docs/Novel allele detection with MentaLiST.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Novel allele detection with MentaLiST 1.0\n",
    "\n",
    "MentaLiST detects and reconstructs putative novel alleles, while also calling non-present loci, allowing its use on wgMLST schemes. Below we will show how to include novel alleles in the analysis.\n",
    "\n",
    "First, let's do a re-cap of MentaLiST methods. If you are familiar with MentaLiST, you can skip until the section '**Updating an MLST scheme with the detected novel alleles**'.\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Running MentaLiST 1.0\n",
    "\n",
    "Because of the new calling algorithm, new information has to be stored on the MentaLiST database, so databases created with previous 0.1.x or 0.2.x versions are not compatible. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# depending on how you installed mentalist, you might have to add it and julia to the PATH:\n",
    "PATH=$PATH:/rhome/pfeijao/sfu/MentaLiST/src:/rhome/pfeijao/bin"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "On this example we will call MLST alleles on a M. tuberculosis WGS sample. Follow the 'Basic Usage' tutorial to download and create the MLST database and to obtain the FASTQ files for this sample. To run the MLST caller: "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Go to the tmp folder:\n",
    "mkdir -p /tmp/mentalist_quick_start\n",
    "cd /tmp/mentalist_quick_start"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Then, we run MentaLiST on the M. tuberculosis  MLST scheme, setting the `--kt` parameter to 10 to search more agressively for novel alleles (default is 6)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mOpening kmer database ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mFinished the JLD load, building alleles list...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mDecompressing weight list...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mBuilding kmer index ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mSample: SRR6152708. Opening fastq file(s) and counting kmers ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mVoting for alleles ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mCalling alleles and novel alleles ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mWriting output ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mDone.\n"
     ]
    }
   ],
   "source": [
    "mentalist call -o sample.call --db mtb_cgmlst.db --kt 10 --output_votes --output_special -1 SRR6152708_1.fastq.gz -2 SRR6152708_2.fastq.gz"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Description of output files\n",
    "\n",
    "Here, a brief description of each output file. All output files have the same prefix, given by the -o option when running MentaLiST call. 'sample.call' in this example.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-rw-rw-r--. 1 pfeijao pfeijao   27602 Feb 14 10:48 sample.call\n",
      "-rw-rw-r--. 1 pfeijao pfeijao   27643 Feb 14 10:48 sample.call.byvote\n",
      "-rw-rw-r--. 1 pfeijao pfeijao  128763 Feb 14 10:48 sample.call.coverage.txt\n",
      "-rw-rw-r--. 1 pfeijao pfeijao   89361 Feb 14 10:48 sample.call.novel.fa\n",
      "-rw-rw-r--. 1 pfeijao pfeijao    5838 Feb 14 10:48 sample.call.novel.txt\n",
      "-rw-rw-r--. 1 pfeijao pfeijao  205768 Feb 14 10:48 sample.call.special_cases.fa\n",
      "-rw-rw-r--. 1 pfeijao pfeijao     719 Feb 14 10:48 sample.call.ties.txt\n",
      "-rw-rw-r--. 1 pfeijao pfeijao 1209964 Feb 14 10:48 sample.call.votes.txt\n"
     ]
    }
   ],
   "source": [
    "ls -l sample.call*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Sample      Rv0014c  Rv0015c  Rv0016c  Rv0017c  Rv0018c  Rv0019c  Rv0021c  Rv0022c  Rv0023  Rv0024  Rv0025\n",
      "SRR6152708  5        2        1        1        2        1        1        1        1       N       1\n"
     ]
    }
   ],
   "source": [
    "# The 'main' file is sample.call, with the allele calls. Let's show the first 12 calls:\n",
    "cut -f1-12 sample.call | column -ts $'\\t' "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The file sample.call.coverage.txt has a description of each the call for each locus. There are different types of call possible:\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- **'Regular' called alleles** - the most voted allele that has 100% coverage; this is the most common case.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SRR6152708\tRv0014c\t1.0\t43\t\u001b[01;31m\u001b[KCalled\u001b[m\u001b[K allele 5.\n",
      "SRR6152708\tRv0015c\t1.0\t18\t\u001b[01;31m\u001b[KCalled\u001b[m\u001b[K allele 2.\n",
      "SRR6152708\tRv0016c\t1.0\t45\t\u001b[01;31m\u001b[KCalled\u001b[m\u001b[K allele 1.\n",
      "SRR6152708\tRv0017c\t1.0\t45\t\u001b[01;31m\u001b[KCalled\u001b[m\u001b[K allele 1.\n",
      "SRR6152708\tRv0018c\t1.0\t33\t\u001b[01;31m\u001b[KCalled\u001b[m\u001b[K allele 2.\n",
      "SRR6152708\tRv0019c\t1.0\t39\t\u001b[01;31m\u001b[KCalled\u001b[m\u001b[K allele 1.\n",
      "SRR6152708\tRv0021c\t1.0\t35\t\u001b[01;31m\u001b[KCalled\u001b[m\u001b[K allele 1.\n",
      "SRR6152708\tRv0022c\t1.0\t32\t\u001b[01;31m\u001b[KCalled\u001b[m\u001b[K allele 1.\n",
      "SRR6152708\tRv0023\t1.0\t57\t\u001b[01;31m\u001b[KCalled\u001b[m\u001b[K allele 1.\n",
      "SRR6152708\tRv0025\t1.0\t55\t\u001b[01;31m\u001b[KCalled\u001b[m\u001b[K allele 1.\n"
     ]
    }
   ],
   "source": [
    "head -n12 sample.call.coverage.txt | grep Called "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- **Missing loci** - either no $k$-mers of these loci have been detected, or some $k$-mers but below 50% threshold, so it is declared missing. Technically should not happen in a cgMLST scheme, so it might be caused by poor sample coverage."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SRR6152708\tRv1417\t0.0\t0\t\u001b[01;31m\u001b[KNot present\u001b[m\u001b[K; allele 58 is the best covered but below threshold with 188/435 missing kmers.\n"
     ]
    }
   ],
   "source": [
    "grep \"Not present\" sample.call.coverage.txt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- **Novel alleles** - when none of the top voted alleles in scheme for this locus the have 100% coverage, `MentaLiST` looks for a novel allele that has 100% coverage, using existing alleles as \"template\" for creating a novel allele. Some novel alleles in the first 100 calls:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SRR6152708\tRv0024\t1.0\t42\t\u001b[01;31m\u001b[KNovel\u001b[m\u001b[K, 1 mutation from allele 98: Del of len 1 at pos 719\n",
      "SRR6152708\tRv0035\t1.0\t46\t\u001b[01;31m\u001b[KNovel\u001b[m\u001b[K, 2 mutations from allele 227: Subst C->G at pos 47, Subst A->T at pos 76\n",
      "SRR6152708\tRv0045c\t1.0\t61\t\u001b[01;31m\u001b[KNovel\u001b[m\u001b[K, 4 mutations from allele 62: Subst C->T at pos 318, Del of len 2 at pos 650, Subst A->G at pos 652\n",
      "SRR6152708\tRv0063\t1.0\t55\t\u001b[01;31m\u001b[KNovel\u001b[m\u001b[K, 1 mutation from allele 140: Ins of base G at pos 334\n",
      "SRR6152708\tRv0101\t1.0\t50\t\u001b[01;31m\u001b[KNovel\u001b[m\u001b[K, 2 mutations from allele 1541: Subst A->G at pos 5360, Subst A->G at pos 6088\n"
     ]
    }
   ],
   "source": [
    "head -n 100 sample.call.coverage.txt | grep Novel "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- **Multiple possible alleles**: when more than one allele has 100% coverage. In the output, the depth of coverage and number of votes of each allele is shown; the best allele is chosen on the call file, and a character \"+\" is added after the allele number on the call file."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SRR6152708\tRv0471c\t1.0\t43\t\u001b[01;31m\u001b[KMultiple\u001b[m\u001b[K possible alleles:1, 118 with depth 43, 39 and votes 0, -724. Most voted (1) is chosen on call file.\n",
      "SRR6152708\tRv1318c\t1.0\t36\t\u001b[01;31m\u001b[KMultiple\u001b[m\u001b[K possible alleles:302, 1 with depth 36, 36 and votes 4427, 0. Most voted (302) is chosen on call file.\n",
      "SRR6152708\tRv1319c\t1.0\t35\t\u001b[01;31m\u001b[KMultiple\u001b[m\u001b[K possible alleles:8, 3 with depth 35, 35 and votes 3930, 3402. Most voted (8) is chosen on call file.\n",
      "SRR6152708\tRv1911c\t1.0\t26\t\u001b[01;31m\u001b[KMultiple\u001b[m\u001b[K possible alleles:1, 118 with depth 26, 26 and votes 0, -244. Most voted (1) is chosen on call file.\n",
      "SRR6152708\tRv2319c\t1.0\t28\t\u001b[01;31m\u001b[KMultiple\u001b[m\u001b[K possible alleles:7, 1 with depth 28, 30 and votes 101, 0. Most voted (7) is chosen on call file.\n"
     ]
    }
   ],
   "source": [
    "grep Multiple sample.call.coverage.txt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- **Partially covered alleles**: coverage for the best allele is >50%, but less than 100%, which triggers a search for a novel allele, but none was found. Most likely either an undetected novel allele or an existing allele that was not fully covered in the WGS sample, for some reason. The most covered allele is chosen on the call file, and a character \"-\" is added after the allele number on the call file, to indicate partial coverage."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SRR6152708\tRv0275c\t0.986\t0\t\u001b[01;31m\u001b[KPartially\u001b[m\u001b[K covered allele or novel allele; Best allele 26 has 10/696 missing kmers, and no novel was found. Gaps on positions: (635, 665)\n",
      "SRR6152708\tRv0581\t0.973\t0\t\u001b[01;31m\u001b[KPartially\u001b[m\u001b[K covered allele or novel allele; Best allele 1 has 5/186 missing kmers, and no novel was found. Gaps on positions: (115, 119)\n",
      "SRR6152708\tRv0860\t0.987\t0\t\u001b[01;31m\u001b[KPartially\u001b[m\u001b[K covered allele or novel allele; Best allele 331 has 28/2133 missing kmers, and no novel was found. Gaps on positions: (2096, 2133)\n",
      "SRR6152708\tRv1860\t0.9526\t0\t\u001b[01;31m\u001b[KPartially\u001b[m\u001b[K covered allele or novel allele; Best allele 152 has 45/948 missing kmers, and no novel was found. Gaps on positions: (855, 901)\n",
      "SRR6152708\tRv1999c\t0.9575\t0\t\u001b[01;31m\u001b[KPartially\u001b[m\u001b[K covered allele or novel allele; Best allele 5 has 55/1293 missing kmers, and no novel was found. Gaps on positions: (1182, 1236)\n",
      "SRR6152708\tRv2249c\t0.998\t0\t\u001b[01;31m\u001b[KPartially\u001b[m\u001b[K covered allele or novel allele; Best allele 1 has 3/1521 missing kmers, and no novel was found. Gaps on positions: (1, 3)\n",
      "SRR6152708\tRv3017c\t0.775\t0\t\u001b[01;31m\u001b[KPartially\u001b[m\u001b[K covered allele or novel allele; Best allele 1 has 75/333 missing kmers, and no novel was found. Gaps on positions: (1, 75)\n",
      "SRR6152708\tRv3394c\t0.9614\t0\t\u001b[01;31m\u001b[KPartially\u001b[m\u001b[K covered allele or novel allele; Best allele 85 has 60/1545 missing kmers, and no novel was found. Gaps on positions: (1462, 1541)\n",
      "SRR6152708\tRv3795\t0.9995\t0\t\u001b[01;31m\u001b[KPartially\u001b[m\u001b[K covered allele or novel allele; Best allele 1 has 2/3267 missing kmers, and no novel was found. Gaps on positions: (28, 29)\n"
     ]
    }
   ],
   "source": [
    "grep Partially sample.call.coverage.txt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Novel alleles output\n",
    "\n",
    "`MentaLiST` outputs two files with novel alleles information: one FASTA file called `<SAMPLE>.novel.fa` with the sequences, and one text file called `<SAMPLE>.novel.txt` with a description of each novel allele found."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">Rv0024_N1 Seen in 1 sample(s).\n",
      "GTGAATACAGCGAGGTCGAGCTGTTGAGTCGCGCTCATCAACTGTTCGCCGGAGACAGTCGGCGACCGGGGTTGGATGCGGGCACCACACCCTACGGGGATCTGCTGTCTCGGGCTGCCG\n",
      "ACCTGAATGTGGGTGCGGGCCAGCGCCGGTATCAACTCGCCGTGGACCACAGCCGGGCGGCCTTGCTGTCTGCTGCGCGAACCGATGCCGCGGCCGGGGCCGTCATCACCGGCGCTCAAC\n",
      "GGGATCGGGCATGGGCCCGGCGGTCGACCGGAACCGTTCTCGACGAGGCTCGCTCGGATACCACCGTTACTGCGGTTATGCCGATAGCCCAGCGCGAAGCCATACGCCGTCGTGTGGCGC\n",
      "GGCTGCGCGCGCAACGAGCCCATGTGCTGACGGCGCGACGACGGGCACGACGGCACCTGGCGGCGCTGCGTGCGCTGCGGTACCGGGTGGCGCACGGCCCGGGGGTCGCGCTGGCCAAAC\n",
      "TTCGGCTGCCGTCGCCGAGCGGTCGCGCCGGCATCGCGGTCCACGCCGCGCTGTCGCGACTTGGCCGTCCCTATGTCTGGGGCGCAACGGGGCCCAACCAGTTCGACTGTTCCGGTTTGG\n",
      "TCCAGTGGGCCTACGCCCAGGCGGGTGTTCACCTGGATCGCACCACCTATCAACAGATCAACGAGGGGATCCCGGTGCCGCGCTCACAGGTCCGGCCGGGCGATCTGGTCTTCCCGCACC\n",
      "CCGGGCACGTGCAGCTGGCGATCGGCAACAATCTGGTCGTCGAGGCGCCCCATGCGGGCGCGTCGGTTCGGGTCAGCTCGCTGGGCAACAACGTGCAGATTCGGCGACCGCTGAGTGGCA\n",
      "GATAA\n",
      ">Rv0035_N1 Seen in 1 sample(s).\n",
      "ATGACGGCGGCCTTGCTTTCACCAGCCATCGCCTGGCAGCAGATCTGGGCTTGCACGGACCGCACGCTGACGATCTCTTGCGAGGATTCCGAGGTAATCAGCTATCAGGACCTCATCGCG\n",
      "CGCGCGGCGGCATGCATCCCCCCGCTACGGCGTCTTGACCTCAAACGCGGTGAACCCGTGCTGATCACCGCCCACACCAACCTGGAATTCCTGTCCTGCTTTTTGGGCCTCATGCTCCAT\n",
      "GGCGCTGTGCCGGTACCCATCCCGCCGCGGGAGGCACTGAAGACCACCGAGCGTTTCATGACTCGGCTCGGCCCACTGCTGCGCCATCACCGCGTGCTGATCTGCACACCGGCCGAACAC\n",
      "GACGAGATACGCGCTGCCGCCAGCACCGACTGCCAGATCAGCAGATTTACTGCCCTAGCCGAGGCTGGCGACGAGCAGTTCGGCCGCGCCACGGCCCAGCAACTCGCCGACACCGCCACC\n",
      "GCCGACTGGCCGCTATGCACCCTCGACGACGACGCCTACGTCCAATACACCTCTGGCAGCACCGCAGCACCACGCGGAGTGGTCATCACCTACCGCAACCTGCTGTCCAACATGCGCGCA\n",
      "ATGGCCGTGGGCTCACAATTCCAGCACGGCGATGTCATGGGCAGCTGGCTGCCCTTGCACCATGACATGGGGCTGGTGGGCAGCCTATTCGCCGCACTCTTCAACAGTGTCAGCGCGGTA\n",
      "TTCACCACGCCACACCGGTTTCTGTATGACCCGTTGGGATTCCTCAGACTGCTCACCAGCTCCGGGGCTACCCACACGTTCATGCCTAACTTCGCTCTGGAGTGGCTGATCAACGCCTAC\n",
      "CACAGGCGCGGCGCCGACATCGAAGGCATCGACCTACACAAAATGCGCCGCTTGATCATCGCCTCCGAACCCGTCCATGCCGAGGGCATGCGGAGATTCGCCGCCACCTTCGCCGGCGTC\n",
      "GGACTTGCCCCCACGGCCCTGGGTTCGGGCTATGGCCTGGCCGAAGCGACCGTCGCCGTGTCAATGTCAGCGCCCAACACGGGATTCCGCACCGAAACCCACGCCGCCGCGGAGGTCGTC\n",
      "ACCGGCGGCCGAGTGCTGCCTGGCTACGAGGTGCGCATTGACGCCGCACCAGGTGCCCGGGCCGGAACGATCAAACTGCGCGGCGACAGCGTGGCCGCCAAAGCCTATGTGGGCGGGAAG\n",
      "AAGCTGGACGCGCTCGACGAGGAAGGCTTCTGCGACACCCACGACTTGGGTTTTCTTGTAGACGACGAAATCGTCATCCTTGGCCGGCAGGACGAGGTGTTCATTGTCCACGGAGAAAAC\n",
      "AGATTCCCCTACGACATCGAGTTCATCATTCGCGGGGAATCCGAGCAGCACCGGACCAAAGTCGCATGTTTCGGGGTCAACGAACGCGTCGTGGTTGTGTTGGAAAGCCCATTGGACAGC\n",
      "ATCATCGACAAGGCCGAAGCCGACCGACTGAGATGTCAAGTCGTTGCCGCGACTGGGCTGCAGTTGGATGAACTGATCACGGTTCGGCGCGGCGCGATTCCCACCACCACCAGCGGCAAG\n",
      "CTCAAACGACGCGCCGTCGCGCAGGCTTATCGAGACGGCACACTGCCCCGTCTTGCCACCCACGCGTGGACGGCGGATCCCGATAGCGCTCCCAAAACGACCCGGTCCAGCCTGGAAGGC\n",
      "GCCCACTGA\n",
      ">Rv0045c_N1 Seen in 1 sample(s).\n",
      "TCAGCGTGTGTCGAGCACCCCGCGCACGATCTCGATCAGGGCGCGCGGTTGGTCACTTTGCACCGAGTGGCCTGACTTCTCGACGATGTGAACGCCACGGAAATGCGTTGCACGCCTGTG\n",
      "GAGTTCGGCGGTGTCCTGGTCGGTGACGAAGCCCGACGAGCCGCCGCGCACGAGTGTGATCGGCGCGGACAGGGCGTCGACGTCGTCCCAGAGCCCTGCGAAATCTCCGAACGTGCGGAT\n",
      "CGCGTCATAGCGCCACACCCAGTTGCCGTTGTCCAGCCGGCGGGAGTTGTGGAACACGCCGCGGCGCAACGACTTGATATCGCGGTGCGGGGCCGCGGCGATCGTTAGGTCCAGCATGGC\n",
      "CTGAAAGCTGGGGAATTCCCGCTCGCCGTGCATCAGCGCCACCGTGCCGCGCTGCTCGGCGGTCAGCTCGGCGTGCCGTTGCAATGCCGACGGGGTGACGTCGACGAGAACGAGTTCGCC\n",
      "GACCAGGTCGGGTGCCATCGCGGCCAGCCGTATCGCAGTCAACCCGCCCAGCGACATGCCGACCACGAATTCGGCACCCGGCGCAAGCTCGCGTAGCACCGGCGCCAAGGTCTCGGAGTT\n",
      "GAGCTGCGGCGAGTAATTGCCGTCCTCCCGCCAAGCGGAATGGCCGTGCTGGAAGGTCCACCGCCAGCGCCGGCTCACCCAGGCCGACGATCACGGTGTCCCAGGTATGGGCGTTCTGTC\n",
      "CGCCGCCGTGCAGAAAGATCACCCGCGGCGCAGAGCCGCCCCAGCGCAGCGCGCTGATGGCTCCCGCTTGGACCCGCTCGACTTCAGGCAGTGGACCATTGACACCGGCCTGCTCAGCGT\n",
      "TCTCAGCCAGCAGGGCAAACTCGTCCAGTCCGGTCAGTTCGTCGTCAGATAGCAC\n",
      ">Rv0063_N1 Seen in 1 sample(s).\n",
      "TTGGCGCGTGAGATCTCACGCCAGACGTTTCTGCGGGGTGCCGCCGGAGCGTTGGCCGCCGGCGCGGTCTTCGGCTCGGTCCGGGCTACCGCGGATCCGGCTGCCTCTGGCTGGGAGGCT\n",
      "CTTTCTTCCGCCCTCGGAGGGAAAGTGCTACAACCGGACGACGGTCCCCAATTCGCAACGGCCAAGCAGGTTTTCAACACCAACTACAACGGCTATACGCCGGCGGTGATCGTTACCCCG\n",
      "ACATCGCAGCTGGACGTGCAGAAGGCGATGGCGTTCGCTGCCGCGAACAACCTCAAGGTGGCCCCACGCGGTGGCGGGCACTCCTACGTGGGGGCGTCCACGGCCAACGGCGCCATGGTG\n",
      "CTCGACCTACGTCAGCTACCTGGGGACATCAACTACGACGCCACCACCGGGCGGGTCACGGTGACGCCCGCCACCGGTTTGTACGCCATGCACCAGGTGTTGGCCGCGGCCGGCCGGGGC\n",
      "ATCCCGACCGGCACCTGCCCGACGGTCGGTGTCGCGGGACACGCGCTGGGCGGCGGGCTGGGCGCCAATTCCCGGCACGCCGGCCTGCTCTGTGACCAATTGACGTCGGCGTCGGTGGTG\n",
      "CTGCCCAGCGGCCAGGCGGTCACCGCGTCCGCCACCGACCACCCCGACCTGTTCTGGGCGTTGCGCGGTGGCGGTGGCGGCAACTTCGGCGTGACAACCTCGCTGACCTTCGCGACGTTC\n",
      "CCCAGCGGGGACCTCGACGTCGTGAACCTCAATTTCCCACCGCAGTCGTTCGCGCAGGTTCTGGTCGGTTGGCAGAATTGGCTGCGAACCGCCGACCGAGGCAGCTGGGCACTGGCCGAT\n",
      "GCCACCGTCGACCCGCTGGGCACGCATTGCCGCATCCTTGCGACCTGCCCGGCCGGGTCGGGCGGCAGCGTGGCGGCCGCCATCGTTTCGGCCGTCGGAACGCAACCGACCGGCACCGAA\n",
      "AACCACACGTTCAACTATCTGGACCTGGTCAGATATCTGGCCGTCGGGAACCTCAACCCGTCGCCGCTGGGATATGTCGGCGGATCCGATGTCTTCACGACGATCACTCCGGCGACCGCC\n",
      "CAGGGAATCGCCTCGGCGGTCGACGCCTTTCCGCGTGGAGCGGGCCGCATGTTGGCGATCATGCACGCCCTCGACGGCGCGCTCGCCACTGTGTCACCGGGGGCCACGGCCTTCCCGTGG\n",
      "CGTCGGCAGTCGGCGCTGGTGCAGTGGTACGTCGAAACATCCGGCTCCCCGTCGGAAGCGACTAGCTGGCTCAACACCGCACATCAAGCGGTGCGAGCGTATTCGGTTGGCGGCTATGTG\n",
      "AACTATCTCGAGGTAAACCAACCGCCGGCACGTTACTTTGGCCCGAATCTGTCCCGGCTGAGCGCAGTACGTCAGAAGTATGACCCCAGCCGGGTCCATGTTCTCCGGGCTGAACTTCTA\n",
      "G\n",
      ">Rv0101_N1 Seen in 1 sample(s).\n",
      "GTGCACCGAGTTCGGTTAAGCCGCTCGCAGCGCAACCTCTACAACGGCGTGCGCCAGGATAACAATCCCGCGTTATATCTGATCGGCAAGAGCTATCGGTTCCGCCGGTTGGAGCTGGCG\n",
      "AGATTCCTGGCCGCTCTGCACGCAACGGTACTGGACAACCCCGTGCAACTTTGCGTCCTGGAGAATTCGGGGGCAGACTATCCGGATCTGGTGCCGCGGCTACGGTTCGGCGACATCGTG\n",
      "CGGGTGGGGTCAGCCGATGAGCACCTGCAGAGCACATGGTGTTCGGGCATCCTGGGCAAGCCACTGGTGCGGCATACGGTGCACACCGACCCGAACGGGTATGTGACCGGTCTGGACGTT\n",
      "CACACCCACCACATCCTGCTGGACGGCGGCGCGACCGGGACGATCGAAGCTGACCTGGCGCGTTACCTGACCACCGACCCGGCGGGCGAAACCCCCAGTGTCGGTGCGGGTCTAGCCAAG\n",
      "CTCAGGGAGGCGCACCGTCGTGAGACGGCCAAGGTGGAAGAATCGCGGGGGCGCCTGTCGGCTGTCGTGCAGCGTGAACTCGCCGACGAAGCATACCACGGCGGGCACGGGCACAGCGTT\n",
      "AGCGACGCTCCCGGGACCGCGGCCAAGGGCGTCCTGCACGAATCGGCAACGATCTGCGGCAACGCGTTTGATGCCATCCTGACCCTTTCGGAAGCGCAGCGGGTCCCGCTTAATGTGCTG\n",
      "GTGGCTGCGGCGGCCGTCGCGGTGGACGCGAGCCTTCGGCAGAACACCGAAACCCTCTTGGTGCACACGGTGGACAACCGGTTCGGAGATTCTGATCTGAATGTCGCGACCTGTTTGGTC\n",
      "AATTCGGTTGCCCAGACCGTCCGGTTTCCCCCATTTGCGTCGGTGTCCGATGTCGTTCGAACGCTTGACCGCGGCTATGTCAAGGCGGTAAGACGCCGGTGGCTTCGTGAGGAGCATTAC\n",
      "CGCCGAATGTATTTGGCGATCAACCGGACATCTCACGTGGAGGCGTTGACGCTAAATTTCATTCGCGAGCCATGCGCACCTGGCCTGCGCCCGTTCTTGTCGGAGGTCCCGATTGCCACG\n",
      "GATATCGGTCCGGTCGAGGGCATGACGGTGGCGTCTGTTCTGGACGAAGAACAGCGCACACTGAACCTAGCCATCTGGAACCGAGCCGATCTGCCCGCGTGCAAGACACACCCCAAGGTC\n",
      "GCGGAACGGATAGCGGCAGCGTTGGAATCGATGGCGGCGATGTGGGATCGGCCGATCGCCATGATCGTCAACGACTGGTTCGGGATCGGCCCGGACGGGACTCGCTGCCAAGGCGATTGG\n",
      "CCAGCCCGTCAGCCGTCGACGCCCGCGTGGTTTCTCGATTCCGCAAGGGGCGTCCACCAATTTCTCGGCAGGCGCCGCTTCGTCTACCCGTGGGTCGCGTGGTTGGTGCAACGCGGCGCC\n",
      "GCACCGGGTGATGTTCTGGTGTTCACCGACGACGACACCGACAAGACCATTGACCTGCTCATCGCGTGTCACCTTGCGGGTTGCGGGTACAGCGTCTGCGACACCGCTGACGAAATTTCC\n",
      "GTGCGGACCAATGCGATTACCGAGCACGGCGATGGCATCTTGGTGACAGTGGTCGACGTGGCCGCCACCCAGCTGGCGGTTGTCGGCCATGACGAGCTGCGGAAGGTCGTTGACGAGCGC\n",
      "GTCACACAGGTGACACACGACGCACTGCTGGCCACCAAGACCGCCTACATCATGCCGACCTCGGGAACTACCGGACAACCCAAGCTGGTGCGAATCTCACACGGCTCGCTCGCGGTTTTC\n",
      "TGTGATGCGATCAGCCGCGCCTACGGTTGGGGAGCCCACGACACCGTTCTGCAGTGCGCTCCGTTGACATCGGACATCAGCGTCGAGGAGATTTTCGGTGGCGCGGCCTGTGGCGCGCGA\n",
      "CTGGTGCGATCCGCGGCTATGAAAACCGGCGACCTGGCGGCGCTGGTTGACGATCTCGTCGCCCGCGAGACGACAATCGTCGACCTGCCGACCGCCGTCTGGCAGCTGTTGTGCGCCGAC\n",
      "GGCGACGCCATTGACGCGATCGGCCGCTCGCGCCTGCGGCAGATCGTAATCGGCGGTGAAGCCATCCGCTGTAGCGCCGTGGACAAGTGGCTTGAATCGGCTGCTTCACAAGGGATCTCG\n",
      "CTGCTCTCGAGCTATGGTCCAACAGAAGCCACGGTCGTCGCCACCTTCTTGCCGATCGTTTGCGACCAGACCACCATGGACGGCGCACTGCTCAGGCTCGGCCGGCCGATCCTACCGAAC\n",
      "ACGGTGTTCCTCGCGTTCGGTGAAGTCGTCATTGTCGGGGATTTAGTCGCCGACGGCTACCTCGGGATCGACGGCGACGGCTTCGGCACCGTGACGGCCGCAGACGGTTCCCGACGCCGT\n",
      "GCCTTTGCCACTGGCGACCGGGTGACCGTCGACGCCGAAGGATTTCCGGTCTTCTCCGGACGCAAAGACGCCGTCGTCAAGATCTCCGGCAAGCGTGTCGATATCGCTGAGGTAACCAGG\n",
      "CGCATCGCCGAAGACCCCGCGGTGTCAGATGTCGCCGTCGAGTTGCACAGCGGAAGCCTCGGAGTGTGGTTCAAGAGCCAACGGACCCGCGAGGGCGAACAAGACGCTGCCGCGGCGACC\n",
      "CGGATCAGGCTCGTCCTCGTGAGTCTGGGAGTGTCGTCGTTTTTCGTTGTCGGCGTGCCGAATATCCCGAGGAAGCCCAACGGGAAGATCGACAGCGACAACCTGCCGAGGCTGCCTCAG\n",
      "TGGTCAGCTGCTGGGCTAAACACCGCCGAGACGGGTCAGCGAGCGGCCGGCCTCTCGCAGATCTGGAGCCGGCAGCTCGGCCGGGCAATCGGGCCGGACTCGTCGCTGCTTGGTGAGGGC\n",
      "ATCGGCTCGTTGGATCTCATCAGAATACTGCCCGAGACGCGTAGGTATCTGGGGTGGCGCCTCTCGCTGCTGGATCTGATCGGTGCCGATACCGCCGCCAATCTGGCCGATTACGCGCCA\n",
      "ACGCCCGACGCGCCGACGGGCGAAGATCGGTTTAGGCCGCTGGTGGCCGCGCAACGGCCCGCGGCGATTCCGTTGTCGTTTGCCCAGCGGCGACTATGGTTTCTCGACCAGTTACAGCGA\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CCCGCTCCGGTCTACAACATGGCGGTGGCGTTGCGGCTGCGCGGGTATCTCGATACCGAGGCGTTGGGCGCGGCGGTCGCCGATGTCGTGGGCCGCCACGAAAGCCTACGGACGGTGTTT\n",
      "CCGGCGGTCGACGGGGTCCCTCGGCAGCTGGTCATCGAAGCGCGGCGGGCAGATCTTGGCTGCGACATCGTCGATGCCACCGCATGGCCGGCTGACCGGCTGCAACGGGCCATCGAGGAG\n",
      "GCGGCGCGCCACAGCTTCGATTTGGCAACCGAGATACCTTTGCGGACGTGGCTTTTCCGGATCGCCGACGACGAACATGTGCTGGTGGCGGTTGCACACCATATCGCCGCCGACGGCTGG\n",
      "TCGGTGGCTCCGCTGACGGCCGATCTGAGTGCGGCATATGCCAGCCGTTGTGCGGGTCGGGCACCGGACTGGGCGCCATTGCCAGTGCAGTATGTCGATTACACGCTGTGGCAGCGGGAA\n",
      "ATCCTCGGTGATCTCGACGACAGCGACAGCCCGATCGCCGCGCAGCTGGCCTACTGGGAAAATGCGTTGGCCGGTATGCCGGAACGGCTGCGGCTGCCCACCGCTCGGCCCTATCCACCG\n",
      "GTTGCCGATCAGCGCGGCGCCAGTTTGGTGGTGGATTGGCCGGCGTCGGTGCAACAGCAGGTGCGTCGGATCGCCCGCCAGCACAACGCGACCAGCTTCATGGTGGTAGCTGCCGGGCTT\n",
      "GCCGTGCTGCTGTCGAAACTCAGCGGAAGCCCCGATGTGGCGGTCGGATTTCCCATCGCCGGCCGCAGCGATCCTGCGCTGGATAACTTGGTGGGCTTTTTTGTCAACACCTTGGTGTTG\n",
      "CGGGTCAACCTGGCCGGTGATCCCAGCTTCGCCGAACTGCTGGGGCAGGTGCGAGCGCGCAGCCTGGCCGCCTACGAAAATCAAGACGTACCTTTCGAGGTGCTCGTTGATCGCCTCAAA\n",
      "CCCACTCGAGCCCTGACCCATCACCCGCTGATCCAGGTGATGTTGGCCTGGCAGGACAATCCGGTTGGACAGCTGAATTTGGGTGATCTGCAGGCCACCCCGATGCCGATCGACACCCGC\n",
      "ACCGCCCGCATGGACTTGGTGTTTTCGTTAGCGGAACGCTTCAGCGAGGGTAGCGAACCTGCCGGGATCGGCGGAGCGGTGGAATACCGCACCGATGTGTTTGAAGCCCAAGCAATCGAC\n",
      "GTGCTTATCGAGCGGTTGCGGAAGGTGTTGGTGGCGGTGGCCGCTGCTCCGGAACGGACGGTGTCGTCGATCGATGCGCTGGATGGGACCGAGCGTGCCCGGTTGGATGAGTGGGGTAAC\n",
      "CGCGCTGTGCTGACTGCGCCCGCGCCCACGCCGGTGTCGATCCCGCAGATGTTGGCCGCCCAGGTGGCACGTATCCCCGAAGCGGAGGCGGTGTGTTGCGGGGACGCGTCGATGACGTAT\n",
      "CGGGAACTCGACGAGGCGTCCAACCGGTTAGCGCATCGGCTGGCAGGTTGTGGGGCCGGCCCGGGCGAGTGTGTGGCGCTGCTGTTCGAGCGGTGCGCGCCGGCGGTCGTGGCGATGGTG\n",
      "GCAGTGCTCAAAACCGGGGCGGCGTATCTGCCGATCGATCCGGCGAATCCTCCGCCGCGGGTGGCGTTCATGCTCGGCGACGCGGTGCCCGTGGCCGCGGTCACCACGGCTGGGCTGCGC\n",
      "TCCCGGTTGGCGGGACACGACTTGCCGATCATCGATGTCGTCGATGCTTTAGCGGCATATCCGGGCACGCCCCCACCCATGCCGGCCGCAGTGAACCTCGCCTACATCCTGTACACCTCG\n",
      "GGCACTACCGGCGAGCCCAAAGGCGTGGGGATCACCCATCGCAACGTCACCAGGCTGTTCGCATCACTGCCGGCACGCTTGTCGGCGGCGCAGGTGTGGTCGCAGTGTCATTCCTATGGC\n",
      "TTCGACGCCTCGGCGTGGGAGATCTGGGGCGCGTTGCTAGGTGGTGGGCGACTGGTGATCGTGCCCGAGTCGGTGGCGGCCTCGCCGAACGACTTTCATGGGCTGCTCGTGGCCGAACAC\n",
      "GTCAGCGTGCTGACTCAGACTCCGGCTGCGGTGGCAATGTTGCCGACGCAGGGTTTGGAGTCGGTGGCGTTGGTGGTGGCCGGTGAGGCATGTCCGGCAGCGCTGGTGGATCGGTGGGCG\n",
      "CCCGGGCGGGTGATGCTAAATGCTTATGGCCCAACCGAGACCACGATCTGTGCGGCGATAAGTGCGCCGTTGCGACCGGGTTCGGGGATGCCGCCGATTGGTGTTCCGGTGTCGGGGGCG\n",
      "GCGTTGTTTGTGCTGGATAGCTGGTTGCGCCCGGTACCGGCCGGGGTGGCCGGAGAGTTGTACATTGCCGGTGCGGGCGTCGGTGTTGGGTATTGGCGTCGGGCGGGGCTGACCGCGTCA\n",
      "CGGTTTGTGGCCTGCCCATTCGGCGGTTCCGGGGCACGCATGTATCGCACCGGGGATCTGGTGTGTTGGCGCGCCGATGGCCAGTTGGAGTTCCTGGGGCGCACCGACGATCAGGTCAAG\n",
      "ATCCGCGGGTATCGCATCGAGCTCGGCGAGGTTGCGACCGCGCTGGCCGAGCTGGCTGGGGTAGGTCAAGCGGTTGTAATCGCCCGTGAAGACCGCCCTGGGGACAAGCGCCTAGTCGGG\n",
      "TATGCCACCGAAATTGCCCCCGGGGCAGTGGACCCGGCCGGGCTGCGGGCGCAACTAGCCCAGCGATTGCCCGGTTACCTGGTGCCAGCCGCGGTGGTAGTGATCGATGCGCTTCCGTTG\n",
      "ACGGTCAACGGCAAACTTGATCATCGTGCGTTGCCGGCACCGGAATACGGTGATACCAACGGATATCGCGCTCCGGCCGGGCCGGTTGAGAAGACCGTGGCCGGCATCTTTGCCCGGGTG\n",
      "CTTGGGCTTGAGCGGGTCGGCGTCGACGACTCGTTCTTCGAGCTCGGCGGCGATTCGCTGGCGGCAATGCGGGTTATCGCCGCGATCGACACCACCCTAAACGCCGATCTGCCGGTGCGC\n",
      "GCGTTGCTGCACGCGTCGTCGACGAGAGGTTTAAGCCAGCTGTTGGGGCGAGATGCCCGACCGACCAGCGATCCGCGCTTGGTGTCTGTGCACGGCGACAACCCCACCGAGGTGCATGCC\n",
      "AGCGACCTCACGCTGGACCGGTTCATCGACGCCGACACGCTGGCCACCGCCGTCAACCTGCCGGGCCCGAGCCCCGAGCTACGGACGGTCCTGCTGACGGGCGCGACGGGTTTCCTCGGA\n",
      "CGGTATCTGGTCCTTGAATTGCTGCGGCGGCTGGACGTCGACGGCAGGCTGATCTGTTTGGTGCGGGCGGAGTCCGACGAGGATGCGCGGCGTCGTCTGGAGAAGACCTTCGATAGCGGT\n",
      "GACCCGGAATTGCTGCGGCACTTCAAGGAGCTTGCCGCCGACCGGCTGGAGGTCGTCGCAGGCGACAAGAGCGAACCCGACCTGGGCCTGGACCAACCGATGTGGCGGCGGCTGGCCGAA\n",
      "ACCGTGGATTTGATTGTCGATTCCGCGGCGATGGTCAACGCGTTTCCCTACCACGAATTGTTCGGGCCCAACGTCGCGGGCACCGCCGAGCTGATCCGAATCGCGCTTACCACCAAGCTC\n",
      "AAACCCTTCACCTACGTGTCAACCGCCGACGTGGGTGCTGCGATCGAGCCGTCGGCGTTCACCGAGGACGCCGACATCCGGGTAATCAGCCCCACCCGCACCGTCGACGGCGGCTGGGCT\n",
      "GGCGGCTACGGCACCAGCAAGTGGGCCGGTGAGGTGCTGCTGCGCGAGGCCAACGACCTGTGCGCGCTGCCGGTCGCGGTGTTTCGCTGCGGGATGATCCTGGCCGACACCAGCTATGCC\n",
      "GGACAGCTCAACATGTCGGACTGGGTCACCCGGATGGTGTTGAGCTTGATGGCTACCGGCATCGCGCCTCGTTCGTTCTACGAACCGGACTCCGAGGGCAATCGGCAACGCGCGCACTTC\n",
      "GACGGGCTGCCAGTCACCTTCGTTGCCGAGGCGATCGCGGTGCTGGGCGCGCGGGTGGCCGGCTCATCGTTGGCGGGATTTGCGACCTATCACGTGATGAACCCGCACGACGACGGTATC\n",
      "GGGCTCGATGAGTATGTGGACTGGCTGATTGAGGCCGGCTACCCGATACGCCGCATCGATGACTTTGCGGAGTGGTTGCAGCGGTTTGAGGCCAGCCTGGGCGCTCTGCCGGATCGGCAA\n",
      "CGCCGGCACTCGGTGCTGCCGATGCTGCTGGCGAGCAATTCCCAGCGATTGCAGCCGCTTAAGCCGACCAGGGGGTGCTCCGCGCCGACCGACCGATTCCGTGCCGCGGTGCGAGCGGCG\n",
      "AAAGTCGGCTCCGACAAGGACAATCCAGACATCCCGCACGTGTCGGCGCCGACCATCATCAACTACGTCACCAACCTACAACTGCTCGGACTGCTGTAG\n",
      ">Rv0134_N1 Seen in 1 sample(s).\n",
      "ATGATCGCTCTGCCCGCCTTGGAAGGTGTCGAACATCGGCACGTGGATGTGGCGGAAGGCGTCAGGATCCACGTTGCGGACGCCGGGCCGGCCGATGGTCCGGCGGTAATGCTGGTGCAC\n",
      "GGCTTCCCGCAGAACTGGTGGGAGTGGCGCGACCTCATCGGCCCGCTGGCCGCCGACGGCAACCGGGTGCTGTGTCCCGACCTGCGCGGCGCGGGCTGGAGTTCGGCGCCCCGCTCGCGG\n",
      "TATACCAAGACCGAGATGGCTGACGATCTGGCTGCGGTTTTGGACGGCCTGGGTGTGGCCAAGGTCAAGCTGGTGGCCCACGATTGGGGTGGGCCGGTCGCGTTCATCATGATGTTGCGC\n",
      "CATCCCGAGAAGGTGACCGGGTTTTCGGCGTGAACACCGTGGCACCCTGGGTGAAGCGCGATCTTGGCATGCTCCGCAATATGTGGCGGTTCTGGTATCAGATCCCCATGTCGCTGCCGG\n",
      "TGATCGGCCCGCGGGTGATCAGCGATCCTAAGGGCCGCTACTTCCGGCTGTTGACCGGGTGGGTCGGGGGCGGATTTCGGGTTCCCGATGACGACGTGCGCCTGTACTTGGACTGCATGC\n",
      "GCGAGCCGGGGCACGCCGAGGCCGGATCGCGGTGGTATCGCACCTTTCAGACCAGGGAAATGCTGCGCTGGCTGCGCGGCGAGTACAACGACGCTCGGGTCGATGTCCCGGTCCGATGGC\n",
      "TGCACGGCACCGGAGATCCGGTGATCACGCCCGACCTGCTGGACGGCTATGCCGAGCGGGCCAGCGATTTCGAGGTGGAGCTGGTCGACGGCGTGGGCCATTGGATCGTCGAGCAGCGAC\n",
      "CCGAGCTGGTGCTCGACCGGGTGCGTGCGTTCCTAGCTGCGGGGACCGAGCAGCGCGATTGA\n",
      ">Rv0165c_N1 Seen in 1 sample(s).\n",
      "TCAGCCAGGGCCTCCGTCAGCCTGCGTGCCCCATCGGTGAACTGCCAGACGGTGTGCTCGATTACGGCGGCTGTGTCGCGGCGGCGCAGCGCGGCGATCAGCTGCCGATGACTGTTCACC\n",
      "GCGTCCGCGCCCCATCGCGGGTCGGCCGCGAACACCTGCGCCGGCATATAGCGCGCGGCATTAAGCAGGAACCAGGCCAACTTGATCCGGCGGCTCGCTTTGTTGAAGACGCGGTGGAAC\n",
      "GCGAACTCGATCGACGCGATGGTTTTGGCATCACCGGACCCGATAGCACCGGCCAGCGCATTGTTGATGCGGTCCAGCTCGTCGATCTCAACGTCGGTGATGTGAGCGGTGGCCGATGTG\n",
      "GCAAGTTCTTGGGCAATGGTGGCCTGCAGCCAGAAAATGTCGTCGATGTCTTGGCGGGTCAACGGCAGCACCACGTGGCCGCGATGTGGCTCCAGCCCGACCATCCCCTCACCGCGCAGT\n",
      "TTCAGCAGCGCCTCCCGCACCGGCGTGACGCTGACTCCGAGCTCGGCTGCCGTCTCGTCCAGACGGATGAACGTTCCAGAGCGCAGGGCGCCCGACATGATGGCGGCCCGCAGGTGGCCC\n",
      "GCGACCTCGTCGGACAACTGTGCCCGGCGCAGGGGAAGCTGGCTCCGCGGCTTCGCCGATAGAGGTGCGTTCAC\n",
      ">Rv0195_N1 Seen in 1 sample(s).\n",
      "ATGGCACCGGTGAATGTCATTTCGGTCGCGGTGGTGGCGAGCGACCCGTTGACCCGCGATGGAGCTTTGGCCCGACTCTCGTCTCACCGGGAGCTCGACGTGCGCGCTTGGCAGGCTGGA\n",
      "TGCGAAACCTCGGTCCTGCTCGTGCTGGCCACCACGATCACCGCGCCTCTTCTATGCCAGATCGAGGACGCGCAGAAGGATGGCCCCAGTCACGCGCCGAAACTGGTCGTCGTCGCCGAC\n",
      "GAATTCTCCGCTGAACAAGTTTTCCGGATGATCAAGCTGGGGTTGACCGGGTTGTTGTATCGCAGCCAGAGCACGTTCGACTGCATCGTCGAGACAATCCGGTTGTCCGCCGAAGGCCGC\n",
      "CTGCGACTCCCCGAACGTGTCCAGCGTTACCTGGTCGGCCGCATCAAGTCCACCCCGACCGCCGAACCTGACACACCGTGCGCCGCCGCTCTTGCCGAGCGTGAGGTGGCGGTGCTGCGT\n",
      "CTGCTAGCGGACGGCTTGAGCACGCACCAAGTGGCGGTGCAGCTCAACTATTGCGAGCGCACGATCAAGAACATCGTTCATGACATAGTGACGCGGCTGAAGCTCCGCAACCGCACGCAT\n",
      "GCCGTCGCACATGCGCTGCGCGCGGGCCTCATTTGA\n",
      ">Rv0226c_N1 Seen in 1 sample(s).\n",
      "TTAATCCTGGGCGCGGCTCGCCGGCGTGTCTTCGCCGTGGTGTAAGTGTCGGCGCACCCAATAGCCGGCCGCGCCAGCGCCGCCGACCAGCAGCATCGAAAGCCACGCCCAATGCGCGAG\n",
      "CATTGTCGCTTTGAGGCGGGCCGACGATGCACCGGAGGTTTGGCCGCCGACCCGATAAAGAGCCAATTCGTCGTCGCGGTGCGCCGCTGCTAGCCGGCCGAGGGTGCGTGCGGCCGCGCC\n",
      "CATGTCGCCGGCGCTGTCGGATTCGACGACCAGCCACCCGACGCCGGCCGCGGCCAAGGTTGACGGATGGGGCCCGGTGAGCAGCAGCTCCTGGACCGCCCGGGCGTGCGCGTCTTCGCC\n",
      "GGGAACGGTCACCCCGGAAATGACCAGATCACCTGTGGTCAGCACATCGGCGCGAACCCAACGGGGGAGCGGATCGAGTACCGGTGCCGAACCGGACCACGAGAAGCGCCGCATGGTGCC\n",
      "CGCGGGCAAGACCGCAACCGTCCGGGGATCGGCATTGATCGCCGCTGCCACCGCCGCCCAACCGGACGGGTAGTGCACAGGCGCAACCTTGCCCCACACCCCCCACGCCAAGTCAGCCAG\n",
      "CGTTAGGACCAGCGCCAGACAGCAGACCACCGCCGCCGTTGCCGGTCGCAGCCAGCGTCGCAGCGTTAGCACCGTGCCCGCACCGGAGAGTGTGTATCCGGGTACCGCCAGCGCGACCCA\n",
      "CTTCTGTCCGTCGCGCAGCACGCCCAGGCCGGGTGCGGCATCGACCACCACCCGTAGCGCGTGCAGACCTGGGCCGGTCGCAAGGACAGCCGGGACCATCACGGACACCGCCGCTAGTGT\n",
      "CAGCAGCGGCACTGCCACGGGCCGGCGCGCCACAGTCGGTAGTCCGATCGCCACCATGGCGAGTAGTACGACGGCGGATGCCACTGCGAAAAGCGTTGTCCGCGAGCTAGGTACGGCCTC\n",
      "GCCGTTCCAGATCCCACCGAGACTGGCCAAGCTGCCAAGCGTGCCCAGCCCCGGTTCGGCGCGTGGCGCGAACGCGGTAACCCCAAGCTGATTGGCTGCCGTGTGGCTGGTCAACGACGA\n",
      "GCCCAGCGCCGACGCCGTCAGCCAGGGCAGCGCACCCACCAGCGCGGAGCCCAACGCCGCGACCCCACATTGCCAGCGCGGGCGGCCCGCGCCGGGCATCGCCACGCACACCACCGCAAC\n",
      "TGTCGCGGCGAGTAGCAGCCCGGACGGGGTCAGGCCGGCCAGCGCAACCCAGAACGCCAGCCCAAAAAGCCCGAACCAACCCGCGCCAACCGTTGTTCGCATCGTTAACATCGCGGTCGC\n",
      "AACCCAGGGCAGACACCCATAGCCGACCAGCAGGCTCCAATGGCCCTGCAAAAGTCGTTCGGCCACATAGGGATTCCAGATCGCCAGCGTGATCGCGACAAACTGGCCGGCTGCCCCCGC\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "TGCGGGTAGTGCCGTTGCGACCAGTCGGGCCGCGCCCCAGCCCGCCAGCCAAAGCCCCAGCAGCAGCAGCGCTTTCACCACGACGCCGCCGTCGACGAGGTGTGACGCCAAAGCGACCGC\n",
      "GAAGTCCTGCGGAGTCGCCCGGGGCGCCGATGTCAGCCCTAGGGCGTTGGCCGACACATACGACCGTGGTGTGGACACTGCATCGCGCAGCAGTAGGTATCCGGGCCGCAGTAGCGGCGC\n",
      "GGCCAACAGCAGCACCAAGACCAGCGCGTACCCCGGTCGGAACCAGCGCAC\n",
      ">Rv0276_N1 Seen in 1 sample(s).\n",
      "ATGGCGATTTCGCTGGTGGCTCACCAGCCCATCCCCCACGTCGAGCGTCGCATGGCCGACCCACCCCGTCTCCAGCTGGCCAGGCGCCGGCGATCGGCGGCCGGCCCCGGCGGTAACGAG\n",
      "GACAGCTTGATGGGAGTGGCGCTGCTAGCCGGCCCGGCCAACGTGATCATGGAGTTGGCGATGCCGGGTGTCGGCTACGGCGTGTTGGAGAGCCGTGTCGAAAGCGGCCGGCTGGACCGC\n",
      "CATCCGATCAAGCGGGCGCGCACCACCTTTACCTACGTTGCGGTGGCCGTTGCCGGCAGCGACGACCAGAAGGCGGCCTTTCGTCGCGCGGTGAATAAGGTTCACGCGCAGGTGTATTCG\n",
      "ACTCCGGAGAGCCCGGTGTCCTACCACGCGTTCGATCCCGAACTACAGCTGTGGGTGGCGGCATGCCTCTATAAGGGCGGCGTCGACGTCTACCGCACCTTCGTCGGCGAGATGGACGAC\n",
      "GAAGAGGCCGACCATCATTACCGCGCGGGCATGGCGATGGGCACCACGTTGCAGGTGCCGCCGCAGATGTGGCCACCGGATCGGGCGGCCTTCGACCGCTACTGGCGGCAATCACTGGAC\n",
      "AGGGTGCACATCGATGACGTCGTTCGCGACTACCTGTATCCGATCGTGGCGCTCCGAATTCGCGGGATCGCACTGCCGGGTCCGCTGCGGCGGCTGTCGGAGGGTATCGCGCTGCTGATC\n",
      "ACCACCGGTTTCCTGCCGCAGCGGTTTCGCGACGAGATGCGGTTGCCGTGGGACGCGACCAAGCAGCGGCGCTTTGACGCGCTCATGGCCGTGCTGCGCACGGTGAATCGCCTGATGCCG\n",
      "CGGTTTGTCCGGGAGTTCCCGTTCAACCTGATGCTCTGGGACCTGGACCGGCGGATGAGGCGCGGGCGCCCGCTGGTGTAA\n",
      ">Rv0290_N1 Seen in 1 sample(s).\n",
      "ATGTCCGGCACCGTCATGCAGATCGTCCGCGTCGCCATTCTTGCGGACAGCAGGTTGACCGAGATGGCCCTGCCCGCGGAGTTGCCACTGCGCGAAATCCTGCCCGCGGTACAACGCTTG\n",
      "GTGGTTCCCTCGGCGCAAAACGGCGATGGTGGCCAAGCCGACTCCGGCGCTGCCGTGCAACTGAGTTTGGCGCCCGTCGGCGGGCAGCCGTTTAGCTTGGATGCCAACCTGGACACCGTC\n",
      "GGTGTCGTCGACGGTGATCTGTTGGTGTTGCAGCCGGTGCCCACCGGTCCGGCCGCGCCGGGCATCGTCGAAGACATCGCCGACGCCGCGATGATCTTTTCGACGTCGCGGTTAAAGCCC\n",
      "TGGGGCATAGCGCATATCCAACGAGGAGCGCTGGCCGCGGTGATTGCCGTGGCTCTGCTGGCTACCGGTTTGACGGTGACCTATCGGGTTGCCACCGGTGTGCTGGCCGGGCTGCTGGCG\n",
      "GTGGCCGGGATCGCGGTGGCTAGCGCGCTGGCCGGATTGTTGATCACCATCCGTTCGCCACGTTCGGGTATCGCGCTGTCGATCGCCGCGCTGGTCCCCATCGGCGCGGCCCTGGCGTTG\n",
      "GCGGTGCCAGGAAAGTTCGGGCCGGCGCAGGTATTGCTGGGTGCAGCTGGGGTAGCCGCATGGTCGCTGATCGCGCTGATGATTCCCAGCACCGAACGGGAACGCGTCGTCGCCTTCTTC\n",
      "ACCGCAGCGGCGGTGGTCGGGGCGTCGGTGGCGCTGGCGGCCGGTGCGCAATTGCTGTGGCAGCTGCCGTTGTTGAGCATCGGCTGCGGGCTGATTGTGGCGGCGCTGTTGGTCACCATC\n",
      "CAGGCGGCTCAGCTTTCCGCACTGTGGGCGCGGTTCCCGTTGCCGGTGATCCCGGCGCCGGGGGATCCCACCCCGTCGGCCCCGCCGTTGCGCCTGCTGGAGGATTTGCCTCGGCGGGTG\n",
      "CGGGTCAGTGACGCCCATCAAAGCGGCTTCATCGCCGCGGCCGTGCTGCTCAGCGTGTTGGGGTCGGTGGCCATCGCGGTGCGCCCAGAGGCGCTCAGCGTTGTGGGCTGGTATCTGGTG\n",
      "GCGGCGACTGCGGCCGCGGCCACCCTGCGCGCGCGGGTGTGGGATTCGGCCGCATGCAAGGCGTGGCTGCTGGCTCAGCCCTATCTGGTAGCCGGGGTCCTGTTGGTGTTCTACACCGCG\n",
      "ACCGGACGCTATGTCGCCGCGTTCGGCGCGGTGCTGGTGCTAGCCGTGCTCATGCTGGCCTGGGTTGTGGTGGCACTGAACCCGGGCATCGCTTCGCCGGAGAGCTACTCGCTGCCGCTG\n",
      "CGCCGGCTGCTGGGTTTGGTCGCCGCCGGGCTGGATGTTTCGCTGATCCCCGTCATGGCCTACCTGGTCGGATTGTTCGCTTGGGTGCTCAACAGATGA\n",
      ">Rv0551c_N1 Seen in 1 sample(s).\n",
      "CTAGCCGACCGCGCGCCCAGCGCCTTCCCAGAACCGTGCGCGCACGGCCTTCTTGTCCGGCTTTCCTAGACCGGTCAACGGCAAAGAGTCGACGACCACCACCCGCTTGGGTGCCTGCAC\n",
      "CGATCCCTTGCGTTGTTTGACCGCTGCCTGGATCTCGGCGGTCATGGCCTCGATCGCGGGCTCATCGCGGGCCGCGTTGGAGCGCAACACCACCACCGCGGTGACGGCCTCGCCCCACTT\n",
      "CTCATCCGGCGCGCCAACCACGCACACCTGAGCAACCGCCGGATGCTCGGCCACCACGTCCTCGACCTCCCGGGGGAACACGTTGAAGCCGCCGGTGACGATCATGTCCTTGACGCGGTC\n",
      "GACGATGTAGTAGAAGCCATCGGAGTCCTCGCGGGCCAGGTCGCCGGTGTGCAGCCAGCCGTCTTTAAAAGTCCGCGACGTCTCGTCTGGCAGATTCCAGTAACCGCCCGCCAACAGCGG\n",
      "TCGCTGACACAGATTTCGCCGACTTCGCCCTGCTTCACCGGCTTGCCATGCTCGTCTAACAGCGCGACGCGGGCGAACAGCGTCGGCCGCCCACATGAGGTCAGCCGCTTCTCGTCGTGA\n",
      "TCGCCCTTGGCCAGATAGGTGATCACCATGGGCGCCTCGGATTGCCCGTAGTACTGGGCGAAGATTGGGCCGAACCGCCGGATCGCCTCGGCTAGTCGCACCGGGTTGATCGCCGAGGCG\n",
      "CCGTAGTAGACGGTTTCCAGCGACGACAGGTCCCGGGTGTGCGAATCCGGGTGGTCCAGCAGCGCGTACAGCATCGATGGCACCAACATGGTCGCTGTAATGCGTTGCTCCTCAATGATT\n",
      "CTGAGTACCTCGGCCGGGTCGAACTTCGCCAGCACTATCATCTCGCCGCCCTTGATCACCGTCGGCGTGAAAAACGCCGCGCCGGCGTGCGACAGCGGGGTGCACATTAAGAACCGCGGG\n",
      "TTGGCCGGCCACTCCCATTCGGCGAGCTGGATCGAGGTCATGGTGGCGATCGACTGCGCGGTGCCTATCACGCCCTTAGGCTTGCCGGTGGTGCCGCCGGTGTAAGTCAGGCCGATAACT\n",
      "TGGTCGGGTGGCAGGTCGGCGGCGACCAGCGGCTGCGGCTGGTATTTGGCGGCCTCGGCGGATAGGTCGACTGCCACATGCTTGAGCGCATCGGGCACCGGCCCAATGGTGAGGATTTGC\n",
      "TGCAGCGAGTCCACCTGCTCCAGCAGAGCCAGTGCGCGCTCGACGAACATCGGGTTGGGGTCGATGATCAGTGAGCTGATGCCGGCGTCGTTCAGCACGTAGGCGTGATCGGCCAGCGAG\n",
      "CCCAACGGGTGCAGCGCGGTGCGCCGATAACCGCGGGCCTGCCCGGCGCCGATGATCATCAAAACTTCAGGACGGTTGAGCGACAGCAGACCGACCGCCACCCCGGTGCCGGCACCTAGC\n",
      "GCCTCGAATGCCTGGATGTACTGGCTGATACGGTCCGCCAGCTGGCCACCGGTCAGCCTGGTGTCGCCGAGGAACAGCACCGGCTTGTTCTGGTGGCGCTTGAGCGCTCCCACTAGCAGA\n",
      "TGGCCGTTGTGGGTCGGGCTGCGCAACAGCTCGCCCGAACAATCCTGGTCACGCATGGCGCCGCTCTCCCTCGCTAGCTGGGGTACCCCCACCGCATCGCTTCGTCCCCCGCAAGCGGGT\n",
      "GGTACCCCCACTGCATCGTCGCCGGCGGTGCTCAT\n",
      ">Rv0654_N1 Seen in 1 sample(s).\n",
      "ATGACCACCGCACAAGCCGCCGAATCCCAAAACCCATATCTCGAGGGCTTCCTGGCGCCGGTGAGCACCGAGGTAACTGCCACCGACCTGCCGGTCACCGGCCGCATTCCGGAACACCTC\n",
      "GACGGGCGTTATCTGCGTAACGGCCCCAACCCGGTCGCGGAGGTCGACCCGGCCACCTACCACTGGTTCACCGGCGACGCCATGGTGCACGGAGTCGCGCTGCGCGACGGGAAGGCCCGC\n",
      "TGGTATCGCAATCGCTGGGTCCGCACACCCGCGGTGTGCGCCGCCCTGGGCGAGCCCATTTCGGCCCGGCCTCACCCGCGCACCGGGATTATCGAGGGCGGTCCCAACACCAACGTGCTG\n",
      "ACCCACGCCGGACGCACCCTGGCCTTGGTTGAGGCCGGCGTGGTCAACTACGAACTCACCGATGAGCTGGACACCGTGGGACCCTGTGACTTCGACGGCACCCTGCACGGCGGTTACACC\n",
      "GCCCATCCGCAGCGTGATCCGCACACGGGTGAACTGCACGCGGTGTCCTACTCGTTCGCCCGCGGACACAGAGTGCAGTACTCGGTGATCGGCACCGACGGACACGCTCGTCGGACGGTT\n",
      "GATATCGAGGTGGCGGGATCGCCGATGATGCACAGCTTCTCCCTGACCGACAACTACGTGGTGATCTACGACCTGCCGGTGACCTTCGACCCAATGCAGGTGGTGCCGGCGTCCGTGCCA\n",
      "CGCTGGCTGCAACGGCCCGCCAGGTTGGTGATCCAGTCGGTCCTGGGCCGTGTCCGCATCCCCGACCCGATAGCGGCGTTGGGCAACCGGATGCAGGGTCACTCCGATCGCCTCCCGTAC\n",
      "GCCTGGAACCCCAGCTACCCGGCGCGCGTCGGTGTCATGCCGCGCGAGGGTGGCAACGAGGACGTGCGGTGGTTCGACATCGAACCCTGCTACGTATACCACCCACTTAACGCCTACTCG\n",
      "GAGTGCCGGAACGGCGCTGAGGTGCTGGTGTTGGACGTGGTGCGCTACTCACGGATGTTTGATCGCGACCGGCGGGGTCCCGGCGGTGACAGCCGGCCCTCGCTGGATCGCTGGACCATC\n",
      "AACCTGGCGACCGGTGCGGTGACCGCCGAATGCCGCGACGATCGGGCGCAGGAGTTTCCCCGCATCAACGAGACTCTGGTGGGTGGGCCGCATCGCTTCGCCTACACCGTCGGCATCGAG\n",
      "GGTGGGTTTCTCGTCGGCGCCGGCGCTGCGTTGTCGACTCCGCTGTATAAACAGGACTGCGTGACCGGGTCCAGCACGGTCGCCTCGCTCGATCCCGACCTGTTGATCGGCGAGATGGTG\n",
      "TTCGTGCCGAACCCGTCGGCGCGTGCAGAAGATGACGGGATTCTCATGGGCTACGGCTGGCACCGCGGCCGCGACGAAGGCCAGCTGCTCTTGCTGGATGCCCAGACTCTCGAGTCGATC\n",
      "GCCACCGTGCACCTGCCACAGCGTGTGCCGATGGGCTTCCACGGCAACTGGGCGCCGACCACCTGA\n",
      ">Rv0739_N1 Seen in 1 sample(s).\n",
      "TTGGTGCTGACGCGGCGCGCGCGCGTGAAGTGGCGCTGACACAGCACATTGGGGTATCCGCGGAGACCGATCGGGCCGTCGTCCCCAAGCTGCGCCAGGCCTATGACAGCCTGGTGTGCG\n",
      "GTCGCCGCCGGCTTGGCGCCATTGGAGCCGAGATCGAGAACGCGGTGGCCCATCAGCGCGCGCTGGGCCTTGACACCCCGGCCGGTGCCCGTAACTTCTCCCGGTTTCTCGCCACCAAAG\n",
      "CACACGACATCACGCGAGTGCTGGCAGCAACCGCCGCGGAATCCCAGGCCGGCGCGGCGCGGTTGCGATCCCTGGCTTCGTCCTATCAGGCTGTGGGATTTGGCCCCAAACCCCAGGAGC\n",
      "CGCCTCCGGATCCAGTGCCATTTCCGCCCTACCAGCCGAAGGTGTGGGCGGCGTGCCGGGCGCGTGGCCAAGACCCGGACAAGGTCGTCAGGACGTTCCATCACGCGCCGATGAGCGCGA\n",
      "GATTCCGCTCGCTACCGGCCGGAGACTCCGTGTTGTACTGCGGCAATGACAAGTACGGGCTGCTGCACATTCAGGCCAAGCATGGACGCCAATGGCACGATATTGCGGATGCACGATGGC\n",
      "CGAGTGCAGGCAATTGGCGCTATCTCGCCGATTACGCAATCGGTGCCACACTGGCCTACCCGGAGCGAGTGGAGTACAACCAAGACAACGACACGTTCGCCGTATACCGGAGAATGTCGT\n",
      "TGCCAGACGGCAGATACGTTTTCACAACCCGCGTCATTATTTCGGCACGCGACGGGAAGATCATTACGGCCTTCCCGCAGACGACGTGA\n",
      ">Rv0757_N1 Seen in 1 sample(s).\n",
      "ATGCGGAAAGGGGTTGATCTCGTGACGGCGGGAACCCCAGGCGAAAACACCACACCGGAGGCTCGTGTCCTCGTGGTCGATGATGAGGCCAACATCGTTGAACTGCTGTCGGTGAGCCTC\n",
      "AAGTTCCAGGGCTTTGAAGTCTACACCGCGACCAACGGGGCACAGGCGCTGGATCGGGCCCGGGAAACCCGGCCGGACGCGGTGATCCTCGATGTGATGATGCCCGGGATGGACGGCTTT\n",
      "GGGGTGCTGCGCCGGCTGCGCGCCGACGGCATCGATGCCCCGGCGTTGTTCCTGACGGCCCGTGACTCGCTACAGGACAAGATCGCGGGTCTGACCCTGGGTGGTGACGACTATGTGACA\n",
      "AAGCCCTTCAGTCTGGAGGAGGTCGTGGCCAGGCTGCGGGTCATCCTGCGACGCGCGGGCAAGGGCAACAAGGAACCACGTAATGTTCGACTGACGTTCGCCGATATCGAGCTCGACGAG\n",
      "GAGACCCACGAAGTGTGGAAGGCGGGCCAACCGGTGTCGCTGTCGCCCACCGAATTCACCCTGCTGCGCTATTTCGTGATCAACGCGGGCACCGTGCTGAGCAAGCCTAAGATTCTCGAC\n",
      "CACGTTTGGCGCTACGACTTCGGTGGTGATGTCAACGTCGTCGAGTCCTACGTGTCGTATCTGCGCCGCAAGATCGACACTGGGGAGAAGCGGCTGCTGCACACGCTGCGCGGGGTGGGC\n",
      "TACGTACTGCGGGAGCCTCGATGA\n",
      ">Rv0818_N1 Seen in 1 sample(s).\n",
      "TTGTTGGAGTTATTACTGCTGACCTCGGAGCTGTATCCGGATCCGGTCCTGCCGGCGCTGTCGCTGCTGCCCCACACCGTGCGGACGGCGCCGGCCGAGGCGTCTTCGTTGCTGGAGGCG\n",
      "GGAAACGCAGACGCTGTGCTCGTCGACGCGCGCAACGACCTGTCGTCCGGGCGAGGCCTGTGCCGCCTGTTGAGCTCGACCGGCCGGTCGATCCCGGTACTGGCGGTGGTGAGCGAAGGC\n",
      "GGGCTGGTGGCGGTCAGCGCTGACTGGGGGCTGGACGAGATCCTGCTGCTCAACACCGGGCCCGCTGAGATCGACGCCAGACTGCGGCTGGTGGTTGGCCGGCGCGGAGATCTGGCTGAC\n",
      "CAGGAGAGTCTGGGCAAGGTGAGCCTGGGCGAGCTGGTGATCGACGAAGGCACCTACACCGCCCGGCTGCGTGGCCGCCCGCTGGATCTCACCTACAAAGAGTTCGAGCTGCTGAAATAC\n",
      "CTGGCGCAGCATGCCGGCCGGGTGTTCACTCGGGCGCAGCTGCTGCACGAAGTATGGGGGTATGACTTCTTCGGGGGCACCCGGACTGTTGATGTGCACGTGCGGCGGTTGCGGGCCAAA\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CTCGGCCCCGAGCATGAAGCGCTGATCGGCACGGTGCGCAACGTCGGATACAAAGCTGTTCGGCCGGCGCGCGGCCGACCGCCGGCCGCGGACCCCGACGACGAAGACGCCGATCCCGGC\n",
      "CGGGATGGTATGCAAGAACCACTGGTCGACCCGTTGCGCAGTCAGTGA\n",
      ">Rv0826_N1 Seen in 1 sample(s).\n",
      "GTGACCCAAGATACGTCTGCTACCTGTCCGCTGACCAGCACCGTGCAGGATTCCTCGCCGGTTGCGGGCCAGCTTGGCAGGCCTATAGGGTTCCGCGGACTGGCCGGCGGTTGCCCCGTG\n",
      "TCACCGCTGGGTTACGAATCGCCGCCGCTGCCGCTGGGGCCGGATTCGCTGACGTGGCGATACTTCGGTGACTGGCGCGGGATGCTGCAGGGACCGTGGGCGGGATCCATGCAGAATATG\n",
      "CATCCGCAGCTGGGCGCGGCGGTCGAAGATCATTCGACGTTCTTCCGGGAACGCTGGCCACGGCTGCTGCGGTCGTTGTACCCGATCGGCGGAGTTGTCTTCGACGGCGATCGAGCCCCA\n",
      "GTCACCGGTGTGCAGGTGCGTGACTACCACATCACCATCAAGGGTGTCGACGGTGCGGGCCGTCGCTACCACGCGTTGAATCCCGACGTCTTCTACTGGGCGCACGCCACCTTCTTTGTC\n",
      "GGCACGTTGCATGTGGCCGAGCGGTTCTGCGGTGGCCTGACCGAGGCGCAGCGGCGCCAGCTATTTGACGAGCACGTCCAGTGGTACCGCATGTACGGCATGAGCATGCGGCCGGTGCCG\n",
      "GCGACCTGGGAGGAGTTTCAGGACTACTGGGACCACATGTGCCGCAACGTGCTGGAGAACAACTTCGCGGCGCGTGCCGTGCTCGACCTGACCGAACTACCCAAACCGCCATTCGCCCAA\n",
      "CGAGTTCCGGATTGGCTGTGGGCCGCGCCGCGCAAGTTGCTGGCCCGGTTCTTCGTCTGGCTGACCGTCGGACTCTACGATCCGCCCGTGCGCGAGCTGATGGGCTACCGGTGGTTGCGC\n",
      "CGCGACGAATGGTTGCACCGCCGCTTTGGCGACATCGTCCGGCTCGTCTTTGCCTTGGTGGCATTCCGGTTTCGCAAGCACCCGCGGGCTCGCGCCGGCTGGGACCGTGCCACCGGCCGC\n",
      "ATCCCCGCCGATGCGCCGCTAGTACAGACGCCCGCGCGCAACCTGCCGCCGCCCGACGAGCGTGACAACCCGACGCACTACTGCCCTAAGGTCTGA\n",
      ">Rv0888_N1 Seen in 1 sample(s).\n",
      "ATGGATTACGCCAAACGCATCGGCCAGGTTGGGGCGTTAGCCGTTGTCCTGGGGGTGGGGGCGGCGGTGACTACCCACGCGATCGGCTCTGCCGCGCCGACGGATCCGAGCTCCTCGAGC\n",
      "ACCGATTCGCCGGTCGACGCGTGCTCGCCGTTGGGTGGGTCCGCCAGTTCGTTGGCTGCGATACCGGGCGCCAGTGTGCCACAGGTCGGCGTGCGACAGGTAGACCCCGGAAGCATCCCC\n",
      "GATGACTTGCTCAATGCCCTGATCGACTTTCTGGCCGCGGTACGCAACGGGTTGGTGCCCATCATCGAAAACCGCACTCCGGTAGCGAATCCGCAACAAGTCAGCGTCCCTGAGGGGGGG\n",
      "CACCGTCGGCCCGGTCCGGTTTGACGCCTGCGACCCCGATGGCAACCGGATGACCTTCGCGGTGCGCGAGCGCGGTGCACCCGGTGGACCCCAGCATGGCATCGTGACCGTCGACCAACG\n",
      "AACGGCCAGCTTCATCTACACAGCCGATCCGGGTTTCGTTGGCACCGATACCTTCAGTGTGAACGTCAGCGATGACACCAGCCTGCACGTGCACGGTCTGGCGGGATACCTGGGTCCGTT\n",
      "CCATGGGCACGACGACGTCGCCACCGTGACCGTGTTCGTCGGCAACACCCCGACCGACACCATCAGCGGCGACTTCAGCATGCTCACCTACAACATCGCGGGGCTGCCCTTCCCGCTATC\n",
      "CAGCGCAATTCTGCCCCGGTTCTTCTACACCAAAGAGATTGGGAAGCGGCTCAACGCCTACTACGTCGCGAACGTCCAGGAGGATTTCGCCTACCACCAATTCCTCATCAAGAAATCCAA\n",
      "GATGCCCAGCCAGACCCCGCCGGAGCCGCCTACCTTGCTGTGGCCTATCGGTGTGCCCTTCTCCGACGGGCTCAATACCCTCTCGGAGTTCAAGGTGCAGCGGCTGGACCGGCAGACATG\n",
      "GTATGAGTGCACATCCGACAACTGCCTCACCTTGAAGGGCTTCACCTACAGCCAGATGCGGCTTCCCGGCGGTGACACGGTCGACGTCTACAACTTACATACCAACACCGGTGGAGGGCC\n",
      "GACCACCAACGCCAACCTCGCGCAGGTCGCCAACTACATCCAGCAGAACTCGGCGGGCCGCGCGGTCATCGTCACCGGCGACTTCAACGCGCGGTACTCCGACGACCAAAGCGCTCTGTT\n",
      "GCAATTTGCGCAGGTCAACGGGCTCACCGATGCCTGGGTGCAGGTAGAACACGGCCCCACCACACCGCCGTTCGCGCCCACTTGCATGGTCGGCAACGAGTGCGAGCTGCTCGACAAGAT\n",
      "CTTCTATCGAAGCGGCCAGGGAGTGACGTTGCAGGCCGTCAGCTACGGCAACGAGGCGCCGAAATTCTTCAATTCCAAGGGTGAGCCACTGTCGGATCACAGCCCGGCGGTGGTCGGCTT\n",
      "CCACTACGTCGCGGACAACGTGGCCGTACGGTGA\n",
      ">Rv0908_N1 Seen in 1 sample(s).\n",
      "ATGACCCGTTCGGCTTCGGCGACAGCCGGTTTGACCGATGCCGAAGTGGCGCAACGGGTCGCCGAAGGCAAGAGCAACGATATCCCGGAACGGGTCACCCGCACCGTCGGGCAGATCGTC\n",
      "CGGGCCAACGTATTCACGCGGATCAACGCGATTCTGGGCGTTTTGCTGCTCATCGTCTTGGCGACGGGCTCGTTGATCAACGGGATGTTCGGCCTGCTCATCATCGCCAACAGCGTCATC\n",
      "GGCATGGTCCAGGAGATCCGTGCCAAGCAGACGCTGGACAAACTCGCGATCATCGGACAGGCGAAACCGTTGGTGCGCAGGCAATCCGGAACGCGCACGCGGTCGACCAACGAGGTGGTG\n",
      "CTGGACGACATCATCGAACTTGGGCCCGGGGACCAGGTTGTCGTCGACGGCGAGGTCGTCGAGGAGGAAAACTTGGAGATCGACGAATCATTGCTGACCGGCGAGGCCGACCCGATTGCC\n",
      "AAAGACGCTGGCGATACCGTGATGTCGGGCAGTTTCGTCGTCTCCGGTGCCGGCGCCTACCGCGCCACCAAGGTCGGCAGCGAAGCATATGCAGCCAAACTGGCCGCCGAGGCCAGCAAG\n",
      "TTCACCCTGGTGAAATCCGAATTGCGCAACGGCATCAACAGGATTCTGCAGTTCATCACTTACTTGTTGGTGCCGGCCGGCCTGCTGACCATCTACACCCAGTTGTTCACCACACACGTG\n",
      "GGATGGCGGGAATCCGTGTTGCGGATGGTGGGCGCGCTGGTGCCGATGGTTCCCGAAGGCCTGGTGCTGATGACCTCGATCGCCTTCGCCGTCGGGGTGGTCAGGCTCGGCCAGCGTCAA\n",
      "TGCCTGGTGCAAGAGTTGCCCGCCATCGAGGGGTTGGCGCGGGTGGACGTGGTCTGCGCCGACAAGACCGGCACACTGACCGAAAGTGGCATGCGGGTCTGCGAGGTCGAAGAGCTCGAC\n",
      "GGGGCTGGTCGACAGGAAAGTGTCGCCGATGTGCTGGCCGCCCTGGCCGCCGCCGACGCCCGTCCCAACGCGAGCATGCAGGCAATCGCCGAGGCCTTTCACTCGCCGCCGGGCTGGGTC\n",
      "GTGGCCGCGAACGCGCCTTTCAAGTCGGCCACCAAGTGGAGCGGCGTCTCCTTTCGCGATCACGGTAACTGGGTGATCGGCGCGCCCGACGTGCTGCTCGATCCGGCTTCGGTGGCGGCC\n",
      "AGACAGGCCGAGCGGATCGGAGCGCAGGGATTGCGGGTGCTGCTGCTGGCTGCTGGCAGTGTGGCCGTCGACCATGCCCAAGCGCCGGGTCAGGTCACCCCGGTAGCGCTGGTTGTGCTG\n",
      "GAGCAGAAGGTGCGGCCCGACGCCCGTGAAACGCTGGATTATTTTGCTGTTCAGAATGTTTCGGTCAAGGTGATCTCCGGTGACAACGCGGTGTCGGTTGGTGCGGTCGCCGACCGGCTC\n",
      "GGGCTGCATGGCGAGGCGATGGATGCGCGTGCGCTGCCGACGGGCCGCGAAGAACTGGCCGACACACTGGACTCTTACACCAGTTTTGGCCGTGTGCGGCCGGACCAGAAGCGTGCGATC\n",
      "GTGCATGCTCTGCAATCACACGGGCATACCGTGGCGATGACCGGCGACGGCGTCAACGACGTGCTTGCCCTCAAGGACGCTGATATCGGTGTGGCGATGGGCTCGGGCAGCCCGGCCTCG\n",
      "CGTGCGGTGGCACAGATCGTGTTGCTGAACAACCGGTTTGCCACGCTGCCCCATGTGGTCGGCGAGGGGCGTCGGGTCATCGGCAATATCGAACGGGTCGCCAATCTATTCCTGACTAAG\n",
      "ACGGTGTATTCCGTGTTGCTGGCGCTGCTGGTGGGTATTGAGTGCTTAATTGCCATACCGCTGCGGCGTGATCCGCTGTTGTTCCCGTTCCAGCCGATCCACGTCACCATCGCGGCCTGG\n",
      "TTCACTATCGGGATCCCAGCGTTCATCCTGTCCTTGGCGCCCAACAACGAGCGGGCCTATCCGGGCTTCGTTCGGCGAGTTATGACGTCTGCGGTGCCGTTCGGACTAGTCATCGGTGTC\n",
      "GCGACTTTCGTCACCTATCTGGCCGCTTACCAGGGTCGCTACGCCTCGTGGCAGGAGCAGGAACAGGCGTCGACCGCTGCGCTGATCACGTTGTTGATGACCGCGTTATGGGTGCTGGCG\n",
      "GTGATCGCACGCCCCTATCAGTGGTGGCGACTGGCGCTGGTGCTTGTCTCCGGACTGGCCTATGTGGTGATCTTCAGCCTTCCGCTGGCGCGGGAGAAGTTCCTGCTGGATGCCTCGAAC\n",
      "CTGGCGACGACGTCAATCGCGCTGGCGGTTGGCGTGGTGGGTGCGGCGACCATTGAGGCGATGTGGTGGATCCGAAGCAGGATGCTCGGTGTGAAACCGAGAGTGTGGCGATAA\n",
      ">Rv1001_N1 Seen in 1 sample(s).\n",
      "GTGGGTGTCGAATTGGGGTCAAATTCCGAGGTCGGCGCGCTAAGAGTGGTCATCCTGCACCGCCCGGGGGCCGAACTGCGCCGGCTCACACCGCGCAACACCGACCAGCTGCTGTTCGAC\n",
      "GGCCTGCCCTGGGTATCCCGCGCGCAGGACGAGCACGACGAATTCGCCGAGCTGCTGGCTTCCCGCGGTGCGGAAGTGCTGTTGCTGTCGGACCTGTTGACTGAGGCACTACATCACAGC\n",
      "GGGGCCGCCCGCATGCAGGGGATCGCCGCTGCCGTCGACGCACCGCGGCTGGGACTGCCGCTGGCGCAAGAGCTTTCGGCCTACCTGCGTAGTCTCGACCCAGGCAGGTTGGCGCATGTG\n",
      "CTGACGGCCGGCATGACCTTCAACGAGCTCCCGTCGGACACGCGGACCGACGTGTCGTTGGTGTTGCGTATGCACCATGGCGGAGACTTCGTCATTGAGCCGTTGCCGAACCTGGTGTTC\n",
      "ACCCGCGACTCGTCGATATGGATCGGGCCGCGGGTGGTGATCCCGTCGCTGGCATTACGGGCACGGGTGCGCGAAGCGTCGCTGACCGACCTCATCTATGCTCATCACCCGCGGTTCACC\n",
      "GGTGTGCGGCGTGCCTATGAATCGCGCACCGCTCCGGTCGAGGGTGGCGACGTGTTGTTGCTCGCCCCGGGTGTGGTCGCTGTCGGAGTGGGCGAGCGGACTACACCAGCAGGCGCGGAA\n",
      "GCATTGGCGCGCAGCCTTTTTGACGATGATCTTGCGCATACCGTGCTCGCCGTGCCGATCGCTCAGCAGCGCGCGCAAATGCATCTGGACACGGTGTGCACGATGGTCGACACCGATACG\n",
      "ATGGTGATGTACGCCAACGTTGTCGACACGCTCGAGGCGTTCACGATCCAGCGCACACCCGACGGCGTGACCATCGGCGATGCGGCCCCGTTCGCGGAGGCGGCTGCCAAGGCGATGGGA\n",
      "ATCGACAAGCTGCGGGTAATTCATACCGGAATGGACCCGTCGTCGCTGAACGCGAACAGTGGGACGACGGCAACAACACGTTGGCGTTGGCGCCCGGTGTCGTTGTCGCCTACGAGCGCA\n",
      "ACGTACAGACCAACGCCCGCCTGCAGGACGCGGGCATCGAAGTGCTTACCATCGCCGGCTCCGAATTGGGTACCGGCCGTGGCGGGCCCCGCTGCATGTCCTGTCCGGCCGCCCGCGATC\n",
      "CGCTTTAG\n",
      ">Rv1097c_N1 Seen in 1 sample(s).\n",
      "TCAGGACTTGTTGACCTTCAGCGCCTCAATGACCCTCTCGACGGTGGCGCGCGAGGTTGCATCACCGATGGGGGTGGCGCCCAGGAAGACGGTGACCGGCTTGGTGTCGACCGCGATGAT\n",
      "CGTGACCGAATCACCTTTGACGTTGCGTGAACTGTCGGCGATTGTGATATCGGCGTCTACCCGGGCGGCCCTGACCCCGTCGACGGTGATCGACGACGTCTTGGTCGGGCCCAGGGTGGG\n",
      "CGACGAGCCTGCGTAGCCGGGGCCGTCGGCCACGCATTGCATCAACTTCGATGCTTGCGCGGCGACGTCCGGTGGTGACGAAGTTGGTTATCGCAACCTCGGCTTGCATCATCCACTGGT\n",
      "CGGCACCGGCCACCTCGTGGCCGACGCCCACCGCGTCGATGAGGTTCGGGTTCTGGTCGTCGGAGAACGCCGACCACCCGGGTGCCGCGCTGGTCGGGAACGACAGCTTACCCGCACTGA\n",
      "TCGAATCGCCGATGGGCTGCACACCGCCGGACACATTTGGGGTACAACCGGTTGCGGTTTGCTGGGAAAACGGTTGCGACGTGGGAGCACTCGTCGCCGGAGAGGTTGCCGTGGTCGACT\n",
      "TGTTGTCGCCGCGGAGGCCGATCACCAGGATCACCACCAGTAGGATGACACCCAGCACCGCGAGGCCGGCGAGGATCAGCCACGGTGTCTTCGATCCTGGCCCGGGCGGAGGTGGTCCTG\n",
      "GCGGATAGGGCCCCGCCGGCCAGCCGGGCGGATACTGCTGGGGTGGGTAGGCCGGCGGATAGGAGCCGCCCTGCGGTTGGCCTCCCCAATACGGGTCCTGCCCATACGTATTCGGGCCGT\n",
      "AGGGGTAGTTGCCGTAGGGGCCAGCGGGAGGAACCGTCAT\n",
      ">Rv1128c_N1 Seen in 1 sample(s).\n",
      "CTACGGGTCGCCTTCGTCGTCTGCCAGGAGCTTTTCCGGGTGATGGAACGTATTGACTCGAGGTTGGCCGTGGTCGAGATGTGGCGGCGGTAGCCACTCGGTGTCGCCGTGGGCGTTCTT\n",
      "GCGGGTCGTCCAGCCACGTTCGGCTAACGGATGATGGCCACCGCAGCCGAGTGTCAGGTCATTGACGTCGGTGTTGCGGCACTGGGCGTACGGCGTGACATGATGGACTTCACAGTAATA\n",
      "GCCGGGCACGTCGCAACCAGGTGCGCTGCAGCCACTGTCCTTGGCGTACAACATAATTCGCTGCGCCGGGGAGGCCAGGCGCTTGGTGTGGTAGAGCGCCAGGGCCTTGCCTCGATCGAA\n",
      "TATCGCGAGGTAGTGGTTTGCGTGGCGGGCCAGCCGGATCACATCCGATATGGGCAAGATCGTACCCCCGCCGGTGAGCCCGCGCCGGCCGCGGCCTCCAAGTCCTTCAGCGTGGTGGTC\n",
      "ACGATGATGCTGGCCGGTAATCCGTTGTGCTGGCCCAGATTGCCACTTGTCAACAAACTACGTAATCCGGCGTTGAGCGCGTCGTGGTTCCGCTGTGGGCAGCTGCGGGTGTCTCGCCGC\n",
      "GCCTGCTCCTTCGAGGGCGCGCCGTTCACACACGGTGCCTTCTGCTCGGGGTTGCACATACCCGGGGCGGCCAGCTTGGCCCACACCGCCTCGATAGTGGCGCGCAGCTCGGGGGTCACA\n",
      "TATCCGCTGAGCCGCGACATCCCATCGACATCTTGCTTTCCTAACGTCAAGCCGCGGCGGCGGGCGCGGTCCTCGTCGGTGTAGTCGCCATCGGGGTTGAGGCAGTCCATGATCCGCGCG\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GCCAATTTGGCCAGCTGGTCGGGACGGTACTGGGTGGCCTGCTTAGCCAAGTCCCGTTCGGCCTTCTCCAGGGTCTTGAGGTCTACCCAGGATGGTAGGCGGTGCACGAAAGCACGGATT\n",
      "ACTTCAACATGGCCGTCACCAATTAACCCGTGGCGCTGTGCCTTTGCGGTGGCGGTGAGTAGCGGTGGCAGCGGCTCGCCGGTCAGCGCACGGCGCTGGCCAAGGTCGGCGGCCTCGGCC\n",
      "ACTCGCCGCTTGGCCTCGCTGCGGGTGATGCGCAACCGGTCGGCCAGCGTCAATCCCAGCTTGCCGCCCAGCTCCTCCTCGGTGGATTGTTCGCCGATCTGATTGATCAACGTGTGTTCG\n",
      "ACGCTGGGCAGCTGGCGTCGCGCGGTCTCGCAGTGCTCCAGCAGCGCCAGGCGCTCCGGGGTGGTCAATGCGTCAAAGGTCAGCCCCAGCACGCGGGACAGCGCGGTAGCCAATGACGCG\n",
      "AAGGCCTCCGTGATCTCCTCCCGAGTGGAACACAT\n",
      ">Rv1145_N1 Seen in 1 sample(s).\n",
      "ATGCTGCAGAGGATCGCTCGGCTCGCCATCGCTGCGCCGCGCCGAATCATCGGGTTTGCGGTCTTCGTCTTCATCGCCGCAGCGGTCTTCGGTGTTCCGGTGGCTGACAGCCTGTCGCCC\n",
      "GGGGGTTTCCAAGATCCGCGATCGGAGTCGGCACGGGCAATCGAGGTGTTGACCGACAAGTTCGGCCAGAGCGGTCAGAAAATGCTGATCGTGGTTACGGCAGCCGCGGGCGCCGACAGC\n",
      "CCACCTGCCCGCGAGGTCGGGACTGACATCGTCGAGGTGCTGCGGCGGTCGCCGTTGGTTTACAACGTGACCTCGCCGTGGACTGTGCCACCGACTGCCGCCGCCGACCTGCTCAGCACC\n",
      "GACGGAAAATCGGGGTTGATCGTCGTCAACGTCAAAGGCGGCGAAAACGACGCGCAGAACCACGCCCAAACCCTGTCAGACGAAGTCGCCCATGACCGCGACGGCGTCACCGTCCGTGCC\n",
      "GGCGGCTCGGCGATGGAGTACGCCCAGATCAATCGGCAGAACAAAGACGACCTGCTGGTGATGGAGTTGATCGCGATTCCGCTGAGCTTCCTGGTGCTGATCTGGGTGTTCGGTGGGCTG\n",
      "TTGGCCGCCGGGCTGCCGATGGCCCAGGCCGTACTGGCCGTTGTGGGATCGATGGCCGTATTGCGACTCGTTACGTTTGCCACCGAGGTGTCGACCTTCGCGCTCAACCTGAGTACAGCG\n",
      "TTGGGCCTCGCGTTGGCTATCGACTACACGCTGCTCATCGTCAGTCGCTATCGCGACGAGCTCGCCGAGGGCAGTGATCGAGACGAAGCACTGATCCGGACCATGGCGACTTCGGGGCGC\n",
      "ACGGTGTTGTTTTCGGCGGTCACCGTGGCGCTGTCGATGTCGGCGACTGCGCTGTTCCCGATGTACTTTCTGA\n",
      ">Rv1225c_N1 Seen in 1 sample(s).\n",
      "CTAACACCCGAGCAACGGCGGCAGGCCGGCCACCGAGTCGATCACGTGGTGCGGCCGGGTCGCGCTGGCGCCGGCCAGCCAGCGATCCAGCGTTTGCTGGCGGAACTTGCCGGTGCGCAC\n",
      "CAGCACACCCGTCATGCCCACCGCCTGGGCGGCCAGCACGTCGTTGTGCAGATCGTCGCCGATCATGACCATCTGCTGTGGATCGACACCGACGCGGTCGGCGGCCGCCAGGAATCCCTC\n",
      "GGCCGCAGGCTTGCCGATGGCGGTGGCGGTCTTGCCGCAGGCCTGTTCCATTCCGGTCAGGTACATCCCGGTGTCGATGCGCAGCCCGTCGGTGGTGTTCCAGGTCATATTGCGGTGCAT\n",
      "CGCCACCACCGGAACGCCGTCGAGCATCCACCCATAGACCCGGCTGAGCGTGCGGTGATCGAACTGGGGGCCGGGCACTGCCGAGCACGACGACGTCGGGGGCTTCGGGGCAATCCTCGG\n",
      "GACCGATCTCGGTCGACAAGACGACGTCGATGCCGGGCAAGTCCTCGGTGATGTCGCCGTTGTTCACCAGGAAGCACCGCGCGCCGGGATAGGCGCCGTGCAGGTACTCGGCCGTCAGCA\n",
      "CCCCGGCCGTGATCACGTCGTCGGCGGCGACGGGGATCCCCGCGGCACCCAGCGCCTCGGCGATCTGCCGGCGGGTGCGCGTCGTGGTGTTGGTCAGATACGCGCAGGCGATTCCCCGAT\n",
      "GGGTCAGTTGCCGCACGGTCTCGGCGGCCCCGGGAATCGCGCGCCACGACAGCACCAGCACGCCGTCGATGTCGAACAGCACCGCCGCGGCCATCAGATGCGCCACGTCCAC\n",
      ">Rv1258c_N1 Seen in 1 sample(s).\n",
      "TCACTGAGCCGATCCTACGGGCCGATCGATGTCCGCTTGGGGCGCCAGATCCAGTTCGCGCAGCGCGGGCAGCCGGATCGCGACCAGCCCGGTGCACACGATGGGCAGTGCCAACGCGAG\n",
      "AAACGTGGCATGCAGTCCAGCGGCGTCGGTCAGTGGACCGGCCAGCAACAGACCCAACGGGCCGGCGGCGTAGGCCAGCGACGTCATCACCCCGACTACCCGGCCGCGCAGATGCTGTGC\n",
      "TGCCCGCGTCTGTATCACGTAGTTATAGATCGGCTGGATGGGTCCGTACACCAGGCCGACCACCGCGCACAACACCATGATGACCGGCAGTGGCGGCAGGAACGCGATGACCATCGATGC\n",
      "CAAACCCAGGGTAAGAACCGCGGTCGACATGGTCACGCGACGGGGAACGCGGATAGCCAACACGGCATACCCCAGCGCTCCCACCAGGCCGCCGCCGGCGATCGCCATCAACGCCCAACC\n",
      "CAGCTGCACCGGTTGCTGGTGGTCGGTGAAGTATTTCGGGAACAGCACGCTCTCCATCGGCAGATACAGCGCGGTGACGGTCAGGTCAATCATCCCGAGGGTGCGCAATACCCGCAGGTT\n",
      "CCAGACGAAGCGCAGCCCCTCGGCGATCCCGGATACCAACCCTTGGGGCCGCGAGGTGTGGTGCGGCTTGCCGGCACCCTGCGAGTTGCAGGGCGGCAATCGCGAGGATGGACAACCCGA\n",
      "ATGCCGTCGCGGTAATCCACATTGTGGTGATGCCGCCAACCGTCGCGATCATCAAGCCACCGATGGCCGGGCCGACAATAAAGGCCAGGTTGAGGATCGCCTCGTAGGCGCCGTTGATGC\n",
      "GGTCCAACGACCAGCCTGCCCGAGCGGCGGCCTCGGGCAGCATCGAGTCACGAGCCGTCATGCCTGCCGGGCCGAAGGCGGCCGCCAGGGCGGCCAATACGGCCAGCACCAGCACGTTGA\n",
      "CCGCGTCGCCGCCGTACCCCCACGCCACCAGGGGGACGCCGGCCACCGCCGCACCCGACAGCGCATCGGCCACCATCGACACCCGGCGACGCCCGAAGTAGTCGACCGCGGTGCCGGCGA\n",
      "CCAGCGTGGCGAACAACAGCGGCAGCATGGTCGCACTGGCCACGATCGAGGCCTGCCCAGCGCTGCCCTCGCGCTGCAACACCAGCCACGGAAACGCGACTATCGAGACGCCATCACCCG\n",
      "CGGCCGCCATCAGCGTTGCGAACAGGATCAGGAATGCCGGGCCGCGGTTGCTGTTTCTCAT\n",
      ">Rv1269c_N1 Seen in 1 sample(s).\n",
      "TTAGTTGCAGGCCCAGGTGTCGATGTAGCCGCCGCCGAGCTTGGTCAGGGCGTCCTTCATGGCGGCGGCCAAGGTGGGTCCAACTCCTCCCTGGTATGCCCTATCGTTGGCGGCGACGGC\n",
      "GCCGCAGGCGGTGAAACTGGTGAGCACCTTGCAGTCGGAGTAGCCACACGACTTGACGGCGGTGGCTTCGGCAGCCGCCCGGGTTGGGTAGTCCCACGATCGGCCCCACGAGCCGTTGCC\n",
      "GGAGTAGGCAATTGCGCCATAGACATCGGCGGCATTTGCTGGTGCGGGAGCCAGGGAGCCAGGGTGACGGTCGTCGCGGCGGCAGTGGCGACGCCGGCGACGGCCACCGCGAACCGTCGC\n",
      "CGAAGAGTAATCATCGTCGTCAT\n",
      ">Rv1326c_N1 Seen in 1 sample(s).\n",
      "CTAGGCGGGCGTCAGCCACAGCGCCGAAGTGGGCGGCAGCACCAGCACCGCGGACGCCGGGCGGCCATGCCAGGGGTCGTCGGTGGCGTCCACGCCGCCGAGGTTGCCGATCCCTGAGCC\n",
      "GTGGTAGATCGTCGCGTCGGTATTGAGCACCTCGCGCCAGCGGCCCGCGCGCGGCAGCCCGAGTCGATAGTCACGGTGTTCGGCACCTGCGAAATTGAACACGCAGGCCAGCACCGAGCC\n",
      "GTCGCTGCCGTAGCGCATAAAGCTCAACACATTGTTGGCGGAGTCGTTGGCGTCGATCCAAGAATAGCCTTCGGGGGTGGTGTCTAAGCTCCACAGCGCCGGGTGGCATCGGTAGATGTC\n",
      "GTTGATGTCGCGCACCAGCCGCTGAATCCCGTTGGAGAAGCCGTTTTCGTCGAGTTGGAACCAGTCCAGGCCGCGCTGCTCGGACCATTCGGCGCGTTGGCCGAATTCCTGACCCATGAA\n",
      "CAGCAATTGCTTGCCGGGGTGTGCCCATTGGTAGGCAAGCAGGCTACGCAGGCCGGCGGCCTTGACGTGATTGTTGCCCGGCATCCGCCCCCACAGCGTGCCTTTGCCGTGCACCACCTC\n",
      "GTCATGACTGAGCGGCAACACGTAATTTTCGCTGAACGCATACAGCATCGAGAACGTCATCTCGTGGTGGTGGTAGCTGCGGTACACCGGATCTCGGCTGACGTAGTCGAGCGTGTCGTG\n",
      "CATCCAGCCCATGTTCCACTTCATCGAAAAGCCCAGGCCGCCAATGTTGGTCGGGCGGGTCACCCCAGGCCACGGCGTGGACTCCTCGGCGATGGTGACGATTCCCGGCGCGACCTTGTG\n",
      "CGCCGTGGCGTTCATCTCCTGCAGGAACTGCACTGCTTCCAGGTTCTCCCGGCCGCCGTGGACGTTGGGGGTCCAGCCGCCCTCGGGTCGCGAGTAGTCTAGATAGAGCATTGAGGCCAC\n",
      "CGCGTCCACCCGCAGGCCGTCGATGTGGAACTCCTGTAGCCAGTACAACGCATTGGCTACCAGAAAGTTGCGCACTTCCGGGCGGCCGAAGTCGAACACGTATGTGCCCCAATCCAGTTG\n",
      "CTCGCCGCGTTTGGGATCGGAATGTTCGTAGAGCGGAGTGCCGTCGAACCGTCCCAGGGCCCACGCGTCCTTCGGGAAGTGCGCTGGGACCCAATCCACGATGACGCCGATGCCGGCCTG\n",
      "GTGCAGGGCGTCGACCAGCGCCCGGAAGTCGTCGGGTGTGCCGAATCGTGATGTCGGCGCATAGTAGGACGTGACCTGATACCCCCATGATCCGGCGAATGGATGCTCGGCGACGGGCAA\n",
      "CAGCTCCACATGGGTAAACCCTTGATCCACAATGTAATCCGTCAACTCACGAGCAAGCTGGCGGTAGCTGAGTCCAGGCCGCCACGAACCGAGATGGACTTCGTAGGTGCTCATCGCCTC\n",
      "GTTCACCGGGTTGCGCAGCGCACGCCCAGCCATCCAGTCGTCGTCACCCCAGGTGTAGTCACTCGACGTCACCCGCGATGCGGTCTGCGGCGGCACCTCGGTGCCGAACGCGAACGGGTC\n",
      "GGCCCGATCGGTAACCACGCCGTCGGCGCCGTGCACGCGGAACTTGTACAGACCGTCGCAAGGGAAGTCGGGCCAGAACAATTCCCATACCCCTGATGGGCCGAGCACCCGCATGGGGGC\n",
      "TTCGTGGCCATTCCAACCGTTGAACTCGCCGATCAAGCTGACGCCCTTGGCGTTGGGCGCCCACACGGCGAACGACACGCCACTCACCACACCGTCGGCCGTGGTAAACGAGCGGGGGTG\n",
      "GGCACCCAGGACTTCCCAAAGCCGTTCGTGGCGGCCCTCGGCGAACAGGTGCAGGTCGACCTCGCCCAGGGTGGGCAGGAATCGGTACGCATCGGCCACGGTGTGTGGCTCGCAACCTTC\n",
      "ATAGGTCACCTGCAGGCGGTAGTCGATGAGGTCGACGAACGGCAATGCGACGGCAAACAGGCCAGAATCGAGGTGCTGCAACGAGAGCCGGTCCTTACCAACGAGCGCGACGACCTCGAC\n",
      "GGCATGCGGACGGAACGCTCGGATGACGGTATGGTCGTCGTATTCGTGGGCGCCCAGGATGCCGTGCGGGTTGTGATGTGTACCCGCCACCAAGCGCGCCATTTCGGCCGGCTCGGGTGC\n",
      "AAGGTGCTCCCCGGTGAGTTTCTCGGATCGACTCAT\n",
      ">Rv1330c_N1 Seen in 1 sample(s).\n",
      "TCAGGCCGGGATCGTGCGTGTCGGAATCGCCGGCTCGCCGGGTGCCAATTTCAGCCCGTCGGCTGGCAGGCTGCGCAACCCGGATGCCACCAGCTGCCGTGCCGCGGCCAGGCTGGTATC\n",
      "GGCTACCGGTTGCCCGGCGCGGACCAGTGGCAGCGTCAAAACCCGGTGCGGCTCGACAATGACCGGCGGACGGCCCGCCGGATGCACGAGCTCCTCGGTGATGGTGCCCGTCGCACGGGA\n",
      "GCGCCGCAGTGCCTCTTTGCGGCCGCCGGGGGATTCTTTGTAGCTGCTGCGCTTTTGCACCGGTACACCGTCTACCTCGACCAGTTTGTAGACCATGTTGGCGGTCGGCGCGCCCGACCC\n",
      "GGTGACCAGCGACGTGCCCACGCCGTAGCTGTCGACGGGTTCACCGCGCAACGCGGCGATGCTGAACTCGTCAAGTTCGCCGGACACCACGATGCGCGTCCGGGTGGCTCCTAGCCGGTC\n",
      "GAGCTGCTCCCGCGCTTGGCGGGCCAGTACCCCAAGCTCACCGGAATCGATGCGGATCGCGCCGAGCTCAGCGCCGGCGGCGGCAACGGCATTGGCCACACCGGTCGTGACGTCATAGGT\n",
      "ATCCACCAGCAGCGTGGTACCGGGTCCCAGCGCTTCGACCTGGGCGCGGAATGCGGCTCGCTCGGCTAGTTCGGTGGGGCCGCCATGCTGGGCGTGCAACATGGTGAATGCGTGTGCCGC\n",
      "GGTGCCGTGCGCGGGCACTCCGTAGCGTCGCTGCGCCGCCAAGTTGGATGACGCGGCGAAACCGGCGATATACGCCGCCCGGGCCGCTGCCACCGCGGCGCGTTCGTGGGTGCGCCGCGA\n",
      "GCCCATCTCGATCAGTGGGCGCCCCCCGGCGGCGCTGACCATGCGCGCCGCTGCCGAGGCGATCGCTGTGTCGTGGTTGAAGATTGACAGCACCAGCGTTTCGAGCAGGACGCATTCGGC\n",
      "GAAGCTGCCGCGTACCGAGAGCACCGGTGACCCGGGAAAATACAGCTCCCCCTCGGCATAGCCGTCGATATCGCCGCGGAACCGGAATTCGCGAAGATACCGCACCGTGGCCGGGTCGAG\n",
      "GAATTGGGCCAGCAACTCGCACGCGTCAGCGTCGAACCTGAACTGCGGCAACGCTTCCAGCAACCGGCCGGTTCCGGCGACAACTCCGTAGCGACGGCCGGTGGGGAGTCGGCGAGCGAA\n",
      "CACCTCGAATGTGGTGGGGCGATTGGCGCTGCCGTCGCGCAGGGCAGCCGCCAGCATGGTCAACTCGTACTTGTCGGTCAACAGCCCGGCTGGGTCTTGATTGTCGGGCTCTCCCTCTCG\n",
      "CCGCCTGGCGGCTGGGGGTGGCCCCAC\n",
      ">Rv1363c_N1 Seen in 1 sample(s).\n",
      "TCACGGTACGAACTCAACTTTCGACATCTTGTACTGTCCCCCCTCTTCGGTCACGGTCACTTTGAGCCGCCACGGACGTGGTTCGTCTTTCGCCCCAGCGGAATTGGTGACCCGTGAAGT\n",
      "CGCCGCGACGAGCACCACGGCGGAATGCTCGTTCATGGATTCGACGGCTGTCGCGTTCACCGTGCCTTCGGTGACCACTTTGGACTGTTCGACAACCTTGGTGAAATCGGCTGCCCGCTG\n",
      "CTGGAAGTCATCCCTGAATTCGCCGGTGGAGCTGTCGATCACACGCGCGACGTCTTCTTTGGCCTTGTTGAAGTCCAGCGAGGTCATGTTGATGACACCTTGCTTGGCTCCGGCGGCGAA\n",
      "CGCCGCGGCGCGCTGCTGGCGTTCGGTGGCCTCATGGTGTTGCCACACAATGTATCCGCTGAGCCCGGTGAAGCCGCAGATGATGACGACTGCGGCCGCCATGGCAATCGTGGACAGTCT\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "TGGTAACCGCACCCGCAACCGCCGTCGCCAGGATGCCGACCGTGCGGCCTCCTGGTCTGCGGCCTCATAGTCGTCATAGTCGTCATAGTCTTCGGCGTCTTCCCAGTCTGCATACTCCTC\n",
      "GGGGACGTTCTCGTCCTCGGCTGGGGCCATCGCCAGCGCCTCACGCTTCAACCGGGCGGCACGGGCACGGGCCCGCGCCGCGGCGGCCAGCGCTTCGGCTTCGGCGGCTTCGGCTTCGGC\n",
      "GGCCAACGCCATCGCGTCGGCTTGCGATGTCCCCGCGTCCGACGGTGGTTCGGTTGTCTCAGCCAT\n",
      ">Rv1413_N1 Seen in 1 sample(s).\n",
      "GTGGCCACCATCGGGGAAGTCGAGGTATTCGTCGACCACGGCGCCGACGACGTATTCATCACCTACCCATTGTGGATCGACACACGCCAAGCCGACCGGCTCCGTCAGCTGGCTGACCGC\n",
      "GCTCGCATCGCTGTCGGTGCGGGCACCGCCGAGGGCGCTTCGAACACCGGCGCACGGCTCGCAGACGCCGCTGGCGCGATCGATGTTCTCATCGAAATCGACAGTGGCCATCACCGCAGC\n",
      "GGCGTCCGTGCCGAACAAGTGTTGGAGGTCGCCCACGCCGTCGGTGAGGCTGGGCTTCACCTGGTGGGGGTGTTCACCTTCCCCGGTCACAGTTATGCGCCAGGTAAACCCGGCGAAGCC\n",
      "GGCGAGCAAGAGCGGCGCGCTCTCAACGACGCGGCGAACGCGCTGGTCGCGGTGGGCTTCCCGATCAGCTGCCGCAGCGGTGGGTCCACTCCCACCGCATTGCTCACCGCCGCGGACGGG\n",
      "GCCTCCGAGACGTCCCGGCGTCTATGTGCTCGGTGA\n",
      ">Rv1420_N1 Seen in 1 sample(s).\n",
      "GTGCCAGATCCCGCAACGTATCGCCCCGCGCCCGGGTCCATCCCGGTCGAGCCGGGCGTGTACCGATTCCGGGACCAGCATGGGCGAGTCATCTACGTCGGCAAGGCCAAGAGCCTGCGT\n",
      "AGCCGGCTGACGTCCTATTTTGCCGACGTGGCCAGCCTAGCGCCGCGGACCCGGCAGCTGGTGACCACCGCGGCCAAGGTCGAATGGACGGCCGTGGGGACCGAGGTTGAGGCACTGCAG\n",
      "CTGGAATACACCTGGATCAAGGAGTTCGATCCGCGATTCAACGTCCGCTACCGCGACGACAAGTCCTACCCTGTGCTGGCGGTCACCCTGGGCGAGGAATTTCCCCGGTTGATGGTCTAT\n",
      "CGCGGTCCGCGGCGCAAGGGTGTGCGCTATTTCGGGCCGTACTCGCACGCGTGGGCAATCCGGGAAACGCTGGATCTGCTCACCCGGGTGTTTCCGGCGCGAACTTGCTCGGCGGGGGTG\n",
      "TTTAAGCGGCACAGGCAGATCGATCGTCCATGCCTGCTCGGCTACATCGACAAATGTTCCGCGCCGTGTATTGGCAGGGTCGATGCGGCCCAGCACCGCCAGATCGTGGCAGACTTCTGC\n",
      "GACTTTCTGTCCGGCAAGACCGACCGGTTCGCCCGCGCCTTGGAACAGCAAATGAACGCCGCGGCCGAGCAACTGGACTTCGAACGAGCGGCGCGGCTTCGCGACGACCTGTCCGCACTG\n",
      "AAGCGTGCCATGGAAAAGCAGGCCGTGGTGCTCGGGGACGGCACCGACGCCGACGTGGTGGCATTCGCCGACGACGAACTCGAGGCGGCGGTGCAAGTGTTCCACGTGCGCGGCGGACGG\n",
      "GTCCGCGGCCAGCGTGGCTGGATTATCGAAAAGCCAGGAGAGCCAGGAGATTCCGGAATCCAGTTGGTCGAGCAATTCCTGACACAGTTCTACGGCGACCAGGCGGCGTTGGACGACGCC\n",
      "GCCGACGAATCCGCCAACCCGGTTCCCCGCGAGGTGCTGGTGCCCTGTTTGCCGTCCAACGCCGAGGAGCTGGCCAGCTGGCTGTCCGGCCTGCGCGGCTCAAGGGTCGTGCTGCGGGTG\n",
      "CCGCGCCGCGGGGACAAGCGGGCACTGGCCGAAACGGTGCACCGAAACGCAGAAGATGCACTGCAACAACACAAGCTGAAGCGGGCCAGCGATTTCAACGCCAGATCCGCTGCGCTGCAG\n",
      "AGCATTCAGGACTCGTTGGGCCTGGCAGACGCACCCTTGCGGATCGAGTGTGTCGACGTCAGCCATGTGCAGGGCACCGACGTGGTCGGGTCACTGGTGGCGTTCGAAGACGGCCTGCCG\n",
      "CGCAAGTCGGACTACCGCCACTTCGGGATCCGGGAAGCCGCAGGCCAGGGGCGCTCCGACGACGTGGCCTGTATTGCCGAGGTGACCCGGCGCCGCTTCCTGCGGCACCTGCGCGATCAG\n",
      "AGCGATCCGGATCTTCTTTCTCCGGAAAGGAAGTCGCGTAGATTCGCCTATCCGCCCAATCTGTACGTCGTCGACGGCGGCGCGCCGCAAGTCAACGCGGCCAGTGCGGTAATCGACGAA\n",
      "CTCGGTGTTACCGACGTCGCGGTGATCGGCCTGGCCAAGCGGCTGGAAGAGGTATGGGTGCCGTCGGAGCCGGACCCGATTATCATGCCGCGCAACAGTGAGGGACTCTATCTGCTGCAG\n",
      "CGAGTGCGAGACGAGGCACACCGGTTCGCTATCACCTACCATCGCAGCAAGCGGTCGACGCGGATGACTGCCTCAGCGCTGGACTCGGTGCCGGGATTGGGGGAGCATCGCCGCAAAGCG\n",
      "CTGGTCACCCATTTCGGATCGATCGCTCGCCTCAAGGAGGCCACCGTCGACGAAATCACCGCTGTTCCCGGTATCGGCGTGGCCACGGCCACGGCCGTCCACGACGCACTGCGACCTGAC\n",
      "TCATCGGGGGCCGCGCGATGA\n",
      ">Rv1551_N1 Seen in 1 sample(s).\n",
      "GTGACTGCACGGGAGGTGGGCCGCATCGGACTGCGAAAGTTGCTGCAGCGCATCGGTATTGTTGCTGAATCAATGACGCCGCTAGCGACCGACCCCGTTGAGGTTACCCAACTGCTGGAT\n",
      "GCCCGATGGTATGACGAGCGGCTGCGTGCGCTGGCCGACGAGCTCGGACGCGATCCGGACAGCGTGCGCGCCGAGGCGGCAGGCTATCTGCGGGAGATGGCCGCCTCGCTGGATGAGCGG\n",
      "GCCGTGCAGGCATGGCGCGGCTTCAGTCGCTGGCTCATGCGCGCCTACGACGTACTGGTCGACGAGGACCAGATCACGCAGCTGCGCAAGCTTGATCGCAAAGCCACCCTGGCGTTCGCG\n",
      "TTCTCGCATCGTTCGTACTTGGATGGGATGCTGCTGCCCGAGGCGATCCTGGCCAACCGGCTCTCGCCGGCGCTGACCTTCGGCGGGGCGAACCTGAACTTCTTTCCGATGGGCGCTTGG\n",
      "GCCAAACGTACCGGGGCTATCTTCATTCGGCGTCAGACGAAAGATATTCCCGTCTACCGCTTCGTATTACGTGCTTACGCCGCGCAGCTGGTGCAAAACCATGTCAACCTCACCTGGTCG\n",
      "ATCGAAGGGGGTCGGACCAGAACGGGCAAGCTACGGCCACCGGTGTTCGGGATCCTGCGTTACATCACCGATGCGGTCGACGAAATCGACGGTCCCGAAGTGTATTTGGTGCCGACCTCG\n",
      "ATCGTGTACGACCAGCTGCACGAGGTGGAAGCCATGACCACCGAGGCCTATGGCGCGGTGAAACGACCCGAAGACCTGCGCTTTCTGGTCCGGTTGGCGCGACAGCAGGGCGAGCGACTG\n",
      "GGCCGCGCCTATCTCGACTTCGGCGAACCGCTGCCGCTTCGCAAGCGCCTGCAGGAGATGCGCGCCGACAAGTCGGCACCGGCAGCGAGATCGAACGGATCGCGTTGGATGTCGAGCACC\n",
      "GGATCAACCGCGCCACACCGGTTACCCCCACCGCGGTGGTGAGTCTGGCCCTGCTGGGCGCGGACCGCTCGTTGTCCATCAGCGAGGTGTTGGCGACGGTTCGCCCGTTGGCCAGCTACA\n",
      "TAGCTGCCCGCAACTGGGCGGTGGCCGGCGCCGCCGATCTGACGAATCGCTCGACGATCCGGTGGACCTTGCATCAGATGGTTGCTTCCGGCGTGGTGAGTGTCTACGACGCGGGCACCG\n",
      "AGGCGGTGTGGGGCATCGGCGAGGACCAGCACCTGGTGGCGGCGTTTTACCGCAACACCGCGATCCATATCCTGGTCGATCGGGCCGTCGCCGAGTTGGCGTTGCTGGCGGCCGCAGAGA\n",
      "CCACAACAAACGGCTCGGTTTCCCCGGCGACCGTGCGTGATGAGGCGTTGAGCCTTCGCGACTTGCTGAAGTTCGAGTTCTTGTTTTCTGGCCGTGCCCAGTTTGAGAAAGACCTCGCAA\n",
      "ACGAGGTACTGCTGATCGGGTCGGTGGTCGACACCTCCAAGCCCGCGGCCGCAGCCGATGTGTGGCGCCTGCTGGAATCGGCCGATGTGCTGCTGGCCCACCTGGTGCTGCGGCCGTTTC\n",
      "TCGATGCCTACCACATTGTCGCCGATCGGCTGGCCGCCCATGAAGACGACTCTTTCGACGAGGAAGGGTTTCTGGCCGAGTGTCTACAGGTCGGCAAGCAGTGGGAGCTGCAGCGCAATA\n",
      "TCGCCAGCGCCGAGTCCAGGTCGATGGAGCTGTTCAAGACCGCACTGCGCCTGGCTCGCCATCGCGAGCTGGTCGACGGTGCCGATGCGACGGACATCGCCAAACGCCGACAGCAGTTCG\n",
      "CCGACGAGATAGCCACGGCAACCAGGCGGGTAAACACAATCGCAGAACTGGCCCGCAGGCAATGA\n",
      ">Rv1564c_N1 Seen in 1 sample(s).\n",
      "TCACAACGTCTTACGCAGGACCAGCAGCGAGCGCGCAGGTACCGAAAACGTGTCAGTGGCGGTTACCGTCAGGTCGATGTCACCGACGGGATCGTTGGTATCCAGCTCTCCGGTCCACTG\n",
      "CTGCGCATAGCCGTCATGCGGCATCACGAACTCCACGTCGTGGTCATGGGCGTTGAAGCACAACAGGAATGAATCGTCGACTACTCGCTCACCACGGGCGTCCGGTGCGGTAATGGCTTC\n",
      "ACCGTTGAGAAACACCGCAACACACCTGTCGAAGCCTCTGCCCCAATCCTCGTGCGTCATCTCCCGACCGCTCGGTGTCAACCAGGCGATATCGCGGACTTCGTCGCCACTGCGGATCGG\n",
      "TTCACCCTCAAAGAACCGGCGTCGGCGAAACACCTTGTGGTTCTTGCGCAAGGTCGTCGCCTTGCGTGCGAAAGCTAGCAGATCGGCATTCTTGTCCACCAATGACCAATCCATCCAAGA\n",
      "TAATTCGGAGTCCTGGCAGTAGACGTTGTTGTTGCCGTATTGGGTGCGCCCAATCTCGTCGCCGTGGGCGATCATCGGCGTGCCCTGGCTGACCATAAGCGTGGCCCACATGTTGCGCAT\n",
      "CTGGCGGGCACGCAGCGCCAAGATGTCGGGGTCATCGGTGGGGCCCTCGACACCGCAGTTCCACGATCGGTTGTAGCTTTCCCCGTCGCGGTTGTTCTCGCCATTGGCCTCGTTGTGCTT\n",
      "GTCGTTGTACGAGACCAGGTCGTTGAGTGTGAACCCGTCGTGGGCGGTGACGAAATTGATACTGGCACTGGGCCGGCGGCCGGTTGCTTCGTAGAGGTCCGACGACCCGGTCAGCCGGGA\n",
      "GGCGAATTCGCCTAGGGTGGCCGGCTCGCCTCGCCAGTAGTCGCGCACGGTGTCGCGGTACTTGCCGTTCCATTCCGTCCACAGTCCTGGGAAGTTGCCAACCTGGTAGCCACCTTCGCC\n",
      "GACATCCCATGGCTCGGCGATCAGCTTGACCTGACTGACCACCGGATCTTGTTGCACCAGATCGAAGAATGCCGACAGCCGGTCGACGTCGTGCAGCTCGCGGGCCAGCGTGGACGCCAG\n",
      "GTCGAACCGGAACCCGTCGACGTGCATTTCGATCACCCAGTAGCGCAGCGAATCCATGATCAGCTGCAGGGTGTGTGGGTGGCGGGCATTGAGGCTGTTGCCGGTACCGGTGAAGTCCTT\n",
      "GTAGAACCTCAAGTCGTGGTCCATCAGTCGGTAGTAGGCGGTGTTGTCGATTCCGCGAAAGTTGATCGTCGGACCCAAGTGGTTGCCTTCAGCGGTGTGGTTGTAGACGACGTCGAGGAT\n",
      "GACCTCGATGCCGGCTTCGTGCAGGCTGCGCACCATGGTTTTGAACTCGGCTACCGCGCTGCCGGCTTGCCGGGTCGACGCGTATTGATGGTGCGGGGCGAAGAATCCGAAGGTGTTGTA\n",
      "ACCCCAGTAGTTTCGCAAGCCGAGGTCCAGCAGCCGGGAGTCGTGTAGGAACTGGTGCACCGGCATCAACTCAACGGCGGTGACGTTGAGCTCGTTGAGGTGGTCGATGATCACCGGGTG\n",
      "GGCAGGCCGGCGTAGGTGCCCCGGAGTTCGGGCGGGATACTGGGATGGGTCTGTGTCATGCCTTTGACATGCGCTTCGTAGATTACGGTCTCGTGGTACGGGGTGCGCGGCGACCGGTCG\n",
      "TATGCCCAGTCGAAGAACGGATTGATCACGACGCTGGTCATAGTGTGGCCCAGCGAGTCGACCATCGGGGGAGTGCTGTCCGGGTCGACGGCGTTGACGTCATAGGAATACAGCGCCTGC\n",
      "CCGAAGGTGAAATCGCCGTGGAACGACTTCCCATACGGGTCGAGCAGCAGCTTGCTGGGGTCACACCGATGGCCGGCCGCCGGGTCGAACGGCCCGTGCACACGAAACCCGTAGCGCTGG\n",
      "CCGGGGGTGATGTTCGGCAGATAGGCATGCCAGACGTACCCGTCCACCTCGTCAAGCGGGATCCGCGACTCGACGCCGTCCTCGTCGATCAGACATAGCTCGACCTTCTCGGCGATCTCG\n",
      "GAGAACAACGAAAAGTTGGTCCCGGCGCCGTCGTAGGTGGCTCCAAGCGGATAGGCGTTGCCCGGCCACACCGTGGGTAGAGCGGGCCCGGTCCCGTCGGACTCCCCGGCGTTGTTCGAC\n",
      "GACAT\n",
      ">Rv1615_N1 Seen in 1 sample(s).\n",
      "ATGGGCCTACGGCCGGCACGGGTCGTGCGCCCGGCTCGATCTGGCATGCTGAAAGGCGTGACCGATCCCCTGCAGCACGGTGCCTTCGAGCCGGGCTGGCAATCCGCACCACCCGGATAT\n",
      "CCACCGCCTTATCCGCAATATCCGGGGCCTGGCTCTTACTTTGACCCGTTCGCGCCATATGGTCGCCATCCGGTCACCGGCCAACCATTTTCCGACAAATCGAAGACTGTTGCCGGCCTG\n",
      "TTGCAGTTGCTTGGACTGTTCGGCATCGCCGGGATCGGGCGAATCTATCTGGGCCATACCGGCCTGGGCATCGCGCAGCTGCTGGTGGGCTGGGTGACGTGCGGTTTGGGCGCCGTCATC\n",
      "TGGGGCGTCATTGACGCCCTGCTGATATTGACCGACAAAGTCGGCGACCCTTGGGGTCGTCCCTTGCGCGATGGAAGCTAG\n",
      ">Rv1775_N1 Seen in 1 sample(s).\n",
      "ATGGCCAGCGATCTGTACCTGGGCTACCGCAACGACGACGCGGACACGCCGTTCGGCAAGTTCTTCAAACCCGAGATGGCCCCGCTGCCACAGCATGTCGTGGTGGCGTTGCAGCATGGC\n",
      "CCCAGGCCGGGATGGCGTTGCTCGCCTTCGACGACGCCGCGAGCATCGTTGATGAGGGCTATCAGCAGACCGAGAACGGCTACGGGATTCTCGGCGACGGCAGCATGCAGGTATCCGTGC\n",
      "GCACCGACATGCCCGGGGTCACTCCCGCGATGTGGGCATGGTGGTTCGGCTGGCACGGCAGCGACACCCGCCGCTACAAGCTGTGGCACCCGCGGGCCCATCTATCGGCGCGGTGGAAGG\n",
      "ACGGCGACCAGGACAGCGGGGCCGGCCGTCGGGGCGCGCAGCGTTACGTCGGCCGCTGGTCGATGATCAGCGAGTACATCGGCTCGACGAAACTGGGTGCCGCAATACAATTCGTCGAGC\n",
      "CGGCGGCCATGGGTCTGCCCGACGACAGCGACGATACGGTGTCGATCTGTGCGCGGTTGGGCTCTGCTGACGCCCCGGTGGATGCGGGCTGGTTCGTCCATCAGGTCCGATCGACGCCGG\n",
      "GCGGGTCCGAGATGCGGTCACGGTTTTGGATGGGCGGACCGCACATCGCGGTGCGCAAGGCACCCGAGGTCGCGTCCAAGGCGGTGCGTCCCATCGCGTCGAAGCTAATCGGCGTCTCGG\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "AATCGACCGCGCGTAATCTGCTGGTGTACTGCGCGCAGGAGATGAACCACCTGGCGGGGTTCTTGGCGGACCTGTGGGAAAGCTTCGGTGACGAGTGA\n",
      ">Rv1915_N1 Seen in 1 sample(s).\n",
      "ATGGCCATCGCCGAAACGGACACCGAGGTCCACACACCGTTCGAGCAGGACTTTGAGAAAGACGTAGCCGCCACTCAGCGATACTTCGACAGCTCGCGCTTTGCTGGGATCATTCGGCTC\n",
      "TACACCGCCCGCCAAGTCGTGGAACAGCGCGGCACGATCCCCGTCGACCACATCGTGGCGCGAGAGGCGGCGGGCGCCTTCTACGAGCGTCTGCGCGAACTCTTTGCAGCCCGCAAGAGC\n",
      "ATCACGACGTTTGGCCCCTACTCGCCGGGGCAGGCGGTGAGCATGAAGCGGATGGGTATCGAGGCGATCTACCTCGGTGGTTGGGCTACCTCAGCTAAGGGCTCCAGCACCGAAGATCCG\n",
      "GGGCCCGACCTCGCCAGCTACCCGCTGAGCCAGGTGCCTGACGATGCCGCGGTGCTGGTGCGCGCCTTGCTCACCGCGGACCGCAACCAACACTATCTACGCCTGCAGATGAGCGAGCGA\n",
      "CAGCGTGCGGCGACACCGGCTTACGACTTCCGCCCGTTTATCATCGCCGACGCCGACACCGGCCACGGCGGCGATCCGCACGTACGCAACCTGATCCGCCGCTTCGTCGAGGTCGGTGTG\n",
      "CCGGGCTACCACATCGAGGACCAACGACCCGGCACCAAGAAGTGCGGCCACCAGGGCGGCAAGGTCCTGGTGCCGTCCGACGAACAGATCAAGCGGCTCAACGCCGCCCGCTTCCAGCTC\n",
      "GACATCATGCGGGTGCCCGGCATCATCGTCGCACGCACCGACGCGGAGGCGGCCAACCTGATCGACAGTCGCGCCGACGAGCGTGACCAGCCGTTCCTTCTCGGCGCGACCAAGCTCGAC\n",
      "GTACCGTCCTACAAGTCCTGTTTCCTGGCAATGGTGCGGCGTTTTTACGAACTGGGCGTCAAGGAGCTCAATGGTCATCTTCTCTATGCGCTTGGCGACAGCGAGTACGCGGCGGCCGGC\n",
      "GGTTGGCTTGAGCGCCAAGGCATTTTCGGCTTGGTCTCCGACGCGGTCAACGCGTGGCGGGAGGACGGCCAGCAGTCGATCGACGGCATTTTCGACCAGGTCGAGTCGCGGTTCGTGGCG\n",
      "GCCTGGGAGGACGACGCGGGCCTGA\n",
      ">Rv2027c_N1 Seen in 1 sample(s).\n",
      "TCAGCGCAGCGGTGCAGACCACCGCAGCAAGGTGCCTCCGGTCGGCATGTTCTCGACTGTGAATTCGCCGCCCGCGTCGTCGGCACGCTGGCGGAGATTGCGCAGGCCGCTTTCGGTGAT\n",
      "GTCGCCGGAGATGCCGACACCGTCGTCGACGACCTCGACCCGCACATCATCCTCGACGCTGACGTTGATGGCCAGGCTGGTCGCGTTCGCGTGCCGGACAGCGTTGCTAACCGCCTCCCG\n",
      "CAGAACCGCTTCGGCGTGGTTGGCCAGGACGGTGTCGACAACGGACAGCGGGCCCGTGTACTGGACCGTGGTGTGCAGCGCGGGGATCGCGAGTTGGTCGATGACCTTGTCCAGTCGGTG\n",
      "GCGCAGACCCGTCGCCCGGGAGGGCCCGGCGTGTAGGTCGAAGATCGCAGATCGAATCTCCTGAATGATTTCCTGGAGATCGTCGATGCTGCTGTAGATGGATTCCCGGACGGCGGGGAC\n",
      "ACGTGCTCGCGGAGCGGCACCCTGCAGGGTGAGCCCGACTGCGAAGAGCCGCTGGATGACGTGGTCATGCAGATCACGTGCGATCCGGTCGCGATCGGTCAGGATCTCCACTTCTCGCAT\n",
      "CTGTCGCTGCGCGGTCGCCAGCCGCCAGGCGAGCGCAGCCTGGTCAGCGAAGGCGGCCATCATATCGAGCTGTTTGTCGCTGAACGGCTGTTCATCGGCACTGCGAAGTGCGACCAGCAC\n",
      "ACCGGCAACAGTGTCGGCGGCACGCAGCGGCAGCACCAGGGCGGGCCCGGGCTCCACCGGGCCGTCGACCGCGAGGTCAAGCCGGTCGAACCGGCGGGGCGTACGGTCGTGAAAGACTCC\n",
      "CCCGATCGACGTTCCGCTGACGGCAACCGTCATTTGCTTGACCGCCGGGGAGATCTCTCCGGCCACCTCTACGATGACCAGGTCGTCGACCTCGCAAGCCGGCGCTTGTCGTCGAGCGGC\n",
      "ACCGCCACCAAGGTGGCTGCCCCAGCCATCAACGTCAACGCTTCCTCGGCGATGAGCCGAAACACCATGGCCGGGTCCGCACCGGCCAGCATCTGCGTTCCGATGTCGCGGGTTGCCTCG\n",
      "ATCCACGCTTCCCGGGTCCGTGATTCCTCGAAGAGACGGGCATTGTCAACGGCAATCCCGGCCGCGGCGGCCAGCGCCTGCACCAGCACCTCGTCGTCATCGCTGAACGGCTGGCCATCT\n",
      "GCCTTCTCGGTCAAGTAAAGATTGCCGAACACCTCGTCGCGGATGCGCACTGGAACCCCGAGGAAGGTCCGCATCGGCGGATGGTGCAGCGGAAATCCAACCGATGCGGGATGCCGCGAG\n",
      "ATATCGTCCAGCCGGATCGGCTTTGGCTCCTCGATCAGCGCGCCGAGAACACCTCGCCCCTCCGGCAATGAGCCGATGAGGTGCCGGGTCTCTTCGTCGATCCCCTCGTAGACGAATTCG\n",
      "ACCAATCTATGGTCGTAACCGCGCACCCCGAGCGCCCCGTAGCGGGCATCCACCAACTCGGCGGCGGTATGCACAATGGCGCGCAGGGTGGCGTCGAGCTTGAGTCCCGATGTGATCGCC\n",
      "AAGATGGCGTCGATCAGACCATCCAGCCGGTCGCGGCCTTCGACGATCTGTTCAATCCGGTCTTGGACTTCCAGCAGCAGCTCTCGCAACCGAAGCTGCGACAGTGTCTCGCGCAATGGC\n",
      "GGGCTGCCAGGGTTAACGTTCGCCCTGTCAGGGTGTGTCAC\n",
      ">Rv2084_N1 Seen in 1 sample(s).\n",
      "GTGAGTGACGATTCGTCGTCGGCGTTCGATCTGATTTGCGCCGAGATCGAACGCCAGTTGCGCGGCGGCGAGCTGCTCATGGATGCCGCAGCAGCATCCGAATTACTACTCACCGTGCGG\n",
      "TATCAGCTCGATACCCAGCCGCGGCCACTTGTCATCGTGCATGGACCGCTGTTTCAGGCCGTCAAAGCGGCCCGCGCACAGGTGTACGGACGCCTGATACAGCTGCGACACGCGCGCTGT\n",
      "GAGGTGCTCGATGAGCGATGGCAGCTACGGCCGACGGGTCAGCGCGATGTGCGCGCACTGCTGATCGATGTGCTGAACGTGTTGTTGGCGGCCATTACCGCCGCAGGCGTGGAACGGGCA\n",
      "TACGCGTGCGCGGAGCGGCGGGCGATGGCCGCCGCGGTTGTCGCCAAGAATTACCGGGACGCGTTGGGTGTCGAGCTGCAGTGCAATTCCGTATGCCGAGCCGCCGCCGAGGCGATCCAC\n",
      "GCGCTGGCGCACCGCACAGGGGCTACCGAGGATGCCGACTGCCTCCCGCCGGTTGATGTGATACACGCCGACGTTACTCGCCGCATGCATGGCGAGGTGGCGACCGACGTTGTCGCGGCC\n",
      "GGCGAACTGGTGATAGCGGCGCGACACTTGCTGGACCCCATGCCCAGGGGCGAGCTCAGTTACGGCCCACTCCACGAGGGGGGAAATGCGGCCCGTAAATCGGTCTATCGACGCCTGGTT\n",
      "CAGCTATGGCAAGCGCGCCGGGCTGTTACCGACGGTGACGTCGACCTGCGCGACGCTCGCACGCTGCTGACCGATCTGGACAGCATTTTGCGTGAGATGCGCACGGCCGCAACCATTCAA\n",
      "CAGGCGTACACACGAGCGGAACGGCGGGCGATGGCGGCGGCGGTCGTCGCCAAGATTCGCGGCGACGCAATGGGCCTCGACGCCCAGCGCGACGCGGTACATCGCGCGGCCGCCGATGCG\n",
      "CTCCACGCGTTGCAATCGGTTGGCATACACCAATAGGCGACCCTTTGGCAGTTGAGGGTGTAGAGGAGATCGGCGCGTCGTTGCCGGGGCGGGAGTCGACGCCTTCCGATGATGGAGGTT\n",
      "CCCTACACCCATCAGGAAGACCTCGACGCGTCCATCGCCGCCGGTGGTGCGGGCTTGGCCTGTGCTGA\n",
      ">Rv2148c_N1 Seen in 1 sample(s).\n",
      "TCAGGTGACCGTAACCGCCGCGGACCCAATAGCGCGGTACCGACACGCACACAGGTCGAACCATGTTTGACGGCGACTTCAAGGTCGTTGGACATGCCCGCCGACAGACCGATCGCGTGC\n",
      "GGGAACATCGCACGCACCCGGTTGTGCTCCGATTGCAGCCGGTCAAAGGCCTCGTCCGGGTCCCAATCCAGCGGCGGAATGCCCATCAACCCGACCAGTTCGAGGCCCTCTGACTCCTGC\n",
      "ACCTGCGCGCAAATCCGGTCTACGGCGCCGGGCGTCGTGCTGTCGACGCCGCCCCGGGATCCGTCACCGTCGAGGCTGACCTGGACGTAAACCCGCAGCCGCTCGCCACGACGGTGTTCG\n",
      "GCCAGCGCCGCAACAACCGCCCGATCCAGCGCGGTCACCAACCGCGAGCTGTCCACCGAGTGAGCGGTGTGCGCCCAGCGAGCCAGCGACCCGGCTTTGTTGCGTTGAATCCGGCCCACC\n",
      "ATGTGCCAGTGCACACCCCCCGAGTGACCCAACTCGGCAGCCGCCAACAACCGATTAAGTTCGGCCATCTTGGCTGAAGCTTCCTGTTCGCGCGATTCGCCAACGGACCGACAACCCAAT\n",
      "CGAAACAAAATCGCAACATCGGTTGCTGGAAAGAATTTGGTAATCGGTAGAAGTTCAATTTCGCCGACATTGCGACCCGCCGCCTCCGCGGCCGCCGCAAGTCGCGATCGCATTGCCGCC\n",
      "AACGCATGCGTCAATTCCGATTCGCGGTCTGGATACGCCGAAAGATCCGCCGCCAT\n",
      ">Rv2176_N1 Seen in 1 sample(s).\n",
      "GTGGTCGAAGCTGGCACGAGGGACCCGTTGGAGAGCGCGCTGCTGGACAGCCGCTATCTGGTCCAGGCCAAGATTGCCAGCGGCGGCACCTCGACGGTCTACCGGGGCCTGGATGTCCGA\n",
      "CTCGACCGGCCCGTCGCGCTGAAAGTGATGGATTCTCGCTACGCGGGCGATGAACAGTTTCTGACCCGCTTTCGACTGGAGGCCCGTGCGGTTGCCCGGCTAAATAACCGCGCGCTGGTC\n",
      "GCGGTCTACGACCAGGGCAAAGACGGCAGGCACCCGTTTCTGGTGATGGAGCTCATCGAGGGCGGTACCCTGCGCGAGCTGCTGATAGAACGTGGTCCCATGCCGCCACATGCCGTTGTG\n",
      "GCGGTGCTGCGCCCAGTGCTTGGCGGGCTGGCTGCCGCCCATCGAGCCGGTCTGGTGCATCGCGATGTCAAGCCCGAGAACATCTTGATCTCCGACGACGGCGACGTCAAACTCGCCGAT\n",
      "TTCGGGTTGGTCCGCGCGGTCGCCGCCGCTTCAATCACGTCTACCGGCGTCATCCTGGGTACCGCGGCCTACCTGTCCCCTGAGCAGGTCCGTGATGGAAACGCCGATCCTCGAAGCGAC\n",
      "GTCTACTCTGTCGGCGTTCTGGTCTACGAGCTGCTAACGGGGCACACACCGTTCACCGGCGACTCGGCCTTGTCGATTGCCTACCAACGGCTTGATGCTGACGTGCCGCGTGCCAGTGCT\n",
      "GTAATCGACGGTGTACCGCCACAATTCGATGAGTTGGTGGCATGTGCAACTGCCCGCAACCCTGCCGACCGATACGCCGATGCGATCGCGATGGGCGCCGATCTGGAGGCGATCGCCGAG\n",
      "GAGCTGGCCCTGCCTGAATTCCGGGTACCGGCGCCGCGCAACTCCGCTCAACACCGGTCGGCCGCGTTGTACCGCAGCCGGATTACCCAGCAAGGGCAGCTGGGTGCCAAACCGGTTCAC\n",
      "CACCCTACTCGCCAGCTGACTCGCCAACCCGGCGACTGCTCCGAGCCGGCTTCAGGGTCGGAGCCCGAACACGAGCCGATCACCGGCCAATTCGCCGGCATCGCAATCGAGGAATTCATC\n",
      "TGGGCGCGACAGCACGCCCGTCGAATGGTGCTTGTCTGGGTGTCGGTGGTGCTGGCGATCACCGGGCTAGTGGCGTCCGCGGCATGGACGATCGGGAGCAACCTGAGCGGCCTGCTCTAA\n",
      ">Rv2185c_N1 Seen in 1 sample(s).\n",
      "TCAGCCCTCGACTCGTTTCTTCAGATCCTTCAACGCGCCGTCTATCAACCTGCGTTCCGCCTTACGCTTGAGCATCCCGATCATGGGGACAGCAAGGTCGACGGCAAGCTCGTAGGTGAC\n",
      "CTCAGTGCCAGAACCCTTGGGCGCCAAGCGATACGTGCCTTCGAGGGACTTTAGCAGCGAGCTGGATTCGAGAGTCCAGCTAAGCGATTGGCGGTCTTCCGGCCACTCGTAGGACATGAT\n",
      "CAAGGTGTCTTTGAAGATGGCTGCGTCCATCAACATTCGCGCTCGTTTCGGGTAGCCCTCGTCGTCGGCCTCTAGGATCTCGACTTCCTTATACTCCGAAATCCATTGCGGGTAGGCGTC\n",
      "GATGTCGGCGATCGCCTTCATCACCTCGCCTGGATCCGCGTCGATGTAAATCGTCTGTGTCGTCTTGTCCGCCAC\n",
      ">Rv2241_N1 Seen in 1 sample(s).\n",
      "GTGGCGTCGTATTTGCCCGACATTGATCCCGAGGAGACCTCGGAGTGGCTGGAGTCCTTTGACACGCTGCTGCAACGCTGCGGCCCGTCGCGGGCCCGCTACCTGATGTTGCGGCTGCTA\n",
      "GAGCGGGCCGGCGAGCAGCGGGTGGCCATCCCGGCATTGACGTCTACCGACTATGTCAACACCATCCCGACCGAGCTGGAGCCGTGGTTCCCCGGCGACGAAGACGTCGAACGTCGTTAT\n",
      "CGAGCGTGGATCAGATGGAATGCGGCCATCATGGTGCACCGTGCGCAACGACCGGGTGTGGGCGTGGGTGGCCATATCTCGACCTACGCGTCGTCCGCGGCGCTCTATGAGGTCGGTTTC\n",
      "AACCACTTCTTCCGCGGCAAGTCGCACCCGGGCGGCGGCGATCAGGTGTTCATCCAGGGCCACGCTTCCCCGGGAATCTACGCGCGCGCCTTCCTCGAAGGGCGGTTGACCGCCGAGCAA\n",
      "CTCGACGGATTCCGCCAGGAACACAGCCATGTCGGCGGCGGGTTGCCGTCCTATCCGCACCCGCGGCTCATGCCCGACTTCTGGGAATTCCCCACCGTGTCGATGGGTTTGGGCCCGCTC\n",
      "AACGCCATCTACCAGGCACGGTTCAACCACTATCTGCATGACCGCGGTATCAAAGACACCTCCGATCAACACGTGTGGTGTTTTTTGGGCGACGGCGAGATGGACGAACCCGAGAGCCGT\n",
      "GGGCTGGCCCACGTCGGCGCGCTGGAAGGCTTGGACAACTTGACCTTCGTGATCAACTGCAATCTGCAGCGACTCGACGGCCCGGTGCGCGGCAACGGCAAGATCATCCAGGAGCTGGAG\n",
      "TCGTTCTTCCGCGGTGCCGGCTGGAACGTCATCAAGGTGGTGTGGGGCCGCGAATGGGATGCCCTGCTGCACGCCGACCGCGACGGTGCGCTGGTGAATTTAATGAATACAACACCCGAT\n",
      "GGCGATTACCAGACCTATAAGGCCAACGACGGCGGCTACGTGCGTGACCACTTCTTCGGCCGCGACCCACGCACCAAGGCGCTGGTGGAGAACATGAGCGACCAGGATATCTGGAACCTC\n",
      "AAACGGGGCGGCCACGATTACCGCAAGGTTTACGCCGCCTACCGCGCCGCCGTCGACCACAAGGGACAGCCGACGGTGATCCTGGCCAAGACCATCAAAGGCTACGCGCTGGGCAAGCAT\n",
      "TTCGAAGGACGCAATGCCACCCACCAGATGAAAAAACTGACCCTGGAAGACCTTAAGGAGTTTCGTGACACGCAGCGGATTCCGGTCAGCGACGCCCAGCTTGAAGAGAATCCGTACCTG\n",
      "CCGCCCTACTACCACCCCGGCCTCAACGCCCCGGAGATTCGTTACATGCTCGACCGGCGCCGGGCCCTCGGGGGCTTTGTTCCCGAGCGCAGGACCAAGTCCAAAGCGCTGACCCTGCCG\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GGTCGCGACATCTACGCGCCGCTGAAAAAGGGCTCTGGGCACCAGGAGGTGGCCACCACCATGGCGACGGTGCGCACGTTCAAAGAAGTGTTGCGCGACAAGCAGATCGGGCCGCGGATA\n",
      "GTCCCGATCATTCCCGACGAGGCCCGCACCTTCGGGATGGACTCCTGGTTCCCGTCGCTAAAGATCTATAACCGCAATGGCCAGCTGTATACCGCGGTTGACGCCGACCTGATGCTGGCC\n",
      "TACAAGGAGAGCGAAGTCGGGCAGATCCTGCACGAGGGCATCAACGAAGCCGGGTCGGTGGGCTCGTTCATCGCGGCCGGCACCTCGTATGCGACGCACAACGAACCGATGATCCCCATT\n",
      "TACATCTTCTACTCGATGTTCGGCTTCCAGCGCACCGGCGATAGCTTCTGGGCCGCGGCCGACCAGATGGCTCGAGGGTTCGTGCTCGGGGCCACCGCCGGGCGCACCACCCTGACCGGT\n",
      "GAGGGCCTGCAACACGCCGACGGTCACTCGTTGCTGCTGGCCGCCACCAACCCGGCGGTGGTTGCCTACGACCCGGCCTTCGCCTACGAAATCGCCTACATCGTGGAAAGCGGACTGGCC\n",
      "AGGATGTGCGGGGAGAACCCGGAGAACATCTTCTTCTACATCACCGTCTACAACGAGCCGTACGTGCAGCCGCCGGAGCCGGAGAACTTCGATCCCGAGGGCGTGCTGCGGGGTATCTAC\n",
      "CGCTATCACGCGGCCACCGAGCAACGCACCAACAAGGCGCAGATCCTGGCCTCCGGGGTAGCGATGCCCGCGGCGCTGCGGGCAGCACAGATGCTGGCCGCCGAGTGGGATGTCGCCGCC\n",
      "GACGTGTGGTCGGTGACCAGTTGGGGCGAGCTAAACCGCGACGGGGTGGCCATCGAGACCGAGAAGCTCCGCCACCCCGATCGGCCGGCGGGCGTGCCCTACGTGACGAGAGCGCTGGAG\n",
      "AATGCTCGGGGCCCGGTGATCGCGGTGTCGGACTGGATGCGCGCGGTCCCCGAGCAGATCCGACCGTGGGTGCCGGGCACATACCTCACGTTGGGCACCGACGGGTTCGGCTTTTCCGAC\n",
      "ACTCGGCCCGCCGCTCGCCGCTACGTCAACACCGACGCCGAATCCCAGGTGGTCGCGGTTTTGGAGGCGTTGGCGGGCGACGGCGAGATCGACCCATCGGTGCCGGTCGCGGCCGCCCGC\n",
      "CAGTACCGGATCGACGACGTGGCGGCTGCGCCCGAGCAGACCACGGATCCCGGTCCCGGGGCCTAA\n",
      ">Rv2264c_N1 Seen in 1 sample(s).\n",
      "TCAGCTACCCGAAATCGCGCTGAACTGTCCGATCCCGGGAACCTGAGGTATTCCGGGAGGGGAGCTGCGGAATCTCCGGAATCGGTGGGATCGGCGGGATCGGTGGAGGGCTGGGGGACG\n",
      "TGGTCGCCGGCGGCTGCGTGGTCGCCGGCGGCTGCGTGGTCGCCGGCGGCGCGGAAGCGGGGGTCGTCGGTGCCGGAGTGATGACATCGGTGGTCACCGCCGGTTGCGTATTCGTCGTTG\n",
      "TCGGCGGAGGCGGCAACGGCTGCTGCAGCGGCGGCGCGGGCCCACCGGTGGCTGGCGCCTGTACGGGAGGTGCGGGCTCGGCAGTGGGGCCATCGGATGCCGGCGCTGGGGACGGGGGCG\n",
      "GTGCGGCGGTCGTGGTCACACCCGGCCTCTGCGGGGTCCCCGGCGCCGTCGGCTGGTCGCCGGTGGACAACCCGATCGCCACGGCGGCACCCACCAGCAACACCGCCACCGTCGTGCCGG\n",
      "TGATGATCACGGCCGGCAGGCGATACCACGGGATTGGCGGGGACTTGGGCTCGGGCTCCGCATGGGCATCGTGGTCGAAGCTCAGCGACGGGCGGGCCGCTGTGTAGCCAGGGGCCGGCC\n",
      "CGATGTGGGAGTCCTCGTCGGCCTCCGACCAGGCCAAAGCGGGCTGCAGGACCGACGCCGGCGCATCGGCCGGCGCCGTCGCCGTCGCCGAGGTGACCGCGGTCAGCACCGTTGCGCTGG\n",
      "TGTCGCCGGGTCTGCGTGCCGCCCACAACGCGCCGCCGAAAGCGGCCGTCAATTGCGGACGAGGCGTCCTGACCACCGGCACGCAGAAACGTCCGGACAGCGTCGTGGTGACTGCCGGGA\n",
      "TATTTGCACCACCACCCACCGAAACGATCGCTACCAGCTCGGCCGTGCGAATTCCGCTGCGGGCCAGGGTTTGTTCCAAGGCCCTGCCCACGCTGTCCAGCGAGTCACGGATTGTGTCCT\n",
      "CGAGCTCGTTGCGGGTCAACCGGATATCCCCGCCCAACGCGTCGGTCAGCGTGGTCACCGTGCTTGACGAAAGCCGTTCCTTGGCTTTGCGACATTCGATCCGCAGCTTAGTCAGTGAGC\n",
      "CGATCGCCGAGGTGCCGGCTGGATCGAACGCGCCCGTGCCCGGTAGTTCGGACATGACGTAGCTCAACAGCGACTGATCGATCAGATCGCCGGAGAAAGCCTGATGGCGCACCGTCGCGG\n",
      "CCACCGGCCGATACTCGTCTGCGGCGTCGACGAGCGTGATGCCGGTCCCGCTGCCACCGAAGTCGCATACCGCGACGATCCCACGGGCCGGTATGCCCGGGTCGGCCCGTATCGCGTACA\n",
      "GCGCTGCCGCGGCGTCAGGGAGCAGTGACAGTGGCTGGGCCGTACTCGAAGTCCCGTGCGACCATTCCGAGGCCCGACGCAGCGCGCTATCCAACGCTGCTACCGCAGCCGGCCCCCAGT\n",
      "GGGCGGGATAGGTCACCGTGACACTTCCGGGAAGAGCACGACCGCCGGTAGCGGTGTAGGCCAGCGCCAGCAGTGCGTCAGCCACTAGCGCCTCGCTGCGGTACACCGAGCCGTCGGCAG\n",
      "CCACGATGCCGACCGAATCTCCCACCCGGTCTACGAAGTCGGTGATCACCAGGCCTGGCTCGTCCAGCCTCGGGTTCTCCGATGGCACACCGACCTCGGGCGGGCGCTGTCGATACAGCG\n",
      "TCAGCACGGGTTTACGTGTGATGGAGTGATCGGCAGCCACAGCCGCTAGGTTGGTGACACCGATCGACAAGCCTAATGCCGGTCTCGCCCCTGTTGCCAT\n",
      ">Rv2293c_N1 Seen in 1 sample(s).\n",
      "TCAGCCAGGGTCCCGCCGCCTGGAAAAAGTTACCGGTATAGCCAAGTGAGCGATCGGGTGCACTACAGGGTTGGCAGCCAAAAACGCTGCCGCCGTTCGGGATGCAAGGAAAAGCCTGGC\n",
      "CGTTGTTCTTGTCGGAGCTAGACCCGTCACCGCCGACGAACAGTTGCGGCTGGCGCCCCAGGTGGTTCAACCGGACGACCGGAACGTTCCTGCACAGACAGACAGGATTGCCGAGCGTGT\n",
      "TGATGTTGTCCAGTACAACAGAAAGCGTCTGGGCAGTAGCCAGCATGCCGGGATCGACCCCACGGAATGTTGCCCCGTTGTCCAGGGTCCACCGTGCTGGTATTGCCACGTCCCCAATGC\n",
      "TGGTGCGGCCGGCACCACCGGCGACGCCCGAGAACATCACGGCGGCAATGGCAATGGAAGAAGCACAGGTAAAGCGTGCGAAGGCGGTCTCGGTGGTGTTGGTAGCGTTCACTAGGCCGA\n",
      "TGCCGGTCATCGCCACAATCACCTTCTTGCCGCTGATCGAGCCCAGGTAGTAGCGACGACGGTCGGCGACCACCACCGGGTTGGCGTCCAGCGCGGTGTGCGCCAGCACCGCGTCGGCCT\n",
      "CAGCCGGAAACGCCGACAAGACCAGCGTGCGCTGTTCGCACGGGATCACATTTGCCACGTATCCGGGATCGGCCGCCGCCACGCCACAGCCCAGCGACAACGCGGCCGCCACCAAAAGAC\n",
      "AGTGCCGCAAAGGCGCGCCCAC\n",
      ">Rv2339_N1 Seen in 1 sample(s).\n",
      "ATGGTGCCGGGCGAAGTCCACATGAGTGATACGCCGTCAGGCCCGCACCCAATCATCCCGCGGACGATTCGCCTGGCCGCGATTCCCATCTTGCTGTGTTGGCTGGGATTTACCGTTTTC\n",
      "GTCAGCGTCGCCGTTCCTCCGTTGGAGGCGATCGGTGAAACCCGGGCCGTGGCAGTTGCCCCCGACGATGCGCAATCGATGCGTGCGATGCGACGTGCGGAAAGGTGTTCAACGAATTCG\n",
      "ATTCCAATAGCATCGCGATGGTCGTCCTGGAAAGCGATCAACCACTAGGCGAGAAGGCCCATAGGTATTACGACCACCTGGTCGATACGCTCGTACTGGACCAGAGCCATATCCAGCACA\n",
      "TTCAAGACTTTTGGCGTGATCCCCTGACGGCGGCGGGTGCGGTCAGCGCAGATGGTAAGGCGGCGTACGTTCAACTTTACCTCGCCGGCAACATGGGTGAAGCACTCGCAAACGAATCCG\n",
      "TTGAAGCCGTCCGGAAAATTGTGGCGAATAGTACACCGCCGGAAGGCATCAGAACCTATGTCACCGGACCGGCGGCCTTGTTTGCCGACCAAATCGCCGCCGGTGACCGAAGCATGAAGC\n",
      "TGATCACCGGATTAACGTTCGCGGTAATCACCGTGTTGCTGCTGCTCGTCTATCGCTCGATCGCCACCACGCTGCTGATTCTTCCCATGGTGTTTATTGGACTCGGCGCGACGCGTGGCA\n",
      "CCATTGCCTTTCTTGGATACCACGGAATGGTCGGCCTTTCGACTTTTGTGGTCAATATCCTCACGGCACTTGCCATTGCTGCCGGTACAGACTACGCGATCTTCCTGGTCGGCCGCTATC\n",
      "AAGAAGCCCGCCATATCGGCCAGAATCGCGAAGCCTCTTTCTACACGATGTACAGGGGCACCGCTAACGTCATTCTCGGATCGGGACTGACCATCGCCGGCGCAACATATTGTCTGAGTT\n",
      "TCGCCCGGCTGACGCTGTTTCACACCATGGGGCCTCCGTTGGCAATAGGCATGCTGGTTTCGGTCGCGGCCGCGCTGACCCTGGCGCCCGCCATCATTGCCATCGCCGGCCGCTTCGGCT\n",
      "TGCTCGACCCCAAGCGAAGACTGAAGACCAGGGGCTGGCGTCGTGTGGGTACCGCAGTCGTGCGCTGGCCCGGGCCAATTCTGGCCACGTCGGTCGCGCTTGCCCTGGTGGGATTGCTCG\n",
      "CACTACCGGGCTACCGGCCCGGCTATAACGATCGCTACTACCTGCGCGCTGGCACGCCTGTCAACCGCGGGTATGCGGCCGCCGACCGGCACTTTGGCCCAGCCCGGATGAACCCCGAGA\n",
      "TGCTGCTGGTCGAGAGCGATCAAGACATGCGAAATCCGGCCGGGATGCTCGTCATCGACAAGATCGCCAAGGAGGTCCTGCACGTGTCCGGGGTCGAGCGGGTGCAAGCGATCACCCGGC\n",
      "CGCAGGGGGTGCCCCTTGAGCATGCGTCGATTCCCTTTCAGATCAGCATGATGGGTGCCACCCAGACGATGAGCCTGCCCTACATGCGCGAACGCATGGCCGATATGTTGACCATGAGCG\n",
      "ACGAAATGCTGGTTGCGATCAATTCCATGGAACAGATGCTCGACTTGGTGCAGCAGCTCAACGACGTTACCCATGAGATGGCAGCCACGACGCGCGAGATCAAAGCTACTACCAGCGAAC\n",
      "TGCGAGATCACCTTGCGGACATCGACGATTTCGTCAGGCCGTTGCGTAGCTATTTCTACTGGGAGCACCATTGCTTCGACATTCCGTTGTGCTCGGCGACGCGATCACTGTTTGACACCC\n",
      "TAGACGGCGTCGACACGCTGACTGACCAATTGCGGGCCCTTACCGACGACATGAATAAGATGGAGGCGCTCACACCGCAATTTCTCGCACTGCTGCCGCCAATGATCACGACCATGAAGA\n",
      "CCATGCGGACCATGATGTTGACCATGCGATCAACAATAAGTGGCGTACAAGATCAAATGGCCGATATGCAAGACCATGCGACTGCGATGGGGCAGGCCTTCGACACCGCAAAAAGCGGCG\n",
      "ATTCATTCTATCTTCCTCCGGAAGCCTTCGATAATGCAGAATTCCAGCAAGGCATGAAGTTGTTTTTGTCGCCGAATGGTAAGGCGGTGCGCTTCGTAATTTCCCACGAGAGCGATCCAG\n",
      "CAAGTACTGAAGGTATCGATCGCATCGAAGCGATAAGGGCCGCGACCAAAGATGCCATCAAGGCGACACCATTGCAAGGCGCTAAAATCTATATCGGTGGCACGGCTGCGACCTACCAAG\n",
      "ACATTCGAGACGGTACCAAGTACGATATCCTCATCGTTGGTATAGCCGCGGTATGCCTGGTATTTATTGTCATGCTCATGATTACCCAGAGCCTGATTGCGTCACTCGTCATTGTTGGCA\n",
      "CGGTACTTCTGTCATTGGGTACTGCGTTCGGACTGTCCGTGCTCATCTGGCAGCACTTTGTCGGTCTCCAGGTGCATTGGACGATCGTCGCGATGTCTGTCATCGTCTTGCTGGCCGTCG\n",
      "GTTCTGACTACAACCTCCTTTTGGTGTCCCGGTTCAAGGAGGAGGTCGGCGCTGGATTAAAGACCGGGATCATCCGGGCGATGGCCGGCACCGGCGCAGTTGTCACGTCGGCCGGTCTGG\n",
      "TATTCGCGTTCACCATGGCGTCCATGGCCGTCAGCGAACTCCGCGTTATCGGACAGGTCGGCACCACCATCGGGCTCGGTCTACTTTTCGATACCCTGGTGGTCCGATCGTTCATGACGC\n",
      "CATCCATCGCAGCGCTGCTAGGTCGCTGGTTCTGGTGGCCGAACATGATCCACTCGAGACCCACCGTCCCGGAGGCGCACACACGCCAGGGCGCTCGCCGAATTCAGCCGCATCTGCACC\n",
      "GGGGTTGA\n",
      ">Rv2437_N1 Seen in 1 sample(s).\n",
      "GTGCTGCAGCGGACCAACGTTGTCCAACCGCTGAATACTCTGCGCATGGTCTGGATTCAGGTTGCCGGCATAATCCCGGCGACGGCCGGGATCGCGGCCACGGTTTCGCCCAGCTTGCGA\n",
      "TGGGCGATTCGTGGCGGATCGGGGTGGACGAGCAGGAGAACACCACTCTGGTGCGCACCGGCCCGTTTAAATGGGTGCGTCACCCCATCTACACGGCCATGATGGCGTTTGGCCTCGGGC\n",
      "TGTTGCTGGTGACTCCGAATCTCGTTGCCCTCGCCGGGTTTATCCTGCTCGTTGCCACGCTCGAGGTGCATGTCCGCCGCGTCGAAGAACCCTACCTGTTGCGGACGCACAGTGCCGTCT\n",
      "ACCGCGGCTACACCGCCAGCGTCGGCCGGTTCGTCCCGGGTGTGGGGTTGATCCGCTAG\n",
      ">Rv2526_N1 Seen in 1 sample(s).\n",
      "ATGACCGTAAAGAGGACCACGATTGAGCTGGACGAAGATCTTGTGCGGGCAGCCCAGGCCGTCACCGGGGACGCGAGCGACGGTCGAGCGCGCGCTGCAGCAGCTGGTGGCCGCGGCTGC\n",
      "CGAGCAGGCCGCCGCGCGCCGGCGGCGGATCGTCGACCATCTCGCGCACGCCGGCACTCACGTGGACGCAGACGTGCTGCTCTCCGAGCAGGCGTGGCGATGA\n",
      ">Rv2545_N1 Seen in 1 sample(s).\n",
      "GTGAGCACCACCATCGTTGCTGGCGTGATCCAGGGTCACCTGCCGGTGATCCTGCCCACGCGCAGGCGGGCTCGCGATCTCGGGCACACGACGGCGTTTTTCGGGCGCAAACGCTCCAAT\n",
      "GCATATATCTCAGTATCGAATACCTATATGTTTGCTCCATGTCTCGGCGTACAACGATCGACATCGATGACATACTGCTGGCCCGCGCGCAAGCGGCGCTCGGTACCACCGGGCTGAAGG\n",
      "ACAGGGTCGATGCCGCTTTGCGAGCCGCGGTGCGCTAG\n",
      ">Rv2587c_N1 Seen in 1 sample(s).\n",
      "CTATCCCCGTCCCGTCCGAGCCATGGCCCGGCGTTCGCGTGCGACCTGCTGCACCGCTCCCAGGCCGTTGTATGCCGGCTTGGCCAGCAGCGACGATTTGGACGCCAGATACACCAACGG\n",
      "CCACGTCACCAAGAACACCACGACGAGGTCCAGGATCGTGGTGAGGCCCAGGGTGAACGCGAACCCCTTCACCTGACCGATCGCCAGAAAGTACAGCACGGCAGCGGCCAGGAAAGTGAC\n",
      "GGCGTTGCCCGACACGATCGTCTTGCGGGCACGCGCCCAACCGCGCGGCACTGCCGACCGGAACGAACGGCCTTCGCGGATCTCGTCTTTGATGCGTTCGAAGAACACCACGAACGAGTC\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GGCGGTGGTCCCGATACCGATGATCAGGCCCGCAATACCAGCCAGATCTAGGGTGTAGTTGATATATCGGCCCAAGAGCACCAGGATCGCAAAAACCATTGAGCCAGAAGCCACTAGCGA\n",
      "CAAGGCCGTGAGCAGTCCCAGCACTCGGTAGTAGAGCAGCGAATACACCAGCACCAACAGCAGGCCGATCGCACCCGCGATCATGCCCGCGCGCAGCGATGACAACCCCAAGGTCGCCGA\n",
      "AACCGTTTGGGCTTCCGACGGTTCGAAGGACAGCGGCAGCGACCCGTACTTGAGGACGTTGGCGAGCTGGCGTGCGGTCGCCGCGGTGAATGGCGGATCCCCACCGCTGATCTGGGTTCG\n",
      "GCCGCCGGGGATCGCTTCCTGGATCTGCGGTGCACTGACAACCTGCGAGTCCAGGGTGAACGCCGTCTGGGTGCCGATATGGGCGGCGGTGTAGTCGGCCCAGATGTTGGCCGCCGGACC\n",
      "CTTGAACTGCAGGTCGACGACGTAGCCGATGCCGCGCTGGTCCATACCCGAGGTGGCGTTTTGGATCTGGTCGCCGCTGATGACCGACGGCGCCAGCAGGTACGCGGTCTTGTGGTCGGT\n",
      "CGAGCAGGTCACCAACGGCAGTTTCGGGTCGTCGTTGCCGGCCAAAATGTCGTCGCTCTCGCAGCGGGTCGCCTGGAATTGCAGTGCAACCATCTGCATGTATTGGTTGGTGCTCTGCCG\n",
      "CAGCTTCTTCTCCTGGGCGATGCGCTCGGCGAGATCCTTGCGCGGATCCGTGGCCGGCGCCTCAGCGGGCGGCGCCGGCGGCGGGCTGGCCGGTGAGGTCGGGTTGGGCGATGGCGCCGG\n",
      "GTCCTGCGGATAGGGCCGCGGTTGGGCCCCAGGTTGCGGTGAAGCCGGCGCCCCCGATTGGGCTGGCGGCGGTGCGGCGGGTTGACCGGGCGGCTGCGGTTCGGCGCTGGGTGCCGGCTG\n",
      "CGGTTCTTCGGCTGCGGGCTGCGCCGGCATCGAGTTGAGCACCGGCCGGATGTACAGCCGAGCGGTCTGTCCGAGGTTGCGTGCCTCGCTGCCGTCGTTGCCGGGCACCGTGATGACCAG\n",
      "GTTGTCACCGTCGACGACCACCTCCGACCCGGACACTCCCAGCCCGTTGACCCGCGCGCTGATGATTTGCTGCGCCTGTGCCAGCGCTTCCCGGCTCGGGGCCGAGCCGTCCGGTGTGCG\n",
      "CGCGGTCAGCGTGACCCTGGTGCCGCCCTGCAGGTCAATGCCGAGTTTGGGGGCGGTGTGCTTGTCCCCGGTGAAAAACACCAGCAAATAGATGCCGATCAGCATCACCAGGAACACCGA\n",
      "CAGGTAACGGGCAGGGTGCACCGGCGCCGAAGACGATGCCAC\n",
      ">Rv2848c_N1 Seen in 1 sample(s).\n",
      "TTACGCTCGTGGAGTATTGCAGGCCGCATGTGCGACGAAACGCGCCACCGCACCGGGGTGTTGCGGCCGGATGGGTATGCAGGTAGGACGCGTGCACGCCGCTGTGCACCGCGCCGTCTC\n",
      "GCACGTCGTCCACGTCTTGGCCCTGGTACACCCACGCGGGCTGATAGCTATCGGCGAATGTGACTGCGGTTCGGTGGAATTCATGTCCAACCACGCGCTCGCCGACGGAGTACAGCGCCG\n",
      "AATCAACAACCGCGACGGCGTCGCGATAACCCAGCTTGAGATGCTGGGTGAACCGCGCCGATCCGGCCACCACACCGCACATCGGGTGTCCGTCGAGTTCAGAAACCAGATAGAGCAGGC\n",
      "CGGCACATTCGGCATGCACCGGGGCGCCGGCAGCGGCCAGTTCGTTGATCTGCCGCCGGACGGTGTCGTTGGCGGACAACTCGGCGGTGAACTGCTCGGGGAATCCGCCGGGCAACACCA\n",
      "CCGCGTCCGTACCCTCGGGCAGAGTTTCGCTGAGCGGGTCGAACTCGACCACTTCAGCCCCGGCGGCGCGCAACATCTCGGCGTGTTCGGCGTAGCCGAAGGTAAACGCCCTTCCGGCCG\n",
      "CGATGGCAACCGTGGCTGGCTGGCGGGCGGTGTTGCCGACGGCAATCACCGGGTCCCATGGCGGGTGGGCCGCCTGGCTCCCGGCGCAGGCGATCACCGCGGCCAGATCGACGTGGCGAG\n",
      "CGACCACAGCAGTCATCGCCTGCACGGCGAGCCGTGCGCGACGGCCGTACTCGACGGCGGTAACCAGACCCAGATACCTTGTCGGCAGCTCTAGTTCAGCTGTGCGTGGAATGGCGCCCA\n",
      "AGACCGCGACACCGGCCTGGTCACACGCCTGTCGCAGCACCTGTTCATGTCGGGCCGATCCGACCCGGTTGAGGATGACACCGGCGATCCGAGTTGCGGTGTCGAACGTGGAAAAGCCGT\n",
      "GCAGCAGTGCGGCAACGCTGTGACTCTGGCCGCGGGCATCGACCACCAGGATCACCGGGGCGCCAAGCAGAGCAGCGACGTGCGCGGTGGACCCCGCTGCGGGCGCGCCCCCGGCAGGCC\n",
      "CAATGCGCCCGTCGAACAGCCCCAGCACCCCTTCGATCACGGCGATGTCCGCGCCCGCAACTCCATGCGCGTACAGGGGGCCGATAAGCCGCTCCCCCACCAGTACCGGGTCGAGATTGC\n",
      "GGCCGGGCCGTCCCGCGGCCAGGGCGTGATAGCCGGGGTCGATAAAATCCGGGCCTACCTTAAACGGCGCGACGGTGTGACCGGCCTGCCGCAGCGCTCCGATCAAGCCCGTCGCGATCG\n",
      "TGGTCTTACCGCTGCCCGACGCAGGCGCGGCGACGGCCACCGCGGATACCCGCAT\n",
      ">Rv2902c_N1 Seen in 1 sample(s).\n",
      "CTAAGTGCCCTGAGCGCGACCCGTGGCCCGCATTGTCGCTGGGTGGGAACTCTTGCTCCATCTTCCCTCACCCGTCTGTGCCGTCCCGTCCCGAGGGTCGGGTTGGCCGTCGGCGACCTC\n",
      "TGCGGTGTTCGACCCACTCGCCACCCGGCGAACATTGATGAACGAGTAACGGTGCTGCGGGCAGGGTCCCAATCGGGCCAGCGCCCGGCTGTGCGCCGGGGTGCTGTAACCCTTGTGCTC\n",
      "CGCGAAACCGTACCCGGGGTAATCGGCGTCCAACGCAACCATCACGCGGTCCCGGCTGACCTTGGCGAGCACGCTAGCCGCGGCGATGCAGGCGGCTGCCGCGTCGCCACCGATCACCGG\n",
      "CAACGACGGCATCGGCAGTCCTGGCACGCGAAAGCCGTCGCTGAGCACATAACCGGGCCGCACCGCCAGACCGGCCACCGCGCGCCGCATACCTTCGATATTGGCCACGTGCACGCCGCG\n",
      "GCGGTCGACCTCGGCCGACGGGATGAACACCACGTGATAGGCCACCGCATACCGGCAGATCAGCGGGAACAGCTTCTCCCGCGCTTGCTCGCTGAGCTTCTTCGAATCATCAAGGGCGGC\n",
      "AAGACTTGCTATCCGCCCGGGGCCAAGCACGCAGGCCGCGACCACCAACGGGCCAGCGCAGGCGCCGCGACCCACTTCGTCGACCCCGGCCACCGGCCCCAGACCACCACGATGCAGCGC\n",
      "GGACTCCAGGGTGCGCATTCCCCGCAAACCCCCAGATTTACGGATCACCGTCCGCGGTGGCCAGGTCTTGGTCAT\n",
      ">Rv2947c_N1 Seen in 1 sample(s).\n",
      "TCACCCACGGCACCATCGACGGCCGCGGCCCGCGGCCCCCGGTGCTTTCGCTCGCCTCAACCGGCGCCTCTGCGGGGGCTGGTACGGGGGCCTCTTCCAAGATCAGATGCGCGTTGGTGC\n",
      "CGCTGATCCCAAAGGAGGACACCGCCGCCCGGCGCGGACGCCCGTCAACCGACCACTCCCTGGCCTCGGTCAACACCGACACCGCGCCGCTGGTCCAATCCACCCGCGGGGAAGGCTCAT\n",
      "CCACATGCAACGTCGCCGGCATCACCCCATGACGCATCGCCTGCACCATCTTGATCACCCCGGCGACCCCCGCGGCGGCCTGGGTGTGGCCCATGTTCGACTTGATTGAGCCCACCCACA\n",
      "GCGGCTGCTCCGCTGGACCTCCCTGCCCGTAGGTGGACAGCAATGCCTGCGCTTCGATGGGATCACCCAACGTGGTGGCGGTCCCGTGTGCCTCCACCACGTCTACGTCTGCGGCGGACA\n",
      "ACCCGGCGTTGGCCAACGCCGCCTGGATCACTCGCTGCTGGGCGAGCCCATTGGGCGCGGTCAGCCCATTGGACGCACCATCCTGGTTGACCGCGCTCCCCCGCACCACCGCCAGCACCG\n",
      "AATGCCCCAACCGCCGGGCGTCCGATAGCCGCTCCAGCACAACCACCCCGGCGCCCTCGCCCCACCCGGTGCCGTCGGCCGCGGCCGCAAACGCCTTACATCGCCCATCGGCAGCCAACC\n",
      "CCCGCTGCCGGGAAAACCCCACAAAAATCGACGGCAGCCCCATCACCGTCACCCCACCGGCCAACGCCAAATCACACTCCCCGGAGCGCAATGACGACATCGCCCAATGGATCGCCACCA\n",
      "ACGACGACGAACAAGCGGTATCCACTGACACCGCCGGGCCCTGCAGCCCCAATACGTACGACACACGTCCCGAGGCCACGCTGATTGACGTGCCGGTCAACCCGTACCCTTGCAGCCCCC\n",
      "CGGTATCCCTATTGCCGTAACTCGCCGCGAAAATGCCGGTGTACACCCCGGTCGCCGAACCACGCAACGACAACGGGTCAATCCCCGCGTGCTCCAACGCCTCCCACGAAACCTCCAGCA\n",
      "TCAACCGCTGCTGAGGATCCATCGCCAACACTTCACTAGGAGCGATGCCGAAGAACCCGGCGTCAAAGCCGGTGGCGTCGTCTAGAAATGCCCCCCATCGCGTGTAGGTTTTGCCCTCAG\n",
      "CGTCGGGATCCGGATCGTATAGCCCCTCAACATCCCAGCCCCGATCGGTCGGAAACTCCGACACCACGTCGCGCCCCGCCGAAACGACATCCCAGAGTCCGTCCGGGCCATCCACGCCGC\n",
      "CCGGAAATCGGCAGCCGATTCCCACCACCGCCACCGGTTCTGTCGCGCGTTGCTCATATTCACGCAGCCGAGCGCGTGTCTCATCGAGCTCGACAGCAACCTTCTTTAGGTAGTGAAAAA\n",
      "GCTTTTCGCTCTGCTGGTCGGCACCTTCAACGCTCATCGTCCGTTGCTCCTCTATCAC\n",
      ">Rv2975c_N1 Seen in 1 sample(s).\n",
      "TCAACGCGCCGGCCGCGAGAGCGGCCGCAACCCGCGCCACGTCTTCGGCGTCAGCCTGCGAATTCGCGTGCAAATCAGCTTCTACGACCGCGGCACGCATGGTGAACAGCATGTTGACGC\n",
      "CGGTATCGGAGTCAGCGACCGGGAACACATTGAGCCGGTTGATCTCGTCGATGTGGAGGATCAGATCGCTGACGACGGCGTGTGCCCAGTCCCGCAAGGCCGAGGCGTCCAACGGCCGAT\n",
      "CCGCCGTCCCCAC\n",
      ">Rv3091_N1 Seen in 1 sample(s).\n",
      "ATGCCGATCCCCTTTGCCGATGGGATGCTCAGCCGGCTGGGTCGCCGCGGGGCAGCGCTCGACCTGATCGAGGAGTTCGAGGACGAGTCCGGGGAGCCCCCCGCATCCCTGAGCCCCGCC\n",
      "GACCTGCTGGCCGCCGAACCGGCCCTGCTGCTGCAGAAGATGGAGAACCGCCTCGTCCGGCACCACCTAGCCAATCCGGACGTGTTGAGCGGCGAACAGCTGCGCAAGCTGCGCTACATC\n",
      "CTCAATTTCGCCAGGCTGGCCGACTTCGAACCGGGGGCCGCGGGGCCGGGCGGAAGCCGCGGTCGCGGGGACATCTCGGTGGGCGGCCAAGTCGCGCCTTGGCGGTCCCGGGTCGTCGAC\n",
      "GCGTTGTACGCACCGCTGCGCGAGGAGCCCGATCCGGTCACGGCGCTGGAGGGCGCGAAAGACGTGCTGGCGACGCTGGTCGACGACCAGGACGATCAGCGTCGAGTGCTCATCGAGCGC\n",
      "CACGGCAGCGACTTCTCCGCGACGGAACTCGACGCCGAGGTCGGCTACAAGAAGCTGGTGACCGTCCTCGGCGGCGGCGGGGGCGCGGGCTTCGTCTACATCGGCGGCATGCAACGGCTG\n",
      "CTGGCGGCCGGCCAGGTGCCCGACTACATGATCGGCTCGTCGTTCGGGTCGATCATCGGCAGCCTGGTGGCCCGTGAACTGCCGGTGCCGATCGACGAGTACGCCGAGTGGGCCAAAACG\n",
      "GTGTCCTACCGCGCCATCCTGGGCCCGGAGCGGCGGCGCAGCCGCCACGGGTTGGCCGGAATGTTCACCCTGCGCTTCGACCAGTTCGCCCATACCCTGCTCAGCCGTGCGGACGGCGAA\n",
      "CGGATGCGCATGTCGGATCTGGCAATCCCGTTCGATGTCGTCGTCGCCGGTGTGCGCAGGCAGCCTTATGCGGCGCTGCCGTCCAGGTTCCGCCATCGCGAGCGGTCTACACTGACGTTG\n",
      "CGGTCGCTGCCGTTTCTGCCGATCGGTATCGGCCCGTGGGTGGCGGCACGCATGTGGCAAGTCGCGGCCTTCATCGACTTGCGGGTGGTCAAGCCGATCGTCATCAGCGCCGACGGCGCG\n",
      "ACACGCGACGTCAACGTCGTTGACGCGGCGTCTTTCTCGTCGGCCATCCCCGGTGTGCTGCACCACGAAACCAGCGACCCGCGGATGCTGCCAATCCTCGACGAGTTGTGCGCCGACCAG\n",
      "GACGTCGCGGCGATGGTCGACGGCGGCGCGGCCAGCAACGTCCCGGTCGAATTGGCGTGGGAGCGGGTCCGCGACGGGCGGCTCGGCACCCGCAACGCATGTTATCTGGCGTTCGACTGC\n",
      "TTCCATCCGCACTGGGACCCCCGACATCTGTGGCTGGTACCGATCACCCAGGCGGTCCAGCTGCAGATGGTGCGCAACCTGCCCTACGCCGACCACCTCGTCCGATTCGAGCCGACGCTG\n",
      "TCGCCGGTGAACCTGGCGCCGTCCGCGGCGGCCATCGACCGGGCTTGCCGGTGGGGGCGCGACAGCGTCGAACCGGCGATTGCGGTGACATCGGCGCTGCTGGAGCCGACGTGGTGGGAA\n",
      "GGCGACAGGCCCCCCGCCGCCGAACCCAAGGAACGCACAAAGTCGGCGGCCTCGTCGATGAGCGCCGTGATGGCCGCGATTCAGGCGCCGACGGGCCGGTTTCGGCGATGGCGAAGCCGC\n",
      "CACCTGACCTAG\n",
      ">Rv3197_N1 Seen in 1 sample(s).\n",
      "ATGGATGATGGGAGTGTGTCAGATATCAAACGGGGCCGCGCCGCGCGCAATGCGAAGCTGGCCAGCATCCCGGTCGGCTTCGCCGGTCGGGCGGCGCTCGGGCTCGGCAAGCGACTGACC\n",
      "GGTAAGTCAAAAGACGAGGTTACCGCCGAGCTGATGGAGAAGGCCGCCAATCAGTTGTTTACCGTCCTCGGCGAACTCAAGGGTGGCGCGATGAAGGTCGGCCAGGCGCTGTCGGTGATG\n",
      "GAGGCCGCCATTCCCGACGAGTTCGGCGAACCCTACCGGGAAGCACTGACCAAGCTGCAGAAGGACGCCCCACCGCTGCCCGCCAGTAAGGTGCACCGGGTGCTCGACGGACAGCTGGGC\n",
      "ACCAAATGGCGGGAGCGGTTCAGCTCGTTCAACGACACCCCAGTGGCATCTGCCAGCATCGGCCAGGTGCACAAAGCAATCTGGTCGGACGGCCGAGAAGTGGCCGTCAAGATCCAGTAT\n",
      "CCCGGCGCCGACGAGGCGCTGCGCGCGGACCTCAAGACCATGCAGCGCATGGTCGGCGTGCTCAAACAGCTCTCACCCGGCGCCGACGTCCAAGGGGTGGTCGACGAACTGGTTGAACGC\n",
      "ACCGAAATGGAACTCGACTACCGGCTGGAGGCCGCCAACCAGCGCGCCTTCGCCAAGGCGTACCACGACCACCCGCGCTTCCAGGTGCCTCACGTCGTGGCAAGCGCACCGAAGGTGGTG\n",
      "ATCCAGGAGTGGATCGAAGGTGTGCCGATGGCAGAGATCATCCGTCACGGGACCACCGAGCAGCGTGATCTGATCGGTACGCTGCTCGCCGAGCTCACCTTCGACGCACCACGGCGGCTG\n",
      "GGGTTGATGCACGGCGACGCCCACCCCGGTAATTTCATGCTGCTGCCCGACGGCCGGATGGGCATCATCGACTTCGGTGCCGTGGCACCGATGCCCGGCGGCTTCCCGATAGAGCTCGGG\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ATGACGATTCGACTGGCCCGCGAGAAGAACTACGACCTCCTGTTGCCGACGATGGAGAAGGCCGGGTTGATCCAGCGAGGACGACAGGTGTCGGTTCGCGAGATCGACGAGATGCTGCGC\n",
      "CAATACGTCGAGCCCATCCAGGTCGAGGTCTTCCACTACACCCGCAAGTGGTTACAGAAAATGACCGTCAGTCAGATCGACCGCTCGGTTGCGCAGATCAGAACGGCGCGCCAGATGGAC\n",
      "CTGCCGGCCAAGCTCGCGATTCCGATGCGGGTTATCGCATCGGTGGGCGCGATCCTATGCCAGCTGGACGCGCATGTGCCGATCAAGGCCCTGTCGGAGGAGCTGATCCCGGGTTTCGCC\n",
      "GAGCCCGACGCGATCGTCGTCTGA\n",
      ">Rv3234c_N1 Seen in 1 sample(s).\n",
      "TCAGCACCACGTCGTGGACGTCACAGTCGTAGCGAGCCCGCACCGTGCGATAGTCATCAAGACTTGCACGGGCAACCGTAAATCGCCGATTACGCGACACGGTGGCATTGAGCGGGCTAC\n",
      "TGGGCGCGGTGCCCCGTGCCACCGTGCGGGCGATATCGAGAACCTTGCGGCCCGTCTCGACGAGTTGGCCGGAATTCGTTACCAACCCGGCGACCGCGGATCCGACGGCCTGTAGTTGTG\n",
      "CGCCCGGCCGCACCAGCCAGTCCCCGACCGCGCGCAGCAGCAACCGCGTGGTGCCGGGGTCCCGTTCCGGGACCCAGATGTCTTCCGGAAACGCCGGTGGACGCCGCGTCCGGTCGGCGA\n",
      "TCACGTGGCCTATCGCCAGCGCGGTCACCCCGTTGATCAGGGCTTGGTGCGACTTGGTGTAGAGGGCAATGCGATTCTTTTCCAGACCCTCGACGAGATACATCTCCCACAATGGCCGCG\n",
      "ATTTGTCCAGCGGCCGAGCGGCCAGCCGTGCGATCAGCTCGTGCAGTTGCTCGTCACTACCCGGCGACGGCAGGGCCGACCGCCGGACGTGGTAGGTGATGTCGAAGTCGCGATCGTCGA\n",
      "TCCACACCGGCCTGGCCAGGCCCAATTTCACTTCCTGGACTTTCTGACGATAGCGCGGTATCTGCGGCAGCCGCTGTTCGACGGTTTCCAGCAGTGCCTCGTAGCTCAATCCGGCACGCG\n",
      "GACGGCGCAGGATCAACAGCAACCCGACATACATTGGGGTGGCTGTGTTCTCCAGCTGATAGAAGGAGGCGTCCGATGCAGACAACCGGGTGACCAC\n",
      ">Rv3253c_N1 Seen in 1 sample(s).\n",
      "TCAACACCTCCGGGTCGCGCTCTCTCGAGCTTGCCGAAGGCCCTGCGCCGAGTGCCGGCGCCCGTAGCCGACATAAATCGCGGTTCCGGCCACCAGCCAGATCCCGAACCGGATCCAAGT\n",
      "CAACGCGGTGAGGTTCAGCATCAGCCACAGGCACGCGCACACTGCGGCGATCGGAAGTAACGGCACCCACGGAGCTGTGAACCCCCGCTGAAGGTCGGGTCGGGTCCGGCGCAGCACGAC\n",
      "CACTCCGGCCGAGACGAGGATGAACGCGAACAGTGTCCCGACGTTGACCATCTCCTCAAGCTTGGTGATCGGAAACACCGACGCCGTCGTGGCCACCAACACCGCGACCAGCACCGTGAC\n",
      "CCGGACCGGGGTGCCGCGCGAACCGGTCTTGGCCAATTGCCGCGGCACCAAGCCGTCGCGCGCCATGGCGAACAGCACGCGGCATTACCCGAGCATCAACACCATCACCACCGTGGTAAG\n",
      "CCCGGCCAGCGCGCCGACGGAGATGATGCCGCTGGCCCAGTACACCCCGTTGGCCTGGAACGCGGTGGCCAGATTTGCCGGCCCGCGGCCCGGTACGGTCCGCAGTTGGGTGTATGGAAC\n",
      "CATGCCCGACAGCACCACCGATACCGCGACGTAGAGAAGGGTCACGACCCCCAGCGACGCGAGAATCCCTCGAGGGACGTCTCGTTGAGGACGCTTGGTCTCCTCGGCCATGGTGGCCAC\n",
      "GATGTCAAACCCGATAAACGCGAAGAACACGATCGATGCCCCGGCCAGCACGCCGTACCATCCGTAGTGGCTGCCTTGGGCTCCGGTCAGCAACGAGAAGACGGATTGATCGAGCCCGCC\n",
      "GCCGTGGTGCTGGACTTCGGGCTCGGGAATGAACGGCGAGTAGTTGGCGGCCCTGATGTAGAAGGCACCGACGACCACCACCAAGACGACCACCGACACCTTGATTGCGGTGACCACCGC\n",
      "GGAAAATCTCGACGACAATTTGGTGCCCAACGCGATCAGGGTCGCCACCAACGTGACGATCACGAGCGCACCCCAGTCGAGCTGCAGCGATCCGAGATGGCCTGTGCCATTACCGAATCC\n",
      "GAACACGGTGCCCAAGTAGCTGGACCAGCCTTTGGCGACCACGGCCGCACCCATCGCCAGTTCCAGCACCAGATTCCAGCCGATCACCCAGGCCAAGAACTCCCCGAAGGTGGCATAAGA\n",
      "GAAGGTATAGGCGCTGCCGGCCACCGGCAGCGTCGAGGCGAACTCGGCGTAGCACAGCGCGGCCAGCGCACAGGTCGCCGCCGCGATCAGAAACGATATCCAGATGGCCGGGCCGGTGAT\n",
      "ATCGCCAGCGGTCGACGCGGTAACCGTGAATATTCCGGCGCCAATCACCACCGAGACGCCGAAAACAACCAGGTCCCACCAGGTGAGGTCCTTGCGCAGCCGAGTGGTGGGCTCGTCGGT\n",
      "GTCGGCGATTGACTGTTCTACCGACTTCATGCGCCGTCGACCGGCCAT\n",
      ">Rv3725_N1 Seen in 1 sample(s).\n",
      "ATGCAGAATGCCACCATGCGCGTTCTGGTCACCGGCGGTACGGGATTTGTGGGCGGGTGGACTGCCAAAGCCATCGCTGACGCGGGCCACTCCGTCCGGTTCCTGGTGCGAAATCCCGCA\n",
      "CGGCTGAAGACGTCTGTCGCGAAACTGGGCGTCGACGTGTCGGACTTTGCGGTTGCAGACATATCCGACCGCGATTCGGTACGGGAGGCGTTGAACGGATGCGACGCCGTCGTGCACAGC\n",
      "GCCGCGCTGGTGGCAACCGACCCGCGTGAGACTTCGCGGATGCTGAGTACGAACATGGCGGGCGCCCAAAATGTTCTCGGTCAAGCCGTCGAGCTCGGAATGGATCCGATCGTGCATGTG\n",
      "TCGAGCTTCACGGCGCTGTTTCGTCCCAACTTGGCGACGCTGAGCGCTGATCTGCCGGTTGCCGGTGGGACGGATGGATACGGACAATCCAAAGCGCAGATCGAAATCTATGCGCGCGGT\n",
      "CTTCAGGACGCCGGCGCACCGGTGAACATCACTTATCCTGGCATGCTCCTCGGCCCGCCGGTGGGCGATCAATTCGGTGAAGCCGGGGAGGGTGTCCGGTCCGCATTGTGGATGCATGTC\n",
      "ATTCCCGGGCGCGGCGCGGCGTGGTTGATCGTCGACGTCCGAGATGTGGCGGCACTGCACGCGGCGTTGTTGGAATCCGGGCGTGGGCCGCGCCGCTACACTGCGGGAGGTCATCGGATT\n",
      "CCGGTGCCCGAGCTCGCGAAAATTCTGGGCGAGGTCGCCGGCACCACGATGCTGGCCGTCCCGGTGCCCGATTCCGCGCTGCGTGTCGCGGGATCGGTGCTGGATCAAGCCGGGCCCTAT\n",
      "CTGCCTTTCAATACTCCGTTCACCGCGGCAGGTATGCAGTACTACACACAGATGCCGGAGTCCGACGATTCGCCGAGCGAAAAAGAACTAG\n",
      ">Rv3736_N1 Seen in 1 sample(s).\n",
      "ATGTCCGTGGTGCGCGGGACCGCTCTGGCTAACTACCCGAGCCTAGTTGCCGGGTTGGGCGGTGACCCGGCCACTCTGCTACGGGCCGCGGGTGTTCGGGATCAGGATGTCGGCAACTAT\n",
      "GACGCGTTCATTTCGATCCGGGCAGCGATTCGGGCAATCGAATCGGCCGCAGCGGTCACCGCCACAATGGATTTCGGGAGACGATTGGCACAGCGGCAAGGGATTGAGATCCTGGGACCG\n",
      "GTCGGTGTGGCGGCCCGCACGGCCGCCACGGTCGGTGACGCTCTGGCGATCTTCAACACCTTCATGGCGGCCTACAGCCCAGTTATCGCCATCCGGATCACGCCGCTGGCCGGACAGCGG\n",
      "TCATTTATTGCACTCGAGTTCCTGCTCGACGAGCCGGCGTCGTATCCGCAGACCATGGAGCTGGCGCTCGGGGTGGCGCTCGGGGTGATCCGGTTGTTGTTGGGCGCTGACTACGCCCCA\n",
      "CTGGCCGTGCACTTACCCCACGACCCACTCACACCCGAAGCCTTCTACCTGCAGTACTTCGGCTGCCGGCCTTACTTCGCCGAACGTGTTGGTGGTTTCACCATGCGCACCGCGGACCTG\n",
      "AGCCGTCCCCTCAACCGCGACGATGTCGCCCACCGGGTGGTCGTCGACTACCTGAGCAGCATCACGCCGCTGGGCGAGGGGATCGTGGAATCGGTGCGCACCATCGTGCGCCAGCTGCTG\n",
      "CCCACCGGAGCGGCGACGCTCAACGTGGTCGCCGGGCAGTTCCACCTGCACCCGAAAACGCTGCAACGTCGACTTGCGGAGGAGAACACCACATTCGTTATTCTGGTCGATCGGGTCCGC\n",
      "AAGGATGTCGCCGATCGCTACCTAAGGACCACCGGGATCGGCCTTACCCATTTGGCACGTGAACTGGGCTACGCCGAACAAAGCGTGTTGACCCGCTCGTGCAAACGCTGGTTCGGAACC\n",
      "GGACCGGCCGCCTACCGCAACCAGGCCAGGTTACAGACAACCGTGAGCGCACCTGGCAGCGGGCGTGGTCCGAATCCAGGTAACGTCTCAGTATCCTGCTGA\n",
      ">Rv3825c_N1 Seen in 1 sample(s).\n",
      "TTACTGTGACGACAGCGCGGCAGCAGGAGCGTCGTCGGGCGCCAGCTGTTCATACAAGTGATCCGCTAAGCCCCGCACCGTGGCGCTGACGTTCTTGGGTGCCAACCGGATTCCGGTCTC\n",
      "GGTCTCGATCCGAGTGCGCAGCTCTAGTGCGCCCAACGAATCAAGTCCATACTCGGGTAGCGGGCGGTCAGGGTCGACGGTGCGCCGCAGAATCAGGCTGACCTGCTCGGCGACCAGCTG\n",
      "CCGAAGCCGCGCCGGCCACTCGTCGCGTGGCAGCTCGTTCAGCTCGACGCGGAATTTGCTTGTGCCCGAACCGTTGCTGCTGGAGAACACTTCGAAAAACCGGCTGCGCTCTGCGAAGGC\n",
      "GACCAGCCACGGGGCTCCGATGACCGGGGCATAGCCGGTATAGACGCGGTTGTGGCGCAATAGCGCCTCGAACGCGTAAGCACCTTCGTCGGGAGTGATCGCCGTGTAGTTGCTTTCCTC\n",
      "CAATGCCGAAGCCCGCGCGGGCGATGCCGACCACCACCCCAACTGGCCGATATCCGACCAGGCTCCCCACGCGATCGCGGTAGCCGGCAGGCCCTGAGCTTGCCGCCAATGCGCGAAGGC\n",
      "GTCCAGCCAGCTGTTGGCCGCTGAGTAGGCACTCTGTCCCGGCGAGCCGGTGAGAGCTGCCGCCGACGAAAACAAGCAGAACCAGTCAAGCGGCTGTCCGCTGGTTGCTTCATGCAACTC\n",
      "CCAGGCACCGTGAACCTTTGGCGCCCAGTCGCGCGCCAGCAACTCGTCGGTGATATTGGCCAAGGTGGCGTCCTCGACCACCGCGGCCGCGTGTAGCACGCCTCGTACCGGAAGCCCGGT\n",
      "GGCCACAGCGGTCGCCACCAACCGCTCCGCGGTACCCGGTTGGGCGATGTCACCGCATTCCACCACGACTTCAGAGCCCATCGCCGCGATGGCCTCGATCGTTTCCCTCATCTTTTGCGT\n",
      "CGGCTGGGTGCGGGAATTCAGCACGATCCGGCCGCAACCGGCCGCGGCCATCTTCTCGGCCAGGAACAGCCCTAGCCCACCGAGGCCGCCGGTGATGATGTAGGAGCCGTCGGGACGGAA\n",
      "CACCTGAGCTTGTTCCGGAGGCAGGGTAACGAGGCTTTTTCCGGTCTGTGGGATGTGGAGGACGAGTTTGCCGGTGTGCTCGGCGTTGCCCATCACACGGATGGCGGTGGCCGCCTCGAC\n",
      "GAGGGGGTAATGGGTGCTCTGCGGCATCGGCAACTCGCCGGCTGCGGTCAAGCGATAGACCGTGCCGAGCAGGTCGCGCAGCTCTTCTGGGTGTGTCGCAGACAGCAACCCCAGGTCTAC\n",
      "GGCGTAGAAGGACAGGTTGCGCCGGAAGGGAAAGAGCCCCAGCTTGGTGTCACCATAGATGTCGCGCTTGCCAATCTCGACGAACCGTCCCCGGAAGGCGAGCAGTTTCAGCCCGGCAAG\n",
      "TTGCGCGGCGCCGGTCACCGAGTTGAGCACGACATCGACACCCCGGCCGTTAGTGTCCCGCCGAATCTGCTCGGCGAACTCGATGCTGCGCGAGTCATAGACATGCTCAATACCCATGTT\n",
      "GCGCAATAGCTCTCGACGCTGTGGGGTACCGGCGGTGGCGAAGATCTCAGCGCCCGCCGCGCGGGCTATAGCGATCGCCGCTTGTCCGACCCCGCCGGTGCCGGAGTGAATTAGCACCGT\n",
      "GTCACCCGCCCTAATCCGGGCGAGCTCATGCAGTCCGTACCAGGCGGTGGCGTGCGCGGTGGTCACCGCAGCGGCCTGTGCGTCACCCAGGCCCGGTGGCAGCGTCGCGGCCAGCCGAGC\n",
      "GTCACACGTGACGAATGTGCCCCAGCAGCCGTTAGGCGACATGCCACCAACATGGTCACCAACCTTGTGGTCAGTGACGCCTGGTCCGACCGCGGTCACCACGCCGGCGAAATCCGTGCC\n",
      "CAGCTGGGGCAGGTGTCCCTCGAAGCTGGGGTAGCGACCGAAAGCGATGAGTACATCGGCAAAGTTGACGCTGGACGCACGGACCGCAACCTCGATCTGTCCTGGTCCTGGTGGAACGCG\n",
      "GTGAAACGCGGCCAGCTCTATCGTTTGCATATCGCCGGGGGTACGGATCTGCAGGCGCATGCCGCTCTGCTGATGATCCGCGACGATGGTGCGCCGCTCCTGAGGACGCAACGGGGTCGG\n",
      "ACACAAGCGCGCCACGTACCACTCGTTGTCTCGCCAGGCGGTCTCGTCTTCTTCCGACGTGGCCAGCAATTGGCGTGCCAGCTGCTCGACACCGGTCTGTTCGTCCACGTCGATCTGGGT\n",
      "GGCACGCAGGTGAGGGTGCTCGGCGCCGATCGTCCGCAGTAGACCACGCAGCCCGCCCTGCTCAAGATTGACGCAGTCGTCGGCCAGCACCCGCTGGGCACCCCGCGTCACGACGTACAT\n",
      "GCGCGGCACCGCCCCGGGAAGGTCTGACAATTCGCGAGCGATACCCACCAGCCGGCGAACGTACTCAGCGCCGCGATCCGCGCTCCCCTGATGCGGCGTACCGGTGTTCGACCCGGTGAG\n",
      "CACGACCACGCCGCTAAACTCGTCGCTACCAACTTGATCGCGTAGCTGGTCGGCGGCGGCCAACTGGTCGTCGTGCAGTGGCCACCGCATCGTCGTGCACGCCGCGCTGTGTTCCCTAAA\n",
      "CGCGTCCGCTAGCCGGGTAGCGGTCACATCAGAGGCAGCGCAGTCACTGATCAGCAGCCATTTTCCAGCGCCAGAGGGGTCCATCTCGGGCAGCTCACGCTGGTGCCATTCGATGGTGAG\n",
      "TAAGCGCTCATTCAGCACCCGATTGTGTTTATCGCGCTCGGACACTCCCGTACCGATTCGCAGTCCGCACACGGCCAGCAACACCGTGCCGTGCGCGTCCAGCACGTCGATATCGGCCTC\n",
      "GACGCCGACCAACTCGACTTTGGTCACCCGCGTGTAGCAATAGCGAGCGGTACGCACCGGAGCATAGGCACGGACTCGGCGCACCCCCAACGGCACCAATAGGCCGCTACCTACCGACTG\n",
      "GCTATCGGGATGCGCGCCGACCGACTGGAAACAGGCATCCAGGAGGGCCGGGTGGATTGCGTACAGGCCCTGCTGCGAACGAATCGAGCCGGGCAGCGCGACTTCGGCCAGCATTGTGGC\n",
      "GGTCGCATCCTCCGCGACATAGGCCACGGCCAGGCCGGTGAAGGCCGGACCATATTGCACACCGTGCTTGTCGAATTGCCGGCGCAGATCCTCACCGTCCACGCGGCAAGGGTGGGCTTC\n",
      "CAATAAGGAGGCCATGTCGTACGCCGGCGGCTCGCATTCGCCGGATACCTGCTGCAGCACCGCCGACGCACGCCGCAAGTGATGCCCAACGCCTTCCTGCAAGGCCTCGACGGCGAAGTC\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GACGACACCGGGCGAGGTCACCGTTGCCACGGTGGACACCGGGGTCTGGTCATCCAGCAGCAGCATCGCCTCAAAGCGCATGTCGCGTACTTCGGACTGCTCGCCGAGGACGGCACGGGC\n",
      "CGCAGACAACGCCATCTCGCAGTAGGCGGCCCCTGGAAGAGCAGCCACGTTGTGTATCCGGTGATCGCCCAACCAGGGCAAGGTTGCGGTACCAACATCGGCCTGCCAGGCGTGGCGTTC\n",
      "CGGCTCTTCGGGCAATCGCACGTGTGCGCCCAACAACGGGTGCACGGCTACCGTGGAGCCACCCGGCGACCGATTGTCAACGCCTTCGCGGTCATAGAACAGGAACCGGTGCGACCACGC\n",
      "CGGCAGCGGAGCATCGACCAAGCGGCCTTGGGGACAGAGCACCGAGAAGTCCACTGCCGCACCAGCGTTGTGCAGATCCGTCAGCAGGCGACGGAGCCCCAGCGGCAATGGCTGCTCCCG\n",
      "CCGCATACCGGCCAGCGCGGCAACCGGCATGCCTACACTGCCGGCAATCTGATCGACCGCGTGGGTCAGCAGCGGGTGCGGCGAAAGCTCGGCGAAGACTCGGTACCCGTCGTCGAGCGC\n",
      "CGAGCGCACCGCAGCGGAGAACCGCACGGTGTGGCGCAAATTGTCGGCCCAGTAACGCGCGTCGCACGCCGGCGCTTCGCGCGGGTCGAAAAGCGTCGCCGAATAGTAGGGAATCTCAGG\n",
      "AGCTTTCGGATTCAGGTCGGCCAGCGCAGCTATCAACTCGTCGAGGATCGGATCCACCTGCGGCGAATGCGAAGCCACGTCGACGGCCACCGCCCGCGCCAGCACGTCTCGCCGCTCCCA\n",
      "TATGTCGACCAGCTTGCGCACCGACTCGGTGCCTCCGGCGATCACGGTGGACTGCGGCGCGGTCACCACGGCGACCACCACATCGTCGATGCCTAGAGCGGTCAATTCCGACTGCACAGC\n",
      "TAAGGCAGGCAACTCCACCGACGCCATCGCCGCGGAACCGGCGATCGTCGCCATCAGTTTTGATCGTCGGCAGATGACGCGTACCCCATCTTCGGCTGACAGCACCCCTGCGACCACAGC\n",
      "CGCGGCCGACTCACCCATTGAGTGGCCGATCACGGCGCCCGGGCGCACTCCGTATGCCGCCATCGTGGCTGCCAACGCGACCTGCATCGCGAAGATGGTCGGCTGAACTCTGTCGATGCC\n",
      "AGTCACGGTCTCGGGCGCCGTCATCGCCTCGGTGACCGAGAACCCGGACTCCGCGGCGATCAATGGCTCTAGCTCCGCAACGGTCGCGGCGAACACCGATTCGTTCGTCAGCAGATCGGC\n",
      "GCCCATCGCTGCCCACTGCGACCCTTGCCCGGAGAATAACCAGACCGGCCCGCGGTCATCCTGCCCCACCGCGGGCTGGTAAACGGTGTCACCGTCGGCGACCTCGCCCAAGCCGGCAAT\n",
      "CAGCTCGTCGACGCTGCTCGCGATGACCGCCGTGCGCACCGACCGGTGCGTACGCCGCCGCGCCAGCGTGTACGCAAGATCCGAGAGCACCAGGGAGTCGGCGTGCTGCTGTATCCAGTC\n",
      "GGTCAACCGCTGAGCAGTCTGCCGCAGCGCGTCGGCCGAGGAAGCGGACAGCGTGAACAAGGCAGGGGTGCCGGTCGGGGGGGTGCTCGCCGCGTGGGGCTGGGCTTCGGTTTGCGGAGC\n",
      "TTGCTCCACAACAGCGTGCACGTTCGTTCCCGAGAACCCATAAGACGACACTGCCGCCCGCCGGGGCACCTGACGACCGTTGGTGGGCCACGGTGTGGTCACCTCGGGCACGAAGAGGTT\n",
      "GGTGGTGATGCCAGCAATCTCATCGGGCAGCCGAGTGAAGTGCAGATTACGTGGAACCACACCATGTTTCAGAGCGAGAACCACCTTGATTAGCCCTAGCACCCCGGCGGTCGACTGGGT\n",
      "GTGTCCGAAGTTGGTCTTCACCGATGCGAGTGCGCACGGGCCGTCGACCCCATACACCTCGGAGACACTTGCATATTCAATGGGGTCACCGATCGGGGTGCCGGGGCCGTGCGCTTCGAC\n",
      "CATGCCGACCGTCGCGGCGTCCACGCCACCGGCAGCCAACGCCGCTCGATAAGCCGCAACCTGTGCGGGCTGCGAAGGCGTCGCGATATTGACCGTGTGGCCATCCTGATTTGCGGACGT\n",
      "GCCACGAATTACCGCCAGGATCCGGTCACCGTCGGCCAATGCATCCGGCAACCGCTTGAGCACCACCACGGCACAACCCTCGCCTGACACGAACCCGTCAGCCGCGACATCGAACGCGCG\n",
      "ACAACGTCCGGTCGGGGACAACATGCCCAAAGCGGATCCAGCAGCGGCCTTGCGTGGCTCCAGCATCAAGGCGACACCCCCCGCCAAGGCAACGTCGCTTTCACCCTCGTGCAGGCTGCG\n",
      "ACACGCCATGTGCACGGCCGTCAGGCCGGACGAGCATGCGGTATCAACGGTTATTGCCGGACCGTGCAGTCGCATCGCGTAGGCGACCCGGCCCGACGCCATGCTGAAGCTGTTGCCCAG\n",
      "ATATCCGTACGGCTCCTCCAATTGTTTGGCGTCGGCCGCCACCATCGTGTAGTCACCATGGGTGACACCCGCGAACACGCCGGTCGCCGAGCCTGCCAGCGTTTGCTGAGTAAGACCGGC\n",
      "GTGCTCCATGGCCTCCCAGGACGTCTCCAGCAACAGACGTTGCTGCGGATCGATCGCAATCGCCTCCCGCTCGCCGATGCCAAAGAACTCGCAATCGAAATCCGCGGGGTTATCCAGGAA\n",
      "ACCGCCCCACTTGCACACCGTCCGACCGGGCACGCCCGGCTGCGGGTCGTAGAACTCGTCGCAATCCCACCGGTCCGGCGGCACCTCGGTGATCAGGTCGTCGCCTCGTAACAACGCCTT\n",
      "CCACAACAACTCGGGGGAATCGATCCCGCCGGGCAGCCGGCAAGCCATGCCGATAACAGCAACCGGAGTCACACGTGGTTCAGCCAACGTCCATGCACCCCTATCTGCACCAGTGCCTGA\n",
      "CGCCGCCGACCCCAAGCCCAA\n",
      ">Rv3829c_N1 Seen in 1 sample(s).\n",
      "CTACCGACCACTCAAAACGCAACAGTTGGCAGCCCTACGATCGGCCAGCGCCTGACGGGCGGCGTTATATCCAGGGATGAACGTGATTCCCGGCCCACCGTGGACAACCGGCACTGCCCA\n",
      "GGTACAACCCGGCTATCGGGATCGGCTGGCCGATAAAGCCTTTCGGGCCAGGCCTGTTGGGGCCGATCTGGTCCGAGTGCAGCAGGGCATGGCAGTAGTCCCCACCCGGGGCACCGAACA\n",
      "TCACACCCATGTGTTTGGGGGTAAAGGTGGTGTACCGGAGAATGCTGCCTTTGAAGTTCGGTGCCAACCTAGTGATCTTGTCGATCACGTTCTGCCCCATTTCGACCTTTGCCCGGCCGT\n",
      "ACCCTCCGTATTTTGAGCCACCCTCGATCGGGAACCACATTGCGAACGCCGACGCGGCCTGCTTACCCGCCGGGGCCAGGCTGGGATCATGCAGCGACGGGATCTGCAACACCACGGTCG\n",
      "GATCGGCCGGGACGATCCCACGCCGGCAATCCTCCCACTGCTGCTGAACCTGCTCCGGTGTACAGAAAATGCCCATCGATGCCTGCATGCTCGGATCGTTGAGTGCCTGGTAGGGCGCCG\n",
      "CGAAGGCCGGTGGCTGCGCGAGCGCAAAATGCATCTGCAGATAGCTGCCGCGGTGGTCGATGCGCAAATAGCGATCGCGGATTTCCGACGGCAACACTGCCGGATCGATCAGCTCGTTGA\n",
      "TGGTGACGTCGGGTGCTATGGCGGAGACCACGATCGGGGAGGTCAAGGTGTCCCCCGCCGCGGTGCGCACGCCCCGCACGCGGGCTGACGACCGACTATTGTCAACCACGATCTCGGTCA\n",
      "CCTTGGAACGTAACCGGACCTCGCCGCCGGTGCGTTCCAGCAATTGCGACAGATGGGTGGTAAGCGCGCCGATGCCACCGCGCAATTTCTTCCACCGCACGAAGTCGCCCTCCGGGACAC\n",
      "CCAATCCGAAGGCGAGCGCGGCAGCGCTGCCCGGTGTGGCCGGCCCGCGATAGAGCGTGTTCACGGCCAGCACGGTCATCGACCCGCGCAGGGCGCCGTGCTTCTCGCGGTCCGGGAAAT\n",
      "GGCGGTCCAACACGTCGGTGACCGATCCGAACAGCATGTCATCGATCGCTGACCGTTCGAATTCATTTGTGGCACAGGCATACATCTCGTCGAAGCTCTTGGGCAGAGTTCCGGCTTCGA\n",
      "AACGCCCCAGCGCCCGGGTCGGCGCCTGGCTCCACGCCAGCAGGCCCGCCATCCCGGTGACGGCGTCTGCCCCGTGCACCCGATGGAGGTGGGTAAGCATCTTCGTCGGGTCGGTGAATT\n",
      "GGACCACCGGATCGTCCCCGACACCGCGCAACGCTACCGACATCACCTCCAGATCGACCGTCGGCAAGCTGTCCAGGCCTAACTCGCTGCTGACCGCCGAGGAGGTCGGGAACTGCACCG\n",
      "ATCCGGCGATCTCGAACCGGTACCCGTCGAACAGCTCCACCGTGGAGGCCATCCCGCCGGCGTAGCGCTTAGCGTCCAGACACGCGGTCCGCAGTCCGGCTCGCTGCAGCAGCACTGCCG\n",
      "CGGTCAGCCCGTTGTGCCCGGCGCCGATAACTATCGCGTCATAACCAGTCAT\n",
      ">Rv3830c_N1 Seen in 1 sample(s).\n",
      "TTATGACGAAAACTGTGAGGGTGGTCCAGGTGTCGGAGATGCCGACGCGCAGCGACTCCAGTGCGACGTGGCAGACCCGCGCCAGCTCCCCGAGCGACCGGTCACTCCCAAGCATCCAGG\n",
      "CTTCCATCGCGCCGAACACCGCCGCGGCGACGCATCGTGCGGTGACGGCGATGTGCAATCGGGCATCGGGTGCACCCGCGATATCGCAGTTACGTCGCCGCAATTGGGCCTGGATGGCAT\n",
      "CGGCGAAGTCGGCTTCCACCTCGCGCATATGGCGGACGATCCGGCTCGGCTCCAACTCGCCGCGCCGCAACGACGCAATCTTCGTCACTGCGTCAACGTCATAAGGAAACGAGAAGATAG\n",
      "CCGCTTGCACGGAATCGATGATCGATTCGTCGGCCGGTCTAGCATCCAGCGCCGCGCGAAACCAGTGCAGTCCGGCGTCGTAGTCGGCAAACAGCAAATCGTGCTTGGATCTGAAGTGGC\n",
      "GATAGAAAGTACGCAGCGACACCCCGGCGTCCTCCGCAATCTGCTCGGCTGAGGTAGCCTCGACGCCCTGGGCCAGAAATCGCACCAGGGCGGCCTGGCGCAGTGCCTCGCGAGTGCGTT\n",
      "CGCTGCGCGCCGTCTGCGGGGGCCGGACCAT\n",
      ">Rv3847_N1 Seen in 1 sample(s).\n",
      "ATGGGTACCGGGTCAGGTGGGCCTATTGGGGTTTCTCCCTTCCATTCGCGTGGTGCCCTGAAAGGGTTCGTGATCTCTGGACGTTGGCCTGATTCGACCAAAGAGTGGGCCCAGCTGCTG\n",
      "ATGGTCGCAGTTCGGGTCGCGTCGTTGCCCGGCTTGCTCTCCACCACAACGGTGTTTGGTGCCCGCGAAGAGTTGCCCGACGAACCCGAGCCGGGGACCGTCGGTCTGGTGCTGGCCGAG\n",
      "GGCACCGTCTTCGGTGAATCAGCAATTCAGCCAGGATATTTCGCTGATCATCAACCCCCTGCATTGCTGATGCTGCATCCACCCTCGGAGACCACGCCGTCGCTGCCGGAATGCACCGGG\n",
      "GCGGCGTCAGGGTGCGTGCTGCTGCCGGGATTACCGTATCTGGGATTGGAACATCGTGCGGCTTGGGTGGAGGCTGAAGCCGACGGCACCATCACATCTATGGTGAGCCGGGTGGGCGTC\n",
      "GACCCGATAAGCCATCCCGACACGCAATTCTGGCAATGCTGCTTGCAGCATAA\n",
      ">Rv3848_N1 Seen in 1 sample(s).\n",
      "ATGCTCGCCGCCACACTGCTAAGTCTGGGAGCCGTTTTCCTTGCTGAGCTCGGCGACAGATCCCAGCTCATCACGATGACCTACACACTTCGCTACCGCTGGTGGGTGGTGCTGACCGGG\n",
      "GTGGCGATCGCAGCGTTCACGGTGCACGGGGTAGCGGTGGCGATCGGCCACTTTTTGGGCTCGACCGTGCCGGCCCGGCCGGCCGCCTGCGTATCGGCGATCGCATTCCTGATCTTTGCC\n",
      "GTGTGGGTCTGGCGGGAGGACACGGCCAGCGACAGCGAAACCTCGCCAACCGCTGCCGAACCCCGACTCGCGCTGTTCACCGTGGTCTCGTCGTTCGCACTGGCTGAGCTGGGTGACAAG\n",
      "ACAACGTTGGCGACGGTGACCTTGGCCAGCGATCACCACTGGGCCGGCGTATGGATCGGCACCACCCTGGGCATGATCCTGGCCGACGGCCTGGCGATCGGCGCAGGGCTGCTGCTGCAC\n",
      "CGGCGCCTTCCGGAGCGGTTGCTGCAGGTCCTGACTGGCCTGCTGTTCCTGCTGTTCGGACTGTGGTTGCTGTTCGACGACGCGTTGGGCTTCAGATCGGTTGCCATCGCCGTGACAGCG\n",
      "GCGGTGGTGCTGGCCGCGGCAACTACGGCGGTATCGGTGCGGGTGGCGCAAACTCGTCGGCGGCGGCCAACCGCTGCTGCGACACCAGAAGATGACTCGACACGCCCCGAGCGGTCGTCG\n",
      "GTCGCGCCGGGCCATCCCGGGAGCATCTTGCTACCGCTTCCGGAAGTGTCTTTGCGGGGGCGCCGACCGCCCTCAGGGTCGCCTGACGAGCGCTGTGCGGACCCAGGCAGCAAAGGAGGC\n",
      "TCTCGGCGAATCTCCGTTGGCTGCTAGTTGCCCGGAGTCGGCCGCATCCGCCCGACACGGTCATCCTGA\n"
     ]
    }
   ],
   "source": [
    "# novel alleles found:\n",
    "cat sample.call.novel.fa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Sample\tLocus\tNovel_id\tMinKmerDepth\tNmut\tDesc\n",
      "SRR6152708\tRv0024\tN1\t42\t1\tFrom allele 98, Del of len 1 at pos 719.\n",
      "SRR6152708\tRv0035\tN1\t46\t2\tFrom allele 227, Subst C->G at pos 47, Subst A->T at pos 76.\n",
      "SRR6152708\tRv0045c\tN1\t61\t4\tFrom allele 62, Subst C->T at pos 318, Del of len 2 at pos 650, Subst A->G at pos 652.\n",
      "SRR6152708\tRv0063\tN1\t55\t1\tFrom allele 140, Ins of base G at pos 334.\n",
      "SRR6152708\tRv0101\tN1\t50\t2\tFrom allele 1541, Subst A->G at pos 5360, Subst A->G at pos 6088.\n",
      "SRR6152708\tRv0134\tN1\t66\t2\tFrom allele 25, Subst G->T at pos 374, Del of len 1 at pos 386.\n",
      "SRR6152708\tRv0165c\tN1\t58\t3\tFrom allele 16, Subst T->C at pos 147, Ins of base G at pos 163, Ins of base G at pos 164.\n",
      "SRR6152708\tRv0195\tN1\t63\t2\tFrom allele 88, Subst G->A at pos 185, Subst T->C at pos 191.\n",
      "SRR6152708\tRv0226c\tN1\t66\t2\tFrom allele 59, Subst A->C at pos 36, Subst A->G at pos 1229.\n",
      "SRR6152708\tRv0276\tN1\t42\t2\tFrom allele 108, Subst C->G at pos 50, Subst T->C at pos 57.\n",
      "SRR6152708\tRv0290\tN1\t51\t2\tFrom allele 253, Subst G->A at pos 691, Subst G->A at pos 1033.\n",
      "SRR6152708\tRv0551c\tN1\t47\t2\tFrom allele 68, Subst T->C at pos 472, Del of len 1 at pos 483.\n",
      "SRR6152708\tRv0654\tN1\t49\t2\tFrom allele 187, Subst C->T at pos 1303, Subst G->A at pos 1315.\n",
      "SRR6152708\tRv0739\tN1\t63\t3\tFrom allele 87, Ins of base C at pos 14, Ins of base G at pos 13, Subst A->G at pos 62.\n",
      "SRR6152708\tRv0757\tN1\t49\t2\tFrom allele 141, Subst T->C at pos 364, Subst T->C at pos 373.\n",
      "SRR6152708\tRv0818\tN1\t56\t3\tFrom allele 89, Subst G->A at pos 275, Subst C->T at pos 290, Subst G->A at pos 293.\n",
      "SRR6152708\tRv0826\tN1\t49\t2\tFrom allele 84, Subst C->G at pos 901, Subst G->A at pos 920.\n",
      "SRR6152708\tRv0888\tN1\t50\t1\tFrom allele 187, Ins of base G at pos 1145.\n",
      "SRR6152708\tRv0908\tN1\t55\t2\tFrom allele 271, Subst T->C at pos 2197, Subst C->T at pos 2207.\n",
      "SRR6152708\tRv1001\tN1\t45\t2\tFrom allele 68, Subst T->C at pos 982, Del of len 1 at pos 999.\n",
      "SRR6152708\tRv1097c\tN1\t62\t3\tFrom allele 135, Subst A->G at pos 302, Del of len 2 at pos 311.\n",
      "SRR6152708\tRv1128c\tN1\t38\t2\tFrom allele 223, Subst T->C at pos 421, Del of len 1 at pos 439.\n",
      "SRR6152708\tRv1145\tN1\t48\t2\tFrom allele 2, Subst A->G at pos 818, Ins of base A at pos 829.\n",
      "SRR6152708\tRv1225c\tN1\t55\t2\tFrom allele 110, Ins of base G at pos 435, Subst T->C at pos 451.\n",
      "SRR6152708\tRv1258c\tN1\t47\t2\tFrom allele 82, Ins of base G at pos 681, Subst T->C at pos 697.\n",
      "SRR6152708\tRv1269c\tN1\t55\t2\tFrom allele 63, Ins of base G at pos 110, Ins of base C at pos 123.\n",
      "SRR6152708\tRv1326c\tN1\t54\t2\tFrom allele 76, Subst A->G at pos 2007, Subst T->C at pos 2034.\n",
      "SRR6152708\tRv1330c\tN1\t58\t2\tFrom allele 169, Subst G->T at pos 436, Subst T->C at pos 447.\n",
      "SRR6152708\tRv1363c\tN1\t43\t2\tFrom allele 61, Subst C->A at pos 59, Subst C->G at pos 75.\n",
      "SRR6152708\tRv1413\tN1\t60\t2\tFrom allele 139, Subst C->A at pos 65, Subst G->A at pos 80.\n",
      "SRR6152708\tRv1420\tN1\t47\t2\tFrom allele 42, Subst C->G at pos 56, Subst T->C at pos 212.\n",
      "SRR6152708\tRv1551\tN1\t48\t2\tFrom allele 279, Subst A->G at pos 907, Del of len 1 at pos 917.\n",
      "SRR6152708\tRv1564c\tN1\t45\t2\tFrom allele 39, Del of len 1 at pos 1564, Subst G->C at pos 1581.\n",
      "SRR6152708\tRv1615\tN1\t47\t2\tFrom allele 97, Subst C->T at pos 275, Subst C->T at pos 288.\n",
      "SRR6152708\tRv1775\tN1\t56\t2\tFrom allele 167, Del of len 1 at pos 124, Subst A->C at pos 128.\n",
      "SRR6152708\tRv1915\tN1\t58\t2\tFrom allele 1, Subst G->A at pos 536, Ins of base T at pos 886.\n",
      "SRR6152708\tRv2027c\tN1\t55\t2\tFrom allele 5, Del of len 1 at pos 948, Subst G->C at pos 969.\n",
      "SRR6152708\tRv2084\tN1\t61\t2\tFrom allele 138, Ins of base T at pos 23, Ins of base G at pos 20.\n",
      "SRR6152708\tRv2148c\tN1\t75\t2\tFrom allele 87, Subst G->C at pos 19, Del of len 1 at pos 4.\n",
      "SRR6152708\tRv2176\tN1\t53\t2\tFrom allele 53, Subst C->T at pos 75, Subst T->C at pos 95.\n",
      "SRR6152708\tRv2185c\tN1\t41\t2\tFrom allele 41, Subst G->T at pos 342, Subst T->G at pos 358.\n",
      "SRR6152708\tRv2241\tN1\t37\t2\tFrom allele 296, Subst T->C at pos 2532, Subst T->G at pos 2545.\n",
      "SRR6152708\tRv2264c\tN1\t48\t3\tFrom allele 1, Ins of base A at pos 57, Subst C->T at pos 28, Subst T->C at pos 322.\n",
      "SRR6152708\tRv2293c\tN1\t60\t1\tFrom allele 66, Ins of base A at pos 602.\n",
      "SRR6152708\tRv2339\tN1\t57\t2\tFrom allele 524, Del of len 1 at pos 219, Subst A->G at pos 224.\n",
      "SRR6152708\tRv2437\tN1\t64\t2\tFrom allele 78, Del of len 1 at pos 107, Subst C->G at pos 113.\n",
      "SRR6152708\tRv2526\tN1\t53\t6\tFrom allele 4, Subst A->G at pos 45, Del of len 2 at pos 72, Del of len 3 at pos 73.\n",
      "SRR6152708\tRv2545\tN1\t46\t2\tFrom allele 48, Subst G->A at pos 91, Del of len 1 at pos 99.\n",
      "SRR6152708\tRv2587c\tN1\t51\t2\tFrom allele 344, Subst C->T at pos 906, Subst T->C at pos 924.\n",
      "SRR6152708\tRv2848c\tN1\t60\t2\tFrom allele 238, Ins of base G at pos 58, Subst A->G at pos 66.\n",
      "SRR6152708\tRv2902c\tN1\t46\t2\tFrom allele 2, Subst T->C at pos 253, Subst G->A at pos 261.\n",
      "SRR6152708\tRv2947c\tN1\t37\t1\tFrom allele 48, Ins of base G at pos 780.\n",
      "SRR6152708\tRv2975c\tN1\t51\t3\tFrom allele 42, Subst G->A at pos 32, Del of len 2 at pos 6.\n",
      "SRR6152708\tRv3091\tN1\t59\t2\tFrom allele 166, Subst T->C at pos 1289, Subst G->A at pos 1299.\n",
      "SRR6152708\tRv3197\tN1\t66\t2\tFrom allele 10, Subst A->G at pos 342, Subst C->A at pos 351.\n",
      "SRR6152708\tRv3234c\tN1\t60\t2\tFrom allele 19, Ins of base C at pos 18, Subst G->T at pos 57.\n",
      "SRR6152708\tRv3253c\tN1\t36\t2\tFrom allele 278, Subst G->A at pos 447, Subst T->C at pos 462.\n",
      "SRR6152708\tRv3725\tN1\t44\t3\tFrom allele 79, Subst G->C at pos 526, Subst A->G at pos 747, Ins of base A at pos 752.\n",
      "SRR6152708\tRv3736\tN1\t75\t2\tFrom allele 83, Subst T->C at pos 510, Subst A->G at pos 755.\n",
      "SRR6152708\tRv3825c\tN1\t40\t2\tFrom allele 480, Subst T->C at pos 4426, Subst G->A at pos 4453.\n",
      "SRR6152708\tRv3829c\tN1\t61\t2\tFrom allele 328, Subst T->A at pos 86, Ins of base G at pos 103.\n",
      "SRR6152708\tRv3830c\tN1\t61\t1\tFrom allele 105, Ins of base G at pos 147.\n",
      "SRR6152708\tRv3847\tN1\t57\t2\tFrom allele 64, Del of len 1 at pos 504, Subst G->A at pos 532.\n",
      "SRR6152708\tRv3848\tN1\t53\t2\tFrom allele 271, Subst G->A at pos 866, Subst G->T at pos 878.\n"
     ]
    }
   ],
   "source": [
    "# Description of novel alleles; number of mutations, and description of the mutation;\n",
    "cat sample.call.novel.txt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "## Updating an MLST scheme with the detected novel alleles\n",
    "\n",
    "You can update your MLST scheme with the novel alleled detected by MentaLiST, specially after running it on many different samples. In the scripts folder, there are python scripts to help select alleles and build an updated scheme. To do that, you will perform the following steps:\n",
    "1. Run MentaLiST on all files in your dataset (first-pass run)\n",
    "1. From the found novel alleles, select a subset that satisfy some restrictions in terms of number of mutations or minimum number of samples that have it.\n",
    "1. Create a new MLST by copying the existing one and adding the novel alleles.\n",
    "1. Run MentaLiST to create a k-mer database for this MLST scheme.\n",
    "1. Re-run MentaLiST again on all files, so each novel allele will have a proper allele id. (second-pass run)\n",
    "\n",
    "\n",
    "Each step will be described below. \n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### For the impatient:\n",
    "Here are the commands for each of the main steps. Below, I will describe each command and also look at the intermediate files being created."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# First pass call:\n",
    "mentalist call -o my_dataset_calls1.txt --db mtb_cgmlst.db -1 SRR6*_1.fastq.gz  -2 SRR6*_2.fastq.gz\n",
    "# Parse the novel alleles output, possibly filtering some alleles.\n",
    "parse_novel_alleles.py -f my_dataset_calls1.txt.novel.fa -o all_novel_alleles \n",
    "# Add the novel alleles to the scheme FASTA files:\n",
    "create_new_scheme_with_novel.py mtb_cgmlst_fasta/*fasta -o MTB_novel_scheme -n all_novel_alleles.fa\n",
    "# Build a new MentaLiST db for this scheme:\n",
    "mentalist build_db --db mtb_novel_cgMLST.db -k 31 -f MTB_novel_scheme/*.fasta \n",
    "# Second pass mentalist call:\n",
    "mentalist call -o my_dataset_novel_calls1.txt --db mtb_novel_cgMLST.db -1 SRR6*_1.fastq.gz  -2 SRR6*_2.fastq.gz\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 1. Run MentaLiST on all files in your dataset \n",
    "\n",
    "Let's download a 4 sample tuberculosis dataset:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "File ‘SRR6397472_1.fastq.gz’ already there; not retrieving.\n",
      "\n",
      "File ‘SRR6397472_2.fastq.gz’ already there; not retrieving.\n",
      "\n",
      "File ‘SRR6398036_1.fastq.gz’ already there; not retrieving.\n",
      "\n",
      "File ‘SRR6398036_2.fastq.gz’ already there; not retrieving.\n",
      "\n",
      "File ‘SRR6152708_1.fastq.gz’ already there; not retrieving.\n",
      "\n",
      "File ‘SRR6152708_2.fastq.gz’ already there; not retrieving.\n",
      "\n",
      "File ‘SRR6398023_1.fastq.gz’ already there; not retrieving.\n",
      "\n",
      "File ‘SRR6398023_2.fastq.gz’ already there; not retrieving.\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# Download a 4 sample tuberculosis dataset:\n",
    "wget ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/002/SRR6397472/SRR6397472_{1,2}.fastq.gz --no-clobber\n",
    "wget ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/006/SRR6398036/SRR6398036_{1,2}.fastq.gz --no-clobber\n",
    "wget ftp.sra.ebi.ac.uk/vol1/fastq/SRR615/008/SRR6152708/SRR6152708_{1,2}.fastq.gz --no-clobber\n",
    "wget ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/003/SRR6398023/SRR6398023_{1,2}.fastq.gz --no-clobber"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "You can run MentaLiST in many samples at one time, by passing all files at once, using the `-1` and `-2` parameters:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mOpening kmer database ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mFinished the JLD load, building alleles list...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mDecompressing weight list...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mBuilding kmer index ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mSample: SRR6152708. Opening fastq file(s) and counting kmers ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mVoting for alleles ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mCalling alleles and novel alleles ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mSample: SRR6397472. Opening fastq file(s) and counting kmers ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mVoting for alleles ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mCalling alleles and novel alleles ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mSample: SRR6398023. Opening fastq file(s) and counting kmers ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mVoting for alleles ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mCalling alleles and novel alleles ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mSample: SRR6398036. Opening fastq file(s) and counting kmers ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mVoting for alleles ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mCalling alleles and novel alleles ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mWriting output ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mDone.\n"
     ]
    }
   ],
   "source": [
    "mentalist call -o my_dataset_calls1.txt --db mtb_cgmlst.db -1 SRR6*_1.fastq.gz  -2 SRR6*_2.fastq.gz"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "### 2. Selecting the novel alleles\n",
    "\n",
    "To do that, we will use a Python script on the `scripts` folder of your MentaLiST installation (it might be already on your PATH if you installed via conda)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 94,
   "metadata": {},
   "outputs": [],
   "source": [
    "# optional: select the python environment and/or PATH to run the scripts;\n",
    "conda config --set changeps1 False # just avoid the PS1 change here on Jupyter, not needed in your console;\n",
    "conda activate mentalist1\n",
    "PATH=$PATH:/rhome/pfeijao/sfu/MentaLiST/scripts"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The 'parse_novel_alleles.py' script collects all novel alleles, creates a report and also outputs a FASTA file with selected alleles, to include in an updated MLST scheme. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "usage: parse_novel_alleles.py [-h] [-f F [F ...]] [-o O] [-t THRESHOLD]\n",
      "                              [-m MUTATION]\n",
      "                              [-ll {DEBUG,INFO,WARNING,ERROR,CRITICAL}]\n",
      "\n",
      "Given a list of FASTA files with novel alleles found with MentaLiST, output a\n",
      "FASTA with a unique list of novel alleles.\n",
      "\n",
      "optional arguments:\n",
      "  -h, --help            show this help message and exit\n",
      "  -f F [F ...]          Fasta files with novel alleles.\n",
      "  -o O                  Output Fasta file with alleles above the threshold\n",
      "                        requirement(s).\n",
      "  -t THRESHOLD, --threshold THRESHOLD\n",
      "                        Minimum number of different samples to appear, to\n",
      "                        include a novel allele in the output fasta.\n",
      "  -m MUTATION, --mutation MUTATION\n",
      "                        Also include if novel allel has equal or less than\n",
      "                        this number of mutations, regardless of times seen.\n",
      "                        Disabled by default.\n",
      "  -ll {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL}\n",
      "                        Set the logging level\n"
     ]
    }
   ],
   "source": [
    "parse_novel_alleles.py -h"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "You must give the novel allele FASTA file(s) found by MentaLiST as parameter -f. If you ran all your samples at once (like we did in this example), there is a single FASTA file, but you can also combine different FASTA files for different runs of MentaLiST on the same MLST scheme. \n",
    "\n",
    "Any given novel allele will be included in the output file (parameter -o) if this exact allele is present in at least (-t) samples. Also, if the parameter -m is given, any novel allele that has -m or more mutations will be excluded; this is useful if you want to include only novel alleles that are very close to existing alleles. \n",
    "\n",
    "Let's run the script, choosing alleles present in at least 2 of the 4 samples:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "02:10:09 PM (217 ms) -> INFO:Reading the new alleles  ...\n",
      "02:10:09 PM (245 ms) -> INFO:Writing output ...\n",
      "02:10:09 PM (248 ms) -> INFO:Done.\n"
     ]
    }
   ],
   "source": [
    "parse_novel_alleles.py -f my_dataset_calls1.txt.novel.fa -o novel_alleles -t 2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "There are three files created as output:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "novel_alleles.fa  novel_alleles.samples.txt  novel_alleles.txt\n"
     ]
    }
   ],
   "source": [
    "ls novel_alleles*"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Both .txt files have a report on *all* novel alleles found in the dataset, including how many times this each allele is seen, the number of mutations, and on which samples."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 62,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Locus\tAlleles found\tSamples x (mutations)\n",
      "Rv0024\t1\t1x (1)\n",
      "Rv0025\t1\t1x (1)\n",
      "Rv0035\t1\t1x (2)\n",
      "Rv0045c\t1\t1x (4)\n",
      "Rv0049\t1\t2x (2)\n",
      "Rv0051\t1\t2x (3)\n",
      "Rv0058\t1\t1x (2)\n",
      "Rv0063\t1\t1x (1)\n",
      "Rv0101\t1\t1x (2)\n",
      "Rv0104\t1\t1x (2)\n",
      "Rv0134\t1\t1x (2)\n",
      "Rv0139\t1\t2x (2)\n",
      "Rv0165c\t1\t1x (3)\n",
      "Rv0187\t1\t1x (2)\n",
      "Rv0195\t1\t1x (2)\n",
      "Rv0226c\t1\t1x (2)\n",
      "Rv0236c\t1\t1x (2)\n",
      "Rv0276\t1\t1x (2)\n",
      "Rv0289\t1\t1x (2)\n",
      "Rv0290\t1\t1x (2)\n",
      "Rv0311\t1\t2x (3)\n",
      "Rv0325\t1\t2x (2)\n",
      "Rv0347\t1\t1x (2)\n",
      "Rv0551c\t2\t2x (4), 1x (2)\n",
      "Rv0574c\t1\t2x (2)\n",
      "Rv0585c\t1\t2x (3)\n",
      "Rv0592\t1\t1x (3)\n",
      "Rv0634c\t1\t1x (2)\n",
      "Rv0654\t1\t1x (2)\n"
     ]
    }
   ],
   "source": [
    "head -n 30 novel_alleles.txt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For instance, locus Rv0311 has one novel allele, which was seen on 2 samples, and it has a distance of 4 mutations in relation to an existing allele in the scheme. On the other has, Rv0551c has 2 novel alleles, where one was seen in two samples, and the other on just one. \n",
    "\n",
    "On the `.samples.txt` file, we can see which samples exactly have the novel alleles.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 63,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Locus\tCount\tSamples\n",
      "Rv0024\t1x\tSRR6152708\n",
      "Rv0025\t1x\tSRR6397472\n",
      "Rv0035\t1x\tSRR6152708\n",
      "Rv0045c\t1x\tSRR6152708\n",
      "Rv0049\t2x\tSRR6398023,SRR6398036\n",
      "Rv0051\t2x\tSRR6398023,SRR6398036\n",
      "Rv0058\t1x\tSRR6398023\n",
      "Rv0063\t1x\tSRR6152708\n",
      "Rv0101\t1x\tSRR6152708\n",
      "Rv0104\t1x\tSRR6397472\n",
      "Rv0134\t1x\tSRR6152708\n",
      "Rv0139\t2x\tSRR6398023,SRR6398036\n",
      "Rv0165c\t1x\tSRR6152708\n",
      "Rv0187\t1x\tSRR6397472\n",
      "Rv0195\t1x\tSRR6152708\n",
      "Rv0226c\t1x\tSRR6152708\n",
      "Rv0236c\t1x\tSRR6397472\n",
      "Rv0276\t1x\tSRR6152708\n",
      "Rv0289\t1x\tSRR6397472\n",
      "Rv0290\t1x\tSRR6152708\n",
      "Rv0311\t2x\tSRR6398023,SRR6398036\n",
      "Rv0325\t2x\tSRR6398023,SRR6398036\n",
      "Rv0347\t1x\tSRR6397472\n",
      "Rv0551c\t2x\tSRR6398023,SRR6398036\n",
      "Rv0551c\t1x\tSRR6152708\n",
      "Rv0574c\t2x\tSRR6398023,SRR6398036\n",
      "Rv0585c\t2x\tSRR6398023,SRR6398036\n",
      "Rv0592\t1x\tSRR6397472\n",
      "Rv0634c\t1x\tSRR6397472\n"
     ]
    }
   ],
   "source": [
    "head -n30 novel_alleles.samples.txt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The third file is the `.fa` FASTA, which has all the *filtered* novel allele sequences. Comparing with the original FASTA file, we can see that from the 172 unique alleles found by MentaLiST, we are keeping 56."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "172\n"
     ]
    }
   ],
   "source": [
    "grep -c \">\" my_dataset_calls1.txt.novel.fa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "56\n"
     ]
    }
   ],
   "source": [
    "grep -c \">\" novel_alleles.fa"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can check that the locus Rv0551c has only one allele in this FASTA file, even though two new alleles were found. This is because one of the alleles was seen in only one sample, and therefore was filtered."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 65,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">\u001b[01;31m\u001b[KRv0551c\u001b[m\u001b[K\n",
      "CTAGCCGACCGCGCGCCCAGCGCCTTCCCAGAACCGTGCGCGCACGGCCTTCTTGTCCGGCTTTCCTAGACCGGTCAACGGCAAAGAGTCGACGACCACCACCCGCTTGGGTGCCTGCACCGATCCCTTGCGTTGTTTGACCGCTGCCTGGATCTCGGCGGTCATGGCCTCGATCGCGGGCTCATCGCGGGCCGCGTTGGAGCGCAACACCACCACCGCGGTGACGGCCTCGCCCCACTTCTCATCCGGCGCGCCAACCACGCACACCTGAGCAACCGCCGGATGCTCGGCCACCACGTCCTCGACCTCCCGGGGGAACACGTTGAAGCCGCCGGTGACGATCATGTCCTTGACGCGGTCGACGATGTAGTAGAAGCCATCGGAGTCCTCGCGGGCCAGGTCGCCGGTGTGCAGCCAGCCGTCTTTAAAAGTCCGCGACGTCTCGTCTGGCAGATTCCAGTAACCGCCCGCCAACAGCGGTCCGCTGACACAGATTTCGCCGACTTCGCCCTGCTTCACCGGCTTGCCATGCTCGTCTAACAGCGCGACGCGGGCGAACAGCGTCGGCCGCCCACATGAGGTCAGCCGCTTCTCGTCGTGATCGCCCTTGGCCAGATAGGTGATCACCATGGGCGCCTCGGATTGCCCGTAGTACTGGGCGAAGATTGGGCCGAACCGCCGGATCGCCTCGGCTAGTCGCACCGGGTTGATCGCCGGCGCCGTAGTAGACGGTTTCCAGCGACGACAGGTCCCGGGTGTGCGAATCCGGGTGGTCCAGCAGCGCGTACAGCATCGATGGCACCAACATGGTCGCTGTAATGCGTTGCTCCTCAATGATTCTGAGTACCTCGGCCGGGTCGAACTTCGCCAGCACTATCATCTCGCCGCCCTTGATCACCGTCGGCGTGAAAAACGCCGCGCCGGCGTGCGACAGCGGGGTGCACATTAAGAACCGCGGGTTGGCCGGCCACTCCCATTCGGCGAGCTGGATCGAGGTCATGGTGGCGATCGACTGCGCGGTGCCTATCACGCCCTTAGGCTTGCCGGTGGTGCCGCCGGTGTAAGTCAGGCCGATAACTTGGTCGGGTGGCAGGTCGGCGGCGACCAGCGGCTGCGGCTGGTATTTGGCGGCCTCGGCGGATAGGTCGACTGCCACATGCTTGAGCGCATCGGGCACCGGCCCAATGGTGAGGATTTGCTGCAGCGAGTCCACCTGCTCCAGCAGAGCCAGTGCGCGCTCGACGAACATCGGGTTGGGGTCGATGATCAGTGAGCTGATGCCGGCGTCGTTCAGCACGTAGGCGTGATCGGCCAGCGAGCCCAACGGGTGCAGCGCGGTGCGCCGATAACCGCGGGCCTGCCCGGCGCCGATGATCATCAAAACTTCAGGACGGTTGAGCGACAGCAGACCGACCGCCACCCCGGTGCCGGCACCTAGCGCCTCGAATGCCTGGATGTACTGGCTGATACGGTCCGCCAGCTGGCCACCGGTCAGCCTGGTGTCGCCGAGGAACAGCACCGGCTTGTTCTGGTGGCGCTTGAGCGCTCCCACTAGCAGATGGCCGTTGTGGGTCGGGCTGCGCAACAGCTCGCCCGAACAATCCTGGTCACGCATGGCGCCGCTCTCCCTCGCTAGCTGGGGTACCCCCACCGCATCGCTTCGTCCCCCGCAAGCGGGTGGTACCCCCACTGCATCGTCGCCGGCGGTGCTCAT\n"
     ]
    }
   ],
   "source": [
    "grep \"Rv0551c\" -A1 novel_alleles.fa"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can run the script again, this time without the parameter `-t 2`, meaning that we don't filter any allele, and we get all novel alleles:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 95,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "03:03:56 PM (935 ms) -> INFO:Reading the new alleles  ...\n",
      "03:03:56 PM (1062 ms) -> INFO:Writing output ...\n",
      "03:03:56 PM (1065 ms) -> INFO:Done.\n"
     ]
    }
   ],
   "source": [
    "parse_novel_alleles.py -f my_dataset_calls1.txt.novel.fa -o all_novel_alleles "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "172\n"
     ]
    }
   ],
   "source": [
    "grep -c \">\" all_novel_alleles.fa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">\u001b[01;31m\u001b[KRv0551c\u001b[m\u001b[K\n",
      "CTAGCCGACCGCGCGCCCAGCGCCTTCCCAGAACCGTGCGCGCACGGCCTTCTTGTCCGGCTTTCCTAGACCGGTCAACGGCAAAGAGTCGACGACCACCACCCGCTTGGGTGCCTGCACCGATCCCTTGCGTTGTTTGACCGCTGCCTGGATCTCGGCGGTCATGGCCTCGATCGCGGGCTCATCGCGGGCCGCGTTGGAGCGCAACACCACCACCGCGGTGACGGCCTCGCCCCACTTCTCATCCGGCGCGCCAACCACGCACACCTGAGCAACCGCCGGATGCTCGGCCACCACGTCCTCGACCTCCCGGGGGAACACGTTGAAGCCGCCGGTGACGATCATGTCCTTGACGCGGTCGACGATGTAGTAGAAGCCATCGGAGTCCTCGCGGGCCAGGTCGCCGGTGTGCAGCCAGCCGTCTTTAAAAGTCCGCGACGTCTCGTCTGGCAGATTCCAGTAACCGCCCGCCAACAGCGGTCGCTGACACAGATTTCGCCGACTTCGCCCTGCTTCACCGGCTTGCCATGCTCGTCTAACAGCGCGACGCGGGCGAACAGCGTCGGCCGCCCACATGAGGTCAGCCGCTTCTCGTCGTGATCGCCCTTGGCCAGATAGGTGATCACCATGGGCGCCTCGGATTGCCCGTAGTACTGGGCGAAGATTGGGCCGAACCGCCGGATCGCCTCGGCTAGTCGCACCGGGTTGATCGCCGAGGCGCCGTAGTAGACGGTTTCCAGCGACGACAGGTCCCGGGTGTGCGAATCCGGGTGGTCCAGCAGCGCGTACAGCATCGATGGCACCAACATGGTCGCTGTAATGCGTTGCTCCTCAATGATTCTGAGTACCTCGGCCGGGTCGAACTTCGCCAGCACTATCATCTCGCCGCCCTTGATCACCGTCGGCGTGAAAAACGCCGCGCCGGCGTGCGACAGCGGGGTGCACATTAAGAACCGCGGGTTGGCCGGCCACTCCCATTCGGCGAGCTGGATCGAGGTCATGGTGGCGATCGACTGCGCGGTGCCTATCACGCCCTTAGGCTTGCCGGTGGTGCCGCCGGTGTAAGTCAGGCCGATAACTTGGTCGGGTGGCAGGTCGGCGGCGACCAGCGGCTGCGGCTGGTATTTGGCGGCCTCGGCGGATAGGTCGACTGCCACATGCTTGAGCGCATCGGGCACCGGCCCAATGGTGAGGATTTGCTGCAGCGAGTCCACCTGCTCCAGCAGAGCCAGTGCGCGCTCGACGAACATCGGGTTGGGGTCGATGATCAGTGAGCTGATGCCGGCGTCGTTCAGCACGTAGGCGTGATCGGCCAGCGAGCCCAACGGGTGCAGCGCGGTGCGCCGATAACCGCGGGCCTGCCCGGCGCCGATGATCATCAAAACTTCAGGACGGTTGAGCGACAGCAGACCGACCGCCACCCCGGTGCCGGCACCTAGCGCCTCGAATGCCTGGATGTACTGGCTGATACGGTCCGCCAGCTGGCCACCGGTCAGCCTGGTGTCGCCGAGGAACAGCACCGGCTTGTTCTGGTGGCGCTTGAGCGCTCCCACTAGCAGATGGCCGTTGTGGGTCGGGCTGCGCAACAGCTCGCCCGAACAATCCTGGTCACGCATGGCGCCGCTCTCCCTCGCTAGCTGGGGTACCCCCACCGCATCGCTTCGTCCCCCGCAAGCGGGTGGTACCCCCACTGCATCGTCGCCGGCGGTGCTCAT\n",
      ">\u001b[01;31m\u001b[KRv0551c\u001b[m\u001b[K\n",
      "CTAGCCGACCGCGCGCCCAGCGCCTTCCCAGAACCGTGCGCGCACGGCCTTCTTGTCCGGCTTTCCTAGACCGGTCAACGGCAAAGAGTCGACGACCACCACCCGCTTGGGTGCCTGCACCGATCCCTTGCGTTGTTTGACCGCTGCCTGGATCTCGGCGGTCATGGCCTCGATCGCGGGCTCATCGCGGGCCGCGTTGGAGCGCAACACCACCACCGCGGTGACGGCCTCGCCCCACTTCTCATCCGGCGCGCCAACCACGCACACCTGAGCAACCGCCGGATGCTCGGCCACCACGTCCTCGACCTCCCGGGGGAACACGTTGAAGCCGCCGGTGACGATCATGTCCTTGACGCGGTCGACGATGTAGTAGAAGCCATCGGAGTCCTCGCGGGCCAGGTCGCCGGTGTGCAGCCAGCCGTCTTTAAAAGTCCGCGACGTCTCGTCTGGCAGATTCCAGTAACCGCCCGCCAACAGCGGTCCGCTGACACAGATTTCGCCGACTTCGCCCTGCTTCACCGGCTTGCCATGCTCGTCTAACAGCGCGACGCGGGCGAACAGCGTCGGCCGCCCACATGAGGTCAGCCGCTTCTCGTCGTGATCGCCCTTGGCCAGATAGGTGATCACCATGGGCGCCTCGGATTGCCCGTAGTACTGGGCGAAGATTGGGCCGAACCGCCGGATCGCCTCGGCTAGTCGCACCGGGTTGATCGCCGGCGCCGTAGTAGACGGTTTCCAGCGACGACAGGTCCCGGGTGTGCGAATCCGGGTGGTCCAGCAGCGCGTACAGCATCGATGGCACCAACATGGTCGCTGTAATGCGTTGCTCCTCAATGATTCTGAGTACCTCGGCCGGGTCGAACTTCGCCAGCACTATCATCTCGCCGCCCTTGATCACCGTCGGCGTGAAAAACGCCGCGCCGGCGTGCGACAGCGGGGTGCACATTAAGAACCGCGGGTTGGCCGGCCACTCCCATTCGGCGAGCTGGATCGAGGTCATGGTGGCGATCGACTGCGCGGTGCCTATCACGCCCTTAGGCTTGCCGGTGGTGCCGCCGGTGTAAGTCAGGCCGATAACTTGGTCGGGTGGCAGGTCGGCGGCGACCAGCGGCTGCGGCTGGTATTTGGCGGCCTCGGCGGATAGGTCGACTGCCACATGCTTGAGCGCATCGGGCACCGGCCCAATGGTGAGGATTTGCTGCAGCGAGTCCACCTGCTCCAGCAGAGCCAGTGCGCGCTCGACGAACATCGGGTTGGGGTCGATGATCAGTGAGCTGATGCCGGCGTCGTTCAGCACGTAGGCGTGATCGGCCAGCGAGCCCAACGGGTGCAGCGCGGTGCGCCGATAACCGCGGGCCTGCCCGGCGCCGATGATCATCAAAACTTCAGGACGGTTGAGCGACAGCAGACCGACCGCCACCCCGGTGCCGGCACCTAGCGCCTCGAATGCCTGGATGTACTGGCTGATACGGTCCGCCAGCTGGCCACCGGTCAGCCTGGTGTCGCCGAGGAACAGCACCGGCTTGTTCTGGTGGCGCTTGAGCGCTCCCACTAGCAGATGGCCGTTGTGGGTCGGGCTGCGCAACAGCTCGCCCGAACAATCCTGGTCACGCATGGCGCCGCTCTCCCTCGCTAGCTGGGGTACCCCCACCGCATCGCTTCGTCCCCCGCAAGCGGGTGGTACCCCCACTGCATCGTCGCCGGCGGTGCTCAT\n"
     ]
    }
   ],
   "source": [
    "grep \"Rv0551c\" -A1 all_novel_alleles.fa"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Even in the case that you don't want to filter any allele, you have to run the `parse_novel_alleles.py` script, as its output will be used on the next step.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 3. Create a new MLST scheme with the novel alleles\n",
    "\n",
    "To create a new MLST scheme with the novel alleles included, provide the original MLST scheme and the novel alleles FASTA file to the script 'create_new_scheme_with_novel.py' "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "usage: create_new_scheme_with_novel.py [-h] [-n NOVEL] [-o OUTPUT] [-i ID]\n",
      "                                       [-ll {DEBUG,INFO,WARNING,ERROR,CRITICAL}]\n",
      "                                       files [files ...]\n",
      "\n",
      "Adds novel alleles to an existing MLST scheme.\n",
      "\n",
      "positional arguments:\n",
      "  files                 MLST Fasta files\n",
      "\n",
      "optional arguments:\n",
      "  -h, --help            show this help message and exit\n",
      "  -n NOVEL, --novel NOVEL\n",
      "                        FASTA with novel alleles.\n",
      "  -o OUTPUT, --output OUTPUT\n",
      "                        Output folder for new scheme.\n",
      "  -i ID, --id ID        Start numbering new alleles on this value, later will\n",
      "                        implement from last allele id +1.\n",
      "  -ll {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL}\n",
      "                        Set the logging level\n"
     ]
    }
   ],
   "source": [
    "create_new_scheme_with_novel.py -h"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "So, to add the novel alleles from the previous step in the small MLST scheme from the initial example, we run:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "02:33:14 PM (133 ms) -> INFO:Opening the novel alleles file ...\n",
      "02:33:14 PM (158 ms) -> INFO:Opening the MLST schema and adding novel alleles ...\n",
      "02:33:36 PM (21784 ms) -> INFO:Done.\n"
     ]
    }
   ],
   "source": [
    "create_new_scheme_with_novel.py mtb_cgmlst_fasta/*fasta -o MTB_novel_scheme -n all_novel_alleles.fa"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can see that the new scheme has more alleles, for instance, on locus Rv0551c:\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">Rv0551c_364\n",
      ">Rv0551c_365\n",
      ">Rv0551c_366\n",
      ">Rv0551c_367\n",
      ">Rv0551c_368\n"
     ]
    }
   ],
   "source": [
    "grep \">\" mtb_cgmlst_fasta/Rv0551c.fasta | tail -n5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 81,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">Rv0551c_366\n",
      ">Rv0551c_367\n",
      ">Rv0551c_368\n",
      ">Rv0551c_369\n",
      ">Rv0551c_370\n"
     ]
    }
   ],
   "source": [
    "grep \">\" MTB_novel_scheme/Rv0551c.fasta | tail -n5"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 4. Run MentaLiST to create a new MLST database file\n",
    "\n",
    "Now we run MentaLiST to create a new MLST scheme database, similarly as it was done before, but now with the new MLST scheme, to include the new alleles. Unfortunately there is now way currently to do this in an incremental way. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 87,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mOpening FASTA files ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mCombining results for each locus ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mSaving DB ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mDone!\n"
     ]
    }
   ],
   "source": [
    "mentalist build_db --db mtb_novel_cgMLST.db -k 31 -f MTB_novel_scheme/*.fasta --threads 4"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 5. MentaLiST call -  second pass \n",
    "\n",
    "Now, we can rerun the MLST calling phase with the new DB:\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 90,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mOpening kmer database ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mFinished the JLD load, building alleles list...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mDecompressing weight list...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mBuilding kmer index ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mSample: SRR6152708. Opening fastq file(s) and counting kmers ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mVoting for alleles ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mCalling alleles and novel alleles ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mSample: SRR6397472. Opening fastq file(s) and counting kmers ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mVoting for alleles ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mCalling alleles and novel alleles ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mSample: SRR6398023. Opening fastq file(s) and counting kmers ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mVoting for alleles ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mCalling alleles and novel alleles ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mSample: SRR6398036. Opening fastq file(s) and counting kmers ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mVoting for alleles ... \n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mCalling alleles and novel alleles ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mWriting output ...\n",
      "\u001b[36m\u001b[1m[ \u001b[22m\u001b[39m\u001b[36m\u001b[1mInfo: \u001b[22m\u001b[39mDone.\n"
     ]
    }
   ],
   "source": [
    "mentalist call -o my_dataset_novel_calls1.txt --db mtb_novel_cgMLST.db -1 SRR6*_1.fastq.gz  -2 SRR6*_2.fastq.gz"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Comparing this call with the previous, we can see that the novel alleles (marked as \"N\") have been called in the new output: "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 91,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Rv0023  Rv0024  Rv0025  Rv0033  Rv0034  Rv0035  Rv0036c  Rv0037c  Rv0038  Rv0039c  Rv0040c\n",
      "1       N       1       1       2       N       4        1        1       2        2\n",
      "1       1       N       1       2       1       1        1        1       1        2\n",
      "1       1       1       1       2       1-      1        1        1       1        2\n",
      "1       1       1       1       2       1-      1        1        1       1        2\n"
     ]
    }
   ],
   "source": [
    "# OLD:\n",
    "cut -f10-20 my_dataset_calls1.txt | column -ts $'\\t'   "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 92,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Rv0023  Rv0024  Rv0025  Rv0033  Rv0034  Rv0035  Rv0036c  Rv0037c  Rv0038  Rv0039c  Rv0040c\n",
      "1       314     1       1       2       562     4        1        1       2        2\n",
      "1       1       123     1       2       1       1        1        1       1        2\n",
      "1       1       1       1       2       1-      1        1        1       1        2\n",
      "1       1       1       1       2       1-      1        1        1       1        2\n"
     ]
    }
   ],
   "source": [
    "# New:\n",
    "cut -f10-20 my_dataset_novel_calls1.txt | column -ts $'\\t'   "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "### Command summary: "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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