<?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 05:29:19"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C00HBa0067O19-yYU7K/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C00HBa0067O19-yYU7K/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-C00HBa0067O19-yYU7K/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E243969" ref_strand="+" ref_description="SGN-E243969 [cLEE-1-A19]">
      <seq>ggaaatctgccaaaacgcggcttggtcgacggaccacgcgacggaccgtcgtggactctgtcgtcccatacttggtgcaatttcttctgctgctttcttcattcccctcgacggcaagtgtaacggaccgtcataggtacaacggtctgtcgagggtcttcgtttcaaaatacttcaactcttggaatctgggtactgggatcacttctctgatcttcacgacgaacctgcaggacggaccgtcatagccatgacggaccgtcacaagcttcgtaatcccacacttggtcagacttccccatcttccttcagcagcttctctacgctaccacctacggaccgtcacaagcacgacagaccttcaaaagctccgtaggtggtctcttctgcatttttttgctcaaaatctccgctttcagcttttgacagatttcctgcaaaacaaagagaaacttatatcaaaattagcacaaaaaaggctttcggacactttaaacttaaggcaaaagtattaattatacc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0067O19-yYU7K/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00HBa0067O19.2" temp_strand="+" temp_description="C00HBa0067O19.2  CU570768.5 htgs_phase:3 submitted_to_sgn_as:C04HBa0067O19 sequenced_by:sanger upload_account_name:uk">
        <position start="44092" stop="45231"/>
      </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="44392" g_stop="44931" g_length="540"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="522" r_length="522" r_score="0.906"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0067O19.2" gen_strand="+" ref_id="SGN-E243969" ref_strand="+">
        <total_alignment_score>0.906</total_alignment_score>
        <cumulative_length_of_scored_exons>540</cumulative_length_of_scored_exons>
        <coverage percentage="1.034" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0067O19.2" gen_strand="+"/>
        <rDNA rDNA_id="SGN-E243969" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="44392" e_stop="44931"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GGAAATCTGCCAAAACGCGGCTGGGTCGACGGACCACGCGACGGAACGTCGTGGTCATGACGGACCGTCGTGGGCTCCGTCGCCCCATACTTGAGTGCAA-TTCTTCTGCTGCTTTCTTCATTCCCCTCGACGGCAAGTGTGACCGACCATCACAGGCACGACGGTCCGTCGAGGGTCTTCGTTACAAAATACTTCAACTTTTGGAATTTGGGTACTGGGATCACTTCTCTGATCTTCACGACGAACCTGCAGGACGGACCGTCATATCCATGACGGACCGTCACAAGCTTCGTAATCCCACACTTGGTCAGACTTCCCCATCTTCCTTCAGCAGCTTCTCTACACTGCCACCTACGGACCGTCACAAGCACGACAGACCGTCATAAGCTCCGTAGGTGGTCTCTTCTGCA-TTTTTCGCTCAAAATCTCCGCATTCAGCTTTAGACAGATTTCCTGCAAAACAAAGAAAAACTTATATCAAAATTAGCACAAAAAGGGCTTCCGGACACACTAAACTTAAGGAAAAATTATTAATTATACC</genome_strand>
        <mrna_strand>GGAAATCTGCCAAAACGCGGCTTGGTCGACGGACCACGCGACGG-AC--C---GTC--G-TGGA-C-TC-T--G-T-CGT---CCCATACTTG-GTGCAATTTCTTCTGCTGCTTTCTTCATTCCCCTCGACGGCAAGTGTAACGGACCGTCATAGGTACAACGGTCTGTCGAGGGTCTTCGTTTCAAAATACTTCAACTCTTGGAATCTGGGTACTGGGATCACTTCTCTGATCTTCACGACGAACCTGCAGGACGGACCGTCATAGCCATGACGGACCGTCACAAGCTTCGTAATCCCACACTTGGTCAGACTTCCCCATCTTCCTTCAGCAGCTTCTCTACGCTACCACCTACGGACCGTCACAAGCACGACAGACCTTCAAAAGCTCCGTAGGTGGTCTCTTCTGCATTTTTTTGCTCAAAATCTCCGCTTTCAGCTTTTGACAGATTTCCTGCAAAACAAAGAGAAACTTATATCAAAATTAGCACAAAAAAGGCTTTCGGACACTTTAAACTTAAGGCAAAAGTATTAATTATACC</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-C00HBa0067O19-yYU7K/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E577891" ref_strand="+" ref_description="SGN-E577891 [LE08BA04]">
      <seq>ttcgtttcaaaatacttcagctcttggaatctgggtactggaatcacttctctgatcttcacgacgaacctgcaggacggaccgtcatagccatgacggaccgtcacaatcttcgtaatcccacacttggtgagacttccccatcttccttcagcagcttctctacgctgccacctacggagcgtcaaaggcacgatggaccgtcataagctcagtaggtggtctcttctacattttttcgctcaaaatctctgctttcagctttggacagatttcctgcaaaataaagagaaacttataccaaaattagcacaaaaaggcttacggacacactaaacttaaggcaaaagtattaattataccgtgaaaccacggtatatcagggacatgaactcgaaggccattgttggc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0067O19-yYU7K/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00HBa0067O19.2" temp_strand="+" temp_description="C00HBa0067O19.2  CU570768.5 htgs_phase:3 submitted_to_sgn_as:C04HBa0067O19 sequenced_by:sanger upload_account_name:uk">
        <position start="44269" stop="45250"/>
      </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="44569" g_stop="44950" g_length="382"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="382" r_length="382" r_score="0.927"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0067O19.2" gen_strand="+" ref_id="SGN-E577891" ref_strand="+">
        <total_alignment_score>0.927</total_alignment_score>
        <cumulative_length_of_scored_exons>382</cumulative_length_of_scored_exons>
        <coverage percentage="0.929" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0067O19.2" gen_strand="+"/>
        <rDNA rDNA_id="SGN-E577891" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="44569" e_stop="44950"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTCGTTACAAAATACTTCAACTTTTGGAATTTGGGTACTGGGATCACTTCTCTGATCTTCACGACGAACCTGCAGGACGGACCGTCATATCCATGACGGACCGTCACAAGCTTCGTAATCCCACACTTGGTCAGACTTCCCCATCTTCCTTCAGCAGCTTCTCTACACTGCCACCTACGGACCGTCACAAGCACGACAGACCGTCATAAGCTCCGTAGGTGGTCTCTTCTGCA-TTTTTCGCTCAAAATCTCCGCATTCAGCTTTAGACAGATTTCCTGCAAAACAAAGAAAAACTTATATCAAAATTAGCACAAAAAGGGCTTCCGGACACACTAAACTTAAGGAAAAATTATTAATTATACCGTGAAACCACGGTATATCA</genome_strand>
        <mrna_strand>TTCGTTTCAAAATACTTCAGCTCTTGGAATCTGGGTACTGGAATCACTTCTCTGATCTTCACGACGAACCTGCAGGACGGACCGTCATAGCCATGACGGACCGTCACAATCTTCGTAATCCCACACTTGGTGAGACTTCCCCATCTTCCTTCAGCAGCTTCTCTACGCTGCCACCTACGGAGCGTCAAAGGCACGATGGACCGTCATAAGCTCAGTAGGTGGTCTCTTCTACATTTTTTCGCTCAAAATCTCTGCTTTCAGCTTTGGACAGATTTCCTGCAAAATAAAGAGAAACTTATACCAAAATTAGCACAAAAA-GGCTTACGGACACACTAAACTTAAGGCAAAAGTATTAATTATACCGTGAAACCACGGTATATCA</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-C00HBa0067O19-yYU7K/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E546519" ref_strand="-" ref_description="SGN-E546519 [TUS-69-O20]">
      <seq>caaggcaatnatagtcagttttcaaggtccacacaacagttccaaggaaatctgttcaaagatgtatgcagaggtttttgagtgaagaaatgcagaagagaccacctacggagcttgtgacggtccgtcatgcttgtgacggtacgtaggtggcagcatagtgcagctgctgaaggaatatggggaagtctgaccaagtgtggggttacggagtccatgacggtccttcgtgtctatgacggtccgtcctgcaggttcttcatgaagttcagagaagtaatcccagtacccatattccaagagtttaagtgttttggaacgaagaccctcgacggaccgttgtgcctttgacggtccgtcatacttgccgtcgagggtaatgaagagagaagcagaagaaatttcatcaagtatgggacgacggagtccatgacggtccgtcgtgaccacgatgatccgtcgcgaggtccgttgacccagccgcgttttgacaaatttccagcaaatagagtccttatttaattaggtttttaatttctataaatagttcaaaaaaacctcatttttgaggttagactctggataattattagactctgtgtattagtgttagacttttgattatcattagactttttgtgagattcttgattactttgaaattcttgcaagtgattgttggtgattaatcaagaaaactttcggattttaaaaaaaaaaaaaaaaaaactcgagactagtctctctctc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0067O19-yYU7K/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00HBa0067O19.2" temp_strand="+" temp_description="C00HBa0067O19.2  CU570768.5 htgs_phase:3 submitted_to_sgn_as:C04HBa0067O19 sequenced_by:sanger upload_account_name:uk">
        <position start="75093" stop="83335"/>
      </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="82197" g_stop="82244" g_length="48"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="46" r_length="46" r_score="0.521"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="82245" i_stop="82397" i_length="153">
            <donor d_prob="0.000" d_score="0.52"/>
            <acceptor a_prob="0.994" a_score="0.80"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="82398" g_stop="83029" g_length="632"/>
          <reference_exon_boundary r_type="cDNA" r_start="47" r_stop="681" r_length="635" r_score="0.915"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="711" polyA_stop="730"/>
      <MATCH_line gen_id="C00HBa0067O19.2" gen_strand="+" ref_id="SGN-E546519" ref_strand="-">
        <total_alignment_score>0.915</total_alignment_score>
        <cumulative_length_of_scored_exons>680</cumulative_length_of_scored_exons>
        <coverage percentage="0.907" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0067O19.2" gen_strand="+"/>
        <rDNA rDNA_id="SGN-E546519" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="82197" e_stop="82244"/>
          <exon e_start="82398" e_stop="83029"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATAGCCAAATGATTGCAAAGGATAAAACATGGATACTATTGTACAAAGATTTTCTATTAAGTCATAGTCAAACAACGAATTTAAGTTGAGGGTGTTGATATACCCTGTTTTCATGATATTATCTATACTTTTTCCTTAAAGTTTAGTGTGTCCAAAAGACTTTTTGTGCTAATTTTTATATAAGTTTCTCTTTATTTGTAGGAAATCTGACCAAAGTTGAATGCGGA-GATTTTGAGCTAAGAAATGCAGAAGAGACCACCTACGGAGATTGTGACGGTCCGCCGTGCTTGTGACGATCCGTAGGTGGCAGCGTAGTGCAGCTGTTGAAGGAAGATGGGGAAGTCTTACCAAGTGTGAGGTTACGAAGTCCATGATGGTCCGTCGTGTCTATGACGGTCCATCCTGCAGGTTCGTCATGAAGTTCAGAGAAGCAATCCCAGTACCCATATTCCAAGAGTTCAAGTTTTTTAGAACGGAGACCCTCGACGGAACGTTGTGCCAATGAAGGTCCTTCATACTTGCCGTCGAGGGTAATGAAGAGAGAAGCAGAAGAAATTGCA-CAAGTATGGGATGACGGAGTCCATGACGGTCTGTCGTGACCACGACGATCCGTCGCGAGGTCCGTCCACCCAGCCGTGTTTTGACAGATTTCCAGCAAATAGAGTCCTTGTTTAATTAGGTTTTTATTTTCTATAAATAGTTC-GAAAAACCTCGTTTTTGATGTTAGACTCTGGATCATTATTAGACTCTGTGTATTAGTGTTAGACTTTTGATTATCATTAGACTTTTTGTGAGATTCTTGATTACTTTGAGATTCTTGCAAGTGATTGTTG</genome_strand>
        <mrna_strand>CAAGGCAA-TNATAG-TCAGTTTTCAAGGTCCACACAACAGTTCCAAG.........................................................................................................................................................GAAATCTGTTCAAAGATGTATGCAGAGGTTTTTGAGTGAAGAAATGCAGAAGAGACCACCTACGGAGCTTGTGACGGTCCGTCATGCTTGTGACGGTACGTAGGTGGCAGCATAGTGCAGCTGCTGAAGGAATATGGGGAAGTCTGACCAAGTGTGGGGTTACGGAGTCCATGACGGTCCTTCGTGTCTATGACGGTCCGTCCTGCAGGTTCTTCATGAAGTTCAGAGAAGTAATCCCAGTACCCATATTCCAAGAGTTTAAGTGTTTTGGAACGAAGACCCTCGACGGACCGTTGTGCCTTTGACGGTCCGTCATACTTGCCGTCGAGGGTAATGAAGAGAGAAGCAGAAGAAATTTCATCAAGTATGGGACGACGGAGTCCATGACGGTCCGTCGTGACCACGATGATCCGTCGCGAGGTCCGTTGACCCAGCCGCGTTTTGACAAATTTCCAGCAAATAGAGTCCTTATTTAATTAGGTTTTTAATTTCTATAAATAGTTCAAAAAAACCTCATTTTTGAGGTTAGACTCTGGATAATTATTAGACTCTGTGTATTAGTGTTAGACTTTTGATTATCATTAGACTTTTTGTGAGATTCTTGATTACTTTGAAATTCTTGCAAGTGATTGTTG</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="44392" PGL_stop="44950"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="44392" e_stop="44950"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.906"/>
        </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="0.906">
            <gDNA_exon_boundary e_start="44392" e_stop="44950" e_length="559"/>
          </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="44392" stop="44931"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E243969" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="44569" stop="44950"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E577891" 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>GGAAATCTGCCAAAACGCGGCTGGGTCGACGGACCACGCGACGGAACGTCGTGGTCATGACGGACCGTCGTGGGCTCCGTCGCCCCATACTTGAGTGCAATTCTTCTGCTGCTTTCTTCATTCCCCTCGACGGCAAGTGTGACCGACCATCACAGGCACGACGGTCCGTCGAGGGTCTTCGTTACAAAATACTTCAACTTTTGGAATTTGGGTACTGGGATCACTTCTCTGATCTTCACGACGAACCTGCAGGACGGACCGTCATATCCATGACGGACCGTCACAAGCTTCGTAATCCCACACTTGGTCAGACTTCCCCATCTTCCTTCAGCAGCTTCTCTACACTGCCACCTACGGACCGTCACAAGCACGACAGACCGTCATAAGCTCCGTAGGTGGTCTCTTCTGCATTTTTCGCTCAAAATCTCCGCATTCAGCTTTAGACAGATTTCCTGCAAAACAAAGAAAAACTTATATCAAAATTAGCACAAAAAGGGCTTCCGGACACACTAAACTTAAGGAAAAATTATTAATTATACCGTGAAACCACGGTATATCA</gDNA_template>
            <first_frame> G  N  L  P  K  R  G  W  V  D  G  P  R  D  G  T  S  W  S  *  R  T  V  V  G  S  V  A  P  Y  L  S  A  I  L  L  L  L  S  S  F  P  S  T  A  S  V  T  D  H  H  R  H  D  G  P  S  R  V  F  V  T  K  Y  F  N  F  W  N  L  G  T  G  I  T  S  L  I  F  T  T  N  L  Q  D  G  P  S  Y  P  *  R  T  V  T  S  F  V  I  P  H  L  V  R  L  P  H  L  P  S  A  A  S  L  H  C  H  L  R  T  V  T  S  T  T  D  R  H  K  L  R  R  W  S  L  L  H  F  S  L  K  I  S  A  F  S  F  R  Q  I  S  C  K  T  K  K  N  L  Y  Q  N  *  H  K  K  G  F  R  T  H  *  T  *  G  K  I  I  N  Y  T  V  K  P  R  Y  I  </first_frame>
            <second_frame>  E  I  C  Q  N  A  A  G  S  T  D  H  A  T  E  R  R  G  H  D  G  P  S  W  A  P  S  P  H  T  *  V  Q  F  F  C  C  F  L  H  S  P  R  R  Q  V  *  P  T  I  T  G  T  T  V  R  R  G  S  S  L  Q  N  T  S  T  F  G  I  W  V  L  G  S  L  L  *  S  S  R  R  T  C  R  T  D  R  H  I  H  D  G  P  S  Q  A  S  *  S  H  T  W  S  D  F  P  I  F  L  Q  Q  L  L  Y  T  A  T  Y  G  P  S  Q  A  R  Q  T  V  I  S  S  V  G  G  L  F  C  I  F  R  S  K  S  P  H  S  A  L  D  R  F  P  A  K  Q  R  K  T  Y  I  K  I  S  T  K  R  A  S  G  H  T  K  L  K  E  K  L  L  I  I  P  *  N  H  G  I  S </second_frame>
            <third_frame>   K  S  A  K  T  R  L  G  R  R  T  T  R  R  N  V  V  V  M  T  D  R  R  G  L  R  R  P  I  L  E  C  N  S  S  A  A  F  F  I  P  L  D  G  K  C  D  R  P  S  Q  A  R  R  S  V  E  G  L  R  Y  K  I  L  Q  L  L  E  F  G  Y  W  D  H  F  S  D  L  H  D  E  P  A  G  R  T  V  I  S  M  T  D  R  H  K  L  R  N  P  T  L  G  Q  T  S  P  S  S  F  S  S  F  S  T  L  P  P  T  D  R  H  K  H  D  R  P  S  *  A  P  *  V  V  S  S  A  F  F  A  Q  N  L  R  I  Q  L  *  T  D  F  L  Q  N  K  E  K  L  I  S  K  L  A  Q  K  G  L  P  D  T  L  N  L  R  K  N  Y  *  L  Y  R  E  T  T  V  Y   </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="C00HBa0067O19.2" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="44394" stop="44777"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>381</number_coding_nucleotides>
                  <number_encoded_amino_acids>127</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>KSAKTRLGRRTTRRNVVVMTDRRGLRRPILECNSSAAFFIPLDGKCDRPSQARRSVEGLRYKILQLLEFGYWDHFSDLHDEPAGRTVISMTDRHKLRNPTLGQTSPSSFSSFSTLPPTDRHKHDRPS*</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="82197" PGL_stop="83029"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="82197" e_stop="82244"/>
            <exon e_start="82398" e_stop="83029"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.000" acc_prob="0.994" e_score="0.521"/>
          <exon-only e_score="0.915"/>
        </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="0.521">
            <gDNA_exon_boundary e_start="82197" e_stop="82244" e_length="48"/>
          </exon>
          <intron i_serial="1" don_prob="0.000" acc_prob="0.994">
            <gDNA_intron_boundary i_start="82245" i_stop="82397" i_length="153"/>
          </intron>
          <exon e_serial="2" e_score="0.915">
            <gDNA_exon_boundary e_start="82398" e_stop="83029" e_length="632"/>
          </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="82197" stop="82244"/>
              <exon start="82398" stop="83029"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E546519" 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>ATAGCCAAATGATTGCAAAGGATAAAACATGGATACTATTGTACAAAG : GAAATCTGACCAAAGTTGAATGCGGAGATTTTGAGCTAAGAAATGCAGAAGAGACCACCTACGGAGATTGTGACGGTCCGCCGTGCTTGTGACGATCCGTAGGTGGCAGCGTAGTGCAGCTGTTGAAGGAAGATGGGGAAGTCTTACCAAGTGTGAGGTTACGAAGTCCATGATGGTCCGTCGTGTCTATGACGGTCCATCCTGCAGGTTCGTCATGAAGTTCAGAGAAGCAATCCCAGTACCCATATTCCAAGAGTTCAAGTTTTTTAGAACGGAGACCCTCGACGGAACGTTGTGCCAATGAAGGTCCTTCATACTTGCCGTCGAGGGTAATGAAGAGAGAAGCAGAAGAAATTGCACAAGTATGGGATGACGGAGTCCATGACGGTCTGTCGTGACCACGACGATCCGTCGCGAGGTCCGTCCACCCAGCCGTGTTTTGACAGATTTCCAGCAAATAGAGTCCTTGTTTAATTAGGTTTTTATTTTCTATAAATAGTTCGAAAAACCTCGTTTTTGATGTTAGACTCTGGATCATTATTAGACTCTGTGTATTAGTGTTAGACTTTTGATTATCATTAGACTTTTTGTGAGATTCTTGATTACTTTGAGATTCTTGCAAGTGATTGTTG</gDNA_template>
            <first_frame> I  A  K  *  L  Q  R  I  K  H  G  Y  Y  C  T  K  :  E  I  *  P  K  L  N  A  E  I  L  S  *  E  M  Q  K  R  P  P  T  E  I  V  T  V  R  R  A  C  D  D  P  *  V  A  A  *  C  S  C  *  R  K  M  G  K  S  Y  Q  V  *  G  Y  E  V  H  D  G  P  S  C  L  *  R  S  I  L  Q  V  R  H  E  V  Q  R  S  N  P  S  T  H  I  P  R  V  Q  V  F  *  N  G  D  P  R  R  N  V  V  P  M  K  V  L  H  T  C  R  R  G  *  *  R  E  K  Q  K  K  L  H  K  Y  G  M  T  E  S  M  T  V  C  R  D  H  D  D  P  S  R  G  P  S  T  Q  P  C  F  D  R  F  P  A  N  R  V  L  V  *  L  G  F  Y  F  L  *  I  V  R  K  T  S  F  L  M  L  D  S  G  S  L  L  D  S  V  Y  *  C  *  T  F  D  Y  H  *  T  F  C  E  I  L  D  Y  F  E  I  L  A  S  D  C   </first_frame>
            <second_frame>  *  P  N  D  C  K  G  *  N  M  D  T  I  V  Q  R :   K  S  D  Q  S  *  M  R  R  F  *  A  K  K  C  R  R  D  H  L  R  R  L  *  R  S  A  V  L  V  T  I  R  R  W  Q  R  S  A  A  V  E  G  R  W  G  S  L  T  K  C  E  V  T  K  S  M  M  V  R  R  V  Y  D  G  P  S  C  R  F  V  M  K  F  R  E  A  I  P  V  P  I  F  Q  E  F  K  F  F  R  T  E  T  L  D  G  T  L  C  Q  *  R  S  F  I  L  A  V  E  G  N  E  E  R  S  R  R  N  C  T  S  M  G  *  R  S  P  *  R  S  V  V  T  T  T  I  R  R  E  V  R  P  P  S  R  V  L  T  D  F  Q  Q  I  E  S  L  F  N  *  V  F  I  F  Y  K  *  F  E  K  P  R  F  *  C  *  T  L  D  H  Y  *  T  L  C  I  S  V  R  L  L  I  I  I  R  L  F  V  R  F  L  I  T  L  R  F  L  Q  V  I  V  </second_frame>
            <third_frame>   S  Q  M  I  A  K  D  K  T  W  I  L  L  Y  K   : G  N  L  T  K  V  E  C  G  D  F  E  L  R  N  A  E  E  T  T  Y  G  D  C  D  G  P  P  C  L  *  R  S  V  G  G  S  V  V  Q  L  L  K  E  D  G  E  V  L  P  S  V  R  L  R  S  P  *  W  S  V  V  S  M  T  V  H  P  A  G  S  S  *  S  S  E  K  Q  S  Q  Y  P  Y  S  K  S  S  S  F  L  E  R  R  P  S  T  E  R  C  A  N  E  G  P  S  Y  L  P  S  R  V  M  K  R  E  A  E  E  I  A  Q  V  W  D  D  G  V  H  D  G  L  S  *  P  R  R  S  V  A  R  S  V  H  P  A  V  F  *  Q  I  S  S  K  *  S  P  C  L  I  R  F  L  F  S  I  N  S  S  K  N  L  V  F  D  V  R  L  W  I  I  I  R  L  C  V  L  V  L  D  F  *  L  S  L  D  F  L  *  D  S  *  L  L  *  D  S  C  K  *  L  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="C00HBa0067O19.2" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="82471" stop="82701"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>228</number_coding_nucleotides>
                  <number_encoded_amino_acids>76</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>RSAVLVTIRRWQRSAAVEGRWGSLTKCEVTKSMMVRRVYDGPSCRFVMKFREAIPVPIFQEFKFFRTETLDGTLCQ*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 112 chains have been computed
$ 
$ memory statistics:
$ 19672 bytes spliced alignments in total
$ 3 spliced alignments have been stored
$ 6557 bytes was the average size of a spliced alignment
$ 6736 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3368 bytes was the average size of a predicted gene location
$ 1 megabytes was the average size of the backtrace matrix
$ 131 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 05:31:53
-->
