<?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="2009-01-15 23:24:39"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0255I02-m8c3I/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C04HBa0255I02-m8c3I/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-C04HBa0255I02-m8c3I/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M1576" ref_strand="+" ref_description="SGN-M1576 T0737 [cos_markers]">
      <seq>ggcgatgtctcacttcggtagatcaggcccaccggacatcaaagacacctactctctgctcgttctcaacgttacttttcgtaccactgctgatgacttgtttcctctatttgataagtatggaaaagtagtcgatgtctttatccctagagaccgaaggactggagattctaggggttttgcatttgtgcgctacaagtatcaggatgaggctcaaaaagcagtggaaaagcttgatggaagagttgtagatggtcgggaaatcatggttcgatttgcgaagtacggccctaatgctgagagaattgacaaaggtagaattttggagcctgtacaaaggccaaaagggaggtcaagaagccgcagtcctagaccaaggcatcgtgatcatagggacaaggattctagaaggagaagccgaagtagaagtagaagtagaagtaggggaaggtatgagcgtgatcagtacc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0255I02-m8c3I/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0255I02.1" temp_strand="-" temp_description="C04HBa0255I02.1  CU326399.2 htgs_phase:3 submitted_to_sgn_as:C04HBa0255I02 sequenced_by:sanger upload_account_name:uk">
        <position start="9319" stop="5079"/>
      </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="9019" g_stop="8940" g_length="80"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="80" r_length="80" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="8939" i_stop="8844" i_length="96">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.997" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="8843" g_stop="8765" g_length="79"/>
          <reference_exon_boundary r_type="cDNA" r_start="81" r_stop="159" r_length="79" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="8764" i_stop="7947" i_length="818">
            <donor d_prob="0.991" d_score="1.00"/>
            <acceptor a_prob="0.990" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="7946" g_stop="7867" g_length="80"/>
          <reference_exon_boundary r_type="cDNA" r_start="160" r_stop="239" r_length="80" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="7866" i_stop="7798" i_length="69">
            <donor d_prob="0.969" d_score="1.00"/>
            <acceptor a_prob="0.975" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="7797" g_stop="7731" g_length="67"/>
          <reference_exon_boundary r_type="cDNA" r_start="240" r_stop="306" r_length="67" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="7730" i_stop="7518" i_length="213">
            <donor d_prob="0.976" d_score="1.00"/>
            <acceptor a_prob="0.923" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="7517" g_stop="7446" g_length="72"/>
          <reference_exon_boundary r_type="cDNA" r_start="307" r_stop="378" r_length="72" r_score="1.000"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="7445" i_stop="5471" i_length="1975">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="0.994" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="5470" g_stop="5379" g_length="92"/>
          <reference_exon_boundary r_type="cDNA" r_start="379" r_stop="470" r_length="92" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0255I02.1" gen_strand="-" ref_id="SGN-M1576" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>470</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0255I02.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M1576" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="9019" e_stop="8940"/>
          <exon e_start="8843" e_stop="8765"/>
          <exon e_start="7946" e_stop="7867"/>
          <exon e_start="7797" e_stop="7731"/>
          <exon e_start="7517" e_stop="7446"/>
          <exon e_start="5470" e_stop="5379"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GGCGATGTCTCACTTCGGTAGATCAGGCCCACCGGACATCAAAGACACCTACTCTCTGCTCGTTCTCAACGTTACTTTTCGTAATTATCCATTCTCTTTCCCTATTTTTAGCAATTTTTTCTTCTTTTCTAGCAAAGTTGTTGAATCTGATAGTTAATTACTGTTTCCCTGTACAGGTACCACTGCTGATGACTTGTTTCCTCTATTTGATAAGTATGGAAAAGTAGTCGATGTCTTTATCCCTAGAGACCGAAGGTTCTTATCTTTCATACTTTTTTTTGCAGAAGCGTACTTTTATAGTATTGTTACTGTATATTTGGCCGAGTTTACGAAGTGGAAGTCTCTTCGGCTTTTTCAGTACCCTTATTGTTTGCATAATTGTATTTGTGATGTTAATTTGATTGCTGTGTTATTTTTTCTCCACCAACTTCGTTATATGATGCCTATATGACACATTTTATTCCAGGACGATCTAAATTGTTCGACATCTTGAAACTAATGAAATCACCATGTAATTTACTTATAACTATGATGAGTCTGAGTTTTGTATGTATTGCTACTTTTGAAAGTATAAATTCATTTGATATATTCTTTATCAAACAGACTTTTCAAATATTATCCTGATATAATATTTAATGACCATTAATATGATGCATACTTTTTGAAAACAGCCTCCTTACCACACAAAGTTAGGGGTAAGGTCTGGGTACATCCTAGTCTCTCTAGACTCTACTTTTGGGATAATACTTGTTATGTTGTTGTAATATAATACATAATTCAAATTATTATTTTAAGTTGTCTTATTTCTTCCTACATGCCTTCCCCTTGGTGAGCAGCTTTAGCCGGTACCTGCACTGTTAGGTAGAAGGATGCAGGTATTCGTTACCATTATATAAAGAAATAGAGTGGGAAGGAAATGATTTCTCCTTTTCAAGTGTTACTTCTGATTATCTTACATTACTTATGAACCGAGATGTATGTATGATGTCTTAGTGTTATCTTGATGTGGAAATAGGCAAAGATGTAGCCATATCTGTAGTCTTAGACTGGTACGATGCTTATTTGTGCTTCAGGACTGGAGATTCTAGGGGTTTTGCATTTGTGCGCTACAAGTATCAGGATGAGGCTCAAAAAGCAGTGGAAAAGCTTGATGGTAACTGATCACATTAATATTTGGATGGTAGCCTATGTTGCTGTTGTTCACACTGATATTTGGTCACAGGAAGAGTTGTAGATGGTCGGGAAATCATGGTTCGATTTGCGAAGTACGGCCCTAATGCTGAGAGAATGTAAGTCTTGTCTGATGCAAGTATTCCTTAAGTTGTGGAGATTTCCTTGTTTAAAGTTGTGATTTTCATACGTGTATTTTTTAGGTTCATCTTTATCCTATAATCTAACATGTATTTTTAGTTGCATCTTTATCCTATAAACTTATTTGTAATAACCTTTTGTTTGTGGGAGTAGAACCATGTCTGACAGACTAGGATTGTTTTTGTGATCAGTGACAAAGGTAGAATTTTGGAGCCTGTACAAAGGCCAAAAGGGAGGTCAAGAAGCCGCAGTCCTAGACCAAGGTAAGAGCTTAATTTAATTATGCCACTTAAAGTGTTATCATGGTCATTGAGATTTCCATTAGAATATAATTGTTTGTTTTAGTGTAATCTTGGTCATTATCTTTGTTGATTTTGTAATCATGAAACATTGGGGATACTTCCTATAGGGAAATTCATGTGAATATTTGATCAGACATGCTTTCTACATCAACGGATTTTTACAAGTGAAACCAAGTGAAGTGCACCGCTTCCTTAAAGCATACAATATGTTTGTTCACTAATCAATTTACTTGTGCTTTGCGTGGTCATAGAAGATGGGGAATTTCAGACATGATCTTGTAATAAAATTGATTTTTTAATGTTATCACACACAACTTCACAACTGCCCATGTCACCAATTCTCAAATTCTATTCATTCAAGTTGTAGAAGTTAAAAATTAATTATCATACAATGAACTTTGGAGCCGAGAAAAAGAAATCTACGACGATTAGGAGAAAGATGTCCCTTCAAGTTGCCCTCTCAATCAGCTAAATAGGAGTAACTGATCAAGAAAATGCTTGTTTCTATACTCACCTTAATTGGTTTAAAACACCCTTTGCTTCTATTCTCACCCTAAGTAATCATTTGCATGTACCAGATGATAAGAATTTCACATTCTTATTTTATAAAAGTTAACAGTGGCGCGGTAGTTTTTCATTTTTTGCGCTGGAAAACTGGAAAAAAGGAGACAATATAGGAACTATTTGCATCTTGCTTGTGAAGTGGGAAATTTACACAAATATATGTTGAGTAGGTCCATCCATATACAAGATGTTATTTTTCTTTGAAGCACATACTCTATGAAAAAGCATAATATGGCATACATGAATTCAGTATTATACAAATGATCAAATTATGAGTAAAATAACTAATTTAGAGCCTGTGGATTAGCTTTTGACTTATAAGTGGCTTATTTTACCATTTTAGCTTAAAACCAAGTGGTTGTAAGCATTTTTTGAAATTATCCAAACACTCCAAACGTGCTTCAAAGTTATTTTGGCTTGAAAAAGCACTTAAAATAGGCCAATCCAAACAGGCTCTAATTCATATTCAGAGAAAGTGTATCCAAATTCAATTTTCTTTGTAAAAAGTATGGTCAAACACGACTCTCCCATTATAATATTTAATTTTTAATGGCCAAATCAGTAAACTCTCTTTCTTTCATCAGCTGTTGTAATTGAACTTGCCTTTAATAAATTTGCAGATTTCTTGATCTTCTTTTTTTGGCTAAGATTTTTCCTCTGATTGAATTGATTGATTGAGTTGATACTGATGTTATATGGTCTTCATGCTTTCAATTCCTCTGCAGTGTGTAACAACCATCTCAATGTGGTAAACTGAGTGAGGGGTAAATAGGGAAATCAGTAACATTGTTATCTTACTTTGAGCCATTAATGTTTATGATAACAATAATGTTGTGATTTTACTTGTTTCCTGCCATTAGTAAATGGATGAAAACATTTGTTATTAATTAGTTAAAGCAATTTAGATTGCCAACATCTCAAAACAACTGAGTAGGTTCACGAACATGTTTCAGTTGGATTAGATGGAGGCGCCTTTATACGTCTAGCATCGTCATCTACTGTCCGACTGGATACTAATATCAGTTTTCTGTCTTGGGATTGTGTACAGAACAAGCTATAACTCCAAAGCTTTTTGTGTGTGTGGTGGAATGTGGTGATCCCATCAAGGCATAAATGTTTGAGCTTTTGTGGATAAGCTTATTTTGGTCTAGAATGGATACGGGCATATTTTGGTTTAGAATAGATACGGGTTTATATTCTTCTTCTATAACTAATTCCTCTCCAAAAACAAGGTGGAAGTATGCACATAATATTGCTTCTCCTTTTGTGTGGTACTTGAGTTGAATGATTGCCATTTTGCTTTTTAGCTAAGAGAGGTTGAAGAGTTGTATCCACAATCTGATCTTCACCCTTTTTTGTTTGTTTATCTTAGGCATCGTGATCATAGGGACAAGGATTCTAGAAGGAGAAGCCGAAGTAGAAGTAGAAGTAGAAGTAGGGGAAGGTATGAGCGTGATCAGTACC</genome_strand>
        <mrna_strand>GGCGATGTCTCACTTCGGTAGATCAGGCCCACCGGACATCAAAGACACCTACTCTCTGCTCGTTCTCAACGTTACTTTTC................................................................................................GTACCACTGCTGATGACTTGTTTCCTCTATTTGATAAGTATGGAAAAGTAGTCGATGTCTTTATCCCTAGAGACCGAAG..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GACTGGAGATTCTAGGGGTTTTGCATTTGTGCGCTACAAGTATCAGGATGAGGCTCAAAAAGCAGTGGAAAAGCTTGATG.....................................................................GAAGAGTTGTAGATGGTCGGGAAATCATGGTTCGATTTGCGAAGTACGGCCCTAATGCTGAGAGAAT.....................................................................................................................................................................................................................TGACAAAGGTAGAATTTTGGAGCCTGTACAAAGGCCAAAAGGGAGGTCAAGAAGCCGCAGTCCTAGACCAAG.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCATCGTGATCATAGGGACAAGGATTCTAGAAGGAGAAGCCGAAGTAGAAGTAGAAGTAGAAGTAGGGGAAGGTATGAGCGTGATCAGTACC</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-C04HBa0255I02-m8c3I/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M6793" ref_strand="+" ref_description="SGN-M6793 C2_At1g35720 [cosii_markers]">
      <seq>ctagtctcgaatttttatttttatttttaaaaagagggccctattgtagatcaaaggtgatctttgtgtctttaaaaagaaaagaagggaagtggaaaaaattgactccatactcatcactctgcattttcgagtcttcacaatcatatcctcctaaccacacacagaagaaaaaaaatggcaagtcttacagttccggcagaagttccttccgtcgctgaagactgtgaacaactccgatctgccttcaaaggatggggaacgaacgagaagttgattatatcaattttggctcatagaaatgctgctcaacgcaaattgattcgacagacttatgctgagacttttggggaagatctacttaaagagttggacagagaacttacccatgattttgagaaattggtgctaatatggacactggatccgtcagaacgtgatgcctatttggctaaggaagctactaagagatggacaaaaagcaactttgttcttgtggagatagcttgtactagatctcctaaagaactggttttggcaagggaagcttatcatgctcgtaacaagaaatctctcgaagaggacgttgcttatcacactactggggatcaccgcaagcttttggtacctcttgtgagctcctaccgatatggaggagacgaggtggacttgcgccttgctaaagcagaatctaaagtgctgcatgagaagatctccgataaggcttacagtgacgatgaggtcattagaattttagccacaaggagcaaagcgcaactcaatgctactttgaatcattacaaagatgaatatggtgaggatatcctaaagcaattggaagatgaggatgagtttgttgcactattgagggccaccataaaaggtcttgtctaccctgagcactatttcgtggaggttcttcgtgatgcaattaacaggagaggaacagaggaagatcatctgagccgagttattgctacaagggctgaggtcgatctgaagactatcgctaacgagtaccagaagagggatagcattcctctgggtcgcgccattgccaaagatacaggaggagattatgagaatatgctggtggctttacttggacaagaggaggaatgaggaggattggctcacttctgttttataatgaccagaataaatatgccatctcccatatatttcagagttggcatctgtttgatgattgagtgtggtctgtttcacatgagcttttagtccttttcttcgtgtgagaaactttgaatatgcatctttgtgctgtctaaaatattttctaataatttgcatcaattacttatcatcttgtatccattacaatatcttcaactacgcctcagtttcaagcaagttgagatctatcaatgtcacttcatttaaactaaaaaaaaaaagaaaaaaacaaaaaaaacaaacaaaaaagac</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0255I02-m8c3I/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0255I02.1" temp_strand="+" temp_description="C04HBa0255I02.1  CU326399.2 htgs_phase:3 submitted_to_sgn_as:C04HBa0255I02 sequenced_by:sanger upload_account_name:uk">
        <position start="51757" stop="54759"/>
      </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="52061" g_stop="52284" g_length="224"/>
          <reference_exon_boundary r_type="cDNA" r_start="35" r_stop="253" r_length="219" r_score="0.915"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="52285" i_stop="52485" i_length="201">
            <donor d_prob="0.984" d_score="0.98"/>
            <acceptor a_prob="0.999" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="52486" g_stop="52631" g_length="146"/>
          <reference_exon_boundary r_type="cDNA" r_start="254" r_stop="399" r_length="146" r_score="0.973"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="52632" i_stop="53013" i_length="382">
            <donor d_prob="0.989" d_score="0.96"/>
            <acceptor a_prob="0.996" a_score="0.92"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="53014" g_stop="53232" g_length="219"/>
          <reference_exon_boundary r_type="cDNA" r_start="400" r_stop="618" r_length="219" r_score="0.973"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="53233" i_stop="53577" i_length="345">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.973" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="53578" g_stop="53790" g_length="213"/>
          <reference_exon_boundary r_type="cDNA" r_start="619" r_stop="831" r_length="213" r_score="0.986"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="53791" i_stop="53900" i_length="110">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="53901" g_stop="54409" g_length="509"/>
          <reference_exon_boundary r_type="cDNA" r_start="832" r_stop="1334" r_length="503" r_score="0.939"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="1405" polyA_stop="1423"/>
      <MATCH_line gen_id="C04HBa0255I02.1" gen_strand="+" ref_id="SGN-M6793" ref_strand="+">
        <total_alignment_score>0.952</total_alignment_score>
        <cumulative_length_of_scored_exons>1311</cumulative_length_of_scored_exons>
        <coverage percentage="0.907" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0255I02.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M6793" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="52061" e_stop="52284"/>
          <exon e_start="52486" e_stop="52631"/>
          <exon e_start="53014" e_stop="53232"/>
          <exon e_start="53578" e_stop="53790"/>
          <exon e_start="53901" e_stop="54409"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGGGCCCTATTGTAGATCAAAAGTGATCTTTGTGCGTCTTTAAAAAGGGAAGAAGGAATGTGTAAAAAATTGACTCCCTACTCATCACCCTGCATTTTCGAGTCTTGACAATCATATCCTCCTCCTGCCCACACAGAGAAGAAGAAAAATGGCAAGTCTTACAGTTCCGGCAGAAGTTCCTTCAGTCGCTGAAGACTGTGAACAACTCCGATCTGCCTTCAAAGGTATTGAAGTCAACTTATAATACCATTAAATCTCTCAACAACGAATATACAGATTCACTACTTTGATTTTTCTAGCATATTCTAAATTCTGTTTACTATCTTTTGCGATTATAGAGATCTTATATTTTTTTAGATTGATCGGTGATGTTAACATCAAAATTGATTGAAGTTTTAACTTCTGGAATGATTTGATTGTTACAGGATGGGGAACGAATGAGAAGTTGATTATATCAATTTTGGCTCATAGAAATGCGGCTCAACGCAAATTGATTCGACAGACTTATGCTGAGACTTTTGGGGAAGATCTGCTTAAAGAGTTGGACAGAGAACTTACTCATGATTTTGAGGTCATTTTCATAATTACAGAATAATTTTTGAATTCTTAGTTGATTATTTGAGTTTCTGAGTTACTCTGTGTGATCAAAGGCAGATCTATGATGTAAAATATATATATACACATTATCCGTATAGTAAAACCATGCTAATTCTGAACCCGATACTCTAGATCATGGATTCAACTTCGATTTTATCAGAGACAGATCTATGAAAAATATGTATTAGTATGTCAAAATATGAAAATGTGTACATATATAATAAAATCATACGTGTTTTGAATTCACTGACTCGAGATCCTGGATTTGCCTTTTGACTTTTTGATCGTATGTGAACTTTGATCAGAAATGATAACCAACACTTGTACTTGTGTTTTCTCTTGAATGTTTCTCGCAGAAATTGGTGGTAGTATGGACACTGGATCCTGCAGAACGTGATGCCTATTTGGCTAAGGAAGCTACTAAGAGATGGACAAAAAGCAACTTTGTTCTTGTGGAGATAGCTTGTACCAGATCTCCTAAAGAACTGGTTTTGGCAAGAGAAGCTTATCATGCTCGTAACAAGAAATCTCTCGAAGAGGACGTTGCTTATCACACTACTGGGGATCACCGCAAGGTATATCATTCAAAGCATTCTAATTGCAAGTAGTCTCATTTGTAGCTCTGTATCCGAGTCCTTAACAATAATTCATTAAGTTGTTGTCAAATTAAATGAGGTTTGAATGGTGCCCATGAAGCATTTGCTCTGTTTTTGGAGATCTAAAGACATATAATCGACAAAGTACAACTTTTTAATCTATAGTTCTTGTTATCGTAACATATTCTCAAGGCAAGAATGTCTTTGTGCCACATTGCAATGTAGGGTATATCTAATGTTCATTGAACTCCATGTTTGTTTGGATGAATACTGACAGTGAATTAACTTTGTGTATTGATCATTTAAGTTTCCAACTTCTTACAGCTTTTGGTACCTCTTGTGAGCTCCTACCGATATGGGGGAGATGAGGTGGACTTGCGACTTGCTAAAGCAGAATCTAAAGTGCTGCATGAGAAGATCTCCGATAAGGCTTACAGTGACGATGAGGTCATTAGAATTTTAGCCACAAGGAGCAAAGCGCAACTCAATGCTACTTTGAATCATTACAAAGATGAATATGGTGAGGATATCCTAAAGGTACAGATTCATCCGTTGCTCCATTTCTTTCAGTCATACGCCTTTCTACTGTAGGACTGGCTTTCTATTTCTGCTATATTGAATTATTGAGTTCTTTTGTCAATGTGCAGCAATTAGAAGATGAGGATGAGTTTGTTGCACTGTTAAGGGCCACCATAAAAGGTCTTGTCTACCCCGAGCACTATTTCGTGGAGGTTCTTCGTGATGCAATTAACAGGAGAGGAACAGAGGAAGATCATCTAACCCGAGTTATCGCTACAAGGGCTGAGGTCGATCTGAAGACTATCGCTAACGAGTACCAGAAGAGGGATAGCGTTCCTCTGGGTCGCGCCATTGCCAAAGATACAGGAGGAGATTATGAGAATATGCTGGTGGCTTTACTTGGACAAGAGGAGGAATAAGAAGCGGATTGGCTCACTTCTGTTTTATAATGACCAGAATAAATATGCCATTCTCCCATATATTTCAGAGTTGGCATGTGTTTGATGATTGAGTGTGGTCTGTTTCACATGAGCTTTTAGTCCTTTTCTTCTTGTGAGAAACTTTGAATATGAATCTTTGTGCTGTCTAAAAATGTTCTCTAATGATTTGCATCCACTACAATAATCTTCAACTACGC</genome_strand>
        <mrna_strand>AGGGCCCTATTGTAGATCAAAGGTGATCTTTGT--GTCTTTAAAAAGAAAAGAAGGGAAGTGGAAAAAATTGACTCCATACTCATCACTCTGCATTTTCGAGTCTTCACAATCATA---TCCTCCTAACCACACACAGAAGAAAAAAAATGGCAAGTCTTACAGTTCCGGCAGAAGTTCCTTCCGTCGCTGAAGACTGTGAACAACTCCGATCTGCCTTCAAAG.........................................................................................................................................................................................................GATGGGGAACGAACGAGAAGTTGATTATATCAATTTTGGCTCATAGAAATGCTGCTCAACGCAAATTGATTCGACAGACTTATGCTGAGACTTTTGGGGAAGATCTACTTAAAGAGTTGGACAGAGAACTTACCCATGATTTTGAG..............................................................................................................................................................................................................................................................................................................................................................................................AAATTGGTGCTAATATGGACACTGGATCCGTCAGAACGTGATGCCTATTTGGCTAAGGAAGCTACTAAGAGATGGACAAAAAGCAACTTTGTTCTTGTGGAGATAGCTTGTACTAGATCTCCTAAAGAACTGGTTTTGGCAAGGGAAGCTTATCATGCTCGTAACAAGAAATCTCTCGAAGAGGACGTTGCTTATCACACTACTGGGGATCACCGCAAG.........................................................................................................................................................................................................................................................................................................................................................CTTTTGGTACCTCTTGTGAGCTCCTACCGATATGGAGGAGACGAGGTGGACTTGCGCCTTGCTAAAGCAGAATCTAAAGTGCTGCATGAGAAGATCTCCGATAAGGCTTACAGTGACGATGAGGTCATTAGAATTTTAGCCACAAGGAGCAAAGCGCAACTCAATGCTACTTTGAATCATTACAAAGATGAATATGGTGAGGATATCCTAAAG..............................................................................................................CAATTGGAAGATGAGGATGAGTTTGTTGCACTATTGAGGGCCACCATAAAAGGTCTTGTCTACCCTGAGCACTATTTCGTGGAGGTTCTTCGTGATGCAATTAACAGGAGAGGAACAGAGGAAGATCATCTGAGCCGAGTTATTGCTACAAGGGCTGAGGTCGATCTGAAGACTATCGCTAACGAGTACCAGAAGAGGGATAGCATTCCTCTGGGTCGCGCCATTGCCAAAGATACAGGAGGAGATTATGAGAATATGCTGGTGGCTTTACTTGGACAAGAGGAGGAAT--GAGGAGGATTGGCTCACTTCTGTTTTATAATGACCAGAATAAATATGCCA-TCTCCCATATATTTCAGAGTTGGCATCTGTTTGATGATTGAGTGTGGTCTGTTTCACATGAGCTTTTAGTCCTTTTCTTCGTGTGAGAAACTTTGAATATGCATCTTTGTGCTGTCT-AAAATATTTTCTAATAATTTGCATCAATTAC--TTATCATCTTGTATCC</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-C04HBa0255I02-m8c3I/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M234-F" ref_strand="-" ref_description="SGN-M234-F CT188-F [rflp_markers_forward]">
      <seq>gaatatggtgaggatatcctaaagcaattagaagatgaggatgagtttgttgcactgttaagggccaccataaaaggtcttgtctaccccgagcactatttcgtggaggttcttcgtgatgcaattaacaggagaggaacagaggaagatcatctaccccgagttatcgctacaagggctgaggtcgatctgaagactatcgctaacgagttccagaagagggatagcgttcctctgggtcgcgccattgccaaagatacaggaggagattatgagaatatgctggtggcttttcttggacaagaggaggaataagaagcggattggctcatttctgttttataatgaccagaataaatatgccattctcccatatatttcagagttggcatgtgtttgatgattgagcgtggtctgtttcacatgagcttttagtccttttcttcttgtgagaaactttgaatatgaatctttgtgctgtctaaaacaaaaaaaaaaaaag</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0255I02-m8c3I/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0255I02.1" temp_strand="+" temp_description="C04HBa0255I02.1  CU326399.2 htgs_phase:3 submitted_to_sgn_as:C04HBa0255I02 sequenced_by:sanger upload_account_name:uk">
        <position start="53467" stop="54663"/>
      </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="53767" g_stop="53790" g_length="24"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="24" r_length="24" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="53791" i_stop="53900" i_length="110">
            <donor d_prob="0.998" d_score="0.00"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="53901" g_stop="54363" g_length="463"/>
          <reference_exon_boundary r_type="cDNA" r_start="25" r_stop="487" r_length="463" r_score="0.989"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="489" polyA_stop="502"/>
      <MATCH_line gen_id="C04HBa0255I02.1" gen_strand="+" ref_id="SGN-M234-F" ref_strand="-">
        <total_alignment_score>0.989</total_alignment_score>
        <cumulative_length_of_scored_exons>487</cumulative_length_of_scored_exons>
        <coverage percentage="0.970" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0255I02.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M234-F" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="53767" e_stop="53790"/>
          <exon e_start="53901" e_stop="54363"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GAATATGGTGAGGATATCCTAAAGGTACAGATTCATCCGTTGCTCCATTTCTTTCAGTCATACGCCTTTCTACTGTAGGACTGGCTTTCTATTTCTGCTATATTGAATTATTGAGTTCTTTTGTCAATGTGCAGCAATTAGAAGATGAGGATGAGTTTGTTGCACTGTTAAGGGCCACCATAAAAGGTCTTGTCTACCCCGAGCACTATTTCGTGGAGGTTCTTCGTGATGCAATTAACAGGAGAGGAACAGAGGAAGATCATCTAACCCGAGTTATCGCTACAAGGGCTGAGGTCGATCTGAAGACTATCGCTAACGAGTACCAGAAGAGGGATAGCGTTCCTCTGGGTCGCGCCATTGCCAAAGATACAGGAGGAGATTATGAGAATATGCTGGTGGCTTTACTTGGACAAGAGGAGGAATAAGAAGCGGATTGGCTCACTTCTGTTTTATAATGACCAGAATAAATATGCCATTCTCCCATATATTTCAGAGTTGGCATGTGTTTGATGATTGAGTGTGGTCTGTTTCACATGAGCTTTTAGTCCTTTTCTTCTTGTGAGAAACTTTGAATATGAATCTTTGTGCTGTCTAAAA</genome_strand>
        <mrna_strand>GAATATGGTGAGGATATCCTAAAG..............................................................................................................CAATTAGAAGATGAGGATGAGTTTGTTGCACTGTTAAGGGCCACCATAAAAGGTCTTGTCTACCCCGAGCACTATTTCGTGGAGGTTCTTCGTGATGCAATTAACAGGAGAGGAACAGAGGAAGATCATCTACCCCGAGTTATCGCTACAAGGGCTGAGGTCGATCTGAAGACTATCGCTAACGAGTTCCAGAAGAGGGATAGCGTTCCTCTGGGTCGCGCCATTGCCAAAGATACAGGAGGAGATTATGAGAATATGCTGGTGGCTTTTCTTGGACAAGAGGAGGAATAAGAAGCGGATTGGCTCATTTCTGTTTTATAATGACCAGAATAAATATGCCATTCTCCCATATATTTCAGAGTTGGCATGTGTTTGATGATTGAGCGTGGTCTGTTTCACATGAGCTTTTAGTCCTTTTCTTCTTGTGAGAAACTTTGAATATGAATCTTTGTGCTGTCTAAAA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>3</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="9019" PGL_stop="5379"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="9019" e_stop="8940"/>
            <exon e_start="8843" e_stop="8765"/>
            <exon e_start="7946" e_stop="7867"/>
            <exon e_start="7797" e_stop="7731"/>
            <exon e_start="7517" e_stop="7446"/>
            <exon e_start="5470" e_stop="5379"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.999" acc_prob="0.997" e_score="1.000"/>
          <exon-intron don_prob="0.991" acc_prob="0.990" e_score="1.000"/>
          <exon-intron don_prob="0.969" acc_prob="0.975" e_score="1.000"/>
          <exon-intron don_prob="0.976" acc_prob="0.923" e_score="1.000"/>
          <exon-intron don_prob="0.998" acc_prob="0.994" e_score="1.000"/>
          <exon-only e_score="1.000"/>
        </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="1.000">
            <gDNA_exon_boundary e_start="9019" e_stop="8940" e_length="80"/>
          </exon>
          <intron i_serial="1" don_prob="0.999" acc_prob="0.997">
            <gDNA_intron_boundary i_start="8939" i_stop="8844" i_length="96"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="8843" e_stop="8765" e_length="79"/>
          </exon>
          <intron i_serial="2" don_prob="0.991" acc_prob="0.990">
            <gDNA_intron_boundary i_start="8764" i_stop="7947" i_length="818"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="7946" e_stop="7867" e_length="80"/>
          </exon>
          <intron i_serial="3" don_prob="0.969" acc_prob="0.975">
            <gDNA_intron_boundary i_start="7866" i_stop="7798" i_length="69"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="7797" e_stop="7731" e_length="67"/>
          </exon>
          <intron i_serial="4" don_prob="0.976" acc_prob="0.923">
            <gDNA_intron_boundary i_start="7730" i_stop="7518" i_length="213"/>
          </intron>
          <exon e_serial="5" e_score="1.000">
            <gDNA_exon_boundary e_start="7517" e_stop="7446" e_length="72"/>
          </exon>
          <intron i_serial="5" don_prob="0.998" acc_prob="0.994">
            <gDNA_intron_boundary i_start="7445" i_stop="5471" i_length="1975"/>
          </intron>
          <exon e_serial="6" e_score="1.000">
            <gDNA_exon_boundary e_start="5470" e_stop="5379" e_length="92"/>
          </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="9019" stop="8940"/>
              <exon start="8843" stop="8765"/>
              <exon start="7946" stop="7867"/>
              <exon start="7797" stop="7731"/>
              <exon start="7517" stop="7446"/>
              <exon start="5470" stop="5379"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1576" 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>GGCGATGTCTCACTTCGGTAGATCAGGCCCACCGGACATCAAAGACACCTACTCTCTGCTCGTTCTCAACGTTACTTTTC : GTACCACTGCTGATGACTTGTTTCCTCTATTTGATAAGTATGGAAAAGTAGTCGATGTCTTTATCCCTAGAGACCGAAG : GACTGGAGATTCTAGGGGTTTTGCATTTGTGCGCTACAAGTATCAGGATGAGGCTCAAAAAGCAGTGGAAAAGCTTGATG : GAAGAGTTGTAGATGGTCGGGAAATCATGGTTCGATTTGCGAAGTACGGCCCTAATGCTGAGAGAAT : TGACAAAGGTAGAATTTTGGAGCCTGTACAAAGGCCAAAAGGGAGGTCAAGAAGCCGCAGTCCTAGACCAAG : GCATCGTGATCATAGGGACAAGGATTCTAGAAGGAGAAGCCGAAGTAGAAGTAGAAGTAGAAGTAGGGGAAGGTATGAGCGTGATCAGTACC</gDNA_template>
            <first_frame> G  D  V  S  L  R  *  I  R  P  T  G  H  Q  R  H  L  L  S  A  R  S  Q  R  Y  F  S :   Y  H  C  *  *  L  V  S  S  I  *  *  V  W  K  S  S  R  C  L  Y  P  *  R  P  K  :  D  W  R  F  *  G  F  C  I  C  A  L  Q  V  S  G  *  G  S  K  S  S  G  K  A  *  W :   K  S  C  R  W  S  G  N  H  G  S  I  C  E  V  R  P  *  C  *  E  N  :  *  Q  R  *  N  F  G  A  C  T  K  A  K  R  E  V  K  K  P  Q  S  *  T  K  :  A  S  *  S  *  G  Q  G  F  *  K  E  K  P  K  *  K  *  K  *  K  *  G  K  V  *  A  *  S  V   </first_frame>
            <second_frame>  A  M  S  H  F  G  R  S  G  P  P  D  I  K  D  T  Y  S  L  L  V  L  N  V  T  F   : R  T  T  A  D  D  L  F  P  L  F  D  K  Y  G  K  V  V  D  V  F  I  P  R  D  R  R :   T  G  D  S  R  G  F  A  F  V  R  Y  K  Y  Q  D  E  A  Q  K  A  V  E  K  L  D   : G  R  V  V  D  G  R  E  I  M  V  R  F  A  K  Y  G  P  N  A  E  R  I :   D  K  G  R  I  L  E  P  V  Q  R  P  K  G  R  S  R  S  R  S  P  R  P  R :   H  R  D  H  R  D  K  D  S  R  R  R  S  R  S  R  S  R  S  R  S  R  G  R  Y  E  R  D  Q  Y  </second_frame>
            <third_frame>   R  C  L  T  S  V  D  Q  A  H  R  T  S  K  T  P  T  L  C  S  F  S  T  L  L  F  :  V  P  L  L  M  T  C  F  L  Y  L  I  S  M  E  K  *  S  M  S  L  S  L  E  T  E   : G  L  E  I  L  G  V  L  H  L  C  A  T  S  I  R  M  R  L  K  K  Q  W  K  S  L  M  :  E  E  L  *  M  V  G  K  S  W  F  D  L  R  S  T  A  L  M  L  R  E   : L  T  K  V  E  F  W  S  L  Y  K  G  Q  K  G  G  Q  E  A  A  V  L  D  Q   : G  I  V  I  I  G  T  R  I  L  E  G  E  A  E  V  E  V  E  V  E  V  G  E  G  M  S  V  I  S  T </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="C04HBa0255I02.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="9018" stop="8940"/>
                    <exon start="8843" stop="8765"/>
                    <exon start="7946" stop="7867"/>
                    <exon start="7797" stop="7731"/>
                    <exon start="7517" stop="7446"/>
                    <exon start="5470" stop="5380"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>468</number_coding_nucleotides>
                  <number_encoded_amino_acids>156</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>AMSHFGRSGPPDIKDTYSLLVLNVTFRTTADDLFPLFDKYGKVVDVFIPRDRRTGDSRGFAFVRYKYQDEAQKAVEKLDGRVVDGREIMVRFAKYGPNAERIDKGRILEPVQRPKGRSRSRSPRPRHRDHRDKDSRRRSRSRSRSRSRGRYERDQY</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="52061" PGL_stop="54409"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="52061" e_stop="52284"/>
            <exon e_start="52486" e_stop="52631"/>
            <exon e_start="53014" e_stop="53232"/>
            <exon e_start="53578" e_stop="53790"/>
            <exon e_start="53901" e_stop="54409"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.984" acc_prob="0.999" e_score="0.915"/>
          <exon-intron don_prob="0.989" acc_prob="0.996" e_score="0.973"/>
          <exon-intron don_prob="1.000" acc_prob="0.973" e_score="0.973"/>
          <exon-intron don_prob="0.998" acc_prob="1.000" e_score="0.986"/>
          <exon-only e_score="0.939"/>
        </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="52061" e_stop="52284" e_length="224"/>
          </exon>
          <intron i_serial="1" don_prob="0.984" acc_prob="0.999">
            <gDNA_intron_boundary i_start="52285" i_stop="52485" i_length="201"/>
          </intron>
          <exon e_serial="2" e_score="0.973">
            <gDNA_exon_boundary e_start="52486" e_stop="52631" e_length="146"/>
          </exon>
          <intron i_serial="2" don_prob="0.989" acc_prob="0.996">
            <gDNA_intron_boundary i_start="52632" i_stop="53013" i_length="382"/>
          </intron>
          <exon e_serial="3" e_score="0.973">
            <gDNA_exon_boundary e_start="53014" e_stop="53232" e_length="219"/>
          </exon>
          <intron i_serial="3" don_prob="1.000" acc_prob="0.973">
            <gDNA_intron_boundary i_start="53233" i_stop="53577" i_length="345"/>
          </intron>
          <exon e_serial="4" e_score="0.986">
            <gDNA_exon_boundary e_start="53578" e_stop="53790" e_length="213"/>
          </exon>
          <intron i_serial="4" don_prob="0.998" acc_prob="1.000">
            <gDNA_intron_boundary i_start="53791" i_stop="53900" i_length="110"/>
          </intron>
          <exon e_serial="5" e_score="0.939">
            <gDNA_exon_boundary e_start="53901" e_stop="54409" e_length="509"/>
          </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="52061" stop="52284"/>
              <exon start="52486" stop="52631"/>
              <exon start="53014" stop="53232"/>
              <exon start="53578" stop="53790"/>
              <exon start="53901" stop="54409"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M6793" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="53767" stop="53790"/>
              <exon start="53901" stop="54363"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M234-F" 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>AGGGCCCTATTGTAGATCAAAAGTGATCTTTGTGCGTCTTTAAAAAGGGAAGAAGGAATGTGTAAAAAATTGACTCCCTACTCATCACCCTGCATTTTCGAGTCTTGACAATCATATCCTCCTCCTGCCCACACAGAGAAGAAGAAAAATGGCAAGTCTTACAGTTCCGGCAGAAGTTCCTTCAGTCGCTGAAGACTGTGAACAACTCCGATCTGCCTTCAAAG : GATGGGGAACGAATGAGAAGTTGATTATATCAATTTTGGCTCATAGAAATGCGGCTCAACGCAAATTGATTCGACAGACTTATGCTGAGACTTTTGGGGAAGATCTGCTTAAAGAGTTGGACAGAGAACTTACTCATGATTTTGAG : AAATTGGTGGTAGTATGGACACTGGATCCTGCAGAACGTGATGCCTATTTGGCTAAGGAAGCTACTAAGAGATGGACAAAAAGCAACTTTGTTCTTGTGGAGATAGCTTGTACCAGATCTCCTAAAGAACTGGTTTTGGCAAGAGAAGCTTATCATGCTCGTAACAAGAAATCTCTCGAAGAGGACGTTGCTTATCACACTACTGGGGATCACCGCAAG : CTTTTGGTACCTCTTGTGAGCTCCTACCGATATGGGGGAGATGAGGTGGACTTGCGACTTGCTAAAGCAGAATCTAAAGTGCTGCATGAGAAGATCTCCGATAAGGCTTACAGTGACGATGAGGTCATTAGAATTTTAGCCACAAGGAGCAAAGCGCAACTCAATGCTACTTTGAATCATTACAAAGATGAATATGGTGAGGATATCCTAAAG : CAATTAGAAGATGAGGATGAGTTTGTTGCACTGTTAAGGGCCACCATAAAAGGTCTTGTCTACCCCGAGCACTATTTCGTGGAGGTTCTTCGTGATGCAATTAACAGGAGAGGAACAGAGGAAGATCATCTAACCCGAGTTATCGCTACAAGGGCTGAGGTCGATCTGAAGACTATCGCTAACGAGTACCAGAAGAGGGATAGCGTTCCTCTGGGTCGCGCCATTGCCAAAGATACAGGAGGAGATTATGAGAATATGCTGGTGGCTTTACTTGGACAAGAGGAGGAATAAGAAGCGGATTGGCTCACTTCTGTTTTATAATGACCAGAATAAATATGCCATTCTCCCATATATTTCAGAGTTGGCATGTGTTTGATGATTGAGTGTGGTCTGTTTCACATGAGCTTTTAGTCCTTTTCTTCTTGTGAGAAACTTTGAATATGAATCTTTGTGCTGTCTAAAAATGTTCTCTAATGATTTGCATCCACTACAATAATCTTCAACTACGC</gDNA_template>
            <first_frame> R  A  L  L  *  I  K  S  D  L  C  A  S  L  K  R  E  E  G  M  C  K  K  L  T  P  Y  S  S  P  C  I  F  E  S  *  Q  S  Y  P  P  P  A  H  T  E  K  K  K  N  G  K  S  Y  S  S  G  R  S  S  F  S  R  *  R  L  *  T  T  P  I  C  L  Q  R :   M  G  N  E  *  E  V  D  Y  I  N  F  G  S  *  K  C  G  S  T  Q  I  D  S  T  D  L  C  *  D  F  W  G  R  S  A  *  R  V  G  Q  R  T  Y  S  *  F  *   : E  I  G  G  S  M  D  T  G  S  C  R  T  *  C  L  F  G  *  G  S  Y  *  E  M  D  K  K  Q  L  C  S  C  G  D  S  L  Y  Q  I  S  *  R  T  G  F  G  K  R  S  L  S  C  S  *  Q  E  I  S  R  R  G  R  C  L  S  H  Y  W  G  S  P  Q   : A  F  G  T  S  C  E  L  L  P  I  W  G  R  *  G  G  L  A  T  C  *  S  R  I  *  S  A  A  *  E  D  L  R  *  G  L  Q  *  R  *  G  H  *  N  F  S  H  K  E  Q  S  A  T  Q  C  Y  F  E  S  L  Q  R  *  I  W  *  G  Y  P  K   : A  I  R  R  *  G  *  V  C  C  T  V  K  G  H  H  K  R  S  C  L  P  R  A  L  F  R  G  G  S  S  *  C  N  *  Q  E  R  N  R  G  R  S  S  N  P  S  Y  R  Y  K  G  *  G  R  S  E  D  Y  R  *  R  V  P  E  E  G  *  R  S  S  G  S  R  H  C  Q  R  Y  R  R  R  L  *  E  Y  A  G  G  F  T  W  T  R  G  G  I  R  S  G  L  A  H  F  C  F  I  M  T  R  I  N  M  P  F  S  H  I  F  Q  S  W  H  V  F  D  D  *  V  W  S  V  S  H  E  L  L  V  L  F  F  L  *  E  T  L  N  M  N  L  C  A  V  *  K  C  S  L  M  I  C  I  H  Y  N  N  L  Q  L  R </first_frame>
            <second_frame>  G  P  Y  C  R  S  K  V  I  F  V  R  L  *  K  G  K  K  E  C  V  K  N  *  L  P  T  H  H  P  A  F  S  S  L  D  N  H  I  L  L  L  P  T  Q  R  R  R  K  M  A  S  L  T  V  P  A  E  V  P  S  V  A  E  D  C  E  Q  L  R  S  A  F  K   : G  W  G  T  N  E  K  L  I  I  S  I  L  A  H  R  N  A  A  Q  R  K  L  I  R  Q  T  Y  A  E  T  F  G  E  D  L  L  K  E  L  D  R  E  L  T  H  D  F  E  :  K  L  V  V  V  W  T  L  D  P  A  E  R  D  A  Y  L  A  K  E  A  T  K  R  W  T  K  S  N  F  V  L  V  E  I  A  C  T  R  S  P  K  E  L  V  L  A  R  E  A  Y  H  A  R  N  K  K  S  L  E  E  D  V  A  Y  H  T  T  G  D  H  R  K  :  L  L  V  P  L  V  S  S  Y  R  Y  G  G  D  E  V  D  L  R  L  A  K  A  E  S  K  V  L  H  E  K  I  S  D  K  A  Y  S  D  D  E  V  I  R  I  L  A  T  R  S  K  A  Q  L  N  A  T  L  N  H  Y  K  D  E  Y  G  E  D  I  L  K  :  Q  L  E  D  E  D  E  F  V  A  L  L  R  A  T  I  K  G  L  V  Y  P  E  H  Y  F  V  E  V  L  R  D  A  I  N  R  R  G  T  E  E  D  H  L  T  R  V  I  A  T  R  A  E  V  D  L  K  T  I  A  N  E  Y  Q  K  R  D  S  V  P  L  G  R  A  I  A  K  D  T  G  G  D  Y  E  N  M  L  V  A  L  L  G  Q  E  E  E  *  E  A  D  W  L  T  S  V  L  *  *  P  E  *  I  C  H  S  P  I  Y  F  R  V  G  M  C  L  M  I  E  C  G  L  F  H  M  S  F  *  S  F  S  S  C  E  K  L  *  I  *  I  F  V  L  S  K  N  V  L  *  *  F  A  S  T  T  I  I  F  N  Y   </second_frame>
            <third_frame>   G  P  I  V  D  Q  K  *  S  L  C  V  F  K  K  G  R  R  N  V  *  K  I  D  S  L  L  I  T  L  H  F  R  V  L  T  I  I  S  S  S  C  P  H  R  E  E  E  K  W  Q  V  L  Q  F  R  Q  K  F  L  Q  S  L  K  T  V  N  N  S  D  L  P  S  K  :  D  G  E  R  M  R  S  *  L  Y  Q  F  W  L  I  E  M  R  L  N  A  N  *  F  D  R  L  M  L  R  L  L  G  K  I  C  L  K  S  W  T  E  N  L  L  M  I  L  R :   N  W  W  *  Y  G  H  W  I  L  Q  N  V  M  P  I  W  L  R  K  L  L  R  D  G  Q  K  A  T  L  F  L  W  R  *  L  V  P  D  L  L  K  N  W  F  W  Q  E  K  L  I  M  L  V  T  R  N  L  S  K  R  T  L  L  I  T  L  L  G  I  T  A  S :   F  W  Y  L  L  *  A  P  T  D  M  G  E  M  R  W  T  C  D  L  L  K  Q  N  L  K  C  C  M  R  R  S  P  I  R  L  T  V  T  M  R  S  L  E  F  *  P  Q  G  A  K  R  N  S  M  L  L  *  I  I  T  K  M  N  M  V  R  I  S  *  S :   N  *  K  M  R  M  S  L  L  H  C  *  G  P  P  *  K  V  L  S  T  P  S  T  I  S  W  R  F  F  V  M  Q  L  T  G  E  E  Q  R  K  I  I  *  P  E  L  S  L  Q  G  L  R  S  I  *  R  L  S  L  T  S  T  R  R  G  I  A  F  L  W  V  A  P  L  P  K  I  Q  E  E  I  M  R  I  C  W  W  L  Y  L  D  K  R  R  N  K  K  R  I  G  S  L  L  F  Y  N  D  Q  N  K  Y  A  I  L  P  Y  I  S  E  L  A  C  V  *  *  L  S  V  V  C  F  T  *  A  F  S  P  F  L  L  V  R  N  F  E  Y  E  S  L  C  C  L  K  M  F  S  N  D  L  H  P  L  Q  *  S  S  T  T  </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="C04HBa0255I02.1" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="52134" stop="52284"/>
                    <exon start="52486" stop="52631"/>
                    <exon start="53014" stop="53232"/>
                    <exon start="53578" stop="53790"/>
                    <exon start="53901" stop="54191"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>1017</number_coding_nucleotides>
                  <number_encoded_amino_acids>339</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LPTHHPAFSSLDNHILLLPTQRRRKMASLTVPAEVPSVAEDCEQLRSAFKGWGTNEKLIISILAHRNAAQRKLIRQTYAETFGEDLLKELDRELTHDFEKLVVVWTLDPAERDAYLAKEATKRWTKSNFVLVEIACTRSPKELVLAREAYHARNKKSLEEDVAYHTTGDHRKLLVPLVSSYRYGGDEVDLRLAKAESKVLHEKISDKAYSDDEVIRILATRSKAQLNATLNHYKDEYGEDILKQLEDEDEFVALLRATIKGLVYPEHYFVEVLRDAINRRGTEEDHLTRVIATRAEVDLKTIANEYQKRDSVPLGRAIAKDTGGDYENMLVALLGQEEE*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 4 chains have been computed
$ 
$ memory statistics:
$ 5816 bytes spliced alignments in total
$ 3 spliced alignments have been stored
$ 1938 bytes was the average size of a spliced alignment
$ 6992 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3496 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 5 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-15 23:24:42
-->
