<?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="2009-12-01 05:47:22"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C00HBa0142A05-mWZNo/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C00HBa0142A05-mWZNo/gth_cdna_fileCXGN::TomatoGenome::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-C00HBa0142A05-mWZNo/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="C2_At1g72790" ref_strand="+" ref_description="C2_At1g72790">
      <seq>tttttttattcaaaatcacacttctttcataacttaggctagtcaagtactacatgaccaacttatcaactgcaacaaagaaacacaaaattaacaaatgttcaatccatagcggaagcttaagtgacctatgatagtttttttttttttaaacaatctctctattttctgtacactaataataactcaaatctcaaatgatgaacaaaaaaaatgacaactttaacaaatcaatcaatgtggtaagaaaagaatctaactgtggcctactcctgggccgagatttgataagcttcgtcctagatcatttttgttgaaggaattgattttttctagctttaatccagctctaaattttgatatgaagttttcagcttttgtgtttacatctgggcttggacaaaacaatggtgacggagcaaacgccatcccttcaccagcgccggcgtcttctgccatcggggtgttttcggctgaatctatatcttcaagttcaggagacccaaaacgtgagctgagggtgctgtctattctcaagtagtcgccttgtactacaaatttccaggcgtgttttc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0142A05-mWZNo/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C00HBa0142A05.2" temp_strand="-" temp_description="C00HBa0142A05.2  CU928192.4 htgs_phase:3 submitted_to_sgn_as:C04HBa0142A05 sequenced_by:sanger upload_account_name:uk">
        <position start="42048" stop="40879"/>
      </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="41753" g_stop="41179" g_length="575"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="575" r_length="575" r_score="0.990"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0142A05.2" gen_strand="-" ref_id="C2_At1g72790" ref_strand="+">
        <total_alignment_score>0.990</total_alignment_score>
        <cumulative_length_of_scored_exons>575</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0142A05.2" gen_strand="-"/>
        <rDNA rDNA_id="C2_At1g72790" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="41753" e_stop="41179"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATCGATTATTCAAAATCACACTTCTTTCATAACTTAGGCTAGTCAAGTACTACATGACCAACTTATCAACTGCAACAAAGAAACACAAAATTAACAAATGTTCAATCCATAGCGGAAGCTTAAGTGACCTATGATAGTTTTTTTTTTTTTAAACAATCTCTCTATTTTCTGTACACTAATAATAACTCAAATCTCAAATGATGAACAAAAAAAATGACAACTTTAACAAATCAATCAATGTGGTAAGAAAAGAATCTAACTGTGGCCTACTCCTGGGCCGAGATTTGATAAGCTTCGTCCTAGATCATTTTTGTTGAAGGAATTGATTTTTTCTAGCTTTAATCCAGCTCTAAATTTTGATATGAAGTTTTCAGCTTTTGTGTTTACATCTGGGCTTGGACAAAACAATGGTGACGGAGCAAACGCCATCCCTTCACCAGCGCCGGCGTCTTCTGCCATCGGGGTGTTTTCGGCTGAATCTATATCTTCAAGTTCAGGAGACCCAGAACGTGAGCTGAGGGTGCTGTCTATTCTCAAGTAGTCGCCTTGTACTACGAATTTCCAGGCGTGTTTTC</genome_strand>
        <mrna_strand>TTTTTTTATTCAAAATCACACTTCTTTCATAACTTAGGCTAGTCAAGTACTACATGACCAACTTATCAACTGCAACAAAGAAACACAAAATTAACAAATGTTCAATCCATAGCGGAAGCTTAAGTGACCTATGATAGTTTTTTTTTTTTTAAACAATCTCTCTATTTTCTGTACACTAATAATAACTCAAATCTCAAATGATGAACAAAAAAAATGACAACTTTAACAAATCAATCAATGTGGTAAGAAAAGAATCTAACTGTGGCCTACTCCTGGGCCGAGATTTGATAAGCTTCGTCCTAGATCATTTTTGTTGAAGGAATTGATTTTTTCTAGCTTTAATCCAGCTCTAAATTTTGATATGAAGTTTTCAGCTTTTGTGTTTACATCTGGGCTTGGACAAAACAATGGTGACGGAGCAAACGCCATCCCTTCACCAGCGCCGGCGTCTTCTGCCATCGGGGTGTTTTCGGCTGAATCTATATCTTCAAGTTCAGGAGACCCAAAACGTGAGCTGAGGGTGCTGTCTATTCTCAAGTAGTCGCCTTGTACTACAAATTTCCAGGCGTGTTTTC</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-C00HBa0142A05-mWZNo/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="C2_At5g13640" ref_strand="+" ref_description="C2_At5g13640">
      <seq>tccttgcaaaagtaagtccagagacgatgctgctcagaattcaggacatcacgagaatcaaactacagattctaaagcaaaatattacagttatggaaggatgatgtcctttggaaaagatgcaacagaggctcatccatcagatcttaagaggattgactttagggatgctgttaagggcactaatgttgcaaataacacctgtgatgtgtggaacgagtaccaagacatgggtgttagtggtactaaagcagtggaagagtacaaggtttatacagctggagagattgtggatttgctcaactttgttgctccgaaaatgatggcccgtggtaatgctcatttttcatatgggatagctgatgatttggatgatcctaagtattcacactacaaatattggtcaaatccattggagacaaagttaccaaatgctcctgacatggagatctattcaatgtatggagttggcattgaaactgaaagagcatatgtttacaagcggatacctacagcaggatgcaatattccattccagattgatacttcagctgatgatggtgatgaaagtagctgcttgaaatctggtggttacacgatagatggtgatgagactgtgcctgcatta</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0142A05-mWZNo/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C00HBa0142A05.2" temp_strand="-" temp_description="C00HBa0142A05.2  CU928192.4 htgs_phase:3 submitted_to_sgn_as:C04HBa0142A05 sequenced_by:sanger upload_account_name:uk">
        <position start="79402" stop="75736"/>
      </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="79102" g_stop="78937" g_length="166"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="166" r_length="166" r_score="0.970"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="78936" i_stop="77144" i_length="1793">
            <donor d_prob="0.999" d_score="0.92"/>
            <acceptor a_prob="0.995" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="77143" g_stop="76887" g_length="257"/>
          <reference_exon_boundary r_type="cDNA" r_start="167" r_stop="423" r_length="257" r_score="0.984"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="76886" i_stop="76241" i_length="646">
            <donor d_prob="0.971" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="76240" g_stop="76036" g_length="205"/>
          <reference_exon_boundary r_type="cDNA" r_start="424" r_stop="628" r_length="205" r_score="0.971"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0142A05.2" gen_strand="-" ref_id="C2_At5g13640" ref_strand="+">
        <total_alignment_score>0.976</total_alignment_score>
        <cumulative_length_of_scored_exons>628</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0142A05.2" gen_strand="-"/>
        <rDNA rDNA_id="C2_At5g13640" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="79102" e_stop="78937"/>
          <exon e_start="77143" e_stop="76887"/>
          <exon e_start="76240" e_stop="76036"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCCTTGCAGAAGTAAGTCCAGAGACGATGCTGCTCAGAATTCAGGACATCACGAGAATCAAACTACAGATTCTAAAGCAAAATATTACAGTTATGGAAGGATGATGTCCTTTGGAAAGGATGCAGCAGAAGCTCATCCATCAGATCTTAAGAGGATTGACTTCAGGGTAATGTTAATCTGAAACCAAATTCTCTCATTGTTTCTCTTGTATACGCTACTTTCCTTTATGTGTTTCAACTTTGAGCATTGATTTTGTTAGTGGTGGGTGTAGGTGATTTCGGATTACCAGTTTAGGGACTTCTATGATCAGCAGACATGCTGTAGTCCAAGGGATTTAGTGAATAAACTGTGTTCATCTCAACCCAGTAGCTTTACCTTGGACCATGTATATGTGTTCAGAAATCATCCAGATAATAGATATCAGACCCAGTTAATATGGGATGTGACAGAATTCCAAATCTGAATCCATATAACTCAAATGTGCCTAAAGTAGCACAAATAAAACTATCTATAAAGTGGTTAGTACTCTAATGTGAAGTTCTTGTTCTGATTATGGTTCTTTTACTTATACTTTTATGCAATAGGCAAGCATGGGTATGACCTGTTGCCTCGCTAAAAACTGCTTCTTTTGGGGAATTGCCAAAGAATGATTTGGATACCTGGCTGGTCATAATAAAACCAGTGGGCTCACATGTCATGAGTTACACGATTCAGAGCCAATGTGTTGTGCTTGGTGTGATGTCAGTGTAAAATAATGGAAATAAATGAAGTCTAATCTTTATATTACAACTGGATGATGTCCTTGTATATCAATTGTTTTTGTACACATTCTTTGCAAGACATTCCCTTTTTTGTGATAATATTAGATGAGGACTTATCCACTAACAAAAGAAAGAAATAAGATAAAGTACTGCATGAGGCATTCCTTTAACACTTGCTATCTCAACGAAATATCTGTTCAGAATTTCCTTTAAAGGAAAATCTGCTGTCAATGTAAATGGGACGAGATGGTTACAATTAAGTTCATATTGGACTTCCTCTTGAAAAGTGTTCCTTTACTTGCATATAATATTCCAAACTTGTCACTTGTCTTCTTCTTTTTTCTTGAACGAGGAACTCCATTCATTTTGTCAGTTCATCTGAATTTATTATGCTCCAAAAAGACCACAAGAGTCAAAAATATTTCCACTGAGTAGAAGCAGAACTAGACAAGCAAAGCATCATAACTGCCAGGAAAAGCAATGAAAAATGGAACCATGTTCTCTCAAATATTTCAAATTTGAAGACCATATTGGTTATGCTATAAGGTGCTTCTTATAGAGCAAAGAAATATCTATTTCCTTCTCTTCTTGTAATTATTACTCATATTTAAGATCCCTACATCAGCAGCAGCACATGTTTAGTGTGCATCAATCAAGTAATCTGAAGAAGATCTGAAGAACCATTCTCATATGCATCTTTTGGACTTATGGATGGAAAGAAATAAGGCTTGCTTTGAAGGAAGAAAGATGCATGTTTCTAGAATTAAGAACTCTTGTTTGCTTAGTTGATATTTCTGGTGTTATATGAGTAGAGTAGACAGCCTGGATCAGTGCATGGATGTCCTTAGCTTGCTAGAAGGGATTACTCGATGTGGTGATGTTTTCTCATGCAGTTGGTTTTTGTACTTCCCTGTACCATCTTGTACTTTTTTAAAATAAAATTGACCTCATCAAGAAAATAAAAAGTTACCAGGAGATTTAACTAAATAACATTAAAGATGGGTGATCTGTGATGTCTCAGTGGCCTTCCATGATATGGGTGCCTTTTCTTCCTATTTATGCAAATATTGTCTGAAGAAGTTGTCTTAACTTCCTTATCAGATTTTTTTTTGTGCTCACAGGCTGTAATTTCCAAAATAAATTGTCTTATCCATTGCTTCCTGATGCCTCTAACTAACTAGCATTTATTTACATGCAGGATGCTGTTAAGGGCAGTAATGTTGCAAATAACACCTGTGATGTGTGGAACGAGTACCAAGACATGGGTGTTAGTGGCACTAAAGCAGTGGAAGAGTACAAGGTTTATACAGCTGGAGAGATTGTGGATTTGCTCAACTTTGTTGCCCCGAAAATGATGGCCCGTGGTAATGCTCACTTTTCATATGGGATAGCTGATGATTTGGATGATCCTAAGTATTCACACTACAAATATTGGTCAAATCCATTGGAGACAAAGTGAGTCCTCTCATATTTTTGCTTTTGTGTCTTATAATGTAGTTCTAACTTATAAGACTACAGGTTTTTTAGACTATGTACAGATCTGCTAGTTTGGTAATAAAATGTTAGTTTTAATTGCCAAAAAAAATGTAGTTCTAACTTGAATCCTTTCAGATAAGACGAAAAGAAGTCTTTTAACTGTATAGGTTGAAGTTCAAGAACCAAAACGAAATTTGGTTTTACAGCCAAGAGCCTCGACTATCCTACTTCAAAACACACAAAATTTCAGTAGCAATTTCCAATCTGAAGAAAGAACCCGACACTTAAGGCAGTAAAGCTCTATCATTGCCTTCTTGTGTGGTAAAGAACATTAATAGCTTCCACTCGGGCAAGAAGTTCCCCCTTAGTACAGTTTTTTAAACAGGAAAAAGATAGGATCACAAGCCCTTTGAGATACTTTTGTTTTCTTGTGGCTCATGGAAATTACCTGATTGTTATTTAGATTCTCTTCTATTGAGTTCTCTTTCCTTTGTCCCCCCTTTGAATTTCTCAGAAGGTTTAGACAAACTTGAATGTCCATGACAAGGCTTTGCTATAATTTGCAGCAGCTTCTTTAGTTCAAACTAATCTTAGTTATTTTGTTTTGATCTGATTTTTTCTTCAGGTTACCAAATGCTCCTGACATGGAGATCTATTCACTGTATGGAGTTGGCATTGAAACTGAAAGAGCATATGTTTACAAGCGGATACCTACAGCAGGATGCAATATTCCATTCCAGATTGATACTTCAGCTGATGATAATGATGAAGGTAGCTGCTTGAAATCTGGTGTTTACACGGTAGATGGTGATGAGACTGTGCCTGCATTA</genome_strand>
        <mrna_strand>TCCTTGCAAAAGTAAGTCCAGAGACGATGCTGCTCAGAATTCAGGACATCACGAGAATCAAACTACAGATTCTAAAGCAAAATATTACAGTTATGGAAGGATGATGTCCTTTGGAAAAGATGCAACAGAGGCTCATCCATCAGATCTTAAGAGGATTGACTTTAGG.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GATGCTGTTAAGGGCACTAATGTTGCAAATAACACCTGTGATGTGTGGAACGAGTACCAAGACATGGGTGTTAGTGGTACTAAAGCAGTGGAAGAGTACAAGGTTTATACAGCTGGAGAGATTGTGGATTTGCTCAACTTTGTTGCTCCGAAAATGATGGCCCGTGGTAATGCTCATTTTTCATATGGGATAGCTGATGATTTGGATGATCCTAAGTATTCACACTACAAATATTGGTCAAATCCATTGGAGACAAA......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTACCAAATGCTCCTGACATGGAGATCTATTCAATGTATGGAGTTGGCATTGAAACTGAAAGAGCATATGTTTACAAGCGGATACCTACAGCAGGATGCAATATTCCATTCCAGATTGATACTTCAGCTGATGATGGTGATGAAAGTAGCTGCTTGAAATCTGGTGGTTACACGATAGATGGTGATGAGACTGTGCCTGCATTA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>2</total_number_ESTs_reported>
    </alignment_module>
  <PGL_module xmlns="http://www.genomethreader.org/GTH_output/PGL_module/">
    <predicted_gene_location>
      <PGL_line PGL_serial="1" PGL_strand="-" PGL_start="41753" PGL_stop="41179"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="41753" e_stop="41179"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.990"/>
        </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="0.990">
            <gDNA_exon_boundary e_start="41753" e_stop="41179" e_length="575"/>
          </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="41753" stop="41179"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="C2_At1g72790" 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>ATCGATTATTCAAAATCACACTTCTTTCATAACTTAGGCTAGTCAAGTACTACATGACCAACTTATCAACTGCAACAAAGAAACACAAAATTAACAAATGTTCAATCCATAGCGGAAGCTTAAGTGACCTATGATAGTTTTTTTTTTTTTAAACAATCTCTCTATTTTCTGTACACTAATAATAACTCAAATCTCAAATGATGAACAAAAAAAATGACAACTTTAACAAATCAATCAATGTGGTAAGAAAAGAATCTAACTGTGGCCTACTCCTGGGCCGAGATTTGATAAGCTTCGTCCTAGATCATTTTTGTTGAAGGAATTGATTTTTTCTAGCTTTAATCCAGCTCTAAATTTTGATATGAAGTTTTCAGCTTTTGTGTTTACATCTGGGCTTGGACAAAACAATGGTGACGGAGCAAACGCCATCCCTTCACCAGCGCCGGCGTCTTCTGCCATCGGGGTGTTTTCGGCTGAATCTATATCTTCAAGTTCAGGAGACCCAGAACGTGAGCTGAGGGTGCTGTCTATTCTCAAGTAGTCGCCTTGTACTACGAATTTCCAGGCGTGTTTTC</gDNA_template>
            <first_frame> I  D  Y  S  K  S  H  F  F  H  N  L  G  *  S  S  T  T  *  P  T  Y  Q  L  Q  Q  R  N  T  K  L  T  N  V  Q  S  I  A  E  A  *  V  T  Y  D  S  F  F  F  F  K  Q  S  L  Y  F  L  Y  T  N  N  N  S  N  L  K  *  *  T  K  K  M  T  T  L  T  N  Q  S  M  W  *  E  K  N  L  T  V  A  Y  S  W  A  E  I  *  *  A  S  S  *  I  I  F  V  E  G  I  D  F  F  *  L  *  S  S  S  K  F  *  Y  E  V  F  S  F  C  V  Y  I  W  A  W  T  K  Q  W  *  R  S  K  R  H  P  F  T  S  A  G  V  F  C  H  R  G  V  F  G  *  I  Y  I  F  K  F  R  R  P  R  T  *  A  E  G  A  V  Y  S  Q  V  V  A  L  Y  Y  E  F  P  G  V  F   </first_frame>
            <second_frame>  S  I  I  Q  N  H  T  S  F  I  T  *  A  S  Q  V  L  H  D  Q  L  I  N  C  N  K  E  T  Q  N  *  Q  M  F  N  P  *  R  K  L  K  *  P  M  I  V  F  F  F  L  N  N  L  S  I  F  C  T  L  I  I  T  Q  I  S  N  D  E  Q  K  K  *  Q  L  *  Q  I  N  Q  C  G  K  K  R  I  *  L  W  P  T  P  G  P  R  F  D  K  L  R  P  R  S  F  L  L  K  E  L  I  F  S  S  F  N  P  A  L  N  F  D  M  K  F  S  A  F  V  F  T  S  G  L  G  Q  N  N  G  D  G  A  N  A  I  P  S  P  A  P  A  S  S  A  I  G  V  F  S  A  E  S  I  S  S  S  S  G  D  P  E  R  E  L  R  V  L  S  I  L  K  *  S  P  C  T  T  N  F  Q  A  C  F  </second_frame>
            <third_frame>   R  L  F  K  I  T  L  L  S  *  L  R  L  V  K  Y  Y  M  T  N  L  S  T  A  T  K  K  H  K  I  N  K  C  S  I  H  S  G  S  L  S  D  L  *  *  F  F  F  F  *  T  I  S  L  F  S  V  H  *  *  *  L  K  S  Q  M  M  N  K  K  N  D  N  F  N  K  S  I  N  V  V  R  K  E  S  N  C  G  L  L  L  G  R  D  L  I  S  F  V  L  D  H  F  C  *  R  N  *  F  F  L  A  L  I  Q  L  *  I  L  I  *  S  F  Q  L  L  C  L  H  L  G  L  D  K  T  M  V  T  E  Q  T  P  S  L  H  Q  R  R  R  L  L  P  S  G  C  F  R  L  N  L  Y  L  Q  V  Q  E  T  Q  N  V  S  *  G  C  C  L  F  S  S  S  R  L  V  L  R  I  S  R  R  V  F </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="C00HBa0142A05.2" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="41494" stop="41213"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>279</number_coding_nucleotides>
                  <number_encoded_amino_acids>93</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LWPTPGPRFDKLRPRSFLLKELIFSSFNPALNFDMKFSAFVFTSGLGQNNGDGANAIPSPAPASSAIGVFSAESISSSSGDPERELRVLSILK*</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="79102" PGL_stop="76036"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="79102" e_stop="78937"/>
            <exon e_start="77143" e_stop="76887"/>
            <exon e_start="76240" e_stop="76036"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.999" acc_prob="0.995" e_score="0.970"/>
          <exon-intron don_prob="0.971" acc_prob="1.000" e_score="0.984"/>
          <exon-only e_score="0.971"/>
        </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="0.970">
            <gDNA_exon_boundary e_start="79102" e_stop="78937" e_length="166"/>
          </exon>
          <intron i_serial="1" don_prob="0.999" acc_prob="0.995">
            <gDNA_intron_boundary i_start="78936" i_stop="77144" i_length="1793"/>
          </intron>
          <exon e_serial="2" e_score="0.984">
            <gDNA_exon_boundary e_start="77143" e_stop="76887" e_length="257"/>
          </exon>
          <intron i_serial="2" don_prob="0.971" acc_prob="1.000">
            <gDNA_intron_boundary i_start="76886" i_stop="76241" i_length="646"/>
          </intron>
          <exon e_serial="3" e_score="0.971">
            <gDNA_exon_boundary e_start="76240" e_stop="76036" e_length="205"/>
          </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="79102" stop="78937"/>
              <exon start="77143" stop="76887"/>
              <exon start="76240" stop="76036"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="C2_At5g13640" 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>TCCTTGCAGAAGTAAGTCCAGAGACGATGCTGCTCAGAATTCAGGACATCACGAGAATCAAACTACAGATTCTAAAGCAAAATATTACAGTTATGGAAGGATGATGTCCTTTGGAAAGGATGCAGCAGAAGCTCATCCATCAGATCTTAAGAGGATTGACTTCAGG : GATGCTGTTAAGGGCAGTAATGTTGCAAATAACACCTGTGATGTGTGGAACGAGTACCAAGACATGGGTGTTAGTGGCACTAAAGCAGTGGAAGAGTACAAGGTTTATACAGCTGGAGAGATTGTGGATTTGCTCAACTTTGTTGCCCCGAAAATGATGGCCCGTGGTAATGCTCACTTTTCATATGGGATAGCTGATGATTTGGATGATCCTAAGTATTCACACTACAAATATTGGTCAAATCCATTGGAGACAAA : GTTACCAAATGCTCCTGACATGGAGATCTATTCACTGTATGGAGTTGGCATTGAAACTGAAAGAGCATATGTTTACAAGCGGATACCTACAGCAGGATGCAATATTCCATTCCAGATTGATACTTCAGCTGATGATAATGATGAAGGTAGCTGCTTGAAATCTGGTGTTTACACGGTAGATGGTGATGAGACTGTGCCTGCATTA</gDNA_template>
            <first_frame> S  L  Q  K  *  V  Q  R  R  C  C  S  E  F  R  T  S  R  E  S  N  Y  R  F  *  S  K  I  L  Q  L  W  K  D  D  V  L  W  K  G  C  S  R  S  S  S  I  R  S  *  E  D  *  L  Q   : G  C  C  *  G  Q  *  C  C  K  *  H  L  *  C  V  E  R  V  P  R  H  G  C  *  W  H  *  S  S  G  R  V  Q  G  L  Y  S  W  R  D  C  G  F  A  Q  L  C  C  P  E  N  D  G  P  W  *  C  S  L  F  I  W  D  S  *  *  F  G  *  S  *  V  F  T  L  Q  I  L  V  K  S  I  G  D  K  :  V  T  K  C  S  *  H  G  D  L  F  T  V  W  S  W  H  *  N  *  K  S  I  C  L  Q  A  D  T  Y  S  R  M  Q  Y  S  I  P  D  *  Y  F  S  *  *  *  *  *  R  *  L  L  E  I  W  C  L  H  G  R  W  *  *  D  C  A  C  I  </first_frame>
            <second_frame>  P  C  R  S  K  S  R  D  D  A  A  Q  N  S  G  H  H  E  N  Q  T  T  D  S  K  A  K  Y  Y  S  Y  G  R  M  M  S  F  G  K  D  A  A  E  A  H  P  S  D  L  K  R  I  D  F  R  :  D  A  V  K  G  S  N  V  A  N  N  T  C  D  V  W  N  E  Y  Q  D  M  G  V  S  G  T  K  A  V  E  E  Y  K  V  Y  T  A  G  E  I  V  D  L  L  N  F  V  A  P  K  M  M  A  R  G  N  A  H  F  S  Y  G  I  A  D  D  L  D  D  P  K  Y  S  H  Y  K  Y  W  S  N  P  L  E  T  K :   L  P  N  A  P  D  M  E  I  Y  S  L  Y  G  V  G  I  E  T  E  R  A  Y  V  Y  K  R  I  P  T  A  G  C  N  I  P  F  Q  I  D  T  S  A  D  D  N  D  E  G  S  C  L  K  S  G  V  Y  T  V  D  G  D  E  T  V  P  A  L </second_frame>
            <third_frame>   L  A  E  V  S  P  E  T  M  L  L  R  I  Q  D  I  T  R  I  K  L  Q  I  L  K  Q  N  I  T  V  M  E  G  *  C  P  L  E  R  M  Q  Q  K  L  I  H  Q  I  L  R  G  L  T  S  G :   M  L  L  R  A  V  M  L  Q  I  T  P  V  M  C  G  T  S  T  K  T  W  V  L  V  A  L  K  Q  W  K  S  T  R  F  I  Q  L  E  R  L  W  I  C  S  T  L  L  P  R  K  *  W  P  V  V  M  L  T  F  H  M  G  *  L  M  I  W  M  I  L  S  I  H  T  T  N  I  G  Q  I  H  W  R  Q   : S  Y  Q  M  L  L  T  W  R  S  I  H  C  M  E  L  A  L  K  L  K  E  H  M  F  T  S  G  Y  L  Q  Q  D  A  I  F  H  S  R  L  I  L  Q  L  M  I  M  M  K  V  A  A  *  N  L  V  F  T  R  *  M  V  M  R  L  C  L  H   </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C00HBa0142A05.2" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="79101" stop="78937"/>
                    <exon start="77143" stop="76887"/>
                    <exon start="76240" stop="76036"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>627</number_coding_nucleotides>
                  <number_encoded_amino_acids>209</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>PCRSKSRDDAAQNSGHHENQTTDSKAKYYSYGRMMSFGKDAAEAHPSDLKRIDFRDAVKGSNVANNTCDVWNEYQDMGVSGTKAVEEYKVYTAGEIVDLLNFVAPKMMARGNAHFSYGIADDLDDPKYSHYKYWSNPLETKLPNAPDMEIYSLYGVGIETERAYVYKRIPTAGCNIPFQIDTSADDNDEGSCLKSGVYTVDGDETVPAL</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 103 chains have been computed
$ 
$ memory statistics:
$ 4320 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 2160 bytes was the average size of a spliced alignment
$ 6768 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3384 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 104 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 05:47:26
-->
