<?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 20:35:17"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0107M13-WbykN/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C04HBa0107M13-WbykN/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-C04HBa0107M13-WbykN/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M6545-2" ref_strand="+" ref_description="SGN-M6545-2 C2_At1g08550-2 [cosii_markers]">
      <seq>ggaagtgcagaaacaagaaaatgtggtgacgttgctaatctaattatcacaaaatgtcttatccatttccccttcactcaactctttcacacttaatacacccaaaattcagaaaaaaaaagtgaatacaaaaatccacaataactccttattctcaatgttcaatctctatagcactctatttacatgaggttggagttggtggtcatctagttgaataatggcgcttgcccctcattcaaactttctgtgcgttcatgaaaccatcaaatgtcaagttgggtcaaagcttcacagtcatacaagatttagctggggtagggcagaatactttggtagtatagtcatagtgaaaatttgttccagaagatggatacctacatacttgcagaaatctcctagaataagatgtggtttggattctaaaggtctgcaactatcatcacaggggaaacaaaatctctcttctgcacatagctataaccagaatgtacctaagggaaatacaatatgtaaatttccagaagatgtagctctgatggtccggaagaaatggtgtcaattggccaaaacagcaattgtaactctattcattttgtcagttgcttcaaaggctgatgctgttgatgcactcaaaacttgtacatgcttactgaaagagtgcaggatagagcttgcaaagtgcattgcaaaccctgcatgtgcagctaatgttgcctgtctccagacttgcaacaatagacctgatgaaacggaatgtcagataaaatgtggtgatttgtttgaaaatagtgttgtagacgaattcaatgagtgtgcagtctcccgggagaaatgtgtacctcgtaaatctgatgttggtgactttcct</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0107M13-WbykN/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0107M13.1" temp_strand="+" temp_description="C04HBa0107M13.1  CU210888.2 htgs_phase:3 submitted_to_sgn_as:C04HBa0107M13 sequenced_by:sanger upload_account_name:uk">
        <position start="4428" stop="7517"/>
      </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="4728" g_stop="4931" g_length="204"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="191" r_length="191" r_score="0.863"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="4932" i_stop="5527" i_length="596">
            <donor d_prob="0.976" d_score="0.88"/>
            <acceptor a_prob="0.712" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="5528" g_stop="5835" g_length="308"/>
          <reference_exon_boundary r_type="cDNA" r_start="192" r_stop="499" r_length="308" r_score="0.916"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="5836" i_stop="5966" i_length="131">
            <donor d_prob="0.996" d_score="0.92"/>
            <acceptor a_prob="0.000" a_score="0.92"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="5967" g_stop="6133" g_length="167"/>
          <reference_exon_boundary r_type="cDNA" r_start="500" r_stop="666" r_length="167" r_score="0.934"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="6134" i_stop="6931" i_length="798">
            <donor d_prob="0.787" d_score="0.94"/>
            <acceptor a_prob="0.994" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="6932" g_stop="7028" g_length="97"/>
          <reference_exon_boundary r_type="cDNA" r_start="667" r_stop="763" r_length="97" r_score="0.948"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="7029" i_stop="7109" i_length="81">
            <donor d_prob="0.976" d_score="0.96"/>
            <acceptor a_prob="0.998" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="7110" g_stop="7217" g_length="108"/>
          <reference_exon_boundary r_type="cDNA" r_start="764" r_stop="871" r_length="108" r_score="0.972"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0107M13.1" gen_strand="+" ref_id="SGN-M6545-2" ref_strand="+">
        <total_alignment_score>0.917</total_alignment_score>
        <cumulative_length_of_scored_exons>884</cumulative_length_of_scored_exons>
        <coverage percentage="1.015" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0107M13.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M6545-2" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="4728" e_stop="4931"/>
          <exon e_start="5528" e_stop="5835"/>
          <exon e_start="5967" e_stop="6133"/>
          <exon e_start="6932" e_stop="7028"/>
          <exon e_start="7110" e_stop="7217"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GGAAGTGCAGAAACAAGAAAATGTGGTGACGTTGCTAAGCTAATTATCACAAAATGTCTTATCCCCCTTCATCCATTTCCCCTTCACTCAACTCTTTCACACTTAAAACACCCAAAAATTCAGAAGAAGAAAAAAAAAGATGCAAAATCCACAACAACTCTTTATACTCAACGTTCAATCTTCATAGCACTCTATTTACATGAGGTCAGTTATTGGGATTTATATTTATATTCACATACTCATCTTTTACTCTTTGAGTATATTATGATTCTGCATTTGACAATTTAACTTGTCAATTTTAGCTTTGTAAATGTGCTGCTCCGTCTCAATTTATGTGATACAAGTCATACAAATGATCCCTTTTACTTAAAATTTATGCTAACTCAAATGGTGTCACACTAATTGGGACGGAAGGAGTAGTATTTAATGTTAAACTGAAGGTGAATAGAGAGGAACATGAAAGGGTGAGTTCTTGATTGATTGTGAACTATGCACCAAAACCTTTAGTTGGAACTGAAGATGAATGTGGGAAGTTGAAAATTTATCTGCATTTCAATATTTGACCTTAAATCCTACTTATGTATCATAGAATTTCAATCAACTAGTGAATGTGGAAAAATTCTTGATTGTGAATCTGATAGTAAGATTTGATATGTGCTGACGTGCAACACACACGCACACACGTAGAATATGCATCTTGGACCAATCAGTCTGATATGTGCGCGTGTGTGTTGCACAGAGTAGATATCAATCAGAAAGATTTAGAAGATAGCACAATCTGATATACTTCATTTCTATAGGTTGGAGTTGGTGGTCATTCAATTGAATAATGGCGCTTGCCCCTCATTCAAACATTCTGTGCAATCATGAGGCCATCAAATGTCAAGTTGGATCAAGGCTTCAGAGTCATACAAGATTTAGCTGGGGTAGAGCAGATTACTTTGGTAGTATAGTCCTAGTGAAAATTTGTTCCAGAAGACAGATACCTACATACTTGCAGAAATCTTCTAGAATATGTTGTGGTTTGGATTCTAGAAGTCTGCAACTATCATCACGGGGGAAACAAAATCTTTCTTCTGCACATAGAATTAACCAGAATGTACCTAAGGTGAGTTTGATATTATTTTGTTCTGTTGCTTCTCGTTTACTACTTTCCGAAGGAATGTGGGGGTCTAGCTCTGTCCTCTGCATCCTTTTCATCCTCTTCTTTCTCTTTGCTGACAGAAGTCCTCTATATAGGGAAATACAATATGGAAATTTCCAGAAGATGTAGCTTTGATGGTCTTGAAGAAATGGGGCCAATTGGCCAAAACAGCAATTGTAACTATATTTATTTTGTCAGTTGCTTCAAAGGCTGATGCCGTTGATGCTCTCAAAACTTGTACTTGCTTACTGAAAGAGTGCAGGTAATTTGCAGATGTTACTAAAGTATGCCGGTATACTTCCTTCTACCGAGCTGCCAATATATTTTGTTTTGCTACCCTTCTTATGTTTCTTTCAAGAGCTTTGAGCTTGTTTACTTCTATTACATATAAAAATACACAAGGAATGTGAAATTGGTTCTTGTTTGTACACTGTGGATTGTCGTCCTGAATTAATAATTGAGTGCAGTGGTAAGGATGTCAAATTCAGTTTTCACGGACATAGACTGTCTCTAGCTTTTTATGATCAACTGTCCATAAGTTCTCGATTCTAGTCGTAATTATCGATAAAATCAAGTTTTAAGCATGTTCAAAGTGAAACATAACCCCAACCGTAATGCTTTTCCATCTATTCCTTTCCGATTTTGAGACTGTTAAGACTTTCTGTGTTCTAATTAGGCCATGAGAATAGCAGTATGAATTTGACTTATTTGGAGCAAGTTTTTTTAGACCTTTACGGTGGTAAAAGCAACTGATACTGTTGCTGTGCTAGGGATGCAGGAAAGTTTTTACTATTATTCCAATTTCCCTGAATCTCAAAAGATATCTTTTTGTCTCGTGCCACAATTTGATGAACTTGTAAAGATATAGCCACACAAATGTCTTAGGTTTATTTTAGACCACAAAATTCACAAGTCTTTTTTTCTTTCTTAAAGTTTTTGCTAAGTCAAACTGTCCAACAAAAATTAGGACGGAGGGAGTAGTATTGATGAGTTTCAACCTCCATCCCTAACATGCATGTCTGATACTCTTAGGTGACTTATTAAAGTATTATGCTTTCAGGATAGAGCTTGCGAAGTGCATCTCAAACCCTGCATGTGCAGCTAATGTTGCCTGTCTCCAAACATGCAACAATAGACCTGATGAAACGGAATGTCAGGTGTCTACAAACATCTTATTAAAACTGAATATTGATTTGATCACATTTATGGAATATTAATATGTTGGAATATGGGTGCAGATAAAATGTGGTGATTTGTTTGAAAACAGTGTTGTAGACGAGTTCAATGAGTGTGCAGTCTCCCGGAAGAAATGTGTACCTCGTAAATCTGATGTTGGTGACTTTCCT</genome_strand>
        <mrna_strand>GGAAGTGCAGAAACAAGAAAATGTGGTGACGTTGCTAATCTAATTATCACAAAATG-----T----CTT-ATCCATTTCCCCTTCACTCAACTCTTTCACACTTAATACACCC-AAAATTCAGAA-AAAAAAAGTGAATA-CAAAAATCCACAATAACTCCTTATTCTCAATGTTCAATCTCTATAGCACTCTATTTACATGAG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTGGAGTTGGTGGTCATCTAGTTGAATAATGGCGCTTGCCCCTCATTCAAACTTTCTGTGCGTTCATGAAACCATCAAATGTCAAGTTGGGTCAAAGCTTCACAGTCATACAAGATTTAGCTGGGGTAGGGCAGAATACTTTGGTAGTATAGTCATAGTGAAAATTTGTTCCAGAAGATGGATACCTACATACTTGCAGAAATCTCCTAGAATAAGATGTGGTTTGGATTCTAAAGGTCTGCAACTATCATCACAGGGGAAACAAAATCTCTCTTCTGCACATAGCTATAACCAGAATGTACCTAAG...................................................................................................................................GGAAATACAATATGTAAATTTCCAGAAGATGTAGCTCTGATGGTCCGGAAGAAATGGTGTCAATTGGCCAAAACAGCAATTGTAACTCTATTCATTTTGTCAGTTGCTTCAAAGGCTGATGCTGTTGATGCACTCAAAACTTGTACATGCTTACTGAAAGAGTGCAG..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GATAGAGCTTGCAAAGTGCATTGCAAACCCTGCATGTGCAGCTAATGTTGCCTGTCTCCAGACTTGCAACAATAGACCTGATGAAACGGAATGTCAG.................................................................................ATAAAATGTGGTGATTTGTTTGAAAATAGTGTTGTAGACGAATTCAATGAGTGTGCAGTCTCCCGGGAGAAATGTGTACCTCGTAAATCTGATGTTGGTGACTTTCCT</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-C04HBa0107M13-WbykN/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M6545" ref_strand="+" ref_description="SGN-M6545 C2_At1g08550 [cosii_markers]">
      <seq>gcacgagccacaacaactctttatactcaacgttcaatcttcatagcactctatttacatgaggttggagttggtggtcattcaattgaataatggcgcttgcccctcattcaaacattctgtgcaatcatgaggccatcaaatgtcaagttggatcaaggcttcagagtcatacaagatttagctggggtagagcagattactttggtagtatagtcctagtgaaaatttgttccagaagacagatacctacatacttgcagaaatcttctagaatatgttgtggtttggattctagaagtctgcaactatcatcacgggggaaacaaaatctttcttctgcacatagaattaaccagaatgtacctaagggaaatacaatatggaaatttccagaagatgtagctttgatggtcttgaagaaatggggccaattggccaaaacagcaattgtaactatatttattttgtcagttgcttcaaaggctgatgccgttgatgctctcaaaacttgtacttgcttactgaaagagtgcaggtaatttgcagatgttactaaagtatgccggatagagcttgcgaagtgcatctcaaaccctgcatgtgcagctaatgttgcctgtctccaaacatgcaacaatagacctgatgaaacggaatgtcagataaaatgtggtgatttgtttgaaaacagtgttgtagacgagttcaatgagtgtgcagt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0107M13-WbykN/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0107M13.1" temp_strand="+" temp_description="C04HBa0107M13.1  CU210888.2 htgs_phase:3 submitted_to_sgn_as:C04HBa0107M13 sequenced_by:sanger upload_account_name:uk">
        <position start="4569" stop="7468"/>
      </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="4869" g_stop="4931" g_length="63"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="63" r_length="63" r_score="0.952"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="4932" i_stop="5527" i_length="596">
            <donor d_prob="0.976" d_score="1.00"/>
            <acceptor a_prob="0.712" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="5528" g_stop="5835" g_length="308"/>
          <reference_exon_boundary r_type="cDNA" r_start="64" r_stop="371" r_length="308" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="5836" i_stop="5966" i_length="131">
            <donor d_prob="0.996" d_score="1.00"/>
            <acceptor a_prob="0.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="5967" g_stop="6163" g_length="197"/>
          <reference_exon_boundary r_type="cDNA" r_start="372" r_stop="568" r_length="197" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="6164" i_stop="6931" i_length="768">
            <donor d_prob="0.935" d_score="1.00"/>
            <acceptor a_prob="0.994" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="6932" g_stop="7028" g_length="97"/>
          <reference_exon_boundary r_type="cDNA" r_start="569" r_stop="665" r_length="97" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="7029" i_stop="7109" i_length="81">
            <donor d_prob="0.976" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="7110" g_stop="7168" g_length="59"/>
          <reference_exon_boundary r_type="cDNA" r_start="666" r_stop="724" r_length="59" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0107M13.1" gen_strand="+" ref_id="SGN-M6545" ref_strand="+">
        <total_alignment_score>0.996</total_alignment_score>
        <cumulative_length_of_scored_exons>724</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0107M13.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M6545" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="4869" e_stop="4931"/>
          <exon e_start="5528" e_stop="5835"/>
          <exon e_start="5967" e_stop="6163"/>
          <exon e_start="6932" e_stop="7028"/>
          <exon e_start="7110" e_stop="7168"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GCAAAATCCACAACAACTCTTTATACTCAACGTTCAATCTTCATAGCACTCTATTTACATGAGGTCAGTTATTGGGATTTATATTTATATTCACATACTCATCTTTTACTCTTTGAGTATATTATGATTCTGCATTTGACAATTTAACTTGTCAATTTTAGCTTTGTAAATGTGCTGCTCCGTCTCAATTTATGTGATACAAGTCATACAAATGATCCCTTTTACTTAAAATTTATGCTAACTCAAATGGTGTCACACTAATTGGGACGGAAGGAGTAGTATTTAATGTTAAACTGAAGGTGAATAGAGAGGAACATGAAAGGGTGAGTTCTTGATTGATTGTGAACTATGCACCAAAACCTTTAGTTGGAACTGAAGATGAATGTGGGAAGTTGAAAATTTATCTGCATTTCAATATTTGACCTTAAATCCTACTTATGTATCATAGAATTTCAATCAACTAGTGAATGTGGAAAAATTCTTGATTGTGAATCTGATAGTAAGATTTGATATGTGCTGACGTGCAACACACACGCACACACGTAGAATATGCATCTTGGACCAATCAGTCTGATATGTGCGCGTGTGTGTTGCACAGAGTAGATATCAATCAGAAAGATTTAGAAGATAGCACAATCTGATATACTTCATTTCTATAGGTTGGAGTTGGTGGTCATTCAATTGAATAATGGCGCTTGCCCCTCATTCAAACATTCTGTGCAATCATGAGGCCATCAAATGTCAAGTTGGATCAAGGCTTCAGAGTCATACAAGATTTAGCTGGGGTAGAGCAGATTACTTTGGTAGTATAGTCCTAGTGAAAATTTGTTCCAGAAGACAGATACCTACATACTTGCAGAAATCTTCTAGAATATGTTGTGGTTTGGATTCTAGAAGTCTGCAACTATCATCACGGGGGAAACAAAATCTTTCTTCTGCACATAGAATTAACCAGAATGTACCTAAGGTGAGTTTGATATTATTTTGTTCTGTTGCTTCTCGTTTACTACTTTCCGAAGGAATGTGGGGGTCTAGCTCTGTCCTCTGCATCCTTTTCATCCTCTTCTTTCTCTTTGCTGACAGAAGTCCTCTATATAGGGAAATACAATATGGAAATTTCCAGAAGATGTAGCTTTGATGGTCTTGAAGAAATGGGGCCAATTGGCCAAAACAGCAATTGTAACTATATTTATTTTGTCAGTTGCTTCAAAGGCTGATGCCGTTGATGCTCTCAAAACTTGTACTTGCTTACTGAAAGAGTGCAGGTAATTTGCAGATGTTACTAAAGTATGCCGGTATACTTCCTTCTACCGAGCTGCCAATATATTTTGTTTTGCTACCCTTCTTATGTTTCTTTCAAGAGCTTTGAGCTTGTTTACTTCTATTACATATAAAAATACACAAGGAATGTGAAATTGGTTCTTGTTTGTACACTGTGGATTGTCGTCCTGAATTAATAATTGAGTGCAGTGGTAAGGATGTCAAATTCAGTTTTCACGGACATAGACTGTCTCTAGCTTTTTATGATCAACTGTCCATAAGTTCTCGATTCTAGTCGTAATTATCGATAAAATCAAGTTTTAAGCATGTTCAAAGTGAAACATAACCCCAACCGTAATGCTTTTCCATCTATTCCTTTCCGATTTTGAGACTGTTAAGACTTTCTGTGTTCTAATTAGGCCATGAGAATAGCAGTATGAATTTGACTTATTTGGAGCAAGTTTTTTTAGACCTTTACGGTGGTAAAAGCAACTGATACTGTTGCTGTGCTAGGGATGCAGGAAAGTTTTTACTATTATTCCAATTTCCCTGAATCTCAAAAGATATCTTTTTGTCTCGTGCCACAATTTGATGAACTTGTAAAGATATAGCCACACAAATGTCTTAGGTTTATTTTAGACCACAAAATTCACAAGTCTTTTTTTCTTTCTTAAAGTTTTTGCTAAGTCAAACTGTCCAACAAAAATTAGGACGGAGGGAGTAGTATTGATGAGTTTCAACCTCCATCCCTAACATGCATGTCTGATACTCTTAGGTGACTTATTAAAGTATTATGCTTTCAGGATAGAGCTTGCGAAGTGCATCTCAAACCCTGCATGTGCAGCTAATGTTGCCTGTCTCCAAACATGCAACAATAGACCTGATGAAACGGAATGTCAGGTGTCTACAAACATCTTATTAAAACTGAATATTGATTTGATCACATTTATGGAATATTAATATGTTGGAATATGGGTGCAGATAAAATGTGGTGATTTGTTTGAAAACAGTGTTGTAGACGAGTTCAATGAGTGTGCAGT</genome_strand>
        <mrna_strand>GCACGAGCCACAACAACTCTTTATACTCAACGTTCAATCTTCATAGCACTCTATTTACATGAG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTGGAGTTGGTGGTCATTCAATTGAATAATGGCGCTTGCCCCTCATTCAAACATTCTGTGCAATCATGAGGCCATCAAATGTCAAGTTGGATCAAGGCTTCAGAGTCATACAAGATTTAGCTGGGGTAGAGCAGATTACTTTGGTAGTATAGTCCTAGTGAAAATTTGTTCCAGAAGACAGATACCTACATACTTGCAGAAATCTTCTAGAATATGTTGTGGTTTGGATTCTAGAAGTCTGCAACTATCATCACGGGGGAAACAAAATCTTTCTTCTGCACATAGAATTAACCAGAATGTACCTAAG...................................................................................................................................GGAAATACAATATGGAAATTTCCAGAAGATGTAGCTTTGATGGTCTTGAAGAAATGGGGCCAATTGGCCAAAACAGCAATTGTAACTATATTTATTTTGTCAGTTGCTTCAAAGGCTGATGCCGTTGATGCTCTCAAAACTTGTACTTGCTTACTGAAAGAGTGCAGGTAATTTGCAGATGTTACTAAAGTATGCCG................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GATAGAGCTTGCGAAGTGCATCTCAAACCCTGCATGTGCAGCTAATGTTGCCTGTCTCCAAACATGCAACAATAGACCTGATGAAACGGAATGTCAG.................................................................................ATAAAATGTGGTGATTTGTTTGAAAACAGTGTTGTAGACGAGTTCAATGAGTGTGCAGT</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-C04HBa0107M13-WbykN/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M1921" ref_strand="+" ref_description="SGN-M1921 T1317 [cos_markers]">
      <seq>tcaacgttcaatcttcatagcactctatttacatgaggttggagttggtggtcattcaattgaataatggcgcttgcccctcattcaaacattctgtgcaatcatgaagccatcaaatgtcaagttggatcaaggctgcagagtcagacaagatttagctggggtagagcagattactttggtagtatagtcctagtgaaaatttgttccagaagacagatacctacatacttgcagaaatcttctagaatatgttgtggtttggattctagaagtctgcaactatcatcacgggggaaacaaaatctttcttctgcacatagaattaaccagaatgtacctaagggaaatacaatatggaaatttccagaagatgtagctttgatggtcttgaagaaatggggccaattggccaaaacagcaattgtaactatatttattttgtcagttgcttcaaaggctgatgccgttgatgctctcaaaacttgtacttgcttactgaaagagtgcaggatagagcttgcgaagtgcatctcaaaccctgcatgtgcagctaatgttgcctgtctccaaacatgcaacaatagacctgatgaaacggaatgtcagataaaatgtggtgatttgtttg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0107M13-WbykN/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0107M13.1" temp_strand="+" temp_description="C04HBa0107M13.1  CU210888.2 htgs_phase:3 submitted_to_sgn_as:C04HBa0107M13 sequenced_by:sanger upload_account_name:uk">
        <position start="4595" stop="7431"/>
      </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="4895" g_stop="4931" g_length="37"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="37" r_length="37" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="4932" i_stop="5527" i_length="596">
            <donor d_prob="0.976" d_score="0.00"/>
            <acceptor a_prob="0.712" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="5528" g_stop="5835" g_length="308"/>
          <reference_exon_boundary r_type="cDNA" r_start="38" r_stop="345" r_length="308" r_score="0.990"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="5836" i_stop="5966" i_length="131">
            <donor d_prob="0.996" d_score="1.00"/>
            <acceptor a_prob="0.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="5967" g_stop="6133" g_length="167"/>
          <reference_exon_boundary r_type="cDNA" r_start="346" r_stop="512" r_length="167" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="6134" i_stop="6931" i_length="798">
            <donor d_prob="0.787" d_score="1.00"/>
            <acceptor a_prob="0.994" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="6932" g_stop="7028" g_length="97"/>
          <reference_exon_boundary r_type="cDNA" r_start="513" r_stop="609" r_length="97" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="7029" i_stop="7109" i_length="81">
            <donor d_prob="0.976" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="7110" g_stop="7131" g_length="22"/>
          <reference_exon_boundary r_type="cDNA" r_start="610" r_stop="631" r_length="22" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0107M13.1" gen_strand="+" ref_id="SGN-M1921" ref_strand="+">
        <total_alignment_score>0.995</total_alignment_score>
        <cumulative_length_of_scored_exons>631</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0107M13.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M1921" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="4895" e_stop="4931"/>
          <exon e_start="5528" e_stop="5835"/>
          <exon e_start="5967" e_stop="6133"/>
          <exon e_start="6932" e_stop="7028"/>
          <exon e_start="7110" e_stop="7131"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCAACGTTCAATCTTCATAGCACTCTATTTACATGAGGTCAGTTATTGGGATTTATATTTATATTCACATACTCATCTTTTACTCTTTGAGTATATTATGATTCTGCATTTGACAATTTAACTTGTCAATTTTAGCTTTGTAAATGTGCTGCTCCGTCTCAATTTATGTGATACAAGTCATACAAATGATCCCTTTTACTTAAAATTTATGCTAACTCAAATGGTGTCACACTAATTGGGACGGAAGGAGTAGTATTTAATGTTAAACTGAAGGTGAATAGAGAGGAACATGAAAGGGTGAGTTCTTGATTGATTGTGAACTATGCACCAAAACCTTTAGTTGGAACTGAAGATGAATGTGGGAAGTTGAAAATTTATCTGCATTTCAATATTTGACCTTAAATCCTACTTATGTATCATAGAATTTCAATCAACTAGTGAATGTGGAAAAATTCTTGATTGTGAATCTGATAGTAAGATTTGATATGTGCTGACGTGCAACACACACGCACACACGTAGAATATGCATCTTGGACCAATCAGTCTGATATGTGCGCGTGTGTGTTGCACAGAGTAGATATCAATCAGAAAGATTTAGAAGATAGCACAATCTGATATACTTCATTTCTATAGGTTGGAGTTGGTGGTCATTCAATTGAATAATGGCGCTTGCCCCTCATTCAAACATTCTGTGCAATCATGAGGCCATCAAATGTCAAGTTGGATCAAGGCTTCAGAGTCATACAAGATTTAGCTGGGGTAGAGCAGATTACTTTGGTAGTATAGTCCTAGTGAAAATTTGTTCCAGAAGACAGATACCTACATACTTGCAGAAATCTTCTAGAATATGTTGTGGTTTGGATTCTAGAAGTCTGCAACTATCATCACGGGGGAAACAAAATCTTTCTTCTGCACATAGAATTAACCAGAATGTACCTAAGGTGAGTTTGATATTATTTTGTTCTGTTGCTTCTCGTTTACTACTTTCCGAAGGAATGTGGGGGTCTAGCTCTGTCCTCTGCATCCTTTTCATCCTCTTCTTTCTCTTTGCTGACAGAAGTCCTCTATATAGGGAAATACAATATGGAAATTTCCAGAAGATGTAGCTTTGATGGTCTTGAAGAAATGGGGCCAATTGGCCAAAACAGCAATTGTAACTATATTTATTTTGTCAGTTGCTTCAAAGGCTGATGCCGTTGATGCTCTCAAAACTTGTACTTGCTTACTGAAAGAGTGCAGGTAATTTGCAGATGTTACTAAAGTATGCCGGTATACTTCCTTCTACCGAGCTGCCAATATATTTTGTTTTGCTACCCTTCTTATGTTTCTTTCAAGAGCTTTGAGCTTGTTTACTTCTATTACATATAAAAATACACAAGGAATGTGAAATTGGTTCTTGTTTGTACACTGTGGATTGTCGTCCTGAATTAATAATTGAGTGCAGTGGTAAGGATGTCAAATTCAGTTTTCACGGACATAGACTGTCTCTAGCTTTTTATGATCAACTGTCCATAAGTTCTCGATTCTAGTCGTAATTATCGATAAAATCAAGTTTTAAGCATGTTCAAAGTGAAACATAACCCCAACCGTAATGCTTTTCCATCTATTCCTTTCCGATTTTGAGACTGTTAAGACTTTCTGTGTTCTAATTAGGCCATGAGAATAGCAGTATGAATTTGACTTATTTGGAGCAAGTTTTTTTAGACCTTTACGGTGGTAAAAGCAACTGATACTGTTGCTGTGCTAGGGATGCAGGAAAGTTTTTACTATTATTCCAATTTCCCTGAATCTCAAAAGATATCTTTTTGTCTCGTGCCACAATTTGATGAACTTGTAAAGATATAGCCACACAAATGTCTTAGGTTTATTTTAGACCACAAAATTCACAAGTCTTTTTTTCTTTCTTAAAGTTTTTGCTAAGTCAAACTGTCCAACAAAAATTAGGACGGAGGGAGTAGTATTGATGAGTTTCAACCTCCATCCCTAACATGCATGTCTGATACTCTTAGGTGACTTATTAAAGTATTATGCTTTCAGGATAGAGCTTGCGAAGTGCATCTCAAACCCTGCATGTGCAGCTAATGTTGCCTGTCTCCAAACATGCAACAATAGACCTGATGAAACGGAATGTCAGGTGTCTACAAACATCTTATTAAAACTGAATATTGATTTGATCACATTTATGGAATATTAATATGTTGGAATATGGGTGCAGATAAAATGTGGTGATTTGTTTG</genome_strand>
        <mrna_strand>TCAACGTTCAATCTTCATAGCACTCTATTTACATGAG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTGGAGTTGGTGGTCATTCAATTGAATAATGGCGCTTGCCCCTCATTCAAACATTCTGTGCAATCATGAAGCCATCAAATGTCAAGTTGGATCAAGGCTGCAGAGTCAGACAAGATTTAGCTGGGGTAGAGCAGATTACTTTGGTAGTATAGTCCTAGTGAAAATTTGTTCCAGAAGACAGATACCTACATACTTGCAGAAATCTTCTAGAATATGTTGTGGTTTGGATTCTAGAAGTCTGCAACTATCATCACGGGGGAAACAAAATCTTTCTTCTGCACATAGAATTAACCAGAATGTACCTAAG...................................................................................................................................GGAAATACAATATGGAAATTTCCAGAAGATGTAGCTTTGATGGTCTTGAAGAAATGGGGCCAATTGGCCAAAACAGCAATTGTAACTATATTTATTTTGTCAGTTGCTTCAAAGGCTGATGCCGTTGATGCTCTCAAAACTTGTACTTGCTTACTGAAAGAGTGCAG..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GATAGAGCTTGCGAAGTGCATCTCAAACCCTGCATGTGCAGCTAATGTTGCCTGTCTCCAAACATGCAACAATAGACCTGATGAAACGGAATGTCAG.................................................................................ATAAAATGTGGTGATTTGTTTG</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="4728" PGL_stop="7217"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="4728" e_stop="4931"/>
            <exon e_start="5528" e_stop="5835"/>
            <exon e_start="5967" e_stop="6133"/>
            <exon e_start="6932" e_stop="7028"/>
            <exon e_start="7110" e_stop="7217"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.976" acc_prob="0.712" e_score="0.863"/>
          <exon-intron don_prob="0.996" acc_prob="0.000" e_score="0.990"/>
          <exon-intron don_prob="0.787" acc_prob="0.994" e_score="1.000"/>
          <exon-intron don_prob="0.976" acc_prob="0.998" e_score="1.000"/>
          <exon-only e_score="0.972"/>
        </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="0.863">
            <gDNA_exon_boundary e_start="4728" e_stop="4931" e_length="204"/>
          </exon>
          <intron i_serial="1" don_prob="0.976" acc_prob="0.712">
            <gDNA_intron_boundary i_start="4932" i_stop="5527" i_length="596"/>
          </intron>
          <exon e_serial="2" e_score="0.990">
            <gDNA_exon_boundary e_start="5528" e_stop="5835" e_length="308"/>
          </exon>
          <intron i_serial="2" don_prob="0.996" acc_prob="0.000">
            <gDNA_intron_boundary i_start="5836" i_stop="5966" i_length="131"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="5967" e_stop="6133" e_length="167"/>
          </exon>
          <intron i_serial="3" don_prob="0.787" acc_prob="0.994">
            <gDNA_intron_boundary i_start="6134" i_stop="6931" i_length="798"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="6932" e_stop="7028" e_length="97"/>
          </exon>
          <intron i_serial="4" don_prob="0.976" acc_prob="0.998">
            <gDNA_intron_boundary i_start="7029" i_stop="7109" i_length="81"/>
          </intron>
          <exon e_serial="5" e_score="0.972">
            <gDNA_exon_boundary e_start="7110" e_stop="7217" e_length="108"/>
          </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="4728" stop="4931"/>
              <exon start="5528" stop="5835"/>
              <exon start="5967" stop="6133"/>
              <exon start="6932" stop="7028"/>
              <exon start="7110" stop="7217"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M6545-2" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="4895" stop="4931"/>
              <exon start="5528" stop="5835"/>
              <exon start="5967" stop="6133"/>
              <exon start="6932" stop="7028"/>
              <exon start="7110" stop="7131"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1921" 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>GGAAGTGCAGAAACAAGAAAATGTGGTGACGTTGCTAAGCTAATTATCACAAAATGTCTTATCCCCCTTCATCCATTTCCCCTTCACTCAACTCTTTCACACTTAAAACACCCAAAAATTCAGAAGAAGAAAAAAAAAGATGCAAAATCCACAACAACTCTTTATACTCAACGTTCAATCTTCATAGCACTCTATTTACATGAG : GTTGGAGTTGGTGGTCATTCAATTGAATAATGGCGCTTGCCCCTCATTCAAACATTCTGTGCAATCATGAGGCCATCAAATGTCAAGTTGGATCAAGGCTTCAGAGTCATACAAGATTTAGCTGGGGTAGAGCAGATTACTTTGGTAGTATAGTCCTAGTGAAAATTTGTTCCAGAAGACAGATACCTACATACTTGCAGAAATCTTCTAGAATATGTTGTGGTTTGGATTCTAGAAGTCTGCAACTATCATCACGGGGGAAACAAAATCTTTCTTCTGCACATAGAATTAACCAGAATGTACCTAAG : GGAAATACAATATGGAAATTTCCAGAAGATGTAGCTTTGATGGTCTTGAAGAAATGGGGCCAATTGGCCAAAACAGCAATTGTAACTATATTTATTTTGTCAGTTGCTTCAAAGGCTGATGCCGTTGATGCTCTCAAAACTTGTACTTGCTTACTGAAAGAGTGCAG : GATAGAGCTTGCGAAGTGCATCTCAAACCCTGCATGTGCAGCTAATGTTGCCTGTCTCCAAACATGCAACAATAGACCTGATGAAACGGAATGTCAG : ATAAAATGTGGTGATTTGTTTGAAAACAGTGTTGTAGACGAGTTCAATGAGTGTGCAGTCTCCCGGAAGAAATGTGTACCTCGTAAATCTGATGTTGGTGACTTTCCT</gDNA_template>
            <first_frame> G  S  A  E  T  R  K  C  G  D  V  A  K  L  I  I  T  K  C  L  I  P  L  H  P  F  P  L  H  S  T  L  S  H  L  K  H  P  K  I  Q  K  K  K  K  K  D  A  K  S  T  T  T  L  Y  T  Q  R  S  I  F  I  A  L  Y  L  H  E  :  V  G  V  G  G  H  S  I  E  *  W  R  L  P  L  I  Q  T  F  C  A  I  M  R  P  S  N  V  K  L  D  Q  G  F  R  V  I  Q  D  L  A  G  V  E  Q  I  T  L  V  V  *  S  *  *  K  F  V  P  E  D  R  Y  L  H  T  C  R  N  L  L  E  Y  V  V  V  W  I  L  E  V  C  N  Y  H  H  G  G  N  K  I  F  L  L  H  I  E  L  T  R  M  Y  L  R :   E  I  Q  Y  G  N  F  Q  K  M  *  L  *  W  S  *  R  N  G  A  N  W  P  K  Q  Q  L  *  L  Y  L  F  C  Q  L  L  Q  R  L  M  P  L  M  L  S  K  L  V  L  A  Y  *  K  S  A   : G  *  S  L  R  S  A  S  Q  T  L  H  V  Q  L  M  L  P  V  S  K  H  A  T  I  D  L  M  K  R  N  V  R :   *  N  V  V  I  C  L  K  T  V  L  *  T  S  S  M  S  V  Q  S  P  G  R  N  V  Y  L  V  N  L  M  L  V  T  F   </first_frame>
            <second_frame>  E  V  Q  K  Q  E  N  V  V  T  L  L  S  *  L  S  Q  N  V  L  S  P  F  I  H  F  P  F  T  Q  L  F  H  T  *  N  T  Q  K  F  R  R  R  K  K  K  M  Q  N  P  Q  Q  L  F  I  L  N  V  Q  S  S  *  H  S  I  Y  M  R :   L  E  L  V  V  I  Q  L  N  N  G  A  C  P  S  F  K  H  S  V  Q  S  *  G  H  Q  M  S  S  W  I  K  A  S  E  S  Y  K  I  *  L  G  *  S  R  L  L  W  *  Y  S  P  S  E  N  L  F  Q  K  T  D  T  Y  I  L  A  E  I  F  *  N  M  L  W  F  G  F  *  K  S  A  T  I  I  T  G  E  T  K  S  F  F  C  T  *  N  *  P  E  C  T  *   : G  K  Y  N  M  E  I  S  R  R  C  S  F  D  G  L  E  E  M  G  P  I  G  Q  N  S  N  C  N  Y  I  Y  F  V  S  C  F  K  G  *  C  R  *  C  S  Q  N  L  Y  L  L  T  E  R  V  Q  :  D  R  A  C  E  V  H  L  K  P  C  M  C  S  *  C  C  L  S  P  N  M  Q  Q  *  T  *  *  N  G  M  S   : D  K  M  W  *  F  V  *  K  Q  C  C  R  R  V  Q  *  V  C  S  L  P  E  E  M  C  T  S  *  I  *  C  W  *  L  S  </second_frame>
            <third_frame>   K  C  R  N  K  K  M  W  *  R  C  *  A  N  Y  H  K  M  S  Y  P  P  S  S  I  S  P  S  L  N  S  F  T  L  K  T  P  K  N  S  E  E  E  K  K  R  C  K  I  H  N  N  S  L  Y  S  T  F  N  L  H  S  T  L  F  T  *   : G  W  S  W  W  S  F  N  *  I  M  A  L  A  P  H  S  N  I  L  C  N  H  E  A  I  K  C  Q  V  G  S  R  L  Q  S  H  T  R  F  S  W  G  R  A  D  Y  F  G  S  I  V  L  V  K  I  C  S  R  R  Q  I  P  T  Y  L  Q  K  S  S  R  I  C  C  G  L  D  S  R  S  L  Q  L  S  S  R  G  K  Q  N  L  S  S  A  H  R  I  N  Q  N  V  P  K  :  G  N  T  I  W  K  F  P  E  D  V  A  L  M  V  L  K  K  W  G  Q  L  A  K  T  A  I  V  T  I  F  I  L  S  V  A  S  K  A  D  A  V  D  A  L  K  T  C  T  C  L  L  K  E  C  R :   I  E  L  A  K  C  I  S  N  P  A  C  A  A  N  V  A  C  L  Q  T  C  N  N  R  P  D  E  T  E  C  Q  :  I  K  C  G  D  L  F  E  N  S  V  V  D  E  F  N  E  C  A  V  S  R  K  K  C  V  P  R  K  S  D  V  G  D  F  P </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="C04HBa0107M13.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="5554" stop="5835"/>
                    <exon start="5967" stop="6133"/>
                    <exon start="6932" stop="7028"/>
                    <exon start="7110" stop="7217"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>654</number_coding_nucleotides>
                  <number_encoded_amino_acids>218</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>IMALAPHSNILCNHEAIKCQVGSRLQSHTRFSWGRADYFGSIVLVKICSRRQIPTYLQKSSRICCGLDSRSLQLSSRGKQNLSSAHRINQNVPKGNTIWKFPEDVALMVLKKWGQLAKTAIVTIFILSVASKADAVDALKTCTCLLKECRIELAKCISNPACAANVACLQTCNNRPDETECQIKCGDLFENSVVDEFNECAVSRKKCVPRKSDVGDFP</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0107M13.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="4728" stop="4931"/>
                    <exon start="5528" stop="5557"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>231</number_coding_nucleotides>
                  <number_encoded_amino_acids>77</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>GSAETRKCGDVAKLIITKCLIPLHPFPLHSTLSHLKHPKIQKKKKKDAKSTTTLYTQRSIFIALYLHEVGVGGHSIE*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
      <AGS_information>
        <AGS_line AGS_serial="2">
          <exon_coordinates>
            <exon e_start="4869" e_stop="4931"/>
            <exon e_start="5528" e_stop="5835"/>
            <exon e_start="5967" e_stop="6163"/>
            <exon e_start="6932" e_stop="7028"/>
            <exon e_start="7110" e_stop="7168"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.976" acc_prob="0.712" e_score="0.952"/>
          <exon-intron don_prob="0.996" acc_prob="0.000" e_score="1.000"/>
          <exon-intron don_prob="0.935" acc_prob="0.994" e_score="1.000"/>
          <exon-intron don_prob="0.976" acc_prob="0.998" 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="0.952">
            <gDNA_exon_boundary e_start="4869" e_stop="4931" e_length="63"/>
          </exon>
          <intron i_serial="1" don_prob="0.976" acc_prob="0.712">
            <gDNA_intron_boundary i_start="4932" i_stop="5527" i_length="596"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="5528" e_stop="5835" e_length="308"/>
          </exon>
          <intron i_serial="2" don_prob="0.996" acc_prob="0.000">
            <gDNA_intron_boundary i_start="5836" i_stop="5966" i_length="131"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="5967" e_stop="6163" e_length="197"/>
          </exon>
          <intron i_serial="3" don_prob="0.935" acc_prob="0.994">
            <gDNA_intron_boundary i_start="6164" i_stop="6931" i_length="768"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="6932" e_stop="7028" e_length="97"/>
          </exon>
          <intron i_serial="4" don_prob="0.976" acc_prob="0.998">
            <gDNA_intron_boundary i_start="7029" i_stop="7109" i_length="81"/>
          </intron>
          <exon e_serial="5" e_score="1.000">
            <gDNA_exon_boundary e_start="7110" e_stop="7168" e_length="59"/>
          </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="4869" stop="4931"/>
              <exon start="5528" stop="5835"/>
              <exon start="5967" stop="6163"/>
              <exon start="6932" stop="7028"/>
              <exon start="7110" stop="7168"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M6545" 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="2" gDNA_strand="+"/>
          <translation>
            <gDNA_template>GCAAAATCCACAACAACTCTTTATACTCAACGTTCAATCTTCATAGCACTCTATTTACATGAG : GTTGGAGTTGGTGGTCATTCAATTGAATAATGGCGCTTGCCCCTCATTCAAACATTCTGTGCAATCATGAGGCCATCAAATGTCAAGTTGGATCAAGGCTTCAGAGTCATACAAGATTTAGCTGGGGTAGAGCAGATTACTTTGGTAGTATAGTCCTAGTGAAAATTTGTTCCAGAAGACAGATACCTACATACTTGCAGAAATCTTCTAGAATATGTTGTGGTTTGGATTCTAGAAGTCTGCAACTATCATCACGGGGGAAACAAAATCTTTCTTCTGCACATAGAATTAACCAGAATGTACCTAAG : GGAAATACAATATGGAAATTTCCAGAAGATGTAGCTTTGATGGTCTTGAAGAAATGGGGCCAATTGGCCAAAACAGCAATTGTAACTATATTTATTTTGTCAGTTGCTTCAAAGGCTGATGCCGTTGATGCTCTCAAAACTTGTACTTGCTTACTGAAAGAGTGCAGGTAATTTGCAGATGTTACTAAAGTATGCCG : GATAGAGCTTGCGAAGTGCATCTCAAACCCTGCATGTGCAGCTAATGTTGCCTGTCTCCAAACATGCAACAATAGACCTGATGAAACGGAATGTCAG : ATAAAATGTGGTGATTTGTTTGAAAACAGTGTTGTAGACGAGTTCAATGAGTGTGCAGT</gDNA_template>
            <first_frame> A  K  S  T  T  T  L  Y  T  Q  R  S  I  F  I  A  L  Y  L  H  E  :  V  G  V  G  G  H  S  I  E  *  W  R  L  P  L  I  Q  T  F  C  A  I  M  R  P  S  N  V  K  L  D  Q  G  F  R  V  I  Q  D  L  A  G  V  E  Q  I  T  L  V  V  *  S  *  *  K  F  V  P  E  D  R  Y  L  H  T  C  R  N  L  L  E  Y  V  V  V  W  I  L  E  V  C  N  Y  H  H  G  G  N  K  I  F  L  L  H  I  E  L  T  R  M  Y  L  R :   E  I  Q  Y  G  N  F  Q  K  M  *  L  *  W  S  *  R  N  G  A  N  W  P  K  Q  Q  L  *  L  Y  L  F  C  Q  L  L  Q  R  L  M  P  L  M  L  S  K  L  V  L  A  Y  *  K  S  A  G  N  L  Q  M  L  L  K  Y  A   : G  *  S  L  R  S  A  S  Q  T  L  H  V  Q  L  M  L  P  V  S  K  H  A  T  I  D  L  M  K  R  N  V  R :   *  N  V  V  I  C  L  K  T  V  L  *  T  S  S  M  S  V  Q  </first_frame>
            <second_frame>  Q  N  P  Q  Q  L  F  I  L  N  V  Q  S  S  *  H  S  I  Y  M  R :   L  E  L  V  V  I  Q  L  N  N  G  A  C  P  S  F  K  H  S  V  Q  S  *  G  H  Q  M  S  S  W  I  K  A  S  E  S  Y  K  I  *  L  G  *  S  R  L  L  W  *  Y  S  P  S  E  N  L  F  Q  K  T  D  T  Y  I  L  A  E  I  F  *  N  M  L  W  F  G  F  *  K  S  A  T  I  I  T  G  E  T  K  S  F  F  C  T  *  N  *  P  E  C  T  *   : G  K  Y  N  M  E  I  S  R  R  C  S  F  D  G  L  E  E  M  G  P  I  G  Q  N  S  N  C  N  Y  I  Y  F  V  S  C  F  K  G  *  C  R  *  C  S  Q  N  L  Y  L  L  T  E  R  V  Q  V  I  C  R  C  Y  *  S  M  P  :  D  R  A  C  E  V  H  L  K  P  C  M  C  S  *  C  C  L  S  P  N  M  Q  Q  *  T  *  *  N  G  M  S   : D  K  M  W  *  F  V  *  K  Q  C  C  R  R  V  Q  *  V  C  S </second_frame>
            <third_frame>   K  I  H  N  N  S  L  Y  S  T  F  N  L  H  S  T  L  F  T  *   : G  W  S  W  W  S  F  N  *  I  M  A  L  A  P  H  S  N  I  L  C  N  H  E  A  I  K  C  Q  V  G  S  R  L  Q  S  H  T  R  F  S  W  G  R  A  D  Y  F  G  S  I  V  L  V  K  I  C  S  R  R  Q  I  P  T  Y  L  Q  K  S  S  R  I  C  C  G  L  D  S  R  S  L  Q  L  S  S  R  G  K  Q  N  L  S  S  A  H  R  I  N  Q  N  V  P  K  :  G  N  T  I  W  K  F  P  E  D  V  A  L  M  V  L  K  K  W  G  Q  L  A  K  T  A  I  V  T  I  F  I  L  S  V  A  S  K  A  D  A  V  D  A  L  K  T  C  T  C  L  L  K  E  C  R  *  F  A  D  V  T  K  V  C  R :   I  E  L  A  K  C  I  S  N  P  A  C  A  A  N  V  A  C  L  Q  T  C  N  N  R  P  D  E  T  E  C  Q  :  I  K  C  G  D  L  F  E  N  S  V  V  D  E  F  N  E  C  A   </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="C04HBa0107M13.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="2" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="5554" stop="5835"/>
                    <exon start="5967" stop="6137"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>450</number_coding_nucleotides>
                  <number_encoded_amino_acids>150</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>IMALAPHSNILCNHEAIKCQVGSRLQSHTRFSWGRADYFGSIVLVKICSRRQIPTYLQKSSRICCGLDSRSLQLSSRGKQNLSSAHRINQNVPKGNTIWKFPEDVALMVLKKWGQLAKTAIVTIFILSVASKADAVDALKTCTCLLKECR*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 15 chains have been computed
$ 
$ memory statistics:
$ 7096 bytes spliced alignments in total
$ 3 spliced alignments have been stored
$ 2365 bytes was the average size of a spliced alignment
$ 5872 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5872 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 15 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-15 20:35:22
-->
