<?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="2009-01-05 14:34:35"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0128L09-11qXg/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C04HBa0128L09-11qXg/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-C04HBa0128L09-11qXg/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M3910" ref_strand="+" ref_description="SGN-M3910 U214856 [unigene_markers]">
      <seq>atttagtatatgtggcttgttctgtttaattcgtaaaaaagtgtgctttgtgtctagaaatctctctgtattgacagcaaagcattcatcagatacagcctaataatactactctttctattttcatttttagatatatagagattcacgggcattgttagagaagcaacgtcgtcgtttctcttgctccgttcccgtctcccgtcctttttctgcattgtcgccggcgacaatggtggatttaggtctcttcggatctcttcttgtagtggtgttggggttcgttgcagttttctgttttttcattggtcgtaacaaaagtaaaaatgatggctcggcaactagcaccactacaactacgctgtataatggagagtccagatcaaaggatggaaacgaagacgttgatatcatcatcgtcggtgccggtgttgccggtgctgctcttgctcacactcttggcaaggaggggcgtcgtgtaaaagtaattgaaagagatttgacggagcctgatcgaattgttggagaactcctacaaccgggtggttatctcaaattgcaggagttgggattggaagattgtgttgagaaaattgatgctcaacgcgtttttgggtatgcccttttcaaggatggaaagagtacacgtctttcttatcccctggagaaatttcactctgatgtttctggaaggagcttccacaatgggcgtttcattcaaagaatgcgagagaaagctgcagctcttcccaatgtcaaactcgagcaaggtactgttacgtctctgcttgaagaaaaggggatcattagaggtgttcagtacaagactaaatccggtgaagagttgaaagcatatgcaccattaactgtagtatgtgatggttgtttctcgaatctgcgacgtaccctctgtgatccaaaggtagaagtcccttcttgttttgttggtctggtcctggagaactgtcagcttccacatgaaaatcacggacatgtcattttggctgatccgtcacctatcttgttctatcccataagcagtactgaagtccgctgtctggttgatgtacctggtcaaaaagtgccttctatttcgaatggtgaaatggccaaatatttgaaaagtgtagttgctccccaggtccctcctgagataaaagatgcattcattgctgcaattgataaaggaaacatcaggacaatgcccaaccgaagcatgccagctgctcctcatcctactcctggtgctcttctcatgggtgatgcattcaacatgcgccaccccttgactggtggaggaatgactgtagcattatctgatatcgttgtattgcgtgatcttctcaaacctcttcgtaatttgaatgatgcatctactctttgcagatatctggagtcattttacaccttgcgtaagcctgtggcctccaccatcaatacattggctggtgccttgtataaggtattttgtgcttcacctgatcaagctaggaaggagatgcgtgaagcatgctttgattatttgagcctcggtggagtattctcagaaggaccagtatctttgctttctggcttaaaccctcgtccattgagtctcgtttgtcatttctttgctgtggctatctttggtgttggccgcttgctgcttcctttcccatcaccgaaacgtatatggattggagcccggctaatatcgagtgcatctgcaatcattttccctatcatcaaggcagaaggggtcagacagatgttcttccctgctactgttcccgcatattacaggaagccctcctgaagtgaggttgtaactgctataaacagaataaggctatgccattgtaccacctccatcagtattctggttgtgagtttcaagagtttagtccaactgttgcacaatttttggtttctagtcttcccttgtaatctttttcctttgttcccatgattgattacactattaactgcaaagtaaatataagttgtaaaagtaaaaaaaaaaaaaacattcatttttttttccttttttaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0128L09-11qXg/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0128L09.1" temp_strand="+" temp_description="C04HBa0128L09.1  CU915722.3 htgs_phase:3 submitted_to_sgn_as:C04HBa0128L09 sequenced_by:sanger upload_account_name:uk">
        <position start="58911" stop="63052"/>
      </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="59211" g_stop="59676" g_length="466"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="466" r_length="466" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="59677" i_stop="59995" i_length="319">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.994" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="59996" g_stop="60107" g_length="112"/>
          <reference_exon_boundary r_type="cDNA" r_start="467" r_stop="578" r_length="112" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="60108" i_stop="60231" i_length="124">
            <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="3">
          <gDNA_exon_boundary g_start="60232" g_stop="60406" g_length="175"/>
          <reference_exon_boundary r_type="cDNA" r_start="579" r_stop="753" r_length="175" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="60407" i_stop="60642" i_length="236">
            <donor d_prob="0.994" d_score="1.00"/>
            <acceptor a_prob="0.995" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="60643" g_stop="60811" g_length="169"/>
          <reference_exon_boundary r_type="cDNA" r_start="754" r_stop="922" r_length="169" r_score="0.994"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="60812" i_stop="61100" i_length="289">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.754" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="61101" g_stop="61319" g_length="219"/>
          <reference_exon_boundary r_type="cDNA" r_start="923" r_stop="1141" r_length="219" r_score="1.000"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="61320" i_stop="61420" i_length="101">
            <donor d_prob="0.989" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="61421" g_stop="61696" g_length="276"/>
          <reference_exon_boundary r_type="cDNA" r_start="1142" r_stop="1417" r_length="276" r_score="0.996"/>
        </exon>
        <intron i_serial="6">
          <gDNA_intron_boundary i_start="61697" i_stop="62087" i_length="391">
            <donor d_prob="0.987" d_score="1.00"/>
            <acceptor a_prob="0.994" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="7">
          <gDNA_exon_boundary g_start="62088" g_stop="62366" g_length="279"/>
          <reference_exon_boundary r_type="cDNA" r_start="1418" r_stop="1696" r_length="279" r_score="0.996"/>
        </exon>
        <intron i_serial="7">
          <gDNA_intron_boundary i_start="62367" i_stop="62453" i_length="87">
            <donor d_prob="0.928" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="8">
          <gDNA_exon_boundary g_start="62454" g_stop="62747" g_length="294"/>
          <reference_exon_boundary r_type="cDNA" r_start="1697" r_stop="1990" r_length="294" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="2030" polyA_stop="2062"/>
      <MATCH_line gen_id="C04HBa0128L09.1" gen_strand="+" ref_id="SGN-M3910" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>1990</cumulative_length_of_scored_exons>
        <coverage percentage="0.965" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0128L09.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M3910" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="59211" e_stop="59676"/>
          <exon e_start="59996" e_stop="60107"/>
          <exon e_start="60232" e_stop="60406"/>
          <exon e_start="60643" e_stop="60811"/>
          <exon e_start="61101" e_stop="61319"/>
          <exon e_start="61421" e_stop="61696"/>
          <exon e_start="62088" e_stop="62366"/>
          <exon e_start="62454" e_stop="62747"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATTTAGTATATGTGGCTTGTTCTGTTTAATTCGTAAAAAAGTGTGCTTTGTGTCTAGAAATCTCTCTGTATTGACAGCAAAGCATTCATCAGATACAGCCTAATAATACTACTCTTTCTATTTTCATTTTTAGATATATAGAGATTCACGGGCATTGTTAGAGAAGCAACGTCGTCGTTTCTCTTGCTCCGTTCCCGTCTCCCGTCCTTTTTCTGCATTGTCGCCGGCGACAATGGTGGATTTAGGTCTCTTCGGATCTCTTCTTGTAGTGGTGTTGGGGTTCGTTGCAGTTTTCTGTTTTTTCATTGGTCGTAACAAAAGTAAAAATGATGGCTCGGCAACTAGCACCACTACAACTACGCTGTATAATGGAGAGTCCAGATCAAAGGATGGAAACGAAGACGTTGATATCATCATCGTCGGTGCCGGTGTTGCCGGTGCTGCTCTTGCTCACACTCTTGGCAAGGTGTTGTTTCTATCTTTGTAATCCTTTTTTAAAAGTTATTGTTCAACTTTGGTCCTTTAACTATTTTTTTTATGTACATATGTGAGGAAACTGTATTTGTTTAGTGAGAAGTAATTAGGTTGATAAGTTGATGTGGTTATTGTTCATTGAAGACTTGAACTTGATTGTTAATTTGATGAAATCATAGAAATGAAAGATGCATTGATGATGAAAGCGTTTGGTGTCGCTGCAAATAATTTTATTGGAGTTCTTTGTTGATAATTCTCTATAAAAAAAGTTCTTTGTTGTGAGATTTATGATTATACATTTGGGACTACAGGAGGGGCGTCGTGTAAAAGTAATTGAAAGAGATTTGACGGAGCCTGATCGAATTGTTGGAGAACTCCTACAACCGGGTGGTTATCTCAAATTGCAGGAGTTGGGATTGGAAGGTAAAGTTCCTAAATGATGTGATTTGTGTCAATTCTGGTTAATTTACTCTCTTGAAGAGAAAAAAAAGGATGTTAGTCTGTCTGTTTTTCGCATTTCTCATGTTTGTATTTGTGTCTGCTGCAGATTGTGTTGAGAAAATTGATGCTCAACGCGTTTTTGGGTATGCCCTTTTCAAGGATGGAAAGAGTACACGTCTTTCTTATCCCCTGGAGAAATTTCACTCTGATGTTTCTGGAAGGAGCTTCCACAATGGGCGTTTCATTCAAAGAATGCGAGAGAAAGCTGCAGCTCTTCCCAAGTATTCCTTCTTACTATTTTTTCTTTTTCCCTTGGCAGATCTATTTCTCTCTTTCTCTTATATGTTATGAAGTATTTGATCTTCAAATAATTTCCTGTTTGATCTTATAGTGAGGATTCATATTGTCGAGTCTTACTAGTTTGGATGGAAGCTTAGTTGATTGATTGAAATAGTTTCCTGTTGAATTATCTCTGCTTTGATTGACTAAATGCATATCGGCTTTGATTTTTTAACAGTGTCAAACTCGAGCAAGGCACTGTTACGTCTCTGCTTGAAGAAAAGGGGATCATTAGAGGTGTTCAGTACAAGACTAAATCCGGTGAAGAGTTGAAAGCATATGCACCATTAACTGTAGTATGTGATGGTTGTTTCTCGAATCTGCGACGTACCCTCTGTGATCCAAAGGTAAGGGCGCTTATCTATATTTCTCTTGATTTTTGTTAAGATAAGAAGGATGATACTGGGTGATTAATTTTTTTCTGAGAAGGATCTTTTGTTTAAAAAGCTCGTCTGTGAAATCGTTTGCTTTTACTTACTGTATATCATCTTTTGCTTTTTTACTTACTGTGTGAGACAATAAGAATTAGTGTACCGAAGTTGTTTGAATGAACAAATATCTTTAAATGAACATCAACTTTGTTGTCCCCTCCTTATGTTTCTCTCAACACTCAGAATGACATGTAACATTGCACAGGTAGAAGTCCCTTCTTGTTTTGTTGGTCTGGTCCTGGAGAACTGTCAGCTTCCACATGAAAATCACGGACATGTCATTTTGGCTGATCCGTCACCTATCTTGTTCTATCCCATAAGCAGTACTGAAGTCCGCTGTCTGGTTGATGTACCTGGTCAAAAAGTGCCTTCTATTTCGAATGGTGAAATGGCCAAATATTTGAAAAGTGTAGTTGCTCCCCAGGTAAAGAATTGTTGAAAAAGTTATCCTGAATGACATACCATGTCATTATAGTAGTATACATACTTATTATGTTCAATGAGATGTTTGTGTGGTTGTTCCAGGTCCCTCCTGAGATAAAAGATGCATTCATTGCTGCAATTGATAAAGGAAACATCAGGACAATGCCCAACCGAAGCATGCCAGCTGCTCCTCATCCTACTCCTGGTGCTCTTCTCATGGGTGATGCATTCAACATGCGCCACCCCTTGACTGGTGGAGGAATGACTGTAGCATTATCTGATATCGTTGTATTGCGTGATCTTCTCAAACCTCTTCGTGATTTGAATGATGCATCTACTCTTTGCAGATATCTGGAGTCATTTTACACCTTGCGTAAGGTAAAAATCTTTTGAAATCCTTCCTTGCATAAGCAACATATTTGGTTGCTGTAAGCACCACATTTTCTACTTTGAGAATCCTTAGTGAAGTAAAAACTCTATGTTGACTAGTGAGTAATTAAGGATCTGGAACCACAAAACTGACATTCCTTTGATGATTTCACCAGCTATCAATCTACCAATAACAATGTAATGTAAAAAGGCTTGGTTCATTACGATGTTTTAGGACTTTTTGAACTCACTCAATTCTCCTATAATTTGCCTTCTACATAAAAAAAAAAAGGGAGAGCAAAAGAGGATGACTCAATTCTCCTGCAGCACTTTCAGACTTAACTAGAATATTATTACCTTTATAGATATTGACTTGTTCTGCTCGCATATTTATCTGCAGCCTGTGGCCTCCACCATCAATACATTGGCTGGTGCCTTGTATAAGGTATTTTGTGCTTCACCTGATCAAGCTAGGAAGGAGATGCGTGAAGCATGCTTTGATTATTTGAGCCTCGGTGGAGTATTCTCAGAAGGACCAGTATCTTTGCTTTCTGGCTTAAACCCTCGTCCATTAAGTCTCGTTTGTCATTTCTTTGCTGTGGCTATCTTTGGTGTTGGCCGCTTGCTGCTTCCTTTCCCATCACCGAAACGTATATGGATTGGAGCCCGGCTAATATCGGTAGGTGTCAATCTTGCTTTTGCTCAAGTATTTACAATCTTACTCGTGTTCTTGTATTTTGACAATTTCATGTTGATTCAAATGCAGAGTGCATCTGCAATCATTTTCCCTATCATCAAGGCAGAAGGGGTCAGACAGATGTTCTTCCCTGCTACTGTTCCCGCATATTACAGGAAGCCCTCCTGAAGTGAGGTTGTAACTGCTATAAACAGAATAAGGCTATGCCATTGTACCACCTCCATCAGTATTCTGGTTGTGAGTTTCAAGAGTTTAGTCCAACTGTTGCACAATTTTTGGTTTCTAGTCTTCCCTTGTAATCTTTTTCCTTTGTTCCCATGATTGATTACACTATTAACTGCAAAGTAAATATAAGTTGTAAAA</genome_strand>
        <mrna_strand>ATTTAGTATATGTGGCTTGTTCTGTTTAATTCGTAAAAAAGTGTGCTTTGTGTCTAGAAATCTCTCTGTATTGACAGCAAAGCATTCATCAGATACAGCCTAATAATACTACTCTTTCTATTTTCATTTTTAGATATATAGAGATTCACGGGCATTGTTAGAGAAGCAACGTCGTCGTTTCTCTTGCTCCGTTCCCGTCTCCCGTCCTTTTTCTGCATTGTCGCCGGCGACAATGGTGGATTTAGGTCTCTTCGGATCTCTTCTTGTAGTGGTGTTGGGGTTCGTTGCAGTTTTCTGTTTTTTCATTGGTCGTAACAAAAGTAAAAATGATGGCTCGGCAACTAGCACCACTACAACTACGCTGTATAATGGAGAGTCCAGATCAAAGGATGGAAACGAAGACGTTGATATCATCATCGTCGGTGCCGGTGTTGCCGGTGCTGCTCTTGCTCACACTCTTGGCAAG...............................................................................................................................................................................................................................................................................................................................GAGGGGCGTCGTGTAAAAGTAATTGAAAGAGATTTGACGGAGCCTGATCGAATTGTTGGAGAACTCCTACAACCGGGTGGTTATCTCAAATTGCAGGAGTTGGGATTGGAAG............................................................................................................................ATTGTGTTGAGAAAATTGATGCTCAACGCGTTTTTGGGTATGCCCTTTTCAAGGATGGAAAGAGTACACGTCTTTCTTATCCCCTGGAGAAATTTCACTCTGATGTTTCTGGAAGGAGCTTCCACAATGGGCGTTTCATTCAAAGAATGCGAGAGAAAGCTGCAGCTCTTCCCAA............................................................................................................................................................................................................................................TGTCAAACTCGAGCAAGGTACTGTTACGTCTCTGCTTGAAGAAAAGGGGATCATTAGAGGTGTTCAGTACAAGACTAAATCCGGTGAAGAGTTGAAAGCATATGCACCATTAACTGTAGTATGTGATGGTTGTTTCTCGAATCTGCGACGTACCCTCTGTGATCCAAAG.................................................................................................................................................................................................................................................................................................GTAGAAGTCCCTTCTTGTTTTGTTGGTCTGGTCCTGGAGAACTGTCAGCTTCCACATGAAAATCACGGACATGTCATTTTGGCTGATCCGTCACCTATCTTGTTCTATCCCATAAGCAGTACTGAAGTCCGCTGTCTGGTTGATGTACCTGGTCAAAAAGTGCCTTCTATTTCGAATGGTGAAATGGCCAAATATTTGAAAAGTGTAGTTGCTCCCCAG.....................................................................................................GTCCCTCCTGAGATAAAAGATGCATTCATTGCTGCAATTGATAAAGGAAACATCAGGACAATGCCCAACCGAAGCATGCCAGCTGCTCCTCATCCTACTCCTGGTGCTCTTCTCATGGGTGATGCATTCAACATGCGCCACCCCTTGACTGGTGGAGGAATGACTGTAGCATTATCTGATATCGTTGTATTGCGTGATCTTCTCAAACCTCTTCGTAATTTGAATGATGCATCTACTCTTTGCAGATATCTGGAGTCATTTTACACCTTGCGTAAG.......................................................................................................................................................................................................................................................................................................................................................................................................CCTGTGGCCTCCACCATCAATACATTGGCTGGTGCCTTGTATAAGGTATTTTGTGCTTCACCTGATCAAGCTAGGAAGGAGATGCGTGAAGCATGCTTTGATTATTTGAGCCTCGGTGGAGTATTCTCAGAAGGACCAGTATCTTTGCTTTCTGGCTTAAACCCTCGTCCATTGAGTCTCGTTTGTCATTTCTTTGCTGTGGCTATCTTTGGTGTTGGCCGCTTGCTGCTTCCTTTCCCATCACCGAAACGTATATGGATTGGAGCCCGGCTAATATCG.......................................................................................AGTGCATCTGCAATCATTTTCCCTATCATCAAGGCAGAAGGGGTCAGACAGATGTTCTTCCCTGCTACTGTTCCCGCATATTACAGGAAGCCCTCCTGAAGTGAGGTTGTAACTGCTATAAACAGAATAAGGCTATGCCATTGTACCACCTCCATCAGTATTCTGGTTGTGAGTTTCAAGAGTTTAGTCCAACTGTTGCACAATTTTTGGTTTCTAGTCTTCCCTTGTAATCTTTTTCCTTTGTTCCCATGATTGATTACACTATTAACTGCAAAGTAAATATAAGTTGTAAAA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>1</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="59211" PGL_stop="62747"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="59211" e_stop="59676"/>
            <exon e_start="59996" e_stop="60107"/>
            <exon e_start="60232" e_stop="60406"/>
            <exon e_start="60643" e_stop="60811"/>
            <exon e_start="61101" e_stop="61319"/>
            <exon e_start="61421" e_stop="61696"/>
            <exon e_start="62088" e_stop="62366"/>
            <exon e_start="62454" e_stop="62747"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="1.000" acc_prob="0.994" e_score="1.000"/>
          <exon-intron don_prob="0.999" acc_prob="0.997" e_score="1.000"/>
          <exon-intron don_prob="0.994" acc_prob="0.995" e_score="1.000"/>
          <exon-intron don_prob="0.999" acc_prob="0.754" e_score="0.994"/>
          <exon-intron don_prob="0.989" acc_prob="1.000" e_score="1.000"/>
          <exon-intron don_prob="0.987" acc_prob="0.994" e_score="0.996"/>
          <exon-intron don_prob="0.928" acc_prob="0.999" e_score="0.996"/>
          <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="59211" e_stop="59676" e_length="466"/>
          </exon>
          <intron i_serial="1" don_prob="1.000" acc_prob="0.994">
            <gDNA_intron_boundary i_start="59677" i_stop="59995" i_length="319"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="59996" e_stop="60107" e_length="112"/>
          </exon>
          <intron i_serial="2" don_prob="0.999" acc_prob="0.997">
            <gDNA_intron_boundary i_start="60108" i_stop="60231" i_length="124"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="60232" e_stop="60406" e_length="175"/>
          </exon>
          <intron i_serial="3" don_prob="0.994" acc_prob="0.995">
            <gDNA_intron_boundary i_start="60407" i_stop="60642" i_length="236"/>
          </intron>
          <exon e_serial="4" e_score="0.994">
            <gDNA_exon_boundary e_start="60643" e_stop="60811" e_length="169"/>
          </exon>
          <intron i_serial="4" don_prob="0.999" acc_prob="0.754">
            <gDNA_intron_boundary i_start="60812" i_stop="61100" i_length="289"/>
          </intron>
          <exon e_serial="5" e_score="1.000">
            <gDNA_exon_boundary e_start="61101" e_stop="61319" e_length="219"/>
          </exon>
          <intron i_serial="5" don_prob="0.989" acc_prob="1.000">
            <gDNA_intron_boundary i_start="61320" i_stop="61420" i_length="101"/>
          </intron>
          <exon e_serial="6" e_score="0.996">
            <gDNA_exon_boundary e_start="61421" e_stop="61696" e_length="276"/>
          </exon>
          <intron i_serial="6" don_prob="0.987" acc_prob="0.994">
            <gDNA_intron_boundary i_start="61697" i_stop="62087" i_length="391"/>
          </intron>
          <exon e_serial="7" e_score="0.996">
            <gDNA_exon_boundary e_start="62088" e_stop="62366" e_length="279"/>
          </exon>
          <intron i_serial="7" don_prob="0.928" acc_prob="0.999">
            <gDNA_intron_boundary i_start="62367" i_stop="62453" i_length="87"/>
          </intron>
          <exon e_serial="8" e_score="1.000">
            <gDNA_exon_boundary e_start="62454" e_stop="62747" e_length="294"/>
          </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="59211" stop="59676"/>
              <exon start="59996" stop="60107"/>
              <exon start="60232" stop="60406"/>
              <exon start="60643" stop="60811"/>
              <exon start="61101" stop="61319"/>
              <exon start="61421" stop="61696"/>
              <exon start="62088" stop="62366"/>
              <exon start="62454" stop="62747"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M3910" 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>ATTTAGTATATGTGGCTTGTTCTGTTTAATTCGTAAAAAAGTGTGCTTTGTGTCTAGAAATCTCTCTGTATTGACAGCAAAGCATTCATCAGATACAGCCTAATAATACTACTCTTTCTATTTTCATTTTTAGATATATAGAGATTCACGGGCATTGTTAGAGAAGCAACGTCGTCGTTTCTCTTGCTCCGTTCCCGTCTCCCGTCCTTTTTCTGCATTGTCGCCGGCGACAATGGTGGATTTAGGTCTCTTCGGATCTCTTCTTGTAGTGGTGTTGGGGTTCGTTGCAGTTTTCTGTTTTTTCATTGGTCGTAACAAAAGTAAAAATGATGGCTCGGCAACTAGCACCACTACAACTACGCTGTATAATGGAGAGTCCAGATCAAAGGATGGAAACGAAGACGTTGATATCATCATCGTCGGTGCCGGTGTTGCCGGTGCTGCTCTTGCTCACACTCTTGGCAAG : GAGGGGCGTCGTGTAAAAGTAATTGAAAGAGATTTGACGGAGCCTGATCGAATTGTTGGAGAACTCCTACAACCGGGTGGTTATCTCAAATTGCAGGAGTTGGGATTGGAAG : ATTGTGTTGAGAAAATTGATGCTCAACGCGTTTTTGGGTATGCCCTTTTCAAGGATGGAAAGAGTACACGTCTTTCTTATCCCCTGGAGAAATTTCACTCTGATGTTTCTGGAAGGAGCTTCCACAATGGGCGTTTCATTCAAAGAATGCGAGAGAAAGCTGCAGCTCTTCCCAA : TGTCAAACTCGAGCAAGGCACTGTTACGTCTCTGCTTGAAGAAAAGGGGATCATTAGAGGTGTTCAGTACAAGACTAAATCCGGTGAAGAGTTGAAAGCATATGCACCATTAACTGTAGTATGTGATGGTTGTTTCTCGAATCTGCGACGTACCCTCTGTGATCCAAAG : GTAGAAGTCCCTTCTTGTTTTGTTGGTCTGGTCCTGGAGAACTGTCAGCTTCCACATGAAAATCACGGACATGTCATTTTGGCTGATCCGTCACCTATCTTGTTCTATCCCATAAGCAGTACTGAAGTCCGCTGTCTGGTTGATGTACCTGGTCAAAAAGTGCCTTCTATTTCGAATGGTGAAATGGCCAAATATTTGAAAAGTGTAGTTGCTCCCCAG : GTCCCTCCTGAGATAAAAGATGCATTCATTGCTGCAATTGATAAAGGAAACATCAGGACAATGCCCAACCGAAGCATGCCAGCTGCTCCTCATCCTACTCCTGGTGCTCTTCTCATGGGTGATGCATTCAACATGCGCCACCCCTTGACTGGTGGAGGAATGACTGTAGCATTATCTGATATCGTTGTATTGCGTGATCTTCTCAAACCTCTTCGTGATTTGAATGATGCATCTACTCTTTGCAGATATCTGGAGTCATTTTACACCTTGCGTAAG : CCTGTGGCCTCCACCATCAATACATTGGCTGGTGCCTTGTATAAGGTATTTTGTGCTTCACCTGATCAAGCTAGGAAGGAGATGCGTGAAGCATGCTTTGATTATTTGAGCCTCGGTGGAGTATTCTCAGAAGGACCAGTATCTTTGCTTTCTGGCTTAAACCCTCGTCCATTAAGTCTCGTTTGTCATTTCTTTGCTGTGGCTATCTTTGGTGTTGGCCGCTTGCTGCTTCCTTTCCCATCACCGAAACGTATATGGATTGGAGCCCGGCTAATATCG : AGTGCATCTGCAATCATTTTCCCTATCATCAAGGCAGAAGGGGTCAGACAGATGTTCTTCCCTGCTACTGTTCCCGCATATTACAGGAAGCCCTCCTGAAGTGAGGTTGTAACTGCTATAAACAGAATAAGGCTATGCCATTGTACCACCTCCATCAGTATTCTGGTTGTGAGTTTCAAGAGTTTAGTCCAACTGTTGCACAATTTTTGGTTTCTAGTCTTCCCTTGTAATCTTTTTCCTTTGTTCCCATGATTGATTACACTATTAACTGCAAAGTAAATATAAGTTGTAAAA</gDNA_template>
            <first_frame> I  *  Y  M  W  L  V  L  F  N  S  *  K  S  V  L  C  V  *  K  S  L  C  I  D  S  K  A  F  I  R  Y  S  L  I  I  L  L  F  L  F  S  F  L  D  I  *  R  F  T  G  I  V  R  E  A  T  S  S  F  L  L  L  R  S  R  L  P  S  F  F  C  I  V  A  G  D  N  G  G  F  R  S  L  R  I  S  S  C  S  G  V  G  V  R  C  S  F  L  F  F  H  W  S  *  Q  K  *  K  *  W  L  G  N  *  H  H  Y  N  Y  A  V  *  W  R  V  Q  I  K  G  W  K  R  R  R  *  Y  H  H  R  R  C  R  C  C  R  C  C  S  C  S  H  S  W  Q   : G  G  A  S  C  K  S  N  *  K  R  F  D  G  A  *  S  N  C  W  R  T  P  T  T  G  W  L  S  Q  I  A  G  V  G  I  G  R :   L  C  *  E  N  *  C  S  T  R  F  W  V  C  P  F  Q  G  W  K  E  Y  T  S  F  L  S  P  G  E  I  S  L  *  C  F  W  K  E  L  P  Q  W  A  F  H  S  K  N  A  R  E  S  C  S  S  S  Q  :  C  Q  T  R  A  R  H  C  Y  V  S  A  *  R  K  G  D  H  *  R  C  S  V  Q  D  *  I  R  *  R  V  E  S  I  C  T  I  N  C  S  M  *  W  L  F  L  E  S  A  T  Y  P  L  *  S  K   : G  R  S  P  F  L  F  C  W  S  G  P  G  E  L  S  A  S  T  *  K  S  R  T  C  H  F  G  *  S  V  T  Y  L  V  L  S  H  K  Q  Y  *  S  P  L  S  G  *  C  T  W  S  K  S  A  F  Y  F  E  W  *  N  G  Q  I  F  E  K  C  S  C  S  P   : G  P  S  *  D  K  R  C  I  H  C  C  N  *  *  R  K  H  Q  D  N  A  Q  P  K  H  A  S  C  S  S  S  Y  S  W  C  S  S  H  G  *  C  I  Q  H  A  P  P  L  D  W  W  R  N  D  C  S  I  I  *  Y  R  C  I  A  *  S  S  Q  T  S  S  *  F  E  *  C  I  Y  S  L  Q  I  S  G  V  I  L  H  L  A  *   : A  C  G  L  H  H  Q  Y  I  G  W  C  L  V  *  G  I  L  C  F  T  *  S  S  *  E  G  D  A  *  S  M  L  *  L  F  E  P  R  W  S  I  L  R  R  T  S  I  F  A  F  W  L  K  P  S  S  I  K  S  R  L  S  F  L  C  C  G  Y  L  W  C  W  P  L  A  A  S  F  P  I  T  E  T  Y  M  D  W  S  P  A  N  I   : E  C  I  C  N  H  F  P  Y  H  Q  G  R  R  G  Q  T  D  V  L  P  C  Y  C  S  R  I  L  Q  E  A  L  L  K  *  G  C  N  C  Y  K  Q  N  K  A  M  P  L  Y  H  L  H  Q  Y  S  G  C  E  F  Q  E  F  S  P  T  V  A  Q  F  L  V  S  S  L  P  L  *  S  F  S  F  V  P  M  I  D  Y  T  I  N  C  K  V  N  I  S  C  K  </first_frame>
            <second_frame>  F  S  I  C  G  L  F  C  L  I  R  K  K  V  C  F  V  S  R  N  L  S  V  L  T  A  K  H  S  S  D  T  A  *  *  Y  Y  S  F  Y  F  H  F  *  I  Y  R  D  S  R  A  L  L  E  K  Q  R  R  R  F  S  C  S  V  P  V  S  R  P  F  S  A  L  S  P  A  T  M  V  D  L  G  L  F  G  S  L  L  V  V  V  L  G  F  V  A  V  F  C  F  F  I  G  R  N  K  S  K  N  D  G  S  A  T  S  T  T  T  T  T  L  Y  N  G  E  S  R  S  K  D  G  N  E  D  V  D  I  I  I  V  G  A  G  V  A  G  A  A  L  A  H  T  L  G  K  :  E  G  R  R  V  K  V  I  E  R  D  L  T  E  P  D  R  I  V  G  E  L  L  Q  P  G  G  Y  L  K  L  Q  E  L  G  L  E   : D  C  V  E  K  I  D  A  Q  R  V  F  G  Y  A  L  F  K  D  G  K  S  T  R  L  S  Y  P  L  E  K  F  H  S  D  V  S  G  R  S  F  H  N  G  R  F  I  Q  R  M  R  E  K  A  A  A  L  P  N :   V  K  L  E  Q  G  T  V  T  S  L  L  E  E  K  G  I  I  R  G  V  Q  Y  K  T  K  S  G  E  E  L  K  A  Y  A  P  L  T  V  V  C  D  G  C  F  S  N  L  R  R  T  L  C  D  P  K  :  V  E  V  P  S  C  F  V  G  L  V  L  E  N  C  Q  L  P  H  E  N  H  G  H  V  I  L  A  D  P  S  P  I  L  F  Y  P  I  S  S  T  E  V  R  C  L  V  D  V  P  G  Q  K  V  P  S  I  S  N  G  E  M  A  K  Y  L  K  S  V  V  A  P  Q  :  V  P  P  E  I  K  D  A  F  I  A  A  I  D  K  G  N  I  R  T  M  P  N  R  S  M  P  A  A  P  H  P  T  P  G  A  L  L  M  G  D  A  F  N  M  R  H  P  L  T  G  G  G  M  T  V  A  L  S  D  I  V  V  L  R  D  L  L  K  P  L  R  D  L  N  D  A  S  T  L  C  R  Y  L  E  S  F  Y  T  L  R  K  :  P  V  A  S  T  I  N  T  L  A  G  A  L  Y  K  V  F  C  A  S  P  D  Q  A  R  K  E  M  R  E  A  C  F  D  Y  L  S  L  G  G  V  F  S  E  G  P  V  S  L  L  S  G  L  N  P  R  P  L  S  L  V  C  H  F  F  A  V  A  I  F  G  V  G  R  L  L  L  P  F  P  S  P  K  R  I  W  I  G  A  R  L  I  S  :  S  A  S  A  I  I  F  P  I  I  K  A  E  G  V  R  Q  M  F  F  P  A  T  V  P  A  Y  Y  R  K  P  S  *  S  E  V  V  T  A  I  N  R  I  R  L  C  H  C  T  T  S  I  S  I  L  V  V  S  F  K  S  L  V  Q  L  L  H  N  F  W  F  L  V  F  P  C  N  L  F  P  L  F  P  *  L  I  T  L  L  T  A  K  *  I  *  V  V  K </second_frame>
            <third_frame>   L  V  Y  V  A  C  S  V  *  F  V  K  K  C  A  L  C  L  E  I  S  L  Y  *  Q  Q  S  I  H  Q  I  Q  P  N  N  T  T  L  S  I  F  I  F  R  Y  I  E  I  H  G  H  C  *  R  S  N  V  V  V  S  L  A  P  F  P  S  P  V  L  F  L  H  C  R  R  R  Q  W  W  I  *  V  S  S  D  L  F  L  *  W  C  W  G  S  L  Q  F  S  V  F  S  L  V  V  T  K  V  K  M  M  A  R  Q  L  A  P  L  Q  L  R  C  I  M  E  S  P  D  Q  R  M  E  T  K  T  L  I  S  S  S  S  V  P  V  L  P  V  L  L  L  L  T  L  L  A  R :   R  G  V  V  *  K  *  L  K  E  I  *  R  S  L  I  E  L  L  E  N  S  Y  N  R  V  V  I  S  N  C  R  S  W  D  W  K  :  I  V  L  R  K  L  M  L  N  A  F  L  G  M  P  F  S  R  M  E  R  V  H  V  F  L  I  P  W  R  N  F  T  L  M  F  L  E  G  A  S  T  M  G  V  S  F  K  E  C  E  R  K  L  Q  L  F  P   : M  S  N  S  S  K  A  L  L  R  L  C  L  K  K  R  G  S  L  E  V  F  S  T  R  L  N  P  V  K  S  *  K  H  M  H  H  *  L  *  Y  V  M  V  V  S  R  I  C  D  V  P  S  V  I  Q  R :   *  K  S  L  L  V  L  L  V  W  S  W  R  T  V  S  F  H  M  K  I  T  D  M  S  F  W  L  I  R  H  L  S  C  S  I  P  *  A  V  L  K  S  A  V  W  L  M  Y  L  V  K  K  C  L  L  F  R  M  V  K  W  P  N  I  *  K  V  *  L  L  P  R :   S  L  L  R  *  K  M  H  S  L  L  Q  L  I  K  E  T  S  G  Q  C  P  T  E  A  C  Q  L  L  L  I  L  L  L  V  L  F  S  W  V  M  H  S  T  C  A  T  P  *  L  V  E  E  *  L  *  H  Y  L  I  S  L  Y  C  V  I  F  S  N  L  F  V  I  *  M  M  H  L  L  F  A  D  I  W  S  H  F  T  P  C  V  S :   L  W  P  P  P  S  I  H  W  L  V  P  C  I  R  Y  F  V  L  H  L  I  K  L  G  R  R  C  V  K  H  A  L  I  I  *  A  S  V  E  Y  S  Q  K  D  Q  Y  L  C  F  L  A  *  T  L  V  H  *  V  S  F  V  I  S  L  L  W  L  S  L  V  L  A  A  C  C  F  L  S  H  H  R  N  V  Y  G  L  E  P  G  *  Y  R :   V  H  L  Q  S  F  S  L  S  S  R  Q  K  G  S  D  R  C  S  S  L  L  L  F  P  H  I  T  G  S  P  P  E  V  R  L  *  L  L  *  T  E  *  G  Y  A  I  V  P  P  P  S  V  F  W  L  *  V  S  R  V  *  S  N  C  C  T  I  F  G  F  *  S  S  L  V  I  F  F  L  C  S  H  D  *  L  H  Y  *  L  Q  S  K  Y  K  L  *   </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="C04HBa0128L09.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="59344" stop="59676"/>
                    <exon start="59996" stop="60107"/>
                    <exon start="60232" stop="60406"/>
                    <exon start="60643" stop="60811"/>
                    <exon start="61101" stop="61319"/>
                    <exon start="61421" stop="61696"/>
                    <exon start="62088" stop="62366"/>
                    <exon start="62454" stop="62552"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>1659</number_coding_nucleotides>
                  <number_encoded_amino_acids>553</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>IYRDSRALLEKQRRRFSCSVPVSRPFSALSPATMVDLGLFGSLLVVVLGFVAVFCFFIGRNKSKNDGSATSTTTTTLYNGESRSKDGNEDVDIIIVGAGVAGAALAHTLGKEGRRVKVIERDLTEPDRIVGELLQPGGYLKLQELGLEDCVEKIDAQRVFGYALFKDGKSTRLSYPLEKFHSDVSGRSFHNGRFIQRMREKAAALPNVKLEQGTVTSLLEEKGIIRGVQYKTKSGEELKAYAPLTVVCDGCFSNLRRTLCDPKVEVPSCFVGLVLENCQLPHENHGHVILADPSPILFYPISSTEVRCLVDVPGQKVPSISNGEMAKYLKSVVAPQVPPEIKDAFIAAIDKGNIRTMPNRSMPAAPHPTPGALLMGDAFNMRHPLTGGGMTVALSDIVVLRDLLKPLRDLNDASTLCRYLESFYTLRKPVASTINTLAGALYKVFCASPDQARKEMREACFDYLSLGGVFSEGPVSLLSGLNPRPLSLVCHFFAVAIFGVGRLLLPFPSPKRIWIGARLISSASAIIFPIIKAEGVRQMFFPATVPAYYRKPS*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 10 chains have been computed
$ 
$ memory statistics:
$ 2024 bytes spliced alignments in total
$ 1 spliced alignments have been stored
$ 2024 bytes was the average size of a spliced alignment
$ 5752 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5752 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 10 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-05 14:34:43
-->
