<?xml version="1.0" encoding="ISO-8859-1"?>
<GTH_output xmlns="http://www.genomethreader.org/GTH_output/" GTH_XML_version="1.1">
  <header xmlns="http://www.genomethreader.org/GTH_output/header/">
    <source program="GenomeThreader" version="0.9.54" build_date="2006-07-28 11:55:15" run_date="2008-11-20 23:02:46"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0213A03-GY2cF/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C04HBa0213A03-GY2cF/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" type="ESTcDNA"/>
    </reference_files>
    <splice_site_parameters parameter_type="Bayesian" species="arabidopsis"/>
    <parameters>
      <parameter name="bssmfile" value="arabidopsis"/>
      <parameter name="scorematrixfile" value="BLOSUM62"/>
      <parameter name="searchmode" value="forward=True,reverse=True)"/>
      <parameter name="translationtable" value="1"/>
      <parameter name="frompos" value="0"/>
      <parameter name="topos" value="0"/>
      <parameter name="width" value="0"/>
      <parameter name="verbose" value="False"/>
      <parameter name="skipalignmentout" value="False"/>
      <parameter name="showintronmaxlen" value="120"/>
      <parameter name="minorflen" value="64"/>
      <parameter name="showseqnums" value="False"/>
      <parameter name="gs2out" value="False"/>
      <parameter name="maskpolyatails" value="False"/>
      <parameter name="noautoindex" value="False"/>
      <parameter name="minmatchlen" value="20"/>
      <parameter name="seedlength" value="16"/>
      <parameter name="exdrop" value="2"/>
      <parameter name="online" value="False"/>
      <parameter name="inverse" value="False"/>
      <parameter name="exact" value="False"/>
      <parameter name="chainwf" value="0.500000"/>
      <parameter name="gcmaxgapwidth" value="1000000"/>
      <parameter name="gcmincoverage" value="50"/>
      <parameter name="introncutout" value="False"/>
      <parameter name="autointroncutout" value="0"/>
      <parameter name="icinitialdelta" value="50"/>
      <parameter name="iciterations" value="2"/>
      <parameter name="icdeltaincrease" value="50"/>
      <parameter name="icminremintronlen" value="10"/>
      <parameter name="nou12intronmodel" value="False"/>
      <parameter name="u12donorprob" value="0.990000"/>
      <parameter name="u12donorprob1mism" value="0.900000"/>
      <parameter name="probies" value="0.500000"/>
      <parameter name="probdelgen" value="0.030000"/>
      <parameter name="identityweight" value="2.000000"/>
      <parameter name="mismatchweight" value="-2.000000"/>
      <parameter name="undetcharweight" value="0.000000"/>
      <parameter name="deletionweight" value="-4.000000"/>
      <parameter name="dpminexonlen" value="5"/>
      <parameter name="dpminintronlen" value="50"/>
      <parameter name="shortexonpenal" value="100"/>
      <parameter name="shortintronpenal" value="100"/>
      <parameter name="wzerotransition" value="80"/>
      <parameter name="wdecreasedoutput" value="80"/>
      <parameter name="leadcutoffsmode" value="RELAXED"/>
      <parameter name="termcutoffsmode" value="STRICT"/>
      <parameter name="cutoffsminexonlen" value="5"/>
      <parameter name="scoreminexonlen" value="50"/>
      <parameter name="minaveragessp" value="0.500000"/>
      <parameter name="minalignmentscore" value="0.900000"/>
      <parameter name="maxalignmentscore" value="1.000000"/>
      <parameter name="mincoverage" value="0.900000"/>
      <parameter name="maxcoverage" value="100.000000"/>
      <parameter name="intermediate" value="False"/>
      <parameter name="sortags" value="False"/>
      <parameter name="sortagswf" value="1.000000"/>
      <parameter name="first" value="0"/>
      <parameter name="exondistri" value="False"/>
      <parameter name="introndistri" value="False"/>
      <parameter name="refseqcovdistri" value="False"/>
    </parameters>
    <overall_reference_type>ESTcDNA</overall_reference_type>
  </header>
  <alignment_module>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C04HBa0213A03-GY2cF/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M6804" ref_strand="+" ref_description="SGN-M6804 C2_At1g43900 [cosii_markers]">
      <seq>aaaaaccgaatgcggcgaccgcgatgaacgttgacaaggaacaatccgatcgcaaccttccagaactttctccaccgtctatggagaaacctgcgccggcgccggcacccgaaccgtcacagcaaccaccaagagagtccactgctccgacgccgtccctgccgcagattaaacagccgccatccctgccgctggtgaaacagccgccgtctctgacgcaggtgaaacagacgccgtctattgatcccagtgcgctctttagtggcggcggtattagctttctgactggaaacaaaaatgctaaattcagctatggatatgctacttttaaggggaaacgggcctccatggaggactactatgagacaagcatatcagaagttgatggtcaaatggtggcattttttggtgtttttgatggtcatggtggttcaagaacagcagaatacttaaagaacaacctctttaagaatttgagtagtcatcctgattttatcaaagatacgaagtcagctatagttgaagcatttaagcagactgatgccgattaccttaatgaagaaaaaggccagcaaaaagatgccggttcaacagcgtcaactgctgttcttttaggtgataaattgcttgtcgcaaatgtgggggactctatagacgtggcttgtagagatggttcanctattcctttgtccatcgatcacaagcctgacagatctgatgagcgtgaaaag</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0213A03-GY2cF/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0213A03.1" temp_strand="-" temp_description="C04HBa0213A03.1  CU914527.4 htgs_phase:3 submitted_to_sgn_as:C04HBa0213A03 sequenced_by:sanger upload_account_name:uk">
        <position start="38719" stop="27606"/>
      </template>
    </gDNA_segment>
    <predicted_gene_structure xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
      <exon-intron_info>
        <exon e_serial="1">
          <gDNA_exon_boundary g_start="38419" g_stop="38172" g_length="248"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="250" r_length="250" r_score="0.915"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="38171" i_stop="35951" i_length="2221">
            <donor d_prob="0.000" d_score="0.85"/>
            <acceptor a_prob="0.000" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="35950" g_stop="35944" g_length="7"/>
          <reference_exon_boundary r_type="cDNA" r_start="251" r_stop="256" r_length="6" r_score="0.714"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="35943" i_stop="34909" i_length="1035">
            <donor d_prob="0.803" d_score="0.00"/>
            <acceptor a_prob="0.679" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="34908" g_stop="34886" g_length="23"/>
          <reference_exon_boundary r_type="cDNA" r_start="257" r_stop="277" r_length="21" r_score="0.522"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="34885" i_stop="34664" i_length="222">
            <donor d_prob="0.128" d_score="0.00"/>
            <acceptor a_prob="0.586" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="34663" g_stop="34521" g_length="143"/>
          <reference_exon_boundary r_type="cDNA" r_start="278" r_stop="420" r_length="143" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="34520" i_stop="33167" i_length="1354">
            <donor d_prob="0.905" d_score="1.00"/>
            <acceptor a_prob="0.983" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="33166" g_stop="33068" g_length="99"/>
          <reference_exon_boundary r_type="cDNA" r_start="421" r_stop="519" r_length="99" r_score="0.990"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="33067" i_stop="32977" i_length="91">
            <donor d_prob="0.977" d_score="0.98"/>
            <acceptor a_prob="0.622" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="32976" g_stop="32818" g_length="159"/>
          <reference_exon_boundary r_type="cDNA" r_start="520" r_stop="678" r_length="159" r_score="0.962"/>
        </exon>
        <intron i_serial="6">
          <gDNA_intron_boundary i_start="32817" i_stop="27960" i_length="4858">
            <donor d_prob="0.995" d_score="0.92"/>
            <acceptor a_prob="0.996" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="7">
          <gDNA_exon_boundary g_start="27959" g_stop="27907" g_length="53"/>
          <reference_exon_boundary r_type="cDNA" r_start="679" r_stop="731" r_length="53" r_score="0.925"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0213A03.1" gen_strand="-" ref_id="SGN-M6804" ref_strand="+">
        <total_alignment_score>0.954</total_alignment_score>
        <cumulative_length_of_scored_exons>732</cumulative_length_of_scored_exons>
        <coverage percentage="1.001" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0213A03.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M6804" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="38419" e_stop="38172"/>
          <exon e_start="35950" e_stop="35944"/>
          <exon e_start="34908" e_stop="34886"/>
          <exon e_start="34663" e_stop="34521"/>
          <exon e_start="33166" e_stop="33068"/>
          <exon e_start="32976" e_stop="32818"/>
          <exon e_start="27959" e_stop="27907"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAAAACCGAATGCGGCGACCGCGATGAACGTTGACAAGGAACAATCCGATTGCAACCTTCCAGAACTTTCTCCACCGTCCATGGAGAAACCTGCACCGGAGCCGGCGCCGGAACCGTCACAGCAACCACCGAGAGAGTCTACTGCTCCGACGCCGTCCATGACGCAGATTAAACAGCCGCCGTCTCTGACGCAGGTGAAACAGCCGCCGTCTCTGACGCAGGTGAAACAGCCGCCGTCT-CTGA-CGCAGGTGAAACAGCCGCCGTCTATTGATCCCAGTGCGCTCTTTAGCGGCGGCGGTATTAGGTAACTGCATTATTGGTCTCTTGCTTAATTTTATTGTTTTCTGCTGAATTTATTAACTGTTTGTTGTTATCAATGTTTATGTTTCGAGAAATGATCAATTTTATTTGATTCCTTTTTCTAGCATTAGAAATGAGAATGACAGTTCGCAGTTGCTATTTCTACTTGACATCATGGTTTAGTAAAAGGTTTTGTTACAATTTTTTCCGTAGCTAGTCTTTGTTTTACAAAGATGGGTAGTATTTACAAAGGAATAGTACATAAACATTACCCTCAACTTGACATCAACGGACAATTATGACCTCTAATTTTGGAGGTGCACAAGTAGAGACTTAAATTTGTACAAAATTGAGCAAATGGACACATTTGTCCTACATGACACCCTACATGAAAATTTTGTGTCCTATGTGTATTATGCCATGCAGAACAAGAGTATCTACTTGTGCATACTCAAAGTTGGAGGACATAGTTGTCCGTTGCAGCCAAGTTAAGGGTTACGTTTATGAATTATGTTATTTACAAACGTGTAATATGATCATATAAAAGAGGCATCCCAAAAGTCTTGCACAATTTGCTAGAATTAAAGAGAGCACTAAGCAATGGTCTCTGTACCCTCCAGGAATGAGGAAGCCCCAAAACCGCAAAAGGAGAAGTCATCCTAATCTTCTTTTTCTTCACACCCACTTTGTTCAACCTTTAGCTTTCCGTTGTTCCTGGCTTCCTGCAACTATTTTAGGAAGTACCTATTGGTTGTTGAAAGTTACAAAATTCAAAGACCACAATTCCAAAGATGCAGTAAGAGATGATTCACATCCTCCCCATGTTTGGTACACATACAACTCCAATTCGTGATGATGCATCTACTCCTTAAATTATCTACCATTAAGAGAGGCTCCCCATGCAACACAACATGTGACAAATATCTCTTCTTTTGGTGCATCTGATAGGAGACTCCCACACGAGATAATGATCCGTCGTAAACAAGTGGTAACACGACGTAACAGAGATGTACTTCTATTACCAGCTTTTTCCATATCAAAAGTAGCTCCATATCACATAATATCATTACTGTAATCTTCATGTGCTTATCGAATTTGAATGAGCTTGGCTTTTTTTTTTTTTAGGCTAATGATGGTTGTGTCTAGTGTTATCAAAGGCAAAAAGCGCAAAAAAGCTTTAGGGTCCATCGGGGCTTTAAGCGCAAAGCGCAAATAAAGCGTGGACTTTAATGAAAAAAGGTGCAAAGGGAGGAAAAAATATAAATATATATGTTTAGTCCAGGACTATAAATTATAAACATGAATGATAAATACATGACCAAGGAAATTGAATTTTTTTAATTATAAAGTGAAATATCAACTATTTAGTGTCAGTTCTTCATAAGAGGCTCATTGGCAAGGAAAAGTTTGCCTTAGAACCTTGATGACGACACTGAACCGCAAATAAAGCGAGGTGAAGCGTTCAATACGTTTTGAGTCTCGCTTCAGGGCTTAAGTGCGCTTAAAGCGCGCCTTTGATAACACTGGTTATGTCTGGGCCAACGTGTTGAGAAATGTGAATTAGTTGGTGAATTTACATTTAAAGTTATTATTACCACATCATACATGATCCAGGAATATGTTCTATATCCCAATGGCGTAGCAAGATTTTTGTGAGGGGTATCACCTTTTAAAATGAACAATAAATAAAATTATGTGACTTCATATTGAAAAAAAGGAACAAAATATAAATAAAATACAGTTCGGGCTCAGTACTATACATTTTCTAAAAAGAAGTACTTTTAAAAAATTAATAAAAACATTCACGTGTCTTTTTTTATTTTGAAATATATTCAAAATAACTTTTAAAATTAATAATATTAAATGCTTCATAAATTGTTTTTAATTAATTTACTGATTAGAAAGATGGTGAAAGTAACCCCTCCCCCACATAAAAAATTAATAATATTAAATGCTTCATAAATTGTTTTTAATTAATTTACTGATTAGAAAGATGGTGAAAGTAACCCCCCCCCCCCCCTCCACATAAAAAATAAGCCTATAAGAAGAGTGAAAGAAGAACTTCAAATGTATAAAAAAAATGACAAGTGCTTGATTCAAACACAAGACCTATACCTTAGAACTAAGGCGCCTGACCAGCTAAGCTAAGTGTGTGTATGTGTCTAGGAGTGTCACTGTATATAACATATTCAGTGTTTCTCCTTTTTCTTTTAGTTATGTATATTAACTAAATTTTTCAGTTGAAGCAGTGTCACATGACACCCTTTGGACTTACGTAGATCTGCCCCTGCTATATCGCTTTAAACCTAGGAACCAATGAACTCAAAGAGTCTTTTTTATGGCTAATGGTGGTAGTTTTCAGGCCAGCTTGTTGGAAAATGTGAATTAGTTGGTGTATTTACATTTCAAGCTTTATATCACACCATACACGGCAAGAAATATGTTCTATCCCCCCTTCAAACCTAGGAACCAATGCACTCAAAAGAGTTTGATCTTATTTCATTTCAATACCCCTCTCCACAAACTCATTCTATAAGGGCGTTTTCAGTGAATCAACCATAATGACAGACTGATGCCATATTTCAGCAGAATCCCCTTCCTGCACATGACCTGTTCTTCTACTGGAAATCTCCATAAATGCCCAACAATGTCTAATGAAAAGTTCCAACCTTGGGATGGCTAATCTCACGATCTTCAAGACATCTTTTTGGACAGTTTCGAAATATAATTCCACTGTTTAGTTTTACAATCTTGTGCTAATCGATGCCGAAGTGAACAAGGACCAAATAAAGTAGGATGCTTAAAATGGCAGCATATAGAAAATGGATCAATGGCGTCATGGAAGAGTTTAGAGGCTCTTCTAACATTACAGTCTCACACATTATATGGAGACCCTTGCAGGGGCGGAGCAAGTGTAGGACGATGTTGGCAAATGATTGTTGAATAGAGTTACTCACCTCGCAACCTAATTTCCTCTATGAGCTTGGCGGGACCCAGTAACTTTGGCATCAAACAGTTTATGTTTAAAATTTCATTTAATATGTACAACACAATCTATTGAGAACCTAGTAAGCAAAAAAAATTGTTATTCCTTATAAGCTAAAAATCCTGTCTCTGCTAATCCTTGTTCTAAGTGATGCTTATGTTTCTCAACACATCCAGATGGTATGAATACTGCAAAATATGCTCTACTGTGGGGTACCTTGTGTAGCTTAAGAGTTGGTCATTGGGCAGGTTAAGTCTTGAATTTCAGCCTGGTTGCTGTTTTTGGTTGTGGATATTTGCATCCATATTTGGACTGATAAATGCATTTCTTTTGTTCGGATCTGTTTATTTTTAATACGACTGTATCTTCATAGTGGGGAGAAACAATTAATGTAATCCTACATTTGTAAAGATATGTTTGGGGATGAACTTTTATAAGAAACCAACTGATTTCTTTTTCTTTTCTTGAAGCTTTCTGACTGGAAACAAAAATGCTAAATTCAGCTATGGATATGCTACTTTTAAGGGGAAACGGGCCTCCATGGAGGACTACTATGAGACAAGCATATCAGAAGTTGATGGTCAAATGGTGGCATTTTTTGGTGTTTTTGATGGTATTTCCTAGAATTTCTTGCATATCTTGTCAGGATGATGTTTCTTTTTTGTAATTAAAGTATTACTACCAAATCGGAAAATTACAGCTCAAACAAAAAAAGAAGAGATTCAAGATTGGACATGCATGTCCATTCTTTTGCTAAGCTACTTTTCATCACCAACTCAGTACTTTAGTAGTATTTATTGCTTATACATCAAGGGTAGTAGTTTAGATCTTGCAATATCCTAGGTACTATGGAACACTAATCTGTCTAACTGTTGCTGCTGTTATTCTTCTTATATTCTGAAACACCCCGTGTTCTTTCCATACATAGTATACTGCTGCAGCCAATTTCGTCTTAAAGATTTCTGCTTGGCTACTCTTTCCTTTATAGTAGGTTACAGCCACCTTATCTCCTCTTGCCATCCATATCTCTTTGCATTTTTTGCCAACGTAACAATTTTAACCATATACTAGAACTTTCAGGACATTGGAAGAGCAAGTGCTGGATACTTTCAGCTTCATTACATAGGGGACATTTGAGGCTAACATTTATTTCCCACTTTACAAGTTAGTAGCCAGCCCTCCAGTATTGCCAGTCTTAGTATAAATATCCATTTTGTAGAACCTCAGTTGTTACATACCAATCTTGTCCAGTCTACTTCTTGGAAGATGCCTTGTAAATTTCTGTATATTGCTTGAATGGATATGCTATCCATTTGCATGAGTTCAGTCAATGTGCAACTTTCCCCCAAAATGTTAATAAAACTATTTACCATATGTCCATATAAAAAAAAAATTATATATATATATATATACTTATTGGATTTGAGTATCTTCCTAGTCATCCATGCAGCCTGTTTTAATTCAATTTGCCAAATAGTTCTCACTTTCCCATAGTAGATGTGCATCCATTTTACCCCTGGGTTGTCCTTCCTTTTGCAAATATTGCATAGGAGTTCACATATTGCAGCTCTATTCCAGATCATGATGTTGATAATGTTCAAGCCTCCAGCTGATTGAGGTTGATAGAGATTTTCCCATGCCACTGGTGGCTTCATAGAAATTTAGCTTTTCTAGTCTTCACATATCTTTTACATATGTTCTCTATCTTCTTATGGAGTATAAACATTTGTCCCAGAATGTTCATTGATAAAATGACGCTCTTTATGAGCTGAGCTCTTCCAACATATGACAGGAACTTAGAAGGATGGGCGTTTTCTACTTTCAGAGTGTTAATCTTGTTTAAATATCATTTTAGTTGTTGTAGATACGAAATTTACTCACGAAGAGACTTTTTTTTGGGTACTCTTGAATTGAGTTTCTTTGCAACCTAGATGATTATTTATCCCTTATACTCTGCTTGGTGTTAGGTCATGGTGGTTCAAGAACAGCAGAATACTTAAAGAACAACCTCTTTAAGAATTTGAGTAGTCATCCTGATTTTATCAAAGATACAAAGTCAGCTATAGGTATGAACCAAAGCAGAGCTCTATGTCATTTCTAGTTTCATTGTATCTTCTCTCTTCTGTATCATTTAATTGGAAAAGCTCTTGAGTGCAGTTGAAGCATTTAAGCAGACTGATGTCGATTACCTTAATGAAGAAAAAGGCCAGCAAAAAGATGCCGGTTCAACAGCGTCAACTGCTGTTCTTTTAGGTGATAGATTGCTTGTCGCAAATGTGGGGGACTCTAGAGTCGTGGCTTGCAGAGATGGTTCAGGTTTGTTGCTTGTTGACTATTTACTATATCCAAAGTTTTCACAAACATGACTTTGGCTATCTCAAGGTCCATTAGTTCTTTTGTGGATTATCTTTGTTATAGGTAAACAAACTTTTTATAAGGGAAGTACATCAGAAAAAATGGGTAAAGGCGTAAAGCTCACAGGGACAGAGGGAGTTTTTCATTAGGTTTAGTCTGAATAGTTTGCATAGGATAACATATTCTTTGGTCTGTACAAAACTGTGATTCTGGAACTACTTTTTGTAATTTCTAGAACTTTCCACATTTTCATATCAATGGAAGTTCATTAATATATCAAAAACGTGTAAAAAAGTACATATACCTGAACAAACAAATTAAAAATAACAAAGCACATTTCAAACCTTCAAGCAATTAAGAACCTCAAACAAATTCAGACACTTGAAACAACTTTGTTACTCGATGCTAGCTTATCACAATTTATGTTAAGCATTCTTACAATCATAGTAACCACTACACTTAATTTGTCTGGCTAGTTGCTTCCGCTATGCGTTATAAATGAACTGATCATTAGGATCACATATATCAGCTTTCTATATCCTCTATTGTTTATACCCTTTGGTCTGATTGTTTGTATAATGATTTATTCAATAATTTAGAAAGCTTGTTATGTTGTCTTTTGTTTTGATTTGGCCATAGCCAGGCAGAACATATTTCTGCTTGGAAGATGTTAACTATGAGACTTTTGCAACAAAGGAATATGACTTGTATAATTTAAAAAATTAACCGATGAAGCATGTTTTGTATTGACTGACCTTAATCATATTTGTCTCCAAGGTCATTTGTCGGTGTAAAATTTTGTTATAGTCTTTTATCTGTAGGTTCTCACAAGAGTTATTAATCTGTGAAAACTGAAAAGCTTGCCCTGTTTTTCATTCAGAATAAGATATGAAGGAATCTGTGGGGTGTTTTATAATTTTTGTATATGGGTTTATCTTATGAATATAGGTTCATTATTACTCATTTAAAAAGAAAAAGAAGACTAGAAAGATAGGATGTTTCTTATGTATACTATCTAGTAAAGTCTCAATGATTTACCGTTTGCAGCCTTTACCATTTAACATTTGGGCTTTCCATCCCCCTATTATCCTTTTAACAACAACAACATCCCCTGTGAAATCTCACAAGTGAGGTCTTAGGAGGGTAAAATGTATGCATACCTTACAACTACCTCGTGGAGGTAGAGAGTCTGTTCCCGACATATTTTTATTAAGACTTTCCATATTTATGGAGTGGAACAATGACAAATCATATGGTTTGATGTAAACACATGGTGAGGTTATGCTTTTTTTGATGAAGTCACAACGGGTTTGGGTAAGTTATCGGTATGATATTCCGTAAGAAGAGAGAACTTCTTAGAAAGCACCATTAAGAATATAGATTGGAAAAAGTCCAAATATACCCATGAATTATACTATTTGGAGCAAATTTATCCTCCCATAAAAATGGCCTATATCTACCCCTATCGTTACACAAATGACTCATATATATCCTGTTCGATAGATGGAGCTCAAATACCCGTCATTGAAATATTTTTCCTAGTGTATTCATTATAAGTAAAGCCATGTGTAAAAAATTAAATCTTGATCAGATAGTAGCTGTTAAATTAAAGAATAGAAGTCCATTAATCCTAGTTTGTTTTGGCCTATTTTGCTTATTGAGGATTAATTTGATCAATTTTGGTGTTAAGATTAAAACAAATTCATTCTTTTTAAGATATTAAGCACTTACATTAAAAGTAAAGAACTACAAGTTGCAACACCGCAATTCAGAAGAACACATTTTACATATTAGTCAAAGCTCACCTAAATTTCATCCTTGGAAAGTTAATAGGGAAATAATTTGGGACATTTAAGGGAAGTTCCGATCTTTCACCTCATGAATTGATAAGGAAATGTACTTTATAATTCATTTTTGTACCGACCAAAAAGGAAATGGGTTATTCCATTTGAAATGGAGGAGGTACTTGTGGTTGAATTAGATTTGCAAGTTAAGAAAAAATCATTATGCAATTTAGGAGTTTTTTTAAAGATGAAGTAGGAATATTATTAACAAAAGAGCATTAACTAGCCCGTATACAAAAAGTAGAAAATCTTTAAAGAAAATATAATTTTTTATGAATGACACCAAATCATCTAAACAAAAAGTAACCTCACGGGTGCACCAAAGATAGCTAAGGGAAACAAGGTAGTTCTCAAGGGTAGAATTTTTCTCTATTCCATCAAAAGCTCTGCTATTCCCCTCTCTCCGTATGGTTCACATCTGTGCTATAGGGGTAATTTCATATGCCTTGCGTCTAGGGGTGTGCATCAGTCAGCTTAGTTCGGTTTTACATATTATTGATTCGATTTACAGTTTTTAATATGCTAAACCCATAAGATATTTTTATCGATTTTGGTCCTTAACGGTTTGGTTCTCGGTTTAACCAATAAGAAAATGCTTATAAAGCAACTATATGATTTTCCAACAATTTGACGCGACAAAACAATAATTATAACTTTACAAATGATCGTAAAAAAATAATAACTAAGGTGAAAAGAACTATACTAGTGTAATACAAAGAGAAATAAGATTCTTACATTAGGTTTTGACGTTTTGAATAATGTGAAGTTGTGAACTCAAAGTCATTGTGAAGTGTGAATTGAAGGCTAAAAGACAAAGACAGTATCTAGTAAGGTATTGAGATTAATATTTAATGTTTTAGTAAATTACTACAGCCTTAATGGGTTACCGATTTATCCAATAACCCAATATTGAAAACCAAAATCGAACCGGTAACTCTATAATGTTTTTGTATTAAATCATTGAAAAACCATTAATCCAGTAACCCAATAGCAATAAATCAATAATACTTTTTCCATTCGATTTATGAGTCGATTCGGATTTTACACACCGCTACCTTCCTCTGCCTTTCTATGAGCCTAGCTGAACATTGTTTCGAGTAAAGTAGTAAATCAGTGCAGTCTTAATTGGTTATTGATTTATCCAATAACCCAACATTGAAAACCAAACCGAACAGACAACCCAATAATATTTTTTTAATATAAAACCATTAACTCAATAGCAATAGACCAATAATACTTTTTCGGTTCGATTTTTCGGTCAGTTTGGTTTTTCACACTCCTACCTGTACCTCCTCCTCCACCTTTCTATGACCCTACATAAACATTGTTTCTTTCATAGTTCTCGACATTACCCACTCAAAACAAAACCGTCTAATTAACTCCCCCCATAACAAAGATGCTACCCGATAATGTAAGAATAGGTGATCTATGTCTTCCCTTGATTCTTTGCAACTGAGGAATTGATTAAGAAAATATAGTGGTATTTCTATCGGTGTAGAAAACAAGTGATACTAAAAGATTACATTTATAATTCAACAACATACCTGGTGAGATTCCACAAGTCGGGTCTGGGAGGATGGTGGGTGTATACATACCTTATTCCTACCTTTGTGGAGTAGAAGAAGTTGTTTCAATAGACCCTCAGACTCGGGAGAAAAGGAACCGTTTTTCCAAAACAGTTCTGAAGAAAAACAAATGCAAGAGTAAATAAGCTATGATAAAAGTATCTCTGAGAGTTTAAGTTATAATTCCTTTAATGATAATAGAATTAAGTAACCACCTCATTGTGTAAATCTTCCTAGCGAGAAACTTAAATGGAAAGATTTAAAAGTCAAACTAAATTATTGACCTAACATAGTGGATAAATAAAGAAAAATATTTCATCATTGATGGAAATTTAACAAAATAATAACTACTCCGTCCATCCCATTTTATGTGGCACCCTTTCCTTTTTAGTCCGTCCCAAAAAGAATGTCACATACTATAATTAGGAACAATTTAACTTTAAAATTCCCTTTTACCCTTGATAAAATGATTTAACAACCGCACAAATATCTAACTATTGTTTTAGACCATAAGTTTTAAAAATCTTCCTTTTTTTCTTAAATAACGTGTCAAATCAAATAGTATCACATAAAATGGGATGGAGGGAGTAAAATGTATATTCGTTTTTATATTTGAATATCATTTCTGAATAACCACCACATAATAAAGAAATATAAGGGACCTATCCATTTTCTTATCTCTTATAAGAGATTTAGCTACTTCAGTTTTTGAATTGAAACAGTAAAGGAAGTGAAATACCAATAGAAATCCATTGAATGAATAAAGTAAAAGTAAAACACTCCTAATCCAACTTGTATGGAGCACTTATTATGAAGAAGTAAAAACAACTTTTTTCTTTACCAAGTTCTTCTTTGAAAATATCTATAAATAATTTTTATTTTTTAAATTTGGTTTTGATTGTACATTCAAAATTGACCAGAAAGTAGGTATGACGTGATATATCTTGGGACTGTTGAAAACTTGGAATAACTCATGTTTTGAAACTGTTAATATGACAGTTGGAATAACTTTCAGCAATTCTAAAGTCCACCTTATCCATTTACTTTTGTATTCATTGTCTTACAAGAAAGTAGTCTTCATTCTCTGCTTTATTGTGTCCGATGCAAAAACTGTGTTTGCTAAATGTTTGTACAAATGGAAACCAGGAAAACTATCATTCTCATTGAACTTGCCACGTGAGCTTTATTCCTAGTATAACACCTAAATCTTGATAAATTAGGTGTTGGAATCTATTTTCTTCTCAAATTTCAACACGCCTAAACTTAATTATTTATTTCTCAGATTTCTAGATCAAATTTAGGAAGTGATTCATCAGTTGAATGATTATTGAACATATTTTAGATTTTTAAAAGATGTTAATTCATTTTAAGCTATTTGGTTATGAGATATAACTGTTGCAATTAATGCAGCTATTCCTTTGTCCATTGATCACAAGCCTGACAGATCAGATGAGCGCGAAAGG</genome_strand>
        <mrna_strand>AAAAACCGAATGCGGCGACCGCGATGAACGTTGACAAGGAACAATCCGATCGCAACCTTCCAGAACTTTCTCCACCGTCTATGGAGAAACCTGCGCCGGCGCCGGCACCCGAACCGTCACAGCAACCACCAAGAGAGTCCACTGCTCCGACGCCGTCCCTGCCGCAGATTAAACAGCCGCCATCCCTGCCGCTGGTGAAACAGCCGCCGTCTCTGACGCAGGTGAAACAGACGCCGTCTATTGATCCCAG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TG-CGCT...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTTTAGTGGCGG-CGGT-ATTAG..............................................................................................................................................................................................................................CTTTCTGACTGGAAACAAAAATGCTAAATTCAGCTATGGATATGCTACTTTTAAGGGGAAACGGGCCTCCATGGAGGACTACTATGAGACAAGCATATCAGAAGTTGATGGTCAAATGGTGGCATTTTTTGGTGTTTTTGATG..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTCATGGTGGTTCAAGAACAGCAGAATACTTAAAGAACAACCTCTTTAAGAATTTGAGTAGTCATCCTGATTTTATCAAAGATACGAAGTCAGCTATAG...........................................................................................TTGAAGCATTTAAGCAGACTGATGCCGATTACCTTAATGAAGAAAAAGGCCAGCAAAAAGATGCCGGTTCAACAGCGTCAACTGCTGTTCTTTTAGGTGATAAATTGCTTGTCGCAAATGTGGGGGACTCTATAGACGTGGCTTGTAGAGATGGTTCAN..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTATTCCTTTGTCCATCGATCACAAGCCTGACAGATCTGATGAGCGTGAAAAG</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C04HBa0213A03-GY2cF/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M1832" ref_strand="-" ref_description="SGN-M1832 T1204 [cos_markers]">
      <seq>atgttttcgatttggttgagtggcgaaaaaggaacgttactggcatataccattactggcaggacaagaacgtggaccgcacattgtggaagcttggcactttaccacctggactgctgaccttctatggattaacagaggctttgaatccttcatggcatgtcttaggttttggttacacgaatgtcgattccaaattgatagaaaagggagctgtgctgcacttcaatggtaactcaaaaccctggttgaagattggtattgagaagtacaagccactctgggacaaatatgttgattatagtcatcctttattacaacaatgcaattttcactaagttgtctttagttaatttaatcttatatagttctcacagaggtggtaattttgggaatctgtaaggggttctgtgagattaagatattgtcatctcttgtgcttattccaatttgttgtagtatagcttttgaaacaaacatcaaggcaccaccagtatcttattacataaaatttcatgttggaaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0213A03-GY2cF/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0213A03.1" temp_strand="+" temp_description="C04HBa0213A03.1  CU914527.4 htgs_phase:3 submitted_to_sgn_as:C04HBa0213A03 sequenced_by:sanger upload_account_name:uk">
        <position start="52520" stop="53640"/>
      </template>
    </gDNA_segment>
    <predicted_gene_structure xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
      <exon-intron_info>
        <exon e_serial="1">
          <gDNA_exon_boundary g_start="52820" g_stop="53309" g_length="490"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="490" r_length="490" r_score="0.980"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="523" polyA_stop="541"/>
      <MATCH_line gen_id="C04HBa0213A03.1" gen_strand="+" ref_id="SGN-M1832" ref_strand="-">
        <total_alignment_score>0.980</total_alignment_score>
        <cumulative_length_of_scored_exons>490</cumulative_length_of_scored_exons>
        <coverage percentage="0.906" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0213A03.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M1832" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="52820" e_stop="53309"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATGTTTTCGATTTGGTTGAGTGGCGCAAAAGGAATGTTACTGGCATATACCATTACTGGCAGGACAAGAACGTGGACCGCACATTGTGGAAGCTTGGTACTTTACCACCTGGATTGCTGACCTTCTATGGATTGACAGAGGCTTTGAATCCTTCATGGCATGTCTTAGGTTTTGGTTACACGAATGTCGACTCCAAATTGATAGAAAAGGGAGCTGTGCTGCACTTCAATGGTAACTCAAAACCCTGGTTGAAGATTGGTATTGAGAAGTACAAGCCACTCTGGGACAAATATGTTGATTATAGTCATCCTTTATTACAACAATGCAATTTTCACTAAGTTGTCTTTAATTAATTTAATCATATATAGTTCTCACAGAGGTGGTAATTTTGGGGATCTGTAATGGGTTCTGTGAGATTAAGATATTGTCATCTCTTGTGCTTATTCCAATTTGTTGTAGTATAGCTTTTGAAACAAACATCAAGGCACCA</genome_strand>
        <mrna_strand>ATGTTTTCGATTTGGTTGAGTGGCGAAAAAGGAACGTTACTGGCATATACCATTACTGGCAGGACAAGAACGTGGACCGCACATTGTGGAAGCTTGGCACTTTACCACCTGGACTGCTGACCTTCTATGGATTAACAGAGGCTTTGAATCCTTCATGGCATGTCTTAGGTTTTGGTTACACGAATGTCGATTCCAAATTGATAGAAAAGGGAGCTGTGCTGCACTTCAATGGTAACTCAAAACCCTGGTTGAAGATTGGTATTGAGAAGTACAAGCCACTCTGGGACAAATATGTTGATTATAGTCATCCTTTATTACAACAATGCAATTTTCACTAAGTTGTCTTTAGTTAATTTAATCTTATATAGTTCTCACAGAGGTGGTAATTTTGGGAATCTGTAAGGGGTTCTGTGAGATTAAGATATTGTCATCTCTTGTGCTTATTCCAATTTGTTGTAGTATAGCTTTTGAAACAAACATCAAGGCACCA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>2</total_number_ESTs_reported>
    </alignment_module>
  <PGL_module xmlns="http://www.genomethreader.org/GTH_output/PGL_module/">
    <predicted_gene_location>
      <PGL_line PGL_serial="1" PGL_strand="-" PGL_start="38419" PGL_stop="27907"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="38419" e_stop="38172"/>
            <exon e_start="35950" e_stop="35944"/>
            <exon e_start="34908" e_stop="34886"/>
            <exon e_start="34663" e_stop="34521"/>
            <exon e_start="33166" e_stop="33068"/>
            <exon e_start="32976" e_stop="32818"/>
            <exon e_start="27959" e_stop="27907"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.000" acc_prob="0.000" e_score="0.915"/>
          <exon-intron don_prob="0.803" acc_prob="0.679" e_score="0.714"/>
          <exon-intron don_prob="0.128" acc_prob="0.586" e_score="0.522"/>
          <exon-intron don_prob="0.905" acc_prob="0.983" e_score="1.000"/>
          <exon-intron don_prob="0.977" acc_prob="0.622" e_score="0.990"/>
          <exon-intron don_prob="0.995" acc_prob="0.996" e_score="0.962"/>
          <exon-only e_score="0.925"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="0.915">
            <gDNA_exon_boundary e_start="38419" e_stop="38172" e_length="248"/>
          </exon>
          <intron i_serial="1" don_prob="0.000" acc_prob="0.000">
            <gDNA_intron_boundary i_start="38171" i_stop="35951" i_length="2221"/>
          </intron>
          <exon e_serial="2" e_score="0.714">
            <gDNA_exon_boundary e_start="35950" e_stop="35944" e_length="7"/>
          </exon>
          <intron i_serial="2" don_prob="0.803" acc_prob="0.679">
            <gDNA_intron_boundary i_start="35943" i_stop="34909" i_length="1035"/>
          </intron>
          <exon e_serial="3" e_score="0.522">
            <gDNA_exon_boundary e_start="34908" e_stop="34886" e_length="23"/>
          </exon>
          <intron i_serial="3" don_prob="0.128" acc_prob="0.586">
            <gDNA_intron_boundary i_start="34885" i_stop="34664" i_length="222"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="34663" e_stop="34521" e_length="143"/>
          </exon>
          <intron i_serial="4" don_prob="0.905" acc_prob="0.983">
            <gDNA_intron_boundary i_start="34520" i_stop="33167" i_length="1354"/>
          </intron>
          <exon e_serial="5" e_score="0.990">
            <gDNA_exon_boundary e_start="33166" e_stop="33068" e_length="99"/>
          </exon>
          <intron i_serial="5" don_prob="0.977" acc_prob="0.622">
            <gDNA_intron_boundary i_start="33067" i_stop="32977" i_length="91"/>
          </intron>
          <exon e_serial="6" e_score="0.962">
            <gDNA_exon_boundary e_start="32976" e_stop="32818" e_length="159"/>
          </exon>
          <intron i_serial="6" don_prob="0.995" acc_prob="0.996">
            <gDNA_intron_boundary i_start="32817" i_stop="27960" i_length="4858"/>
          </intron>
          <exon e_serial="7" e_score="0.925">
            <gDNA_exon_boundary e_start="27959" e_stop="27907" e_length="53"/>
          </exon>
        </exon-intron_info>
        <supporting_evidence xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/supporting_evidence/">
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="38419" stop="38172"/>
              <exon start="35950" stop="35944"/>
              <exon start="34908" stop="34886"/>
              <exon start="34663" stop="34521"/>
              <exon start="33166" stop="33068"/>
              <exon start="32976" stop="32818"/>
              <exon start="27959" stop="27907"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M6804" strand="+"/>
          </PGS_line>
        </supporting_evidence>
        <three_phase_translation xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/">
          <description PGL_serial="1" AGS_serial="1" gDNA_strand="-"/>
          <translation>
            <gDNA_template>AAAAACCGAATGCGGCGACCGCGATGAACGTTGACAAGGAACAATCCGATTGCAACCTTCCAGAACTTTCTCCACCGTCCATGGAGAAACCTGCACCGGAGCCGGCGCCGGAACCGTCACAGCAACCACCGAGAGAGTCTACTGCTCCGACGCCGTCCATGACGCAGATTAAACAGCCGCCGTCTCTGACGCAGGTGAAACAGCCGCCGTCTCTGACGCAGGTGAAACAGCCGCCGTCTCTGACGCAG : TGTCACT : CTTAAGAGTTGGTCATTGGGCAG : CTTTCTGACTGGAAACAAAAATGCTAAATTCAGCTATGGATATGCTACTTTTAAGGGGAAACGGGCCTCCATGGAGGACTACTATGAGACAAGCATATCAGAAGTTGATGGTCAAATGGTGGCATTTTTTGGTGTTTTTGATG : GTCATGGTGGTTCAAGAACAGCAGAATACTTAAAGAACAACCTCTTTAAGAATTTGAGTAGTCATCCTGATTTTATCAAAGATACAAAGTCAGCTATAG : TTGAAGCATTTAAGCAGACTGATGTCGATTACCTTAATGAAGAAAAAGGCCAGCAAAAAGATGCCGGTTCAACAGCGTCAACTGCTGTTCTTTTAGGTGATAGATTGCTTGTCGCAAATGTGGGGGACTCTAGAGTCGTGGCTTGCAGAGATGGTTCAG : CTATTCCTTTGTCCATTGATCACAAGCCTGACAGATCAGATGAGCGCGAAAGG</gDNA_template>
            <first_frame> K  N  R  M  R  R  P  R  *  T  L  T  R  N  N  P  I  A  T  F  Q  N  F  L  H  R  P  W  R  N  L  H  R  S  R  R  R  N  R  H  S  N  H  R  E  S  L  L  L  R  R  R  P  *  R  R  L  N  S  R  R  L  *  R  R  *  N  S  R  R  L  *  R  R  *  N  S  R  R  L  *  R  S :   V  T  :  L  K  S  W  S  L  G  S :   F  L  T  G  N  K  N  A  K  F  S  Y  G  Y  A  T  F  K  G  K  R  A  S  M  E  D  Y  Y  E  T  S  I  S  E  V  D  G  Q  M  V  A  F  F  G  V  F  D   : G  H  G  G  S  R  T  A  E  Y  L  K  N  N  L  F  K  N  L  S  S  H  P  D  F  I  K  D  T  K  S  A  I   : V  E  A  F  K  Q  T  D  V  D  Y  L  N  E  E  K  G  Q  Q  K  D  A  G  S  T  A  S  T  A  V  L  L  G  D  R  L  L  V  A  N  V  G  D  S  R  V  V  A  C  R  D  G  S   : A  I  P  L  S  I  D  H  K  P  D  R  S  D  E  R  E  R </first_frame>
            <second_frame>  K  T  E  C  G  D  R  D  E  R  *  Q  G  T  I  R  L  Q  P  S  R  T  F  S  T  V  H  G  E  T  C  T  G  A  G  A  G  T  V  T  A  T  T  E  R  V  Y  C  S  D  A  V  H  D  A  D  *  T  A  A  V  S  D  A  G  E  T  A  A  V  S  D  A  G  E  T  A  A  V  S  D  A   : V  S  L :   L  R  V  G  H  W  A   : A  F  *  L  E  T  K  M  L  N  S  A  M  D  M  L  L  L  R  G  N  G  P  P  W  R  T  T  M  R  Q  A  Y  Q  K  L  M  V  K  W  W  H  F  L  V  F  L  M  :  V  M  V  V  Q  E  Q  Q  N  T  *  R  T  T  S  L  R  I  *  V  V  I  L  I  L  S  K  I  Q  S  Q  L  *  :  L  K  H  L  S  R  L  M  S  I  T  L  M  K  K  K  A  S  K  K  M  P  V  Q  Q  R  Q  L  L  F  F  *  V  I  D  C  L  S  Q  M  W  G  T  L  E  S  W  L  A  E  M  V  Q  :  L  F  L  C  P  L  I  T  S  L  T  D  Q  M  S  A  K   </second_frame>
            <third_frame>   K  P  N  A  A  T  A  M  N  V  D  K  E  Q  S  D  C  N  L  P  E  L  S  P  P  S  M  E  K  P  A  P  E  P  A  P  E  P  S  Q  Q  P  P  R  E  S  T  A  P  T  P  S  M  T  Q  I  K  Q  P  P  S  L  T  Q  V  K  Q  P  P  S  L  T  Q  V  K  Q  P  P  S  L  T  Q  :  C  H   : S  *  E  L  V  I  G  Q  :  L  S  D  W  K  Q  K  C  *  I  Q  L  W  I  C  Y  F  *  G  E  T  G  L  H  G  G  L  L  *  D  K  H  I  R  S  *  W  S  N  G  G  I  F  W  C  F  *  W :   S  W  W  F  K  N  S  R  I  L  K  E  Q  P  L  *  E  F  E  *  S  S  *  F  Y  Q  R  Y  K  V  S  Y  S :   *  S  I  *  A  D  *  C  R  L  P  *  *  R  K  R  P  A  K  R  C  R  F  N  S  V  N  C  C  S  F  R  *  *  I  A  C  R  K  C  G  G  L  *  S  R  G  L  Q  R  W  F  S :   Y  S  F  V  H  *  S  Q  A  *  Q  I  R  *  A  R  K  </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0213A03.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="38176" stop="38172"/>
                    <exon start="35950" stop="35944"/>
                    <exon start="34908" stop="34886"/>
                    <exon start="34663" stop="34521"/>
                    <exon start="33166" stop="33068"/>
                    <exon start="32976" stop="32818"/>
                    <exon start="27959" stop="27907"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>489</number_coding_nucleotides>
                  <number_encoded_amino_acids>163</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>RSVTLKSWSLGSFLTGNKNAKFSYGYATFKGKRASMEDYYETSISEVDGQMVAFFGVFDGHGGSRTAEYLKNNLFKNLSSHPDFIKDTKSAIVEAFKQTDVDYLNEEKGQQKDAGSTASTAVLLGDRLLVANVGDSRVVACRDGSAIPLSIDHKPDRSDERER</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0213A03.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="38417" stop="38172"/>
                    <exon start="35950" stop="35944"/>
                    <exon start="34908" stop="34904"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>255</number_coding_nucleotides>
                  <number_encoded_amino_acids>85</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>KPNAATAMNVDKEQSDCNLPELSPPSMEKPAPEPAPEPSQQPPRESTAPTPSMTQIKQPPSLTQVKQPPSLTQVKQPPSLTQCHS*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="2" PGL_strand="+" PGL_start="52820" PGL_stop="53309"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="52820" e_stop="53309"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.980"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="0.980">
            <gDNA_exon_boundary e_start="52820" e_stop="53309" e_length="490"/>
          </exon>
        </exon-intron_info>
        <supporting_evidence xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/supporting_evidence/">
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="52820" stop="53309"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1832" strand="-"/>
          </PGS_line>
        </supporting_evidence>
        <three_phase_translation xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/">
          <description PGL_serial="2" AGS_serial="1" gDNA_strand="+"/>
          <translation>
            <gDNA_template>ATGTTTTCGATTTGGTTGAGTGGCGCAAAAGGAATGTTACTGGCATATACCATTACTGGCAGGACAAGAACGTGGACCGCACATTGTGGAAGCTTGGTACTTTACCACCTGGATTGCTGACCTTCTATGGATTGACAGAGGCTTTGAATCCTTCATGGCATGTCTTAGGTTTTGGTTACACGAATGTCGACTCCAAATTGATAGAAAAGGGAGCTGTGCTGCACTTCAATGGTAACTCAAAACCCTGGTTGAAGATTGGTATTGAGAAGTACAAGCCACTCTGGGACAAATATGTTGATTATAGTCATCCTTTATTACAACAATGCAATTTTCACTAAGTTGTCTTTAATTAATTTAATCATATATAGTTCTCACAGAGGTGGTAATTTTGGGGATCTGTAATGGGTTCTGTGAGATTAAGATATTGTCATCTCTTGTGCTTATTCCAATTTGTTGTAGTATAGCTTTTGAAACAAACATCAAGGCACCA</gDNA_template>
            <first_frame> M  F  S  I  W  L  S  G  A  K  G  M  L  L  A  Y  T  I  T  G  R  T  R  T  W  T  A  H  C  G  S  L  V  L  Y  H  L  D  C  *  P  S  M  D  *  Q  R  L  *  I  L  H  G  M  S  *  V  L  V  T  R  M  S  T  P  N  *  *  K  R  E  L  C  C  T  S  M  V  T  Q  N  P  G  *  R  L  V  L  R  S  T  S  H  S  G  T  N  M  L  I  I  V  I  L  Y  Y  N  N  A  I  F  T  K  L  S  L  I  N  L  I  I  Y  S  S  H  R  G  G  N  F  G  D  L  *  W  V  L  *  D  *  D  I  V  I  S  C  A  Y  S  N  L  L  *  Y  S  F  *  N  K  H  Q  G  T  </first_frame>
            <second_frame>  C  F  R  F  G  *  V  A  Q  K  E  C  Y  W  H  I  P  L  L  A  G  Q  E  R  G  P  H  I  V  E  A  W  Y  F  T  T  W  I  A  D  L  L  W  I  D  R  G  F  E  S  F  M  A  C  L  R  F  W  L  H  E  C  R  L  Q  I  D  R  K  G  S  C  A  A  L  Q  W  *  L  K  T  L  V  E  D  W  Y  *  E  V  Q  A  T  L  G  Q  I  C  *  L  *  S  S  F  I  T  T  M  Q  F  S  L  S  C  L  *  L  I  *  S  Y  I  V  L  T  E  V  V  I  L  G  I  C  N  G  F  C  E  I  K  I  L  S  S  L  V  L  I  P  I  C  C  S  I  A  F  E  T  N  I  K  A  P </second_frame>
            <third_frame>   V  F  D  L  V  E  W  R  K  R  N  V  T  G  I  Y  H  Y  W  Q  D  K  N  V  D  R  T  L  W  K  L  G  T  L  P  P  G  L  L  T  F  Y  G  L  T  E  A  L  N  P  S  W  H  V  L  G  F  G  Y  T  N  V  D  S  K  L  I  E  K  G  A  V  L  H  F  N  G  N  S  K  P  W  L  K  I  G  I  E  K  Y  K  P  L  W  D  K  Y  V  D  Y  S  H  P  L  L  Q  Q  C  N  F  H  *  V  V  F  N  *  F  N  H  I  *  F  S  Q  R  W  *  F  W  G  S  V  M  G  S  V  R  L  R  Y  C  H  L  L  C  L  F  Q  F  V  V  V  *  L  L  K  Q  T  S  R  H   </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0213A03.1" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="52822" stop="53157"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>333</number_coding_nucleotides>
                  <number_encoded_amino_acids>111</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>VFDLVEWRKRNVTGIYHYWQDKNVDRTLWKLGTLPPGLLTFYGLTEALNPSWHVLGFGYTNVDSKLIEKGAVLHFNGNSKPWLKIGIEKYKPLWDKYVDYSHPLLQQCNFH*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 12 chains have been computed
$ 
$ memory statistics:
$ 4064 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 2032 bytes was the average size of a spliced alignment
$ 6896 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3448 bytes was the average size of a predicted gene location
$ 2 megabytes was the average size of the backtrace matrix
$ 14 backtrace matrices have been allocated
$ 
$ date finished: 2008-11-20 23:02:58
-->
