatcgccatt attttggcat ctttttctgc ttccacaagt gcttttgtgg aaactgtgaa\n",
    "     1741 aggtttggat tataaagcat tcaaacaaat tgttgaatcc tgtggtaatt ttaaagttac\n",
    "     1801 aaaaggaaaa gctaaaaaag gtgcctggaa tattggtgaa cagaaatcaa tactgagtcc\n",
    "     1861 tctttatgca tttgcatcag aggctgctcg tgttgtacga tcaattttct cccgcactct\n",
    "     1921 tgaaactgct caaaattctg tgcgtgtttt acagaaggcc gctataacaa tactagatgg\n",
    "     1981 aatttcacag tattcactga gactcattga tgctatgatg ttcacatctg atttggctac\n",
    "     2041 taacaatcta gttgtaatgg cctacattac aggtggtgtt gttcagttga cttcgcagtg\n",
    "     2101 gctaactaac atctttggca ctgtttatga aaaactcaaa cccgtccttg attggcttga\n",
    "     2161 agagaagttt aaggaaggtg tagagtttct tagagacggt tgggaaattg ttaaatttat\n",
    "     2221 ctcaacctgt gcttgtgaaa ttgtcggtgg acaaattgtc acctgtgcaa aggaaattaa\n",
    "     2281 ggagagtgtt cagacattct ttaagcttgt aaataaattt ttggctttgt gtgctgactc\n",
    "     2341 tatcattatt ggtggagcta aacttaaagc cttgaattta ggtgaaacat ttgtcacgca\n",
    "     2401 ctcaaaggga ttgtacagaa agtgtgttaa atccagagaa gaaactggcc tactcatgcc\n",
    "     2461 tctaaaagcc ccaaaagaaa ttatcttctt agagggagaa acacttccca cagaagtgtt\n",
    "     2521 aacagaggaa gttgtcttga aaactggtga tttacaacca ttagaacaac ctactagtga\n",
    "     2581 agctgttgaa gctccattgg ttggtacacc agtttgtatt aacgggctta tgttgctcga\n",
    "     2641 aatcaaagac acagaaaagt actgtgccct tgcacctaat atgatggtaa caaacaatac\n",
    "     2701 cttcacactc aaaggcggtg caccaacaaa ggttactttt ggtgatgaca ctgtgataga\n",
    "     2761 agtgcaaggt tacaagagtg tgaatatcac ttttgaactt gatgaaagga ttgataaagt\n",
    "     2821 acttaatgag aagtgctctg cctatacagt tgaactcggt acagaagtaa atgagttcgc\n",
    "     2881 ctgtgttgtg gcagatgctg tcataaaaac tttgcaacca gtatctgaat tacttacacc\n",
    "     2941 actgggcatt gatttagatg agtggagtat ggctacatac tacttatttg atgagtctgg\n",
    "     3001 tgagtttaaa ttggcttcac atatgtattg ttctttctac cctccagatg aggatgaaga\n",
    "     3061 agaaggtgat tgtgaagaag aagagtttga gccatcaact caatatgagt atggtactga\n",
    "     3121 agatgattac caaggtaaac ctttggaatt tggtgccact tctgctgctc ttcaacctga\n",
    "     3181 agaagagcaa gaagaagatt ggttagatga tgatagtcaa caaactgttg gtcaacaaga\n",
    "     3241 cggcagtgag gacaatcaga caactactat tcaaacaatt gttgaggttc aacctcaatt\n",
    "     3301 agagatggaa cttacaccag ttgttcagac tattgaagtg aatagtttta gtggttattt\n",
    "     3361 aaaacttact gacaatgtat acattaaaaa tgcagacatt gtggaagaag ctaaaaaggt\n",
    "     3421 aaaaccaaca gtggttgtta atgcagccaa tgtttacctt aaacatggag gaggtgttgc\n",
    "     3481 aggagcctta aataaggcta ctaacaatgc catgcaagtt gaatctgatg attacatagc\n",
    "     3541 tactaatgga ccacttaaag tgggtggtag ttgtgtttta agcggacaca atcttgctaa\n",
    "     3601 acactgtctt catgttgtcg gcccaaatgt taacaaaggt gaagacattc aacttcttaa\n",
    "     3661 gagtgcttat gaaaatttta atcagcacga agttctactt gcaccattat tatcagctgg\n",
    "     3721 tatttttggt gctgacccta tacattcttt aagagtttgt gtagatactg ttcgcacaaa\n",
    "     3781 tgtctactta gctgtctttg ataaaaatct ctatgacaaa cttgtttcaa gctttttgga\n",
    "     3841 aatgaagagt gaaaagcaag ttgaacaaaa gatcgctgag attcctaaag aggaagttaa\n",
    "     3901 gccatttata actgaaagta aaccttcagt tgaacagaga aaacaagatg ataagaaaat\n",
    "     3961 caaagcttgt gttgaagaag ttacaacaac tctggaagaa actaagttcc tcacagaaaa\n",
    "     4021 cttgttactt tatattgaca ttaatggcaa tcttcatcca gattctgcca ctcttgttag\n",
    "     4081 tgacattgac atcactttct taaagaaaga tgctccatat atagtgggtg atgttgttca\n",
    "     4141 agagggtgtt ttaactgctg tggttatacc tactaaaaag gctggtggca ctactgaaat\n",
    "     4201 gctagcgaaa gctttgagaa aagtgccaac agacaattat ataaccactt acccgggtca\n",
    "     4261 gggtttaaat ggttacactg tagaggaggc aaagacagtg cttaaaaagt gtaaaagtgc\n",
    "     4321 cttttacatt ctaccatcta ttatctctaa tgagaagcaa gaaattcttg gaactgtttc\n",
    "     4381 ttggaatttg cgagaaatgc ttgcacatgc agaagaaaca cgcaaattaa tgcctgtctg\n",
    "     4441 tgtggaaact aaagccatag tttcaactat acagcgtaaa tataagggta ttaaaataca\n",
    "     4501 agagggtgtg gttgattatg gtgctagatt ttacttttac accagtaaaa caactgtagc\n",
    "     4561 gtcacttatc aacacactta acgatctaaa tgaaactctt gttacaatgc cacttggcta\n",
    "     4621 tgtaacacat ggcttaaatt tggaagaagc tgctcggtat atgagatctc tcaaagtgcc\n",
    "     4681 agctacagtt tctgtttctt cacctgatgc tgttacagcg tataatggtt atcttacttc\n",
    "     4741 ttcttctaaa acacctgaag aacattttat tgaaaccatc tcacttgctg gttcctataa\n",
    "     4801 agattggtcc tattctggac aatctacaca actaggtata gaatttctta agagaggtga\n",
    "     4861 taaaagtgta tattacacta gtaatcctac cacattccac ctagatggtg aagttatcac\n",
    "     4921 ctttgacaat cttaagacac ttctttcttt gagagaagtg aggactatta aggtgtttac\n",
    "     4981 aacagtagac aacattaacc tccacacgca agttgtggac atgtcaatga catatggaca\n",
    "     5041 acagtttggt ccaacttatt tggatggagc tgatgttact aaaataaaac ctcataattc\n",
    "     5101 acatgaaggt aaaacatttt atgttttacc taatgatgac actctacgtg ttgaggcttt\n",
    "     5161 tgagtactac cacacaactg atcctagttt tctgggtagg tacatgtcag cattaaatca\n",
    "     5221 cactaaaaag tggaaatacc cacaagttaa tggtttaact tctattaaat gggcagataa\n",
    "     5281 caactgttat cttgccactg cattgttaac actccaacaa atagagttga agtttaatcc\n",
    "     5341 acctgctcta caagatgctt attacagagc aagggctggt gaagctgcta acttttgtgc\n",
    "     5401 acttatctta gcctactgta ataagacagt aggtgagtta ggtgatgtta gagaaacaat\n",
    "     5461 gagttacttg tttcaacatg ccaatttaga ttcttgcaaa agagtcttga acgtggtgtg\n",
    "     5521 taaaacttgt ggacaacagc agacaaccct taagggtgta gaagctgtta tgtacatggg\n",
    "     5581 cacactttct tatgaacaat ttaagaaagg tgttcagata ccttgtacgt gtggtaaaca\n",
    "     5641 agctacaaaa tatctagtac aacaggagtc accttttgtt atgatgtcag caccacctgc\n",
    "     5701 tcagtatgaa cttaagcatg gtacatttac ttgtgctagt gagtacactg gtaattacca\n",
    "     5761 gtgtggtcac tataaacata taacttctaa agaaactttg tattgcatag acggtgcttt\n",
    "     5821 acttacaaag tcctcagaat acaaaggtcc tattacggat gttttctaca aagaaaacag\n",
    "     5881 ttacacaaca accataaaac cagttactta taaattggat ggtgttgttt gtacagaaat\n",
    "     5941 tgaccctaag ttggacaatt attataagaa agacaattct tatttcacag agcaaccaat\n",
    "     6001 tgatcttgta ccaaaccaac catatccaaa cgcaagcttc gataatttta agtttgtatg\n",
    "     6061 tgataatatc aaatttgctg atgatttaaa ccagttaact ggttataaga aacctgcttc\n",
    "     6121 aagagagctt aaagttacat ttttccctga cttaaatggt gatgtggtgg ctattgatta\n",
    "     6181 taaacactac acaccctctt ttaagaaagg agctaaattg ttacataaac ctattgtttg\n",
    "     6241 gcatgttaac aatgcaacta ataaagccac gtataaacca aatacctggt gtatacgttg\n",
    "     6301 tctttggagc acaaaaccag ttgaaacatc aaattcgttt gatgtactga agtcagagga\n",
    "     6361 cgcgcaggga atggataatc ttgcctgcga agatctaaaa ccagtctctg aagaagtagt\n",
    "     6421 ggaaaatcct accatacaga aagacgttct tgagtgtaat gtgaaaacta ccgaagttgt\n",
    "     6481 aggagacatt atacttaaac cagcaaataa tagtttaaaa attacagaag aggttggcca\n",
    "     6541 cacagatcta atggctgctt atgtagacaa ttctagtctt actattaaga aacctaatga\n",
    "     6601 attatctaga gtattaggtt tgaaaaccct tgctactcat ggtttagctg ctgttaatag\n",
    "     6661 tgtcccttgg gatactatag ctaattatgc taagcctttt cttaacaaag ttgttagtac\n",
    "     6721 aactactaac atagttacac ggtgtttaaa ccgtgtttgt actaattata tgccttattt\n",
    "     6781 ctttacttta ttgctacaat tgtgtacttt tactagaagt acaaattcta gaattaaagc\n",
    "     6841 atctatgccg actactatag caaagaatac tgttaagagt gtcggtaaat tttgtctaga\n",
    "     6901 ggcttcattt aattatttga agtcacctaa tttttctaaa ctgataaata ttataatttg\n",
    "     6961 gtttttacta ttaagtgttt gcctaggttc tttaatctac tcaaccgctg ctttaggtgt\n",
    "     7021 tttaatgtct aatttaggca tgccttctta ctgtactggt tacagagaag gctatttgaa\n",
    "     7081 ctctactaat gtcactattg caacctactg tactggttct ataccttgta gtgtttgtct\n",
    "     7141 tagtggttta gattctttag acacctatcc ttctttagaa actatacaaa ttaccatttc\n",
    "     7201 atcttttaaa tgggatttaa ctgcttttgg cttagttgca gagtggtttt tggcatatat\n",
    "     7261 tcttttcact aggtttttct atgtacttgg attggctgca atcatgcaat tgtttttcag\n",
    "     7321 ctattttgca gtacatttta ttagtaattc ttggcttatg tggttaataa ttaatcttgt\n",
    "     7381 acaaatggcc ccgatttcag ctatggttag aatgtacatc ttctttgcat cattttatta\n",
    "     7441 tgtatggaaa agttatgtgc atgttgtaga cggttgtaat tcatcaactt gtatgatgtg\n",
    "     7501 ttacaaacgt aatagagcaa caagagtcga atgtacaact attgttaatg gtgttagaag\n",
    "     7561 gtccttttat gtctatgcta atggaggtaa aggcttttgc aaactacaca attggaattg\n",
    "     7621 tgttaattgt gatacattct gtgctggtag tacatttatt agtgatgaag ttgcgagaga\n",
    "     7681 cttgtcacta cagtttaaaa gaccaataaa tcctactgac cagtcttctt acatcgttga\n",
    "     7741 tagtgttaca gtgaagaatg gttccatcca tctttacttt gataaagctg gtcaaaagac\n",
    "     7801 ttatgaaaga cattctctct ctcattttgt taacttagac aacctgagag ctaataacac\n",
    "     7861 taaaggttca ttgcctatta atgttatagt ttttgatggt aaatcaaaat gtgaagaatc\n",
    "     7921 atctgcaaaa tcagcgtctg tttactacag tcagcttatg tgtcaaccta tactgttact\n",
    "     7981 agatcaggca ttagtgtctg atgttggtga tagtgcggaa gttgcagtta aaatgtttga\n",
    "     8041 tgcttacgtt aatacgtttt catcaacttt taacgtacca atggaaaaac tcaaaacact\n",
    "     8101 agttgcaact gcagaagctg aacttgcaaa gaatgtgtcc ttagacaatg tcttatctac\n",
    "     8161 ttttatttca gcagctcggc aagggtttgt tgattcagat gtagaaacta aagatgttgt\n",
    "     8221 tgaatgtctt aaattgtcac atcaatctga catagaagtt actggcgata gttgtaataa\n",
    "     8281 ctatatgctc acctataaca aagttgaaaa catgacaccc cgtgaccttg gtgcttgtat\n",
    "     8341 tgactgtagt gcgcgtcata ttaatgcgca ggtagcaaaa agtcacaaca ttgctttgat\n",
    "     8401 atggaacgtt aaagatttca tgtcattgtc tgaacaacta cgaaaacaaa tacgtagtgc\n",
    "     8461 tgctaaaaag aataacttac cttttaagtt gacatgtgca actactagac aagttgttaa\n",
    "     8521 tgttgtaaca acaaagatag cacttaaggg tggtaaaatt gttaataatt ggttgaagca\n",
    "     8581 gttaattaaa gttacacttg tgttcctttt tgttgctgct attttctatt taataacacc\n",
    "     8641 tgttcatgtc atgtctaaac atactgactt ttcaagtgaa atcataggat acaaggctat\n",
    "     8701 tgatggtggt gtcactcgtg acatagcatc tacagatact tgttttgcta acaaacatgc\n",
    "     8761 tgattttgac acatggttta gccagcgtgg tggtagttat actaatgaca aagcttgccc\n",
    "     8821 attgattgct gcagtcataa caagagaagt gggttttgtc gtgcctggtt tgcctggcac\n",
    "     8881 gatattacgc acaactaatg gtgacttttt gcatttctta cctagagttt ttagtgcagt\n",
    "     8941 tggtaacatc tgttacacac catcaaaact tatagagtac actgactttg caacatcagc\n",
    "     9001 ttgtgttttg gctgctgaat gtacaatttt taaagatgct tctggtaagc cagtaccata\n",
    "     9061 ttgttatgat accaatgtac tagaaggttc tgttgcttat gaaagtttac gccctgacac\n",
    "     9121 acgttatgtg ctcatggatg gctctattat tcaatttcct aacacctacc ttgaaggttc\n",
    "     9181 tgttagagtg gtaacaactt ttgattctga gtactgtagg cacggcactt gtgaaagatc\n",
    "     9241 agaagctggt gtttgtgtat ctactagtgg tagatgggta cttaacaatg attattacag\n",
    "     9301 atctttacca ggagttttct gtggtgtaga tgctgtaaat ttacttacta atatgtttac\n",
    "     9361 accactaatt caacctattg gtgctttgga catatcagca tctatagtag ctggtggtat\n",
    "     9421 tgtagctatc gtagtaacat gccttgccta ctattttatg aggtttagaa gagcttttgg\n",
    "     9481 tgaatacagt catgtagttg cctttaatac tttactattc cttatgtcat tcactgtact\n",
    "     9541 ctgtttaaca ccagtttact cattcttacc tggtgtttat tctgttattt acttgtactt\n",
    "     9601 gacattttat cttactaatg atgtttcttt tttagcacat attcagtgga tggttatgtt\n",
    "     9661 cacaccttta gtacctttct ggataacaat tgcttatatc atttgtattt ccacaaagca\n",
    "     9721 tttctattgg ttctttagta attacctaaa gagacgtgta gtctttaatg gtgtttcctt\n",
    "     9781 tagtactttt gaagaagctg cgctgtgcac ctttttgtta aataaagaaa tgtatctaaa\n",
    "     9841 gttgcgtagt gatgtgctat tacctcttac gcaatataat agatacttag ctctttataa\n",
    "     9901 taagtacaag tattttagtg gagcaatgga tacaactagc tacagagaag ctgcttgttg\n",
    "     9961 tcatctcgca aaggctctca atgacttcag taactcaggt tctgatgttc tttaccaacc\n",
    "    10021 accacaaacc tctatcacct cagctgtttt gcagagtggt tttagaaaaa tggcattccc\n",
    "    10081 atctggtaaa gttgagggtt gtatggtaca agtaacttgt ggtacaacta cacttaacgg\n",
    "    10141 tctttggctt gatgacgtag tttactgtcc aagacatgtg atctgcacct ctgaagacat\n",
    "    10201 gcttaaccct aattatgaag atttactcat tcgtaagtct aatcataatt tcttggtaca\n",
    "    10261 ggctggtaat gttcaactca gggttattgg acattctatg caaaattgtg tacttaagct\n",
    "    10321 taaggttgat acagccaatc ctaagacacc taagtataag tttgttcgca ttcaaccagg\n",
    "    10381 acagactttt tcagtgttag cttgttacaa tggttcacca tctggtgttt accaatgtgc\n",
    "    10441 tatgaggccc aatttcacta ttaagggttc attccttaat ggttcatgtg gtagtgttgg\n",
    "    10501 ttttaacata gattatgact gtgtctcttt ttgttacatg caccatatgg aattaccaac\n",
    "    10561 tggagttcat gctggcacag acttagaagg taacttttat ggaccttttg ttgacaggca\n",
    "    10621 aacagcacaa gcagctggta cggacacaac tattacagtt aatgttttag cttggttgta\n",
    "    10681 cgctgctgtt ataaatggag acaggtggtt tctcaatcga tttaccacaa ctcttaatga\n",
    "    10741 ctttaacctt gtggctatga agtacaatta tgaacctcta acacaagacc atgttgacat\n",
    "    10801 actaggacct ctttctgctc aaactggaat tgccgtttta gatatgtgtg cttcattaaa\n",
    "    10861 agaattactg caaaatggta tgaatggacg taccatattg ggtagtgctt tattagaaga\n",
    "    10921 tgaatttaca ccttttgatg ttgttagaca atgctcaggt gttactttcc aaagtgcagt\n",
    "    10981 gaaaagaaca atcaagggta cacaccactg gttgttactc acaattttga cttcactttt\n",
    "    11041 agttttagtc cagagtactc aatggtcttt gttctttttt ttgtatgaaa atgccttttt\n",
    "    11101 accttttgct atgggtatta ttgctatgtc tgcttttgca atgatgtttg tcaaacataa\n",
    "    11161 gcatgcattt ctctgtttgt ttttgttacc ttctcttgcc actgtagctt attttaatat\n",
    "    11221 ggtctatatg cctgctagtt gggtgatgcg tattatgaca tggttggata tggttgatac\n",
    "    11281 tagtttgtct ggttttaagc taaaagactg tgttatgtat gcatcagctg tagtgttact\n",
    "    11341 aatccttatg acagcaagaa ctgtgtatga tgatggtgct aggagagtgt ggacacttat\n",
    "    11401 gaatgtcttg acactcgttt ataaagttta ttatggtaat gctttagatc aagccatttc\n",
    "    11461 catgtgggct cttataatct ctgttacttc taactactca ggtgtagtta caactgtcat\n",
    "    11521 gtttttggcc agaggtattg tttttatgtg tgttgagtat tgccctattt tcttcataac\n",
    "    11581 tggtaataca cttcagtgta taatgctagt ttattgtttc ttaggctatt tttgtacttg\n",
    "    11641 ttactttggc ctcttttgtt tactcaaccg ctactttaga ctgactcttg gtgtttatga\n",
    "    11701 ttacttagtt tctacacagg agtttagata tatgaattca cagggactac tcccacccaa\n",
    "    11761 gaatagcata gatgccttca aactcaacat taaattgttg ggtgttggtg gcaaaccttg\n",
    "    11821 tatcaaagta gccactgtac agtctaaaat gtcagatgta aagtgcacat cagtagtctt\n",
    "    11881 actctcagtt ttgcaacaac tcagagtaga atcatcatct aaattgtggg ctcaatgtgt\n",
    "    11941 ccagttacac aatgacattc tcttagctaa agatactact gaagcctttg aaaaaatggt\n",
    "    12001 ttcactactt tctgttttgc tttccatgca gggtgctgta gacataaaca agctttgtga\n",
    "    12061 agaaatgctg gacaacaggg caaccttaca agctatagcc tcagagttta gttcccttcc\n",
    "    12121 atcatatgca gcttttgcta ctgctcaaga agcttatgag caggctgttg ctaatggtga\n",
    "    12181 ttctgaagtt gttcttaaaa agttgaagaa gtctttgaat gtggctaaat ctgaatttga\n",
    "    12241 ccgtgatgca gccatgcaac gtaagttgga aaagatggct gatcaagcta tgacccaaat\n",
    "    12301 gtataaacag gctagatctg aggacaagag ggcaaaagtt actagtgcta tgcagacaat\n",
    "    12361 gcttttcact atgcttagaa agttggataa tgatgcactc aacaacatta tcaacaatgc\n",
    "    12421 aagagatggt tgtgttccct tgaacataat acctcttaca acagcagcca aactaatggt\n",
    "    12481 tgtcatacca gactataaca catataaaaa tacgtgtgat ggtacaacat ttacttatgc\n",
    "    12541 atcagcattg tgggaaatcc aacaggttgt agatgcagat agtaaaattg ttcaacttag\n",
    "    12601 tgaaattagt atggacaatt cacctaattt agcatggcct cttattgtaa cagctttaag\n",
    "    12661 ggccaattct gctgtcaaat tacagaataa tgagcttagt cctgttgcac tacgacagat\n",
    "    12721 gtcttgtgct gccggtacta cacaaactgc ttgcactgat gacaatgcgt tagcttacta\n",
    "    12781 caacacaaca aagggaggta ggtttgtact tgcactgtta tccgatttac aggatttgaa\n",
    "    12841 atgggctaga ttccctaaga gtgatggaac tggtactatc tatacagaac tggaaccacc\n",
    "    12901 ttgtaggttt gttacagaca cacctaaagg tcctaaagtg aagtatttat actttattaa\n",
    "    12961 aggattaaac aacctaaata gaggtatggt acttggtagt ttagctgcca cagtacgtct\n",
    "    13021 acaagctggt aatgcaacag aagtgcctgc caattcaact gtattatctt tctgtgcttt\n",
    "    13081 tgctgtagat gctgctaaag cttacaaaga ttatctagct agtgggggac aaccaatcac\n",
    "    13141 taattgtgtt aagatgttgt gtacacacac tggtactggt caggcaataa cagttacacc\n",
    "    13201 ggaagccaat atggatcaag aatcctttgg tggtgcatcg tgttgtctgt actgccgttg\n",
    "    13261 ccacatagat catccaaatc ctaaaggatt ttgtgactta aaaggtaagt atgtacaaat\n",
    "    13321 acctacaact tgtgctaatg accctgtggg ttttacactt aaaaacacag tctgtaccgt\n",
    "    13381 ctgcggtatg tggaaaggtt atggctgtag ttgtgatcaa ctccgcgaac ccatgcttca\n",
    "    13441 gtcagctgat gcacaatcgt ttttaaacgg gtttgcggtg taagtgcagc ccgtcttaca\n",
    "    13501 ccgtgcggca caggcactag tactgatgtc gtatacaggg cttttgacat ctacaatgat\n",
    "    13561 aaagtagctg gttttgctaa attcctaaaa actaattgtt gtcgcttcca agaaaaggac\n",
    "    13621 gaagatgaca atttaattga ttcttacttt gtagttaaga gacacacttt ctctaactac\n",
    "    13681 caacatgaag aaacaattta taatttactt aaggattgtc cagctgttgc taaacatgac\n",
    "    13741 ttctttaagt ttagaataga cggtgacatg gtaccacata tatcacgtca acgtcttact\n",
    "    13801 aaatacacaa tggcagacct cgtctatgct ttaaggcatt ttgatgaagg taattgtgac\n",
    "    13861 acattaaaag aaatacttgt cacatacaat tgttgtgatg atgattattt caataaaaag\n",
    "    13921 gactggtatg attttgtaga aaacccagat atattacgcg tatacgccaa cttaggtgaa\n",
    "    13981 cgtgtacgcc aagctttgtt aaaaacagta caattctgtg atgccatgcg aaatgctggt\n",
    "    14041 attgttggtg tactgacatt agataatcaa gatctcaatg gtaactggta tgatttcggt\n",
    "    14101 gatttcatac aaaccacgcc aggtagtgga gttcctgttg tagattctta ttattcattg\n",
    "    14161 ttaatgccta tattaacctt gaccagggct ttaactgcag agtcacatgt tgacactgac\n",
    "    14221 ttaacaaagc cttacattaa gtgggatttg ttaaaatatg acttcacgga agagaggtta\n",
    "    14281 aaactctttg accgttattt taaatattgg gatcagacat accacccaaa ttgtgttaac\n",
    "    14341 tgtttggatg acagatgcat tctgcattgt gcaaacttta atgttttatt ctctacagtg\n",
    "    14401 ttcccaccta caagttttgg accactagtg agaaaaatat ttgttgatgg tgttccattt\n",
    "    14461 gtagtttcaa ctggatacca cttcagagag ctaggtgttg tacataatca ggatgtaaac\n",
    "    14521 ttacatagct ctagacttag ttttaaggaa ttacttgtgt atgctgctga ccctgctatg\n",
    "    14581 cacgctgctt ctggtaatct attactagat aaacgcacta cgtgcttttc agtagctgca\n",
    "    14641 cttactaaca atgttgcttt tcaaactgtc aaacccggta attttaacaa agacttctat\n",
    "    14701 gactttgctg tgtctaaggg tttctttaag gaaggaagtt ctgttgaatt aaaacacttc\n",
    "    14761 ttctttgctc aggatggtaa tgctgctatc agcgattatg actactatcg ttataatcta\n",
    "    14821 ccaacaatgt gtgatatcag acaactacta tttgtagttg aagttgttga taagtacttt\n",
    "    14881 gattgttacg atggtggctg tattaatgct aaccaagtca tcgtcaacaa cctagacaaa\n",
    "    14941 tcagctggtt ttccatttaa taaatggggt aaggctagac tttattatga ttcaatgagt\n",
    "    15001 tatgaggatc aagatgcact tttcgcatat acaaaacgta atgtcatccc tactataact\n",
    "    15061 caaatgaatc ttaagtatgc cattagtgca aagaatagag ctcgcaccgt agctggtgtc\n",
    "    15121 tctatctgta gtactatgac caatagacag tttcatcaaa aattattgaa atcaatagcc\n",
    "    15181 gccactagag gagctactgt agtaattgga acaagcaaat tctatggtgg ttggcacaac\n",
    "    15241 atgttaaaaa ctgtttatag tgatgtagaa aaccctcacc ttatgggttg ggattatcct\n",
    "    15301 aaatgtgata gagccatgcc taacatgctt agaattatgg cctcacttgt tcttgctcgc\n",
    "    15361 aaacatacaa cgtgttgtag cttgtcacac cgtttctata gattagctaa tgagtgtgct\n",
    "    15421 caagtattga gtgaaatggt catgtgtggc ggttcactat atgttaaacc aggtggaacc\n",
    "    15481 tcatcaggag atgccacaac tgcttatgct aatagtgttt ttaacatttg tcaagctgtc\n",
    "    15541 acggccaatg ttaatgcact tttatctact gatggtaaca aaattgccga taagtatgtc\n",
    "    15601 cgcaatttac aacacagact ttatgagtgt ctctatagaa atagagatgt tgacacagac\n",
    "    15661 tttgtgaatg agttttacgc atatttgcgt aaacatttct caatgatgat actctctgac\n",
    "    15721 gatgctgttg tgtgtttcaa tagcacttat gcatctcaag gtctagtggc tagcataaag\n",
    "    15781 aactttaagt cagttcttta ttatcaaaac aatgttttta tgtctgaagc aaaatgttgg\n",
    "    15841 actgagactg accttactaa aggacctcat gaattttgct ctcaacatac aatgctagtt\n",
    "    15901 aaacagggtg atgattatgt gtaccttcct tacccagatc catcaagaat cctaggggcc\n",
    "    15961 ggctgttttg tagatgatat cgtaaaaaca gatggtacac ttatgattga acggttcgtg\n",
    "    16021 tctttagcta tagatgctta cccacttact aaacatccta atcaggagta tgctgatgtc\n",
    "    16081 tttcatttgt acttacaata cataagaaag ctacatgatg agttaacagg acacatgtta\n",
    "    16141 gacatgtatt ctgttatgct tactaatgat aacacttcaa ggtattggga acctgagttt\n",
    "    16201 tatgaggcta tgtacacacc gcatacagtc ttacaggctg ttggggcttg tgttctttgc\n",
    "    16261 aattcacaga cttcattaag atgtggtgct tgcatacgta gaccattctt atgttgtaaa\n",
    "    16321 tgctgttacg accatgtcat atcaacatca cataaattag tcttgtctgt taatccgtat\n",
    "    16381 gtttgcaatg ctccaggttg tgatgtcaca gatgtgactc aactttactt aggaggtatg\n",
    "    16441 agctattatt gtaaatcaca taaaccaccc attagttttc cattgtgtgc taatggacaa\n",
    "    16501 gtttttggtt tatataaaaa tacatgtgtt ggtagcgata atgttactga ctttaatgca\n",
    "    16561 attgcaacat gtgactggac aaatgctggt gattacattt tagctaacac ctgtactgaa\n",
    "    16621 agactcaagc tttttgcagc agaaacgctc aaagctactg aggagacatt taaactgtct\n",
    "    16681 tatggtattg ctactgtacg tgaagtgctg tctgacagag aattacatct ttcatgggaa\n",
    "    16741 gttggtaaac ctagaccacc acttaaccga aattatgtct ttactggtta tcgtgtaact\n",
    "    16801 aaaaacagta aagtacaaat aggagagtac acctttgaaa aaggtgacta tggtgatgct\n",
    "    16861 gttgtttacc gaggtacaac aacttacaaa ttaaatgttg gtgattattt tgtgctgaca\n",
    "    16921 tcacatacag taatgccatt aagtgcacct acactagtgc cacaagagca ctatgttaga\n",
    "    16981 attactggct tatacccaac actcaatatc tcagatgagt tttctagcaa tgttgcaaat\n",
    "    17041 tatcaaaagg ttggtatgca aaagtattct acactccagg gaccacctgg tactggtaag\n",
    "    17101 agtcattttg ctattggcct agctctctac tacccttctg ctcgcatagt gtatacagct\n",
    "    17161 tgctctcatg ccgctgttga tgcactatgt gagaaggcat taaaatattt gcctatagat\n",
    "    17221 aaatgtagta gaattatacc tgcacgtgct cgtgtagagt gttttgataa attcaaagtg\n",
    "    17281 aattcaacat tagaacagta tgtcttttgt actgtaaatg cattgcctga gacgacagca\n",
    "    17341 gatatagttg tctttgatga aatttcaatg gccacaaatt atgatttgag tgttgtcaat\n",
    "    17401 gccagattac gtgctaagca ctatgtgtac attggcgacc ctgctcaatt acctgcacca\n",
    "    17461 cgcacattgc taactaaggg cacactagaa ccagaatatt tcaattcagt gtgtagactt\n",
    "    17521 atgaaaacta taggtccaga catgttcctc ggaacttgtc ggcgttgtcc tgctgaaatt\n",
    "    17581 gttgacactg tgagtgcttt ggtttatgat aataagctta aagcacataa agacaaatca\n",
    "    17641 gctcaatgct ttaaaatgtt ttataagggt gttatcacgc atgatgtttc atctgcaatt\n",
    "    17701 aacaggccac aaataggcgt ggtaagagaa ttccttacac gtaaccctgc ttggagaaaa\n",
    "    17761 gctgtcttta tttcacctta taattcacag aatgctgtag cctcaaagat tttgggacta\n",
    "    17821 ccaactcaaa ctgttgattc atcacagggc tcagaatatg actatgtcat attcactcaa\n",
    "    17881 accactgaaa cagctcactc ttgtaatgta aacagattta atgttgctat taccagagca\n",
    "    17941 aaagtaggca tactttgcat aatgtctgat agagaccttt atgacaagtt gcaatttaca\n",
    "    18001 agtcttgaaa ttccacgtag gaatgtggca actttacaag ctgaaaatgt aacaggactc\n",
    "    18061 tttaaagatt gtagtaaggt aatcactggg ttacatccta cacaggcacc tacacacctc\n",
    "    18121 agtgttgaca ctaaattcaa aactgaaggt ttatgtgttg acatacctgg catacctaag\n",
    "    18181 gacatgacct atagaagact catctctatg atgggtttta aaatgaatta tcaagttaat\n",
    "    18241 ggttacccta acatgtttat cacccgcgaa gaagctataa gacatgtacg tgcatggatt\n",
    "    18301 ggcttcgatg tcgaggggtg tcatgctact agagaagctg ttggtaccaa tttaccttta\n",
    "    18361 cagctaggtt tttctacagg tgttaaccta gttgctgtac ctacaggtta tgttgataca\n",
    "    18421 cctaataata cagatttttc cagagttagt gctaaaccac cgcctggaga tcaatttaaa\n",
    "    18481 cacctcatac cacttatgta caaaggactt ccttggaatg tagtgcgtat aaagattgta\n",
    "    18541 caaatgttaa gtgacacact taaaaatctc tctgacagag tcgtatttgt cttatgggca\n",
    "    18601 catggctttg agttgacatc tatgaagtat tttgtgaaaa taggacctga gcgcacctgt\n",
    "    18661 tgtctatgtg atagacgtgc cacatgcttt tccactgctt cagacactta tgcctgttgg\n",
    "    18721 catcattcta ttggatttga ttacgtctat aatccgttta tgattgatgt tcaacaatgg\n",
    "    18781 ggttttacag gtaacctaca aagcaaccat gatctgtatt gtcaagtcca tggtaatgca\n",
    "    18841 catgtagcta gttgtgatgc aatcatgact aggtgtctag ctgtccacga gtgctttgtt\n",
    "    18901 aagcgtgttg actggactat tgaatatcct ataattggtg atgaactgaa gattaatgcg\n",
    "    18961 gcttgtagaa aggttcaaca catggttgtt aaagctgcat tattagcaga caaattccca\n",
    "    19021 gttcttcacg acattggtaa ccctaaagct attaagtgtg tacctcaagc tgatgtagaa\n",
    "    19081 tggaagttct atgatgcaca gccttgtagt gacaaagctt ataaaataga agaattattc\n",
    "    19141 tattcttatg ccacacattc tgacaaattc acagatggtg tatgcctatt ttggaattgc\n",
    "    19201 aatgtcgata gatatcctgc taattccatt gtttgtagat ttgacactag agtgctatct\n",
    "    19261 aaccttaact tgcctggttg tgatggtggc agtttgtatg taaataaaca tgcattccac\n",
    "    19321 acaccagctt ttgataaaag tgcttttgtt aatttaaaac aattaccatt tttctattac\n",
    "    19381 tctgacagtc catgtgagtc tcatggaaaa caagtagtgt cagatataga ttatgtacca\n",
    "    19441 ctaaagtctg ctacgtgtat aacacgttgc aatttaggtg gtgctgtctg tagacatcat\n",
    "    19501 gctaatgagt acagattgta tctcgatgct tataacatga tgatctcagc tggctttagc\n",
    "    19561 ttgtgggttt acaaacaatt tgatacttat aacctctgga acacttttac aagacttcag\n",
    "    19621 agtttagaaa atgtggcttt taatgttgta aataagggac actttgatgg acaacagggt\n",
    "    19681 gaagtaccag tttctatcat taataacact gtttacacaa aagttgatgg tgttgatgta\n",
    "    19741 gaattgtttg aaaataaaac aacattacct gttaatgtag catttgagct ttgggctaag\n",
    "    19801 cgcaacatta aaccagtacc agaggtgaaa atactcaata atttgggtgt ggacattgct\n",
    "    19861 gctaatactg tgatctggga ctacaaaaga gatgctccag cacatatatc tactattggt\n",
    "    19921 gtttgttcta tgactgacat agccaagaaa ccaactgaaa cgatttgtgc accactcact\n",
    "    19981 gtcttttttg atggtagagt tgatggtcaa gtagacttat ttagaaatgc ccgtaatggt\n",
    "    20041 gttcttatta cagaaggtag tgttaaaggt ttacaaccat ctgtaggtcc caaacaagct\n",
    "    20101 agtcttaatg gagtcacatt aattggagaa gccgtaaaaa cacagttcaa ttattataag\n",
    "    20161 aaagttgatg gtgttgtcca acaattacct gaaacttact ttactcagag tagaaattta\n",
    "    20221 caagaattta aacccaggag tcaaatggaa attgatttct tagaattagc tatggatgaa\n",
    "    20281 ttcattgaac ggtataaatt agaaggctat gccttcgaac atatcgttta tggagatttt\n",
    "    20341 agtcatagtc agttaggtgg tttacatcta ctgattggac tagctaaacg ttttaaggaa\n",
    "    20401 tcaccttttg aattagaaga ttttattcct atggacagta cagttaaaaa ctatttcata\n",
    "    20461 acagatgcgc aaacaggttc atctaagtgt gtgtgttctg ttattgattt attacttgat\n",
    "    20521 gattttgttg aaataataaa atcccaagat ttatctgtag tttctaaggt tgtcaaagtg\n",
    "    20581 actattgact atacagaaat ttcatttatg ctttggtgta aagatggcca tgtagaaaca\n",
    "    20641 ttttacccaa aattacaatc tagtcaagcg tggcaaccgg gtgttgctat gcctaatctt\n",
    "    20701 tacaaaatgc aaagaatgct attagaaaag tgtgaccttc aaaattatgg tgatagtgca\n",
    "    20761 acattaccta aaggcataat gatgaatgtc gcaaaatata ctcaactgtg tcaatattta\n",
    "    20821 aacacattaa cattagctgt accctataat atgagagtta tacattttgg tgctggttct\n",
    "    20881 gataaaggag ttgcaccagg tacagctgtt ttaagacagt ggttgcctac gggtacgctg\n",
    "    20941 cttgtcgatt cagatcttaa tgactttgtc tctgatgcag attcaacttt gattggtgat\n",
    "    21001 tgtgcaactg tacatacagc taataaatgg gatctcatta ttagtgatat gtacgaccct\n",
    "    21061 aagactaaaa atgttacaaa agaaaatgac tctaaagagg gttttttcac ttacatttgt\n",
    "    21121 gggtttatac aacaaaagct agctcttgga ggttccgtgg ctataaagat aacagaacat\n",
    "    21181 tcttggaatg ctgatcttta taagctcatg ggacacttcg catggtggac agcctttgtt\n",
    "    21241 actaatgtga atgcgtcatc atctgaagca tttttaattg gatgtaatta tcttggcaaa\n",
    "    21301 ccacgcgaac aaatagatgg ttatgtcatg catgcaaatt acatattttg gaggaataca\n",
    "    21361 aatccaattc agttgtcttc ctattcttta tttgacatga gtaaatttcc ccttaaatta\n",
    "    21421 aggggtactg ctgttatgtc tttaaaagaa ggtcaaatca atgatatgat tttatctctt\n",
    "    21481 cttagtaaag gtagacttat aattagagaa aacaacagag ttgttatttc tagtgatgtt\n",
    "    21541 cttgttaaca actaaacgaa caatgtttgt ttttcttgtt ttattgccac tagtctctag\n",
    "    21601 tcagtgtgtt aatcttacaa ccagaactca attaccccct gcatacacta attctttcac\n",
    "    21661 acgtggtgtt tattaccctg acaaagtttt cagatcctca gttttacatt caactcagga\n",
    "    21721 cttgttctta cctttctttt ccaatgttac ttggttccat gctatacatg tctctgggac\n",
    "    21781 caatggtact aagaggtttg ataaccctgt cctaccattt aatgatggtg tttattttgc\n",
    "    21841 ttccactgag aagtctaaca taataagagg ctggattttt ggtactactt tagattcgaa\n",
    "    21901 gacccagtcc ctacttattg ttaataacgc tactaatgtt gttattaaag tctgtgaatt\n",
    "    21961 tcaattttgt aatgatccat ttttgggtgt ttattaccac aaaaacaaca aaagttggat\n",
    "    22021 ggaaagtgag ttcagagttt attctagtgc gaataattgc acttttgaat atgtctctca\n",
    "    22081 gccttttctt atggaccttg aaggaaaaca gggtaatttc aaaaatctta gggaatttgt\n",
    "    22141 gtttaagaat attgatggtt attttaaaat atattctaag cacacgccta ttaatttagt\n",
    "    22201 gcgtgatctc cctcagggtt tttcggcttt agaaccattg gtagatttgc caataggtat\n",
    "    22261 taacatcact aggtttcaaa ctttacttgc tttacataga agttatttga ctcctggtga\n",
    "    22321 ttcttcttca ggttggacag ctggtgctgc agcttattat gtgggttatc ttcaacctag\n",
    "    22381 gacttttcta ttaaaatata atgaaaatgg aaccattaca gatgctgtag actgtgcact\n",
    "    22441 tgaccctctc tcagaaacaa agtgtacgtt gaaatccttc actgtagaaa aaggaatcta\n",
    "    22501 tcaaacttct aactttagag tccaaccaac agaatctatt gttagatttc ctaatattac\n",
    "    22561 aaacttgtgc ccttttggtg aagtttttaa cgccaccaga tttgcatctg tttatgcttg\n",
    "    22621 gaacaggaag agaatcagca actgtgttgc tgattattct gtcctatata attccgcatc\n",
    "    22681 attttccact tttaagtgtt atggagtgtc tcctactaaa ttaaatgatc tctgctttac\n",
    "    22741 taatgtctat gcagattcat ttgtaattag aggtgatgaa gtcagacaaa tcgctccagg\n",
    "    22801 gcaaactgga aagattgctg attataatta taaattacca gatgatttta caggctgcgt\n",
    "    22861 tatagcttgg aattctaaca atcttgattc taaggttggt ggtaattata attacctgta\n",
    "    22921 tagattgttt aggaagtcta atctcaaacc ttttgagaga gatatttcaa ctgaaatcta\n",
    "    22981 tcaggccggt agcacacctt gtaatggtgt tgaaggtttt aattgttact ttcctttaca\n",
    "    23041 atcatatggt ttccaaccca ctaatggtgt tggttaccaa ccatacagag tagtagtact\n",
    "    23101 ttcttttgaa cttctacatg caccagcaac tgtttgtgga cctaaaaagt ctactaattt\n",
    "    23161 ggttaaaaac aaatgtgtca atttcaactt caatggttta acaggcacag gtgttcttac\n",
    "    23221 tgagtctaac aaaaagtttc tgcctttcca acaatttggc agagacattg ctgacactac\n",
    "    23281 tgatgctgtc cgtgatccac agacacttga gattcttgac attacaccat gttcttttgg\n",
    "    23341 tggtgtcagt gttataacac caggaacaaa tacttctaac caggttgctg ttctttatca\n",
    "    23401 ggatgttaac tgcacagaag tccctgttgc tattcatgca gatcaactta ctcctacttg\n",
    "    23461 gcgtgtttat tctacaggtt ctaatgtttt tcaaacacgt gcaggctgtt taataggggc\n",
    "    23521 tgaacatgtc aacaactcat atgagtgtga catacccatt ggtgcaggta tatgcgctag\n",
    "    23581 ttatcagact cagactaatt ctcctcggcg ggcacgtagt gtagctagtc aatccatcat\n",
    "    23641 tgcctacact atgtcacttg gtgcagaaaa ttcagttgct tactctaata actctattgc\n",
    "    23701 catacccaca aattttacta ttagtgttac cacagaaatt ctaccagtgt ctatgaccaa\n",
    "    23761 gacatcagta gattgtacaa tgtacatttg tggtgattca actgaatgca gcaatctttt\n",
    "    23821 gttgcaatat ggcagttttt gtacacaatt aaaccgtgct ttaactggaa tagctgttga\n",
    "    23881 acaagacaaa aacacccaag aagtttttgc acaagtcaaa caaatttaca aaacaccacc\n",
    "    23941 aattaaagat tttggtggtt ttaatttttc acaaatatta ccagatccat caaaaccaag\n",
    "    24001 caagaggtca tttattgaag atctactttt caacaaagtg acacttgcag atgctggctt\n",
    "    24061 catcaaacaa tatggtgatt gccttggtga tattgctgct agagacctca tttgtgcaca\n",
    "    24121 aaagtttaac ggccttactg ttttgccacc tttgctcaca gatgaaatga ttgctcaata\n",
    "    24181 cacttctgca ctgttagcgg gtacaatcac ttctggttgg acctttggtg caggtgctgc\n",
    "    24241 attacaaata ccatttgcta tgcaaatggc ttataggttt aatggtattg gagttacaca\n",
    "    24301 gaatgttctc tatgagaacc aaaaattgat tgccaaccaa tttaatagtg ctattggcaa\n",
    "    24361 aattcaagac tcactttctt ccacagcaag tgcacttgga aaacttcaag atgtggtcaa\n",
    "    24421 ccaaaatgca caagctttaa acacgcttgt taaacaactt agctccaatt ttggtgcaat\n",
    "    24481 ttcaagtgtt ttaaatgata tcctttcacg tcttgacaaa gttgaggctg aagtgcaaat\n",
    "    24541 tgataggttg atcacaggca gacttcaaag tttgcagaca tatgtgactc aacaattaat\n",
    "    24601 tagagctgca gaaatcagag cttctgctaa tcttgctgct actaaaatgt cagagtgtgt\n",
    "    24661 acttggacaa tcaaaaagag ttgatttttg tggaaagggc tatcatctta tgtccttccc\n",
    "    24721 tcagtcagca cctcatggtg tagtcttctt gcatgtgact tatgtccctg cacaagaaaa\n",
    "    24781 gaacttcaca actgctcctg ccatttgtca tgatggaaaa gcacactttc ctcgtgaagg\n",
    "    24841 tgtctttgtt tcaaatggca cacactggtt tgtaacacaa aggaattttt atgaaccaca\n",
    "    24901 aatcattact acagacaaca catttgtgtc tggtaactgt gatgttgtaa taggaattgt\n",
    "    24961 caacaacaca gtttatgatc ctttgcaacc tgaattagac tcattcaagg aggagttaga\n",
    "    25021 taaatatttt aagaatcata catcaccaga tgttgattta ggtgacatct ctggcattaa\n",
    "    25081 tgcttcagtt gtaaacattc aaaaagaaat tgaccgcctc aatgaggttg ccaagaattt\n",
    "    25141 aaatgaatct ctcatcgatc tccaagaact tggaaagtat gagcagtata taaaatggcc\n",
    "    25201 atggtacatt tggctaggtt ttatagctgg cttgattgcc atagtaatgg tgacaattat\n",
    "    25261 gctttgctgt atgaccagtt gctgtagttg tctcaagggc tgttgttctt gtggatcctg\n",
    "    25321 ctgcaaattt gatgaagacg actctgagcc agtgctcaaa ggagtcaaat tacattacac\n",
    "    25381 ataaacgaac ttatggattt gtttatgaga atcttcacaa ttggaactgt aactttgaag\n",
    "    25441 caaggtgaaa tcaaggatgc tactccttca gattttgttc gcgctactgc aacgataccg\n",
    "    25501 atacaagcct cactcccttt cggatggctt attgttggcg ttgcacttct tgctgttttt\n",
    "    25561 cagagcgctt ccaaaatcat aaccctcaaa aagagatggc aactagcact ctccaagggt\n",
    "    25621 gttcactttg tttgcaactt gctgttgttg tttgtaacag tttactcaca ccttttgctc\n",
    "    25681 gttgctgctg gccttgaagc cccttttctc tatctttatg ctttagtcta cttcttgcag\n",
    "    25741 agtataaact ttgtaagaat aataatgagg ctttggcttt gctggaaatg ccgttccaaa\n",
    "    25801 aacccattac tttatgatgc caactatttt ctttgctggc atactaattg ttacgactat\n",
    "    25861 tgtatacctt acaatagtgt aacttcttca attgtcatta cttcaggtga tggcacaaca\n",
    "    25921 agtcctattt ctgaacatga ctaccagatt ggtggttata ctgaaaaatg ggaatctgga\n",
    "    25981 gtaaaagact gtgttgtatt acacagttac ttcacttcag actattacca gctgtactca\n",
    "    26041 actcaattga gtacagacac tggtgttgaa catgttacct tcttcatcta caataaaatt\n",
    "    26101 gttgatgagc ctgaagaaca tgtccaaatt cacacaatcg acggttcatc cggagttgtt\n",
    "    26161 aatccagtaa tggaaccaat ttatgatgaa ccgacgacga ctactagcgt gcctttgtaa\n",
    "    26221 gcacaagctg atgagtacga acttatgtac tcattcgttt cggaagagac aggtacgtta\n",
    "    26281 atagttaata gcgtacttct ttttcttgct ttcgtggtat tcttgctagt tacactagcc\n",
    "    26341 atccttactg cgcttcgatt gtgtgcgtac tgctgcaata ttgttaacgt gagtcttgta\n",
    "    26401 aaaccttctt tttacgttta ctctcgtgtt aaaaatctga attcttctag agttcctgat\n",
    "    26461 cttctggtct aaacgaacta aatattatat tagtttttct gtttggaact ttaattttag\n",
    "    26521 ccatggcaga ttccaacggt actattaccg ttgaagagct taaaaagctc cttgaacaat\n",
    "    26581 ggaacctagt aataggtttc ctattcctta catggatttg tcttctacaa tttgcctatg\n",
    "    26641 ccaacaggaa taggtttttg tatataatta agttaatttt cctctggctg ttatggccag\n",
    "    26701 taactttagc ttgttttgtg cttgctgctg tttacagaat aaattggatc accggtggaa\n",
    "    26761 ttgctatcgc aatggcttgt cttgtaggct tgatgtggct cagctacttc attgcttctt\n",
    "    26821 tcagactgtt tgcgcgtacg cgttccatgt ggtcattcaa tccagaaact aacattcttc\n",
    "    26881 tcaacgtgcc actccatggc actattctga ccagaccgct tctagaaagt gaactcgtaa\n",
    "    26941 tcggagctgt gatccttcgt ggacatcttc gtattgctgg acaccatcta ggacgctgtg\n",
    "    27001 acatcaagga cctgcctaaa gaaatcactg ttgctacatc acgaacgctt tcttattaca\n",
    "    27061 aattgggagc ttcgcagcgt gtagcaggtg actcaggttt tgctgcatac agtcgctaca\n",
    "    27121 ggattggcaa ctataaatta aacacagacc attccagtag cagtgacaat attgctttgc\n",
    "    27181 ttgtacagta agtgacaaca gatgtttcat ctcgttgact ttcaggttac tatagcagag\n",
    "    27241 atattactaa ttattatgag gacttttaaa gtttccattt ggaatcttga ttacatcata\n",
    "    27301 aacctcataa ttaaaaattt atctaagtca ctaactgaga ataaatattc tcaattagat\n",
    "    27361 gaagagcaac caatggagat tgattaaacg aacatgaaaa ttattctttt cttggcactg\n",
    "    27421 ataacactcg ctacttgtga gctttatcac taccaagagt gtgttagagg tacaacagta\n",
    "    27481 cttttaaaag aaccttgctc ttctggaaca tacgagggca attcaccatt tcatcctcta\n",
    "    27541 gctgataaca aatttgcact gacttgcttt agcactcaat ttgcttttgc ttgtcctgac\n",
    "    27601 ggcgtaaaac acgtctatca gttacgtgcc agatcagttt cacctaaact gttcatcaga\n",
    "    27661 caagaggaag ttcaagaact ttactctcca atttttctta ttgttgcggc aatagtgttt\n",
    "    27721 ataacacttt gcttcacact caaaagaaag acagaatgat tgaactttca ttaattgact\n",
    "    27781 tctatttgtg ctttttagcc tttctgctat tccttgtttt aattatgctt attatctttt\n",
    "    27841 ggttctcact tgaactgcaa gatcataatg aaacttgtca cgcctaaacg aacatgaaat\n",
    "    27901 ttcttgtttt cttaggaatc atcacaactg tagctgcatt tcaccaagaa tgtagtttac\n",
    "    27961 agtcatgtac tcaacatcaa ccatatgtag ttgatgaccc gtgtcctatt cacttctatt\n",
    "    28021 ctaaatggta tattagagta ggagctagaa aatcagcacc tttaattgaa ttgtgcgtgg\n",
    "    28081 atgaggctgg ttctaaatca cccattcagt acatcgatat cggtaattat acagtttcct\n",
    "    28141 gtttaccttt tacaattaat tgccaggaac ctaaattggg tagtcttgta gtgcgttgtt\n",
    "    28201 cgttctatga agacttttta gagtatcatg acgttcgtgt tgttttagat ttcatctaaa\n",
    "    28261 cgaacaaact aaaatgtctg ataatggacc ccaaaatcag cgaaatgcac cccgcattac\n",
    "    28321 gtttggtgga ccctcagatt caactggcag taaccagaat ggagaacgca gtggggcgcg\n",
    "    28381 atcaaaacaa cgtcggcccc aaggtttacc caataatact gcgtcttggt tcaccgctct\n",
    "    28441 cactcaacat ggcaaggaag accttaaatt ccctcgagga caaggcgttc caattaacac\n",
    "    28501 caatagcagt ccagatgacc aaattggcta ctaccgaaga gctaccagac gaattcgtgg\n",
    "    28561 tggtgacggt aaaatgaaag atctcagtcc aagatggtat ttctactacc taggaactgg\n",
    "    28621 gccagaagct ggacttccct atggtgctaa caaagacggc atcatatggg ttgcaactga\n",
    "    28681 gggagccttg aatacaccaa aagatcacat tggcacccgc aatcctgcta acaatgctgc\n",
    "    28741 aatcgtgcta caacttcctc aaggaacaac attgccaaaa ggcttctacg cagaagggag\n",
    "    28801 cagaggcggc agtcaagcct cttctcgttc ctcatcacgt agtcgcaaca gttcaagaaa\n",
    "    28861 ttcaactcca ggcagcagta ggggaacttc tcctgctaga atggctggca atggcggtga\n",
    "    28921 tgctgctctt gctttgctgc tgcttgacag attgaaccag cttgagagca aaatgtctgg\n",
    "    28981 taaaggccaa caacaacaag gccaaactgt cactaagaaa tctgctgctg aggcttctaa\n",
    "    29041 gaagcctcgg caaaaacgta ctgccactaa agcatacaat gtaacacaag ctttcggcag\n",
    "    29101 acgtggtcca gaacaaaccc aaggaaattt tggggaccag gaactaatca gacaaggaac\n",
    "    29161 tgattacaaa cattggccgc aaattgcaca atttgccccc agcgcttcag cgttcttcgg\n",
    "    29221 aatgtcgcgc attggcatgg aagtcacacc ttcgggaacg tggttgacct acacaggtgc\n",
    "    29281 catcaaattg gatgacaaag atccaaattt caaagatcaa gtcattttgc tgaataagca\n",
    "    29341 tattgacgca tacaaaacat tcccaccaac agagcctaaa aaggacaaaa agaagaaggc\n",
    "    29401 tgatgaaact caagccttac cgcagagaca gaagaaacag caaactgtga ctcttcttcc\n",
    "    29461 tgctgcagat ttggatgatt tctccaaaca attgcaacaa tccatgagca gtgctgactc\n",
    "    29521 aactcaggcc taaactcatg cagaccacac aaggcagatg ggctatataa acgttttcgc\n",
    "    29581 ttttccgttt acgatatata gtctactctt gtgcagaatg aattctcgta actacatagc\n",
    "    29641 acaagtagat gtagttaact ttaatctcac atagcaatct ttaatcagtg tgtaacatta\n",
    "    29701 gggaggactt gaaagagcca ccacattttc accgaggcca cgcggagtac gatcgagtgt\n",
    "    29761 acagtgaaca atgctaggga gagctgccta tatggaagag ccctaatgtg taaaattaat\n",
    "    29821 tttagtagtg ctatccccat gtgattttaa tagcttctta ggagaatgac aaaaaaaaaa\n",
    "    29881 aaaaaaaaaa aaaaaaaaaa aaa\"\"\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> **This genome can be replaced in this notebook by saving it on the disk by creating a txt file and calling it like we've done in the next cell**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open('/Users/pranjal27bhardwaj/Desktop/Corona main/covid_genome.txt', 'r') as file:\n",
    "    corona = file.read()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'1 atattaggtt tttacctacc caggaaaagc caaccaacct cgatctcttg tagatctgtt\\n61 ctctaaacga actttaaaat ctgtgtagct gtcgctcggc tgcatgccta gtgcacctac\\n121 gcagtataaa caataataaa ttttactgtc gttgacaaga aacgagtaac tcgtccctct\\n181 tctgcagact gcttacggtt tcgtccgtgt tgcagtcgat catcagcata cctaggtttc\\n241 gtccgggtgt gaccgaaagg taagatggag agccttgttc ttggtgtcaa cgagaaaaca\\n301 cacgtccaac tcagtttgcc tgtccttcag gttagagacg tgctagtgcg tggcttcggg\\n361 gactctgtgg aagaggccct atcggaggca cgtgaacacc tcaaaaatgg cacttgtggt\\n421 ctagtagagc tggaaaaagg cgtactgccc cagcttgaac agccctatgt gttcattaaa\\n481 cgttctgatg ccttaagcac caatcacggc cacaaggtcg ttgagctggt tgcagaaatg\\n541 gacggcattc agtacggtcg tagcggtata acactgggag tactcgtgcc acatgtgggc\\n601 gaaaccccaa ttgcataccg caatgttctt cttcgtaaga acggtaataa gggagccggt\\n661 ggtcatagct atggcatcga tctaaagtct tatgacttag gtgacgagct tggcactgat\\n721 cccattgaag attatgaaca aaactggaac actaagcatg gcagtggtgc actccgtgaa\\n781 ctcactcgtg agctcaatgg aggtgcagtc actcgctatg tcgacaacaa tttctgtggc\\n841 ccagatgggt accctcttga ttgcatcaaa gattttctcg cacgcgcggg caagtcaatg\\n901 tgcactcttt ccgaacaact tgattacatc gagtcgaaga gaggtgtcta ctgctgccgt\\n961 gaccatgagc atgaaattgc ctggttcact gagcgctctg ataagagcta cgagcaccag\\n1021 acacccttcg aaattaagag tgccaagaaa tttgacactt tcaaagggga atgcccaaag\\n1081 tttgtgtttc ctcttaactc aaaagtcaaa gtcattcaac cacgtgttga aaagaaaaag\\n1141 actgagggtt tcatggggcg tatacgctct gtgtaccctg ttgcatctcc acaggagtgt\\n1201 aacaatatgc acttgtctac cttgatgaaa tgtaatcatt gcgatgaagt ttcatggcag\\n1261 acgtgcgact ttctgaaagc cacttgtgaa cattgtggca ctgaaaattt agttattgaa\\n1321 ggacctacta catgtgggta cctacctact aatgctgtag tgaaaatgcc atgtcctgcc\\n1381 tgtcaagacc cagagattgg acctgagcat agtgttgcag attatcacaa ccactcaaac\\n1441 attgaaactc gactccgcaa gggaggtagg actagatgtt ttggaggctg tgtgtttgcc\\n1501 tatgttggct gctataataa gcgtgcctac tgggttcctc gtgctagtgc tgatattggc\\n1561 tcaggccata ctggcattac tggtgacaat gtggagacct tgaatgagga tctccttgag\\n1621 atactgagtc gtgaacgtgt taacattaac attgttggcg attttcattt gaatgaagag\\n1681 gttgccatca ttttggcatc tttctctgct tctacaagtg cctttattga cactataaag\\n1741 agtcttgatt acaagtcttt caaaaccatt gttgagtcct gcggtaacta taaagttacc\\n1801 aagggaaagc ccgtaaaagg tgcttggaac attggacaac agagatcagt tttaacacca\\n1861 ctgtgtggtt ttccctcaca ggctgctggt gttatcagat caatttttgc gcgcacactt\\n1921 gatgcagcaa accactcaat tcctgatttg caaagagcag ctgtcaccat acttgatggt\\n1981 atttctgaac agtcattacg tcttgtcgac gccatggttt atacttcaga cctgctcacc\\n2041 aacagtgtca ttattatggc atatgtaact ggtggtcttg tacaacagac ttctcagtgg\\n2101 ttgtctaatc ttttgggcac tactgttgaa aaactcaggc ctatctttga atggattgag\\n2161 gcgaaactta gtgcaggagt tgaatttctc aaggatgctt gggagattct caaatttctc\\n2221 attacaggtg tttttgacat cgtcaagggt caaatacagg ttgcttcaga taacatcaag\\n2281 gattgtgtaa aatgcttcat tgatgttgtt aacaaggcac tcgaaatgtg cattgatcaa\\n2341 gtcactatcg ctggcgcaaa gttgcgatca ctcaacttag gtgaagtctt catcgctcaa\\n2401 agcaagggac tttaccgtca gtgtatacgt ggcaaggagc agctgcaact actcatgcct\\n2461 cttaaggcac caaaagaagt aacctttctt gaaggtgatt cacatgacac agtacttacc\\n2521 tctgaggagg ttgttctcaa gaacggtgaa ctcgaagcac tcgagacgcc cgttgatagc\\n2581 ttcacaaatg gagctatcgt tggcacacca gtctgtgtaa atggcctcat gctcttagag\\n2641 attaaggaca aagaacaata ctgcgcattg tctcctggtt tactggctac aaacaatgtc\\n2701 tttcgcttaa aagggggtgc accaattaaa ggtgtaacct ttggagaaga tactgtttgg\\n2761 gaagttcaag gttacaagaa tgtgagaatc acatttgagc ttgatgaacg tgttgacaaa\\n2821 gtgcttaatg aaaagtgctc tgtctacact gttgaatccg gtaccgaagt tactgagttt\\n2881 gcatgtgttg tagcagaggc tgttgtgaag actttacaac cagtttctga tctccttacc\\n2941 aacatgggta ttgatcttga tgagtggagt gtagctacat tctacttatt tgatgatgct\\n3001 ggtgaagaaa acttttcatc acgtatgtat tgttcctttt accctccaga tgaggaagaa\\n3061 gaggacgatg cagagtgtga ggaagaagaa attgatgaaa cctgtgaaca tgagtacggt\\n3121 acagaggatg attatcaagg tctccctctg gaatttggtg cctcagctga aacagttcga\\n3181 gttgaggaag aagaagagga agactggctg gatgatacta ctgagcaatc agagattgag\\n3241 ccagaaccag aacctacacc tgaagaacca gttaatcagt ttactggtta tttaaaactt\\n3301 actgacaatg ttgccattaa atgtgttgac atcgttaagg aggcacaaag tgctaatcct\\n3361 atggtgattg taaatgctgc taacatacac ctgaaacatg gtggtggtgt agcaggtgca\\n3421 ctcaacaagg caaccaatgg tgccatgcaa aaggagagtg atgattacat taagctaaat\\n3481 ggccctctta cagtaggagg gtcttgtttg ctttctggac ataatcttgc taagaagtgt\\n3541 ctgcatgttg ttggacctaa cctaaatgca ggtgaggaca tccagcttct taaggcagca\\n3601 tatgaaaatt tcaattcaca ggacatctta cttgcaccat tgttgtcagc aggcatattt\\n3661 ggtgctaaac cacttcagtc tttacaagtg tgcgtgcaga cggttcgtac acaggtttat\\n3721 attgcagtca atgacaaagc tctttatgag caggttgtca tggattatct tgataacctg\\n3781 aagcctagag tggaagcacc taaacaagag gagccaccaa acacagaaga ttccaaaact\\n3841 gaggagaaat ctgtcgtaca gaagcctgtc gatgtgaagc caaaaattaa ggcctgcatt\\n3901 gatgaggtta ccacaacact ggaagaaact aagtttctta ccaataagtt actcttgttt\\n3961 gctgatatca atggtaagct ttaccatgat tctcagaaca tgcttagagg tgaagatatg\\n4021 tctttccttg agaaggatgc accttacatg gtaggtgatg ttatcactag tggtgatatc\\n4081 acttgtgttg taataccctc caaaaaggct ggtggcacta ctgagatgct ctcaagagct\\n4141 ttgaagaaag tgccagttga tgagtatata accacgtacc ctggacaagg atgtgctggt\\n4201 tatacacttg aggaagctaa gactgctctt aagaaatgca aatctgcatt ttatgtacta\\n4261 ccttcagaag cacctaatgc taaggaagag attctaggaa ctgtatcctg gaatttgaga\\n4321 gaaatgcttg ctcatgctga agagacaaga aaattaatgc ctatatgcat ggatgttaga\\n4381 gccataatgg caaccatcca acgtaagtat aaaggaatta aaattcaaga gggcatcgtt\\n4441 gactatggtg tccgattctt cttttatact agtaaagagc ctgtagcttc tattattacg\\n4501 aagctgaact ctctaaatga gccgcttgtc acaatgccaa ttggttatgt gacacatggt\\n4561 tttaatcttg aagaggctgc gcgctgtatg cgttctctta aagctcctgc cgtagtgtca\\n4621 gtatcatcac cagatgctgt tactacatat aatggatacc tcacttcgtc atcaaagaca\\n4681 tctgaggagc actttgtaga aacagtttct ttggctggct cttacagaga ttggtcctat\\n4741 tcaggacagc gtacagagtt aggtgttgaa tttcttaagc gtggtgacaa aattgtgtac\\n4801 cacactctgg agagccccgt cgagtttcat cttgacggtg aggttctttc acttgacaaa\\n4861 ctaaagagtc tcttatccct gcgggaggtt aagactataa aagtgttcac aactgtggac\\n4921 aacactaatc tccacacaca gcttgtggat atgtctatga catatggaca gcagtttggt\\n4981 ccaacatact tggatggtgc tgatgttaca aaaattaaac ctcatgtaaa tcatgagggt\\n5041 aagactttct ttgtactacc tagtgatgac acactacgta gtgaagcttt cgagtactac\\n5101 catactcttg atgagagttt tcttggtagg tacatgtctg ctttaaacca cacaaagaaa\\n5161 tggaaatttc ctcaagttgg tggtttaact tcaattaaat gggctgataa caattgttat\\n5221 ttgtctagtg ttttattagc acttcaacag cttgaagtca aattcaatgc accagcactt\\n5281 caagaggctt attatagagc ccgtgctggt gatgctgcta acttttgtgc actcatactc\\n5341 gcttacagta ataaaactgt tggcgagctt ggtgatgtca gagaaactat gacccatctt\\n5401 ctacagcatg ctaatttgga atctgcaaag cgagttctta atgtggtgtg taaacattgt\\n5461 ggtcagaaaa ctactacctt aacgggtgta gaagctgtga tgtatatggg tactctatct\\n5521 tatgataatc ttaagacagg tgtttccatt ccatgtgtgt gtggtcgtga tgctacacaa\\n5581 tatctagtac aacaagagtc ttcttttgtt atgatgtctg caccacctgc tgagtataaa\\n5641 ttacagcaag gtacattctt atgtgcgaat gagtacactg gtaactatca gtgtggtcat\\n5701 tacactcata taactgctaa ggagaccctc tatcgtattg acggagctca ccttacaaag\\n5761 atgtcagagt acaaaggacc agtgactgat gttttctaca aggaaacatc ttacactaca\\n5821 accatcaagc ctgtgtcgta taaactcgat ggagttactt acacagagat tgaaccaaaa\\n5881 ttggatgggt attataaaaa ggataatgct tactatacag agcagcctat agaccttgta\\n5941 ccaactcaac cattaccaaa tgcgagtttt gataatttca aactcacatg ttctaacaca\\n6001 aaatttgctg atgatttaaa tcaaatgaca ggcttcacaa agccagcttc acgagagcta\\n6061 tctgtcacat tcttcccaga cttgaatggc gatgtagtgg ctattgacta tagacactat\\n6121 tcagcgagtt tcaagaaagg tgctaaatta ctgcataagc caattgtttg gcacattaac\\n6181 caggctacaa ccaagacaac gttcaaacca aacacttggt gtttacgttg tctttggagt\\n6241 acaaagccag tagatacttc aaattcattt gaagttctgg cagtagaaga cacacaagga\\n6301 atggacaatc ttgcttgtga aagtcaacaa cccacctctg aagaagtagt ggaaaatcct\\n6361 accatacaga aggaagtcat agagtgtgac gtgaaaacta ccgaagttgt aggcaatgtc\\n6421 atacttaaac catcagatga aggtgttaaa gtaacacaag agttaggtca tgaggatctt\\n6481 atggctgctt atgtggaaaa cacaagcatt accattaaga aacctaatga gctttcacta\\n6541 gccttaggtt taaaaacaat tgccactcat ggtattgctg caattaatag tgttccttgg\\n6601 agtaaaattt tggcttatgt caaaccattc ttaggacaag cagcaattac aacatcaaat\\n6661 tgcgctaaga gattagcaca acgtgtgttt aacaattata tgccttatgt gtttacatta\\n6721 ttgttccaat tgtgtacttt tactaaaagt accaattcta gaattagagc ttcactacct\\n6781 acaactattg ctaaaaatag tgttaagagt gttgctaaat tatgtttgga tgccggcatt\\n6841 aattatgtga agtcacccaa attttctaaa ttgttcacaa tcgctatgtg gctattgttg\\n6901 ttaagtattt gcttaggttc tctaatctgt gtaactgctg cttttggtgt actcttatct\\n6961 aattttggtg ctccttctta ttgtaatggc gttagagaat tgtatcttaa ttcgtctaac\\n7021 gttactacta tggatttctg tgaaggttct tttccttgca gcatttgttt aagtggatta\\n7081 gactcccttg attcttatcc agctcttgaa accattcagg tgacgatttc atcgtacaag\\n7141 ctagacttga caattttagg tctggccgct gagtgggttt tggcatatat gttgttcaca\\n7201 aaattctttt atttattagg tctttcagct ataatgcagg tgttctttgg ctattttgct\\n7261 agtcatttca tcagcaattc ttggctcatg tggtttatca ttagtattgt acaaatggca\\n7321 cccgtttctg caatggttag gatgtacatc ttctttgctt ctttctacta catatggaag\\n7381 agctatgttc atatcatgga tggttgcacc tcttcgactt gcatgatgtg ctataagcgc\\n7441 aatcgtgcca cacgcgttga gtgtacaact attgttaatg gcatgaagag atctttctat\\n7501 gtctatgcaa atggaggccg tggcttctgc aagactcaca attggaattg tctcaattgt\\n7561 gacacatttt gcactggtag tacattcatt agtgatgaag ttgctcgtga tttgtcactc\\n7621 cagtttaaaa gaccaatcaa ccctactgac cagtcatcgt atattgttga tagtgttgct\\n7681 gtgaaaaatg gcgcgcttca cctctacttt gacaaggctg gtcaaaagac ctatgagaga\\n7741 catccgctct cccattttgt caatttagac aatttgagag ctaacaacac taaaggttca\\n7801 ctgcctatta atgtcatagt ttttgatggc aagtccaaat gcgacgagtc tgcttctaag\\n7861 tctgcttctg tgtactacag tcagctgatg tgccaaccta ttctgttgct tgaccaagct\\n7921 cttgtatcag acgttggaga tagtactgaa gtttccgtta agatgtttga tgcttatgtc\\n7981 gacacctttt cagcaacttt tagtgttcct atggaaaaac ttaaggcact tgttgctaca\\n8041 gctcacagcg agttagcaaa gggtgtagct ttagatggtg tcctttctac attcgtgtca\\n8101 gctgcccgac aaggtgttgt tgataccgat gttgacacaa aggatgttat tgaatgtctc\\n8161 aaactttcac atcactctga cttagaagtg acaggtgaca gttgtaacaa tttcatgctc\\n8221 acctataata aggttgaaaa catgacgccc agagatcttg gcgcatgtat tgactgtaat\\n8281 gcaaggcata tcaatgccca agtagcaaaa agtcacaatg tttcactcat ctggaatgta\\n8341 aaagactaca tgtctttatc tgaacagctg cgtaaacaaa ttcgtagtgc tgccaagaag\\n8401 aacaacatac cttttagact aacttgtgct acaactagac aggttgtcaa tgtcataact\\n8461 actaaaatct cactcaaggg tggtaagatt gttagtactt gttttaaact tatgcttaag\\n8521 gccacattat tgtgcgttct tgctgcattg gtttgttata tcgttatgcc agtacataca\\n8581 ttgtcaatcc atgatggtta cacaaatgaa atcattggtt acaaagccat tcaggatggt\\n8641 gtcactcgtg acatcatttc tactgatgat tgttttgcaa ataaacatgc tggttttgac\\n8701 gcatggttta gccagcgtgg tggttcatac aaaaatgaca aaagctgccc tgtagtagct\\n8761 gctatcatta caagagagat tggtttcata gtgcctggct taccgggtac tgtgctgaga\\n8821 gcaatcaatg gtgacttctt gcattttcta cctcgtgttt ttagtgctgt tggcaacatt\\n8881 tgctacacac cttccaaact cattgagtat agtgattttg ctacctctgc ttgcgttctt\\n8941 gctgctgagt gtacaatttt taaggatgct atgggcaaac ctgtgccata ttgttatgac\\n9001 actaatttgc tagagggttc tatttcttat agtgagcttc gtccagacac tcgttatgtg\\n9061 cttatggatg gttccatcat acagtttcct aacacttacc tggagggttc tgttagagta\\n9121 gtaacaactt ttgatgctga gtactgtaga catggtacat gcgaaaggtc agaagtaggt\\n9181 atttgcctat ctaccagtgg tagatgggtt cttaataatg agcattacag agctctatca\\n9241 ggagttttct gtggtgttga tgcgatgaat ctcatagcta acatctttac tcctcttgtg\\n9301 caacctgtgg gtgctttaga tgtgtctgct tcagtagtgg ctggtggtat tattgccata\\n9361 ttggtgactt gtgctgccta ctactttatg aaattcagac gtgtttttgg tgagtacaac\\n9421 catgttgttg ctgctaatgc acttttgttt ttgatgtctt tcactatact ctgtctggta\\n9481 ccagcttaca gctttctgcc gggagtctac tcagtctttt acttgtactt gacattctat\\n9541 ttcaccaatg atgtttcatt cttggctcac cttcaatggt ttgccatgtt ttctcctatt\\n9601 gtgccttttt ggataacagc aatctatgta ttctgtattt ctctgaagca ctgccattgg\\n9661 ttctttaaca actatcttag gaaaagagtc atgtttaatg gagttacatt tagtaccttc\\n9721 gaggaggctg ctttgtgtac ctttttgctc aacaaggaaa tgtacctaaa attgcgtagc\\n9781 gagacactgt tgccacttac acagtataac aggtatcttg ctctatataa caagtacaag\\n9841 tatttcagtg gagccttaga tactaccagc tatcgtgaag cagcttgctg ccacttagca\\n9901 aaggctctaa atgactttag caactcaggt gctgatgttc tctaccaacc accacagaca\\n9961 tcaatcactt ctgctgttct gcagagtggt tttaggaaaa tggcattccc gtcaggcaaa\\n10021 gttgaagggt gcatggtaca agtaacctgt ggaactacaa ctcttaatgg attgtggttg\\n10081 gatgacacag tatactgtcc aagacatgtc atttgcacag cagaagacat gcttaatcct\\n10141 aactatgaag atctgctcat tcgcaaatcc aaccatagct ttcttgttca ggctggcaat\\n10201 gttcaacttc gtgttattgg ccattctatg caaaattgtc tgcttaggct taaagttgat\\n10261 acttctaacc ctaagacacc caagtataaa tttgtccgta tccaacctgg tcaaacattt\\n10321 tcagttctag catgctacaa tggttcacca tctggtgttt atcagtgtgc catgagacct\\n10381 aatcatacca ttaaaggttc tttccttaat ggatcatgtg gtagtgttgg ttttaacatt\\n10441 gattatgatt gcgtgtcttt ctgctatatg catcatatgg agcttccaac aggagtacac\\n10501 gctggtactg acttagaagg taaattctat ggtccatttg ttgacagaca aactgcacag\\n10561 gctgcaggta cagacacaac cataacatta aatgttttgg catggctgta tgctgctgtt\\n10621 atcaatggtg ataggtggtt tcttaataga ttcaccacta ctttgaatga ctttaacctt\\n10681 gtggcaatga agtacaacta tgaacctttg acacaagatc atgttgacat attgggacct\\n10741 ctttctgctc aaacaggaat tgccgtctta gatatgtgtg ctgctttgaa agagctgctg\\n10801 cagaatggta tgaatggtcg tactatcctt ggtagcacta ttttagaaga tgagtttaca\\n10861 ccatttgatg ttgttagaca atgctctggt gttaccttcc aaggtaagtt caagaaaatt\\n10921 gttaagggca ctcatcattg gatgctttta actttcttga catcactatt gattcttgtt\\n10981 caaagtacac agtggtcact gtttttcttt gtttacgaga atgctttctt gccatttact\\n11041 cttggtatta tggcaattgc tgcatgtgct atgctgcttg ttaagcataa gcacgcattc\\n11101 ttgtgcttgt ttctgttacc ttctcttgca acagttgctt actttaatat ggtctacatg\\n11161 cctgctagct gggtgatgcg tatcatgaca tggcttgaat tggctgacac tagcttgtct\\n11221 ggttataggc ttaaggattg tgttatgtat gcttcagctt tagttttgct tattctcatg\\n11281 acagctcgca ctgtttatga tgatgctgct agacgtgttt ggacactgat gaatgtcatt\\n11341 acacttgttt acaaagtcta ctatggtaat gctttagatc aagctatttc catgtgggcc\\n11401 ttagttattt ctgtaacctc taactattct ggtgtcgtta cgactatcat gtttttagct\\n11461 agagctatag tgtttgtgtg tgttgagtat tacccattgt tatttattac tggcaacacc\\n11521 ttacagtgta tcatgcttgt ttattgtttc ttaggctatt gttgctgctg ctactttggc\\n11581 cttttctgtt tactcaaccg ttacttcagg cttactcttg gtgtttatga ctacttggtc\\n11641 tctacacaag aatttaggta tatgaactcc caggggcttt tgcctcctaa gagtagtatt\\n11701 gatgctttca agcttaacat taagttgttg ggtattggag gtaaaccatg tatcaaggtt\\n11761 gctactgtac agtctaaaat gtctgacgta aagtgcacat ctgtggtact gctctcggtt\\n11821 cttcaacaac ttagagtaga gtcatcttct aaattgtggg cacaatgtgt acaactccac\\n11881 aatgatattc ttcttgcaaa agacacaact gaagctttcg agaagatggt ttctcttttg\\n11941 tctgttttgc tatccatgca gggtgctgta gacattaata ggttgtgcga ggaaatgctc\\n12001 gataaccgtg ctactcttca ggctattgct tcagaattta gttctttacc atcatatgcc\\n12061 gcttatgcca ctgcccagga ggcctatgag caggctgtag ctaatggtga ttctgaagtc\\n12121 gttctcaaaa agttaaagaa atctttgaat gtggctaaat ctgagtttga ccgtgatgct\\n12181 gccatgcaac gcaagttgga aaagatggca gatcaggcta tgacccaaat gtacaaacag\\n12241 gcaagatctg aggacaagag ggcaaaagta actagtgcta tgcaaacaat gctcttcact\\n12301 atgcttagga agcttgataa tgatgcactt aacaacatta tcaacaatgc gcgtgatggt\\n12361 tgtgttccac tcaacatcat accattgact acagcagcca aactcatggt tgttgtccct\\n12421 gattatggta cctacaagaa cacttgtgat ggtaacacct ttacatatgc atctgcactc\\n12481 tgggaaatcc agcaagttgt tgatgcggat agcaagattg ttcaacttag tgaaattaac\\n12541 atggacaatt caccaaattt ggcttggcct cttattgtta cagctctaag agccaactca\\n12601 gctgttaaac tacagaataa tgaactgagt ccagtagcac tacgacagat gtcctgtgcg\\n12661 gctggtacca cacaaacagc ttgtactgat gacaatgcac ttgcctacta taacaattcg\\n12721 aagggaggta ggtttgtgct ggcattacta tcagaccacc aagatctcaa atgggctaga\\n12781 ttccctaaga gtgatggtac aggtacaatt tacacagaac tggaaccacc ttgtaggttt\\n12841 gttacagaca caccaaaagg gcctaaagtg aaatacttgt acttcatcaa aggcttaaac\\n12901 aacctaaata gaggtatggt gctgggcagt ttagctgcta cagtacgtct tcaggctgga\\n12961 aatgctacag aagtacctgc caattcaact gtgctttcct tctgtgcttt tgcagtagac\\n13021 cctgctaaag catataagga ttacctagca agtggaggac aaccaatcac caactgtgtg\\n13081 aagatgttgt gtacacacac tggtacagga caggcaatta ctgtaacacc agaagctaac\\n13141 atggaccaag agtcctttgg tggtgcttca tgttgtctgt attgtagatg ccacattgac\\n13201 catccaaatc ctaaaggatt ctgtgacttg aaaggtaagt acgtccaaat acctaccact\\n13261 tgtgctaatg acccagtggg ttttacactt agaaacacag tctgtaccgt ctgcggaatg\\n13321 tggaaaggtt atggctgtag ttgtgaccaa ctccgcgaac ccttgatgca gtctgcggat\\n13381 gcatcaacgt ttttaaacgg gtttgcggtg taagtgcagc ccgtcttaca ccgtgcggca\\n13441 caggcactag tactgatgtc gtctacaggg cttttgatat ttacaacgaa aaagttgctg\\n13501 gttttgcaaa gttcctaaaa actaattgct gtcgcttcca ggagaaggat gaggaaggca\\n13561 atttattaga ctcttacttt gtagttaaga ggcatactat gtctaactac caacatgaag\\n13621 agactattta taacttggtt aaagattgtc cagcggttgc tgtccatgac tttttcaagt\\n13681 ttagagtaga tggtgacatg gtaccacata tatcacgtca gcgtctaact aaatacacaa\\n13741 tggctgattt agtctatgct ctacgtcatt ttgatgaggg taattgtgat acattaaaag\\n13801 aaatactcgt cacatacaat tgctgtgatg atgattattt caataagaag gattggtatg\\n13861 acttcgtaga gaatcctgac atcttacgcg tatatgctaa cttaggtgag cgtgtacgcc\\n13921 aatcattatt aaagactgta caattctgcg atgctatgcg tgatgcaggc attgtaggcg\\n13981 tactgacatt agataatcag gatcttaatg ggaactggta cgatttcggt gatttcgtac\\n14041 aagtagcacc aggctgcgga gttcctattg tggattcata ttactcattg ctgatgccca\\n14101 tcctcacttt gactagggca ttggctgctg agtcccatat ggatgctgat ctcgcaaaac\\n14161 cacttattaa gtgggatttg ctgaaatatg attttacgga agagagactt tgtctcttcg\\n14221 accgttattt taaatattgg gaccagacat accatcccaa ttgtattaac tgtttggatg\\n14281 ataggtgtat ccttcattgt gcaaacttta atgtgttatt ttctactgtg tttccaccta\\n14341 caagttttgg accactagta agaaaaatat ttgtagatgg tgttcctttt gttgtttcaa\\n14401 ctggatacca ttttcgtgag ttaggagtcg tacataatca ggatgtaaac ttacatagct\\n14461 cgcgtctcag tttcaaggaa cttttagtgt atgctgctga tccagctatg catgcagctt\\n14521 ctggcaattt attgctagat aaacgcacta catgcttttc agtagctgca ctaacaaaca\\n14581 atgttgcttt tcaaactgtc aaacccggta attttaataa agacttttat gactttgctg\\n14641 tgtctaaagg tttctttaag gaaggaagtt ctgttgaact aaaacacttc ttctttgctc\\n14701 aggatggcaa cgctgctatc agtgattatg actattatcg ttataatctg ccaacaatgt\\n14761 gtgatatcag acaactccta ttcgtagttg aagttgttga taaatacttt gattgttacg\\n14821 atggtggctg tattaatgcc aaccaagtaa tcgttaacaa tctggataaa tcagctggtt\\n14881 tcccatttaa taaatggggt aaggctagac tttattatga ctcaatgagt tatgaggatc\\n14941 aagatgcact tttcgcgtat actaagcgta atgtcatccc tactataact caaatgaatc\\n15001 ttaagtatgc cattagtgca aagaatagag ctcgcaccgt agctggtgtc tctatctgta\\n15061 gtactatgac aaatagacag tttcatcaga aattattgaa gtcaatagcc gccactagag\\n15121 gagctactgt ggtaattgga acaagcaagt tttacggtgg ctggcataat atgttaaaaa\\n15181 ctgtttacag tgatgtagaa actccacacc ttatgggttg ggattatcca aaatgtgaca\\n15241 gagccatgcc taacatgctt aggataatgg cctctcttgt tcttgctcgc aaacataaca\\n15301 cttgctgtaa cttatcacac cgtttctaca ggttagctaa cgagtgtgcg caagtattaa\\n15361 gtgagatggt catgtgtggc ggctcactat atgttaaacc aggtggaaca tcatccggtg\\n15421 atgctacaac tgcttatgct aatagtgtct ttaacatttg tcaagctgtt acagccaatg\\n15481 taaatgcact tctttcaact gatggtaata agatagctga caagtatgtc cgcaatctac\\n15541 aacacaggct ctatgagtgt ctctatagaa atagggatgt tgatcatgaa ttcgtggatg\\n15601 agttttacgc ttacctgcgt aaacatttct ccatgatgat tctttctgat gatgccgttg\\n15661 tgtgctataa cagtaactat gcggctcaag gtttagtagc tagcattaag aactttaagg\\n15721 cagttcttta ttatcaaaat aatgtgttca tgtctgaggc aaaatgttgg actgagactg\\n15781 accttactaa aggacctcac gaattttgct cacagcatac aatgctagtt aaacaaggag\\n15841 atgattacgt gtacctgcct tacccagatc catcaagaat attaggcgca ggctgttttg\\n15901 tcgatgatat tgtcaaaaca gatggtacac ttatgattga aaggttcgtg tcactggcta\\n15961 ttgatgctta cccacttaca aaacatccta atcaggagta tgctgatgtc tttcacttgt\\n16021 atttacaata cattagaaag ttacatgatg agcttactgg ccacatgttg gacatgtatt\\n16081 ccgtaatgct aactaatgat aacacctcac ggtactggga acctgagttt tatgaggcta\\n16141 tgtacacacc acatacagtc ttgcaggctg taggtgcttg tgtattgtgc aattcacaga\\n16201 cttcacttcg ttgcggtgcc tgtattagga gaccattcct atgttgcaag tgctgctatg\\n16261 accatgtcat ttcaacatca cacaaattag tgttgtctgt taatccctat gtttgcaatg\\n16321 ccccaggttg tgatgtcact gatgtgacac aactgtatct aggaggtatg agctattatt\\n16381 gcaagtcaca taagcctccc attagttttc cattatgtgc taatggtcag gtttttggtt\\n16441 tatacaaaaa cacatgtgta ggcagtgaca atgtcactga cttcaatgcg atagcaacat\\n16501 gtgattggac taatgctggc gattacatac ttgccaacac ttgtactgag agactcaagc\\n16561 ttttcgcagc agaaacgctc aaagccactg aggaaacatt taagctgtca tatggtattg\\n16621 ccactgtacg cgaagtactc tctgacagag aattgcatct ttcatgggag gttggaaaac\\n16681 ctagaccacc attgaacaga aactatgtct ttactggtta ccgtgtaact aaaaatagta\\n16741 aagtacagat tggagagtac acctttgaaa aaggtgacta tggtgatgct gttgtgtaca\\n16801 gaggtactac gacatacaag ttgaatgttg gtgattactt tgtgttgaca tctcacactg\\n16861 taatgccact tagtgcacct actctagtgc cacaagagca ctatgtgaga attactggct\\n16921 tgtacccaac actcaacatc tcagatgagt tttctagcaa tgttgcaaat tatcaaaagg\\n16981 tcggcatgca aaagtactct acactccaag gaccacctgg tactggtaag agtcattttg\\n17041 ccatcggact tgctctctat tacccatctg ctcgcatagt gtatacggca tgctctcatg\\n17101 cagctgttga tgccctatgt gaaaaggcat taaaatattt gcccatagat aaatgtagta\\n17161 gaatcatacc tgcgcgtgcg cgcgtagagt gttttgataa attcaaagtg aattcaacac\\n17221 tagaacagta tgttttctgc actgtaaatg cattgccaga aacaactgct gacattgtag\\n17281 tctttgatga aatctctatg gctactaatt atgacttgag tgttgtcaat gctagacttc\\n17341 gtgcaaaaca ctacgtctat attggcgatc ctgctcaatt accagccccc cgcacattgc\\n17401 tgactaaagg cacactagaa ccagaatatt ttaattcagt gtgcagactt atgaaaacaa\\n17461 taggtccaga catgttcctt ggaacttgtc gccgttgtcc tgctgaaatt gttgacactg\\n17521 tgagtgcttt agtttatgac aataagctaa aagcacacaa ggataagtca gctcaatgct\\n17581 tcaaaatgtt ctacaaaggt gttattacac atgatgtttc atctgcaatc aacagacctc\\n17641 aaataggcgt tgtaagagaa tttcttacac gcaatcctgc ttggagaaaa gctgttttta\\n17701 tctcacctta taattcacag aacgctgtag cttcaaaaat cttaggattg cctacgcaga\\n17761 ctgttgattc atcacagggt tctgaatatg actatgtcat attcacacaa actactgaaa\\n17821 cagcacactc ttgtaatgtc aaccgcttca atgtggctat cacaagggca aaaattggca\\n17881 ttttgtgcat aatgtctgat agagatcttt atgacaaact gcaatttaca agtctagaaa\\n17941 taccacgtcg caatgtggct acattacaag cagaaaatgt aactggactt tttaaggact\\n18001 gtagtaagat cattactggt cttcatccta cacaggcacc tacacacctc agcgttgata\\n18061 taaagttcaa gactgaagga ttatgtgttg acataccagg cataccaaag gacatgacct\\n18121 accgtagact catctctatg atgggtttca aaatgaatta ccaagtcaat ggttacccta\\n18181 atatgtttat cacccgcgaa gaagctattc gtcacgttcg tgcgtggatt ggctttgatg\\n18241 tagagggctg tcatgcaact agagatgctg tgggtactaa cctacctctc cagctaggat\\n18301 tttctacagg tgttaactta gtagctgtac cgactggtta tgttgacact gaaaataaca\\n18361 cagaattcac cagagttaat gcaaaacctc caccaggtga ccagtttaaa catcttatac\\n18421 cactcatgta taaaggcttg ccctggaatg tagtgcgtat taagatagta caaatgctca\\n18481 gtgatacact gaaaggattg tcagacagag tcgtgttcgt cctttgggcg catggctttg\\n18541 agcttacatc aatgaagtac tttgtcaaga ttggacctga aagaacgtgt tgtctgtgtg\\n18601 acaaacgtgc aacttgcttt tctacttcat cagatactta tgcctgctgg aatcattctg\\n18661 tgggttttga ctatgtctat aacccattta tgattgatgt tcagcagtgg ggctttacgg\\n18721 gtaaccttca gagtaaccat gaccaacatt gccaggtaca tggaaatgca catgtggcta\\n18781 gttgtgatgc tatcatgact agatgtttag cagtccatga gtgctttgtt aagcgcgttg\\n18841 attggtctgt tgaataccct attataggag atgaactgag ggttaattct gcttgcagaa\\n18901 aagtacaaca catggttgtg aagtctgcat tgcttgctga taagtttcca gttcttcatg\\n18961 acattggaaa tccaaaggct atcaagtgtg tgcctcaggc tgaagtagaa tggaagttct\\n19021 acgatgctca gccatgtagt gacaaagctt acaaaataga ggaactcttc tattcttatg\\n19081 ctacacatca cgataaattc actgatggtg tttgtttgtt ttggaattgt aacgttgatc\\n19141 gttacccagc caatgcaatt gtgtgtaggt ttgacacaag agtcttgtca aacttgaact\\n19201 taccaggctg tgatggtggt agtttgtatg tgaataagca tgcattccac actccagctt\\n19261 tcgataaaag tgcatttact aatttaaagc aattgccttt cttttactat tctgatagtc\\n19321 cttgtgagtc tcatggcaaa caagtagtgt cggatattga ttatgttcca ctcaaatctg\\n19381 ctacgtgtat tacacgatgc aatttaggtg gtgctgtttg cagacaccat gcaaatgagt\\n19441 accgacagta cttggatgca tataatatga tgatttctgc tggatttagc ctatggattt\\n19501 acaaacaatt tgatacttat aacctgtgga atacatttac caggttacag agtttagaaa\\n19561 atgtggctta taatgttgtt aataaaggac actttgatgg acacgccggc gaagcacctg\\n19621 tttccatcat taataatgct gtttacacaa aggtagatgg tattgatgtg gagatctttg\\n19681 aaaataagac aacacttcct gttaatgttg catttgagct ttgggctaag cgtaacatta\\n19741 aaccagtgcc agagattaag atactcaata atttgggtgt tgatatcgct gctaatactg\\n19801 taatctggga ctacaaaaga gaagccccag cacatgtatc tacaataggt gtctgcacaa\\n19861 tgactgacat tgccaagaaa cctactgaga gtgcttgttc ttcacttact gtcttgtttg\\n19921 atggtagagt ggaaggacag gtagaccttt ttagaaacgc ccgtaatggt gttttaataa\\n19981 cagaaggttc agtcaaaggt ctaacacctt caaagggacc agcacaagct agcgtcaatg\\n20041 gagtcacatt aattggagaa tcagtaaaaa cacagtttaa ctactttaag aaagtagacg\\n20101 gcattattca acagttgcct gaaacctact ttactcagag cagagactta gaggatttta\\n20161 agcccagatc acaaatggaa actgactttc tcgagctcgc tatggatgaa ttcatacagc\\n20221 gatataagct cgagggctat gccttcgaac acatcgttta tggagatttc agtcatggac\\n20281 aacttggcgg tcttcattta atgataggct tagccaagcg ctcacaagat tcaccactta\\n20341 aattagagga ttttatccct atggacagca cagtgaaaaa ttacttcata acagatgcgc\\n20401 aaacaggttc atcaaaatgt gtgtgttctg tgattgatct tttacttgat gactttgtcg\\n20461 agataataaa gtcacaagat ttgtcagtga tttcaaaagt ggtcaaggtt acaattgact\\n20521 atgctgaaat ttcattcatg ctttggtgta aggatggaca tgttgaaacc ttctacccaa\\n20581 aactacaagc aagtcaagcg tggcaaccag gtgttgcgat gcctaacttg tacaagatgc\\n20641 aaagaatgct tcttgaaaag tgtgaccttc agaattatgg tgaaaatgct gttataccaa\\n20701 aaggaataat gatgaatgtc gcaaagtata ctcaactgtg tcaatactta aatacactta\\n20761 ctttagctgt accctacaac atgagagtta ttcactttgg tgctggctct gataaaggag\\n20821 ttgcaccagg tacagctgtg ctcagacaat ggttgccaac tggcacacta cttgtcgatt\\n20881 cagatcttaa tgacttcgtc tccgacgcag attctacttt aattggagac tgtgcaacag\\n20941 tacatacggc taataaatgg gaccttatta ttagcgatat gtatgaccct aggaccaaac\\n21001 atgtgacaaa agagaatgac tctaaagaag ggtttttcac ttatctgtgt ggatttataa\\n21061 agcaaaaact agccctgggt ggttctatag ctgtaaagat aacagagcat tcttggaatg\\n21121 ctgaccttta caagcttatg ggccatttct catggtggac agcttttgtt acaaatgtaa\\n21181 atgcatcatc atcggaagca tttttaattg gggctaacta tcttggcaag ccgaaggaac\\n21241 aaattgatgg ctataccatg catgctaact acattttctg gaggaacaca aatcctatcc\\n21301 agttgtcttc ctattcactc tttgacatga gcaaatttcc tcttaaatta agaggaactg\\n21361 ctgtaatgtc tcttaaggag aatcaaatca atgatatgat ttattctctt ctggaaaaag\\n21421 gtaggcttat cattagagaa aacaacagag ttgtggtttc aagtgatatt cttgttaaca\\n21481 actaaacgaa catgtttatt ttcttattat ttcttactct cactagtggt agtgaccttg\\n21541 accggtgcac cacttttgat gatgttcaag ctcctaatta cactcaacat acttcatcta\\n21601 tgaggggggt ttactatcct gatgaaattt ttagatcaga cactctttat ttaactcagg\\n21661 atttatttct tccattttat tctaatgtta cagggtttca tactattaat catacgtttg\\n21721 gcaaccctgt catacctttt aaggatggta tttattttgc tgccacagag aaatcaaatg\\n21781 ttgtccgtgg ttgggttttt ggttctacca tgaacaacaa gtcacagtcg gtgattatta\\n21841 ttaacaattc tactaatgtt gttatacgag catgtaactt tgaattgtgt gacaaccctt\\n21901 tctttgctgt ttctaaaccc atgggtacac agacacatac tatgatattc gataatgcat\\n21961 ttaattgcac tttcgagtac atatctgatg ccttttcgct tgatgtttca gaaaagtcag\\n22021 gtaattttaa acacttacga gagtttgtgt ttaaaaataa agatgggttt ctctatgttt\\n22081 ataagggcta tcaacctata gatgtagttc gtgatctacc ttctggtttt aacactttga\\n22141 aacctatttt taagttgcct cttggtatta acattacaaa ttttagagcc attcttacag\\n22201 ccttttcacc tgctcaagac atttggggca cgtcagctgc agcctatttt gttggctatt\\n22261 taaagccaac tacatttatg ctcaagtatg atgaaaatgg tacaatcaca gatgctgttg\\n22321 attgttctca aaatccactt gctgaactca aatgctctgt taagagcttt gagattgaca\\n22381 aaggaattta ccagacctct aatttcaggg ttgttccctc aggagatgtt gtgagattcc\\n22441 ctaatattac aaacttgtgt ccttttggag aggtttttaa tgctactaaa ttcccttctg\\n22501 tctatgcatg ggagagaaaa aaaatttcta attgtgttgc tgattactct gtgctctaca\\n22561 actcaacatt tttttcaacc tttaagtgct atggcgtttc tgccactaag ttgaatgatc\\n22621 tttgcttctc caatgtctat gcagattctt ttgtagtcaa gggagatgat gtaagacaaa\\n22681 tagcgccagg acaaactggt gttattgctg attataatta taaattgcca gatgatttca\\n22741 tgggttgtgt ccttgcttgg aatactagga acattgatgc tacttcaact ggtaattata\\n22801 attataaata taggtatctt agacatggca agcttaggcc ctttgagaga gacatatcta\\n22861 atgtgccttt ctcccctgat ggcaaacctt gcaccccacc tgctcttaat tgttattggc\\n22921 cattaaatga ttatggtttt tacaccacta ctggcattgg ctaccaacct tacagagttg\\n22981 tagtactttc ttttgaactt ttaaatgcac cggccacggt ttgtggacca aaattatcca\\n23041 ctgaccttat taagaaccag tgtgtcaatt ttaattttaa tggactcact ggtactggtg\\n23101 tgttaactcc ttcttcaaag agatttcaac catttcaaca atttggccgt gatgtttctg\\n23161 atttcactga ttccgttcga gatcctaaaa catctgaaat attagacatt tcaccttgcg\\n23221 cttttggggg tgtaagtgta attacacctg gaacaaatgc ttcatctgaa gttgctgttc\\n23281 tatatcaaga tgttaactgc actgatgttt ctacagcaat tcatgcagat caactcacac\\n23341 cagcttggcg catatattct actggaaaca atgtattcca gactcaagca ggctgtctta\\n23401 taggagctga gcatgtcgac acttcttatg agtgcgacat tcctattgga gctggcattt\\n23461 gtgctagtta ccatacagtt tctttattac gtagtactag ccaaaaatct attgtggctt\\n23521 atactatgtc tttaggtgct gatagttcaa ttgcttactc taataacacc attgctatac\\n23581 ctactaactt ttcaattagc attactacag aagtaatgcc tgtttctatg gctaaaacct\\n23641 ccgtagattg taatatgtac atctgcggag attctactga atgtgctaat ttgcttctcc\\n23701 aatatggtag cttttgcaca caactaaatc gtgcactctc aggtattgct gctgaacagg\\n23761 atcgcaacac acgtgaagtg ttcgctcaag tcaaacaaat gtacaaaacc ccaactttga\\n23821 aatattttgg tggttttaat ttttcacaaa tattacctga ccctctaaag ccaactaaga\\n23881 ggtcttttat tgaggacttg ctctttaata aggtgacact cgctgatgct ggcttcatga\\n23941 agcaatatgg cgaatgccta ggtgatatta atgctagaga tctcatttgt gcgcagaagt\\n24001 tcaatggact tacagtgttg ccacctctgc tcactgatga tatgattgct gcctacactg\\n24061 ctgctctagt tagtggtact gccactgctg gatggacatt tggtgctggc gctgctcttc\\n24121 aaataccttt tgctatgcaa atggcatata ggttcaatgg cattggagtt acccaaaatg\\n24181 ttctctatga gaaccaaaaa caaatcgcca accaatttaa caaggcgatt agtcaaattc\\n24241 aagaatcact tacaacaaca tcaactgcat tgggcaagct gcaagacgtt gttaaccaga\\n24301 atgctcaagc attaaacaca cttgttaaac aacttagctc taattttggt gcaatttcaa\\n24361 gtgtgctaaa tgatatcctt tcgcgacttg ataaagtcga ggcggaggta caaattgaca\\n24421 ggttaattac aggcagactt caaagccttc aaacctatgt aacacaacaa ctaatcaggg\\n24481 ctgctgaaat cagggcttct gctaatcttg ctgctactaa aatgtctgag tgtgttcttg\\n24541 gacaatcaaa aagagttgac ttttgtggaa agggctacca ccttatgtcc ttcccacaag\\n24601 cagccccgca tggtgttgtc ttcctacatg tcacgtatgt gccatcccag gagaggaact\\n24661 tcaccacagc gccagcaatt tgtcatgaag gcaaagcata cttccctcgt gaaggtgttt\\n24721 ttgtgtttaa tggcacttct tggtttatta cacagaggaa cttcttttct ccacaaataa\\n24781 ttactacaga caatacattt gtctcaggaa attgtgatgt cgttattggc atcattaaca\\n24841 acacagttta tgatcctctg caacctgagc ttgactcatt caaagaagag ctggacaagt\\n24901 acttcaaaaa tcatacatca ccagatgttg atcttggcga catttcaggc attaacgctt\\n24961 ctgtcgtcaa cattcaaaaa gaaattgacc gcctcaatga ggtcgctaaa aatttaaatg\\n25021 aatcactcat tgaccttcaa gaattgggaa aatatgagca atatattaaa tggccttggt\\n25081 atgtttggct cggcttcatt gctggactaa ttgccatcgt catggttaca atcttgcttt\\n25141 gttgcatgac tagttgttgc agttgcctca agggtgcatg ctcttgtggt tcttgctgca\\n25201 agtttgatga ggatgactct gagccagttc tcaagggtgt caaattacat tacacataaa\\n25261 cgaacttatg gatttgttta tgagattttt tactcttaga tcaattactg cacagccagt\\n25321 aaaaattgac aatgcttctc ctgcaagtac tgttcatgct acagcaacga taccgctaca\\n25381 agcctcactc cctttcggat ggcttgttat tggcgttgca tttcttgctg tttttcagag\\n25441 cgctaccaaa ataattgcgc tcaataaaag atggcagcta gccctttata agggcttcca\\n25501 gttcatttgc aatttactgc tgctatttgt taccatctat tcacatcttt tgcttgtcgc\\n25561 tgcaggtatg gaggcgcaat ttttgtacct ctatgccttg atatattttc tacaatgcat\\n25621 caacgcatgt agaattatta tgagatgttg gctttgttgg aagtgcaaat ccaagaaccc\\n25681 attactttat gatgccaact actttgtttg ctggcacaca cataactatg actactgtat\\n25741 accatataac agtgtcacag atacaattgt cgttactgaa ggtgacggca tttcaacacc\\n25801 aaaactcaaa gaagactacc aaattggtgg ttattctgag gataggcact caggtgttaa\\n25861 agactatgtc gttgtacatg gctatttcac cgaagtttac taccagcttg agtctacaca\\n25921 aattactaca gacactggta ttgaaaatgc tacattcttc atctttaaca agcttgttaa\\n25981 agacccaccg aatgtgcaaa tacacacaat cgacggctct tcaggagttg ctaatccagc\\n26041 aatggatcca atttatgatg agccgacgac gactactagc gtgcctttgt aagcacaaga\\n26101 aagtgagtac gaacttatgt actcattcgt ttcggaagaa acaggtacgt taatagttaa\\n26161 tagcgtactt ctttttcttg ctttcgtggt attcttgcta gtcacactag ccatccttac\\n26221 tgcgcttcga ttgtgtgcgt actgctgcaa tattgttaac gtgagtttag taaaaccaac\\n26281 ggtttacgtc tactcgcgtg ttaaaaatct gaactcttct gaaggagttc ctgatcttct\\n26341 ggtctaaacg aactaactat tattattatt ctgtttggaa ctttaacatt gcttatcatg\\n26401 gcagacaacg gtactattac cgttgaggag cttaaacaac tcctggaaca atggaaccta\\n26461 gtaataggtt tcctattcct agcctggatt atgttactac aatttgccta ttctaatcgg\\n26521 aacaggtttt tgtacataat aaagcttgtt ttcctctggc tcttgtggcc agtaacactt\\n26581 gcttgttttg tgcttgctgc tgtctacaga attaattggg tgactggcgg gattgcgatt\\n26641 gcaatggctt gtattgtagg cttgatgtgg cttagctact tcgttgcttc cttcaggctg\\n26701 tttgctcgta cccgctcaat gtggtcattc aacccagaaa caaacattct tctcaatgtg\\n26761 cctctccggg ggacaattgt gaccagaccg ctcatggaaa gtgaacttgt cattggtgct\\n26821 gtgatcattc gtggtcactt gcgaatggcc ggacactccc tagggcgctg tgacattaag\\n26881 gacctgccaa aagagatcac tgtggctaca tcacgaacgc tttcttatta caaattagga\\n26941 gcgtcgcagc gtgtaggcac tgattcaggt tttgctgcat acaaccgcta ccgtattgga\\n27001 aactataaat taaatacaga ccacgccggt agcaacgaca atattgcttt gctagtacag\\n27061 taagtgacaa cagatgtttc atcttgttga cttccaggtt acaatagcag agatattgat\\n27121 tatcattatg aggactttca ggattgctat ttggaatctt gacgttataa taagttcaat\\n27181 agtgagacaa ttatttaagc ctctaactaa gaagaattat tcggagttag atgatgaaga\\n27241 acctatggag ttagattatc cataaaacga acatgaaaat tattctcttc ctgacattga\\n27301 ttgtatttac atcttgcgag ctatatcact atcaggagtg tgttagaggt acgactgtac\\n27361 tactaaaaga accttgccca tcaggaacat acgagggcaa ttcaccattt caccctcttg\\n27421 ctgacaataa atttgcacta acttgcacta gcacacactt tgcttttgct tgtgctgacg\\n27481 gtactcgaca tacctatcag ctgcgtgcaa gatcagtttc accaaaactt ttcatcagac\\n27541 aagaggaggt tcaacaagag ctctactcgc cactttttct cattgttgct gctctagtat\\n27601 ttttaatact ttgcttcacc attaagagaa agacagaatg aatgagctca ctttaattga\\n27661 cttctatttg tgctttttag cctttctgct attccttgtt ttaataatgc ttattatatt\\n27721 ttggttttca ctcgaaatcc aggatctaga agaaccttgt accaaagtct aaacgaacat\\n27781 gaaacttctc attgttttga cttgtatttc tctatgcagt tgcatatgca ctgtagtaca\\n27841 gcgctgtgca tctaataaac ctcatgtgct tgaagatcct tgtaaggtac aacactaggg\\n27901 gtaatactta tagcactgct tggctttgtg ctctaggaaa ggttttacct tttcatagat\\n27961 ggcacactat ggttcaaaca tgcacaccta atgttactat caactgtcaa gatccagctg\\n28021 gtggtgcgct tatagctagg tgttggtacc ttcatgaagg tcaccaaact gctgcattta\\n28081 gagacgtact tgttgtttta aataaacgaa caaattaaaa tgtctgataa tggaccccaa\\n28141 tcaaaccaac gtagtgcccc ccgcattaca tttggtggac ccacagattc aactgacaat\\n28201 aaccagaatg gaggacgcaa tggggcaagg ccaaaacagc gccgacccca aggtttaccc\\n28261 aataatactg cgtcttggtt cacagctctc actcagcatg gcaaggagga acttagattc\\n28321 cctcgaggcc agggcgttcc aatcaacacc aatagtggtc cagatgacca aattggctac\\n28381 taccgaagag ctacccgacg agttcgtggt ggtgacggca aaatgaaaga gctcagcccc\\n28441 agatggtact tctattacct aggaactggc ccagaagctt cacttcccta cggcgctaac\\n28501 aaagaaggca tcgtatgggt tgcaactgag ggagccttga atacacccaa agaccacatt\\n28561 ggcacccgca atcctaataa caatgctgcc accgtgctac aacttcctca aggaacaaca\\n28621 ttgccaaaag gcttctacgc agagggaagc agaggcggca gtcaagcctc ttctcgctcc\\n28681 tcatcacgta gtcgcggtaa ttcaagaaat tcaactcctg gcagcagtag gggaaattct\\n28741 cctgctcgaa tggctagcgg aggtggtgaa actgccctcg cgctattgct gctagacaga\\n28801 ttgaaccagc ttgagagcaa agtttctggt aaaggccaac aacaacaagg ccaaactgtc\\n28861 actaagaaat ctgctgctga ggcatctaaa aagcctcgcc aaaaacgtac tgccacaaaa\\n28921 cagtacaacg tcactcaagc atttgggaga cgtggtccag aacaaaccca aggaaatttc\\n28981 ggggaccaag acctaatcag acaaggaact gattacaaac attggccgca aattgcacaa\\n29041 tttgctccaa gtgcctctgc attctttgga atgtcacgca ttggcatgga agtcacacct\\n29101 tcgggaacat ggctgactta tcatggagcc attaaattgg atgacaaaga tccacaattc\\n29161 aaagacaacg tcatactgct gaacaagcac attgacgcat acaaaacatt cccaccaaca\\n29221 gagcctaaaa aggacaaaaa gaaaaagact gatgaagctc agcctttgcc gcagagacaa\\n29281 aagaagcagc ccactgtgac tcttcttcct gcggctgaca tggatgattt ctccagacaa\\n29341 cttcaaaatt ccatgagtgg agcttctgct gattcaactc aggcataaac actcatgatg\\n29401 accacacaag gcagatgggc tatgtaaacg ttttcgcaat tccgtttacg atacatagtc\\n29461 tactcttgtg cagaatgaat tctcgtaact aaacagcaca agtaggttta gttaacttta\\n29521 atctcacata gcaatcttta atcaatgtgt aacattaggg aggacttgaa agagccacca\\n29581 cattttcatc gaggccacgc ggagtacgat cgagggtaca gtgaataatg ctagggagag\\n29641 ctgcctatat ggaagagccc taatgtgtaa aattaatttt agtagtgcta tccccatgtg\\n29701 attttaatag cttcttagga gaatgacaaa aaaaaaaaaa aaaaaaaaaa a'"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "corona"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### To remove all the numbers and spaces in the genome and just get the string of A, T, G, C. So using the replace function:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "for a in \" \\n0123456789\":\n",
    "    corona = corona.replace(a, \"\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       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      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "corona"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Number of base pairs i.e. nucleotides in the modelule that made up the RNA and DNA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "29751"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(corona)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Kolmogorov complexity\n",
    "\n",
    "#### Predicting the size of virus by compressing the genome of Corona virus. 'Kolmogorov complexity' (upperbounding because lower bounding is not possible). "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Compressing using zlib "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "8890"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import zlib\n",
    "len(zlib.compress(corona.encode(\"utf-8\")))\n",
    "## for python 3 or more we need to utf-8 format encoding"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### The above result means - The RNA of Coronavirus can contain '8858' bytes of information. This is just an upper-bound. This means - Coronavirus cannot contain more than '8858' bytes of information. Let's see if we can compress it a little more. HEre we used the zlib method of compression. We can look for better compression types like lzma."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Compressing furthermore using lzma"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "8412"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import lzma\n",
    "lzc = lzma.compress(corona.encode(\"utf-8\"))\n",
    "len(lzc)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### So, The RNA of Coronavirus can contain '8308' bytes of information. This is just an upper-bound. Hence it's a better compression way."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# How to extract imformation from this genome information?\n",
    "\n",
    "The genome contains the information about the proteins it can make. These proteins determine the characteristics of the cell in which they are produced. So we need to extract information about the proteins. To extract this info, we must know - how proteins are formed from the genetic material i.e. DNA/RNA.\n",
    "\n",
    "> **Learning before applying:** RNAs and DNAs form proteins. This is how proteins are formed from DNA. In DNA, A-T/U and G-C form pairs. This pair formation is because - the chemical structure of A, T/U, G and C is such that - A and T are attracted towards each other by 2 hydrogen bonds and G and C together are attracted by 3 hydrogen bonds. A-C and G-T can't form such stable bonds. \n",
    "\n",
    "<img src=\"./images_copy/AT-GC.jpg\" width=\"480\">\n",
    "\n",
    "<img src=\"./images_copy/codon2.png\">\n",
    "\n",
    "> What happens during protein formation is:\n",
    "\n",
    "<img src=\"./images_copy/transcript-translate-cell.jpg\">\n",
    "\n",
    "<img src=\"./images_copy/Codons_patterns.png\">\n",
    "\n",
    "> An enzyme called 'RNA polymerase' breaks these hydrogen bonds for a small part, takes one strand of DNA and forms its corresponding paired RNA. This process happens inside the nucleus of the cell. We call this RNA generated as 'mRNA' or 'messenger RNA' because this RNA will come out of nucleus and act like a messaage to Ribosome which will generate proteins accordingly. This process of generation of mRNA is called - **Transcription.** Now Ribosome will read the mRNA in sets of 3 bases. This set of 3 bases is called codon. Codons decide the Amino acids. Depending on the codon read by Ribosome, tRNA (transfer-RNA) brings the appropiate amino acid. These amino acids are then linked using peptide bonds to form a chain called *Polypeptide chain*. At the other end of Ribosome, tRNA is free and can go to take another amino acid. \n",
    "\n",
    "> *Note:* Amino acids are organic compounds that contain amine (-NH2) and carboxyl (-COOH) functional groups. There are 20 standard amino acids and 2 non-standard. Of the 20 standard amino acids, nine (His, Ile, Leu, Lys, Met, Phe, Thr, Trp and Val) are called essential amino acids because the human body cannot synthesize them from other compounds at the level needed for normal growth, so they must be obtained from food. Here is the table of codons and their corresponding Amino acids. 'Met' is usually the starting amino acid i.e. 'AUG' forms the start of mRNA. Hence 'AUG' is called *start codon.* 'UAA', 'UGA' and 'UAG' are *stop codons* as they mark the ending of the polypeptide chain, so that a new chain should start from the next codon. \n",
    "\n",
    "<img src=\"./images_copy/genetic-code-table.jpg\" width=\"600\">\n",
    "\n",
    "> This process of generation of chains of amino acids is called - **Translation.** A very long chain of amino acids is called *Protein.* In summary, we can understand the process as:\n",
    "\n",
    "<img src=\"./images_copy/transcription-translation.png\" width=\"600\">\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now since in Coronavirus, we only has RNA, the process of Transcription won't occur and only Translation will happen. So what we now need to write is - *a translation function*, which takes corona's genome as input and gives back all the polypeptide chains that could be formed from that genome. For that, we first need a dictionary of codons. Following codons' string is copied from 'Genetic code' - Wikipedia. (https://en.wikipedia.org/wiki/DNA_codon_table)\n",
    "\n",
    "<img src=\"./images_copy/codons.png\">\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['Ala / A', 'GCU, GCC, GCA, GCG']\n",
      "['Ile / I', 'AUU, AUC, AUA']\n",
      "['Arg / R', 'CGU, CGC, CGA, CGG; AGA, AGG, AGR;']\n",
      "['Leu / L', 'CUU, CUC, CUA, CUG; UUA, UUG, UUR;']\n",
      "['Asn / N', 'AAU, AAC']\n",
      "['Lys / K', 'AAA, AAG']\n",
      "['Asp / D', 'GAU, GAC']\n",
      "['Met / M', 'AUG']\n",
      "['Phe / F', 'UUU, UUC']\n",
      "['Cys / C', 'UGU, UGC']\n",
      "['Pro / P', 'CCU, CCC, CCA, CCG']\n",
      "['Gln / Q', 'CAA, CAG']\n",
      "['Ser / S', 'UCU, UCC, UCA, UCG; AGU, AGC;']\n",
      "['Glu / E', 'GAA, GAG']\n",
      "['Thr / T', 'ACU, ACC, ACA, ACG']\n",
      "['Trp / W', 'UGG']\n",
      "['Gly / G', 'GGU, GGC, GGA, GGG']\n",
      "['Tyr / Y', 'UAU, UAC']\n",
      "['His / H', 'CAU, CAC']\n",
      "['Val / V', 'GUU, GUC, GUA, GUG']\n",
      "['STOP', 'UAA, UGA, UAG']\n"
     ]
    }
   ],
   "source": [
    "# Asn or Asp / B\tAAU, AAC; GAU, GAC\n",
    "# Gln or Glu / Z\tCAA, CAG; GAA, GAG\n",
    "# START\tAUG\n",
    "## Seperating them from the table because these duplicates was creating problems\n",
    "codons = \"\"\"\n",
    "Ala / A\tGCU, GCC, GCA, GCG\n",
    "Ile / I\tAUU, AUC, AUA\n",
    "Arg / R\tCGU, CGC, CGA, CGG; AGA, AGG, AGR;\n",
    "Leu / L\tCUU, CUC, CUA, CUG; UUA, UUG, UUR;\n",
    "Asn / N\tAAU, AAC\n",
    "Lys / K\tAAA, AAG\n",
    "Asp / D\tGAU, GAC\n",
    "Met / M\tAUG\n",
    "Phe / F\tUUU, UUC\n",
    "Cys / C\tUGU, UGC\n",
    "Pro / P\tCCU, CCC, CCA, CCG\n",
    "Gln / Q\tCAA, CAG\n",
    "Ser / S\tUCU, UCC, UCA, UCG; AGU, AGC;\n",
    "Glu / E\tGAA, GAG\n",
    "Thr / T\tACU, ACC, ACA, ACG\n",
    "Trp / W\tUGG\n",
    "Gly / G\tGGU, GGC, GGA, GGG\n",
    "Tyr / Y\tUAU, UAC\n",
    "His / H\tCAU, CAC\n",
    "Val / V\tGUU, GUC, GUA, GUG\n",
    "STOP\tUAA, UGA, UAG\"\"\".strip()\n",
    "\n",
    "for t in codons.split('\\n'):\n",
    "    print(t.split('\\t'))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> **To make this in a better readable format we'll making it into a decoder dictionary. Then making the decoder for DNA . We will also conevert the \"U\" to \"T\" in the list because the CoronaVIrus is a RNA virus and we will convert to DNA only dictionary.**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'gct': 'A',\n",
       " 'gcc': 'A',\n",
       " 'gca': 'A',\n",
       " 'gcg': 'A',\n",
       " 'att': 'I',\n",
       " 'atc': 'I',\n",
       " 'ata': 'I',\n",
       " 'cgt': 'R',\n",
       " 'cgc': 'R',\n",
       " 'cga': 'R',\n",
       " 'cgg': 'R',\n",
       " 'aga': 'R',\n",
       " 'agg': 'R',\n",
       " 'agr': 'R',\n",
       " 'ctt': 'L',\n",
       " 'ctc': 'L',\n",
       " 'cta': 'L',\n",
       " 'ctg': 'L',\n",
       " 'tta': 'L',\n",
       " 'ttg': 'L',\n",
       " 'ttr': 'L',\n",
       " 'aat': 'N',\n",
       " 'aac': 'N',\n",
       " 'aaa': 'K',\n",
       " 'aag': 'K',\n",
       " 'gat': 'D',\n",
       " 'gac': 'D',\n",
       " 'atg': 'M',\n",
       " 'ttt': 'F',\n",
       " 'ttc': 'F',\n",
       " 'tgt': 'C',\n",
       " 'tgc': 'C',\n",
       " 'cct': 'P',\n",
       " 'ccc': 'P',\n",
       " 'cca': 'P',\n",
       " 'ccg': 'P',\n",
       " 'caa': 'Q',\n",
       " 'cag': 'Q',\n",
       " 'tct': 'S',\n",
       " 'tcc': 'S',\n",
       " 'tca': 'S',\n",
       " 'tcg': 'S',\n",
       " 'agt': 'S',\n",
       " 'agc': 'S',\n",
       " 'gaa': 'E',\n",
       " 'gag': 'E',\n",
       " 'act': 'T',\n",
       " 'acc': 'T',\n",
       " 'aca': 'T',\n",
       " 'acg': 'T',\n",
       " 'tgg': 'W',\n",
       " 'ggt': 'G',\n",
       " 'ggc': 'G',\n",
       " 'gga': 'G',\n",
       " 'ggg': 'G',\n",
       " 'tat': 'Y',\n",
       " 'tac': 'Y',\n",
       " 'cat': 'H',\n",
       " 'cac': 'H',\n",
       " 'gtt': 'V',\n",
       " 'gtc': 'V',\n",
       " 'gta': 'V',\n",
       " 'gtg': 'V',\n",
       " 'taa': '*',\n",
       " 'tga': '*',\n",
       " 'tag': '*'}"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "##decoder dictionary\n",
    "dec = {}  \n",
    "\n",
    "for t in codons.split('\\n'):\n",
    "    k, v = t.split('\\t')\n",
    "    if '/' in k:\n",
    "        k = k.split('/')[-1].strip()\n",
    "    k = k.replace(\"STOP\", \"*\")\n",
    "    v = v.replace(\",\", \"\").replace(\";\", \"\").lower().replace(\"u\", \"t\").split(\" \")\n",
    "    for vv in v:\n",
    "        if vv in dec:\n",
    "            print(\"duplicate\", vv)\n",
    "        dec[vv] = k\n",
    "dec\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## We had to add the duplicate function because AUG is at multiple places, IT can bee seen in \"Met\" and in \"Start\" both. Which was creating problem in translation."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "21"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(set(dec.values())) "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> This means we have 21 amino acids in our decoder. Which can also be verified by the following chart, which shows there can be only 20 amino acids. Here we have a 'STOP' being the 21th amino acid. Which shows that the decoder works well.\n",
    " \n",
    " <img src=\"./images_copy/aminoproof.png\">"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> Now, decoding the genome can result in one of the three possible ways. These 3 ways are called 'reading frames'. \n",
    "\n",
    "<img src=\"./images_copy/reading-frames.png\" width=\"480\">\n",
    "\n",
    "In molecular biology, a reading frame is a way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'ILGFYLPRKSQPTSISCRSVL*TNFKICVAVARLHA*CTYAV*TIINFTVVDKKRVTRPSSADCLRFRPCCSRSSAYLGFVRV*PKGKMESLVLGVNEKTHVQLSLPVLQVRDVLVRGFGDSVEEALSEAREHLKNGTCGLVELEKGVLPQLEQPYVFIKRSDALSTNHGHKVVELVAEMDGIQYGRSGITLGVLVPHVGETPIAYRNVLLRKNGNKGAGGHSYGIDLKSYDLGDELGTDPIEDYEQNWNTKHGSGALRELTRELNGGAVTRYVDNNFCGPDGYPLDCIKDFLARAGKSMCTLSEQLDYIESKRGVYCCRDHEHEIAWFTERSDKSYEHQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRIRSVYPVASPQECNNMHLSTLMKCNHCDEVSWQTCDFLKATCEHCGTENLVIEGPTTCGYLPTNAVVKMPCPACQDPEIGPEHSVADYHNHSNIETRLRKGGRTRCFGGCVFAYVGCYNKRAYWVPRASADIGSGHTGITGDNVETLNEDLLEILSRERVNINIVGDFHLNEEVAIILASFSASTSAFIDTIKSLDYKSFKTIVESCGNYKVTKGKPVKGAWNIGQQRSVLTPLCGFPSQAAGVIRSIFARTLDAANHSIPDLQRAAVTILDGISEQSLRLVDAMVYTSDLLTNSVIIMAYVTGGLVQQTSQWLSNLLGTTVEKLRPIFEWIEAKLSAGVEFLKDAWEILKFLITGVFDIVKGQIQVASDNIKDCVKCFIDVVNKALEMCIDQVTIAGAKLRSLNLGEVFIAQSKGLYRQCIRGKEQLQLLMPLKAPKEVTFLEGDSHDTVLTSEEVVLKNGELEALETPVDSFTNGAIVGTPVCVNGLMLLEIKDKEQYCALSPGLLATNNVFRLKGGAPIKGVTFGEDTVWEVQGYKNVRITFELDERVDKVLNEKCSVYTVESGTEVTEFACVVAEAVVKTLQPVSDLLTNMGIDLDEWSVATFYLFDDAGEENFSSRMYCSFYPPDEEEEDDAECEEEEIDETCEHEYGTEDDYQGLPLEFGASAETVRVEEEEEEDWLDDTTEQSEIEPEPEPTPEEPVNQFTGYLKLTDNVAIKCVDIVKEAQSANPMVIVNAANIHLKHGGGVAGALNKATNGAMQKESDDYIKLNGPLTVGGSCLLSGHNLAKKCLHVVGPNLNAGEDIQLLKAAYENFNSQDILLAPLLSAGIFGAKPLQSLQVCVQTVRTQVYIAVNDKALYEQVVMDYLDNLKPRVEAPKQEEPPNTEDSKTEEKSVVQKPVDVKPKIKACIDEVTTTLEETKFLTNKLLLFADINGKLYHDSQNMLRGEDMSFLEKDAPYMVGDVITSGDITCVVIPSKKAGGTTEMLSRALKKVPVDEYITTYPGQGCAGYTLEEAKTALKKCKSAFYVLPSEAPNAKEEILGTVSWNLREMLAHAEETRKLMPICMDVRAIMATIQRKYKGIKIQEGIVDYGVRFFFYTSKEPVASIITKLNSLNEPLVTMPIGYVTHGFNLEEAARCMRSLKAPAVVSVSSPDAVTTYNGYLTSSSKTSEEHFVETVSLAGSYRDWSYSGQRTELGVEFLKRGDKIVYHTLESPVEFHLDGEVLSLDKLKSLLSLREVKTIKVFTTVDNTNLHTQLVDMSMTYGQQFGPTYLDGADVTKIKPHVNHEGKTFFVLPSDDTLRSEAFEYYHTLDESFLGRYMSALNHTKKWKFPQVGGLTSIKWADNNCYLSSVLLALQQLEVKFNAPALQEAYYRARAGDAANFCALILAYSNKTVGELGDVRETMTHLLQHANLESAKRVLNVVCKHCGQKTTTLTGVEAVMYMGTLSYDNLKTGVSIPCVCGRDATQYLVQQESSFVMMSAPPAEYKLQQGTFLCANEYTGNYQCGHYTHITAKETLYRIDGAHLTKMSEYKGPVTDVFYKETSYTTTIKPVSYKLDGVTYTEIEPKLDGYYKKDNAYYTEQPIDLVPTQPLPNASFDNFKLTCSNTKFADDLNQMTGFTKPASRELSVTFFPDLNGDVVAIDYRHYSASFKKGAKLLHKPIVWHINQATTKTTFKPNTWCLRCLWSTKPVDTSNSFEVLAVEDTQGMDNLACESQQPTSEEVVENPTIQKEVIECDVKTTEVVGNVILKPSDEGVKVTQELGHEDLMAAYVENTSITIKKPNELSLALGLKTIATHGIAAINSVPWSKILAYVKPFLGQAAITTSNCAKRLAQRVFNNYMPYVFTLLFQLCTFTKSTNSRIRASLPTTIAKNSVKSVAKLCLDAGINYVKSPKFSKLFTIAMWLLLLSICLGSLICVTAAFGVLLSNFGAPSYCNGVRELYLNSSNVTTMDFCEGSFPCSICLSGLDSLDSYPALETIQVTISSYKLDLTILGLAAEWVLAYMLFTKFFYLLGLSAIMQVFFGYFASHFISNSWLMWFIISIVQMAPVSAMVRMYIFFASFYYIWKSYVHIMDGCTSSTCMMCYKRNRATRVECTTIVNGMKRSFYVYANGGRGFCKTHNWNCLNCDTFCTGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVAVKNGALHLYFDKAGQKTYERHPLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCDESASKSASVYYSQLMCQPILLLDQALVSDVGDSTEVSVKMFDAYVDTFSATFSVPMEKLKALVATAHSELAKGVALDGVLSTFVSAARQGVVDTDVDTKDVIECLKLSHHSDLEVTGDSCNNFMLTYNKVENMTPRDLGACIDCNARHINAQVAKSHNVSLIWNVKDYMSLSEQLRKQIRSAAKKNNIPFRLTCATTRQVVNVITTKISLKGGKIVSTCFKLMLKATLLCVLAALVCYIVMPVHTLSIHDGYTNEIIGYKAIQDGVTRDIISTDDCFANKHAGFDAWFSQRGGSYKNDKSCPVVAAIITREIGFIVPGLPGTVLRAINGDFLHFLPRVFSAVGNICYTPSKLIEYSDFATSACVLAAECTIFKDAMGKPVPYCYDTNLLEGSISYSELRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDAEYCRHGTCERSEVGICLSTSGRWVLNNEHYRALSGVFCGVDAMNLIANIFTPLVQPVGALDVSASVVAGGIIAILVTCAAYYFMKFRRVFGEYNHVVAANALLFLMSFTILCLVPAYSFLPGVYSVFYLYLTFYFTNDVSFLAHLQWFAMFSPIVPFWITAIYVFCISLKHCHWFFNNYLRKRVMFNGVTFSTFEEAALCTFLLNKEMYLKLRSETLLPLTQYNRYLALYNKYKYFSGALDTTSYREAACCHLAKALNDFSNSGADVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTFQGKFKKIVKGTHHWMLLTFLTSLLILVQSTQWSLFFFVYENAFLPFTLGIMAIAACAMLLVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLELADTSLSGYRLKDCVMYASALVLLILMTARTVYDDAARRVWTLMNVITLVYKVYYGNALDQAISMWALVISVTSNYSGVVTTIMFLARAIVFVCVEYYPLLFITGNTLQCIMLVYCFLGYCCCCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKSSIDAFKLNIKLLGIGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINRLCEEMLDNRATLQAIASEFSSLPSYAAYATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVVDADSKIVQLSEINMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNNSKGGRFVLALLSDHQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDPAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLRNTVCTVCGMWKGYGCSCDQLREPLMQSADASTFLNGFAV*VQPVLHRAAQALVLMSSTGLLIFTTKKLLVLQSS*KLIAVASRRRMRKAIY*TLTL*LRGILCLTTNMKRLFITWLKIVQRLLSMTFSSLE*MVTWYHIYHVSV*LNTQWLI*SMLYVILMRVIVIH*KKYSSHTIAVMMIISIRRIGMTS*RILTSYAYMLT*VSVYANHY*RLYNSAMLCVMQAL*AY*H*IIRILMGTGTISVISYK*HQAAEFLLWIHITHC*CPSSL*LGHWLLSPIWMLISQNHLLSGIC*NMILRKRDFVSSTVILNIGTRHTIPIVLTVWMIGVSFIVQTLMCYFLLCFHLQVLDH**EKYL*MVFLLLFQLDTIFVS*ESYIIRM*TYIARVSVSRNF*CMLLIQLCMQLLAIYC*INALHAFQ*LH*QTMLLFKLSNPVILIKTFMTLLCLKVSLRKEVLLN*NTSSLLRMATLLSVIMTIIVIICQQCVISDNSYS*LKLLINTLIVTMVAVLMPTK*SLTIWINQLVSHLINGVRLDFIMTQ*VMRIKMHFSRILSVMSSLL*LK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HQSRPQGR*AGCRNGRHSVRS*RYNTGSTRATCGRNPNCIPQCSSS*ER**GSRWS*LWHRSKVL*LR*RAWH*SH*RL*TKLEH*AWQWCTP*THS*AQWRCSHSLCRQQFLWPRWVPS*LHQRFSRTRGQVNVHSFRTT*LHRVEERCLLLP*P*A*NCLVH*AL**ELRAPDTLRN*ECQEI*HFQRGMPKVCVSS*LKSQSHSTTC*KEKD*GFHGAYTLCVPCCISTGV*QYALVYLDEM*SLR*SFMADVRLSESHL*TLWH*KFSY*RTYYMWVPTY*CCSENAMSCLSRPRDWT*A*CCRLSQPLKH*NSTPQGR*D*MFWRLCVCLCWLL**ACLLGSSC*C*YWLRPYWHYW*QCGDLE*GSP*DTES*TC*H*HCWRFSFE*RGCHHFGIFLCFYKCLY*HYKES*LQVFQNHC*VLR*L*SYQGKARKRCLEHWTTEISFNTTVWFSLTGCWCYQINFCAHT*CSKPLNS*FAKSSCHHT*WYF*TVITSCRRHGLYFRPAHQQCHYYGICNWWSCTTDFSVVV*SFGHYC*KTQAYL*MD*GET*CRS*ISQGCLGDSQISHYRCF*HRQGSNTGCFR*HQGLCKMLH*CC*QGTRNVH*SSHYRWRKVAITQLR*SLHRSKQGTLPSVYTWQGAAATTHAS*GTKRSNLS*R*FT*HSTYL*GGCSQER*TRSTRDAR**LHKWSYRWHTSLCKWPHALRD*GQRTILRIVSWFTGYKQCLSLKRGCTN*RCNLWRRYCLGSSRLQECENHI*A**TC*QSA**KVLCLHC*IRYRSY*VCMCCSRGCCEDFTTSF*SPYQHGY*S**VECSYILLI**CW*RKLFITYVLFLLPSR*GRRGRCRV*GRRN**NL*T*VRYRG*LSRSPSGIWCLS*NSSS*GRRRGRLAG*YY*AIRD*ARTRTYT*RTS*SVYWLFKTY*QCCH*MC*HR*GGTKC*SYGDCKCC*HTPETWWWCSRCTQQGNQWCHAKGE**LH*AKWPSYSRRVLFAFWT*SC*EVSACCWT*PKCR*GHPAS*GSI*KFQFTGHLTCTIVVSRHIWC*TTSVFTSVRADGSYTGLYCSQ*QSSL*AGCHGLS**PEA*SGST*TRGATKHRRFQN*GEICRTEACRCEAKN*GLH**GYHNTGRN*VSYQ*VTLVC*YQW*ALP*FSEHA*R*RYVFP*EGCTLHGR*CYH*W*YHLCCNTLQKGWWHY*DALKSFEESAS**VYNHVPWTRMCWLYT*GS*DCS*EMQICILCTTFRST*C*GRDSRNCILEFERNACSC*RDKKINAYMHGC*SHNGNHPT*V*RN*NSRGHR*LWCPILLLY**RACSFYYYEAELSK*AACHNANWLCDTWF*S*RGCALYAFS*SSCRSVSIITRCCYYI*WIPHFVIKDI*GALCRNSFFGWLLQRLVLFRTAYRVRC*IS*AW*QNCVPHSGEPRRVSS*R*GSFT*QTKESLIPAGG*DYKSVHNCGQH*SPHTACGYVYDIWTAVWSNILGWC*CYKN*TSCKS*G*DFLCTT***HTT**SFRVLPYS**EFSW*VHVCFKPHKEMEISSSWWFNFN*MG**QLLFV*CFISTSTA*SQIQCTSTSRGLL*SPCW*CC*LLCTHTRLQ**NCWRAW*CQRNYDPSSTAC*FGICKASS*CGV*TLWSENYYLNGCRSCDVYGYSIL**S*DRCFHSMCVWS*CYTISSTTRVFFCYDVCTTC*V*ITARYILMCE*VHW*LSVWSLHSYNC*GDPLSY*RSSPYKDVRVQRTSD*CFLQGNILHYNHQACVV*TRWSYLHRD*TKIGWVL*KG*CLLYRAAYRPCTNSTITKCEF**FQTHMF*HKIC**FKSNDRLHKASFTRAICHILPRLEWRCSGY*L*TLFSEFQERC*ITA*ANCLAH*PGYNQDNVQTKHLVFTLSLEYKASRYFKFI*SSGSRRHTRNGQSCL*KSTTHL*RSSGKSYHTEGSHRV*RENYRSCRQCHT*TIR*RC*SNTRVRS*GSYGCLCGKHKHYH*ET**AFTSLRFKNNCHSWYCCN**CSLE*NFGLCQTILRTSSNYNIKLR*EISTTCV*QLYALCVYIIVPIVYFY*KYQF*N*SFTTYNYC*K*C*ECC*IMFGCRH*LCEVTQIF*IVHNRYVAIVVKYLLRFSNLCNCCFWCTLI*FWCSFLL*WR*RIVS*FV*RYYYGFL*RFFSLQHLFKWIRLP*FLSSS*NHSGDDFIVQARLDNFRSGR*VGFGIYVVHKILLFIRSFSYNAGVLWLFC*SFHQQFLAHVVYH*YCTNGTRFCNG*DVHLLCFFLLHMEELCSYHGWLHLFDLHDVL*AQSCHTR*VYNYC*WHEEIFLCLCKWRPWLLQDSQLELSQL*HILHW*YIH***SCS*FVTPV*KTNQPY*PVIVYC**CCCEKWRASPLL*QGWSKDL*ETSALPFCQFRQFES*QH*RFTAY*CHSF*WQVQMRRVCF*VCFCVLQSADVPTYSVA*PSSCIRRWR*Y*SFR*DV*CLCRHLFSNF*CSYGKT*GTCCYSSQRVSKGCSFRWCPFYIRVSCPTRCC*YRC*HKGCY*MSQTFTSL*LRSDR*QL*QFHAHL**G*KHDAQRSWRMY*L*CKAYQCPSSKKSQCFTHLECKRLHVFI*TAA*TNS*CCQEEQHTF*TNLCYN*TGCQCHNY*NLTQGW*DC*YLF*TYA*GHIIVRSCCIGLLYRYASTYIVNP*WLHK*NHWLQSHSGWCHS*HHFY**LFCK*TCWF*RMV*PAWWFIQK*QKLPCSSCYHYKRDWFHSAWLTGYCAESNQW*LLAFSTSCF*CCWQHLLHTFQTH*V**FCYLCLRSCC*VYNF*GCYGQTCAILL*H*FARGFYFL**ASSRHSLCAYGWFHHTVS*HLPGGFC*SSNNF*C*VL*TWYMRKVRSRYLPIYQW*MGS***ALQSSIRSFLWC*CDESHS*HLYSSCATCGCFRCVCFSSGWWYYCHIGDLCCLLLYEIQTCFW*VQPCCCC*CTFVFDVFHYTLSGTSLQLSAGSLLSLLLVLDILFHQ*CFILGSPSMVCHVFSYCAFLDNSNLCILYFSEALPLVL*QLS*EKSHV*WSYI*YLRGGCFVYLFAQQGNVPKIA*RDTVATYTV*QVSCSI*QVQVFQWSLRYYQLS*SSLLPLSKGSK*L*QLRC*CSLPTTTDINHFCCSAEWF*ENGIPVRQS*RVHGTSNLWNYNS*WIVVG*HSILSKTCHLHSRRHA*S*L*RSAHSQIQP*LSCSGWQCSTSCYWPFYAKLSA*A*S*YF*P*DTQV*ICPYPTWSNIFSSSMLQWFTIWCLSVCHET*SYH*RFFP*WIMW*CWF*H*L*LRVFLLYASYGASNRSTRWY*LRR*ILWSIC*QTNCTGCRYRHNHNIKCFGMAVCCCYQW**VVS**IHHYFE*L*PCGNEVQL*TFDTRSC*HIGTSFCSNRNCRLRYVCCFERAAAEWYEWSYYPW*HYFRR*VYTI*CC*TMLWCYLPR*VQENC*GHSSLDAFNFLDITIDSCSKYTVVTVFLCLRECFLAIYSWYYGNCCMCYAAC*A*ARILVLVSVTFSCNSCLL*YGLHAC*LGDAYHDMA*IG*H*LVWL*A*GLCYVCFSFSFAYSHDSSHCL**CC*TCLDTDECHYTCLQSLLW*CFRSSYFHVGLSYFCNL*LFWCRYDYHVFS*SYSVCVC*VLPIVIYYWQHLTVYHACLLFLRLLLLLLLWPFLFTQPLLQAYSWCL*LLGLYTRI*VYELPGAFAS*E*Y*CFQA*H*VVGYWR*TMYQGCYCTV*NV*RKVHICGTALGSSTT*SRVIF*IVGTMCTTPQ*YSSCKRHN*SFREDGFSFVCFAIHAGCCRH**VVRGNAR*PCYSSGYCFRI*FFTIICRLCHCPGGL*AGCS*W*F*SRSQKVKEIFECG*I*V*P*CCHATQVGKDGRSGYDPNVQTGKI*GQEGKSN*CYANNALHYA*EA***CT*QHYQQCA*WLCSTQHHTIDYSSQTHGCCP*LWYLQEHL*W*HLYICICTLGNPASC*CG*QDCST**N*HGQFTKFGLASYCYSSKSQLSC*TTE**TESSSTTTDVLCGWYHTNSLY**QCTCLL*QFEGR*VCAGITIRPPRSQMG*IP*E*WYRYNLHRTGTTL*VCYRHTKRA*SEILVLHQRLKQPK*RYGAGQFSCYSTSSGWKCYRSTCQFNCAFLLCFCSRPC*SI*GLPSKWRTTNHQLCEDVVYTHWYRTGNYCNTRS*HGPRVLWWCFMLSVL*MPH*PSKS*RIL*LER*VRPNTYHLC**PSGFYT*KHSLYRLRNVERLWL*L*PTPRTLDAVCGCINVFKRVCGVSAARLTPCGTGTSTDVVYRAFDIYNEKVAGFAKFLKTNCCRFQEKDEEGNLLDSYFVVKRHTMSNYQHEETIYNLVKDCPAVAVHDFFKFRVDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQSLLKTVQFCDAMRDAGIVGVLTLDNQDLNGNWYDFGDFVQVAPGCGVPIVDSYYSLLMPILTLTRALAAESHMDADLAKPLIKWDLLKYDFTEERLCLFDRYFKYWDQTYHPNCINCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVETPHLMGWDYPKCDRAMPNMLRIMASLVLARKHNTCCNLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDHEFVDEFYAYLRKHFSMMILSDDAVVCYNSNYAAQGLVASIKNFKAVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKIGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKIITGLHPTQAPTHLSVDIKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATRDAVGTNLPLQLGFSTGVNLVAVPTGYVDTENNTEFTRVNAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKGLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDKRATCFSTSSDTYACWNHSVGFDYVYNPFMIDVQQWGFTGNLQSNHDQHCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWSVEYPIIGDELRVNSACRKVQHMVVKSALLADKFPVLHDIGNPKAIKCVPQAEVEWKFYDAQPCSDKAYKIEELFYSYATHHDKFTDGVCLFWNCNVDRYPANAIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFTNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRQYLDAYNMMISAGFSLWIYKQFDTYNLWNTFTRLQSLENVAYNVVNKGHFDGHAGEAPVSIINNAVYTKVDGIDVEIFENKTTLPVNVAFELWAKRNIKPVPEIKILNNLGVDIAANTVIWDYKREAPAHVSTIGVCTMTDIAKKPTESACSSLTVLFDGRVEGQVDLFRNARNGVLITEGSVKGLTPSKGPAQASVNGVTLIGESVKTQFNYFKKVDGIIQQLPETYFTQSRDLEDFKPRSQMETDFLELAMDEFIQRYKLEGYAFEHIVYGDFSHGQLGGLHLMIGLAKRSQDSPLKLEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVISKVVKVTIDYAEISFMLWCKDGHVETFYPKLQASQAWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPRTKHVTKENDSKEGFFTYLCGFIKQKLALGGSIAVKITEHSWNADLYKLMGHFSWWTAFVTNVNASSSEAFLIGANYLGKPKEQIDGYTMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKENQINDMIYSLLEKGRLIIRENNRVVVSSDILVNN*TNMFIFLLFLTLTSGSDLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLGINITNFRAILTAFSPAQDIWGTSAAAYFVGYLKPTTFMLKYDENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDPKTSEILDISPCAFGGVSVITPGTNASSEVAVLYQDVNCTDVSTAIHADQLTPAWRIYSTGNNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASYHTVSLLRSTSQKSIVAYTMSLGADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVDCNMYICGDSTECANLLLQYGSFCTQLNRALSGIAAEQDRNTREVFAQVKQMYKTPTLKYFGGFNFSQILPDPLKPTKRSFIEDLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDNTFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTSCCSCLKGACSCGSCCKFDEDDSEPVLKGVKLHYT*TNLWICL*DFLLLDQLLHSQ*KLTMLLLQVLFMLQQRYRYKPHSLSDGLLLALHFLLFFRALPK*LRSIKDGS*PFIRASSSFAIYCCYLLPSIHIFCLSLQVWRRNFCTSMP*YIFYNASTHVELL*DVGFVGSANPRTHYFMMPTTLFAGTHITMTTVYHITVSQIQLSLLKVTAFQHQNSKKTTKLVVILRIGTQVLKTMSLYMAISPKFTTSLSLHKLLQTLVLKMLHSSSLTSLLKTHRMCKYTQSTALQELLIQQWIQFMMSRRRLLACLCKHKKVSTNLCTHSFRKKQVR**LIAYFFFLLSWYSC*SH*PSLLRFDCVRTAAILLT*V**NQRFTSTRVLKI*TLLKEFLIFWSKRTNYYYYSVWNFNIAYHGRQRYYYR*GA*TTPGTMEPSNRFPIPSLDYVTTICLF*SEQVFVHNKACFPLALVASNTCLFCACCCLQN*LGDWRDCDCNGLYCRLDVA*LLRCFLQAVCSYPLNVVIQPRNKHSSQCASPGDNCDQTAHGK*TCHWCCDHSWSLANGRTLPRAL*H*GPAKRDHCGYITNAFLLQIRSVAACRH*FRFCCIQPLPYWKL*IKYRPRR*QRQYCFASTVSDNRCFILLTSRLQ*QRY*LSL*GLSGLLFGILTL**VQ**DNYLSL*LRRIIRS*MMKNLWS*IIHKTNMKIILFLTLIVFTSCELYHYQECVRGTTVLLKEPCPSGTYEGNSPFHPLADNKFALTCTSTHFAFACADGTRHTYQLRARSVSPKLFIRQEEVQQELYSPLFLIVAALVFLILCFTIKRKTE*MSSL*LTSICAF*PFCYSLF**CLLYFGFHSKSRI*KNLVPKSKRT*NFSLF*LVFLYAVAYAL*YSAVHLINLMCLKILVRYNTRGNTYSTAWLCALGKVLPFHRWHTMVQTCTPNVTINCQDPAGGALIARCWYLHEGHQTAAFRDVLVVLNKRTN*NV**WTPIKPT*CPPHYIWWTHRFN*Q*PEWRTQWGKAKTAPTPRFTQ*YCVLVHSSHSAWQGGT*IPSRPGRSNQHQ*WSR*PNWLLPKSYPTSSWW*RQNERAQPQMVLLLPRNWPRSFTSLRR*QRRHRMGCN*GSLEYTQRPHWHPQS**QCCHRATTSSRNNIAKRLLRRGKQRRQSSLFSLLIT*SR*FKKFNSWQQ*GKFSCSNG*RRW*NCPRAIAARQIEPA*EQSFW*RPTTTRPNCH*EICC*GI*KASPKTYCHKTVQRHSSIWETWSRTNPRKFRGPRPNQTRN*LQTLAANCTICSKCLCILWNVTHWHGSHTFGNMADLSWSH*IG*QRSTIQRQRHTAEQAH*RIQNIPTNRA*KGQKEKD**SSAFAAETKEAAHCDSSSCG*HG*FLQTTSKFHEWSFC*FNSGINTHDDHTRQMGYVNVFAIPFTIHSLLLCRMNSRN*TAQVGLVNFNLT*QSLINV*H*GGLERATTFSSRPRGVRSRVQ*IMLGRAAYMEEP*CVKLILVVLSPCDFNSFLGE*QKKKKKKK'"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "def translation(x, isProtein = False):\n",
    "    aa = []\n",
    "    for i in range(0, len(x)-2, 3):\n",
    "        aa.append(dec[x[i:i+3]])\n",
    "    aa = ''.join(aa)\n",
    "    if isProtein:\n",
    "        if aa[0] != \"M\" or aa[-1] != \"*\":\n",
    "            print(\"BAD PROTEIN!\")\n",
    "            return None\n",
    "        aa = aa[:-1]\n",
    "    return aa\n",
    "\n",
    "aa = translation(corona[0:]) + translation(corona[1:]) + translation(corona[2:])\n",
    "\n",
    "##Refer to reading of codons for the above algorithm\n",
    "\n",
    "aa"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Polypeptides\n",
    ">In molecular biology, a reading frame is a way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets. Where these triplets equate to amino acids or stop signals during translation, they are called codons.\n",
    "\n",
    ">A polypeptide is a longer, continuous, and unbranched peptide chain of up to fifty amino acids. Hence, peptides fall under the broad chemical classes of biological oligomers and polymers, alongside nucleic acids, oligosaccharides, polysaccharides, and others.\n",
    "\n",
    ">When a polypeptide contains more than fifty amino acids it is known as a protein. Proteins consist of one or more polypeptides arranged in a biologically functional way, often bound to ligands such as coenzymes and cofactors, or to another protein or other macromolecule such as DNA or RNA, or to complex macromolecular assemblies."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['ILGFYLPRKSQPTSISCRSVL',\n",
       " 'TNFKICVAVARLHA',\n",
       " 'CTYAV',\n",
       " 'TIINFTVVDKKRVTRPSSADCLRFRPCCSRSSAYLGFVRV',\n",
       " 'PKGKMESLVLGVNEKTHVQLSLPVLQVRDVLVRGFGDSVEEALSEAREHLKNGTCGLVELEKGVLPQLEQPYVFIKRSDALSTNHGHKVVELVAEMDGIQYGRSGITLGVLVPHVGETPIAYRNVLLRKNGNKGAGGHSYGIDLKSYDLGDELGTDPIEDYEQNWNTKHGSGALRELTRELNGGAVTRYVDNNFCGPDGYPLDCIKDFLARAGKSMCTLSEQLDYIESKRGVYCCRDHEHEIAWFTERSDKSYEHQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRIRSVYPVASPQECNNMHLSTLMKCNHCDEVSWQTCDFLKATCEHCGTENLVIEGPTTCGYLPTNAVVKMPCPACQDPEIGPEHSVADYHNHSNIETRLRKGGRTRCFGGCVFAYVGCYNKRAYWVPRASADIGSGHTGITGDNVETLNEDLLEILSRERVNINIVGDFHLNEEVAIILASFSASTSAFIDTIKSLDYKSFKTIVESCGNYKVTKGKPVKGAWNIGQQRSVLTPLCGFPSQAAGVIRSIFARTLDAANHSIPDLQRAAVTILDGISEQSLRLVDAMVYTSDLLTNSVIIMAYVTGGLVQQTSQWLSNLLGTTVEKLRPIFEWIEAKLSAGVEFLKDAWEILKFLITGVFDIVKGQIQVASDNIKDCVKCFIDVVNKALEMCIDQVTIAGAKLRSLNLGEVFIAQSKGLYRQCIRGKEQLQLLMPLKAPKEVTFLEGDSHDTVLTSEEVVLKNGELEALETPVDSFTNGAIVGTPVCVNGLMLLEIKDKEQYCALSPGLLATNNVFRLKGGAPIKGVTFGEDTVWEVQGYKNVRITFELDERVDKVLNEKCSVYTVESGTEVTEFACVVAEAVVKTLQPVSDLLTNMGIDLDEWSVATFYLFDDAGEENFSSRMYCSFYPPDEEEEDDAECEEEEIDETCEHEYGTEDDYQGLPLEFGASAETVRVEEEEEEDWLDDTTEQSEIEPEPEPTPEEPVNQFTGYLKLTDNVAIKCVDIVKEAQSANPMVIVNAANIHLKHGGGVAGALNKATNGAMQKESDDYIKLNGPLTVGGSCLLSGHNLAKKCLHVVGPNLNAGEDIQLLKAAYENFNSQDILLAPLLSAGIFGAKPLQSLQVCVQTVRTQVYIAVNDKALYEQVVMDYLDNLKPRVEAPKQEEPPNTEDSKTEEKSVVQKPVDVKPKIKACIDEVTTTLEETKFLTNKLLLFADINGKLYHDSQNMLRGEDMSFLEKDAPYMVGDVITSGDITCVVIPSKKAGGTTEMLSRALKKVPVDEYITTYPGQGCAGYTLEEAKTALKKCKSAFYVLPSEAPNAKEEILGTVSWNLREMLAHAEETRKLMPICMDVRAIMATIQRKYKGIKIQEGIVDYGVRFFFYTSKEPVASIITKLNSLNEPLVTMPIGYVTHGFNLEEAARCMRSLKAPAVVSVSSPDAVTTYNGYLTSSSKTSEEHFVETVSLAGSYRDWSYSGQRTELGVEFLKRGDKIVYHTLESPVEFHLDGEVLSLDKLKSLLSLREVKTIKVFTTVDNTNLHTQLVDMSMTYGQQFGPTYLDGADVTKIKPHVNHEGKTFFVLPSDDTLRSEAFEYYHTLDESFLGRYMSALNHTKKWKFPQVGGLTSIKWADNNCYLSSVLLALQQLEVKFNAPALQEAYYRARAGDAANFCALILAYSNKTVGELGDVRETMTHLLQHANLESAKRVLNVVCKHCGQKTTTLTGVEAVMYMGTLSYDNLKTGVSIPCVCGRDATQYLVQQESSFVMMSAPPAEYKLQQGTFLCANEYTGNYQCGHYTHITAKETLYRIDGAHLTKMSEYKGPVTDVFYKETSYTTTIKPVSYKLDGVTYTEIEPKLDGYYKKDNAYYTEQPIDLVPTQPLPNASFDNFKLTCSNTKFADDLNQMTGFTKPASRELSVTFFPDLNGDVVAIDYRHYSASFKKGAKLLHKPIVWHINQATTKTTFKPNTWCLRCLWSTKPVDTSNSFEVLAVEDTQGMDNLACESQQPTSEEVVENPTIQKEVIECDVKTTEVVGNVILKPSDEGVKVTQELGHEDLMAAYVENTSITIKKPNELSLALGLKTIATHGIAAINSVPWSKILAYVKPFLGQAAITTSNCAKRLAQRVFNNYMPYVFTLLFQLCTFTKSTNSRIRASLPTTIAKNSVKSVAKLCLDAGINYVKSPKFSKLFTIAMWLLLLSICLGSLICVTAAFGVLLSNFGAPSYCNGVRELYLNSSNVTTMDFCEGSFPCSICLSGLDSLDSYPALETIQVTISSYKLDLTILGLAAEWVLAYMLFTKFFYLLGLSAIMQVFFGYFASHFISNSWLMWFIISIVQMAPVSAMVRMYIFFASFYYIWKSYVHIMDGCTSSTCMMCYKRNRATRVECTTIVNGMKRSFYVYANGGRGFCKTHNWNCLNCDTFCTGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVAVKNGALHLYFDKAGQKTYERHPLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCDESASKSASVYYSQLMCQPILLLDQALVSDVGDSTEVSVKMFDAYVDTFSATFSVPMEKLKALVATAHSELAKGVALDGVLSTFVSAARQGVVDTDVDTKDVIECLKLSHHSDLEVTGDSCNNFMLTYNKVENMTPRDLGACIDCNARHINAQVAKSHNVSLIWNVKDYMSLSEQLRKQIRSAAKKNNIPFRLTCATTRQVVNVITTKISLKGGKIVSTCFKLMLKATLLCVLAALVCYIVMPVHTLSIHDGYTNEIIGYKAIQDGVTRDIISTDDCFANKHAGFDAWFSQRGGSYKNDKSCPVVAAIITREIGFIVPGLPGTVLRAINGDFLHFLPRVFSAVGNICYTPSKLIEYSDFATSACVLAAECTIFKDAMGKPVPYCYDTNLLEGSISYSELRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDAEYCRHGTCERSEVGICLSTSGRWVLNNEHYRALSGVFCGVDAMNLIANIFTPLVQPVGALDVSASVVAGGIIAILVTCAAYYFMKFRRVFGEYNHVVAANALLFLMSFTILCLVPAYSFLPGVYSVFYLYLTFYFTNDVSFLAHLQWFAMFSPIVPFWITAIYVFCISLKHCHWFFNNYLRKRVMFNGVTFSTFEEAALCTFLLNKEMYLKLRSETLLPLTQYNRYLALYNKYKYFSGALDTTSYREAACCHLAKALNDFSNSGADVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTFQGKFKKIVKGTHHWMLLTFLTSLLILVQSTQWSLFFFVYENAFLPFTLGIMAIAACAMLLVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLELADTSLSGYRLKDCVMYASALVLLILMTARTVYDDAARRVWTLMNVITLVYKVYYGNALDQAISMWALVISVTSNYSGVVTTIMFLARAIVFVCVEYYPLLFITGNTLQCIMLVYCFLGYCCCCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKSSIDAFKLNIKLLGIGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINRLCEEMLDNRATLQAIASEFSSLPSYAAYATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVVDADSKIVQLSEINMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNNSKGGRFVLALLSDHQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDPAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLRNTVCTVCGMWKGYGCSCDQLREPLMQSADASTFLNGFAV',\n",
       " 'VQPVLHRAAQALVLMSSTGLLIFTTKKLLVLQSS',\n",
       " 'KLIAVASRRRMRKAIY',\n",
       " 'TLTL',\n",
       " 'LRGILCLTTNMKRLFITWLKIVQRLLSMTFSSLE',\n",
       " 'MVTWYHIYHVSV',\n",
       " 'LNTQWLI',\n",
       " 'SMLYVILMRVIVIH',\n",
       " 'KKYSSHTIAVMMIISIRRIGMTS',\n",
       " 'RILTSYAYMLT',\n",
       " 'VSVYANHY',\n",
       " 'RLYNSAMLCVMQAL',\n",
       " 'AY',\n",
       " 'H',\n",
       " 'IIRILMGTGTISVISYK',\n",
       " 'HQAAEFLLWIHITHC',\n",
       " 'CPSSL',\n",
       " 'LGHWLLSPIWMLISQNHLLSGIC',\n",
       " 'NMILRKRDFVSSTVILNIGTRHTIPIVLTVWMIGVSFIVQTLMCYFLLCFHLQVLDH',\n",
       " '',\n",
       " 'EKYL',\n",
       " 'MVFLLLFQLDTIFVS',\n",
       " 'ESYIIRM',\n",
       " 'TYIARVSVSRNF',\n",
       " 'CMLLIQLCMQLLAIYC',\n",
       " 'INALHAFQ',\n",
       " 'LH',\n",
       " 'QTMLLFKLSNPVILIKTFMTLLCLKVSLRKEVLLN',\n",
       " 'NTSSLLRMATLLSVIMTIIVIICQQCVISDNSYS',\n",
       " 'LKLLINTLIVTMVAVLMPTK',\n",
       " 'SLTIWINQLVSHLINGVRLDFIMTQ',\n",
       " 'VMRIKMHFSRILSVMSSLL',\n",
       " 'LK',\n",
       " 'ILSMPLVQRIELAP',\n",
       " 'LVSLSVVL',\n",
       " 'QIDSFIRNY',\n",
       " 'SQ',\n",
       " 'PPLEELLW',\n",
       " 'LEQASFTVAGIIC',\n",
       " 'KLFTVM',\n",
       " 'KLHTLWVGIIQNVTEPCLTCLG',\n",
       " 'WPLLFLLANITLAVTYHTVSTG',\n",
       " 'LTSVRKY',\n",
       " 'VRWSCVAAHYMLNQVEHHPVMLQLLMLIVSLTFVKLLQPM',\n",
       " 'MHFFQLMVIR',\n",
       " 'LTSMSAIYNTGSMSVSIEIGMLIMNSWMSFTLTCVNISP',\n",
       " '',\n",
       " 'FFLMMPLCAITVTMRLKV',\n",
       " '',\n",
       " 'LALRTLRQFFIIKIMCSCLRQNVGLRLTLLKDLTNFAHSIQC',\n",
       " 'LNKEMITCTCLTQIHQEY',\n",
       " 'AQAVLSMILSKQMVHL',\n",
       " 'LKGSCHWLLMLTHLQNILIRSMLMSFTCIYNTLESYMMSLLATCWTCIP',\n",
       " 'C',\n",
       " 'LMITPHGTGNLSFMRLCTHHIQSCRL',\n",
       " 'VLVYCAIHRLHFVAVPVLGDHSYVASAAMTMSFQHHTN',\n",
       " 'CCLLIPMFAMPQVVMSLM',\n",
       " 'HNCI',\n",
       " 'EV',\n",
       " 'AIIASHISLPLVFHYVLMVRFLVYTKTHV',\n",
       " 'AVTMSLTSMR',\n",
       " 'QHVIGLMLAITYLPTLVLRDSSFSQQKRSKPLRKHLSCHMVLPLYAKYSLTENCIFHGRLENLDHH',\n",
       " 'TETMSLLVTV',\n",
       " 'LKIVKYRLESTPLKKVTMVMLLCTEVLRHTS',\n",
       " 'MLVITLC',\n",
       " 'HLTL',\n",
       " 'CHLVHLL',\n",
       " 'CHKSTM',\n",
       " 'ELLACTQHSTSQMSFLAMLQIIKRSACKSTLHSKDHLVLVRVILPSDLLSITHLLA',\n",
       " 'CIRHALMQLLMPYVKRH',\n",
       " 'NICP',\n",
       " 'INVVESYLRVRA',\n",
       " 'SVLINSK',\n",
       " 'IQH',\n",
       " 'NSMFSAL',\n",
       " 'MHCQKQLLTL',\n",
       " 'SLMKSLWLLIMT',\n",
       " 'VLSMLDFVQNTTSILAILLNYQPPAHC',\n",
       " 'LKAH',\n",
       " 'NQNILIQCADL',\n",
       " 'KQ',\n",
       " 'VQTCSLELVAVVLLKLLTL',\n",
       " 'VL',\n",
       " 'FMTIS',\n",
       " 'KHTRISQLNASKCSTKVLLHMMFHLQSTDLK',\n",
       " 'AL',\n",
       " 'ENFLHAILLGEKLFLSHLIIHRTL',\n",
       " 'LQKS',\n",
       " 'DCLRRLLIHHRVLNMTMSYSHKLLKQHTLVMSTASMWLSQGQKLAFCA',\n",
       " 'CLIEIFMTNCNLQV',\n",
       " 'KYHVAMWLHYKQKM',\n",
       " 'LDFLRTVVRSLLVFILHRHLHTSALI',\n",
       " 'SSRLKDYVLTYQAYQRT',\n",
       " 'PTVDSSL',\n",
       " 'WVSK',\n",
       " 'ITKSMVTLICLSPAKKLFVTFVRGLALM',\n",
       " 'RAVMQLEMLWVLTYLSS',\n",
       " 'DFLQVLT',\n",
       " '',\n",
       " 'LYRLVMLTLKITQNSPELMQNLHQVTSLNILYHSCIKACPGM',\n",
       " 'CVLR',\n",
       " 'YKCSVIH',\n",
       " 'KDCQTESCSSFGRMALSLHQ',\n",
       " 'STLSRLDLKERVVCVTNVQLAFLLHQILMPAGIILWVLTMSITHL',\n",
       " 'LMFSSGALRVTFRVTMTNIARYMEMHMWLVVMLS',\n",
       " 'LDV',\n",
       " 'QSMSALLSALIGLLNTLL',\n",
       " 'EMN',\n",
       " 'GLILLAEKYNTWL',\n",
       " 'SLHCLLISFQFFMTLEIQRLSSVCLRLK',\n",
       " 'NGSSTMLSHVVTKLTK',\n",
       " 'RNSSILMLHITINSLMVFVCFGIVTLIVTQPMQLCVGLTQESCQT',\n",
       " 'TYQAVMVVVCM',\n",
       " 'ISMHSTLQLSIKVHLLI',\n",
       " 'SNCLSFTILIVLVSLMANK',\n",
       " 'CRILIMFHSNLLRVLHDAI',\n",
       " 'VVLFADTMQMSTDSTWMHII',\n",
       " '',\n",
       " 'FLLDLAYGFTNNLILITCGIHLPGYRV',\n",
       " 'KMWLIMLLIKDTLMDTPAKHLFPSLIMLFTQR',\n",
       " 'MVLMWRSLKIRQHFLLMLHLSFGLSVTLNQCQRLRYSIIWVLISLLIL',\n",
       " 'SGTTKEKPQHMYLQ',\n",
       " 'VSAQ',\n",
       " 'LTLPRNLLRVLVLHLLSCLMVEWKDR',\n",
       " 'TFLETPVMVF',\n",
       " '',\n",
       " 'QKVQSKV',\n",
       " 'HLQRDQHKLASMESH',\n",
       " 'LENQ',\n",
       " 'KHSLTTLRK',\n",
       " 'TALFNSCLKPTLLRAET',\n",
       " 'RILSPDHKWKLTFSSSLWMNSYSDISSRAMPSNTSFMEISVMDNLAVFI',\n",
       " '',\n",
       " '',\n",
       " 'A',\n",
       " 'PSAHKIHHLN',\n",
       " 'RILSLWTAQ',\n",
       " 'KITS',\n",
       " 'QMRKQVHQNVCVL',\n",
       " 'LIFYLMTLSR',\n",
       " '',\n",
       " 'SHKICQ',\n",
       " 'FQKWSRLQLTMLKFHSCFGVRMDMLKPSTQNYKQVKRGNQVLRCLTCTRCKECFLKSVTFRIMVKMLLYQKE',\n",
       " '',\n",
       " '',\n",
       " 'MSQSILNCVNT',\n",
       " 'IHLL',\n",
       " 'LYPTT',\n",
       " 'ELFTLVLALIKELHQVQLCSDNGCQLAHYLSIQILMTSSPTQILL',\n",
       " 'LETVQQYIRLINGTLLLAICMTLGPNM',\n",
       " 'QKRMTLKKGFSLICVDL',\n",
       " 'SKN',\n",
       " 'PWVVL',\n",
       " 'L',\n",
       " 'R',\n",
       " 'QSILGMLTFTSLWAISHGGQLLLQM',\n",
       " 'MHHHRKHF',\n",
       " 'LGLTILASRRNKLMAIPCMLTTFSGGTQILSSCLPIHSLT',\n",
       " 'ANFLLN',\n",
       " 'EELL',\n",
       " 'CLLRRIKSMI',\n",
       " 'FILFWKKVGLSLEKTTELWFQVIFLLTTKRTCLFSYYFLLSLVVVTLTGAPLLMMFKLLITLNILHL',\n",
       " 'GGFTILMKFLDQTLFI',\n",
       " 'LRIYFFHFILMLQGFILLIIRLATLSYLLRMVFILLPQRNQMLSVVGFLVLP',\n",
       " 'TTSHSR',\n",
       " 'LLLTILLMLLYEHVTLNCVTTLSLLFLNPWVHRHIL',\n",
       " 'YSIMHLIALSSTYLMPFRLMFQKSQVILNTYESLCLKIKMGFSMFIRAINL',\n",
       " 'M',\n",
       " 'FVIYLLVLTL',\n",
       " 'NLFLSCLLVLTLQILEPFLQPFHLLKTFGARQLQPILLAI',\n",
       " 'SQLHLCSSMMKMVQSQMLLIVLKIHLLNSNALLRALRLTKEFTRPLISGLFPQEML',\n",
       " 'DSLILQTCVLLERFLMLLNSLLSMHGREKKFLIVLLITLCSTTQHFFQPLSAMAFLPLS',\n",
       " 'MIFASPMSMQILL',\n",
       " 'SREMM',\n",
       " 'DK',\n",
       " 'RQDKLVLLLIIIINCQMISWVVSLLGILGTLMLLQLVIIIINIGILDMASLGPLRETYLMCLSPLMANLAPHLLLIVIGH',\n",
       " 'MIMVFTPLLALATNLTEL',\n",
       " 'YFLLNF',\n",
       " 'MHRPRFVDQNYPLTLLRTSVSILILMDSLVLVC',\n",
       " 'LLLQRDFNHFNNLAVMFLISLIPFEILKHLKY',\n",
       " 'TFHLALLGV',\n",
       " 'V',\n",
       " 'LHLEQMLHLKLLFYIKMLTALMFLQQFMQINSHQLGAYILLETMYSRLKQAVL',\n",
       " 'ELSMSTLLMSATFLLELAFVLVTIQFLYYVVLAKNLLWLILCL',\n",
       " 'VLIVQLLTLITPLLYLLTFQLALLQK',\n",
       " 'CLFLWLKPP',\n",
       " 'IVICTSAEILLNVLICFSNMVAFAHN',\n",
       " 'IVHSQVLLLNRIATHVKCSLKSNKCTKPQL',\n",
       " 'NILVVLIFHKYYLTL',\n",
       " 'SQLRGLLLRTCSLIR',\n",
       " 'HSLMLAS',\n",
       " 'SNMANA',\n",
       " 'VILMLEISFVRRSSMDLQCCHLCSLMI',\n",
       " 'LLPTLLL',\n",
       " 'LVVLPLLDGHLVLALLFKYLLLCKWHIGSMALELPKMFSMRTKNKSPTNLTRRLVKFKNHLQQHQLHWASCKTLLTRMLKH',\n",
       " 'THLLNNLALILVQFQVC',\n",
       " 'MISFRDLIKSRRRYKLTG',\n",
       " 'LQADFKAFKPM',\n",
       " 'HNN',\n",
       " 'SGLLKSGLLLILLLLKCLSVFLDNQKELTFVERATTLCPSHKQPRMVLSSYMSRMCHPRRGTSPQRQQFVMKAKHTSLVKVFLCLMALLGLLHRGTSFLHK',\n",
       " 'LLQTIHLSQEIVMSLLASLTTQFMILCNLSLTHSKKSWTSTSKIIHHQMLILATFQALTLLSSTFKKKLTASMRSLKI',\n",
       " 'MNHSLTFKNWENMSNILNGLGMFGSASLLD',\n",
       " 'LPSSWLQSCFVA',\n",
       " 'LVVAVASRVHALVVLAASLMRMTLSQFSRVSNYITHKRTYGFVYEIFYS',\n",
       " 'INYCTASKN',\n",
       " 'QCFSCKYCSCYSNDTATSLTPFRMACYWRCISCCFSERYQNNCAQ',\n",
       " 'KMAASPL',\n",
       " 'GLPVHLQFTAAICYHLFTSFACRCRYGGAIFVPLCLDIFSTMHQRM',\n",
       " 'NYYEMLALLEVQIQEPITL',\n",
       " 'CQLLCLLAHT',\n",
       " 'L',\n",
       " 'LLYTI',\n",
       " 'QCHRYNCRY',\n",
       " 'R',\n",
       " 'RHFNTKTQRRLPNWWLF',\n",
       " 'G',\n",
       " 'ALRC',\n",
       " 'RLCRCTWLFHRSLLPA',\n",
       " 'VYTNYYRHWY',\n",
       " 'KCYILHL',\n",
       " 'QAC',\n",
       " 'RPTECANTHNRRLFRSC',\n",
       " 'SSNGSNL',\n",
       " '',\n",
       " 'ADDDY',\n",
       " 'RAFVSTRK',\n",
       " 'VRTYVLIRFGRNRYVNS',\n",
       " '',\n",
       " 'RTSFSCFRGILASHTSHPYCASIVCVLLQYC',\n",
       " 'REFSKTNGLRLLAC',\n",
       " 'KSELF',\n",
       " 'RSS',\n",
       " 'SSGLNELTIIIILFGTLTLLIMADNGTITVEELKQLLEQWNLVIGFLFLAWIMLLQFAYSNRNRFLYIIKLVFLWLLWPVTLACFVLAAVYRINWVTGGIAIAMACIVGLMWLSYFVASFRLFARTRSMWSFNPETNILLNVPLRGTIVTRPLMESELVIGAVIIRGHLRMAGHSLGRCDIKDLPKEITVATSRTLSYYKLGASQRVGTDSGFAAYNRYRIGNYKLNTDHAGSNDNIALLVQ',\n",
       " 'VTTDVSSC',\n",
       " 'LPGYNSRDIDYHYEDFQDCYLES',\n",
       " 'RYNKFNSETII',\n",
       " 'ASN',\n",
       " 'EELFGVR',\n",
       " '',\n",
       " 'RTYGVRLSIKRT',\n",
       " 'KLFSS',\n",
       " 'H',\n",
       " 'LYLHLASYITIRSVLEVRLYY',\n",
       " 'KNLAHQEHTRAIHHFTLLLTINLH',\n",
       " 'LALAHTLLLLVLTVLDIPISCVQDQFHQNFSSDKRRFNKSSTRHFFSLLLL',\n",
       " 'YF',\n",
       " 'YFASPLRERQNE',\n",
       " 'AHFN',\n",
       " 'LLFVLFSLSAIPCFNNAYYILVFTRNPGSRRTLYQSLNEHETSHCFDLYFSMQLHMHCSTALCI',\n",
       " '',\n",
       " 'TSCA',\n",
       " 'RSL',\n",
       " 'GTTLGVILIALLGFVL',\n",
       " 'ERFYLFIDGTLWFKHAHLMLLSTVKIQLVVRL',\n",
       " 'LGVGTFMKVTKLLHLETYLLF',\n",
       " 'INEQIKMSDNGPQSNQRSAPRITFGGPTDSTDNNQNGGRNGARPKQRRPQGLPNNTASWFTALTQHGKEELRFPRGQGVPINTNSGPDDQIGYYRRATRRVRGGDGKMKELSPRWYFYYLGTGPEASLPYGANKEGIVWVATEGALNTPKDHIGTRNPNNNAATVLQLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRGNSRNSTPGSSRGNSPARMASGGGETALALLLLDRLNQLESKVSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKQYNVTQAFGRRGPEQTQGNFGDQDLIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYHGAIKLDDKDPQFKDNVILLNKHIDAYKTFPPTEPKKDKKKKTDEAQPLPQRQKKQPTVTLLPAADMDDFSRQLQNSMSGASADSTQA',\n",
       " 'TLMMTTQGRWAM',\n",
       " 'TFSQFRLRYIVYSCAE',\n",
       " 'ILVTKQHK',\n",
       " 'V',\n",
       " 'LTLISHSNL',\n",
       " 'SMCNIREDLKEPPHFHRGHAEYDRGYSE',\n",
       " 'C',\n",
       " 'GELPIWKSPNV',\n",
       " 'N',\n",
       " 'F',\n",
       " '',\n",
       " 'CYPHVILIAS',\n",
       " 'ENDKKKKKKKKY',\n",
       " 'VFTYPGKANQPRSLVDLFSKRTLKSV',\n",
       " 'LSLGCMPSAPTQYKQ',\n",
       " '',\n",
       " 'ILLSLTRNE',\n",
       " 'LVPLLQTAYGFVRVAVDHQHT',\n",
       " 'VSSGCDRKVRWRALFLVSTRKHTSNSVCLSFRLETC',\n",
       " 'CVASGTLWKRPYRRHVNTSKMALVV',\n",
       " '',\n",
       " 'SWKKAYCPSLNSPMCSLNVLMP',\n",
       " 'APITATRSLSWLQKWTAFSTVVAV',\n",
       " 'HWEYSCHMWAKPQLHTAMFFFVRTVIREPVVIAMASI',\n",
       " 'SLMT',\n",
       " 'VTSLALIPLKIMNKTGTLSMAVVHSVNSLVSSMEVQSLAMSTTISVAQMGTLLIASKIFSHARASQCALFPNNLITSSRREVSTAAVTMSMKLPGSLSALIRATSTRHPSKLRVPRNLTLSKGNAQSLCFLLTQKSKSFNHVLKRKRLRVSWGVYALCTLLHLHRSVTICTCLP',\n",
       " '',\n",
       " 'NVIIAMKFHGRRATF',\n",
       " 'KPLVNIVALKI',\n",
       " 'LLKDLLHVGTYLLML',\n",
       " '',\n",
       " 'KCHVLPVKTQRLDLSIVLQIITTTQTLKLDSAREVGLDVLEAVCLPMLAAIISVPTGFLVLVLILAQAILALLVTMWRP',\n",
       " 'MRISLRY',\n",
       " 'VVNVLTLTLLAIFI',\n",
       " 'MKRLPSFWHLSLLLQVPLLTL',\n",
       " 'RVLITSLSKPLLSPAVTIKLPRESP',\n",
       " 'KVLGTLDNRDQF',\n",
       " 'HHCVVFPHRLLVLSDQFLRAHLMQQTTQFLICKEQLSPYLMVFLNSHYVLSTPWFILQTCSPTVSLLWHM',\n",
       " 'LVVLYNRLLSGCLIFWALLLKNSGLSLNGLRRNLVQELNFSRMLGRFSNFSLQVFLTSSRVKYRLLQITSRIV',\n",
       " 'NASLMLLTRHSKCALIKSLSLAQSCDHST',\n",
       " 'VKSSSLKARDFTVSVYVARSSCNYSCLLRHQKK',\n",
       " 'PFLKVIHMTQYLPLRRLFSRTVNSKHSRRPLIASQMELSLAHQSV',\n",
       " 'MASCS',\n",
       " 'RLRTKNNTAHCLLVYWLQTMSFA',\n",
       " 'KGVHQLKV',\n",
       " 'PLEKILFGKFKVTRM',\n",
       " 'ESHLSLMNVLTKCLMKSALSTLLNPVPKLLSLHVL',\n",
       " 'QRLL',\n",
       " 'RLYNQFLISLPTWVLILMSGV',\n",
       " 'LHSTYLMMLVKKTFHHVCIVPFTLQMRKKRTMQSVRKKKLMKPVNMSTVQRMIIKVSLWNLVPQLKQFELRKKKRKTGWMILLSNQRLSQNQNLHLKNQLISLLVI',\n",
       " 'NLLTMLPLNVLTSLRRHKVLILW',\n",
       " 'L',\n",
       " 'MLLTYT',\n",
       " 'NMVVV',\n",
       " 'QVHSTRQPMVPCKRRVMITLS',\n",
       " 'MALLQ',\n",
       " 'EGLVCFLDIILLRSVCMLLDLT',\n",
       " 'MQVRTSSFLRQHMKISIHRTSYLHHCCQQAYLVLNHFSLYKCACRRFVHRFILQSMTKLFMSRLSWIILIT',\n",
       " 'SLEWKHLNKRSHQTQKIPKLRRNLSYRSLSM',\n",
       " 'SQKLRPALMRLPQHWKKLSFLPISYSCLLISMVSFTMILRTCLEVKICLSLRRMHLTW',\n",
       " 'VMLSLVVISLVL',\n",
       " 'YPPKRLVALLRCSQEL',\n",
       " 'RKCQLMSI',\n",
       " 'PRTLDKDVLVIHLRKLRLLLRNANLHFMYYLQKHLMLRKRF',\n",
       " 'ELYPGI',\n",
       " 'EKCLLMLKRQEN',\n",
       " 'CLYAWMLEP',\n",
       " 'WQPSNVSIKELKFKRASLTMVSDSSFILVKSL',\n",
       " 'LLLLRS',\n",
       " 'TL',\n",
       " 'MSRLSQCQLVM',\n",
       " 'HMVLILKRLRAVCVLLKLLP',\n",
       " 'CQYHHQMLLLHIMDTSLRHQRHLRSTL',\n",
       " 'KQFLWLALTEIGPIQDSVQS',\n",
       " 'VLNFLSVVTKLCTTLWRAPSSFILTVRFFHLTN',\n",
       " 'RVSYPCGRLRL',\n",
       " 'KCSQLWTTLISTHSLWICL',\n",
       " 'HMDSSLVQHTWMVLMLQKLNLM',\n",
       " 'IMRVRLSLYYLVMTHYVVKLSSTTILLMRVFLVGTCLL',\n",
       " 'TTQRNGNFLKLVV',\n",
       " 'LQLNGLITIVICLVFY',\n",
       " 'HFNSLKSNSMHQHFKRLIIEPVLVMLLTFVHSYSLTVIKLLASLVMSEKL',\n",
       " 'PIFYSMLIWNLQSEFLMWCVNIVVRKLLP',\n",
       " 'RV',\n",
       " 'KL',\n",
       " 'CIWVLYLMIILRQVFPFHVCVVVMLHNI',\n",
       " 'YNKSLLLL',\n",
       " 'CLHHLLSINYSKVHSYVRMSTLVTISVVITLI',\n",
       " 'LLRRPSIVLTELTLQRCQSTKDQ',\n",
       " 'LMFSTRKHLTLQPSSLCRINSMELLTQRLNQNWMGIIKRIMLTIQSSL',\n",
       " 'TLYQLNHYQMRVLIISNSHVLTQNLLMI',\n",
       " 'IK',\n",
       " 'QASQSQLHESYLSHSSQT',\n",
       " 'MAM',\n",
       " 'WLLTIDTIQRVSRKVLNYCISQLFGTLTRLQPRQRSNQTLGVYVVFGVQSQ',\n",
       " 'ILQIHLKFWQ',\n",
       " 'KTHKEWTILLVKVNNPPLKK',\n",
       " 'WKILPYRRKS',\n",
       " 'SVT',\n",
       " 'KLPKL',\n",
       " 'AMSYLNHQMKVLK',\n",
       " 'HKS',\n",
       " 'VMRILWLLMWKTQALPLRNLMSFH',\n",
       " 'P',\n",
       " 'V',\n",
       " 'KQLPLMVLLQLIVFLGVKFWLMSNHS',\n",
       " 'DKQQLQHQIALRD',\n",
       " 'HNVCLTIICLMCLHYCSNCVLLLKVPILELELHYLQLLLKIVLRVLLNYVWMPALIM',\n",
       " 'SHPNFLNCSQSLCGYCC',\n",
       " 'VFA',\n",
       " 'VL',\n",
       " 'SV',\n",
       " 'LLLLVYSYLILVLLLIVMALENCILIRLTLLLWISVKVLFLAAFV',\n",
       " 'VD',\n",
       " 'TPLILIQLLKPFR',\n",
       " 'RFHRTS',\n",
       " 'T',\n",
       " 'QF',\n",
       " 'VWPLSGFWHICCSQNSFIY',\n",
       " 'VFQL',\n",
       " 'CRCSLAILLVISSAILGSCGLSLVLYKWHPFLQWLGCTSSLLLSTTYGRAMFISWMVAPLRLA',\n",
       " 'CAISAIVPHALSVQLLLMA',\n",
       " 'RDLSMSMQMEAVASARLTIGIVSIVTHFALVVHSLVMKLLVICHSSLKDQSTLLTSHRILLIVLL',\n",
       " 'KMARFTSTLTRLVKRPMRDIRSPILSI',\n",
       " 'TI',\n",
       " 'ELTTLKVHCLLMS',\n",
       " 'FLMASPNATSLLLSLLLCTTVS',\n",
       " 'CANLFCCLTKLLYQTLEIVLKFPLRCLMLMSTPFQQLLVFLWKNLRHLLLQLTAS',\n",
       " 'QRV',\n",
       " 'L',\n",
       " 'MVSFLHSCQLPDKVLLIPMLTQRMLLNVSNFHITLT',\n",
       " 'K',\n",
       " 'QVTVVTISCSPIIRLKT',\n",
       " 'RPEILAHVLTVMQGISMPK',\n",
       " 'QKVTMFHSSGM',\n",
       " 'KTTCLYLNSCVNKFVVLPRRTTYLLD',\n",
       " 'LVLQLDRLSMS',\n",
       " 'LLKSHSRVVRLLVLVLNLCLRPHYCAFLLHWFVISLCQYIHCQSMMVTQMKSLVTKPFRMVSLVTSFLLMIVLQINMLVLTHGLASVVVHTKMTKAAL',\n",
       " '',\n",
       " 'LLSLQERLVS',\n",
       " 'CLAYRVLC',\n",
       " 'EQSMVTSCIFYLVFLVLLATFATHLPNSLSIVILLPLLAFLLLSVQFLRMLWANLCHIVMTLIC',\n",
       " 'RVLFLIVSFVQTLVMCLWMVPSYSFLTLTWRVLLE',\n",
       " '',\n",
       " 'QLLMLSTVDMVHAKGQK',\n",
       " 'VFAYLPVVDGFLIMSITELYQEFSVVLMR',\n",
       " 'IS',\n",
       " 'LTSLLLLCNLWVL',\n",
       " 'MCLLQ',\n",
       " 'WLVVLLPYW',\n",
       " 'LVLPTTL',\n",
       " 'NSDVFLVSTTMLLLLMHFCF',\n",
       " 'CLSLYSVWYQLTAFCRESTQSFTCT',\n",
       " 'HSISPMMFHSWLTFNGLPCFLLLCLFG',\n",
       " 'QQSMYSVFL',\n",
       " 'STAIGSLTTILGKESCLMELHLVPSRRLLCVPFCSTRKCT',\n",
       " 'NCVARHCCHLHSITGILLYITSTSISVEP',\n",
       " 'ILPAIVKQLAAT',\n",
       " 'QRL',\n",
       " 'MTLATQVLMFSTNHHRHQSLLLFCRVVLGKWHSRQAKLKGAWYK',\n",
       " 'PVELQLLMDCGWMTQYTVQDMSFAQQKTCLILTMKICSFANPTIAFLFRLAMFNFVLLAILCKIVCLGLKLILLTLRHPSINLSVSNLVKHFQF',\n",
       " 'HATMVHHLVFISVP',\n",
       " 'DLIIPLKVLSLMDHVVVLVLTLIMIACLSAICIIWSFQQEYTLVLT',\n",
       " 'KVNSMVHLLTDKLHRLQVQTQP',\n",
       " 'H',\n",
       " 'MFWHGCMLLLSMVIGGFLIDSPLL',\n",
       " 'MTLTLWQ',\n",
       " 'STTMNL',\n",
       " 'HKIMLTYWDLFLLKQELPS',\n",
       " 'ICVLL',\n",
       " 'KSCCRMV',\n",
       " 'MVVLSLVALF',\n",
       " 'KMSLHHLMLLDNALVLPSKVSSRKLLRALIIGCF',\n",
       " 'LS',\n",
       " 'HHY',\n",
       " 'FLFKVHSGHCFSLFTRMLSCHLLLVLWQLLHVLCCLLSISTHSCACFCYLLLQQLLTLIWSTCLLAG',\n",
       " 'CVS',\n",
       " 'HGLNWLTLACLVIGLRIVLCMLQL',\n",
       " 'FCLFS',\n",
       " 'QLALFMMMLLDVFGH',\n",
       " '',\n",
       " 'MSLHLFTKSTMVML',\n",
       " 'IKLFPCGP',\n",
       " 'LFL',\n",
       " 'PLTILVSLRLSCF',\n",
       " 'LEL',\n",
       " 'CLCVLSITHCYLLLATPYSVSCLFIVS',\n",
       " 'AIVAAATLAFSVYSTVTSGLLLVFMTTWSLHKNLGI',\n",
       " 'TPRGFCLLRVVLMLSSLTLSCWVLEVNHVSRLLLYSLKCLT',\n",
       " 'SAHLWYCSRFFNNLE',\n",
       " 'SHLLNCGHNVYNSTMIFFLQKTQLKLSRRWFLFCLFCYPCRVL',\n",
       " 'TLIGCARKCSITVLLFRLLLQNLVLYHHMPLMPLPRRPMSRL',\n",
       " 'LMVILKSFSKS',\n",
       " 'RNL',\n",
       " 'MWLNLSLTVMLPCNASWKRWQIRL',\n",
       " 'PKCTNRQDLRTRGQK',\n",
       " 'LVLCKQCSSLCLGSLIMMHLTTLSTMRVMVVFHSTSYH',\n",
       " 'LQQPNSWLLSLIMVPTRTLVMVTPLHMHLHSGKSSKLLMRIARLFNLVKLTWTIHQIWLGLLLLQL',\n",
       " 'EPTQLLNYRIMN',\n",
       " 'VQ',\n",
       " 'HYDRCPVRLVPHKQLVLMTMHLPTITIRREVGLCWHYYQTTKISNGLDSLRVMVQVQFTQNWNHLVGLLQTHQKGLK',\n",
       " 'NTCTSSKA',\n",
       " 'TT',\n",
       " 'IEVWCWAV',\n",
       " 'LLQYVFRLEMLQKYLPIQLCFPSVLLQ',\n",
       " 'TLLKHIRIT',\n",
       " 'QVEDNQSPTV',\n",
       " 'RCCVHTLVQDRQLL',\n",
       " 'HQKLTWTKSPLVVLHVVCIVDATLTIQILKDSVT',\n",
       " 'KVSTSKYLPLVLMTQWVLHLETQSVPSAECGKVMAVVVTNSANP',\n",
       " 'CSLRMHQRF',\n",
       " 'TGLRCKCSPSYTVRHRH',\n",
       " 'Y',\n",
       " 'CRLQGF',\n",
       " 'YLQRKSCWFCKVPKN',\n",
       " 'LLSLPGEG',\n",
       " 'GRQFIRLLLCS',\n",
       " 'EAYYV',\n",
       " 'LPT',\n",
       " 'RDYL',\n",
       " 'LG',\n",
       " 'RLSSGCCP',\n",
       " 'LFQV',\n",
       " 'SRW',\n",
       " 'HGTTYITSASN',\n",
       " 'IHNG',\n",
       " 'FSLCSTSF',\n",
       " '',\n",
       " 'G',\n",
       " 'L',\n",
       " 'YIKRNTRHIQLL',\n",
       " '',\n",
       " '',\n",
       " 'LFQ',\n",
       " 'EGLV',\n",
       " 'LRRES',\n",
       " 'HLTRIC',\n",
       " 'LR',\n",
       " 'ACTPIIIKDCTILRCYA',\n",
       " 'CRHCRRTDIR',\n",
       " 'SGS',\n",
       " 'WELVRFR',\n",
       " 'FRTSSTRLRSSYCGFILLIADAHPHFD',\n",
       " 'GIGC',\n",
       " 'VPYGC',\n",
       " 'SRKTTY',\n",
       " 'VGFAEI',\n",
       " 'FYGRETLSLRPLF',\n",
       " 'ILGPDIPSQLY',\n",
       " 'LFG',\n",
       " '',\n",
       " 'VYPSLCKL',\n",
       " 'CVIFYCVSTYKFWTTSKKNICRWCSFCCFNWIPFS',\n",
       " 'VRSRT',\n",
       " 'SGCKLT',\n",
       " 'LASQFQGTFSVCC',\n",
       " 'SSYACSFWQFIAR',\n",
       " 'THYMLFSSCTNKQCCFSNCQTR',\n",
       " 'F',\n",
       " '',\n",
       " 'RLL',\n",
       " 'LCCV',\n",
       " 'RFL',\n",
       " 'GRKFC',\n",
       " 'TKTLLLCSGWQRCYQ',\n",
       " 'L',\n",
       " 'LLSL',\n",
       " 'SANNV',\n",
       " 'YQTTPIRS',\n",
       " 'SC',\n",
       " '',\n",
       " 'IL',\n",
       " 'LLRWWLY',\n",
       " 'CQPSNR',\n",
       " 'QSG',\n",
       " 'ISWFPI',\n",
       " '',\n",
       " 'MG',\n",
       " 'G',\n",
       " 'TLL',\n",
       " 'LNEL',\n",
       " 'GSRCTFRVY',\n",
       " 'A',\n",
       " 'CHPYYNSNES',\n",
       " 'VCH',\n",
       " 'CKE',\n",
       " 'SSHRSWCLYL',\n",
       " 'YYDK',\n",
       " 'TVSSEIIEVNSRH',\n",
       " 'RSYCGNWNKQVLRWLA',\n",
       " 'YVKNCLQ',\n",
       " 'CRNSTPYGLGLSKM',\n",
       " 'QSHA',\n",
       " 'HA',\n",
       " 'DNGLSCSCSQT',\n",
       " 'HLL',\n",
       " 'LITPFLQVS',\n",
       " 'RVCASIK',\n",
       " 'DGHVWRLTIC',\n",
       " 'TRWNIIR',\n",
       " 'CYNCLC',\n",
       " '',\n",
       " 'CL',\n",
       " 'HLSSCYSQCKCTSFN',\n",
       " 'W',\n",
       " '',\n",
       " 'DS',\n",
       " 'QVCPQSTTQAL',\n",
       " 'VSL',\n",
       " 'K',\n",
       " 'GC',\n",
       " 'S',\n",
       " 'IRG',\n",
       " 'VLRLPA',\n",
       " 'TFLHDDSF',\n",
       " '',\n",
       " 'CRCVL',\n",
       " 'Q',\n",
       " 'LCGSRFSS',\n",
       " 'H',\n",
       " 'EL',\n",
       " 'GSSLLSK',\n",
       " 'CVHV',\n",
       " 'GKMLD',\n",
       " 'D',\n",
       " 'PY',\n",
       " 'RTSRILLTAYNAS',\n",
       " 'TRR',\n",
       " 'LRVPALPRSIKNIRRRLFCR',\n",
       " 'YCQNRWYTYD',\n",
       " 'KVRVTGY',\n",
       " 'CLPTYKTS',\n",
       " 'SGVC',\n",
       " 'CLSLVFTIH',\n",
       " 'KVT',\n",
       " '',\n",
       " 'AYWPHVGHVFRNAN',\n",
       " '',\n",
       " '',\n",
       " 'HLTVLGT',\n",
       " 'VL',\n",
       " 'GYVHTTYSLAGCRCLCIVQFTDFTSLRCLY',\n",
       " 'ETIPMLQVLL',\n",
       " 'PCHFNITQISVVC',\n",
       " 'SLCLQCPRL',\n",
       " 'CH',\n",
       " 'CDTTVSRRYELLLQVT',\n",
       " 'ASH',\n",
       " 'FSIMC',\n",
       " 'WSGFWFIQKHMCRQ',\n",
       " 'QCH',\n",
       " 'LQCDSNM',\n",
       " 'LD',\n",
       " 'CWRLHTCQHLY',\n",
       " 'ETQAFRSRNAQSH',\n",
       " 'GNI',\n",
       " 'AVIWYCHCTRSTL',\n",
       " 'QRIASFMGGWKT',\n",
       " 'TTIEQKLCLYWLPCN',\n",
       " 'K',\n",
       " '',\n",
       " 'STDWRVHL',\n",
       " 'KR',\n",
       " 'LW',\n",
       " 'CCCVQRYYDIQVECW',\n",
       " 'LLCVDISHCNAT',\n",
       " 'CTYSSATRALCENYWLVPNTQHLR',\n",
       " 'VF',\n",
       " 'QCCKLSKGRHAKVLYTPRTTWYW',\n",
       " 'ESFCHRTCSLLPICSHSVYGMLSCSC',\n",
       " 'CPM',\n",
       " 'KGIKIFAHR',\n",
       " 'M',\n",
       " '',\n",
       " 'NHTCACARRVF',\n",
       " '',\n",
       " 'IQSEFNTRTVCFLHCKCIARNNC',\n",
       " 'HCSL',\n",
       " '',\n",
       " 'NLYGY',\n",
       " 'L',\n",
       " 'LECCQC',\n",
       " 'TSCKTLRLYWRSCSITSPPHIAD',\n",
       " 'RHTRTRIF',\n",
       " 'FSVQTYENNRSRHVPWNLSPLSC',\n",
       " 'NC',\n",
       " 'HCECFSL',\n",
       " 'Q',\n",
       " 'AKSTQG',\n",
       " 'VSSMLQNVLQRCYYT',\n",
       " 'CFICNQQTSNRRCKRISYTQSCLEKSCFYLTL',\n",
       " 'FTERCSFKNLRIAYADC',\n",
       " 'FITGF',\n",
       " 'I',\n",
       " 'LCHIHTNY',\n",
       " 'NSTLL',\n",
       " 'CQPLQCGYHKGKNWHFVHNV',\n",
       " '',\n",
       " 'RSL',\n",
       " 'QTAIYKSRNTTSQCGYITSRKCNWTF',\n",
       " 'GL',\n",
       " '',\n",
       " 'DHYWSSSYTGTYTPQR',\n",
       " 'YKVQD',\n",
       " 'RIMC',\n",
       " 'HTRHTKGHDLP',\n",
       " 'THLYDGFQNELPSQWLP',\n",
       " 'YVYHPRRSYSSRSCVDWL',\n",
       " 'CRGLSCN',\n",
       " 'RCCGY',\n",
       " 'PTSPARIFYRC',\n",
       " 'LSSCTDWLC',\n",
       " 'H',\n",
       " 'K',\n",
       " 'HRIHQS',\n",
       " 'CKTSTR',\n",
       " 'PV',\n",
       " 'TSYTTHV',\n",
       " 'RLALECSAY',\n",
       " 'DSTNAQ',\n",
       " 'YTERIVRQSRVRPLGAWL',\n",
       " 'AYINEVLCQDWT',\n",
       " 'KNVLSV',\n",
       " 'QTCNLLFYFIRYLCLLESFCGF',\n",
       " 'LCL',\n",
       " 'PIYD',\n",
       " 'CSAVGLYG',\n",
       " 'PSE',\n",
       " 'P',\n",
       " 'PTLPGTWKCTCG',\n",
       " 'L',\n",
       " 'CYHD',\n",
       " 'MFSSP',\n",
       " 'VLC',\n",
       " 'AR',\n",
       " 'LVC',\n",
       " 'IPYYRR',\n",
       " 'TEG',\n",
       " 'FCLQKSTTHGCEVCIAC',\n",
       " '',\n",
       " 'VSSSS',\n",
       " 'HWKSKGYQVCASG',\n",
       " 'SRMEVLRCSAM',\n",
       " '',\n",
       " 'QSLQNRGTLLFLCYTSR',\n",
       " 'IH',\n",
       " 'WCLFVLEL',\n",
       " 'R',\n",
       " 'SLPSQCNCV',\n",
       " 'V',\n",
       " 'HKSLVKLELTRL',\n",
       " 'WW',\n",
       " 'FVCE',\n",
       " 'ACIPHSSFR',\n",
       " 'KCIY',\n",
       " 'FKAIAFLLLF',\n",
       " '',\n",
       " 'SL',\n",
       " 'VSWQTSSVGY',\n",
       " 'LCSTQICYVYYTMQFRWCCLQTPCK',\n",
       " 'VPTVLGCI',\n",
       " 'YDDFCWI',\n",
       " 'PMDLQTI',\n",
       " 'YL',\n",
       " 'PVEYIYQVTEFRKCGL',\n",
       " 'CC',\n",
       " '',\n",
       " 'RTL',\n",
       " 'WTRRRSTCFHH',\n",
       " '',\n",
       " 'CCLHKGRWY',\n",
       " 'CGDL',\n",
       " 'K',\n",
       " 'DNTSC',\n",
       " 'CCI',\n",
       " 'ALG',\n",
       " 'A',\n",
       " 'H',\n",
       " 'TSARD',\n",
       " 'DTQ',\n",
       " 'FGC',\n",
       " 'YRC',\n",
       " 'YCNLGLQKRSPSTCIYNRCLHND',\n",
       " 'HCQETY',\n",
       " 'ECLFFTYCLV',\n",
       " 'W',\n",
       " 'SGRTGRPF',\n",
       " 'KRP',\n",
       " 'WCFNNRRFSQRSNTFKGTSTS',\n",
       " 'RQWSHINWRISKNTV',\n",
       " 'LL',\n",
       " 'ESRRHYSTVA',\n",
       " 'NLLYSEQRLRGF',\n",
       " 'AQITNGN',\n",
       " 'LSRARYG',\n",
       " 'IHTAI',\n",
       " 'ARGLCLRTHRLWRFQSWTTWRSSFNDRLSQALTRFTT',\n",
       " 'IRGFYPYGQHSEKLLHNRCANRFIKMCVFCD',\n",
       " 'SFT',\n",
       " '',\n",
       " 'LCRDNKVTRFVSDFKSGQGYN',\n",
       " 'LC',\n",
       " 'NFIHALV',\n",
       " 'GWTC',\n",
       " 'NLLPKTTSKSSVATRCCDA',\n",
       " 'LVQDAKNAS',\n",
       " 'KV',\n",
       " 'PSELW',\n",
       " 'KCCYTKRNNDECRKVYSTVSILKYTYFSCTLQHESYSLWCWL',\n",
       " '',\n",
       " 'RSCTRYSCAQTMVANWHTTCRFRS',\n",
       " '',\n",
       " 'LRLRRRFYFNWRLCNSTYG',\n",
       " '',\n",
       " 'MGPYY',\n",
       " 'RYV',\n",
       " 'P',\n",
       " 'DQTCDKRE',\n",
       " 'L',\n",
       " 'RRVFHLSVWIYKAKTSPGWFYSCKDNRAFLEC',\n",
       " 'PLQAYGPFLMVDSFCYKCKCIIIGSIFNWG',\n",
       " 'LSWQAEGTN',\n",
       " 'WLYHAC',\n",
       " 'LHFLEEHKSYPVVFLFTL',\n",
       " 'HEQISS',\n",
       " 'IKRNCCNVS',\n",
       " 'GESNQ',\n",
       " 'YDLFSSGKR',\n",
       " 'AYH',\n",
       " 'RKQQSCGFK',\n",
       " 'YSC',\n",
       " 'QLNEHVYFLIISYSH',\n",
       " 'W',\n",
       " '',\n",
       " 'P',\n",
       " 'PVHHF',\n",
       " '',\n",
       " 'CSSS',\n",
       " 'LHSTYFIYEGGLLS',\n",
       " '',\n",
       " 'NF',\n",
       " 'IRHSLFNSGFISSILF',\n",
       " 'CYRVSYY',\n",
       " 'SYVWQPCHTF',\n",
       " 'GWYLFCCHREIKCCPWLGFWFYHEQQVTVGDYY',\n",
       " 'QFY',\n",
       " 'CCYTSM',\n",
       " 'L',\n",
       " 'IV',\n",
       " 'QPFLCCF',\n",
       " 'THGYTDTYYDIR',\n",
       " 'CI',\n",
       " 'LHFRVHI',\n",
       " 'CLFA',\n",
       " 'CFRKVR',\n",
       " 'F',\n",
       " 'TLTRVCV',\n",
       " 'K',\n",
       " 'RWVSLCL',\n",
       " 'GLSTYRCSS',\n",
       " 'STFWF',\n",
       " 'HFETYF',\n",
       " 'VASWY',\n",
       " 'HYKF',\n",
       " 'SHSYSLFTCSRHLGHVSCSLFCWLFKANYIYAQV',\n",
       " '',\n",
       " 'KWYNHRCC',\n",
       " 'LFSKSTC',\n",
       " 'TQMLC',\n",
       " 'EL',\n",
       " 'D',\n",
       " 'QRNLPDL',\n",
       " 'FQGCSLRRCCEIP',\n",
       " 'YYKLVSFWRGF',\n",
       " 'CY',\n",
       " 'IPFCLCMGEKKNF',\n",
       " 'LCC',\n",
       " 'LLCALQLNIFFNL',\n",
       " 'VLWRFCH',\n",
       " 'VE',\n",
       " 'SLLLQCLCRFFCSQGR',\n",
       " 'CKTNSARTNWCYC',\n",
       " 'L',\n",
       " 'L',\n",
       " 'IAR',\n",
       " 'FHGLCPCLEY',\n",
       " 'EH',\n",
       " 'CYFNW',\n",
       " 'L',\n",
       " 'L',\n",
       " 'I',\n",
       " 'VS',\n",
       " 'TWQA',\n",
       " 'AL',\n",
       " 'ERHI',\n",
       " 'CAFLP',\n",
       " 'WQTLHPTCS',\n",
       " 'LLLAIK',\n",
       " 'LWFLHHYWHWLPTLQSCSTFF',\n",
       " 'TFKCTGHGLWTKIIH',\n",
       " 'PY',\n",
       " 'EPVCQF',\n",
       " 'F',\n",
       " 'WTHWYWCVNSFFKEISTISTIWP',\n",
       " 'CF',\n",
       " 'FH',\n",
       " 'FRSRS',\n",
       " 'NI',\n",
       " 'NIRHFTLRFWGCKCNYTWNKCFI',\n",
       " 'SCCSISRC',\n",
       " 'LH',\n",
       " 'CFYSNSCRSTHTSLAHIFYWKQCIPDSSRLSYRS',\n",
       " 'ACRHFL',\n",
       " 'VRHSYWSWHLC',\n",
       " 'LPYSFFIT',\n",
       " 'Y',\n",
       " 'PKIYCGLYYVFRC',\n",
       " '',\n",
       " 'FNCLL',\n",
       " '',\n",
       " 'HHCYTY',\n",
       " 'LFN',\n",
       " 'HYYRSNACFYG',\n",
       " 'NLRRL',\n",
       " 'YVHLRRFY',\n",
       " 'MC',\n",
       " 'FASPIW',\n",
       " 'LLHTTKSCTLRYCC',\n",
       " 'TGSQHT',\n",
       " 'SVRSSQTNVQNPNFEIFWWF',\n",
       " 'FFTNIT',\n",
       " 'PSKAN',\n",
       " 'EVFY',\n",
       " 'GLAL',\n",
       " '',\n",
       " 'GDTR',\n",
       " 'CWLHEAIWRMPR',\n",
       " 'Y',\n",
       " 'C',\n",
       " 'RSHLCAEVQWTYSVATSAH',\n",
       " '',\n",
       " 'YDCCLHCCSS',\n",
       " 'WYCHCWMDIWCWRCSSNTFCYANGI',\n",
       " 'VQWHWSYPKCSL',\n",
       " 'EPKTNRQPI',\n",
       " 'QGD',\n",
       " 'SNSRITYNNINCIGQAARRC',\n",
       " 'PECSSIKHTC',\n",
       " 'TT',\n",
       " 'L',\n",
       " 'FWCNFKCAK',\n",
       " 'YPFAT',\n",
       " '',\n",
       " 'SRGGGTN',\n",
       " 'QVNYRQTSKPSNLCNTTTNQGC',\n",
       " 'NQGFC',\n",
       " 'SCCY',\n",
       " 'NV',\n",
       " 'VCSWTIKKS',\n",
       " 'LLWKGLPPYVLPTSSPAWCCLPTCHVCAIPGEELHHSASNLS',\n",
       " 'RQSILPS',\n",
       " 'RCFCV',\n",
       " 'WHFLVYYTEELLFSTNNYYRQYICLRKL',\n",
       " 'CRYWHH',\n",
       " 'QHSL',\n",
       " 'SSAT',\n",
       " 'A',\n",
       " 'LIQRRAGQVLQKSYITRC',\n",
       " 'SWRHFRH',\n",
       " 'RFCRQHSKRN',\n",
       " 'PPQ',\n",
       " 'GR',\n",
       " 'KFK',\n",
       " 'ITH',\n",
       " 'PSRIGKI',\n",
       " 'AIY',\n",
       " 'MALVCLARLHCWTNCHRHGYNLALLHD',\n",
       " 'LLQLPQGCMLLWFLLQV',\n",
       " '',\n",
       " 'G',\n",
       " 'L',\n",
       " 'ASSQGCQITLHINELMDLFMRFFTLRSITAQPVKIDNASPASTVHATATIPLQASLPFGWLVIGVAFLAVFQSATKIIALNKRWQLALYKGFQFICNLLLLFVTIYSHLLLVAAGMEAQFLYLYALIYFLQCINACRIIMRCWLCWKCKSKNPLLYDANYFVCWHTHNYDYCIPYNSVTDTIVVTEGDGISTPKLKEDYQIGGYSEDRHSGVKDYVVVHGYFTEVYYQLESTQITTDTGIENATFFIFNKLVKDPPNVQIHTIDGSSGVANPAMDPIYDEPTTTTSVPL',\n",
       " 'AQESEYELMYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPTVYVYSRVKNLNSSEGVPDLLV',\n",
       " 'TN',\n",
       " 'LLLLFCLEL',\n",
       " 'HCLSWQTTVLLPLRSLNNSWNNGT',\n",
       " '',\n",
       " '',\n",
       " 'VSYS',\n",
       " 'PGLCYYNLPILIGTGFCT',\n",
       " '',\n",
       " 'SLFSSGSCGQ',\n",
       " 'HLLVLCLLLSTELIG',\n",
       " 'LAGLRLQWLVL',\n",
       " 'A',\n",
       " 'CGLATSLLPSGCLLVPAQCGHSTQKQTFFSMCLSGGQL',\n",
       " 'PDRSWKVNLSLVL',\n",
       " 'SFVVTCEWPDTP',\n",
       " 'GAVTLRTCQKRSLWLHHERFLITN',\n",
       " 'ERRSV',\n",
       " 'ALIQVLLHTTATVLETIN',\n",
       " 'IQTTPVATTILLC',\n",
       " 'YSK',\n",
       " 'QQMFHLVDFQVTIAEILIIIMRTFRIAIWNLDVIISSIVRQLFKPLTKKNYSELDDEEPMELDYP',\n",
       " 'NEHENYSLPDIDCIYILRAISLSGVC',\n",
       " 'RYDCTTKRTLPIRNIRGQFTISPSC',\n",
       " 'Q',\n",
       " 'ICTNLH',\n",
       " 'HTLCFCLC',\n",
       " 'RYSTYLSAACKISFTKTFHQTRGGSTRALLATFSHCCCSSIFNTLLHH',\n",
       " 'EKDRMNELTLIDFYLCFLAFLLFLVLIMLIIFWFSLEIQDLEEPCTKV',\n",
       " 'TNMKLLIVLTCISLCSCICTVVQRCASNKPHVLEDPCKVQH',\n",
       " 'G',\n",
       " 'YL',\n",
       " 'HCLALCSRKGFTFS',\n",
       " 'MAHYGSNMHT',\n",
       " 'CYYQLSRSSWWCAYS',\n",
       " 'VLVPS',\n",
       " 'RSPNCCI',\n",
       " 'RRTCCFK',\n",
       " 'TNKLKCLIMDPNQTNVVPPALHLVDPQIQLTITRMEDAMGQGQNSADPKVYPIILRLGSQLSLSMARRNLDSLEARAFQSTPIVVQMTKLATTEELPDEFVVVTAK',\n",
       " 'KSSAPDGTSIT',\n",
       " 'ELAQKLHFPTALTKKASYGLQLREP',\n",
       " 'IHPKTTLAPAILITMLPPCYNFLKEQHCQKASTQREAEAAVKPLLAPHHVVAVIQEIQLLAAVGEILLLEWLAEVVKLPSRYCC',\n",
       " 'TD',\n",
       " 'TSLRAKFLVKANNNKAKLSLRNLLLRHLKSLAKNVLPQNSTTSLKHLGDVVQNKPKEISGTKT',\n",
       " 'SDKELITNIGRKLHNLLQVPLHSLECHALAWKSHLREHG',\n",
       " 'LIMEPLNWMTKIHNSKTTSYC',\n",
       " 'TSTLTHTKHSHQQSLKRTKRKRLMKLSLCRRDKRSSPL',\n",
       " 'LFFLRLTWMISPDNFKIP',\n",
       " 'VELLLIQLRHKHS',\n",
       " '',\n",
       " 'PHKADGLCKRFRNSVYDT',\n",
       " 'STLVQNEFS',\n",
       " 'LNSTSRFS',\n",
       " 'L',\n",
       " 'SHIAIFNQCVTLGRT',\n",
       " 'KSHHIFIEATRSTIEGTVNNARESCLYGRALMCKINFSSAIPM',\n",
       " 'F',\n",
       " '',\n",
       " ...]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "polypeptides = aa.split(\"*\")\n",
    "\n",
    "polypeptides"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1578"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(polypeptides)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['PKGKMESLVLGVNEKTHVQLSLPVLQVRDVLVRGFGDSVEEALSEAREHLKNGTCGLVELEKGVLPQLEQPYVFIKRSDALSTNHGHKVVELVAEMDGIQYGRSGITLGVLVPHVGETPIAYRNVLLRKNGNKGAGGHSYGIDLKSYDLGDELGTDPIEDYEQNWNTKHGSGALRELTRELNGGAVTRYVDNNFCGPDGYPLDCIKDFLARAGKSMCTLSEQLDYIESKRGVYCCRDHEHEIAWFTERSDKSYEHQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRIRSVYPVASPQECNNMHLSTLMKCNHCDEVSWQTCDFLKATCEHCGTENLVIEGPTTCGYLPTNAVVKMPCPACQDPEIGPEHSVADYHNHSNIETRLRKGGRTRCFGGCVFAYVGCYNKRAYWVPRASADIGSGHTGITGDNVETLNEDLLEILSRERVNINIVGDFHLNEEVAIILASFSASTSAFIDTIKSLDYKSFKTIVESCGNYKVTKGKPVKGAWNIGQQRSVLTPLCGFPSQAAGVIRSIFARTLDAANHSIPDLQRAAVTILDGISEQSLRLVDAMVYTSDLLTNSVIIMAYVTGGLVQQTSQWLSNLLGTTVEKLRPIFEWIEAKLSAGVEFLKDAWEILKFLITGVFDIVKGQIQVASDNIKDCVKCFIDVVNKALEMCIDQVTIAGAKLRSLNLGEVFIAQSKGLYRQCIRGKEQLQLLMPLKAPKEVTFLEGDSHDTVLTSEEVVLKNGELEALETPVDSFTNGAIVGTPVCVNGLMLLEIKDKEQYCALSPGLLATNNVFRLKGGAPIKGVTFGEDTVWEVQGYKNVRITFELDERVDKVLNEKCSVYTVESGTEVTEFACVVAEAVVKTLQPVSDLLTNMGIDLDEWSVATFYLFDDAGEENFSSRMYCSFYPPDEEEEDDAECEEEEIDETCEHEYGTEDDYQGLPLEFGASAETVRVEEEEEEDWLDDTTEQSEIEPEPEPTPEEPVNQFTGYLKLTDNVAIKCVDIVKEAQSANPMVIVNAANIHLKHGGGVAGALNKATNGAMQKESDDYIKLNGPLTVGGSCLLSGHNLAKKCLHVVGPNLNAGEDIQLLKAAYENFNSQDILLAPLLSAGIFGAKPLQSLQVCVQTVRTQVYIAVNDKALYEQVVMDYLDNLKPRVEAPKQEEPPNTEDSKTEEKSVVQKPVDVKPKIKACIDEVTTTLEETKFLTNKLLLFADINGKLYHDSQNMLRGEDMSFLEKDAPYMVGDVITSGDITCVVIPSKKAGGTTEMLSRALKKVPVDEYITTYPGQGCAGYTLEEAKTALKKCKSAFYVLPSEAPNAKEEILGTVSWNLREMLAHAEETRKLMPICMDVRAIMATIQRKYKGIKIQEGIVDYGVRFFFYTSKEPVASIITKLNSLNEPLVTMPIGYVTHGFNLEEAARCMRSLKAPAVVSVSSPDAVTTYNGYLTSSSKTSEEHFVETVSLAGSYRDWSYSGQRTELGVEFLKRGDKIVYHTLESPVEFHLDGEVLSLDKLKSLLSLREVKTIKVFTTVDNTNLHTQLVDMSMTYGQQFGPTYLDGADVTKIKPHVNHEGKTFFVLPSDDTLRSEAFEYYHTLDESFLGRYMSALNHTKKWKFPQVGGLTSIKWADNNCYLSSVLLALQQLEVKFNAPALQEAYYRARAGDAANFCALILAYSNKTVGELGDVRETMTHLLQHANLESAKRVLNVVCKHCGQKTTTLTGVEAVMYMGTLSYDNLKTGVSIPCVCGRDATQYLVQQESSFVMMSAPPAEYKLQQGTFLCANEYTGNYQCGHYTHITAKETLYRIDGAHLTKMSEYKGPVTDVFYKETSYTTTIKPVSYKLDGVTYTEIEPKLDGYYKKDNAYYTEQPIDLVPTQPLPNASFDNFKLTCSNTKFADDLNQMTGFTKPASRELSVTFFPDLNGDVVAIDYRHYSASFKKGAKLLHKPIVWHINQATTKTTFKPNTWCLRCLWSTKPVDTSNSFEVLAVEDTQGMDNLACESQQPTSEEVVENPTIQKEVIECDVKTTEVVGNVILKPSDEGVKVTQELGHEDLMAAYVENTSITIKKPNELSLALGLKTIATHGIAAINSVPWSKILAYVKPFLGQAAITTSNCAKRLAQRVFNNYMPYVFTLLFQLCTFTKSTNSRIRASLPTTIAKNSVKSVAKLCLDAGINYVKSPKFSKLFTIAMWLLLLSICLGSLICVTAAFGVLLSNFGAPSYCNGVRELYLNSSNVTTMDFCEGSFPCSICLSGLDSLDSYPALETIQVTISSYKLDLTILGLAAEWVLAYMLFTKFFYLLGLSAIMQVFFGYFASHFISNSWLMWFIISIVQMAPVSAMVRMYIFFASFYYIWKSYVHIMDGCTSSTCMMCYKRNRATRVECTTIVNGMKRSFYVYANGGRGFCKTHNWNCLNCDTFCTGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVAVKNGALHLYFDKAGQKTYERHPLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCDESASKSASVYYSQLMCQPILLLDQALVSDVGDSTEVSVKMFDAYVDTFSATFSVPMEKLKALVATAHSELAKGVALDGVLSTFVSAARQGVVDTDVDTKDVIECLKLSHHSDLEVTGDSCNNFMLTYNKVENMTPRDLGACIDCNARHINAQVAKSHNVSLIWNVKDYMSLSEQLRKQIRSAAKKNNIPFRLTCATTRQVVNVITTKISLKGGKIVSTCFKLMLKATLLCVLAALVCYIVMPVHTLSIHDGYTNEIIGYKAIQDGVTRDIISTDDCFANKHAGFDAWFSQRGGSYKNDKSCPVVAAIITREIGFIVPGLPGTVLRAINGDFLHFLPRVFSAVGNICYTPSKLIEYSDFATSACVLAAECTIFKDAMGKPVPYCYDTNLLEGSISYSELRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDAEYCRHGTCERSEVGICLSTSGRWVLNNEHYRALSGVFCGVDAMNLIANIFTPLVQPVGALDVSASVVAGGIIAILVTCAAYYFMKFRRVFGEYNHVVAANALLFLMSFTILCLVPAYSFLPGVYSVFYLYLTFYFTNDVSFLAHLQWFAMFSPIVPFWITAIYVFCISLKHCHWFFNNYLRKRVMFNGVTFSTFEEAALCTFLLNKEMYLKLRSETLLPLTQYNRYLALYNKYKYFSGALDTTSYREAACCHLAKALNDFSNSGADVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTFQGKFKKIVKGTHHWMLLTFLTSLLILVQSTQWSLFFFVYENAFLPFTLGIMAIAACAMLLVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLELADTSLSGYRLKDCVMYASALVLLILMTARTVYDDAARRVWTLMNVITLVYKVYYGNALDQAISMWALVISVTSNYSGVVTTIMFLARAIVFVCVEYYPLLFITGNTLQCIMLVYCFLGYCCCCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKSSIDAFKLNIKLLGIGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINRLCEEMLDNRATLQAIASEFSSLPSYAAYATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVVDADSKIVQLSEINMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNNSKGGRFVLALLSDHQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDPAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLRNTVCTVCGMWKGYGCSCDQLREPLMQSADASTFLNGFAV',\n",
       " 'SGLLKSGLLLILLLLKCLSVFLDNQKELTFVERATTLCPSHKQPRMVLSSYMSRMCHPRRGTSPQRQQFVMKAKHTSLVKVFLCLMALLGLLHRGTSFLHK',\n",
       " 'SSGLNELTIIIILFGTLTLLIMADNGTITVEELKQLLEQWNLVIGFLFLAWIMLLQFAYSNRNRFLYIIKLVFLWLLWPVTLACFVLAAVYRINWVTGGIAIAMACIVGLMWLSYFVASFRLFARTRSMWSFNPETNILLNVPLRGTIVTRPLMESELVIGAVIIRGHLRMAGHSLGRCDIKDLPKEITVATSRTLSYYKLGASQRVGTDSGFAAYNRYRIGNYKLNTDHAGSNDNIALLVQ',\n",
       " 'INEQIKMSDNGPQSNQRSAPRITFGGPTDSTDNNQNGGRNGARPKQRRPQGLPNNTASWFTALTQHGKEELRFPRGQGVPINTNSGPDDQIGYYRRATRRVRGGDGKMKELSPRWYFYYLGTGPEASLPYGANKEGIVWVATEGALNTPKDHIGTRNPNNNAATVLQLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRGNSRNSTPGSSRGNSPARMASGGGETALALLLLDRLNQLESKVSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKQYNVTQAFGRRGPEQTQGNFGDQDLIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYHGAIKLDDKDPQFKDNVILLNKHIDAYKTFPPTEPKKDKKKKTDEAQPLPQRQKKQPTVTLLPAADMDDFSRQLQNSMSGASADSTQA',\n",
       " 'VTSLALIPLKIMNKTGTLSMAVVHSVNSLVSSMEVQSLAMSTTISVAQMGTLLIASKIFSHARASQCALFPNNLITSSRREVSTAAVTMSMKLPGSLSALIRATSTRHPSKLRVPRNLTLSKGNAQSLCFLLTQKSKSFNHVLKRKRLRVSWGVYALCTLLHLHRSVTICTCLP',\n",
       " 'LHSTYLMMLVKKTFHHVCIVPFTLQMRKKRTMQSVRKKKLMKPVNMSTVQRMIIKVSLWNLVPQLKQFELRKKKRKTGWMILLSNQRLSQNQNLHLKNQLISLLVI',\n",
       " 'ASSQGCQITLHINELMDLFMRFFTLRSITAQPVKIDNASPASTVHATATIPLQASLPFGWLVIGVAFLAVFQSATKIIALNKRWQLALYKGFQFICNLLLLFVTIYSHLLLVAAGMEAQFLYLYALIYFLQCINACRIIMRCWLCWKCKSKNPLLYDANYFVCWHTHNYDYCIPYNSVTDTIVVTEGDGISTPKLKEDYQIGGYSEDRHSGVKDYVVVHGYFTEVYYQLESTQITTDTGIENATFFIFNKLVKDPPNVQIHTIDGSSGVANPAMDPIYDEPTTTTSVPL',\n",
       " 'TNKLKCLIMDPNQTNVVPPALHLVDPQIQLTITRMEDAMGQGQNSADPKVYPIILRLGSQLSLSMARRNLDSLEARAFQSTPIVVQMTKLATTEELPDEFVVVTAK',\n",
       " 'PTPRTLDAVCGCINVFKRVCGVSAARLTPCGTGTSTDVVYRAFDIYNEKVAGFAKFLKTNCCRFQEKDEEGNLLDSYFVVKRHTMSNYQHEETIYNLVKDCPAVAVHDFFKFRVDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQSLLKTVQFCDAMRDAGIVGVLTLDNQDLNGNWYDFGDFVQVAPGCGVPIVDSYYSLLMPILTLTRALAAESHMDADLAKPLIKWDLLKYDFTEERLCLFDRYFKYWDQTYHPNCINCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVETPHLMGWDYPKCDRAMPNMLRIMASLVLARKHNTCCNLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDHEFVDEFYAYLRKHFSMMILSDDAVVCYNSNYAAQGLVASIKNFKAVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKIGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKIITGLHPTQAPTHLSVDIKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATRDAVGTNLPLQLGFSTGVNLVAVPTGYVDTENNTEFTRVNAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKGLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDKRATCFSTSSDTYACWNHSVGFDYVYNPFMIDVQQWGFTGNLQSNHDQHCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWSVEYPIIGDELRVNSACRKVQHMVVKSALLADKFPVLHDIGNPKAIKCVPQAEVEWKFYDAQPCSDKAYKIEELFYSYATHHDKFTDGVCLFWNCNVDRYPANAIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFTNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRQYLDAYNMMISAGFSLWIYKQFDTYNLWNTFTRLQSLENVAYNVVNKGHFDGHAGEAPVSIINNAVYTKVDGIDVEIFENKTTLPVNVAFELWAKRNIKPVPEIKILNNLGVDIAANTVIWDYKREAPAHVSTIGVCTMTDIAKKPTESACSSLTVLFDGRVEGQVDLFRNARNGVLITEGSVKGLTPSKGPAQASVNGVTLIGESVKTQFNYFKKVDGIIQQLPETYFTQSRDLEDFKPRSQMETDFLELAMDEFIQRYKLEGYAFEHIVYGDFSHGQLGGLHLMIGLAKRSQDSPLKLEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVISKVVKVTIDYAEISFMLWCKDGHVETFYPKLQASQAWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPRTKHVTKENDSKEGFFTYLCGFIKQKLALGGSIAVKITEHSWNADLYKLMGHFSWWTAFVTNVNASSSEAFLIGANYLGKPKEQIDGYTMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKENQINDMIYSLLEKGRLIIRENNRVVVSSDILVNN',\n",
       " 'TNMFIFLLFLTLTSGSDLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLGINITNFRAILTAFSPAQDIWGTSAAAYFVGYLKPTTFMLKYDENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDPKTSEILDISPCAFGGVSVITPGTNASSEVAVLYQDVNCTDVSTAIHADQLTPAWRIYSTGNNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASYHTVSLLRSTSQKSIVAYTMSLGADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVDCNMYICGDSTECANLLLQYGSFCTQLNRALSGIAAEQDRNTREVFAQVKQMYKTPTLKYFGGFNFSQILPDPLKPTKRSFIEDLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDNTFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTSCCSCLKGACSCGSCCKFDEDDSEPVLKGVKLHYT',\n",
       " 'DVGFVGSANPRTHYFMMPTTLFAGTHITMTTVYHITVSQIQLSLLKVTAFQHQNSKKTTKLVVILRIGTQVLKTMSLYMAISPKFTTSLSLHKLLQTLVLKMLHSSSLTSLLKTHRMCKYTQSTALQELLIQQWIQFMMSRRRLLACLCKHKKVSTNLCTHSFRKKQVR',\n",
       " 'IIHKTNMKIILFLTLIVFTSCELYHYQECVRGTTVLLKEPCPSGTYEGNSPFHPLADNKFALTCTSTHFAFACADGTRHTYQLRARSVSPKLFIRQEEVQQELYSPLFLIVAALVFLILCFTIKRKTE']"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "long_polypep_chains = list(filter(lambda x: len(x) > 100, aa.split(\"*\")))\n",
    "\n",
    "long_polypep_chains"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "12"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(long_polypep_chains)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This is the genome organisation of Sars-Cov-2. _(Genome organisation is the linear order of genetic material (DNA/RNA) and its division into segments performing some specific function.)_ \n",
    "\n",
    "> Note: ORF stands for 'Open Reading Frame', the reading frame in which protein starts with M and ends with *.\n",
    "\n",
    "Source: https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2#Phylogenetics_and_taxonomy\n",
    "\n",
    "<img src=\"./images_copy/SARS-CoV-2-genome.png\" width=\"900\">\n",
    "\n",
    "Let's see if we can extract all the segments as mentioned here. We will refer to the following source again. Source: https://www.ncbi.nlm.nih.gov/nuccore/NC_045512\n",
    "\n",
    "Also, if you will see the following genome organisation of Sars-Cov (old coronavirus), you will notice - the structure is very similar to Sars-CoV-2. _(Ignore the detailing given in the structure.)_\n",
    "\n",
    "<img src=\"./images_copy/SARS-CoV-1-genome.png\" width=\"800\">"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open('/Users/pranjal27bhardwaj/Desktop/corona/sars_cov2_data _c/genome/sars_cov2_genome.txt', 'r') as file:\n",
    "    corona = file.read()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "for s in \"\\n01234567789 \":\n",
    "    corona = corona.replace(s, \"\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIALKGGKIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNGFAV'"
      ]
     },
     "execution_count": 44,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# https://www.ncbi.nlm.nih.gov/protein/1802476803 -  \n",
    "# Orf1a polyprotein, found in Sars-Cov-2 (new Covid 19)\n",
    "orf1a_poly_v2 = translation(corona[265:13483], True)\n",
    "\n",
    "orf1a_v2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'MESLVLGVNEKTHVQLSLPVLQVRDVLVRGFGDSVEEALSEAREHLKNGTCGLVELEKGVLPQLEQPYVFIKRSDALSTNHGHKVVELVAEMDGIQYGRSGITLGVLVPHVGETPIAYRNVLLRKNGNKGAGGHSYGIDLKSYDLGDELGTDPIEDYEQNWNTKHGSGALRELTRELNGGAVTRYVDNNFCGPDGYPLDCIKDFLARAGKSMCTLSEQLDYIESKRGVYCCRDHEHEIAWFTERSDKSYEHQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRIRSVYPVASPQECNNMHLSTLMKCNHCDEVSWQTCDFLKATCEHCGTENLVIEGPTTCGYLPTNAVVKMPCPACQDPEIGPEHSVADYHNHSNIETRLRKGGRTRCFGGCVFAYVGCYNKRAYWVPRASADIGSGHTGITGDNVETLNEDLLEILSRERVNINIVGDFHLNEEVAIILASFSASTSAFIDTIKSLDYKSFKTIVESCGNYKVTKGKPVKGAWNIGQQRSVLTPLCGFPSQAAGVIRSIFARTLDAANHSIPDLQRAAVTILDGISEQSLRLVDAMVYTSDLLTNSVIIMAYVTGGLVQQTSQWLSNLLGTTVEKLRPIFEWIEAKLSAGVEFLKDAWEILKFLITGVFDIVKGQIQVASDNIKDCVKCFIDVVNKALEMCIDQVTIAGAKLRSLNLGEVFIAQSKGLYRQCIRGKEQLQLLMPLKAPKEVTFLEGDSHDTVLTSEEVVLKNGELEALETPVDSFTNGAIVGTPVCVNGLMLLEIKDKEQYCALSPGLLATNNVFRLKGGAPIKGVTFGEDTVWEVQGYKNVRITFELDERVDKVLNEKCSVYTVESGTEVTEFACVVAEAVVKTLQPVSDLLTNMGIDLDEWSVATFYLFDDAGEENFSSRMYCSFYPPDEEEEDDAECEEEEIDETCEHEYGTEDDYQGLPLEFGASAETVRVEEEEEEDWLDDTTEQSEIEPEPEPTPEEPVNQFTGYLKLTDNVAIKCVDIVKEAQSANPMVIVNAANIHLKHGGGVAGALNKATNGAMQKESDDYIKLNGPLTVGGSCLLSGHNLAKKCLHVVGPNLNAGEDIQLLKAAYENFNSQDILLAPLLSAGIFGAKPLQSLQVCVQTVRTQVYIAVNDKALYEQVVMDYLDNLKPRVEAPKQEEPPNTEDSKTEEKSVVQKPVDVKPKIKACIDEVTTTLEETKFLTNKLLLFADINGKLYHDSQNMLRGEDMSFLEKDAPYMVGDVITSGDITCVVIPSKKAGGTTEMLSRALKKVPVDEYITTYPGQGCAGYTLEEAKTALKKCKSAFYVLPSEAPNAKEEILGTVSWNLREMLAHAEETRKLMPICMDVRAIMATIQRKYKGIKIQEGIVDYGVRFFFYTSKEPVASIITKLNSLNEPLVTMPIGYVTHGFNLEEAARCMRSLKAPAVVSVSSPDAVTTYNGYLTSSSKTSEEHFVETVSLAGSYRDWSYSGQRTELGVEFLKRGDKIVYHTLESPVEFHLDGEVLSLDKLKSLLSLREVKTIKVFTTVDNTNLHTQLVDMSMTYGQQFGPTYLDGADVTKIKPHVNHEGKTFFVLPSDDTLRSEAFEYYHTLDESFLGRYMSALNHTKKWKFPQVGGLTSIKWADNNCYLSSVLLALQQLEVKFNAPALQEAYYRARAGDAANFCALILAYSNKTVGELGDVRETMTHLLQHANLESAKRVLNVVCKHCGQKTTTLTGVEAVMYMGTLSYDNLKTGVSIPCVCGRDATQYLVQQESSFVMMSAPPAEYKLQQGTFLCANEYTGNYQCGHYTHITAKETLYRIDGAHLTKMSEYKGPVTDVFYKETSYTTTIKPVSYKLDGVTYTEIEPKLDGYYKKDNAYYTEQPIDLVPTQPLPNASFDNFKLTCSNTKFADDLNQMTGFTKPASRELSVTFFPDLNGDVVAIDYRHYSASFKKGAKLLHKPIVWHINQATTKTTFKPNTWCLRCLWSTKPVDTSNSFEVLAVEDTQGMDNLACESQQPTSEEVVENPTIQKEVIECDVKTTEVVGNVILKPSDEGVKVTQELGHEDLMAAYVENTSITIKKPNELSLALGLKTIATHGIAAINSVPWSKILAYVKPFLGQAAITTSNCAKRLAQRVFNNYMPYVFTLLFQLCTFTKSTNSRIRASLPTTIAKNSVKSVAKLCLDAGINYVKSPKFSKLFTIAMWLLLLSICLGSLICVTAAFGVLLSNFGAPSYCNGVRELYLNSSNVTTMDFCEGSFPCSICLSGLDSLDSYPALETIQVTISSYKLDLTILGLAAEWVLAYMLFTKFFYLLGLSAIMQVFFGYFASHFISNSWLMWFIISIVQMAPVSAMVRMYIFFASFYYIWKSYVHIMDGCTSSTCMMCYKRNRATRVECTTIVNGMKRSFYVYANGGRGFCKTHNWNCLNCDTFCTGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVAVKNGALHLYFDKAGQKTYERHPLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCDESASKSASVYYSQLMCQPILLLDQALVSDVGDSTEVSVKMFDAYVDTFSATFSVPMEKLKALVATAHSELAKGVALDGVLSTFVSAARQGVVDTDVDTKDVIECLKLSHHSDLEVTGDSCNNFMLTYNKVENMTPRDLGACIDCNARHINAQVAKSHNVSLIWNVKDYMSLSEQLRKQIRSAAKKNNIPFRLTCATTRQVVNVITTKISLKGGKIVSTCFKLMLKATLLCVLAALVCYIVMPVHTLSIHDGYTNEIIGYKAIQDGVTRDIISTDDCFANKHAGFDAWFSQRGGSYKNDKSCPVVAAIITREIGFIVPGLPGTVLRAINGDFLHFLPRVFSAVGNICYTPSKLIEYSDFATSACVLAAECTIFKDAMGKPVPYCYDTNLLEGSISYSELRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDAEYCRHGTCERSEVGICLSTSGRWVLNNEHYRALSGVFCGVDAMNLIANIFTPLVQPVGALDVSASVVAGGIIAILVTCAAYYFMKFRRVFGEYNHVVAANALLFLMSFTILCLVPAYSFLPGVYSVFYLYLTFYFTNDVSFLAHLQWFAMFSPIVPFWITAIYVFCISLKHCHWFFNNYLRKRVMFNGVTFSTFEEAALCTFLLNKEMYLKLRSETLLPLTQYNRYLALYNKYKYFSGALDTTSYREAACCHLAKALNDFSNSGADVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTFQGKFKKIVKGTHHWMLLTFLTSLLILVQSTQWSLFFFVYENAFLPFTLGIMAIAACAMLLVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLELADTSLSGYRLKDCVMYASALVLLILMTARTVYDDAARRVWTLMNVITLVYKVYYGNALDQAISMWALVISVTSNYSGVVTTIMFLARAIVFVCVEYYPLLFITGNTLQCIMLVYCFLGYCCCCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKSSIDAFKLNIKLLGIGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINRLCEEMLDNRATLQAIASEFSSLPSYAAYATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVVDADSKIVQLSEINMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNNSKGGRFVLALLSDHQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDPAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLRNTVCTVCGMWKGYGCSCDQLREPLMQSADASTFLNGFAV'"
      ]
     },
     "execution_count": 53,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# https://www.uniprot.org/uniprot/A7J8L3\n",
    "# Orf1a polyprotein, found in Sars-Cov\n",
    "with open('sars_cov2_data/proteins_copy/orf1a.txt', 'r') as file:\n",
    "    orf1a_poly_v1 = file.read().replace('\\n', '')\n",
    "\n",
    "orf1a_poly_v1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(4382, 4405)"
      ]
     },
     "execution_count": 47,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(orf1a_poly_v1), len(orf1a_poly_v2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> Usually orf1b is not studied alone but along with orf1a. So we need to look at 'orf1ab'. But just to prove that the length of orf1b is 2595, here is just finding the length of orf1b in SARS-CoV-2."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2595"
      ]
     },
     "execution_count": 48,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# For orf1b_v1, refer - https://www.uniprot.org/uniprot/A0A0A0QGJ0\n",
    "orf1a_poly_v2 = translation(corona[13467:21555])\n",
    "\n",
    "# Length calculated from first 'M'. The last base is *, so extra -1 for that. \n",
    "len(orf1a_poly_v2) - orf1a_poly_v2.find('M') - 1  "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [],
   "source": [
    "# https://www.ncbi.nlm.nih.gov/protein/1796318597 - \n",
    "# Orf1ab polyprotein - found in Sars-cov-2\n",
    "orf1a_poly_v2 = translation(corona[265:13468]) + translation(corona[13467:21555])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [],
   "source": [
    "# https://www.uniprot.org/uniprot/A7J8L2\n",
    "# Orf1ab polyprotein - found in Sars-cov\n",
    "\n",
    "with open('sars_cov2_data/proteins_copy/orf1ab.txt', 'r') as file:\n",
    "    orf1a_poly_v2 = file.read().replace('\\n', '')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(7073, 4382)"
      ]
     },
     "execution_count": 51,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(orf1a_poly_v2), len(orf1a_poly_v1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> So by now, we have extracted Orf1a and Orf1b RNA segments."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT'"
      ]
     },
     "execution_count": 52,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# https://www.ncbi.nlm.nih.gov/protein/1796318598\n",
    "# Spike glycoprotein - found in Sars-cov-2\n",
    "\n",
    "spike_pro_v2 = translation(corona[21562:25384], True)\n",
    "\n",
    "# https://www.ncbi.nlm.nih.gov/Structure/pdb/6VXX CLOSED FORM of glycoprotein (structure of glycoprotein before delivering the payload)\n",
    "# https://www.ncbi.nlm.nih.gov/Structure/pdb/6VYB OPEN FORM of glycoprotein (structure of glycoprotein after delivering the payload)\n",
    "spike_pro_v2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": [
    "cn3 = open('/Users/pranjal27bhardwaj/Desktop/Corona main/mmdb_6VXX.cn3', 'rb').read"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> Spike gylcoprotein is has catalystic properties which is responsible for attacking the body and multiplying the number of cells. The infection begins when the viral spike(S) glycoprotein attaches to it's compliementary host cell receptor, which usually is ACE2."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "# https://www.uniprot.org/uniprot/P59594\n",
    "# Spike glycoprotein - found in Sars-cov\n",
    "\n",
    "with open('sars_cov2_data/proteins_copy/spike.txt', 'r') as file:\n",
    "    spike_v1 = file.read().replace('\\n', '')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(1273, 1255)"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(spike_v2), len(spike_v1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "8265063b0add4455b70a5ff1024f56fd",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import nglview\n",
    "view = nglview.show_pdbid(\"6VXX\")  # load \"3pqr\" from RCSB PDB and display viewer widget\n",
    "\n",
    "view"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "6f4946d20b8b4105bd205e825ec1ea9c",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import nglview\n",
    "view = nglview.show_pdbid(\"6VYB\")  # load \"3pqr\" from RCSB PDB and display viewer widget\n",
    "\n",
    "view"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {},
   "outputs": [],
   "source": [
    "# https://www.ncbi.nlm.nih.gov/gene/43740569\n",
    "# orf3a protein found in Sars-cov-2.\n",
    "\n",
    "orf3a_pro_v2 = translation(corona[25392:26220], True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [],
   "source": [
    "# https://www.uniprot.org/uniprot/J9TEM7\n",
    "\n",
    "with open('sars_cov2_data/proteins_copy/orf3a.txt', 'r') as file:\n",
    "    orf3a_pro_v1 = file.read().replace('\\n', '')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(275, 274)"
      ]
     },
     "execution_count": 58,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(orf3a_pro_v2), len(orf3a_pro_v1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "By now we have observed that there is very little difference in the corresponding protein lengths of SARS-CoV and SARS-CoV-2.\n",
    "**So, Can we say that there isn't much difference between the proteins of two viruses?** Well, **Not Really** \n",
    "\n",
    "Reason for that is that the length of both the proteins is not the most accurate measure of how dissimilar they are. That arises a different question in front of us.\n",
    "\n",
    "### Q. 3 How much different is the protein of this novel coronavirus as compared to the older one?\n",
    "\n",
    "The answer is - **The Edit Distance.** In computational linguistics and computer science, edit distance is a way of quantifying how dissimilar two strings (e.g., words) are to one another by counting the minimum number of operations required to transform one string into the other. In bioinformatics, it can be used to quantify the similarity of DNA sequences, which can be viewed as strings of the letters A, C, G and T. \n",
    "\n",
    "Source: https://en.wikipedia.org/wiki/Edit_distance\n",
    "\n",
    "Let's calculate the edit distance of the genomes of the two versions of coronaviruses. \n",
    "\n",
    "Source of complete genome of old coronavirus: https://www.ncbi.nlm.nih.gov/nuccore/30271926"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1 atattaggtt tttacctacc caggaaaagc caaccaacct cgatctcttg tagatctgtt\n",
      "61 ctctaaacga actttaaaat ctgtgtagct gtcgctcggc tgcatgccta gtgcacctac\n",
      "121 gcagtataaa caataataaa ttttactgtc gttgacaaga aacgagtaac tcgtccctct\n",
      "181 tctgcagact gcttacggtt tcgtccgtgt tgcagtcgat catcagcata cctaggtttc\n",
      "241 gtccgggtgt gaccgaaagg taagatggag agccttgttc ttggtgtcaa cgagaaaaca\n",
      "301 cacgtccaac tcagtttgcc tgtccttcag gttagagacg tgctagtgcg tggcttcggg\n",
      "361 gactctgtgg aagaggccct atcggaggca cgtgaacacc tcaaaaatgg cacttgtggt\n",
      "421 ctagtagagc tggaaaaagg cgtactgccc cagcttgaac agccctatgt gttcattaaa\n",
      "481 cgttctgatg ccttaagcac caatcacggc cacaaggtcg ttgagctggt tgcagaaatg\n",
      "541 gacggcattc agtacggtcg tagcggtata acactgggag tactcgtgcc acatgtgggc\n",
      "601 gaaaccccaa ttgcataccg caatgttctt cttcgtaaga acggtaataa gggagccggt\n",
      "661 ggtcatagct atggcatcga tctaaagtct tatgacttag gtgacgagct tggcactgat\n",
      "721 cccattgaag attatgaaca aaactggaac actaagcatg gcagtggtgc actccgtgaa\n",
      "781 ctcactcgtg agctcaatgg aggtgcagtc actcgctatg tcgacaacaa tttctgtggc\n",
      "841 ccagatgggt accctcttga ttgcatcaaa gattttctcg cacgcgcggg caagtcaatg\n",
      "901 tgcactcttt ccgaacaact tgattacatc gagtcgaaga gaggtgtcta ctgctgccgt\n",
      "961 gaccatgagc atgaaattgc ctggttcact gagcgctctg ataagagcta cgagcaccag\n",
      "1021 acacccttcg aaattaagag tgccaagaaa tttgacactt tcaaagggga atgcccaaag\n",
      "1081 tttgtgtttc ctcttaactc aaaagtcaaa gtcattcaac cacgtgttga aaagaaaaag\n",
      "1141 actgagggtt tcatggggcg tatacgctct gtgtaccctg ttgcatctcc acaggagtgt\n",
      "1201 aacaatatgc acttgtctac cttgatgaaa tgtaatcatt gcgatgaagt ttcatggcag\n",
      "1261 acgtgcgact ttctgaaagc cacttgtgaa cattgtggca ctgaaaattt agttattgaa\n",
      "1321 ggacctacta catgtgggta cctacctact aatgctgtag tgaaaatgcc atgtcctgcc\n",
      "1381 tgtcaagacc cagagattgg acctgagcat agtgttgcag attatcacaa ccactcaaac\n",
      "1441 attgaaactc gactccgcaa gggaggtagg actagatgtt ttggaggctg tgtgtttgcc\n",
      "1501 tatgttggct gctataataa gcgtgcctac tgggttcctc gtgctagtgc tgatattggc\n",
      "1561 tcaggccata ctggcattac tggtgacaat gtggagacct tgaatgagga tctccttgag\n",
      "1621 atactgagtc gtgaacgtgt taacattaac attgttggcg attttcattt gaatgaagag\n",
      "1681 gttgccatca ttttggcatc tttctctgct tctacaagtg cctttattga cactataaag\n",
      "1741 agtcttgatt acaagtcttt caaaaccatt gttgagtcct gcggtaacta taaagttacc\n",
      "1801 aagggaaagc ccgtaaaagg tgcttggaac attggacaac agagatcagt tttaacacca\n",
      "1861 ctgtgtggtt ttccctcaca ggctgctggt gttatcagat caatttttgc gcgcacactt\n",
      "1921 gatgcagcaa accactcaat tcctgatttg caaagagcag ctgtcaccat acttgatggt\n",
      "1981 atttctgaac agtcattacg tcttgtcgac gccatggttt atacttcaga cctgctcacc\n",
      "2041 aacagtgtca ttattatggc atatgtaact ggtggtcttg tacaacagac ttctcagtgg\n",
      "2101 ttgtctaatc ttttgggcac tactgttgaa aaactcaggc ctatctttga atggattgag\n",
      "2161 gcgaaactta gtgcaggagt tgaatttctc aaggatgctt gggagattct caaatttctc\n",
      "2221 attacaggtg tttttgacat cgtcaagggt caaatacagg ttgcttcaga taacatcaag\n",
      "2281 gattgtgtaa aatgcttcat tgatgttgtt aacaaggcac tcgaaatgtg cattgatcaa\n",
      "2341 gtcactatcg ctggcgcaaa gttgcgatca ctcaacttag gtgaagtctt catcgctcaa\n",
      "2401 agcaagggac tttaccgtca gtgtatacgt ggcaaggagc agctgcaact actcatgcct\n",
      "2461 cttaaggcac caaaagaagt aacctttctt gaaggtgatt cacatgacac agtacttacc\n",
      "2521 tctgaggagg ttgttctcaa gaacggtgaa ctcgaagcac tcgagacgcc cgttgatagc\n",
      "2581 ttcacaaatg gagctatcgt tggcacacca gtctgtgtaa atggcctcat gctcttagag\n",
      "2641 attaaggaca aagaacaata ctgcgcattg tctcctggtt tactggctac aaacaatgtc\n",
      "2701 tttcgcttaa aagggggtgc accaattaaa ggtgtaacct ttggagaaga tactgtttgg\n",
      "2761 gaagttcaag gttacaagaa tgtgagaatc acatttgagc ttgatgaacg tgttgacaaa\n",
      "2821 gtgcttaatg aaaagtgctc tgtctacact gttgaatccg gtaccgaagt tactgagttt\n",
      "2881 gcatgtgttg tagcagaggc tgttgtgaag actttacaac cagtttctga tctccttacc\n",
      "2941 aacatgggta ttgatcttga tgagtggagt gtagctacat tctacttatt tgatgatgct\n",
      "3001 ggtgaagaaa acttttcatc acgtatgtat tgttcctttt accctccaga tgaggaagaa\n",
      "3061 gaggacgatg cagagtgtga ggaagaagaa attgatgaaa cctgtgaaca tgagtacggt\n",
      "3121 acagaggatg attatcaagg tctccctctg gaatttggtg cctcagctga aacagttcga\n",
      "3181 gttgaggaag aagaagagga agactggctg gatgatacta ctgagcaatc agagattgag\n",
      "3241 ccagaaccag aacctacacc tgaagaacca gttaatcagt ttactggtta tttaaaactt\n",
      "3301 actgacaatg ttgccattaa atgtgttgac atcgttaagg aggcacaaag tgctaatcct\n",
      "3361 atggtgattg taaatgctgc taacatacac ctgaaacatg gtggtggtgt agcaggtgca\n",
      "3421 ctcaacaagg caaccaatgg tgccatgcaa aaggagagtg atgattacat taagctaaat\n",
      "3481 ggccctctta cagtaggagg gtcttgtttg ctttctggac ataatcttgc taagaagtgt\n",
      "3541 ctgcatgttg ttggacctaa cctaaatgca ggtgaggaca tccagcttct taaggcagca\n",
      "3601 tatgaaaatt tcaattcaca ggacatctta cttgcaccat tgttgtcagc aggcatattt\n",
      "3661 ggtgctaaac cacttcagtc tttacaagtg tgcgtgcaga cggttcgtac acaggtttat\n",
      "3721 attgcagtca atgacaaagc tctttatgag caggttgtca tggattatct tgataacctg\n",
      "3781 aagcctagag tggaagcacc taaacaagag gagccaccaa acacagaaga ttccaaaact\n",
      "3841 gaggagaaat ctgtcgtaca gaagcctgtc gatgtgaagc caaaaattaa ggcctgcatt\n",
      "3901 gatgaggtta ccacaacact ggaagaaact aagtttctta ccaataagtt actcttgttt\n",
      "3961 gctgatatca atggtaagct ttaccatgat tctcagaaca tgcttagagg tgaagatatg\n",
      "4021 tctttccttg agaaggatgc accttacatg gtaggtgatg ttatcactag tggtgatatc\n",
      "4081 acttgtgttg taataccctc caaaaaggct ggtggcacta ctgagatgct ctcaagagct\n",
      "4141 ttgaagaaag tgccagttga tgagtatata accacgtacc ctggacaagg atgtgctggt\n",
      "4201 tatacacttg aggaagctaa gactgctctt aagaaatgca aatctgcatt ttatgtacta\n",
      "4261 ccttcagaag cacctaatgc taaggaagag attctaggaa ctgtatcctg gaatttgaga\n",
      "4321 gaaatgcttg ctcatgctga agagacaaga aaattaatgc ctatatgcat ggatgttaga\n",
      "4381 gccataatgg caaccatcca acgtaagtat aaaggaatta aaattcaaga gggcatcgtt\n",
      "4441 gactatggtg tccgattctt cttttatact agtaaagagc ctgtagcttc tattattacg\n",
      "4501 aagctgaact ctctaaatga gccgcttgtc acaatgccaa ttggttatgt gacacatggt\n",
      "4561 tttaatcttg aagaggctgc gcgctgtatg cgttctctta aagctcctgc cgtagtgtca\n",
      "4621 gtatcatcac cagatgctgt tactacatat aatggatacc tcacttcgtc atcaaagaca\n",
      "4681 tctgaggagc actttgtaga aacagtttct ttggctggct cttacagaga ttggtcctat\n",
      "4741 tcaggacagc gtacagagtt aggtgttgaa tttcttaagc gtggtgacaa aattgtgtac\n",
      "4801 cacactctgg agagccccgt cgagtttcat cttgacggtg aggttctttc acttgacaaa\n",
      "4861 ctaaagagtc tcttatccct gcgggaggtt aagactataa aagtgttcac aactgtggac\n",
      "4921 aacactaatc tccacacaca gcttgtggat atgtctatga catatggaca gcagtttggt\n",
      "4981 ccaacatact tggatggtgc tgatgttaca aaaattaaac ctcatgtaaa tcatgagggt\n",
      "5041 aagactttct ttgtactacc tagtgatgac acactacgta gtgaagcttt cgagtactac\n",
      "5101 catactcttg atgagagttt tcttggtagg tacatgtctg ctttaaacca cacaaagaaa\n",
      "5161 tggaaatttc ctcaagttgg tggtttaact tcaattaaat gggctgataa caattgttat\n",
      "5221 ttgtctagtg ttttattagc acttcaacag cttgaagtca aattcaatgc accagcactt\n",
      "5281 caagaggctt attatagagc ccgtgctggt gatgctgcta acttttgtgc actcatactc\n",
      "5341 gcttacagta ataaaactgt tggcgagctt ggtgatgtca gagaaactat gacccatctt\n",
      "5401 ctacagcatg ctaatttgga atctgcaaag cgagttctta atgtggtgtg taaacattgt\n",
      "5461 ggtcagaaaa ctactacctt aacgggtgta gaagctgtga tgtatatggg tactctatct\n",
      "5521 tatgataatc ttaagacagg tgtttccatt ccatgtgtgt gtggtcgtga tgctacacaa\n",
      "5581 tatctagtac aacaagagtc ttcttttgtt atgatgtctg caccacctgc tgagtataaa\n",
      "5641 ttacagcaag gtacattctt atgtgcgaat gagtacactg gtaactatca gtgtggtcat\n",
      "5701 tacactcata taactgctaa ggagaccctc tatcgtattg acggagctca ccttacaaag\n",
      "5761 atgtcagagt acaaaggacc agtgactgat gttttctaca aggaaacatc ttacactaca\n",
      "5821 accatcaagc ctgtgtcgta taaactcgat ggagttactt acacagagat tgaaccaaaa\n",
      "5881 ttggatgggt attataaaaa ggataatgct tactatacag agcagcctat agaccttgta\n",
      "5941 ccaactcaac cattaccaaa tgcgagtttt gataatttca aactcacatg ttctaacaca\n",
      "6001 aaatttgctg atgatttaaa tcaaatgaca ggcttcacaa agccagcttc acgagagcta\n",
      "6061 tctgtcacat tcttcccaga cttgaatggc gatgtagtgg ctattgacta tagacactat\n",
      "6121 tcagcgagtt tcaagaaagg tgctaaatta ctgcataagc caattgtttg gcacattaac\n",
      "6181 caggctacaa ccaagacaac gttcaaacca aacacttggt gtttacgttg tctttggagt\n",
      "6241 acaaagccag tagatacttc aaattcattt gaagttctgg cagtagaaga cacacaagga\n",
      "6301 atggacaatc ttgcttgtga aagtcaacaa cccacctctg aagaagtagt ggaaaatcct\n",
      "6361 accatacaga aggaagtcat agagtgtgac gtgaaaacta ccgaagttgt aggcaatgtc\n",
      "6421 atacttaaac catcagatga aggtgttaaa gtaacacaag agttaggtca tgaggatctt\n",
      "6481 atggctgctt atgtggaaaa cacaagcatt accattaaga aacctaatga gctttcacta\n",
      "6541 gccttaggtt taaaaacaat tgccactcat ggtattgctg caattaatag tgttccttgg\n",
      "6601 agtaaaattt tggcttatgt caaaccattc ttaggacaag cagcaattac aacatcaaat\n",
      "6661 tgcgctaaga gattagcaca acgtgtgttt aacaattata tgccttatgt gtttacatta\n",
      "6721 ttgttccaat tgtgtacttt tactaaaagt accaattcta gaattagagc ttcactacct\n",
      "6781 acaactattg ctaaaaatag tgttaagagt gttgctaaat tatgtttgga tgccggcatt\n",
      "6841 aattatgtga agtcacccaa attttctaaa ttgttcacaa tcgctatgtg gctattgttg\n",
      "6901 ttaagtattt gcttaggttc tctaatctgt gtaactgctg cttttggtgt actcttatct\n",
      "6961 aattttggtg ctccttctta ttgtaatggc gttagagaat tgtatcttaa ttcgtctaac\n",
      "7021 gttactacta tggatttctg tgaaggttct tttccttgca gcatttgttt aagtggatta\n",
      "7081 gactcccttg attcttatcc agctcttgaa accattcagg tgacgatttc atcgtacaag\n",
      "7141 ctagacttga caattttagg tctggccgct gagtgggttt tggcatatat gttgttcaca\n",
      "7201 aaattctttt atttattagg tctttcagct ataatgcagg tgttctttgg ctattttgct\n",
      "7261 agtcatttca tcagcaattc ttggctcatg tggtttatca ttagtattgt acaaatggca\n",
      "7321 cccgtttctg caatggttag gatgtacatc ttctttgctt ctttctacta catatggaag\n",
      "7381 agctatgttc atatcatgga tggttgcacc tcttcgactt gcatgatgtg ctataagcgc\n",
      "7441 aatcgtgcca cacgcgttga gtgtacaact attgttaatg gcatgaagag atctttctat\n",
      "7501 gtctatgcaa atggaggccg tggcttctgc aagactcaca attggaattg tctcaattgt\n",
      "7561 gacacatttt gcactggtag tacattcatt agtgatgaag ttgctcgtga tttgtcactc\n",
      "7621 cagtttaaaa gaccaatcaa ccctactgac cagtcatcgt atattgttga tagtgttgct\n",
      "7681 gtgaaaaatg gcgcgcttca cctctacttt gacaaggctg gtcaaaagac ctatgagaga\n",
      "7741 catccgctct cccattttgt caatttagac aatttgagag ctaacaacac taaaggttca\n",
      "7801 ctgcctatta atgtcatagt ttttgatggc aagtccaaat gcgacgagtc tgcttctaag\n",
      "7861 tctgcttctg tgtactacag tcagctgatg tgccaaccta ttctgttgct tgaccaagct\n",
      "7921 cttgtatcag acgttggaga tagtactgaa gtttccgtta agatgtttga tgcttatgtc\n",
      "7981 gacacctttt cagcaacttt tagtgttcct atggaaaaac ttaaggcact tgttgctaca\n",
      "8041 gctcacagcg agttagcaaa gggtgtagct ttagatggtg tcctttctac attcgtgtca\n",
      "8101 gctgcccgac aaggtgttgt tgataccgat gttgacacaa aggatgttat tgaatgtctc\n",
      "8161 aaactttcac atcactctga cttagaagtg acaggtgaca gttgtaacaa tttcatgctc\n",
      "8221 acctataata aggttgaaaa catgacgccc agagatcttg gcgcatgtat tgactgtaat\n",
      "8281 gcaaggcata tcaatgccca agtagcaaaa agtcacaatg tttcactcat ctggaatgta\n",
      "8341 aaagactaca tgtctttatc tgaacagctg cgtaaacaaa ttcgtagtgc tgccaagaag\n",
      "8401 aacaacatac cttttagact aacttgtgct acaactagac aggttgtcaa tgtcataact\n",
      "8461 actaaaatct cactcaaggg tggtaagatt gttagtactt gttttaaact tatgcttaag\n",
      "8521 gccacattat tgtgcgttct tgctgcattg gtttgttata tcgttatgcc agtacataca\n",
      "8581 ttgtcaatcc atgatggtta cacaaatgaa atcattggtt acaaagccat tcaggatggt\n",
      "8641 gtcactcgtg acatcatttc tactgatgat tgttttgcaa ataaacatgc tggttttgac\n",
      "8701 gcatggttta gccagcgtgg tggttcatac aaaaatgaca aaagctgccc tgtagtagct\n",
      "8761 gctatcatta caagagagat tggtttcata gtgcctggct taccgggtac tgtgctgaga\n",
      "8821 gcaatcaatg gtgacttctt gcattttcta cctcgtgttt ttagtgctgt tggcaacatt\n",
      "8881 tgctacacac cttccaaact cattgagtat agtgattttg ctacctctgc ttgcgttctt\n",
      "8941 gctgctgagt gtacaatttt taaggatgct atgggcaaac ctgtgccata ttgttatgac\n",
      "9001 actaatttgc tagagggttc tatttcttat agtgagcttc gtccagacac tcgttatgtg\n",
      "9061 cttatggatg gttccatcat acagtttcct aacacttacc tggagggttc tgttagagta\n",
      "9121 gtaacaactt ttgatgctga gtactgtaga catggtacat gcgaaaggtc agaagtaggt\n",
      "9181 atttgcctat ctaccagtgg tagatgggtt cttaataatg agcattacag agctctatca\n",
      "9241 ggagttttct gtggtgttga tgcgatgaat ctcatagcta acatctttac tcctcttgtg\n",
      "9301 caacctgtgg gtgctttaga tgtgtctgct tcagtagtgg ctggtggtat tattgccata\n",
      "9361 ttggtgactt gtgctgccta ctactttatg aaattcagac gtgtttttgg tgagtacaac\n",
      "9421 catgttgttg ctgctaatgc acttttgttt ttgatgtctt tcactatact ctgtctggta\n",
      "9481 ccagcttaca gctttctgcc gggagtctac tcagtctttt acttgtactt gacattctat\n",
      "9541 ttcaccaatg atgtttcatt cttggctcac cttcaatggt ttgccatgtt ttctcctatt\n",
      "9601 gtgccttttt ggataacagc aatctatgta ttctgtattt ctctgaagca ctgccattgg\n",
      "9661 ttctttaaca actatcttag gaaaagagtc atgtttaatg gagttacatt tagtaccttc\n",
      "9721 gaggaggctg ctttgtgtac ctttttgctc aacaaggaaa tgtacctaaa attgcgtagc\n",
      "9781 gagacactgt tgccacttac acagtataac aggtatcttg ctctatataa caagtacaag\n",
      "9841 tatttcagtg gagccttaga tactaccagc tatcgtgaag cagcttgctg ccacttagca\n",
      "9901 aaggctctaa atgactttag caactcaggt gctgatgttc tctaccaacc accacagaca\n",
      "9961 tcaatcactt ctgctgttct gcagagtggt tttaggaaaa tggcattccc gtcaggcaaa\n",
      "10021 gttgaagggt gcatggtaca agtaacctgt ggaactacaa ctcttaatgg attgtggttg\n",
      "10081 gatgacacag tatactgtcc aagacatgtc atttgcacag cagaagacat gcttaatcct\n",
      "10141 aactatgaag atctgctcat tcgcaaatcc aaccatagct ttcttgttca ggctggcaat\n",
      "10201 gttcaacttc gtgttattgg ccattctatg caaaattgtc tgcttaggct taaagttgat\n",
      "10261 acttctaacc ctaagacacc caagtataaa tttgtccgta tccaacctgg tcaaacattt\n",
      "10321 tcagttctag catgctacaa tggttcacca tctggtgttt atcagtgtgc catgagacct\n",
      "10381 aatcatacca ttaaaggttc tttccttaat ggatcatgtg gtagtgttgg ttttaacatt\n",
      "10441 gattatgatt gcgtgtcttt ctgctatatg catcatatgg agcttccaac aggagtacac\n",
      "10501 gctggtactg acttagaagg taaattctat ggtccatttg ttgacagaca aactgcacag\n",
      "10561 gctgcaggta cagacacaac cataacatta aatgttttgg catggctgta tgctgctgtt\n",
      "10621 atcaatggtg ataggtggtt tcttaataga ttcaccacta ctttgaatga ctttaacctt\n",
      "10681 gtggcaatga agtacaacta tgaacctttg acacaagatc atgttgacat attgggacct\n",
      "10741 ctttctgctc aaacaggaat tgccgtctta gatatgtgtg ctgctttgaa agagctgctg\n",
      "10801 cagaatggta tgaatggtcg tactatcctt ggtagcacta ttttagaaga tgagtttaca\n",
      "10861 ccatttgatg ttgttagaca atgctctggt gttaccttcc aaggtaagtt caagaaaatt\n",
      "10921 gttaagggca ctcatcattg gatgctttta actttcttga catcactatt gattcttgtt\n",
      "10981 caaagtacac agtggtcact gtttttcttt gtttacgaga atgctttctt gccatttact\n",
      "11041 cttggtatta tggcaattgc tgcatgtgct atgctgcttg ttaagcataa gcacgcattc\n",
      "11101 ttgtgcttgt ttctgttacc ttctcttgca acagttgctt actttaatat ggtctacatg\n",
      "11161 cctgctagct gggtgatgcg tatcatgaca tggcttgaat tggctgacac tagcttgtct\n",
      "11221 ggttataggc ttaaggattg tgttatgtat gcttcagctt tagttttgct tattctcatg\n",
      "11281 acagctcgca ctgtttatga tgatgctgct agacgtgttt ggacactgat gaatgtcatt\n",
      "11341 acacttgttt acaaagtcta ctatggtaat gctttagatc aagctatttc catgtgggcc\n",
      "11401 ttagttattt ctgtaacctc taactattct ggtgtcgtta cgactatcat gtttttagct\n",
      "11461 agagctatag tgtttgtgtg tgttgagtat tacccattgt tatttattac tggcaacacc\n",
      "11521 ttacagtgta tcatgcttgt ttattgtttc ttaggctatt gttgctgctg ctactttggc\n",
      "11581 cttttctgtt tactcaaccg ttacttcagg cttactcttg gtgtttatga ctacttggtc\n",
      "11641 tctacacaag aatttaggta tatgaactcc caggggcttt tgcctcctaa gagtagtatt\n",
      "11701 gatgctttca agcttaacat taagttgttg ggtattggag gtaaaccatg tatcaaggtt\n",
      "11761 gctactgtac agtctaaaat gtctgacgta aagtgcacat ctgtggtact gctctcggtt\n",
      "11821 cttcaacaac ttagagtaga gtcatcttct aaattgtggg cacaatgtgt acaactccac\n",
      "11881 aatgatattc ttcttgcaaa agacacaact gaagctttcg agaagatggt ttctcttttg\n",
      "11941 tctgttttgc tatccatgca gggtgctgta gacattaata ggttgtgcga ggaaatgctc\n",
      "12001 gataaccgtg ctactcttca ggctattgct tcagaattta gttctttacc atcatatgcc\n",
      "12061 gcttatgcca ctgcccagga ggcctatgag caggctgtag ctaatggtga ttctgaagtc\n",
      "12121 gttctcaaaa agttaaagaa atctttgaat gtggctaaat ctgagtttga ccgtgatgct\n",
      "12181 gccatgcaac gcaagttgga aaagatggca gatcaggcta tgacccaaat gtacaaacag\n",
      "12241 gcaagatctg aggacaagag ggcaaaagta actagtgcta tgcaaacaat gctcttcact\n",
      "12301 atgcttagga agcttgataa tgatgcactt aacaacatta tcaacaatgc gcgtgatggt\n",
      "12361 tgtgttccac tcaacatcat accattgact acagcagcca aactcatggt tgttgtccct\n",
      "12421 gattatggta cctacaagaa cacttgtgat ggtaacacct ttacatatgc atctgcactc\n",
      "12481 tgggaaatcc agcaagttgt tgatgcggat agcaagattg ttcaacttag tgaaattaac\n",
      "12541 atggacaatt caccaaattt ggcttggcct cttattgtta cagctctaag agccaactca\n",
      "12601 gctgttaaac tacagaataa tgaactgagt ccagtagcac tacgacagat gtcctgtgcg\n",
      "12661 gctggtacca cacaaacagc ttgtactgat gacaatgcac ttgcctacta taacaattcg\n",
      "12721 aagggaggta ggtttgtgct ggcattacta tcagaccacc aagatctcaa atgggctaga\n",
      "12781 ttccctaaga gtgatggtac aggtacaatt tacacagaac tggaaccacc ttgtaggttt\n",
      "12841 gttacagaca caccaaaagg gcctaaagtg aaatacttgt acttcatcaa aggcttaaac\n",
      "12901 aacctaaata gaggtatggt gctgggcagt ttagctgcta cagtacgtct tcaggctgga\n",
      "12961 aatgctacag aagtacctgc caattcaact gtgctttcct tctgtgcttt tgcagtagac\n",
      "13021 cctgctaaag catataagga ttacctagca agtggaggac aaccaatcac caactgtgtg\n",
      "13081 aagatgttgt gtacacacac tggtacagga caggcaatta ctgtaacacc agaagctaac\n",
      "13141 atggaccaag agtcctttgg tggtgcttca tgttgtctgt attgtagatg ccacattgac\n",
      "13201 catccaaatc ctaaaggatt ctgtgacttg aaaggtaagt acgtccaaat acctaccact\n",
      "13261 tgtgctaatg acccagtggg ttttacactt agaaacacag tctgtaccgt ctgcggaatg\n",
      "13321 tggaaaggtt atggctgtag ttgtgaccaa ctccgcgaac ccttgatgca gtctgcggat\n",
      "13381 gcatcaacgt ttttaaacgg gtttgcggtg taagtgcagc ccgtcttaca ccgtgcggca\n",
      "13441 caggcactag tactgatgtc gtctacaggg cttttgatat ttacaacgaa aaagttgctg\n",
      "13501 gttttgcaaa gttcctaaaa actaattgct gtcgcttcca ggagaaggat gaggaaggca\n",
      "13561 atttattaga ctcttacttt gtagttaaga ggcatactat gtctaactac caacatgaag\n",
      "13621 agactattta taacttggtt aaagattgtc cagcggttgc tgtccatgac tttttcaagt\n",
      "13681 ttagagtaga tggtgacatg gtaccacata tatcacgtca gcgtctaact aaatacacaa\n",
      "13741 tggctgattt agtctatgct ctacgtcatt ttgatgaggg taattgtgat acattaaaag\n",
      "13801 aaatactcgt cacatacaat tgctgtgatg atgattattt caataagaag gattggtatg\n",
      "13861 acttcgtaga gaatcctgac atcttacgcg tatatgctaa cttaggtgag cgtgtacgcc\n",
      "13921 aatcattatt aaagactgta caattctgcg atgctatgcg tgatgcaggc attgtaggcg\n",
      "13981 tactgacatt agataatcag gatcttaatg ggaactggta cgatttcggt gatttcgtac\n",
      "14041 aagtagcacc aggctgcgga gttcctattg tggattcata ttactcattg ctgatgccca\n",
      "14101 tcctcacttt gactagggca ttggctgctg agtcccatat ggatgctgat ctcgcaaaac\n",
      "14161 cacttattaa gtgggatttg ctgaaatatg attttacgga agagagactt tgtctcttcg\n",
      "14221 accgttattt taaatattgg gaccagacat accatcccaa ttgtattaac tgtttggatg\n",
      "14281 ataggtgtat ccttcattgt gcaaacttta atgtgttatt ttctactgtg tttccaccta\n",
      "14341 caagttttgg accactagta agaaaaatat ttgtagatgg tgttcctttt gttgtttcaa\n",
      "14401 ctggatacca ttttcgtgag ttaggagtcg tacataatca ggatgtaaac ttacatagct\n",
      "14461 cgcgtctcag tttcaaggaa cttttagtgt atgctgctga tccagctatg catgcagctt\n",
      "14521 ctggcaattt attgctagat aaacgcacta catgcttttc agtagctgca ctaacaaaca\n",
      "14581 atgttgcttt tcaaactgtc aaacccggta attttaataa agacttttat gactttgctg\n",
      "14641 tgtctaaagg tttctttaag gaaggaagtt ctgttgaact aaaacacttc ttctttgctc\n",
      "14701 aggatggcaa cgctgctatc agtgattatg actattatcg ttataatctg ccaacaatgt\n",
      "14761 gtgatatcag acaactccta ttcgtagttg aagttgttga taaatacttt gattgttacg\n",
      "14821 atggtggctg tattaatgcc aaccaagtaa tcgttaacaa tctggataaa tcagctggtt\n",
      "14881 tcccatttaa taaatggggt aaggctagac tttattatga ctcaatgagt tatgaggatc\n",
      "14941 aagatgcact tttcgcgtat actaagcgta atgtcatccc tactataact caaatgaatc\n",
      "15001 ttaagtatgc cattagtgca aagaatagag ctcgcaccgt agctggtgtc tctatctgta\n",
      "15061 gtactatgac aaatagacag tttcatcaga aattattgaa gtcaatagcc gccactagag\n",
      "15121 gagctactgt ggtaattgga acaagcaagt tttacggtgg ctggcataat atgttaaaaa\n",
      "15181 ctgtttacag tgatgtagaa actccacacc ttatgggttg ggattatcca aaatgtgaca\n",
      "15241 gagccatgcc taacatgctt aggataatgg cctctcttgt tcttgctcgc aaacataaca\n",
      "15301 cttgctgtaa cttatcacac cgtttctaca ggttagctaa cgagtgtgcg caagtattaa\n",
      "15361 gtgagatggt catgtgtggc ggctcactat atgttaaacc aggtggaaca tcatccggtg\n",
      "15421 atgctacaac tgcttatgct aatagtgtct ttaacatttg tcaagctgtt acagccaatg\n",
      "15481 taaatgcact tctttcaact gatggtaata agatagctga caagtatgtc cgcaatctac\n",
      "15541 aacacaggct ctatgagtgt ctctatagaa atagggatgt tgatcatgaa ttcgtggatg\n",
      "15601 agttttacgc ttacctgcgt aaacatttct ccatgatgat tctttctgat gatgccgttg\n",
      "15661 tgtgctataa cagtaactat gcggctcaag gtttagtagc tagcattaag aactttaagg\n",
      "15721 cagttcttta ttatcaaaat aatgtgttca tgtctgaggc aaaatgttgg actgagactg\n",
      "15781 accttactaa aggacctcac gaattttgct cacagcatac aatgctagtt aaacaaggag\n",
      "15841 atgattacgt gtacctgcct tacccagatc catcaagaat attaggcgca ggctgttttg\n",
      "15901 tcgatgatat tgtcaaaaca gatggtacac ttatgattga aaggttcgtg tcactggcta\n",
      "15961 ttgatgctta cccacttaca aaacatccta atcaggagta tgctgatgtc tttcacttgt\n",
      "16021 atttacaata cattagaaag ttacatgatg agcttactgg ccacatgttg gacatgtatt\n",
      "16081 ccgtaatgct aactaatgat aacacctcac ggtactggga acctgagttt tatgaggcta\n",
      "16141 tgtacacacc acatacagtc ttgcaggctg taggtgcttg tgtattgtgc aattcacaga\n",
      "16201 cttcacttcg ttgcggtgcc tgtattagga gaccattcct atgttgcaag tgctgctatg\n",
      "16261 accatgtcat ttcaacatca cacaaattag tgttgtctgt taatccctat gtttgcaatg\n",
      "16321 ccccaggttg tgatgtcact gatgtgacac aactgtatct aggaggtatg agctattatt\n",
      "16381 gcaagtcaca taagcctccc attagttttc cattatgtgc taatggtcag gtttttggtt\n",
      "16441 tatacaaaaa cacatgtgta ggcagtgaca atgtcactga cttcaatgcg atagcaacat\n",
      "16501 gtgattggac taatgctggc gattacatac ttgccaacac ttgtactgag agactcaagc\n",
      "16561 ttttcgcagc agaaacgctc aaagccactg aggaaacatt taagctgtca tatggtattg\n",
      "16621 ccactgtacg cgaagtactc tctgacagag aattgcatct ttcatgggag gttggaaaac\n",
      "16681 ctagaccacc attgaacaga aactatgtct ttactggtta ccgtgtaact aaaaatagta\n",
      "16741 aagtacagat tggagagtac acctttgaaa aaggtgacta tggtgatgct gttgtgtaca\n",
      "16801 gaggtactac gacatacaag ttgaatgttg gtgattactt tgtgttgaca tctcacactg\n",
      "16861 taatgccact tagtgcacct actctagtgc cacaagagca ctatgtgaga attactggct\n",
      "16921 tgtacccaac actcaacatc tcagatgagt tttctagcaa tgttgcaaat tatcaaaagg\n",
      "16981 tcggcatgca aaagtactct acactccaag gaccacctgg tactggtaag agtcattttg\n",
      "17041 ccatcggact tgctctctat tacccatctg ctcgcatagt gtatacggca tgctctcatg\n",
      "17101 cagctgttga tgccctatgt gaaaaggcat taaaatattt gcccatagat aaatgtagta\n",
      "17161 gaatcatacc tgcgcgtgcg cgcgtagagt gttttgataa attcaaagtg aattcaacac\n",
      "17221 tagaacagta tgttttctgc actgtaaatg cattgccaga aacaactgct gacattgtag\n",
      "17281 tctttgatga aatctctatg gctactaatt atgacttgag tgttgtcaat gctagacttc\n",
      "17341 gtgcaaaaca ctacgtctat attggcgatc ctgctcaatt accagccccc cgcacattgc\n",
      "17401 tgactaaagg cacactagaa ccagaatatt ttaattcagt gtgcagactt atgaaaacaa\n",
      "17461 taggtccaga catgttcctt ggaacttgtc gccgttgtcc tgctgaaatt gttgacactg\n",
      "17521 tgagtgcttt agtttatgac aataagctaa aagcacacaa ggataagtca gctcaatgct\n",
      "17581 tcaaaatgtt ctacaaaggt gttattacac atgatgtttc atctgcaatc aacagacctc\n",
      "17641 aaataggcgt tgtaagagaa tttcttacac gcaatcctgc ttggagaaaa gctgttttta\n",
      "17701 tctcacctta taattcacag aacgctgtag cttcaaaaat cttaggattg cctacgcaga\n",
      "17761 ctgttgattc atcacagggt tctgaatatg actatgtcat attcacacaa actactgaaa\n",
      "17821 cagcacactc ttgtaatgtc aaccgcttca atgtggctat cacaagggca aaaattggca\n",
      "17881 ttttgtgcat aatgtctgat agagatcttt atgacaaact gcaatttaca agtctagaaa\n",
      "17941 taccacgtcg caatgtggct acattacaag cagaaaatgt aactggactt tttaaggact\n",
      "18001 gtagtaagat cattactggt cttcatccta cacaggcacc tacacacctc agcgttgata\n",
      "18061 taaagttcaa gactgaagga ttatgtgttg acataccagg cataccaaag gacatgacct\n",
      "18121 accgtagact catctctatg atgggtttca aaatgaatta ccaagtcaat ggttacccta\n",
      "18181 atatgtttat cacccgcgaa gaagctattc gtcacgttcg tgcgtggatt ggctttgatg\n",
      "18241 tagagggctg tcatgcaact agagatgctg tgggtactaa cctacctctc cagctaggat\n",
      "18301 tttctacagg tgttaactta gtagctgtac cgactggtta tgttgacact gaaaataaca\n",
      "18361 cagaattcac cagagttaat gcaaaacctc caccaggtga ccagtttaaa catcttatac\n",
      "18421 cactcatgta taaaggcttg ccctggaatg tagtgcgtat taagatagta caaatgctca\n",
      "18481 gtgatacact gaaaggattg tcagacagag tcgtgttcgt cctttgggcg catggctttg\n",
      "18541 agcttacatc aatgaagtac tttgtcaaga ttggacctga aagaacgtgt tgtctgtgtg\n",
      "18601 acaaacgtgc aacttgcttt tctacttcat cagatactta tgcctgctgg aatcattctg\n",
      "18661 tgggttttga ctatgtctat aacccattta tgattgatgt tcagcagtgg ggctttacgg\n",
      "18721 gtaaccttca gagtaaccat gaccaacatt gccaggtaca tggaaatgca catgtggcta\n",
      "18781 gttgtgatgc tatcatgact agatgtttag cagtccatga gtgctttgtt aagcgcgttg\n",
      "18841 attggtctgt tgaataccct attataggag atgaactgag ggttaattct gcttgcagaa\n",
      "18901 aagtacaaca catggttgtg aagtctgcat tgcttgctga taagtttcca gttcttcatg\n",
      "18961 acattggaaa tccaaaggct atcaagtgtg tgcctcaggc tgaagtagaa tggaagttct\n",
      "19021 acgatgctca gccatgtagt gacaaagctt acaaaataga ggaactcttc tattcttatg\n",
      "19081 ctacacatca cgataaattc actgatggtg tttgtttgtt ttggaattgt aacgttgatc\n",
      "19141 gttacccagc caatgcaatt gtgtgtaggt ttgacacaag agtcttgtca aacttgaact\n",
      "19201 taccaggctg tgatggtggt agtttgtatg tgaataagca tgcattccac actccagctt\n",
      "19261 tcgataaaag tgcatttact aatttaaagc aattgccttt cttttactat tctgatagtc\n",
      "19321 cttgtgagtc tcatggcaaa caagtagtgt cggatattga ttatgttcca ctcaaatctg\n",
      "19381 ctacgtgtat tacacgatgc aatttaggtg gtgctgtttg cagacaccat gcaaatgagt\n",
      "19441 accgacagta cttggatgca tataatatga tgatttctgc tggatttagc ctatggattt\n",
      "19501 acaaacaatt tgatacttat aacctgtgga atacatttac caggttacag agtttagaaa\n",
      "19561 atgtggctta taatgttgtt aataaaggac actttgatgg acacgccggc gaagcacctg\n",
      "19621 tttccatcat taataatgct gtttacacaa aggtagatgg tattgatgtg gagatctttg\n",
      "19681 aaaataagac aacacttcct gttaatgttg catttgagct ttgggctaag cgtaacatta\n",
      "19741 aaccagtgcc agagattaag atactcaata atttgggtgt tgatatcgct gctaatactg\n",
      "19801 taatctggga ctacaaaaga gaagccccag cacatgtatc tacaataggt gtctgcacaa\n",
      "19861 tgactgacat tgccaagaaa cctactgaga gtgcttgttc ttcacttact gtcttgtttg\n",
      "19921 atggtagagt ggaaggacag gtagaccttt ttagaaacgc ccgtaatggt gttttaataa\n",
      "19981 cagaaggttc agtcaaaggt ctaacacctt caaagggacc agcacaagct agcgtcaatg\n",
      "20041 gagtcacatt aattggagaa tcagtaaaaa cacagtttaa ctactttaag aaagtagacg\n",
      "20101 gcattattca acagttgcct gaaacctact ttactcagag cagagactta gaggatttta\n",
      "20161 agcccagatc acaaatggaa actgactttc tcgagctcgc tatggatgaa ttcatacagc\n",
      "20221 gatataagct cgagggctat gccttcgaac acatcgttta tggagatttc agtcatggac\n",
      "20281 aacttggcgg tcttcattta atgataggct tagccaagcg ctcacaagat tcaccactta\n",
      "20341 aattagagga ttttatccct atggacagca cagtgaaaaa ttacttcata acagatgcgc\n",
      "20401 aaacaggttc atcaaaatgt gtgtgttctg tgattgatct tttacttgat gactttgtcg\n",
      "20461 agataataaa gtcacaagat ttgtcagtga tttcaaaagt ggtcaaggtt acaattgact\n",
      "20521 atgctgaaat ttcattcatg ctttggtgta aggatggaca tgttgaaacc ttctacccaa\n",
      "20581 aactacaagc aagtcaagcg tggcaaccag gtgttgcgat gcctaacttg tacaagatgc\n",
      "20641 aaagaatgct tcttgaaaag tgtgaccttc agaattatgg tgaaaatgct gttataccaa\n",
      "20701 aaggaataat gatgaatgtc gcaaagtata ctcaactgtg tcaatactta aatacactta\n",
      "20761 ctttagctgt accctacaac atgagagtta ttcactttgg tgctggctct gataaaggag\n",
      "20821 ttgcaccagg tacagctgtg ctcagacaat ggttgccaac tggcacacta cttgtcgatt\n",
      "20881 cagatcttaa tgacttcgtc tccgacgcag attctacttt aattggagac tgtgcaacag\n",
      "20941 tacatacggc taataaatgg gaccttatta ttagcgatat gtatgaccct aggaccaaac\n",
      "21001 atgtgacaaa agagaatgac tctaaagaag ggtttttcac ttatctgtgt ggatttataa\n",
      "21061 agcaaaaact agccctgggt ggttctatag ctgtaaagat aacagagcat tcttggaatg\n",
      "21121 ctgaccttta caagcttatg ggccatttct catggtggac agcttttgtt acaaatgtaa\n",
      "21181 atgcatcatc atcggaagca tttttaattg gggctaacta tcttggcaag ccgaaggaac\n",
      "21241 aaattgatgg ctataccatg catgctaact acattttctg gaggaacaca aatcctatcc\n",
      "21301 agttgtcttc ctattcactc tttgacatga gcaaatttcc tcttaaatta agaggaactg\n",
      "21361 ctgtaatgtc tcttaaggag aatcaaatca atgatatgat ttattctctt ctggaaaaag\n",
      "21421 gtaggcttat cattagagaa aacaacagag ttgtggtttc aagtgatatt cttgttaaca\n",
      "21481 actaaacgaa catgtttatt ttcttattat ttcttactct cactagtggt agtgaccttg\n",
      "21541 accggtgcac cacttttgat gatgttcaag ctcctaatta cactcaacat acttcatcta\n",
      "21601 tgaggggggt ttactatcct gatgaaattt ttagatcaga cactctttat ttaactcagg\n",
      "21661 atttatttct tccattttat tctaatgtta cagggtttca tactattaat catacgtttg\n",
      "21721 gcaaccctgt catacctttt aaggatggta tttattttgc tgccacagag aaatcaaatg\n",
      "21781 ttgtccgtgg ttgggttttt ggttctacca tgaacaacaa gtcacagtcg gtgattatta\n",
      "21841 ttaacaattc tactaatgtt gttatacgag catgtaactt tgaattgtgt gacaaccctt\n",
      "21901 tctttgctgt ttctaaaccc atgggtacac agacacatac tatgatattc gataatgcat\n",
      "21961 ttaattgcac tttcgagtac atatctgatg ccttttcgct tgatgtttca gaaaagtcag\n",
      "22021 gtaattttaa acacttacga gagtttgtgt ttaaaaataa agatgggttt ctctatgttt\n",
      "22081 ataagggcta tcaacctata gatgtagttc gtgatctacc ttctggtttt aacactttga\n",
      "22141 aacctatttt taagttgcct cttggtatta acattacaaa ttttagagcc attcttacag\n",
      "22201 ccttttcacc tgctcaagac atttggggca cgtcagctgc agcctatttt gttggctatt\n",
      "22261 taaagccaac tacatttatg ctcaagtatg atgaaaatgg tacaatcaca gatgctgttg\n",
      "22321 attgttctca aaatccactt gctgaactca aatgctctgt taagagcttt gagattgaca\n",
      "22381 aaggaattta ccagacctct aatttcaggg ttgttccctc aggagatgtt gtgagattcc\n",
      "22441 ctaatattac aaacttgtgt ccttttggag aggtttttaa tgctactaaa ttcccttctg\n",
      "22501 tctatgcatg ggagagaaaa aaaatttcta attgtgttgc tgattactct gtgctctaca\n",
      "22561 actcaacatt tttttcaacc tttaagtgct atggcgtttc tgccactaag ttgaatgatc\n",
      "22621 tttgcttctc caatgtctat gcagattctt ttgtagtcaa gggagatgat gtaagacaaa\n",
      "22681 tagcgccagg acaaactggt gttattgctg attataatta taaattgcca gatgatttca\n",
      "22741 tgggttgtgt ccttgcttgg aatactagga acattgatgc tacttcaact ggtaattata\n",
      "22801 attataaata taggtatctt agacatggca agcttaggcc ctttgagaga gacatatcta\n",
      "22861 atgtgccttt ctcccctgat ggcaaacctt gcaccccacc tgctcttaat tgttattggc\n",
      "22921 cattaaatga ttatggtttt tacaccacta ctggcattgg ctaccaacct tacagagttg\n",
      "22981 tagtactttc ttttgaactt ttaaatgcac cggccacggt ttgtggacca aaattatcca\n",
      "23041 ctgaccttat taagaaccag tgtgtcaatt ttaattttaa tggactcact ggtactggtg\n",
      "23101 tgttaactcc ttcttcaaag agatttcaac catttcaaca atttggccgt gatgtttctg\n",
      "23161 atttcactga ttccgttcga gatcctaaaa catctgaaat attagacatt tcaccttgcg\n",
      "23221 cttttggggg tgtaagtgta attacacctg gaacaaatgc ttcatctgaa gttgctgttc\n",
      "23281 tatatcaaga tgttaactgc actgatgttt ctacagcaat tcatgcagat caactcacac\n",
      "23341 cagcttggcg catatattct actggaaaca atgtattcca gactcaagca ggctgtctta\n",
      "23401 taggagctga gcatgtcgac acttcttatg agtgcgacat tcctattgga gctggcattt\n",
      "23461 gtgctagtta ccatacagtt tctttattac gtagtactag ccaaaaatct attgtggctt\n",
      "23521 atactatgtc tttaggtgct gatagttcaa ttgcttactc taataacacc attgctatac\n",
      "23581 ctactaactt ttcaattagc attactacag aagtaatgcc tgtttctatg gctaaaacct\n",
      "23641 ccgtagattg taatatgtac atctgcggag attctactga atgtgctaat ttgcttctcc\n",
      "23701 aatatggtag cttttgcaca caactaaatc gtgcactctc aggtattgct gctgaacagg\n",
      "23761 atcgcaacac acgtgaagtg ttcgctcaag tcaaacaaat gtacaaaacc ccaactttga\n",
      "23821 aatattttgg tggttttaat ttttcacaaa tattacctga ccctctaaag ccaactaaga\n",
      "23881 ggtcttttat tgaggacttg ctctttaata aggtgacact cgctgatgct ggcttcatga\n",
      "23941 agcaatatgg cgaatgccta ggtgatatta atgctagaga tctcatttgt gcgcagaagt\n",
      "24001 tcaatggact tacagtgttg ccacctctgc tcactgatga tatgattgct gcctacactg\n",
      "24061 ctgctctagt tagtggtact gccactgctg gatggacatt tggtgctggc gctgctcttc\n",
      "24121 aaataccttt tgctatgcaa atggcatata ggttcaatgg cattggagtt acccaaaatg\n",
      "24181 ttctctatga gaaccaaaaa caaatcgcca accaatttaa caaggcgatt agtcaaattc\n",
      "24241 aagaatcact tacaacaaca tcaactgcat tgggcaagct gcaagacgtt gttaaccaga\n",
      "24301 atgctcaagc attaaacaca cttgttaaac aacttagctc taattttggt gcaatttcaa\n",
      "24361 gtgtgctaaa tgatatcctt tcgcgacttg ataaagtcga ggcggaggta caaattgaca\n",
      "24421 ggttaattac aggcagactt caaagccttc aaacctatgt aacacaacaa ctaatcaggg\n",
      "24481 ctgctgaaat cagggcttct gctaatcttg ctgctactaa aatgtctgag tgtgttcttg\n",
      "24541 gacaatcaaa aagagttgac ttttgtggaa agggctacca ccttatgtcc ttcccacaag\n",
      "24601 cagccccgca tggtgttgtc ttcctacatg tcacgtatgt gccatcccag gagaggaact\n",
      "24661 tcaccacagc gccagcaatt tgtcatgaag gcaaagcata cttccctcgt gaaggtgttt\n",
      "24721 ttgtgtttaa tggcacttct tggtttatta cacagaggaa cttcttttct ccacaaataa\n",
      "24781 ttactacaga caatacattt gtctcaggaa attgtgatgt cgttattggc atcattaaca\n",
      "24841 acacagttta tgatcctctg caacctgagc ttgactcatt caaagaagag ctggacaagt\n",
      "24901 acttcaaaaa tcatacatca ccagatgttg atcttggcga catttcaggc attaacgctt\n",
      "24961 ctgtcgtcaa cattcaaaaa gaaattgacc gcctcaatga ggtcgctaaa aatttaaatg\n",
      "25021 aatcactcat tgaccttcaa gaattgggaa aatatgagca atatattaaa tggccttggt\n",
      "25081 atgtttggct cggcttcatt gctggactaa ttgccatcgt catggttaca atcttgcttt\n",
      "25141 gttgcatgac tagttgttgc agttgcctca agggtgcatg ctcttgtggt tcttgctgca\n",
      "25201 agtttgatga ggatgactct gagccagttc tcaagggtgt caaattacat tacacataaa\n",
      "25261 cgaacttatg gatttgttta tgagattttt tactcttaga tcaattactg cacagccagt\n",
      "25321 aaaaattgac aatgcttctc ctgcaagtac tgttcatgct acagcaacga taccgctaca\n",
      "25381 agcctcactc cctttcggat ggcttgttat tggcgttgca tttcttgctg tttttcagag\n",
      "25441 cgctaccaaa ataattgcgc tcaataaaag atggcagcta gccctttata agggcttcca\n",
      "25501 gttcatttgc aatttactgc tgctatttgt taccatctat tcacatcttt tgcttgtcgc\n",
      "25561 tgcaggtatg gaggcgcaat ttttgtacct ctatgccttg atatattttc tacaatgcat\n",
      "25621 caacgcatgt agaattatta tgagatgttg gctttgttgg aagtgcaaat ccaagaaccc\n",
      "25681 attactttat gatgccaact actttgtttg ctggcacaca cataactatg actactgtat\n",
      "25741 accatataac agtgtcacag atacaattgt cgttactgaa ggtgacggca tttcaacacc\n",
      "25801 aaaactcaaa gaagactacc aaattggtgg ttattctgag gataggcact caggtgttaa\n",
      "25861 agactatgtc gttgtacatg gctatttcac cgaagtttac taccagcttg agtctacaca\n",
      "25921 aattactaca gacactggta ttgaaaatgc tacattcttc atctttaaca agcttgttaa\n",
      "25981 agacccaccg aatgtgcaaa tacacacaat cgacggctct tcaggagttg ctaatccagc\n",
      "26041 aatggatcca atttatgatg agccgacgac gactactagc gtgcctttgt aagcacaaga\n",
      "26101 aagtgagtac gaacttatgt actcattcgt ttcggaagaa acaggtacgt taatagttaa\n",
      "26161 tagcgtactt ctttttcttg ctttcgtggt attcttgcta gtcacactag ccatccttac\n",
      "26221 tgcgcttcga ttgtgtgcgt actgctgcaa tattgttaac gtgagtttag taaaaccaac\n",
      "26281 ggtttacgtc tactcgcgtg ttaaaaatct gaactcttct gaaggagttc ctgatcttct\n",
      "26341 ggtctaaacg aactaactat tattattatt ctgtttggaa ctttaacatt gcttatcatg\n",
      "26401 gcagacaacg gtactattac cgttgaggag cttaaacaac tcctggaaca atggaaccta\n",
      "26461 gtaataggtt tcctattcct agcctggatt atgttactac aatttgccta ttctaatcgg\n",
      "26521 aacaggtttt tgtacataat aaagcttgtt ttcctctggc tcttgtggcc agtaacactt\n",
      "26581 gcttgttttg tgcttgctgc tgtctacaga attaattggg tgactggcgg gattgcgatt\n",
      "26641 gcaatggctt gtattgtagg cttgatgtgg cttagctact tcgttgcttc cttcaggctg\n",
      "26701 tttgctcgta cccgctcaat gtggtcattc aacccagaaa caaacattct tctcaatgtg\n",
      "26761 cctctccggg ggacaattgt gaccagaccg ctcatggaaa gtgaacttgt cattggtgct\n",
      "26821 gtgatcattc gtggtcactt gcgaatggcc ggacactccc tagggcgctg tgacattaag\n",
      "26881 gacctgccaa aagagatcac tgtggctaca tcacgaacgc tttcttatta caaattagga\n",
      "26941 gcgtcgcagc gtgtaggcac tgattcaggt tttgctgcat acaaccgcta ccgtattgga\n",
      "27001 aactataaat taaatacaga ccacgccggt agcaacgaca atattgcttt gctagtacag\n",
      "27061 taagtgacaa cagatgtttc atcttgttga cttccaggtt acaatagcag agatattgat\n",
      "27121 tatcattatg aggactttca ggattgctat ttggaatctt gacgttataa taagttcaat\n",
      "27181 agtgagacaa ttatttaagc ctctaactaa gaagaattat tcggagttag atgatgaaga\n",
      "27241 acctatggag ttagattatc cataaaacga acatgaaaat tattctcttc ctgacattga\n",
      "27301 ttgtatttac atcttgcgag ctatatcact atcaggagtg tgttagaggt acgactgtac\n",
      "27361 tactaaaaga accttgccca tcaggaacat acgagggcaa ttcaccattt caccctcttg\n",
      "27421 ctgacaataa atttgcacta acttgcacta gcacacactt tgcttttgct tgtgctgacg\n",
      "27481 gtactcgaca tacctatcag ctgcgtgcaa gatcagtttc accaaaactt ttcatcagac\n",
      "27541 aagaggaggt tcaacaagag ctctactcgc cactttttct cattgttgct gctctagtat\n",
      "27601 ttttaatact ttgcttcacc attaagagaa agacagaatg aatgagctca ctttaattga\n",
      "27661 cttctatttg tgctttttag cctttctgct attccttgtt ttaataatgc ttattatatt\n",
      "27721 ttggttttca ctcgaaatcc aggatctaga agaaccttgt accaaagtct aaacgaacat\n",
      "27781 gaaacttctc attgttttga cttgtatttc tctatgcagt tgcatatgca ctgtagtaca\n",
      "27841 gcgctgtgca tctaataaac ctcatgtgct tgaagatcct tgtaaggtac aacactaggg\n",
      "27901 gtaatactta tagcactgct tggctttgtg ctctaggaaa ggttttacct tttcatagat\n",
      "27961 ggcacactat ggttcaaaca tgcacaccta atgttactat caactgtcaa gatccagctg\n",
      "28021 gtggtgcgct tatagctagg tgttggtacc ttcatgaagg tcaccaaact gctgcattta\n",
      "28081 gagacgtact tgttgtttta aataaacgaa caaattaaaa tgtctgataa tggaccccaa\n",
      "28141 tcaaaccaac gtagtgcccc ccgcattaca tttggtggac ccacagattc aactgacaat\n",
      "28201 aaccagaatg gaggacgcaa tggggcaagg ccaaaacagc gccgacccca aggtttaccc\n",
      "28261 aataatactg cgtcttggtt cacagctctc actcagcatg gcaaggagga acttagattc\n",
      "28321 cctcgaggcc agggcgttcc aatcaacacc aatagtggtc cagatgacca aattggctac\n",
      "28381 taccgaagag ctacccgacg agttcgtggt ggtgacggca aaatgaaaga gctcagcccc\n",
      "28441 agatggtact tctattacct aggaactggc ccagaagctt cacttcccta cggcgctaac\n",
      "28501 aaagaaggca tcgtatgggt tgcaactgag ggagccttga atacacccaa agaccacatt\n",
      "28561 ggcacccgca atcctaataa caatgctgcc accgtgctac aacttcctca aggaacaaca\n",
      "28621 ttgccaaaag gcttctacgc agagggaagc agaggcggca gtcaagcctc ttctcgctcc\n",
      "28681 tcatcacgta gtcgcggtaa ttcaagaaat tcaactcctg gcagcagtag gggaaattct\n",
      "28741 cctgctcgaa tggctagcgg aggtggtgaa actgccctcg cgctattgct gctagacaga\n",
      "28801 ttgaaccagc ttgagagcaa agtttctggt aaaggccaac aacaacaagg ccaaactgtc\n",
      "28861 actaagaaat ctgctgctga ggcatctaaa aagcctcgcc aaaaacgtac tgccacaaaa\n",
      "28921 cagtacaacg tcactcaagc atttgggaga cgtggtccag aacaaaccca aggaaatttc\n",
      "28981 ggggaccaag acctaatcag acaaggaact gattacaaac attggccgca aattgcacaa\n",
      "29041 tttgctccaa gtgcctctgc attctttgga atgtcacgca ttggcatgga agtcacacct\n",
      "29101 tcgggaacat ggctgactta tcatggagcc attaaattgg atgacaaaga tccacaattc\n",
      "29161 aaagacaacg tcatactgct gaacaagcac attgacgcat acaaaacatt cccaccaaca\n",
      "29221 gagcctaaaa aggacaaaaa gaaaaagact gatgaagctc agcctttgcc gcagagacaa\n",
      "29281 aagaagcagc ccactgtgac tcttcttcct gcggctgaca tggatgattt ctccagacaa\n",
      "29341 cttcaaaatt ccatgagtgg agcttctgct gattcaactc aggcataaac actcatgatg\n",
      "29401 accacacaag gcagatgggc tatgtaaacg ttttcgcaat tccgtttacg atacatagtc\n",
      "29461 tactcttgtg cagaatgaat tctcgtaact aaacagcaca agtaggttta gttaacttta\n",
      "29521 atctcacata gcaatcttta atcaatgtgt aacattaggg aggacttgaa agagccacca\n",
      "29581 cattttcatc gaggccacgc ggagtacgat cgagggtaca gtgaataatg ctagggagag\n",
      "29641 ctgcctatat ggaagagccc taatgtgtaa aattaatttt agtagtgcta tccccatgtg\n",
      "29701 attttaatag cttcttagga gaatgacaaa aaaaaaaaaa aaaaaaaaaa a\n"
     ]
    }
   ],
   "source": [
    "with open('sars_cov_data/genome/sars_cov_genome.txt', 'r') as file:\n",
    "    sars_cov = file.read()\n",
    "\n",
    "print(sars_cov)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       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      ]
     },
     "execution_count": 60,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "for s in \"\\n01234567789 \":\n",
    "    sars_cov = sars_cov.replace(s, \"\")\n",
    "    \n",
    "sars_cov"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "8412"
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import lzma\n",
    "lzc_v1 = lzma.compress(sars_cov.encode(\"utf-8\"))\n",
    "len(lzc_v1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(lzc_v1) - len(lzc)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "152"
      ]
     },
     "execution_count": 38,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(corona) - len(sars_cov)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "5992"
      ]
     },
     "execution_count": 39,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import editdistance\n",
    "editdistance.eval(sars_cov, corona)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "From this, we can see that - Novel coronavirus differ alot than expected from old coronavirus. Now that we know - the difference between two DNAs/RNAs is measured by calculating edit-distance, we can now just simply complete extracting other proteins. "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> Cross verifying the length of Envelope protein as 75 aa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 63,
   "metadata": {},
   "outputs": [],
   "source": [
    "# https://www.ncbi.nlm.nih.gov/gene/43740570 - Envelope protein in Cov-2\n",
    "envelope_pro_v2 = translation(corona[26244:26472], True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "75"
      ]
     },
     "execution_count": 64,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(envelope_pro_v2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> Cross verifying the length of Memberane protein which ia supposed to be 222aa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "metadata": {},
   "outputs": [],
   "source": [
    "# https://www.ncbi.nlm.nih.gov/gene/43740571 - Membrane Glycoprotein in Cov-2\n",
    "membrane_pro_v2 = translation(corona[26522:27191], True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "222"
      ]
     },
     "execution_count": 67,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(membrane_pro_v2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> Cross verifying the length of ORF6 protein which is supposed to be 61 aa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {},
   "outputs": [],
   "source": [
    "# https://www.ncbi.nlm.nih.gov/gene/43740572 - Orf6 in Cov-2\n",
    "orf6_pro_v2 = translation(corona[27201:27387], True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "61"
      ]
     },
     "execution_count": 70,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(orf6_pro_v2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> Cross verifying the length of ORF7a protein which is supposed to be 121aa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "metadata": {},
   "outputs": [],
   "source": [
    "# https://www.ncbi.nlm.nih.gov/gene/43740573 - orf7a in Cov-2\n",
    "orf7a_pro = translation(corona[27393:27759], True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "121"
      ]
     },
     "execution_count": 73,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(orf7a_pro)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> Cross verifying the length of ORF7b protein which is supposed to be 43aa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "metadata": {},
   "outputs": [],
   "source": [
    "# https://www.ncbi.nlm.nih.gov/gene/43740574 - orf7b in Cov-2\n",
    "orf7b_pro = translation(corona[27755:27887], True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "43"
      ]
     },
     "execution_count": 75,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(orf7b_pro)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> Cross verifying the length of ORF8 protein which is supposed to be 121aa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 76,
   "metadata": {},
   "outputs": [],
   "source": [
    "# https://www.ncbi.nlm.nih.gov/gene/43740577 - orf8 in Cov-2\n",
    "orf8_pro = translation(corona[27893:28259], True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 77,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "121"
      ]
     },
     "execution_count": 77,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(orf8_pro)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> Cross verifying the length of ORF10 protein which is supposed to be 38aa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 78,
   "metadata": {},
   "outputs": [],
   "source": [
    "# https://www.ncbi.nlm.nih.gov/gene/43740576 - orf10 in Cov-2\n",
    "orf10_pro = translation(corona[29557:29674], True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "38"
      ]
     },
     "execution_count": 79,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(orf10_pro)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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