<?xml version="1.0" encoding="ISO-8859-1"?>
<GTH_output xmlns="http://www.genomethreader.org/GTH_output/" GTH_XML_version="1.1">
  <header xmlns="http://www.genomethreader.org/GTH_output/header/">
    <source program="GenomeThreader" version="0.9.54" build_date="2006-07-28 11:55:15" run_date="2009-01-16 20:51:21"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C06HBa0308F14-2BU5g/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C06HBa0308F14-2BU5g/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_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-C06HBa0308F14-2BU5g/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U335934" ref_strand="+" ref_description="SGN-U335934        Tomato 200607 #1 [1 ESTs aligned] genbank/nr: hypothetical(evalue: 5e-22, score=107)">
      <seq>gatacctaggcacccagagacgaggaagggcgtagtaatcgacgaaatgcttcggggagttgaaaataagcatagatccggagattcccgaatagggcaacctttcgaactgctgctgaatccatgggcaggcaagagacaacctggcgaactgaaacatcttagtagccagaggaaaagaaagcaaaagcgattcccgtagtagcggcgagcgaaatgggagcagcctaaaccgtgaaaacggggttgtgggagagcaatacaagcgtcgtgctgctaggcgaagcagcctgaatgctgcacccatatggcgaaagtccagtagccgaaagcatcactagcttacgctctgacccgagtagcatggggcacgtggaatcccgtgtgaatcagcaaggaccaccttgcaaggctaaatactcctgggtgaccgatagcgaagtagtaccgtgagggaagggtgaaaagaacccccatcggggagtgaaatagaacatgaaaccgtaagctcccaagcagtgggaggagccagggctctgaccgcgtgcctgttgaagaatgagccggcgactcataggcagtggcttggttaagggaacccaccggagccgtagcgaaagcgagtcttcatagggcaattgtcactgcttatggacccgaacctgggtgatctatccatgaccaggatgaagcttgggtgaaactaagtggaggtccgaaccgactgatgttgaagaatcagcggatgagttgtggttaggggtgaaatgccactcgaacccagagctagctggttctccccgaaatgcgttgagccaaaaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C06HBa0308F14-2BU5g/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C06HBa0308F14.2" temp_strand="+" temp_description="C06HBa0308F14.2  AC211076.1 htgs_phase:1 submitted_to_sgn_as:C06HBa0308F14 sequenced_by:cbsg upload_account_name:netherlands [organism=Solanum lycopersicum]">
        <position start="75179" stop="76599"/>
      </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="75479" g_stop="76288" g_length="810"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="809" r_length="809" r_score="0.967"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="818" polyA_stop="838"/>
      <MATCH_line gen_id="C06HBa0308F14.2" gen_strand="+" ref_id="SGN-U335934" ref_strand="+">
        <total_alignment_score>0.967</total_alignment_score>
        <cumulative_length_of_scored_exons>810</cumulative_length_of_scored_exons>
        <coverage percentage="0.967" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C06HBa0308F14.2" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U335934" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="75479" e_stop="76288"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GATACCTAGGCACCCAGTGACGAGGAAGGTCGTAGTAATTGACGAAATGCTTTGGGGAGTTGAAAATAAGCATAGATCCAGAGATTCCCGAATAGGGCAAACTTTCGAACTGCTGCTGAATCCATGGGCAGGCAAGAGACAACCTGGCGAACTGAAACATCTTAGTAGCTAGAGGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGATCAGCCTAAACCATGAAAATGGGGTTGTGGGAGAGCAATACAAACGTCGTGCTGCTAGGCGAAGCAGCCTGAATGCTGCATCCTAGATGGCGAAAGTATAGTAGCCAAAAGCATCACAAGCTTACGCTCTGACCCGAGTAACATGGGGCACGTGGAATCCCGTGTGAATTAGCAAGGACCACCTTGCAAGGCTAAATACTCCTGGGTGACCGATAGAGAAGAAGTACCGTGAGGGAAGGGTGAAAAGGACCCCCATCGGGCAGTGAAATAGAACATGAAACCGTAAGCTCCCAAGAAGTGGGAGGAGCCAGGGCCCTAACCGCGTGCCTGTTGAAGAATGAGCCGGCGACTCATAGGCAGTGGCTTGGTTAAGGGAACCCACCGGAGCCGTAGCGAAAGCGAGTCTTCATAGGGCAATTGTCACTGCTTATGGACCCGAACCTGGGTGATCTATCCATGACCAGGATGAAGCTTGGGTGAAACTAAGTGGAGGTCCGAACCGACTGATGTTGAAGAATCAGCGGATGAGTTGTGGTTAGGGGTGAAATGCCACTCGAACCCAGAGCTAGCTGGTTCTCCCCGAAATGC</genome_strand>
        <mrna_strand>GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGTAATCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCGAATAGGGCAACCTTTCGAACTGCTGCTGAATCCATGGGCAGGCAAGAGACAACCTGGCGAACTGAAACATCTTAGTAGCCAGAGGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGTCGTGCTGCTAGGCGAAGCAGCCTGAATGCTGCA-CCCATATGGCGAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTGGGTGACCGATAGCGAAGTAGTACCGTGAGGGAAGGGTGAAAAGAACCCCCATCGGGGAGTGAAATAGAACATGAAACCGTAAGCTCCCAAGCAGTGGGAGGAGCCAGGGCTCTGACCGCGTGCCTGTTGAAGAATGAGCCGGCGACTCATAGGCAGTGGCTTGGTTAAGGGAACCCACCGGAGCCGTAGCGAAAGCGAGTCTTCATAGGGCAATTGTCACTGCTTATGGACCCGAACCTGGGTGATCTATCCATGACCAGGATGAAGCTTGGGTGAAACTAAGTGGAGGTCCGAACCGACTGATGTTGAAGAATCAGCGGATGAGTTGTGGTTAGGGGTGAAATGCCACTCGAACCCAGAGCTAGCTGGTTCTCCCCGAAATGC</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="75479" PGL_stop="76288"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="75479" e_stop="76288"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.967"/>
        </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="0.967">
            <gDNA_exon_boundary e_start="75479" e_stop="76288" e_length="810"/>
          </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="75479" stop="76288"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U335934" 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>GATACCTAGGCACCCAGTGACGAGGAAGGTCGTAGTAATTGACGAAATGCTTTGGGGAGTTGAAAATAAGCATAGATCCAGAGATTCCCGAATAGGGCAAACTTTCGAACTGCTGCTGAATCCATGGGCAGGCAAGAGACAACCTGGCGAACTGAAACATCTTAGTAGCTAGAGGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGATCAGCCTAAACCATGAAAATGGGGTTGTGGGAGAGCAATACAAACGTCGTGCTGCTAGGCGAAGCAGCCTGAATGCTGCATCCTAGATGGCGAAAGTATAGTAGCCAAAAGCATCACAAGCTTACGCTCTGACCCGAGTAACATGGGGCACGTGGAATCCCGTGTGAATTAGCAAGGACCACCTTGCAAGGCTAAATACTCCTGGGTGACCGATAGAGAAGAAGTACCGTGAGGGAAGGGTGAAAAGGACCCCCATCGGGCAGTGAAATAGAACATGAAACCGTAAGCTCCCAAGAAGTGGGAGGAGCCAGGGCCCTAACCGCGTGCCTGTTGAAGAATGAGCCGGCGACTCATAGGCAGTGGCTTGGTTAAGGGAACCCACCGGAGCCGTAGCGAAAGCGAGTCTTCATAGGGCAATTGTCACTGCTTATGGACCCGAACCTGGGTGATCTATCCATGACCAGGATGAAGCTTGGGTGAAACTAAGTGGAGGTCCGAACCGACTGATGTTGAAGAATCAGCGGATGAGTTGTGGTTAGGGGTGAAATGCCACTCGAACCCAGAGCTAGCTGGTTCTCCCCGAAATGC</gDNA_template>
            <first_frame> D  T  *  A  P  S  D  E  E  G  R  S  N  *  R  N  A  L  G  S  *  K  *  A  *  I  Q  R  F  P  N  R  A  N  F  R  T  A  A  E  S  M  G  R  Q  E  T  T  W  R  T  E  T  S  *  *  L  E  E  K  K  A  K  A  I  P  V  V  A  A  S  E  M  G  S  A  *  T  M  K  M  G  L  W  E  S  N  T  N  V  V  L  L  G  E  A  A  *  M  L  H  P  R  W  R  K  Y  S  S  Q  K  H  H  K  L  T  L  *  P  E  *  H  G  A  R  G  I  P  C  E  L  A  R  T  T  L  Q  G  *  I  L  L  G  D  R  *  R  R  S  T  V  R  E  G  *  K  G  P  P  S  G  S  E  I  E  H  E  T  V  S  S  Q  E  V  G  G  A  R  A  L  T  A  C  L  L  K  N  E  P  A  T  H  R  Q  W  L  G  *  G  N  P  P  E  P  *  R  K  R  V  F  I  G  Q  L  S  L  L  M  D  P  N  L  G  D  L  S  M  T  R  M  K  L  G  *  N  *  V  E  V  R  T  D  *  C  *  R  I  S  G  *  V  V  V  R  G  E  M  P  L  E  P  R  A  S  W  F  S  P  K  C </first_frame>
            <second_frame>  I  P  R  H  P  V  T  R  K  V  V  V  I  D  E  M  L  W  G  V  E  N  K  H  R  S  R  D  S  R  I  G  Q  T  F  E  L  L  L  N  P  W  A  G  K  R  Q  P  G  E  L  K  H  L  S  S  *  R  K  R  K  Q  K  R  F  P  *  *  R  R  A  K  W  D  Q  P  K  P  *  K  W  G  C  G  R  A  I  Q  T  S  C  C  *  A  K  Q  P  E  C  C  I  L  D  G  E  S  I  V  A  K  S  I  T  S  L  R  S  D  P  S  N  M  G  H  V  E  S  R  V  N  *  Q  G  P  P  C  K  A  K  Y  S  W  V  T  D  R  E  E  V  P  *  G  K  G  E  K  D  P  H  R  A  V  K  *  N  M  K  P  *  A  P  K  K  W  E  E  P  G  P  *  P  R  A  C  *  R  M  S  R  R  L  I  G  S  G  L  V  K  G  T  H  R  S  R  S  E  S  E  S  S  *  G  N  C  H  C  L  W  T  R  T  W  V  I  Y  P  *  P  G  *  S  L  G  E  T  K  W  R  S  E  P  T  D  V  E  E  S  A  D  E  L  W  L  G  V  K  C  H  S  N  P  E  L  A  G  S  P  R  N   </second_frame>
            <third_frame>   Y  L  G  T  Q  *  R  G  R  S  *  *  L  T  K  C  F  G  E  L  K  I  S  I  D  P  E  I  P  E  *  G  K  L  S  N  C  C  *  I  H  G  Q  A  R  D  N  L  A  N  *  N  I  L  V  A  R  G  K  E  S  K  S  D  S  R  S  S  G  E  R  N  G  I  S  L  N  H  E  N  G  V  V  G  E  Q  Y  K  R  R  A  A  R  R  S  S  L  N  A  A  S  *  M  A  K  V  *  *  P  K  A  S  Q  A  Y  A  L  T  R  V  T  W  G  T  W  N  P  V  *  I  S  K  D  H  L  A  R  L  N  T  P  G  *  P  I  E  K  K  Y  R  E  G  R  V  K  R  T  P  I  G  Q  *  N  R  T  *  N  R  K  L  P  R  S  G  R  S  Q  G  P  N  R  V  P  V  E  E  *  A  G  D  S  *  A  V  A  W  L  R  E  P  T  G  A  V  A  K  A  S  L  H  R  A  I  V  T  A  Y  G  P  E  P  G  *  S  I  H  D  Q  D  E  A  W  V  K  L  S  G  G  P  N  R  L  M  L  K  N  Q  R  M  S  C  G  *  G  *  N  A  T  R  T  Q  S  *  L  V  L  P  E  M  </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="C06HBa0308F14.2"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 52 chains have been computed
$ 
$ memory statistics:
$ 1528 bytes spliced alignments in total
$ 1 spliced alignments have been stored
$ 1528 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
$ 2 megabytes was the average size of the backtrace matrix
$ 66 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-16 20:52:15
-->
