<?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 06:24:06"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C00SLm0061F09-o4CMa/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C00SLm0061F09-o4CMa/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" 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-C00SLm0061F09-o4CMa/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E207049" ref_strand="+" ref_description="SGN-E207049 [cLEC-30-C22]">
      <seq>tttttagaagcatgtgtcatttttgttcactggagaagggtgtacatcaaattattggcaagtacctttggttgtcttggtcatatggaagggttccttgatgcattattcatgacaaattttaattctattggtgatactatgtttttggtgctttcgaaaaattgaaatgggttaactgaaacaccttaatcta</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLm0061F09-o4CMa/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLm0061F09.2" temp_strand="-" temp_description="C00SLm0061F09.2  CU928196.3 htgs_phase:3 submitted_to_sgn_as:C04SLm0061F09 sequenced_by:sanger upload_account_name:uk">
        <position start="42786" stop="41991"/>
      </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="42486" g_stop="42291" g_length="196"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="196" r_length="196" r_score="0.974"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLm0061F09.2" gen_strand="-" ref_id="SGN-E207049" ref_strand="+">
        <total_alignment_score>0.974</total_alignment_score>
        <cumulative_length_of_scored_exons>196</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLm0061F09.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E207049" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="42486" e_stop="42291"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTTTTAGAAGCATGTGTCATTTTTGTTCACTGGAGAAGGGTGTACATCAAATTATTGGCAAGTACCTTTGGTTGTCTTGGTCATATGGAAGGTTTCCTTGATGCATTATTCATGACAAATTTTAGTTCTATTGTTGATACTATGTTTTTGTTGCTTTCGAAAAATTGAAATGGGTTAGCTGAAACACCTTAATCTA</genome_strand>
        <mrna_strand>TTTTTAGAAGCATGTGTCATTTTTGTTCACTGGAGAAGGGTGTACATCAAATTATTGGCAAGTACCTTTGGTTGTCTTGGTCATATGGAAGGGTTCCTTGATGCATTATTCATGACAAATTTTAATTCTATTGGTGATACTATGTTTTTGGTGCTTTCGAAAAATTGAAATGGGTTAACTGAAACACCTTAATCTA</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-C00SLm0061F09-o4CMa/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E258337" ref_strand="+" ref_description="SGN-E258337 [cLEG-49-B24]">
      <seq>cgctgataacacgaaggaatcgaccagtaggtggttagctgtctgttttgtcgttctcttgcaacggctctttccccctttctatgtttcgtacgaatttcagcgggctacaacattcgtataatccttcattctccagctgtgtagccccgcctcttggagataagtacacatctttcgtcaaggacgaaagagacgatccaaccctctattcctctttattccattgagaggctggaatctcgcgagaatattcggtggatatcggataggatttaaggattggatttcaaacctagggttgcaaatacgattataccctcgtttgttttcttcagggaagctcctctaaataaactctctttcttcttccgattatggggtgga</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLm0061F09-o4CMa/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLm0061F09.2" temp_strand="-" temp_description="C00SLm0061F09.2  CU928196.3 htgs_phase:3 submitted_to_sgn_as:C04SLm0061F09 sequenced_by:sanger upload_account_name:uk">
        <position start="44491" stop="43505"/>
      </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="44191" g_stop="43805" g_length="387"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="387" r_length="387" r_score="0.990"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLm0061F09.2" gen_strand="-" ref_id="SGN-E258337" ref_strand="+">
        <total_alignment_score>0.990</total_alignment_score>
        <cumulative_length_of_scored_exons>387</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLm0061F09.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E258337" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="44191" e_stop="43805"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CGCTGATAACACGAAGGAATCGACCAGTAGGTGGTTAGCTGTCTGTTTTGTCGTTCTCTTGCAACGGCTCTTTCCCCCTTTCTATGTTTCGTACGAATTTCAGCGGGCTACAACATTCGTATAATCCTTCATTCTCCAGCTGTGTAGCCCCGCCTCTTGGAGATAAGTACACATCTTTCGTCAAGGACGAAAGAGACGATCCAACCCTCTATTCCTCTTTATTCCATTGAGAGGCTGGAATCTCGCGAGAATATTCGGTGGATATCGGATAGGATTTAAGGATTGGATTTCAAACCTAGGGTTGCAAATACGATTATACCCTCGTTTGTTTTCTTCAGGGAAGCTCCTCTATATAAACTCTCTTTCTTCTTCGGATTAGGGGTTGGA</genome_strand>
        <mrna_strand>CGCTGATAACACGAAGGAATCGACCAGTAGGTGGTTAGCTGTCTGTTTTGTCGTTCTCTTGCAACGGCTCTTTCCCCCTTTCTATGTTTCGTACGAATTTCAGCGGGCTACAACATTCGTATAATCCTTCATTCTCCAGCTGTGTAGCCCCGCCTCTTGGAGATAAGTACACATCTTTCGTCAAGGACGAAAGAGACGATCCAACCCTCTATTCCTCTTTATTCCATTGAGAGGCTGGAATCTCGCGAGAATATTCGGTGGATATCGGATAGGATTTAAGGATTGGATTTCAAACCTAGGGTTGCAAATACGATTATACCCTCGTTTGTTTTCTTCAGGGAAGCTCCTCTAAATAAACTCTCTTTCTTCTTCCGATTATGGGGTGGA</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-C00SLm0061F09-o4CMa/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E345230" ref_strand="+" ref_description="SGN-E345230 [cTOF-13-E18]">
      <seq>cagaacaaacgtgaaatacctagaacccagacactaaaatccccccagaggcgaaagaaatttatttcccgaaaaccatcctcacgtcatctgcgtgtgagtttcaatcccccttccctcaagcgacgacaacgcacgctgataacgcgaaggaattgaccagtaggtggttagctgtccgttttgtcgttctctcgcaacggctctttccccctttctgcgttttgtacgaatttcagcaggctacaacattcgtatcgtccttcattctctagttgtatagccccgcctcttggagatgatgacacgtctttcgtcaatgacgaaagagacgatccagccctctattcttttttattccgttaagaggctggaatctcgcctgaatgttcggtggatatcggataggatttggggattggaattcaaacctagggttgcaaatacgattataccctcgtttgttttcttcagggaagctcctctatataaaccctcttccctcttcggattaggggttggagatttggagagatagttttatcacgaagagtaagaagaatttttgggaaaatatttgtttcttcttctgtctggtgtagaagaacagttaaaaaattcttgggaaaattggggaaaaattatttggattcttc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLm0061F09-o4CMa/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLm0061F09.2" temp_strand="-" temp_description="C00SLm0061F09.2  CU928196.3 htgs_phase:3 submitted_to_sgn_as:C04SLm0061F09 sequenced_by:sanger upload_account_name:uk">
        <position start="62584" stop="61329"/>
      </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="62284" g_stop="61629" g_length="656"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="656" r_length="656" r_score="0.998"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLm0061F09.2" gen_strand="-" ref_id="SGN-E345230" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>656</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLm0061F09.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E345230" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="62284" e_stop="61629"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CAGAACAAACGTGAAATACCTAGAACCCAGACACTAAAATCCCCCCAGAGGCGAAAGAAATTTATTTCCCGAAAACCATCCTCACGTCATCTGCGTGTGAGTTTCAATCCCCCTTCCCTCAAGCGACGACAACGCACGCTGATAACGCGAAGGAATTGACCAGTAGGTGGTTAGCTGTCCGTTTTGTCGTTCTCTCGCAACGGCTCTTTCCCCCTTTCTGCGTTTTGTACGAATTTCAGCAGGCTACAACATTCGTATCGTCCTTCATTCTCTAGTTGTATAGCCCCGCCTCTTGGAGATGATGACACGTCTTTCGTCAATGACGAAAGAGACGATCCAGCCCTCTATTCTTTTTTATTCCGTTAAGAGGCTGGAATCTCGCCTGAATGTTCGGTGGATATCGGATAGGATTTGGGGATTGGAATTCAAACCTAGGGTTGCAAATACGATTATACCCTCGTTTGTTTTCTTCAGGGAAGCTCCTCTATATAAACCCTCTTCCCTCTTCGGATTAGGGGTTGGAGATTTGGAGAGATAGTTTTATCACGAAGAGTAAGAAGAATTTTTGGGAAAATATTTGTTTCTTCTTCTGTCTGTTGTAGAAGAACAGTTAAAAAATTCTTGGGAAAATTGGGGAAAAATTATTTGGATTCTTC</genome_strand>
        <mrna_strand>CAGAACAAACGTGAAATACCTAGAACCCAGACACTAAAATCCCCCCAGAGGCGAAAGAAATTTATTTCCCGAAAACCATCCTCACGTCATCTGCGTGTGAGTTTCAATCCCCCTTCCCTCAAGCGACGACAACGCACGCTGATAACGCGAAGGAATTGACCAGTAGGTGGTTAGCTGTCCGTTTTGTCGTTCTCTCGCAACGGCTCTTTCCCCCTTTCTGCGTTTTGTACGAATTTCAGCAGGCTACAACATTCGTATCGTCCTTCATTCTCTAGTTGTATAGCCCCGCCTCTTGGAGATGATGACACGTCTTTCGTCAATGACGAAAGAGACGATCCAGCCCTCTATTCTTTTTTATTCCGTTAAGAGGCTGGAATCTCGCCTGAATGTTCGGTGGATATCGGATAGGATTTGGGGATTGGAATTCAAACCTAGGGTTGCAAATACGATTATACCCTCGTTTGTTTTCTTCAGGGAAGCTCCTCTATATAAACCCTCTTCCCTCTTCGGATTAGGGGTTGGAGATTTGGAGAGATAGTTTTATCACGAAGAGTAAGAAGAATTTTTGGGAAAATATTTGTTTCTTCTTCTGTCTGGTGTAGAAGAACAGTTAAAAAATTCTTGGGAAAATTGGGGAAAAATTATTTGGATTCTTC</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="42486" PGL_stop="42291"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="42486" e_stop="42291"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.974"/>
        </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="0.974">
            <gDNA_exon_boundary e_start="42486" e_stop="42291" e_length="196"/>
          </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="42486" stop="42291"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E207049" 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>TTTTTAGAAGCATGTGTCATTTTTGTTCACTGGAGAAGGGTGTACATCAAATTATTGGCAAGTACCTTTGGTTGTCTTGGTCATATGGAAGGTTTCCTTGATGCATTATTCATGACAAATTTTAGTTCTATTGTTGATACTATGTTTTTGTTGCTTTCGAAAAATTGAAATGGGTTAGCTGAAACACCTTAATCTA</gDNA_template>
            <first_frame> F  L  E  A  C  V  I  F  V  H  W  R  R  V  Y  I  K  L  L  A  S  T  F  G  C  L  G  H  M  E  G  F  L  D  A  L  F  M  T  N  F  S  S  I  V  D  T  M  F  L  L  L  S  K  N  *  N  G  L  A  E  T  P  *  S  </first_frame>
            <second_frame>  F  *  K  H  V  S  F  L  F  T  G  E  G  C  T  S  N  Y  W  Q  V  P  L  V  V  L  V  I  W  K  V  S  L  M  H  Y  S  *  Q  I  L  V  L  L  L  I  L  C  F  C  C  F  R  K  I  E  M  G  *  L  K  H  L  N  L </second_frame>
            <third_frame>   F  R  S  M  C  H  F  C  S  L  E  K  G  V  H  Q  I  I  G  K  Y  L  W  L  S  W  S  Y  G  R  F  P  *  C  I  I  H  D  K  F  *  F  Y  C  *  Y  Y  V  F  V  A  F  E  K  L  K  W  V  S  *  N  T  L  I   </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <none gDNA_id="C00SLm0061F09.2"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="2" PGL_strand="-" PGL_start="44191" PGL_stop="43805"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="44191" e_stop="43805"/>
          </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="44191" e_stop="43805" e_length="387"/>
          </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="44191" stop="43805"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E258337" 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>CGCTGATAACACGAAGGAATCGACCAGTAGGTGGTTAGCTGTCTGTTTTGTCGTTCTCTTGCAACGGCTCTTTCCCCCTTTCTATGTTTCGTACGAATTTCAGCGGGCTACAACATTCGTATAATCCTTCATTCTCCAGCTGTGTAGCCCCGCCTCTTGGAGATAAGTACACATCTTTCGTCAAGGACGAAAGAGACGATCCAACCCTCTATTCCTCTTTATTCCATTGAGAGGCTGGAATCTCGCGAGAATATTCGGTGGATATCGGATAGGATTTAAGGATTGGATTTCAAACCTAGGGTTGCAAATACGATTATACCCTCGTTTGTTTTCTTCAGGGAAGCTCCTCTATATAAACTCTCTTTCTTCTTCGGATTAGGGGTTGGA</gDNA_template>
            <first_frame> R  *  *  H  E  G  I  D  Q  *  V  V  S  C  L  F  C  R  S  L  A  T  A  L  S  P  F  L  C  F  V  R  I  S  A  G  Y  N  I  R  I  I  L  H  S  P  A  V  *  P  R  L  L  E  I  S  T  H  L  S  S  R  T  K  E  T  I  Q  P  S  I  P  L  Y  S  I  E  R  L  E  S  R  E  N  I  R  W  I  S  D  R  I  *  G  L  D  F  K  P  R  V  A  N  T  I  I  P  S  F  V  F  F  R  E  A  P  L  Y  K  L  S  F  F  F  G  L  G  V  G </first_frame>
            <second_frame>  A  D  N  T  K  E  S  T  S  R  W  L  A  V  C  F  V  V  L  L  Q  R  L  F  P  P  F  Y  V  S  Y  E  F  Q  R  A  T  T  F  V  *  S  F  I  L  Q  L  C  S  P  A  S  W  R  *  V  H  I  F  R  Q  G  R  K  R  R  S  N  P  L  F  L  F  I  P  L  R  G  W  N  L  A  R  I  F  G  G  Y  R  I  G  F  K  D  W  I  S  N  L  G  L  Q  I  R  L  Y  P  R  L  F  S  S  G  K  L  L  Y  I  N  S  L  S  S  S  D  *  G  L   </second_frame>
            <third_frame>   L  I  T  R  R  N  R  P  V  G  G  *  L  S  V  L  S  F  S  C  N  G  S  F  P  L  S  M  F  R  T  N  F  S  G  L  Q  H  S  Y  N  P  S  F  S  S  C  V  A  P  P  L  G  D  K  Y  T  S  F  V  K  D  E  R  D  D  P  T  L  Y  S  S  L  F  H  *  E  A  G  I  S  R  E  Y  S  V  D  I  G  *  D  L  R  I  G  F  Q  T  *  G  C  K  Y  D  Y  T  L  V  C  F  L  Q  G  S  S  S  I  *  T  L  F  L  L  R  I  R  G  W  </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="C00SLm0061F09.2" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="44025" stop="43813"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>210</number_coding_nucleotides>
                  <number_encoded_amino_acids>70</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>VHIFRQGRKRRSNPLFLFIPLRGWNLARIFGGYRIGFKDWISNLGLQIRLYPRLFSSGKLLYINSLSSSD*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="3" PGL_strand="-" PGL_start="62284" PGL_stop="61629"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="62284" e_stop="61629"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.998"/>
        </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="0.998">
            <gDNA_exon_boundary e_start="62284" e_stop="61629" e_length="656"/>
          </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="62284" stop="61629"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E345230" 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="3" AGS_serial="1" gDNA_strand="-"/>
          <translation>
            <gDNA_template>CAGAACAAACGTGAAATACCTAGAACCCAGACACTAAAATCCCCCCAGAGGCGAAAGAAATTTATTTCCCGAAAACCATCCTCACGTCATCTGCGTGTGAGTTTCAATCCCCCTTCCCTCAAGCGACGACAACGCACGCTGATAACGCGAAGGAATTGACCAGTAGGTGGTTAGCTGTCCGTTTTGTCGTTCTCTCGCAACGGCTCTTTCCCCCTTTCTGCGTTTTGTACGAATTTCAGCAGGCTACAACATTCGTATCGTCCTTCATTCTCTAGTTGTATAGCCCCGCCTCTTGGAGATGATGACACGTCTTTCGTCAATGACGAAAGAGACGATCCAGCCCTCTATTCTTTTTTATTCCGTTAAGAGGCTGGAATCTCGCCTGAATGTTCGGTGGATATCGGATAGGATTTGGGGATTGGAATTCAAACCTAGGGTTGCAAATACGATTATACCCTCGTTTGTTTTCTTCAGGGAAGCTCCTCTATATAAACCCTCTTCCCTCTTCGGATTAGGGGTTGGAGATTTGGAGAGATAGTTTTATCACGAAGAGTAAGAAGAATTTTTGGGAAAATATTTGTTTCTTCTTCTGTCTGTTGTAGAAGAACAGTTAAAAAATTCTTGGGAAAATTGGGGAAAAATTATTTGGATTCTTC</gDNA_template>
            <first_frame> Q  N  K  R  E  I  P  R  T  Q  T  L  K  S  P  Q  R  R  K  K  F  I  S  R  K  P  S  S  R  H  L  R  V  S  F  N  P  P  S  L  K  R  R  Q  R  T  L  I  T  R  R  N  *  P  V  G  G  *  L  S  V  L  S  F  S  R  N  G  S  F  P  L  S  A  F  C  T  N  F  S  R  L  Q  H  S  Y  R  P  S  F  S  S  C  I  A  P  P  L  G  D  D  D  T  S  F  V  N  D  E  R  D  D  P  A  L  Y  S  F  L  F  R  *  E  A  G  I  S  P  E  C  S  V  D  I  G  *  D  L  G  I  G  I  Q  T  *  G  C  K  Y  D  Y  T  L  V  C  F  L  Q  G  S  S  S  I  *  T  L  F  P  L  R  I  R  G  W  R  F  G  E  I  V  L  S  R  R  V  R  R  I  F  G  K  I  F  V  S  S  S  V  C  C  R  R  T  V  K  K  F  L  G  K  L  G  K  N  Y  L  D  S   </first_frame>
            <second_frame>  R  T  N  V  K  Y  L  E  P  R  H  *  N  P  P  R  G  E  R  N  L  F  P  E  N  H  P  H  V  I  C  V  *  V  S  I  P  L  P  S  S  D  D  N  A  R  *  *  R  E  G  I  D  Q  *  V  V  S  C  P  F  C  R  S  L  A  T  A  L  S  P  F  L  R  F  V  R  I  S  A  G  Y  N  I  R  I  V  L  H  S  L  V  V  *  P  R  L  L  E  M  M  T  R  L  S  S  M  T  K  E  T  I  Q  P  S  I  L  F  Y  S  V  K  R  L  E  S  R  L  N  V  R  W  I  S  D  R  I  W  G  L  E  F  K  P  R  V  A  N  T  I  I  P  S  F  V  F  F  R  E  A  P  L  Y  K  P  S  S  L  F  G  L  G  V  G  D  L  E  R  *  F  Y  H  E  E  *  E  E  F  L  G  K  Y  L  F  L  L  L  S  V  V  E  E  Q  L  K  N  S  W  E  N  W  G  K  I  I  W  I  L  </second_frame>
            <third_frame>   E  Q  T  *  N  T  *  N  P  D  T  K  I  P  P  E  A  K  E  I  Y  F  P  K  T  I  L  T  S  S  A  C  E  F  Q  S  P  F  P  Q  A  T  T  T  H  A  D  N  A  K  E  L  T  S  R  W  L  A  V  R  F  V  V  L  S  Q  R  L  F  P  P  F  C  V  L  Y  E  F  Q  Q  A  T  T  F  V  S  S  F  I  L  *  L  Y  S  P  A  S  W  R  *  *  H  V  F  R  Q  *  R  K  R  R  S  S  P  L  F  F  F  I  P  L  R  G  W  N  L  A  *  M  F  G  G  Y  R  I  G  F  G  D  W  N  S  N  L  G  L  Q  I  R  L  Y  P  R  L  F  S  S  G  K  L  L  Y  I  N  P  L  P  S  S  D  *  G  L  E  I  W  R  D  S  F  I  T  K  S  K  K  N  F  W  E  N  I  C  F  F  F  C  L  L  *  K  N  S  *  K  I  L  G  K  I  G  E  K  L  F  G  F  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="C00SLm0061F09.2" strand="-"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="62001" stop="61747"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>252</number_coding_nucleotides>
                  <number_encoded_amino_acids>84</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>PRLLEMMTRLSSMTKETIQPSILFYSVKRLESRLNVRWISDRIWGLEFKPRVANTIIPSFVFFREAPLYKPSSLFGLGVGDLER*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C00SLm0061F09.2" strand="-"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="62261" stop="62010"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>249</number_coding_nucleotides>
                  <number_encoded_amino_acids>83</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>NPDTKIPPEAKEIYFPKTILTSSACEFQSPFPQATTTHADNAKELTSRWLAVRFVVLSQRLFPPFCVLYEFQQATTFVSSFIL*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 176 chains have been computed
$ 
$ memory statistics:
$ 6120 bytes spliced alignments in total
$ 3 spliced alignments have been stored
$ 2040 bytes was the average size of a spliced alignment
$ 7880 bytes predicted gene locations in total
$ 3 predicted gene locations have been stored
$ 2626 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 196 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 06:26:09
-->
