demo.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a4c6c59e-e0a0-4de8-be50-4ce8f84bcb33",
   "metadata": {},
   "outputs": [],
   "source": [
    "!pip install SQUARNA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "f417482e-597d-478c-a4f3-5e64b91a1276",
   "metadata": {},
   "outputs": [],
   "source": [
    "import SQUARNA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6c3f2f87-8f32-4a96-b964-14311a48ffe9",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "bc7c4a31-7f9b-481d-a564-96f4255b7295",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Help on function Predict in module SQUARNA.SQUARNA:\n",
      "\n",
      "Predict(inputfile=None, fileformat='unknown', inputseq=None, configfile=None, inputformat='qtrf', maxstemnum=None, threads=8, byseq=False, algorithms='', entropy=False, rankby='s', evalonly=False, hardrest=False, interchainonly=False, toplim=5, outplim=None, conslim=1, poollim=1000, reactformat=3, alignment=False, levellimit=None, freqlimit=0.35, verbose=False, step3='u', ignorewarn=False, HOME_DIR=None, write_to=None, priority=None, i=None, ff=None, c=None, config=None, s=None, seq=None, a=None, ali=None, algo=None, algorithm=None, rb=None, fl=None, freqlim=None, ll=None, levlim=None, tl=None, ol=None, cl=None, pl=None, pr=None, s3=None, msn=None, rf=None, eo=None, hr=None, ico=None, iw=None, ignore=None, t=None, bs=None, v=None)\n",
      "    -----------------------------------------------------------------------\n",
      "    Prints SQUARNA RNA secondary structure predictions from the given input\n",
      "    \n",
      "    Parameters:\n",
      "        i / inputfile : string\n",
      "            Path to the input file.\n",
      "        ff / fileformat : unknown/fasta/default/stockholm/clustal\n",
      "            Input file format. For the details of the default SQUARNA input\n",
      "            format see https://github.com/febos/SQUARNA/blob/main/examples/seq_input.fas.\n",
      "            \"unknown\"   - the format will be identified automatically.\n",
      "            \"default\"   - default fasta-like format.\n",
      "            \"fasta\"     - FASTA format.\n",
      "            \"stockholm\" - STOCKHOLM format.\n",
      "            \"clustal\"   - CLUSTAL format.\n",
      "        s / seq / inputseq : string\n",
      "            RNA sequence input, alternative to inputfile (higher priority).\n",
      "        c / config / configfile : string\n",
      "            Path to a config file or a name of a built-in config, \n",
      "            see https://github.com/febos/SQUARNA/blob/main/def.conf\n",
      "            for the format details. \n",
      "            In the alignment-based mode, the default config \n",
      "            file is ali.conf. In the single-sequence mode the default\n",
      "            config for sequences under 500nts is def.conf, for sequences\n",
      "            between 500 and 1000nts - 500.conf, and for sequences over\n",
      "            1000nts in length - 1000.conf.\n",
      "            Built-in configs:\n",
      "            def (def.conf) is recommended by default for RNAs under 500nts.\n",
      "            alt (alt.conf) is recommended for short pseudoknotted RNAs.\n",
      "            500 (500.conf) is recommended for RNAs longer 500 nts.\n",
      "            1000 (1000.conf) is recommended for RNAs longer 1000 nts.\n",
      "            sk (sk.conf) is recommended with SHAPE data input.\n",
      "            c=nussinov (nussinov.conf) - Nussinov algorithm config.\n",
      "            c=hungarian (hungarian.conf) - Hungarian algorithm config.\n",
      "            c=edmonds (edmonds.conf) - Edmonds algorithm config.\n",
      "            c=greedy (greedy.conf) - Greedy algorithm config.\n",
      "        inputformat : string\n",
      "            The order of the lines in the input file. By default, SQUARNA \n",
      "            reads the first line of the entry (among the lines after \n",
      "            the \">\" line) as the seQuence (q), the second line as the \n",
      "            reacTivities (t), the third line as the Restraints (r), \n",
      "            the fourth line as the reFerence (f), and all the further lines \n",
      "            are ignored. inputformat should be a subset of qtrfx letters \n",
      "            in any order, with q being mandatory. All \"x\" lines will be ignored.\n",
      "        msn / maxstemnum : int\n",
      "            Maximum number of stems to predict in each structure. By default,\n",
      "            maxstemnum is defined in a config file for each parameter set. \n",
      "            If specified explicitly it will overwrite the maxstemnum \n",
      "            values for all the parameter sets.\n",
      "        t / threads : int\n",
      "            Number of CPUs to use.\n",
      "        bs / byseq : bool\n",
      "            Parallelize the execution over the input sequences\n",
      "            in the single-sequence mode. \n",
      "            By default, the execution in the single-sequence mode\n",
      "            is parallelized over the structure pool within each sequence.\n",
      "            Parallelizing over input sequences is recommended for \n",
      "            large input files along with fast configs.\n",
      "        algo / algorithm / algorithms: string\n",
      "            The algorithms to be used in single-sequence predictions.\n",
      "            By default, the algorithms are derived from the config file.\n",
      "            If the algorithms parameter is specified, it will overwrite the\n",
      "            algorithms listed in the config file.\n",
      "            The choice should be a subset of the four algorithms:\n",
      "            e - Edomnds algorithm [10.6028/jres.069B.013]\n",
      "            g - Greedy SQUARNA algorithm [10.1101/2023.08.28.555103]\n",
      "            h - Hungarian algorithm [10.1002/nav.3800020109]\n",
      "            n - Nussinov algorithm [10.1073/pnas.77.11.6309]\n",
      "        rb / rankby : string\n",
      "            How to rank the predicted structures. rankby should be a subset of\n",
      "            letters r, s, and d in any order (r / s / rs / rd / sd / rsd).\n",
      "            If both r and s are present, the structures will be ranked according\n",
      "            to the total_score = structure_score * reactivity_score. If only \n",
      "            r is present, the structures will be ranked by the reactivity_score,\n",
      "            and if only s is present, the structures will be ranked by the \n",
      "            structure_score. Independently, if d is present, the mutually \n",
      "            divergent structures will be put first.\n",
      "        eo / evalonly : bool\n",
      "            Ignored in the alignment mode.\n",
      "            If specified, no predictions are made and just the reference structure\n",
      "            scores are returned provided the reference is specified. \n",
      "            If non-canonical base pairs are present in the reference structure, \n",
      "            they will be considered with 0.0 weight).\n",
      "        hr / hardrest : bool\n",
      "            If specified, all the base pairs from the restraints line will be\n",
      "            forced to be present in the predicted structures. However, it will\n",
      "            not affect the structure scores, as the forced base pairs won't\n",
      "            contribute to the structure score unless they were predicted without\n",
      "            forcing as well.\n",
      "        ico / interchainonly : bool\n",
      "            Allow only inter-chain base pairs to be predicted.\n",
      "        tl / toplim : int\n",
      "            How many top-N structures will be subject to comparison with the reference.\n",
      "        ol / outplim : int\n",
      "            How many top-N structures will be printed into the stdout.\n",
      "            By default, outplim = toplim.\n",
      "        cl / conslim : int\n",
      "            How many top-N structures will be used to derive the predicted structure consensus.\n",
      "        pl / poollim : int\n",
      "            Maximum number of structures allowed to populate the current structure pool (if exceeded, no bifurcation will occur anymore).\n",
      "        rf / reactformat : 3/10/26\n",
      "            Encoding used to output the reactivities line.\n",
      "            rf=3:   0.0  <= \"_\" <   1/3; \n",
      "                    1/3  <= \"+\" <   2/3;\n",
      "                    2/3  <= \"#\" <=  1.0;\n",
      "            rf=10:  0.0  <= \"0\" <   0.1;\n",
      "                    ....................\n",
      "                    0.5  <= \"5\" <   0.6;\n",
      "                    ....................\n",
      "                    0.9  <= \"9\" <=  1.0;\n",
      "            rf=26:  0.00 <= \"a\" <  0.02;\n",
      "                    0.02 <= \"b\" <  0.06;\n",
      "                    ....................\n",
      "                    0.50 <= \"n\" <  0.54;\n",
      "                    ....................\n",
      "                    0.94 <= \"y\" <  0.98;\n",
      "                    0.98 <= \"z\" <= 1.00.\n",
      "        a / ali/ alignment : bool\n",
      "            Run SQUARNA in the alignment-based mode. If specified,\n",
      "            ali.conf will be used as the config file by default, \n",
      "            unless another config file is explicitly specified \n",
      "            by the user. The bpweights, minlen, and minbpscore \n",
      "            parameters for step-1 will be derived from the first \n",
      "            parameter set in the config file.\n",
      "        ll / levlim / levellimit : int\n",
      "            Ignored in the single-sequence mode.\n",
      "            The allowed number of pseudoknot levels. All the base pairs\n",
      "            of the higher levels will be removed from the structure predicted\n",
      "            at step-1 and from the structure predicted at step-2. By default, \n",
      "            levellimit=3 for short alignments of no more than 500 columns, \n",
      "            and levellimit=2 for longer alignments.\n",
      "        fl / freqlim / freqlimit : 0.0 <= float <= 1.0\n",
      "            Ignored in the single-sequence mode.\n",
      "            The percentage of sequences required to contain a base pair,\n",
      "            in order for it to be added to the predicted consensus structure\n",
      "            at step-2. The consensus will include all the base pairs present\n",
      "            in at least \"fl\" share of the sequences given that the base pair\n",
      "            is not in conflict (does not share a position) with a more \n",
      "            populated base pair.\n",
      "        v / verbose : bool\n",
      "            Run SQUARNA in the verbose mode.\n",
      "            Ignored in the single-sequence mode.\n",
      "        s3 / step3 : \"i\"/\"u\"/\"1\"/\"2\"\n",
      "            Ignored in the single-sequence mode.\n",
      "            Defines the structure that will be printed at step-3. If step3=1,\n",
      "            the structure from step-1 will be printed, and the step-2 will\n",
      "            be skipped completely, meaning the prediction will be super fast.\n",
      "            If step3=2, the structure from step-2 will be printed. If step3=u,\n",
      "            the union of base pairs of the two structures will be printed. \n",
      "            If step3=i, the intersection of base pairs of the two structures \n",
      "            will be printed.\n",
      "        iw / ignore / ignorewarn : bool\n",
      "            Ignore warnings.\n",
      "        HOME_DIR : string\n",
      "            Path to the folder with built-in configs.\n",
      "        write_to : IO_object\n",
      "            Where to write the output. By default, write_to = sys.stdout.\n",
      "        pr / priority : string\n",
      "            Comma-separated list of prioritized paramset names. Default: bppN,bppH1,bppH2.\n",
      "\n"
     ]
    }
   ],
   "source": [
    "help(SQUARNA.Predict)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ec48ed23-48b4-4064-9877-45ef486e1f58",
   "metadata": {},
   "source": [
    "## Single sequence, printing the result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "b0094040-74d4-4c3b-b251-445a91835772",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">inputseq\n",
      "GGGCGGCUAGCUCAGCGGAAGAGCGCUCGCCUCACACGCGAGAGGUCGUAGGUUCAAGUCCUACGCCGCCCACCA\n",
      "___________________________________________________________________________\n",
      "(((((((..((((.......)))).(((((.......))))).....(((((.......))))))))))))....\ttop-1_consensus\n",
      "===========================================================================\n",
      "(((((((..((((.......)))).(((((.......))))).....(((((.......))))))))))))....\t#1\t300.806\t601.611\t0.5\tdefG1,defG2,defN,bppN,bppG1,bppG2\n",
      "(((((((..((((.......))))..((((.......))))......(((((.......))))))))))))....\t#2\t277.661\t555.321\t0.5\tdefE,defH,bppH1,bppH2,bppE1,bppE2\n",
      "((((((...((((.......)))).(((((.......)))))....((((((.......))))))))))))....\t#3\t292.243\t584.486\t0.5\tdefG1,defG2,bppG1,bppG2\n",
      "(((((((..((((.......))))....(((((........))))).(((((.......))))))))))))....\t#4\t275.067\t550.133\t0.5\tbppG2\n",
      "((((((...((((.......))))....(((((........)))))((((((.......))))))))))))....\t#5\t266.504\t533.008\t0.5\tbppG2\n"
     ]
    }
   ],
   "source": [
    "seq = \"GGGCGGCUAGCUCAGCGGAAGAGCGCUCGCCUCACACGCGAGAGGUCGUAGGUUCAAGUCCUACGCCGCCCACCA\"\n",
    "\n",
    "SQUARNA.Predict(inputseq = seq)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4e15e6b2-e145-4637-8ab6-fd968737e3d4",
   "metadata": {},
   "source": [
    "## Single sequence, write the result to a file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "1d26a5c0-fb0a-43b3-8ddb-d8aaca0471db",
   "metadata": {},
   "outputs": [],
   "source": [
    "seq = \"GGGCGGCUAGCUCAGCGGAAGAGCGCUCGCCUCACACGCGAGAGGUCGUAGGUUCAAGUCCUACGCCGCCCACCA\"\n",
    "\n",
    "outpfile = \"demo.txt\"\n",
    "\n",
    "with open(outpfile,\"w\") as file:\n",
    "    SQUARNA.Predict(inputseq = seq, write_to = file)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "89356995-6552-4d78-9ee4-88a727a62670",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">inputseq\r\n",
      "GGGCGGCUAGCUCAGCGGAAGAGCGCUCGCCUCACACGCGAGAGGUCGUAGGUUCAAGUCCUACGCCGCCCACCA\r\n",
      "___________________________________________________________________________\r\n",
      "(((((((..((((.......)))).(((((.......))))).....(((((.......))))))))))))....\ttop-1_consensus\r\n",
      "===========================================================================\r\n",
      "(((((((..((((.......)))).(((((.......))))).....(((((.......))))))))))))....\t#1\t300.806\t601.611\t0.5\tdefG1,defG2,defN,bppN,bppG1,bppG2\r\n",
      "(((((((..((((.......))))..((((.......))))......(((((.......))))))))))))....\t#2\t277.661\t555.321\t0.5\tdefE,defH,bppH1,bppH2,bppE1,bppE2\r\n",
      "((((((...((((.......)))).(((((.......)))))....((((((.......))))))))))))....\t#3\t292.243\t584.486\t0.5\tdefG1,defG2,bppG1,bppG2\r\n",
      "(((((((..((((.......))))....(((((........))))).(((((.......))))))))))))....\t#4\t275.067\t550.133\t0.5\tbppG2\r\n",
      "((((((...((((.......))))....(((((........)))))((((((.......))))))))))))....\t#5\t266.504\t533.008\t0.5\tbppG2\r\n"
     ]
    }
   ],
   "source": [
    "!cat demo.txt"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a6bfc561-bd8d-4d6c-aac9-10f20eb0d1c8",
   "metadata": {},
   "source": [
    "## Single sequence, capture the result into a string"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "10275c9e-c406-48b2-87de-ae270f25503f",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['>inputseq', 'GGGCGGCUAGCUCAGCGGAAGAGCGCUCGCCUCACACGCGAGAGGUCGUAGGUUCAAGUCCUACGCCGCCCACCA', '___________________________________________________________________________', '(((((((..((((.......)))).(((((.......))))).....(((((.......))))))))))))....\\ttop-1_consensus', '===========================================================================', '(((((((..((((.......)))).(((((.......))))).....(((((.......))))))))))))....\\t#1\\t300.806\\t601.611\\t0.5\\tdefG1,defG2,defN,bppN,bppG1,bppG2', '(((((((..((((.......))))..((((.......))))......(((((.......))))))))))))....\\t#2\\t277.661\\t555.321\\t0.5\\tdefE,defH,bppH1,bppH2,bppE1,bppE2', '((((((...((((.......)))).(((((.......)))))....((((((.......))))))))))))....\\t#3\\t292.243\\t584.486\\t0.5\\tdefG1,defG2,bppG1,bppG2', '(((((((..((((.......))))....(((((........))))).(((((.......))))))))))))....\\t#4\\t275.067\\t550.133\\t0.5\\tbppG2', '((((((...((((.......))))....(((((........)))))((((((.......))))))))))))....\\t#5\\t266.504\\t533.008\\t0.5\\tbppG2', '']\n"
     ]
    }
   ],
   "source": [
    "import io\n",
    "seq = \"GGGCGGCUAGCUCAGCGGAAGAGCGCUCGCCUCACACGCGAGAGGUCGUAGGUUCAAGUCCUACGCCGCCCACCA\"\n",
    "\n",
    "with io.StringIO() as stream:\n",
    "    SQUARNA.Predict(inputseq = seq, write_to = stream)\n",
    "    result = stream.getvalue()\n",
    "\n",
    "lines = result.split('\\n')\n",
    "print(lines)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4607552b-e218-4eb4-9e03-30f99058f0f4",
   "metadata": {},
   "source": [
    "## Input file, printing the result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "6e9b6ab8-48d2-40cf-b8b7-91743211c8cc",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">External loop 1\n",
      "CCCAAAAGGG;CCCAAAAGGG\n",
      "_____________________\n",
      "(((....)));(((....)))\ttop-1_consensus\n",
      "=====================\n",
      "(((....)));(((....)))\t#1\t68.329\t136.659\t0.5\tdefG1,defG2,defN,bppN,bppH1,bppH2,bppE1,bppE2,bppG1,bppG2\n",
      "(((....(((;)))....)))\t#2\t68.329\t136.659\t0.5\tdefG1,defG2,defE,bppG1\n",
      "..........;..........\t#3\t0.0\t0\t0.5\tdefH\n",
      ">testcase\n",
      "CGAAGUCCUUUACGUA\n",
      "________________\n",
      "((..........))..\ttop-1_consensus\n",
      "================\n",
      "((..........))..\t#1\t17.148\t34.297\t0.5\tdefN,bppN,defE,defH,bppH1,bppH2,bppE1,bppE2\n",
      ".(((....))).....\t#2\t2.374\t4.748\t0.5\tdefG2\n",
      "................\t#3\t0.0\t0\t0.5\tdefG1,bppG1,bppG2\n",
      ">testcase with reactivities\n",
      "CGAAGUCCUUUACGUA\n",
      "#+++++++++++++++\treactivities\n",
      "________________\n",
      "((..........))..\ttop-1_consensus\n",
      "================\n",
      "((..........))..\t#1\t16.077\t34.297\t0.469\tdefN,bppN,defE,defH,bppH1,bppH2,bppE1,bppE2\n",
      ".(((....))).....\t#2\t2.522\t4.748\t0.531\tdefG2\n",
      "................\t#3\t0.0\t0\t0.531\tdefG1,bppG1,bppG2\n",
      ">multiple chains (separated by ; or &)\n",
      "GGGGGAAAACCCCCAAA;AAAGGGGGAAAACCCCC\n",
      "___________________________________\n",
      "(((((....(((((...;...)))))....)))))\ttop-1_consensus\n",
      "===================================\n",
      "(((((....(((((...;...)))))....)))))\t#1\t162.836\t325.672\t0.5\tdefG1,defG2,defN,bppN,defE,bppH1,bppH2,bppE1,bppE2,bppG1,bppG2\n",
      "(((((....)))))...;...(((((....)))))\t#2\t162.836\t325.672\t0.5\tdefG1,defG2,bppG1,bppG2\n",
      "((((.....(((((...;...)))))....)))).\t#3\t137.133\t274.267\t0.5\tdefG1,defG2\n",
      ".((((....(((((...;...))))).....))))\t#4\t137.133\t274.267\t0.5\tdefG1,defG2\n",
      "((((.....))))....;...(((((....)))))\t#5\t137.133\t274.267\t0.5\tdefG1,defG2\n",
      ">multiple chains with reactivities (with separators included but ignored)\n",
      "GGGGGAAAACCCCCAAA;AAAGGGGGAAAACCCCC\n",
      "#####++++#####+++;+++++++++++++++++\treactivities\n",
      "___________________________________\n",
      "(((((....(((((...;...)))))....)))))\ttop-1_consensus\n",
      "===================================\n",
      "(((((....(((((...;...)))))....)))))\t#1\t114.943\t325.672\t0.353\tdefN,bppN,bppH2,bppE2,bppG1\n",
      ".................;...(((((....)))))\t#2\t105.365\t162.836\t0.647\tdefG1,defG2,defE,defH,bppH1,bppE1,bppG1,bppG2\n",
      ".................;...((((.....)))).\t#3\t72.102\t111.43\t0.647\tdefG1,defG2\n",
      ".................;....((((.....))))\t#4\t72.102\t111.43\t0.647\tdefG1,defG2\n",
      ">multiple chains with bp-to-the-right restraints\n",
      "GGGGGAAAACCCCCAAA;AAAGGGGGAAAACCCCC\n",
      "........./////...;.................\trestraints\n",
      "___________________________________\n",
      "(((((....(((((...;...)))))....)))))\ttop-1_consensus\n",
      "===================================\n",
      "(((((....(((((...;...)))))....)))))\t#1\t162.836\t325.672\t0.5\tdefG1,defG2,defN,bppN,defE,defH,bppH1,bppH2,bppE1,bppE2,bppG1,bppG2\n",
      "((((.....(((((...;...)))))....)))).\t#2\t137.133\t274.267\t0.5\tdefG1,defG2\n",
      ".((((....(((((...;...))))).....))))\t#3\t137.133\t274.267\t0.5\tdefG1,defG2\n",
      ".................;...(((((....)))))\t#4\t81.418\t162.836\t0.5\tdefG1,defG2,bppG1,bppG2\n",
      ".................;...((((.....)))).\t#5\t55.715\t111.43\t0.5\tdefG1,defG2\n",
      ">multiple chains with bp-to-the-left and unpaired restraints\n",
      "GGGGGAAAACCCCCAAA;AAAGGGGGAAAACCCCC\n",
      ".........\\\\\\\\\\...;..._____.........\trestraints\n",
      "___________________________________\n",
      "(((((............;............)))))\ttop-1_consensus\n",
      "===================================\n",
      "(((((............;............)))))\t#1\t81.418\t162.836\t0.5\tdefG1,defG2,defN,bppN,defE,bppH1,bppH2,bppE1,bppE2,bppG1,bppG2\n",
      "(((((....)))))...;.................\t#2\t81.418\t162.836\t0.5\tdefG1,defG2,defH,bppG1,bppG2\n",
      "((((.............;............)))).\t#3\t55.715\t111.43\t0.5\tdefG1,defG2\n",
      ".((((............;.............))))\t#4\t55.715\t111.43\t0.5\tdefG1,defG2\n",
      "((((.....))))....;.................\t#5\t55.715\t111.43\t0.5\tdefG1,defG2\n",
      ">7QR4 [69],1.B.G.1.:1.B.U.69. with reference\n",
      "GGGGGCCACAGCAGAAGCGUUCACGUCGCAGCCCCUGUCAGCCAUUGCACUCCGGCUGCGAAUUCUGCU\n",
      "[[[[[[...((((((((((.......))).]]]]]]..(((((..........)))))....)))))))\treference\t245.103\t490.206\t0.5\n",
      "_____________________________________________________________________\n",
      "((...))..(((((((.((....))((((((((...((..((....))))...)))))))).)))))))\ttop-1_consensus\tTP=7,FP=16,FN=14,FS=0.318,PR=0.304,RC=0.333\n",
      "=====================================================================\n",
      "((...))..(((((((.((....))((((((((...((..((....))))...)))))))).)))))))\t#1\t264.19\t528.38\t0.5\tbppH1,bppE1\n",
      "((...))..(((((((.((....))((((((((...(((((...))).))...)))))))).)))))))\t#2\t254.755\t509.509\t0.5\tbppN\n",
      ".........(((((((.((....))((((((((.......((....)).....)))))))).)))))))\t#3\t237.972\t475.944\t0.5\tbppH2,bppE2\n",
      "((...))..(((((((.((....))((((((((.......((....)).....)))))))).)))))))\t#4\t255.121\t510.241\t0.5\tdefN\n",
      "[[[[[[...((((((((((.......))).]]]]]]..(((((..........)))))....)))))))\t#5\t245.103\t490.206\t0.5\tdefG1,defG2\tTP=21,FP=0,FN=0,FS=1.0,PR=1.0,RC=1.0,RK=5\n",
      ">7QR4 [69],1.B.G.1.:1.B.U.69. with reference and reactivities\n",
      "GGGGGCCACAGCAGAAGCGUUCACGUCGCAGCCCCUGUCAGCCAUUGCACUCCGGCUGCGAAUUCUGCU\n",
      "______++++++++++++++++++++++++++++++++++++++++####+++++++++++++++++++\treactivities\n",
      ".....................................................................\trestraints\n",
      "[[[[[[...((((((((((.......))).]]]]]]..(((((..........)))))....)))))))\treference\t280.625\t490.206\t0.572\n",
      "_____________________________________________________________________\n",
      "((...))..(((((((.((....))((((((((....................)))))))).)))))))\ttop-1_consensus\tTP=7,FP=12,FN=14,FS=0.35,PR=0.368,RC=0.333\n",
      "=====================================================================\n",
      "((...))..(((((((.((....))((((((((....................)))))))).)))))))\t#1\t251.768\t475.944\t0.529\tbppN,bppH1,bppE1\n",
      ".........(((((((.((....))((((((((....................)))))))).)))))))\t#2\t214.423\t441.648\t0.486\tbppH2,bppE2\n",
      "((...))..(((((((.((....))((((((((.......((....)).....)))))))).)))))))\t#3\t255.121\t510.241\t0.5\tdefN\n",
      "[[[[[[...(((((((.........((((((((.......]]].......]]])))))))).)))))))\t#4\t289.903\t506.413\t0.572\tdefG1,bppG1\n",
      "[[[[[[...(((((((.((....))(((((]]]]]]....(((..........)))))))).)))))))\t#5\t283.133\t494.587\t0.572\tdefE,defH\tTP=16,FP=7,FN=5,FS=0.727,PR=0.696,RC=0.762,RK=5\n",
      ">7QR4 [69],1.B.G.1.:1.B.U.69. with restraints\n",
      "GGGGGCCACAGCAGAAGCGUUCACGUCGCAGCCCCUGUCAGCCAUUGCACUCCGGCUGCGAAUUCUGCU\n",
      "[[[[[[........................]]]]]].................................\trestraints\n",
      "_____________________________________________________________________\n",
      "[[[[[[...(((((((.((....))(((((]]]]]]....(((..........)))))))).)))))))\ttop-1_consensus\n",
      "=====================================================================\n",
      "[[[[[[...(((((((.((....))(((((]]]]]]....(((..........)))))))).)))))))\t#1\t247.294\t494.587\t0.5\tbppH2,bppE2\n",
      ".........(((((((.((....))(((((......((..((....))))......))))).)))))))\t#2\t161.359\t322.717\t0.5\tbppH1,bppE1\n",
      ".........(((((((.((....))(((((......(((((...))).))......))))).)))))))\t#3\t151.923\t303.846\t0.5\tbppN\n",
      "[[[[[[...((((((((((.......))).]]]]]]..(((((..........)))))....)))))))\t#4\t245.103\t490.206\t0.5\tdefG1,defG2,bppG1\n",
      "[[[[[[...(((((((.((....))((...]]]]]]..(((((..........))))).)).)))))))\t#5\t237.156\t474.312\t0.5\tdefE,defH\n",
      ">Twister ribozyme with reference\n",
      "GAAAUAAUGCUACCAGACUGCACAAAAAGUCUGCCCGUUCCAAGUCGGGAUGAAAGCAGAGGAUUUC\n",
      "((((...(((({{((((((........))))))(((..[[[..}}.))).....))))..]]]))))\treference\t173.386\t346.771\t0.5\n",
      "___________________________________________________________________\n",
      "(((((..((((..((((((........))))))((((........)))).....))))....)))))\ttop-1_consensus\tTP=17,FP=2,FN=5,FS=0.829,PR=0.895,RC=0.773\n",
      "===================================================================\n",
      "(((((..((((..((((((........))))))((((........)))).....))))....)))))\t#1\t168.949\t337.898\t0.5\tdefG1,defG2,bppN,bppH1,bppH2,bppE1,bppE2,bppG1,bppG2\tTP=17,FP=2,FN=5,FS=0.829,PR=0.895,RC=0.773,RK=1\n",
      "(((((..((((..((((((........))))))..((((((.....))))))..))))....)))))\t#2\t149.854\t299.707\t0.5\tdefG2,defN,bppG1,bppG2\n",
      "(((((.......((...((((............((((........))))......)))).)))))))\t#3\t139.662\t279.323\t0.5\tdefG1\n",
      "(((((..(((.........))).......(((((.((((((.....))))))...)))))..)))))\t#4\t134.572\t269.144\t0.5\tdefG1,defG2\n",
      "(((((..(((.........))).......((((((((........))).......)))))..)))))\t#5\t132.117\t264.233\t0.5\tdefG1\n",
      ">5UD5 [70],1.C.G.1.:1.C.C.7.,1.C.U.9.:1.C.U.15.,1.C.G.18.:1.C.G.47.,1.C.C.49.:1.C.C.74. with reference\n",
      "GGAAACCUGAUCAUGUAGAUCGAAUGGACUCUAAAUCCGUUCAGCCGGGUUAGAUUCCCGGGGUUUCCGC\n",
      "(((((((.((((...[.))))(((((((.......)))))))..(((((..]....))))))))))))..\treference\t252.505\t505.01\t0.5\n",
      "______________________________________________________________________\n",
      "(((((((.((((.....))))(((((((.......)))))))..(((((.......))))))))))))..\ttop-1_consensus\tTP=23,FP=0,FN=1,FS=0.979,PR=1.0,RC=0.958\n",
      "======================================================================\n",
      "(((((((.((((.....))))(((((((.......)))))))..(((((.......))))))))))))..\t#1\t251.509\t503.018\t0.5\tdefG1,defG2,defN,bppN,bppH1,bppH2,bppE1,bppE2,bppG1,bppG2\tTP=23,FP=0,FN=1,FS=0.979,PR=1.0,RC=0.958,RK=1\n",
      "((((((((((((.....)))))((((((.......))))))...(((((.......))))))))))))..\t#2\t227.718\t455.436\t0.5\tbppG2\n",
      "((((((((((((.....))))(((((((.......)))))))...((((.......))))))))))))..\t#3\t222.316\t444.631\t0.5\tdefG1,defG2,defE,defH,bppG1,bppG2\n",
      "((((((((((((.....))))....(((.(((.((((((......))))))))).)))..))))))))..\t#4\t194.648\t389.295\t0.5\tdefG2\n",
      "((((((((((((.....))))((((.....((.((((((......))))))))))))...))))))))..\t#5\t186.095\t372.189\t0.5\tdefG2\n",
      ">External loop 2\n",
      "CCAAAAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA;AAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCAAAAGG\n",
      "_____________________________________________________________________________\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "((....))..............................;..............................((....))\ttop-1_consensus\n",
      "=============================================================================\n",
      "((....))..............................;..............................((....))\t#1\t34.297\t68.594\t0.5\tbppN,bppH1,bppH2,bppE1,bppE2\n",
      "((....((..............................;..............................))....))\t#2\t34.297\t68.594\t0.5\tdefN,defE\n",
      "......................................;......................................\t#3\t0.0\t0\t0.5\tdefG1,defG2,defH,bppG1,bppG2\n",
      ">Aligned sequences (un-align -> predict -> re-align)\n",
      "UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGU-GGUCCGACCUGGG---CAU-CCGAA-GGAGGACGG-AC--GUC-C--ACUC--GG--AUGGCUAAGGGAGUGCCGGC\n",
      "___________________________________________________________________________________________________________________\n",
      "....((((((((((.....))......).(((((.((..((((((..((((...(.(.(((.........))).)...))).)..).))..))..)).))...))))))))))))\ttop-1_consensus\n",
      "===================================================================================================================\n",
      "....((((((((((.....))......).(((((.((..((((((..((((...(.(.(((.........))).)...))).)..).))..))..)).))...))))))))))))\t#1\t308.529\t617.058\t0.5\tbppN,bppG1\n",
      "....((((((((((.....)).........((((.((..((((((..((((...(.(.(((.........))).)...))).)..).))..))..)).))...))))))))))))\t#2\t276.015\t552.03\t0.5\tbppH1,bppE1\n",
      "....((((((((((.....)).........((((......(((((....((...(.(.(((.........))).)...)))......))..))..).......))))))))))))\t#3\t250.826\t501.653\t0.5\tbppH2,bppE2\n",
      "....((((((((((.....))......).(((((.((.((((((.(((......[[[.[[[[....))).))).))......)..))]]..]]..]]].....))))))))))))\t#4\t372.035\t744.07\t0.5\tdefG1\n",
      "....((((((((((.....))......).(((((....(((...))).......(((.((((.....((((.......))).)....))..))..))).....))))))))))))\t#5\t325.923\t651.847\t0.5\tdefN\n",
      ">Aligned sequences (un-align -> predict -> re-align)\n",
      "UCGGGUCGGCAUGGCAUCUCC------ACCUCCUCGC-GGUCCGACCUGGG---CAU-CCGAA-GGAGG-ACGCAC--GUC-C--ACUC--GG--AUGGCUAAGGGAGAGCCACU\n",
      "___________________________________________________________________________________________________________________\n",
      "(((((((((..[[[[.[[[[[.......[[[[[[.......)))))))))....(((.((((].]]]]].((......)).......))..))..)))......]]]]]]]]]..\ttop-1_consensus\n",
      "===================================================================================================================\n",
      "(((((((((..[[[[.[[[[[.......[[[[[[.......)))))))))....(((.((((].]]]]].((......)).......))..))..)))......]]]]]]]]]..\t#1\t375.223\t750.447\t0.5\tbppH1,bppH2,bppE1,bppE2\n",
      "(((((((((....((....................))....)))))))))....(((.((((.....((.((......))).)....))..))..))).....((.....))...\t#2\t275.905\t551.811\t0.5\tbppN\n",
      "(((((((((..[[[[.[[[[[.........[[[[.......)))))))))....(((.((((].]]]((.((......))).)....))..))..)))......]]]]]]]]]..\t#3\t362.74\t725.48\t0.5\tbppG1,bppG2\n",
      "(((((((((.......[[[[[.......[[[[[[.......)))))))))....(((.((((].]]]]].((......)).......))..))..)))((....]]]]]))....\t#4\t350.633\t701.266\t0.5\tdefE\n",
      "(((((((((.......[[[[[.......[[[[[[.......)))))))))....(((.((((].]]]]]..................))..))..)))((....]]]]]))....\t#5\t341.564\t683.127\t0.5\tdefH\n",
      ">SAM riboswitch with reference\n",
      "GUUCUUAUCAAGAGAAGCAGAGGGACUGGCCCGACGAAGCUUCAGCAACCGGUGUAAUGGCGAAAGCCAUGACCAAGGUGCUAAAUCCAGCAAGCUCGAACAGCUUGGAAGAUAAGAACA\n",
      "(((((((((....(((((...(((.[[[[)))......)))))(((..(((((...(((((....))))).)))..)).)))...(]]]](((((.......)))))..)))))))))).\treference\t378.218\t756.436\t0.5\n",
      "________________________________________________________________________________________________________________________\n",
      "(((((((((....(((((...(((.[[[[)))......)))))((((.((......(((((....)))))......))))))....]]]]((((((.....))))))...))))))))).\ttop-1_consensus\tTP=36,FP=2,FN=4,FS=0.923,PR=0.947,RC=0.9\n",
      "========================================================================================================================\n",
      "(((((((((....(((((...(((.[[[[)))......)))))((((.((......(((((....)))))......))))))....]]]]((((((.....))))))...))))))))).\t#1\t369.537\t739.074\t0.5\tbppH2,bppE2\tTP=36,FP=2,FN=4,FS=0.923,PR=0.947,RC=0.9,RK=1\n",
      "(((((((((....(((((...(((.....)))......)))))((((.(((((...(((((....))))).)))..))))))...((...((((((.....)))))))).))))))))).\t#2\t359.835\t719.669\t0.5\tdefN,bppN,bppH1,bppE1\n",
      "(((((((((....(((((...(((.....)))......)))))((((.(((((...(((((....))))).)))..))))))........((((((.....))))))...))))))))).\t#3\t350.765\t701.53\t0.5\tdefG1,bppG1,bppG2\n",
      "(((((((((....(((((...(((.....)))......)))))(((.((((((...(((((....))))).)))..))))))........((((((.....))))))...))))))))).\t#4\t350.083\t700.166\t0.5\tdefG1,bppG1,bppG2\n",
      "(((((((((....(((((...(((.....)))......)))))(((..........(((((....))))).........)))........((((((.....))))))...))))))))).\t#5\t304.15\t608.299\t0.5\tdefE\n",
      ">SAM riboswitch with reference and reactivities\n",
      "GUUCUUAUCAAGAGAAGCAGAGGGACUGGCCCGACGAAGCUUCAGCAACCGGUGUAAUGGCGAAAGCCAUGACCAAGGUGCUAAAUCCAGCAAGCUCGAACAGCUUGGAAGAUAAGAACA\n",
      "+++++++++++++++++++++___#_______++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\n",
      "(((((((((....(((((...(((.[[[[)))......)))))(((..(((((...(((((....))))).)))..)).)))...(]]]](((((.......)))))..)))))))))).\treference\t389.565\t756.436\t0.515\n",
      "________________________________________________________________________________________________________________________\n",
      "(((((((((....(((((...(((.....)))......)))))((((.(((((...(((((....))))).)))..))))))...((...((((((.....)))))))).))))))))).\ttop-1_consensus\tTP=35,FP=4,FN=5,FS=0.886,PR=0.897,RC=0.875\n",
      "========================================================================================================================\n",
      "(((((((((....(((((...(((.....)))......)))))((((.(((((...(((((....))))).)))..))))))...((...((((((.....)))))))).))))))))).\t#1\t352.638\t719.669\t0.49\tdefN,bppN,bppH1,bppE1\n",
      "(((((((((....(((((...(((.[[[[)))......)))))((((.........(((((....)))))........))))....]]]]((((((.....))))))...))))))))).\t#2\t367.659\t704.777\t0.522\tbppH2,bppE2\n",
      "(((((((((....(((((...(((.[[[[)))......)))))((((.(((((...(((((....))))).)))..))))))....]]]]((((((.....))))))...))))))))).\t#3\t402.97\t785.007\t0.513\tdefG1,bppG1\tTP=39,FP=2,FN=1,FS=0.963,PR=0.951,RC=0.975,RK=3\n",
      "(((((((((....(((((...(((.[[[[)))......)))))(((.((((((...(((((....))))).)))..))))))....]]]]((((((.....))))))...))))))))).\t#4\t402.27\t783.644\t0.513\tdefG1,bppG1\n",
      "(((((((((....(((((...(((.[[[[)))......)))))(((.(((...((.(((((....))))).))...))))))....]]]]((((((.....))))))...))))))))).\t#5\t389.262\t755.849\t0.515\tbppG1\n"
     ]
    }
   ],
   "source": [
    "SQUARNA.Predict(inputfile = \"examples/seq_input.fas\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2886a598-513f-47d6-8c46-8bf5d62173a8",
   "metadata": {},
   "source": [
    "## Alignment mode, printing the result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "2223f58f-6383-42de-9283-8e60ca23ceb7",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\n",
      "...................................................................................................................\trestraints\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\n",
      "___________________________________________________________________________________________________________________\n",
      "(((((((((..[[[[.[[[[[......((......[[..)))))))))))....((((((((..(((............)).)....))..)).))))]]....]]]]]]]]]..\tStep-1\t0.5\tTP=27,FP=6,FN=4,FS=0.844,PR=0.818,RC=0.871\n",
      "(((((((((..[[[[.[[[[[......(((........))))))))))))((..((((((((..(((............)).)....))..)).))))))....]]]]]]]]]..\tStep-2\t0.5\tTP=28,FP=6,FN=3,FS=0.862,PR=0.824,RC=0.903\n",
      "(((((((((..[[[[.[[[[[......(((.....[[.))))))))))))....((((((((..(((............)).)....))..)).))))]]....]]]]]]]]]..\tStep-3(u)\t0.5\tTP=28,FP=6,FN=3,FS=0.862,PR=0.824,RC=0.903\n"
     ]
    }
   ],
   "source": [
    "SQUARNA.Predict(inputfile = \"examples/ali_input.afa\", alignment = True)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7d1a14a6-7705-4d1b-a127-209c597eb78c",
   "metadata": {},
   "source": [
    "## Alignment mode, verbose output, writing the result to a file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "e8e08c4b-d1a8-44e3-ba41-698d9441b78c",
   "metadata": {},
   "outputs": [],
   "source": [
    "outpfile = \"demo_ali.txt\"\n",
    "\n",
    "with open(outpfile,'w') as file:\n",
    "    SQUARNA.Predict(inputfile = \"examples/ali_input.afa\", \n",
    "                    alignment = True, verbose = True, write_to = file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "e9fef896-05fd-419a-a60f-eae939ee575f",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">Step 1, Iteration 1\r\n",
      ">Conserved base pairs (one by one)\r\n",
      "............................................................(...........................)..........................\t607.5\r\n",
      ".(..............................................)..................................................................\t606.25\r\n",
      "..(............................................)...................................................................\t606.25\r\n",
      "...(..........................................)....................................................................\t606.25\r\n",
      "....(........................................).....................................................................\t606.25\r\n",
      ".....(......................................)......................................................................\t606.25\r\n",
      ".......(..................................)........................................................................\t605.0\r\n",
      "........(................................).........................................................................\t605.0\r\n",
      "......(....................................).......................................................................\t598.5\r\n",
      "..........................................................(.................................)......................\t585.75\r\n",
      ".................(.........................................................................................).......\t571.5\r\n",
      "..................(.......................................................................................)........\t571.5\r\n",
      "...........................................................(...............................).......................\t570.0\r\n",
      "................(...........................................................................................)......\t548.0\r\n",
      "............(..................................................................................................)...\t524.5\r\n",
      ".............(................................................................................................)....\t524.5\r\n",
      "..............(..............................................................................................).....\t509.5\r\n",
      "...........(....................................................................................................)..\t497.75\r\n",
      ".............................................................(.........................)...........................\t495.75\r\n",
      "................................................................(.................)................................\t469.25\r\n",
      ".................................................................(..............)..................................\t469.25\r\n",
      "..................................................................(............)...................................\t469.25\r\n",
      "................................(...............................)..................................................\t456.25\r\n",
      ".......(............................)..............................................................................\t455.5\r\n",
      "..............................(...................................)................................................\t450.0\r\n",
      "...............................(.................................).................................................\t450.0\r\n",
      "......................................................(..........................................).................\t439.25\r\n",
      ".......................................................(........................................)..................\t439.25\r\n",
      "........................................................(......................................)...................\t439.25\r\n",
      ".............................(.....................................)...............................................\t436.0\r\n",
      "..............(...................................)................................................................\t426.5\r\n",
      "................(................................).................................................................\t361.5\r\n",
      ".................(..............................)..................................................................\t361.5\r\n",
      "...........................(..................)....................................................................\t361.5\r\n",
      "............................(................).....................................................................\t361.5\r\n",
      ".............................(..............)......................................................................\t361.5\r\n",
      "..................(............................)...................................................................\t342.0\r\n",
      "..................................(.........................)......................................................\t331.75\r\n",
      ".......(......................................)....................................................................\t322.0\r\n",
      "........(....................................).....................................................................\t322.0\r\n",
      "...........(...........................................................)...........................................\t317.25\r\n",
      "............(.........................................................)............................................\t317.25\r\n",
      "...................................(.......................).......................................................\t316.75\r\n",
      ".............................(.............................................................................).......\t312.25\r\n",
      ".............................(..................................)..................................................\t308.0\r\n",
      "...........................(............)..........................................................................\t303.0\r\n",
      "............................(..........)...........................................................................\t303.0\r\n",
      ".............................(........)............................................................................\t303.0\r\n",
      "............................(....................................).................................................\t302.75\r\n",
      "................(.................................................)................................................\t299.0\r\n",
      ".................(...............................................).................................................\t299.0\r\n",
      ".................................................(..............................)..................................\t295.0\r\n",
      "..................................................(............................)...................................\t295.0\r\n",
      "(................................................).................................................................\t292.5\r\n",
      ".............(......................................................)..............................................\t290.0\r\n",
      "................................................(.................................)................................\t289.5\r\n",
      "..............(....................................................)...............................................\t287.0\r\n",
      "..........(.............................................................)..........................................\t281.25\r\n",
      "..(..........................).....................................................................................\t273.0\r\n",
      "...(........................)......................................................................................\t273.0\r\n",
      "............................(.....................................................................)................\t273.0\r\n",
      ".............................(...................................................................).................\t273.0\r\n",
      ".......(.......................................................................................................)...\t267.5\r\n",
      ".................................(...........................).....................................................\t267.5\r\n",
      "...(......................................................)........................................................\t265.75\r\n",
      "................................(..................................)...............................................\t262.25\r\n",
      ".................................................(.............................................................)...\t260.75\r\n",
      "................(......................)...........................................................................\t259.25\r\n",
      ".................(....................)............................................................................\t259.25\r\n",
      ".........(.................................................................).......................................\t256.5\r\n",
      "..........................................(........................)...............................................\t253.5\r\n",
      ".(..........................................................)......................................................\t252.75\r\n",
      "..(........................................................).......................................................\t252.75\r\n",
      "...(......................................)........................................................................\t252.75\r\n",
      "....(....................................).........................................................................\t252.75\r\n",
      "...(....................................)..........................................................................\t250.75\r\n",
      "....(..................................)...........................................................................\t250.75\r\n",
      ".....(................................)............................................................................\t250.75\r\n",
      "......(..............................).............................................................................\t250.75\r\n",
      "...................................................................(...........................................)...\t249.0\r\n",
      "...................................................................(..............)................................\t248.5\r\n",
      ".......................................................................(...................).......................\t244.75\r\n",
      ".....(...........................................).................................................................\t243.0\r\n",
      "............................(.....................)................................................................\t242.0\r\n",
      ".............................(...................).................................................................\t242.0\r\n",
      "..............................(.................)..................................................................\t242.0\r\n",
      "...........................(........)..............................................................................\t241.0\r\n",
      "............................(......)...............................................................................\t241.0\r\n",
      "..................................................................................(........................).......\t240.75\r\n",
      ".......................................(...................................).......................................\t238.5\r\n",
      "..............................................(.............................................)......................\t236.75\r\n",
      "........................................................................(...............)..........................\t236.25\r\n",
      "..................................................................(....................)...........................\t235.5\r\n",
      "..............................(..............................).....................................................\t234.0\r\n",
      ".................................(...............................).................................................\t233.75\r\n",
      "........................................(.........)................................................................\t233.25\r\n",
      "..................(..................).............................................................................\t231.25\r\n",
      "(...........................................)......................................................................\t231.0\r\n",
      ".(.........................................).......................................................................\t231.0\r\n",
      "..(.......................................)........................................................................\t231.0\r\n",
      "...(.....................................).........................................................................\t231.0\r\n",
      "....(...................................)..........................................................................\t231.0\r\n",
      ".....(.................................)...........................................................................\t231.0\r\n",
      "......(...............................)............................................................................\t231.0\r\n",
      "..............(..................................................................................).................\t229.75\r\n",
      "............................................(..................................)...................................\t228.0\r\n",
      "..................................(.............................)..................................................\t226.25\r\n",
      "....................................................................(......).......................................\t226.25\r\n",
      "....(............................................).................................................................\t224.5\r\n",
      ".....(..........................................)..................................................................\t224.5\r\n",
      "......(........................................)...................................................................\t224.5\r\n",
      "........(..........................)...............................................................................\t224.5\r\n",
      "...............................................(...........................................).......................\t223.75\r\n",
      "...........................................................................(..................................)....\t223.5\r\n",
      "...............................(..................)................................................................\t222.75\r\n",
      "................................(................).................................................................\t222.75\r\n",
      ".................................(..............)..................................................................\t222.75\r\n",
      "................................................(.......................................)..........................\t221.5\r\n",
      ".................................................(.....................................)...........................\t221.5\r\n",
      "...................(.....................................................................................).........\t219.25\r\n",
      "....................(...................................................................................)..........\t219.25\r\n",
      "........................................................................(......................................)...\t219.0\r\n",
      "...(...........................................................................................................)...\t217.75\r\n",
      "...............................(............................................................)......................\t217.25\r\n",
      "..............................(.............................................................................)......\t217.0\r\n",
      "...............................(............................)......................................................\t217.0\r\n",
      "...............................(...........................................................................).......\t217.0\r\n",
      "...............................................................................(.............................).....\t216.5\r\n",
      "................................................................................(...........................)......\t216.5\r\n",
      "............................(.......................................)..............................................\t215.5\r\n",
      "......................................(....................).......................................................\t215.25\r\n",
      ".......................................(..................)........................................................\t215.25\r\n",
      "............................(....................).................................................................\t214.5\r\n",
      ".............................(..................)..................................................................\t214.5\r\n",
      ".........................................(.........................................................)...............\t210.5\r\n",
      "..........................................(.......................................................)................\t210.5\r\n",
      "...................................(....................................................)..........................\t210.0\r\n",
      "...................................(...............................................................)...............\t210.0\r\n",
      "..(...............................)................................................................................\t209.75\r\n",
      "...(.............................).................................................................................\t209.75\r\n",
      "...................................................................(.......).......................................\t209.0\r\n",
      "...............................(.......)...........................................................................\t208.0\r\n",
      "...............................(..................................................................)................\t208.0\r\n",
      "................................(.....)............................................................................\t208.0\r\n",
      "................................(................................................................).................\t208.0\r\n",
      "..........................................(......).................................................................\t208.0\r\n",
      ".................................................................(......................)..........................\t208.0\r\n",
      "..............(...................................................................................)................\t207.0\r\n",
      ".............................(...............................................................................).....\t206.5\r\n",
      ".................................................(..............................................................)..\t206.0\r\n",
      "..................................................(............................................................)...\t206.0\r\n",
      "................................(.................)................................................................\t205.5\r\n",
      ".................................(...............).................................................................\t205.5\r\n",
      "..................................(.............)..................................................................\t205.5\r\n",
      "................................................(................................................................).\t204.75\r\n",
      ".........................................................(....................................)....................\t204.25\r\n",
      "....................................(.............................................................)................\t203.5\r\n",
      "...............................................................................(............................)......\t203.5\r\n",
      "................................................................................(..........................).......\t203.5\r\n",
      ".................................(................................)................................................\t202.75\r\n",
      "..................................(..............................).................................................\t202.75\r\n",
      "..................................................(................................................)...............\t202.5\r\n",
      "................................(..........................................................).......................\t201.5\r\n",
      ".................................................(.........).......................................................\t201.5\r\n",
      "..................................................(.......)........................................................\t201.5\r\n",
      "..........................................................(.......................................)................\t201.25\r\n",
      "...........................................................(.....................................).................\t201.25\r\n",
      "............................................................(...................................)..................\t201.25\r\n",
      "...........................................(.....................................................).................\t200.75\r\n",
      "............................................(...................................................)..................\t200.75\r\n",
      "......................................(........)...................................................................\t200.0\r\n",
      ".......................................(......)....................................................................\t200.0\r\n",
      "................................................................................(.................)................\t198.0\r\n",
      "..................................................................................(..............).................\t198.0\r\n",
      ".(.................................)...............................................................................\t197.75\r\n",
      "......................................(...........................................)................................\t197.75\r\n",
      ".......................................(........................................)..................................\t197.75\r\n",
      ".....(......................................................................................................)......\t196.25\r\n",
      "................(...........................)......................................................................\t196.0\r\n",
      "...................................(...........)...................................................................\t195.75\r\n",
      "..............................(...........................................................................)........\t195.25\r\n",
      "...............................(.........................................................................).........\t195.25\r\n",
      "................................(.......................................................................)..........\t195.25\r\n",
      ".................................(.....................................................................)...........\t195.25\r\n",
      "......(....................................................).......................................................\t195.0\r\n",
      ".......(..................................................)........................................................\t195.0\r\n",
      ".....(.................................................)...........................................................\t194.75\r\n",
      ".......................................(...........................................................)...............\t193.5\r\n",
      "........................................(.........................................................)................\t193.5\r\n",
      "..(.............................)..................................................................................\t193.0\r\n",
      "...(...........................)...................................................................................\t193.0\r\n",
      "...................................(......)........................................................................\t193.0\r\n",
      ".......................................(........................................................)..................\t191.25\r\n",
      "........................................(......................................................)...................\t191.25\r\n",
      "...................................................................(..........)....................................\t191.0\r\n",
      "......................................................................(.....................)......................\t188.75\r\n",
      "..............................................(.................)..................................................\t188.5\r\n",
      "................................(.................................)................................................\t188.25\r\n",
      ".................................(..........................................................)......................\t187.75\r\n",
      "............(.........................................)............................................................\t187.5\r\n",
      "..............................(.....................................)..............................................\t185.75\r\n",
      "...............................(...................................)...............................................\t185.75\r\n",
      ".................................................................(...............................................).\t185.25\r\n",
      ".................................................(................................)................................\t185.0\r\n",
      "..................................................(.............................)..................................\t185.0\r\n",
      ".................................................................................................(.............)...\t184.75\r\n",
      "..................................................................................................(...........)....\t184.75\r\n",
      ".....(............................................................)................................................\t184.0\r\n",
      ".................................................................(................)................................\t183.75\r\n",
      "..............(........................)...........................................................................\t182.0\r\n",
      "..................................(........................................................).......................\t181.25\r\n",
      "......................................................(....................................................).......\t181.25\r\n",
      ".......................................................(..................................................)........\t181.25\r\n",
      "........................................................(.............................................)............\t181.25\r\n",
      ".........................................................(...........................................).............\t181.25\r\n",
      "............(......................................)...............................................................\t181.0\r\n",
      ".............(....................................)................................................................\t181.0\r\n",
      "............................................(..........................................)...........................\t181.0\r\n",
      "..........................................................(.........................................)..............\t180.25\r\n",
      ".(......................................................................)..........................................\t179.0\r\n",
      "........(.....................................................................................................)....\t176.5\r\n",
      ".............................(....................)................................................................\t176.0\r\n",
      "..............................(..................).................................................................\t176.0\r\n",
      "..............................(...................)................................................................\t176.0\r\n",
      "...............................(................)..................................................................\t176.0\r\n",
      "...............................(.................).................................................................\t176.0\r\n",
      "................................(...............)..................................................................\t176.0\r\n",
      "....................................................................(...........)..................................\t175.75\r\n",
      "...(...............................................)...............................................................\t175.5\r\n",
      "....(......................).......................................................................................\t175.5\r\n",
      "....(.............................................)................................................................\t175.5\r\n",
      ".....(......................................................)......................................................\t175.5\r\n",
      "......(......................).....................................................................................\t175.5\r\n",
      ".......(....................)......................................................................................\t175.5\r\n",
      "........(..................).......................................................................................\t175.5\r\n",
      "...........................(.......................................................................)...............\t175.5\r\n",
      "....(...................................................)..........................................................\t175.25\r\n",
      "..........................................(................................................).......................\t174.5\r\n",
      "...........................................(............................................)..........................\t174.5\r\n",
      ".................................................(........)........................................................\t174.0\r\n",
      ".......(...................................................................).......................................\t173.25\r\n",
      ".............................................(................................)....................................\t173.25\r\n",
      "...............................................................................(..................)................\t173.25\r\n",
      "................................................................................(................).................\t173.25\r\n",
      "....................................................................(........................).....................\t173.0\r\n",
      "................................................................................................(...............)..\t173.0\r\n",
      ".........................................(.........)...............................................................\t172.25\r\n",
      "..........................................(.......)................................................................\t172.25\r\n",
      "............................................(..............).......................................................\t172.25\r\n",
      ".............................................(............)........................................................\t172.25\r\n",
      "..................................................................(.............................................)..\t172.25\r\n",
      "............(...................................................................)..................................\t170.0\r\n",
      "...........(...............................).......................................................................\t169.75\r\n",
      "............(.............................)........................................................................\t169.75\r\n",
      ".............(...........................).........................................................................\t169.75\r\n",
      ".......(........................................................................)..................................\t168.0\r\n",
      ".............................(....................................)................................................\t168.0\r\n",
      "..............................(..................................).................................................\t168.0\r\n",
      "................(................................................).................................................\t167.75\r\n",
      "...................................................................................................(.........).....\t167.75\r\n",
      "..................................................................(.............)..................................\t167.5\r\n",
      "...................................................................(...........)...................................\t167.5\r\n",
      "...(...............................................................................................)...............\t167.25\r\n",
      "....(.............................................................................................)................\t167.25\r\n",
      ".....(...........................................................................................).................\t167.25\r\n",
      "......(.........................................................................................)..................\t167.25\r\n",
      "............................(...............................................................)......................\t167.0\r\n",
      ".............................(.............................................................).......................\t167.0\r\n",
      "..........................................................(........)...............................................\t166.75\r\n",
      "................................................................(................................................).\t166.5\r\n",
      "........................................(...........................................................)..............\t165.75\r\n",
      ".........................................(..................................................)......................\t165.75\r\n",
      "...........................................(.....).................................................................\t165.75\r\n",
      "...........................................(................)......................................................\t165.75\r\n",
      "........................................................................(..........................)...............\t165.0\r\n",
      ".......................................................................................(....................)......\t164.75\r\n",
      "................................(..........................................................................).......\t162.75\r\n",
      "...........................................................(............)..........................................\t162.5\r\n",
      "............................................................(..........)...........................................\t162.5\r\n",
      ".................................................................(..............................................)..\t162.5\r\n",
      "..................................................................(............................................)...\t162.5\r\n",
      ".................(..............................................)..................................................\t162.25\r\n",
      "................................................................(......................)...........................\t162.25\r\n",
      "....(...........................)..................................................................................\t162.0\r\n",
      "..............(..................................).................................................................\t161.5\r\n",
      "................(...............................)..................................................................\t161.5\r\n",
      "............................................(..........................)...........................................\t161.5\r\n",
      ".............................................(........................)............................................\t161.5\r\n",
      ".........................................................(..........)..............................................\t161.5\r\n",
      "...............................................(............)......................................................\t161.0\r\n",
      "................................................(..........).......................................................\t161.0\r\n",
      "...................................................................(............)..................................\t160.25\r\n",
      "......(................................................................)...........................................\t159.5\r\n",
      ".......(..............................................................)............................................\t159.5\r\n",
      "...........................(.......................)...............................................................\t159.5\r\n",
      "..(....................................................................)...........................................\t159.25\r\n",
      ".................................(..........................................................................)......\t159.0\r\n",
      "..................................(........................................................................).......\t159.0\r\n",
      ".........................................(..........................)..............................................\t158.0\r\n",
      ".......(.........................).................................................................................\t157.25\r\n",
      "................................................(...............................)..................................\t157.25\r\n",
      ".................................................(.............................)...................................\t157.25\r\n",
      "...............................(................................)..................................................\t157.0\r\n",
      "................................................................(.......................)..........................\t157.0\r\n",
      ".................................................................(.....................)...........................\t157.0\r\n",
      "................................(................................).................................................\t155.75\r\n",
      ".................................(..............................)..................................................\t155.75\r\n",
      "..(...............................................................................)................................\t155.0\r\n",
      "...(............................................................................)..................................\t155.0\r\n",
      "..............(...................................................)................................................\t155.0\r\n",
      ".......................................(..............................)............................................\t154.25\r\n",
      ".................................................................(.............)...................................\t154.25\r\n",
      "........................................................................................(..................).......\t154.25\r\n",
      "...........................................................................................................(.....).\t154.25\r\n",
      "............................(......................................)...............................................\t154.0\r\n",
      "......................................(................................)...........................................\t154.0\r\n",
      "...........................................(............................)..........................................\t154.0\r\n",
      "................(...................................................)..............................................\t153.5\r\n",
      ".................(.................................................)...............................................\t153.5\r\n",
      "..................(...............................................)................................................\t153.5\r\n",
      "...................(.............................................).................................................\t153.5\r\n",
      "....................(...........................................)..................................................\t153.5\r\n",
      "..................................................(...............................)................................\t153.5\r\n",
      ".(................)................................................................................................\t153.0\r\n",
      "..(..............).................................................................................................\t153.0\r\n",
      "...(............)..................................................................................................\t153.0\r\n",
      "................................................(..............................................................)...\t153.0\r\n",
      ".................................................(............................................................)....\t153.0\r\n",
      ".......................................................................(............................)..............\t153.0\r\n",
      "...............................................................................(...............)...................\t152.5\r\n",
      "...(.........).....................................................................................................\t152.25\r\n",
      "....(.......)......................................................................................................\t152.25\r\n",
      ".....(.....).......................................................................................................\t152.25\r\n",
      "......(...)........................................................................................................\t152.25\r\n",
      "...........(.....................................................................................................).\t152.25\r\n",
      "..................................(.....................................)..........................................\t151.25\r\n",
      "...................................(...................................)...........................................\t151.25\r\n",
      ".............(.....................................................)...............................................\t150.75\r\n",
      "...............................(....................................)..............................................\t150.5\r\n",
      "..................................................(...........................................................)....\t150.25\r\n",
      ".(..........................................)......................................................................\t148.75\r\n",
      "..(........................................).......................................................................\t148.75\r\n",
      "................................................................(...............)..................................\t148.75\r\n",
      "................................(............................................................................).....\t148.5\r\n",
      "....................................(.............)................................................................\t148.5\r\n",
      "..................................................(........................).......................................\t148.5\r\n",
      "..................................................................(...............)................................\t148.5\r\n",
      ">Conserved base pairs (assembled)\r\n",
      "((((((((({{[[[[.[[[[[......(([{[(<.<<.))))))))))))]...((((((((..(((]}..[}..}...)).)....))..)).))))>>]..>]]]]]]]]]..\r\n",
      ".{.[{{{{(..((([.[[[........[[[((((((}}}<A}<}]]]]]]]....{{{])))..)))>).))[..>...((.(.....].......<<a..}}...}))))>>..\r\n",
      "([[((<[[[..[A.{.{((........({<{<B.<B))))CD)])]]](((...a...A]]}..>}}}(..[{..)...)).).....b..]>..c.bad.......>>..}...\r\n",
      ".[[[[AA(A..{{{(.{(.........]]((BD<.a..a}B}]<<<CC)ab}......{.b...))(d{...]..[..>>[......)>..cc}...).(}......]>)]).}.\r\n",
      ".{{(<([[(.......[..........)B(AA<A}}..)))({.].{.BC>)....>.]((...}a<((.<][......[).).....b..}>..]))b].......aa..c>..\r\n",
      ".([{{<(A..).D.....)........((][[([B(..[[}}{{{{.)>))...<..(]]<...CB]C).}>...a...Ad.......b..b....}}}).....]]>a..c.c.\r\n",
      "..{({[C(....{.<.((A........[(<.{<[A)..[}BB}(<(.]]}D]...]..)c)...)aa[)..}...]....)......>(..>b....>>db......)...)...\r\n",
      "..([({<<....)....)..........((.AB]((..[[..)A{.][))C........}]...BD}{).>]a.....}...(....[b.......>)a.....b...]..c.d.\r\n",
      "..((.[.(............A.......)[B))({...({.(..<...]{(.......){]...ab[[)..>}......][.)....}....).....]}.......}...]...\r\n",
      ".(([.{.(.....[..............[<.{{)<<...A...))...(]]]............((}}...>>.......a.)....).........}(..........>)..).\r\n",
      "..[(.([....)..(.(...........<].[{(.....{..(.....])[.......[.....)))]...........(].].........>...}.)).......}.......\r\n",
      "...([.........[.)...........((.{(......]........)<).............}[[)............(.]....].........)]........(....>).\r\n",
      "...({........)..[............((<}(.....A........]))..............[)(>.a.........)...............................]..\r\n",
      "....[............(...........{..(...............<(]........).....)[)............]..........}...................>...\r\n",
      "...(.........(..................[.........(.....[{)........].....[.)...........]).}..........................].....\r\n",
      "...................(..........(.................[){..............)..............].}................................\r\n",
      "...............................(.................)(.............(...............).............................)....\r\n",
      "....................................(............[).......]........................................................\r\n",
      "...........................................(.....)(........................).......................................\r\n",
      "..............(..................................).................................................................\r\n",
      ".................................................(.............................)...................................\r\n",
      ".................................................(............................................................)....\r\n",
      ">Step 1, Iteration 2\r\n",
      ">Conserved base pairs (one by one)\r\n",
      ".(..............................................)..................................................................\t606.25\r\n",
      "..(............................................)...................................................................\t606.25\r\n",
      "...(..........................................)....................................................................\t606.25\r\n",
      "....(........................................).....................................................................\t606.25\r\n",
      ".....(......................................)......................................................................\t606.25\r\n",
      ".......(..................................)........................................................................\t605.0\r\n",
      "........(................................).........................................................................\t605.0\r\n",
      "......(....................................).......................................................................\t598.5\r\n",
      "............................................................(...........................)..........................\t555.75\r\n",
      ".................(.........................................................................................).......\t555.5\r\n",
      "..................(.......................................................................................)........\t555.5\r\n",
      "..........................................................(.................................)......................\t545.0\r\n",
      "...........................................................(...............................).......................\t545.0\r\n",
      "................(...........................................................................................)......\t532.0\r\n",
      "............(..................................................................................................)...\t516.0\r\n",
      ".............(................................................................................................)....\t516.0\r\n",
      "..............(..............................................................................................).....\t507.5\r\n",
      "...........(....................................................................................................)..\t489.25\r\n",
      ".............................................................(.........................)...........................\t444.0\r\n",
      "......................................................(..........................................).................\t439.25\r\n",
      ".......................................................(........................................)..................\t439.25\r\n",
      "........................................................(......................................)...................\t439.25\r\n",
      ".................................................................(..............)..................................\t424.0\r\n",
      "..................................................................(............)...................................\t424.0\r\n",
      "................................................................(.................)................................\t418.75\r\n",
      "(................................................).................................................................\t292.5\r\n",
      ".........................................................(....................................)....................\t204.25\r\n",
      "...................(.....................................................................................).........\t202.25\r\n",
      "....................(...................................................................................)..........\t202.25\r\n",
      "...........................(............)..........................................................................\t195.75\r\n",
      "............................(..........)...........................................................................\t195.75\r\n",
      "...................................(...............................................................)...............\t156.0\r\n",
      "....................................(.............................................................)................\t156.0\r\n",
      ">Conserved base pairs (assembled)\r\n",
      "(((((((((..[[[[.[[[[[......((......[[..)))))))))))....((((((((..(((............)).)....))..)).))))]]....]]]]]]]]]..\r\n",
      ">Step 1, Result\r\n",
      "(((((((((..[[[[.[[[[[......((......[[..)))))))))))....((((((((..(((............)).)....))..)).))))]]....]]]]]]]]]..\r\n",
      ">Step 2, Individuals\r\n",
      ">RF00094__AF425644_1_679_767\r\n",
      "AUGGCCGGCAUGGUC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGAA-GGGGA-CCG--U---CC-C----UC--GGUAAUGGCGAA---UGGGACCCA\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t357.576\t715.151\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((.......)...)).)....))..)).))))))......]]]]]]]..\ttop-1_consensus\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903\r\n",
      "===================================================================================================================\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((.......)...)).)....))..)).))))))......]]]]]]]..\t#1\t350.35\t700.7\t0.5\tali\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903,RK=1\r\n",
      ">RF00094__AF425645_1_687_774\r\n",
      "GUGGCCGGCAUGGUC-CCA--------GCCUCCCCGCUGGCGCCGGCUGGGCAACAUUCCGA--GGGGA-CCG--U---CC-C----UC--GGUAAUGGCGAA---UGGGACCCA\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t404.724\t809.449\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((.......)...)).)....))..)).))))))......]]]]]]]..\ttop-1_consensus\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903\r\n",
      "===================================================================================================================\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((.......)...)).)....))..)).))))))......]]]]]]]..\t#1\t395.81\t791.619\t0.5\tali\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903,RK=1\r\n",
      ">RF00094__AB037947_1_685_775\r\n",
      "GUGGCCGGCAUGGCC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACGAUCCGA--GGGGA-CUG--U-CCCU-C----UC-GAGAAUCGGCAAA---UGGGGCCCC\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t356.35\t712.7\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((.(((..((((..........))).)....)).)...))))))......]]]]]]]..\ttop-1_consensus\tTP=26,FP=5,FN=5,FS=0.839,PR=0.839,RC=0.839\r\n",
      "===================================================================================================================\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((.(((..((((..........))).)....)).)...))))))......]]]]]]]..\t#1\t395.545\t791.091\t0.5\tali\tTP=26,FP=5,FN=5,FS=0.839,PR=0.839,RC=0.839,RK=1\r\n",
      ">RF00094__AB037948_1_685_775\r\n",
      "GUGGCCGGCAUGGCC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACGAUCCGA--GGGGA-CUA--U-CCCU-C----UC-GAGAAUCGGCAAA---UGGGGCCCC\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t356.35\t712.7\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((.(((..((((..........))).)....)).)...))))))......]]]]]]]..\ttop-1_consensus\tTP=26,FP=5,FN=5,FS=0.839,PR=0.839,RC=0.839\r\n",
      "===================================================================================================================\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((.(((..((((..........))).)....)).)...))))))......]]]]]]]..\t#1\t395.545\t791.091\t0.5\tali\tTP=26,FP=5,FN=5,FS=0.839,PR=0.839,RC=0.839,RK=1\r\n",
      ">RF00094__X77627_1_679_767\r\n",
      "AUGGCCGGCAUGGUC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGAG-GGGGA-CCG--U---CC-C----UC--GGUAAUGGCGAA---UGGGACCCA\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t357.576\t715.151\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..(((((((((.(((........)...)).)....))..)).))))))......]]]]]]]..\ttop-1_consensus\tTP=25,FP=7,FN=6,FS=0.794,PR=0.781,RC=0.806\r\n",
      "===================================================================================================================\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..(((((((((.(((........)...)).)....))..)).))))))......]]]]]]]..\t#1\t395.81\t791.619\t0.5\tali\tTP=25,FP=7,FN=6,FS=0.794,PR=0.781,RC=0.806,RK=1\r\n",
      ">RF00094__L22063_1_691_781\r\n",
      "GUGGCCGGCAUGGCC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACGAUCCGA--GGGAG-CUA--C-UCCU-C----UC-GAGAAUCGGCAAA---UGGGGCCCC\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t360.632\t721.264\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((.(((..(((((......).).)).)....)).)...))))))......]]]]]]]..\ttop-1_consensus\tTP=27,FP=5,FN=4,FS=0.857,PR=0.844,RC=0.871\r\n",
      "===================================================================================================================\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((.(((..(((((......).).)).)....)).)...))))))......]]]]]]]..\t#1\t377.919\t755.839\t0.5\tali\tTP=27,FP=5,FN=4,FS=0.857,PR=0.844,RC=0.871,RK=1\r\n",
      ">RF00094__AJ309877_1_318_405\r\n",
      "GUGGCCGGCAUGGUC-CCA--------GCCUCCUCGUUGGCGCCGGCCGGGCAACAUUCCGA--GGGGA-CCG--U---CC-C----UC--GGUAAUGGCGAA---UGGGACCCA\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t441.883\t883.766\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((.......)...)).)....))..)).))))))......]]]]]]]..\ttop-1_consensus\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903\r\n",
      "===================================================================================================================\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((.......)...)).)....))..)).))))))......]]]]]]]..\t#1\t432.461\t864.923\t0.5\tali\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903,RK=1\r\n",
      ">RF00094__M84917_1_684_773\r\n",
      "GUGGCCGGCAUGGUC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGA--GGGGA-CCG--U-CCUC-C----UC--GGUAAUGGCGAA---UGGGACCCA\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t370.132\t740.263\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((..........))).)....))..)).))))))......]]]]]]]..\ttop-1_consensus\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903\r\n",
      "===================================================================================================================\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((..........))).)....))..)).))))))......]]]]]]]..\t#1\t395.81\t791.619\t0.5\tali\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903,RK=1\r\n",
      ">RF00094__X85253_1_682_769\r\n",
      "AUGGCCGGCAUGGUC-CCA--------GCCUCCUUCGUGGCGCCGGCUGGGCAACAUUCCGA--GGGGA-CCG--U---CC-C----UC--GGUAAUGGCGAA---UGGGACCCA\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t404.724\t809.449\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((.......)...)).)....))..)).))))))......]]]]]]]..\ttop-1_consensus\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903\r\n",
      "===================================================================================================================\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((.......)...)).)....))..)).))))))......]]]]]]]..\t#1\t395.81\t791.619\t0.5\tali\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903,RK=1\r\n",
      ">RF00094__U81988_1_679_767\r\n",
      "AUGGCCGGCAUGGUC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGA--GGGGA-CCG--C--CCC-C----UC--GGUAAUGGCGAA---UGGGACCCA\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t403.728\t807.456\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((..........))).)....))..)).))))))......]]]]]]]..\ttop-1_consensus\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903\r\n",
      "===================================================================================================================\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((..........))).)....))..)).))))))......]]]]]]]..\t#1\t434.472\t868.943\t0.5\tali\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903,RK=1\r\n",
      ">RF00094__AF209859_1_689_775\r\n",
      "-UGGCCGGCAUGGUC-CCA--------GCCUCCUCGUCGGCGCCGGCCGGGCAACAUUCCGA--GGGGA-CCG--U---CC-C----UC--GGUAAUGGCGAA---UGGGACCCA\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t441.883\t883.766\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((.......)...)).)....))..)).))))))......]]]]]]]..\ttop-1_consensus\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903\r\n",
      "===================================================================================================================\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((.......)...)).)....))..)).))))))......]]]]]]]..\t#1\t432.461\t864.923\t0.5\tali\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903,RK=1\r\n",
      ">RF00094__M28267_1_687_775\r\n",
      "AUGGCCGGCAUGGUC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGA--GGGGA-CCG--U--CCC-C----UC--GGUAAUGGCGAA---UGGGACGCA\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t376.089\t752.179\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((.[[[[[.[[[........(((........))))))))))).((..((((((((..(((((......)..))).)....))..)).))))))......]]]]]].]]\ttop-1_consensus\tTP=28,FP=6,FN=3,FS=0.862,PR=0.824,RC=0.903\r\n",
      "===================================================================================================================\r\n",
      ".((((((((.[[[[[.[[[........(((........))))))))))).((..((((((((..(((((......)..))).)....))..)).))))))......]]]]]].]]\t#1\t428.774\t857.549\t0.5\tali\tTP=28,FP=6,FN=3,FS=0.862,PR=0.824,RC=0.903,RK=1\r\n",
      ">RF00094__AF104263_1_681_769\r\n",
      "AUGGCCGGCAUGGUC-CCA--------GCCUCCCCGGUGGCGCCGGCUGGGCAACAUUCCGAA-GGGGA-CCG--U---CC-C----UC--GGUAAUGGCGAA---UGGGACCCA\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t357.576\t715.151\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((.......)...)).)....))..)).))))))......]]]]]]]..\ttop-1_consensus\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903\r\n",
      "===================================================================================================================\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((.......)...)).)....))..)).))))))......]]]]]]]..\t#1\t350.35\t700.7\t0.5\tali\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903,RK=1\r\n",
      ">RF00094__AF104264_1_691_778\r\n",
      "GUGGCCGGCAUGGUC-CCA--------GCCUCCCCCGUGGCGCCGGCUGGGCAACAUUCCGA--GGGGA-CCG--U---CC-C----UC--GGUAAUGGCGAA---UGGGACCCA\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t404.724\t809.449\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((.......)...)).)....))..)).))))))......]]]]]]]..\ttop-1_consensus\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903\r\n",
      "===================================================================================================================\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..((((.......)...)).)....))..)).))))))......]]]]]]]..\t#1\t395.81\t791.619\t0.5\tali\tTP=28,FP=4,FN=3,FS=0.889,PR=0.875,RC=0.903,RK=1\r\n",
      ">RF00094__M92448_1_681_769\r\n",
      "AUGGCCGGCAUGGUC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGA--AGGGA-CCG--U--CCC-U----UC--GGUAAUGGCGAA---UGGGACCCA\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t384.926\t769.853\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..(((((......)..))).)....))..)).))))))......]]]]]]]..\ttop-1_consensus\tTP=29,FP=4,FN=2,FS=0.906,PR=0.879,RC=0.935\r\n",
      "===================================================================================================================\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..(((((......)..))).)....))..)).))))))......]]]]]]]..\t#1\t425.495\t850.991\t0.5\tali\tTP=29,FP=4,FN=2,FS=0.906,PR=0.879,RC=0.935,RK=1\r\n",
      ">RF00094__X04451_1_684_772\r\n",
      "AUGGCCGGCAUGGUC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGA--GGGGA-CCG--U--CCC-C----UC--GGUAAUGGCGAA---UGGGACCCA\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t404.724\t809.449\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..(((((......)..))).)....))..)).))))))......]]]]]]]..\ttop-1_consensus\tTP=29,FP=4,FN=2,FS=0.906,PR=0.879,RC=0.935\r\n",
      "===================================================================================================================\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..(((((......)..))).)....))..)).))))))......]]]]]]]..\t#1\t448.34\t896.679\t0.5\tali\tTP=29,FP=4,FN=2,FS=0.906,PR=0.879,RC=0.935,RK=1\r\n",
      ">RF00094__AJ584845_1_918_825\r\n",
      "UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGC-GGUCCGACCUGGG---CAU-CCGAA-GGAGGACAGAAC--GUC-C--ACUC--GG--AUGGCUAAGGGAGAGCCAGU\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t297.132\t594.264\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))....(((.((((..(((]]].........)).)....))..))..)))......]]]]]]]]]..\ttop-1_consensus\tTP=27,FP=7,FN=3,FS=0.844,PR=0.794,RC=0.9\r\n",
      "===================================================================================================================\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))....(((.((((..(((]]].........)).)....))..))..)))......]]]]]]]]]..\t#1\t360.435\t720.87\t0.5\tali\tTP=27,FP=7,FN=3,FS=0.844,PR=0.794,RC=0.9,RK=1\r\n",
      ">RF00094__AJ309880_1_911_818\r\n",
      "UCGGGUCGGCAUGGCAUCUCC------ACCUCCUCGC-GGUCCGACCUGGG---CAUCCGUA--GGAGGACAG-AC--GUC-C----UACUCG-GAUGGCUAAGGGAGAGCCAGU\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t300.496\t600.992\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))....((((((((..(((]]].........)).)....))..)).))))......]]]]]]]]]..\ttop-1_consensus\tTP=28,FP=7,FN=3,FS=0.848,PR=0.8,RC=0.903\r\n",
      "===================================================================================================================\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))....((((((((..(((]]].........)).)....))..)).))))......]]]]]]]]]..\t#1\t363.799\t727.597\t0.5\tali\tTP=28,FP=7,FN=3,FS=0.848,PR=0.8,RC=0.903,RK=1\r\n",
      ">RF00094__EF514905_2_675_762\r\n",
      "GUGGCCGGCAUGGU--CCA--------GCCUACUCGCUGGCGCGGGCUGGGCAACAUUCCGA--GGGGA-CCC--G--UCC-C----UC--GGUAAUGGCGAA---UGGGACCCA\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t305.426\t610.853\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "...[[[[[[...((..(((........((((....]]]]]]..)))))))))..((((((((..((((..........))).)....))..)).))))........(((...)))\ttop-1_consensus\tTP=11,FP=19,FN=19,FS=0.367,PR=0.367,RC=0.367\r\n",
      "===================================================================================================================\r\n",
      "...[[[[[[...((..(((........((((....]]]]]]..)))))))))..((((((((..((((..........))).)....))..)).))))........(((...)))\t#1\t353.905\t707.81\t0.5\tali\tTP=11,FP=19,FN=19,FS=0.367,PR=0.367,RC=0.367,RK=1\r\n",
      ">RF00094__L22063_1_906_814\r\n",
      "UCGGGUCGGCAUGGGAUCUCC------ACCUCCUCGC-GGUCCGACCUGGG---CAU-CCGUAAGGAGA-GCG--UAGCUC-C---CUC--GG--AUGGCAAAGGGAGAUCCACC\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t261.772\t523.545\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "(((((((((....[[[[[[[[......(((........))))))))))))....(((.(((...((((..........))).).....)..))..)))......]]]]]]]]...\ttop-1_consensus\tTP=22,FP=8,FN=8,FS=0.733,PR=0.733,RC=0.733\r\n",
      "===================================================================================================================\r\n",
      "(((((((((....[[[[[[[[......(((........))))))))))))....(((.(((...((((..........))).).....)..))..)))......]]]]]]]]...\t#1\t369.248\t738.495\t0.5\tali\tTP=22,FP=8,FN=8,FS=0.733,PR=0.733,RC=0.733,RK=1\r\n",
      ">RF00094__AB221936_1_165_71\r\n",
      "UCGGGUCGGCAUGGCAUCUCC------ACCUCCUCGC-GGUCCGACCUGGG---CAU-CCGUA-GGAGG-ACGAAC--GUC-CUACCUC--GG--AUGGCUAAGGGAGAGCCAGU\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t286.843\t573.686\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))....(((.(((((.(((]].]........)).)))...)..))..)))......]]]]]]]]]..\ttop-1_consensus\tTP=26,FP=9,FN=4,FS=0.8,PR=0.743,RC=0.867\r\n",
      "===================================================================================================================\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))....(((.(((((.(((]].]........)).)))...)..))..)))......]]]]]]]]]..\t#1\t363.799\t727.597\t0.5\tali\tTP=26,FP=9,FN=4,FS=0.8,PR=0.743,RC=0.867,RK=1\r\n",
      ">RF00094__AB118827_1_904_812\r\n",
      "UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGU-GGUCCGACCUGGG---CAU-CCGAA-GGAGG-ACAAAC--GUC-C--ACUC--GG--AUGGCUAAGGGAGAGCCAGU\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t297.132\t594.264\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))....(((.((((..(((]].]........)).)....))..))..)))......]]]]]]]]]..\ttop-1_consensus\tTP=27,FP=7,FN=3,FS=0.844,PR=0.794,RC=0.9\r\n",
      "===================================================================================================================\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))....(((.((((..(((]].]........)).)....))..))..)))......]]]]]]]]]..\t#1\t360.435\t720.87\t0.5\tali\tTP=27,FP=7,FN=3,FS=0.844,PR=0.794,RC=0.9,RK=1\r\n",
      ">RF00094__AM183327_1_684_771\r\n",
      "GUGGCCGGCAUGGUC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGA--GGGGA-CCG--U---CC-C----CC--GGUAAUGGCAGA---UGGGACCCA\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t392.674\t785.348\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..(((((((...((((.......)...)).).....)..)).))))))......]]]]]]]..\ttop-1_consensus\tTP=27,FP=4,FN=4,FS=0.871,PR=0.871,RC=0.871\r\n",
      "===================================================================================================================\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..(((((((...((((.......)...)).).....)..)).))))))......]]]]]]]..\t#1\t342.776\t685.552\t0.5\tali\tTP=27,FP=4,FN=4,FS=0.871,PR=0.871,RC=0.871,RK=1\r\n",
      ">RF00094__AB037949_1_902_810\r\n",
      "UCGGGUCGGCAUGGGAUCUCC------ACCUCCUCGC-GGUCCGACCUGGG---CAU-CCGUAAGGAGG-ACG--U-AGUC-C--CCUC--GG--AUGGCAAAGGGAGAUCCACC\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t260.776\t521.552\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "(((((((((....[[[[[[[[......((([[[.....))))))))))))....(((.(((...(((]].]........)).).....)..))..)))......]]]]]]]]...\ttop-1_consensus\tTP=22,FP=10,FN=8,FS=0.71,PR=0.688,RC=0.733\r\n",
      "===================================================================================================================\r\n",
      "(((((((((....[[[[[[[[......((([[[.....))))))))))))....(((.(((...(((]].]........)).).....)..))..)))......]]]]]]]]...\t#1\t373.443\t746.885\t0.5\tali\tTP=22,FP=10,FN=8,FS=0.71,PR=0.688,RC=0.733,RK=1\r\n",
      ">RF00094__AJ584849_1_902_810\r\n",
      "UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGU-GGUCCGACCUGGG---CAU-CCGAA-GGAGGACAG-AC--GUC-C--ACUC--GG--AUGGCUAAGGGAGUGCCAGC\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t292.536\t585.072\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "(((((((((..[[[[[[.[[[......((([[[.....))))))))))))....(((.((((..(((]]].........)).)....))..))..)))......]]]]]]]]]..\ttop-1_consensus\tTP=25,FP=9,FN=5,FS=0.781,PR=0.735,RC=0.833\r\n",
      "===================================================================================================================\r\n",
      "(((((((((..[[[[[[.[[[......((([[[.....))))))))))))....(((.((((..(((]]].........)).)....))..))..)))......]]]]]]]]]..\t#1\t338.867\t677.734\t0.5\tali\tTP=25,FP=9,FN=5,FS=0.781,PR=0.735,RC=0.833,RK=1\r\n",
      ">RF00094__AM183332_1_902_810\r\n",
      "UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGC-GGUCCGACCUGGG---CAU-CCGUA-GGAGG-ACGGAC--GUC-C--ACUC--GG--AUGGCGAAGGGAGAGCCAGU\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t286.843\t573.686\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "(((((((((..[[[[.[[[[[......(((....[[[.))))))))))))....(((.(((...(((............)).).....)..))..)))]]]...]]]]]]]]]..\ttop-1_consensus\tTP=26,FP=7,FN=4,FS=0.825,PR=0.788,RC=0.867\r\n",
      "===================================================================================================================\r\n",
      "(((((((((..[[[[.[[[[[......(((....[[[.))))))))))))....(((.(((...(((............)).).....)..))..)))]]]...]]]]]]]]]..\t#1\t361.343\t722.687\t0.5\tali\tTP=26,FP=7,FN=4,FS=0.825,PR=0.788,RC=0.867,RK=1\r\n",
      ">RF00094__AB221996_1_162_71\r\n",
      "UCGGGUCGGCAUGGCAUCUCC------ACCUCCUCAC-GGUCCGACCUGGG---CAU-CCGAA-GGAGG-ACA-AC--GUC-C--CCUC--GG--AUGGCUAAGGGAGAGCCAGU\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t297.132\t594.264\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))....(((.((((..(((]].]........)).)....))..))..)))......]]]]]]]]]..\ttop-1_consensus\tTP=27,FP=7,FN=3,FS=0.844,PR=0.794,RC=0.9\r\n",
      "===================================================================================================================\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))....(((.((((..(((]].]........)).)....))..))..)))......]]]]]]]]]..\t#1\t360.435\t720.87\t0.5\tali\tTP=27,FP=7,FN=3,FS=0.844,PR=0.794,RC=0.9,RK=1\r\n",
      ">RF00094__AJ309877_1_537_443\r\n",
      "UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGC-GGUCCGACCUGGG---CAUCCGUAA-GGAGGACAG-AC--GUC-C----UACUCG-GAUGGCUAAGGGAGAGCCACU\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t290.079\t580.159\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))....((((((..(.(((]]].........)).)....)...)).))))......]]]]]]]]]..\ttop-1_consensus\tTP=26,FP=8,FN=5,FS=0.8,PR=0.765,RC=0.839\r\n",
      "===================================================================================================================\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))....((((((..(.(((]]].........)).)....)...)).))))......]]]]]]]]]..\t#1\t356.646\t713.292\t0.5\tali\tTP=26,FP=8,FN=5,FS=0.8,PR=0.765,RC=0.839,RK=1\r\n",
      ">RF00094__EF514904_1_897_798\r\n",
      "UCGGGUCGGCAUGGCAUCUCCACCUCCACCUCCUCGC-GGUCCGACCUGGG---CAU-CCGAA-GGAGGAGCGGAC--GUC-C--ACUC--GG--AUGGCUAAGGGAGAGCCCAG\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t289.558\t579.117\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "(((((((((...[[[.[[[[[......((([[[.....))))))))))))....(((.((((..(((]]].........)).)....))..))..)))......]]]]]]]]...\ttop-1_consensus\tTP=26,FP=7,FN=4,FS=0.825,PR=0.788,RC=0.867\r\n",
      "===================================================================================================================\r\n",
      "(((((((((...[[[.[[[[[......((([[[.....))))))))))))....(((.((((..(((]]].........)).)....))..))..)))......]]]]]]]]...\t#1\t352.861\t705.722\t0.5\tali\tTP=26,FP=7,FN=4,FS=0.825,PR=0.788,RC=0.867,RK=1\r\n",
      ">RF00094__U19598_1_901_809\r\n",
      "UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGC-GGUCCGACCUGGG---CAU-CCGUA-GAGAG-ACGAAC--GUC-C--ACUC--GG--AUGGCUAAGGGAGAGCCAGU\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t268.082\t536.164\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "(((((((((..[[[[.[[[[[......(((........))))))))))))....(((.(((.......(.((......))).......)..))..)))......]]]]]]]]]..\ttop-1_consensus\tTP=23,FP=7,FN=7,FS=0.767,PR=0.767,RC=0.767\r\n",
      "===================================================================================================================\r\n",
      "(((((((((..[[[[.[[[[[......(((........))))))))))))....(((.(((.......(.((......))).......)..))..)))......]]]]]]]]]..\t#1\t327.179\t654.357\t0.5\tali\tTP=23,FP=7,FN=7,FS=0.767,PR=0.767,RC=0.767,RK=1\r\n",
      ">RF00094__AF104264_1_907_816\r\n",
      "UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGC-GGUCCGACCUGGG---CAU-CCGUA-GGAGG-ACGAAC--GUCAC----UC--GG--AUGGCUAAGGGAGAGCCAGU\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t278.224\t556.447\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "(((((((((..[[[[.[[[[[.......[[[[[........)))))))))....(((.(((...]]]]]...................)..))..)))......]]]]]]]]]..\ttop-1_consensus\tTP=20,FP=9,FN=10,FS=0.678,PR=0.69,RC=0.667\r\n",
      "===================================================================================================================\r\n",
      "(((((((((..[[[[.[[[[[.......[[[[[........)))))))))....(((.(((...]]]]]...................)..))..)))......]]]]]]]]]..\t#1\t346.129\t692.257\t0.5\tali\tTP=20,FP=9,FN=10,FS=0.678,PR=0.69,RC=0.667,RK=1\r\n",
      ">RF00094__AM183330_1_903_811\r\n",
      "UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGU-GGUCCGACCUGGG---CAU-CCGAA-GGAGGACGG-AC--GUC-C--ACUC--GG--AUGGCUAAGGGAGUGCCGGC\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t282.577\t565.155\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "(((((((((..[[[[[.[[[[......((([[[.....))))))))))))....(((.((((..(((]]].........)).)....))..))..)))......]]]]]]]]]..\ttop-1_consensus\tTP=26,FP=8,FN=4,FS=0.812,PR=0.765,RC=0.867\r\n",
      "===================================================================================================================\r\n",
      "(((((((((..[[[[[.[[[[......((([[[.....))))))))))))....(((.((((..(((]]].........)).)....))..))..)))......]]]]]]]]]..\t#1\t349.654\t699.307\t0.5\tali\tTP=26,FP=8,FN=4,FS=0.812,PR=0.765,RC=0.867,RK=1\r\n",
      ">RF00094__X04451_1_902_810\r\n",
      "UCGGGUCGGCAUGGCAUCUCC------ACCUCCUCGC-GGUCCGACCUGGG---CAU-CCGAA-GGAGG-ACGCAC--GUC-C--ACUC--GG--AUGGCUAAGGGAGAGCCACU\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\t297.132\t594.264\t0.5\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))....(((.((((..(((]].]........)).)....))..))..)))......]]]]]]]]]..\ttop-1_consensus\tTP=27,FP=7,FN=3,FS=0.844,PR=0.794,RC=0.9\r\n",
      "===================================================================================================================\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))....(((.((((..(((]].]........)).)....))..))..)))......]]]]]]]]]..\t#1\t360.435\t720.87\t0.5\tali\tTP=27,FP=7,FN=3,FS=0.844,PR=0.794,RC=0.9,RK=1\r\n",
      ">Step 2, Populated base pairs\r\n",
      "......................................................(..........................................)................. 33\r\n",
      ".......................................................(........................................).................. 33\r\n",
      "........................................................(......................................)................... 33\r\n",
      ".(..............................................).................................................................. 32\r\n",
      "..(............................................)................................................................... 32\r\n",
      "...(..........................................).................................................................... 32\r\n",
      "....(........................................)..................................................................... 32\r\n",
      ".....(......................................)...................................................................... 32\r\n",
      "......(....................................)....................................................................... 32\r\n",
      ".......(..................................)........................................................................ 32\r\n",
      "........(................................)......................................................................... 32\r\n",
      "..................(.......................................................................................)........ 32\r\n",
      "............................................................(...........................).......................... 32\r\n",
      ".................(.........................................................................................)....... 31\r\n",
      "...........................(............).......................................................................... 31\r\n",
      "............................(..........)........................................................................... 31\r\n",
      ".............................(........)............................................................................ 31\r\n",
      "............(..................................................................................................)... 30\r\n",
      ".............(................................................................................................).... 30\r\n",
      "..............(..............................................................................................)..... 30\r\n",
      "................(...........................................................................................)...... 30\r\n",
      "..........................................................(.................................)...................... 30\r\n",
      "...........................................................(...............................)....................... 30\r\n",
      "................................................................(.................)................................ 30\r\n",
      ".................................................................(..............).................................. 30\r\n",
      "..................................................................(............)................................... 30\r\n",
      "...........(....................................................................................................).. 28\r\n",
      ".............................................................(.........................)........................... 25\r\n",
      ".........................................................(....................................).................... 20\r\n",
      "..................................................(................................................)............... 17\r\n",
      "...................................................(..............................................)................ 17\r\n",
      "(................................................)................................................................. 15\r\n",
      "...................(.....................................................................................)......... 15\r\n",
      "....................(...................................................................................).......... 15\r\n",
      "...............................(....................................).............................................. 11\r\n",
      "................................(..................................)............................................... 11\r\n",
      "...................................................................(..........).................................... 9\r\n",
      "...................................................................(.......)....................................... 8\r\n",
      "..............................(......................................)............................................. 6\r\n",
      "..............................(.......................................)............................................ 5\r\n",
      "....................................................................(......)....................................... 4\r\n",
      "...........................................................(..............................)........................ 3\r\n",
      ".............(.................................................................................................)... 2\r\n",
      "..............(...............................................................................................).... 2\r\n",
      "...............(.............................................................................................)..... 2\r\n",
      "...............(............................................................................................)...... 2\r\n",
      "..............................................................(...................)................................ 1\r\n",
      "................................................................(...............).................................. 1\r\n",
      ".................................................................(.............)................................... 1\r\n",
      "..................................................................(........)....................................... 1\r\n",
      "...................................................................(.........)..................................... 1\r\n",
      "..........(.......................................................................................................) 1\r\n",
      "...........(.....................................................................................................). 1\r\n",
      "...(....................................).......................................................................... 1\r\n",
      "....(..................................)........................................................................... 1\r\n",
      ".....(................................)............................................................................ 1\r\n",
      "......(..............................)............................................................................. 1\r\n",
      ".......(............................).............................................................................. 1\r\n",
      "........(..........................)............................................................................... 1\r\n",
      "............(......................................)............................................................... 1\r\n",
      ".............(....................................)................................................................ 1\r\n",
      "................(................................)................................................................. 1\r\n",
      ".................(..............................).................................................................. 1\r\n",
      "..................(............................)................................................................... 1\r\n",
      "...........................(..................).................................................................... 1\r\n",
      "............................(................)..................................................................... 1\r\n",
      ".............................(..............)...................................................................... 1\r\n",
      "..............................(............)....................................................................... 1\r\n",
      "..........................................................................................................(.......) 1\r\n",
      "...........................................................................................................(.....). 1\r\n",
      "............................................................................................................(...).. 1\r\n",
      ".............................................................(......................).............................. 1\r\n",
      "..............................................................(....................)............................... 1\r\n",
      "................(..........................................................................................)....... 1\r\n",
      "..................................(.................................................................).............. 1\r\n",
      "...................................(...............................................................)............... 1\r\n",
      "....................................(.............................................................)................ 1\r\n",
      "..............................................................(........................)........................... 1\r\n",
      "....................................................................(...........).................................. 1\r\n",
      "......................................................................(........)................................... 1\r\n",
      ".......................................................................(......).................................... 1\r\n",
      "............................(.......................................).............................................. 1\r\n",
      ".............................(.....................................)............................................... 1\r\n",
      "..............................(...................................)................................................ 1\r\n",
      "...............................(.................................)................................................. 1\r\n",
      "................................(...............................).................................................. 1\r\n",
      ">Step 2, Consensus\r\n",
      "(((((((((.[[[[[.[[[[[......((([[[.{...))))))))))))((..(((((((((.(((]]].(......))).))...))..)).))))))}...]]]]]]]]].]\t0%\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))((..((((((((..(((]]].........)).)....))..)).))))))....]]]]]]]]]..\t5%\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))((..((((((((..(((]]].........)).)....))..)).))))))....]]]]]]]]]..\t10%\r\n",
      "(((((((((..[[[[.[[[[[......((([[[.....))))))))))))((..((((((((..(((]]].........)).)....))..)).))))))....]]]]]]]]]..\t15%\r\n",
      "(((((((((..[[[[.[[[[[......(((.[[.....))))))))))))((..((((((((..(((]]..........)).)....))..)).))))))....]]]]]]]]]..\t20%\r\n",
      "(((((((((..[[[[.[[[[[......(((.[[.....))))))))))))((..((((((((..(((]]..........)).)....))..)).))))))....]]]]]]]]]..\t25%\r\n",
      "(((((((((..[[[[.[[[[[......(((.[[.....))))))))))))((..((((((((..(((]]..........)).)....))..)).))))))....]]]]]]]]]..\t30%\r\n",
      "(((((((((..[[[[.[[[[[......(((........))))))))))))((..((((((((..(((............)).)....))..)).))))))....]]]]]]]]]..\t35%\r\n",
      "(((((((((..[[[[.[[[[[......(((........))))))))))))((..((((((((..(((............)).)....))..)).))))))....]]]]]]]]]..\t40%\r\n",
      "(((((((((..[[[[.[[[[[......(((........))))))))))))((..((((((((..(((............)).)....))..)).))))))....]]]]]]]]]..\t45%\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).((..((((((((..(((............)).)....))..)).))))))......]]]]]]]..\t50%\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).....((((((((..(((............)).)....))..)).))))........]]]]]]]..\t55%\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).....((((((((..(((............)).)....))..)).))))........]]]]]]]..\t60%\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).....(((.((((..(((............)).)....))..))..)))........]]]]]]]..\t65%\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).....(((.((((..(((............)).)....))..))..)))........]]]]]]]..\t70%\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).....(((.((((..(((............)).)....))..))..)))........]]]]]]]..\t75%\r\n",
      ".((((((((..[[[[.[[[........(((........))))))))))).....(((.(((...(((............)).).....)..))..)))........]]]]]]]..\t80%\r\n",
      ".((((((((...[[[.[[[........(((........))))))))))).....(((.(((...(((............)).).....)..))..)))........]]]]]]...\t85%\r\n",
      ".((((((((...[[[.[[[........(((........))))))))))).....(((.(((...(((............)).).....)..))..)))........]]]]]]...\t90%\r\n",
      ".((((((((.........[......................)))))))).....(((...(...........................)......)))........]........\t95%\r\n",
      "......................................................(((......................................))).................\t100%\r\n",
      "===================================================================================================================\r\n",
      "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\treactivities\r\n",
      "...................................................................................................................\trestraints\r\n",
      "..(((((((..[[[[.[[[........(((.[[.....))))))))))]]....((((((((..(((.(......)...)).)....))..)).))))........]]]]]]]..\treference\r\n",
      "___________________________________________________________________________________________________________________\r\n",
      "(((((((((..[[[[.[[[[[......((......[[..)))))))))))....((((((((..(((............)).)....))..)).))))]]....]]]]]]]]]..\tStep-1\t0.5\tTP=27,FP=6,FN=4,FS=0.844,PR=0.818,RC=0.871\r\n",
      "(((((((((..[[[[.[[[[[......(((........))))))))))))((..((((((((..(((............)).)....))..)).))))))....]]]]]]]]]..\tStep-2\t0.5\tTP=28,FP=6,FN=3,FS=0.862,PR=0.824,RC=0.903\r\n",
      "(((((((((..[[[[.[[[[[......(((.....[[.))))))))))))....((((((((..(((............)).)....))..)).))))]]....]]]]]]]]]..\tStep-3(u)\t0.5\tTP=28,FP=6,FN=3,FS=0.862,PR=0.824,RC=0.903\r\n"
     ]
    }
   ],
   "source": [
    "!cat demo_ali.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a52c005a-d072-4efd-83c1-b52ecbd48fc0",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d34f42f3-dddb-4894-a18b-de41e4d333a7",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8c3c0192-2d59-4181-88e0-0be92edfa652",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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