<?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 06:46:36"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C00HBa0027M11-EoEcd/GenomeThreader_SGN_E_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C00HBa0027M11-EoEcd/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato" 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-C00HBa0027M11-EoEcd/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato" ref_id="SGN-E745033" ref_strand="+" ref_description="SGN-E745033 [GI|82754258]">
      <seq>tataaaaatgcggagctacgtcgttcggcagacgaaaaacagccagagctaaaagaagacgttgggaaactccttaaaacccatgacattactgatgctgcaggtacaagcaaaaaagctatggagaaacctacaccaaaaaacataaacctaaatagcatatttaccaaaccatttactccaaagatacagatagtagatgcttcaacaccacaaacatctacctatgcaactagcctgcataaagagaagaaaacatacaaccatatagcccgaacatatattgaaaacctatacaaaatacaaaactttttaaatcaaaaacccaaatctaccacaacttagaaaaaacccaagactacctaacccaaaaactacaaggctataacaagttaattgcacaaccaaaaactaatccaaacctagttaaaacttgttataactatggattattaaatacagtctatacatatacaggtgaagagataagtggaatcccagaggtccacaaagcatttttaatatataaaaagataacaaaaggaaacttatttttcataagattctacacagcaccagcagagatactctatgatgaaataaagccaatgattcagatagtcaaaattgggctaacacgagaaatgataatcccagaagatagaggccaacagccagagataacaagagttgagatacccagtttctatgccaataaaaggataattggattatcaactattatacaagagctagcaaataactatctacaaggcaacgccatat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0027M11-EoEcd/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C00HBa0027M11.1" temp_strand="-" temp_description="C00HBa0027M11.1  AC232687.1 htgs_phase:2 submitted_to_sgn_as:gi|206597339|gb|AC232687.1| upload_account_name:france Solanum lycopersicum chromosome 0 clone C00HBa0027M11, *** SEQUENCING IN PROGRESS ***, 6 ordered pieces">
        <position start="8969" stop="7584"/>
      </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="8669" g_stop="7884" g_length="786"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="786" r_length="786" r_score="0.941"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0027M11.1" gen_strand="-" ref_id="SGN-E745033" ref_strand="+">
        <total_alignment_score>0.941</total_alignment_score>
        <cumulative_length_of_scored_exons>786</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0027M11.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E745033" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="8669" e_stop="7884"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCTAAAAATGCGAAACTACGTCGTTCGGCAGACAAAAAACAGCCAGAACTAAAAGGAGACGTTGGGAAACTCCTTAAAATCCATGACATTACTGATGGTGCAGGTACAAGCAAAGGAGCTATGGAGAAACCTACACCAAAAAACACAAACCTAAATAGCGTATTTACCAAACCATTTACTCCAATGGTACAGATAATAGATACTTCAGCACCACAAACATCTACATATGCAGCTAGCCTGCATAAAGAGAAGAAAACATATAACAATATATCCCGAACATATATTGAAAACCAATACAAGATACAAAACTTTTTGAATCAAAAACCCAAATCTACCACGACATTAAAAAAAACCCATGCCTACCTAACCCAAAAAC-ACAAGGTTATAACAAGTTAATTGCACAACCAAAAACTAATCCGAACCTAGTAAAAACATGTTATAACTATGGATTATTAAATACAGTCTATACATATACTGGTGAAGAAATAAGTGGAATCCCAGAGGTCCACAAAGCATTTTTAATATATAAAAAGATAACAAAAGGAAACTTATTTTTCATAAGATTCTACACAGCACCAGCGGAGATACTCTATGATGAAATAAAGCCAATGATCCAGATAGTCAAAATTGGGCTAACGCGGGAAATGATAATCCCAGAAGATATAGGTCAACAGCCAGAGATAACAAGAGTTGAGATACCCAGTTTCTATGCCAATAAAAGGATAATTGGATTATCAACTATTATACAAGAGCTAGCAAATACCTATCTACAAGGCAACGCCACAT</genome_strand>
        <mrna_strand>TATAAAAATGCGGAGCTACGTCGTTCGGCAGACGAAAAACAGCCAGAGCTAAAAGAAGACGTTGGGAAACTCCTTAAAACCCATGACATTACTGATGCTGCAGGTACAAGCAAAAAAGCTATGGAGAAACCTACACCAAAAAACATAAACCTAAATAGCATATTTACCAAACCATTTACTCCAAAGATACAGATAGTAGATGCTTCAACACCACAAACATCTACCTATGCAACTAGCCTGCATAAAGAGAAGAAAACATACAACCATATAGCCCGAACATATATTGAAAACCTATACAAAATACAAAACTTTTTAAATCAAAAACCCAAATCTACCACAAC-TTAGAAAAAACCCAAGACTACCTAACCCAAAAACTACAAGGCTATAACAAGTTAATTGCACAACCAAAAACTAATCCAAACCTAGTTAAAACTTGTTATAACTATGGATTATTAAATACAGTCTATACATATACAGGTGAAGAGATAAGTGGAATCCCAGAGGTCCACAAAGCATTTTTAATATATAAAAAGATAACAAAAGGAAACTTATTTTTCATAAGATTCTACACAGCACCAGCAGAGATACTCTATGATGAAATAAAGCCAATGATTCAGATAGTCAAAATTGGGCTAACACGAGAAATGATAATCCCAGAAGATAGAGGCCAACAGCCAGAGATAACAAGAGTTGAGATACCCAGTTTCTATGCCAATAAAAGGATAATTGGATTATCAACTATTATACAAGAGCTAGCAAATAACTATCTACAAGGCAACGCCATAT</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="8669" PGL_stop="7884"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="8669" e_stop="7884"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.941"/>
        </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="0.941">
            <gDNA_exon_boundary e_start="8669" e_stop="7884" e_length="786"/>
          </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="8669" stop="7884"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E745033" 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>TCTAAAAATGCGAAACTACGTCGTTCGGCAGACAAAAAACAGCCAGAACTAAAAGGAGACGTTGGGAAACTCCTTAAAATCCATGACATTACTGATGGTGCAGGTACAAGCAAAGGAGCTATGGAGAAACCTACACCAAAAAACACAAACCTAAATAGCGTATTTACCAAACCATTTACTCCAATGGTACAGATAATAGATACTTCAGCACCACAAACATCTACATATGCAGCTAGCCTGCATAAAGAGAAGAAAACATATAACAATATATCCCGAACATATATTGAAAACCAATACAAGATACAAAACTTTTTGAATCAAAAACCCAAATCTACCACGACATTAAAAAAAACCCATGCCTACCTAACCCAAAAACACAAGGTTATAACAAGTTAATTGCACAACCAAAAACTAATCCGAACCTAGTAAAAACATGTTATAACTATGGATTATTAAATACAGTCTATACATATACTGGTGAAGAAATAAGTGGAATCCCAGAGGTCCACAAAGCATTTTTAATATATAAAAAGATAACAAAAGGAAACTTATTTTTCATAAGATTCTACACAGCACCAGCGGAGATACTCTATGATGAAATAAAGCCAATGATCCAGATAGTCAAAATTGGGCTAACGCGGGAAATGATAATCCCAGAAGATATAGGTCAACAGCCAGAGATAACAAGAGTTGAGATACCCAGTTTCTATGCCAATAAAAGGATAATTGGATTATCAACTATTATACAAGAGCTAGCAAATACCTATCTACAAGGCAACGCCACAT</gDNA_template>
            <first_frame> S  K  N  A  K  L  R  R  S  A  D  K  K  Q  P  E  L  K  G  D  V  G  K  L  L  K  I  H  D  I  T  D  G  A  G  T  S  K  G  A  M  E  K  P  T  P  K  N  T  N  L  N  S  V  F  T  K  P  F  T  P  M  V  Q  I  I  D  T  S  A  P  Q  T  S  T  Y  A  A  S  L  H  K  E  K  K  T  Y  N  N  I  S  R  T  Y  I  E  N  Q  Y  K  I  Q  N  F  L  N  Q  K  P  K  S  T  T  T  L  K  K  T  H  A  Y  L  T  Q  K  H  K  V  I  T  S  *  L  H  N  Q  K  L  I  R  T  *  *  K  H  V  I  T  M  D  Y  *  I  Q  S  I  H  I  L  V  K  K  *  V  E  S  Q  R  S  T  K  H  F  *  Y  I  K  R  *  Q  K  E  T  Y  F  S  *  D  S  T  Q  H  Q  R  R  Y  S  M  M  K  *  S  Q  *  S  R  *  S  K  L  G  *  R  G  K  *  *  S  Q  K  I  *  V  N  S  Q  R  *  Q  E  L  R  Y  P  V  S  M  P  I  K  G  *  L  D  Y  Q  L  L  Y  K  S  *  Q  I  P  I  Y  K  A  T  P  H </first_frame>
            <second_frame>  L  K  M  R  N  Y  V  V  R  Q  T  K  N  S  Q  N  *  K  E  T  L  G  N  S  L  K  S  M  T  L  L  M  V  Q  V  Q  A  K  E  L  W  R  N  L  H  Q  K  T  Q  T  *  I  A  Y  L  P  N  H  L  L  Q  W  Y  R  *  *  I  L  Q  H  H  K  H  L  H  M  Q  L  A  C  I  K  R  R  K  H  I  T  I  Y  P  E  H  I  L  K  T  N  T  R  Y  K  T  F  *  I  K  N  P  N  L  P  R  H  *  K  K  P  M  P  T  *  P  K  N  T  R  L  *  Q  V  N  C  T  T  K  N  *  S  E  P  S  K  N  M  L  *  L  W  I  I  K  Y  S  L  Y  I  Y  W  *  R  N  K  W  N  P  R  G  P  Q  S  I  F  N  I  *  K  D  N  K  R  K  L  I  F  H  K  I  L  H  S  T  S  G  D  T  L  *  *  N  K  A  N  D  P  D  S  Q  N  W  A  N  A  G  N  D  N  P  R  R  Y  R  S  T  A  R  D  N  K  S  *  D  T  Q  F  L  C  Q  *  K  D  N  W  I  I  N  Y  Y  T  R  A  S  K  Y  L  S  T  R  Q  R  H   </second_frame>
            <third_frame>   *  K  C  E  T  T  S  F  G  R  Q  K  T  A  R  T  K  R  R  R  W  E  T  P  *  N  P  *  H  Y  *  W  C  R  Y  K  Q  R  S  Y  G  E  T  Y  T  K  K  H  K  P  K  *  R  I  Y  Q  T  I  Y  S  N  G  T  D  N  R  Y  F  S  T  T  N  I  Y  I  C  S  *  P  A  *  R  E  E  N  I  *  Q  Y  I  P  N  I  Y  *  K  P  I  Q  D  T  K  L  F  E  S  K  T  Q  I  Y  H  D  I  K  K  N  P  C  L  P  N  P  K  T  Q  G  Y  N  K  L  I  A  Q  P  K  T  N  P  N  L  V  K  T  C  Y  N  Y  G  L  L  N  T  V  Y  T  Y  T  G  E  E  I  S  G  I  P  E  V  H  K  A  F  L  I  Y  K  K  I  T  K  G  N  L  F  F  I  R  F  Y  T  A  P  A  E  I  L  Y  D  E  I  K  P  M  I  Q  I  V  K  I  G  L  T  R  E  M  I  I  P  E  D  I  G  Q  Q  P  E  I  T  R  V  E  I  P  S  F  Y  A  N  K  R  I  I  G  L  S  T  I  I  Q  E  L  A  N  T  Y  L  Q  G  N  A  T  </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="C00HBa0027M11.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="8382" stop="7885"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>498</number_coding_nucleotides>
                  <number_encoded_amino_acids>166</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>KPIQDTKLFESKTQIYHDIKKNPCLPNPKTQGYNKLIAQPKTNPNLVKTCYNYGLLNTVYTYTGEEISGIPEVHKAFLIYKKITKGNLFFIRFYTAPAEILYDEIKPMIQIVKIGLTREMIIPEDIGQQPEITRVEIPSFYANKRIIGLSTIIQELANTYLQGNAT</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 47 chains have been computed
$ 
$ memory statistics:
$ 2296 bytes spliced alignments in total
$ 1 spliced alignments have been stored
$ 2296 bytes was the average size of a spliced alignment
$ 5528 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5528 bytes was the average size of a predicted gene location
$ 1 megabytes was the average size of the backtrace matrix
$ 69 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 06:48:12
-->
