<?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 07:04:26"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C00SLm0081L19-OFMio/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C00SLm0081L19-OFMio/gth_cdna_fileCXGN::TomatoGenome::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-C00SLm0081L19-OFMio/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" ref_id="SGN-U593741" ref_strand="-" ref_description="SGN-U593741 Tomato 200607#2 [1 ESTs aligned] ">
      <seq>agtatgtattaagcaatatcataaaattaactaatatccttagcatgcagcatttgcaattaccataacccttggttgcatcaccaagcacatcaatgaggactcacacctcctcatcatacttatttgggaatttagttcattggattgcatatattaacatatttcaagattcatcatatttattcccctcgtgtccttacgtgacactccactcctcaatatactatcctggcaccggaacgtggcacccgatccatattctatcctggtgtcagaacgtgacacccgatccatattctatcctggtgtcggaacgtgacacccgatccatattctatcctggtaccggaacgtggcacccgatccatattctatcctggtgtcggaacgtgacacccgatccatattctatcctggtaccggaacgtggcacccgatcccctaatctcaccactttcgttcatcaagccttcttttataccaaggcatcattattaacaaagtagattagggctg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLm0081L19-OFMio/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C00SLm0081L19.1" temp_strand="+" temp_description="C00SLm0081L19.1  CU928680.5 htgs_phase:3 submitted_to_sgn_as:C00SLm0081L19 sequenced_by:sanger upload_account_name:uk">
        <position start="62531" stop="63727"/>
      </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="62831" g_stop="63074" g_length="244"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="244" r_length="244" r_score="0.930"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="63075" i_stop="63151" i_length="77">
            <donor d_prob="0.000" d_score="0.88"/>
            <acceptor a_prob="0.000" a_score="0.82"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="63152" g_stop="63428" g_length="277"/>
          <reference_exon_boundary r_type="cDNA" r_start="245" r_stop="519" r_length="275" r_score="0.928"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLm0081L19.1" gen_strand="+" ref_id="SGN-U593741" ref_strand="-">
        <total_alignment_score>0.929</total_alignment_score>
        <cumulative_length_of_scored_exons>521</cumulative_length_of_scored_exons>
        <coverage percentage="1.004" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLm0081L19.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U593741" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="62831" e_stop="63074"/>
          <exon e_start="63152" e_stop="63428"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGTATGTATTAAGCAATATCATAAAATCAACTAATATCCTTAGCATGCAGCATTTACAGTTACCATAACCCTTGGTTACAACACCAAGCACATCAATGAGGACTCACACCTCCTCATCATACTCATTTGGGAATTTAGTTCATTAGATTTGATATATTAACATATTTCAAGATTCATTATCTTTATTCCCCTCGTGTCGGTACGTGACACTCCGCTCCTCAATATACTATCCTGGTGTCGGAACGTGACACTCTGATCCTCATATACTATCCTGGTACCGGAACATCGCACCCGATCCATATTCTATCCTGGTGTCGGAACGTGACACTCCGATCCTCATATACTATCCTGGTACCGGAACGTGGCACCCGATCCATATTCTATCCTGGTGTCGGAACGTGACACCCGATCCATATTCTATCCTGGTGTCGGAATGTGACACCCGATCCATATTCTATCCTGGTGTCGGAACGTGACACCCGATCTATATTCTATCCTGGTACCGGAACGTGGCACCCGATCCCCTAATCTCACCACTTTCGTTCATCAAGCCTTC-TTTATACCAAGCCATCATCATTAACAAAGTAGATTAGGGTTT</genome_strand>
        <mrna_strand>AGTATGTATTAAGCAATATCATAAAATTAACTAATATCCTTAGCATGCAGCATTTGCAATTACCATAACCCTTGGTTGCATCACCAAGCACATCAATGAGGACTCACACCTCCTCATCATACTTATTTGGGAATTTAGTTCATTGGATTGCATATATTAACATATTTCAAGATTCATCATATTTATTCCCCTCGTGTCCTTACGTGACACTCCACTCCTCAATATACTATCCTGGCACCGGAAC.............................................................................GTGGCAC-CCGAT-C-CATATTCTATCCTGGTGTCAGAACGTGACACCCGATCCATATTCTATCCTGGTGTCGGAACGTGACACCCGATCCATATTCTATCCTGGTACCGGAACGTGGCACCCGATCCATATTCTATCCTGGTGTCGGAACGTGACACCCGATCCATATTCTATCCTGGTACCGGAACGTGGCACCCGATCCCCTAATCTCACCACTTTCGTTCATCAAGCCTTCTTTTATACCAAGGCATCATTATTAACAAAGTAGATTAGGGCTG</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="62831" PGL_stop="63428"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="62831" e_stop="63074"/>
            <exon e_start="63152" e_stop="63428"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.000" acc_prob="0.000" e_score="0.930"/>
          <exon-only e_score="0.928"/>
        </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="0.930">
            <gDNA_exon_boundary e_start="62831" e_stop="63074" e_length="244"/>
          </exon>
          <intron i_serial="1" don_prob="0.000" acc_prob="0.000">
            <gDNA_intron_boundary i_start="63075" i_stop="63151" i_length="77"/>
          </intron>
          <exon e_serial="2" e_score="0.928">
            <gDNA_exon_boundary e_start="63152" e_stop="63428" e_length="277"/>
          </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="62831" stop="63074"/>
              <exon start="63152" stop="63428"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U593741" 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>AGTATGTATTAAGCAATATCATAAAATCAACTAATATCCTTAGCATGCAGCATTTACAGTTACCATAACCCTTGGTTACAACACCAAGCACATCAATGAGGACTCACACCTCCTCATCATACTCATTTGGGAATTTAGTTCATTAGATTTGATATATTAACATATTTCAAGATTCATTATCTTTATTCCCCTCGTGTCGGTACGTGACACTCCGCTCCTCAATATACTATCCTGGTGTCGGAAC : GTGACACTCCGATCCTCATATACTATCCTGGTACCGGAACGTGGCACCCGATCCATATTCTATCCTGGTGTCGGAACGTGACACCCGATCCATATTCTATCCTGGTGTCGGAATGTGACACCCGATCCATATTCTATCCTGGTGTCGGAACGTGACACCCGATCTATATTCTATCCTGGTACCGGAACGTGGCACCCGATCCCCTAATCTCACCACTTTCGTTCATCAAGCCTTCTTTATACCAAGCCATCATCATTAACAAAGTAGATTAGGGTTT</gDNA_template>
            <first_frame> S  M  Y  *  A  I  S  *  N  Q  L  I  S  L  A  C  S  I  Y  S  Y  H  N  P  W  L  Q  H  Q  A  H  Q  *  G  L  T  P  P  H  H  T  H  L  G  I  *  F  I  R  F  D  I  L  T  Y  F  K  I  H  Y  L  Y  S  P  R  V  G  T  *  H  S  A  P  Q  Y  T  I  L  V  S  E   : R  D  T  P  I  L  I  Y  Y  P  G  T  G  T  W  H  P  I  H  I  L  S  W  C  R  N  V  T  P  D  P  Y  S  I  L  V  S  E  C  D  T  R  S  I  F  Y  P  G  V  G  T  *  H  P  I  Y  I  L  S  W  Y  R  N  V  A  P  D  P  L  I  S  P  L  S  F  I  K  P  S  L  Y  Q  A  I  I  I  N  K  V  D  *  G   </first_frame>
            <second_frame>  V  C  I  K  Q  Y  H  K  I  N  *  Y  P  *  H  A  A  F  T  V  T  I  T  L  G  Y  N  T  K  H  I  N  E  D  S  H  L  L  I  I  L  I  W  E  F  S  S  L  D  L  I  Y  *  H  I  S  R  F  I  I  F  I  P  L  V  S  V  R  D  T  P  L  L  N  I  L  S  W  C  R  N  :  V  T  L  R  S  S  Y  T  I  L  V  P  E  R  G  T  R  S  I  F  Y  P  G  V  G  T  *  H  P  I  H  I  L  S  W  C  R  N  V  T  P  D  P  Y  S  I  L  V  S  E  R  D  T  R  S  I  F  Y  P  G  T  G  T  W  H  P  I  P  *  S  H  H  F  R  S  S  S  L  L  Y  T  K  P  S  S  L  T  K  *  I  R  V  </second_frame>
            <third_frame>   Y  V  L  S  N  I  I  K  S  T  N  I  L  S  M  Q  H  L  Q  L  P  *  P  L  V  T  T  P  S  T  S  M  R  T  H  T  S  S  S  Y  S  F  G  N  L  V  H  *  I  *  Y  I  N  I  F  Q  D  S  L  S  L  F  P  S  C  R  Y  V  T  L  R  S  S  I  Y  Y  P  G  V  G  T :   *  H  S  D  P  H  I  L  S  W  Y  R  N  V  A  P  D  P  Y  S  I  L  V  S  E  R  D  T  R  S  I  F  Y  P  G  V  G  M  *  H  P  I  H  I  L  S  W  C  R  N  V  T  P  D  L  Y  S  I  L  V  P  E  R  G  T  R  S  P  N  L  T  T  F  V  H  Q  A  F  F  I  P  S  H  H  H  *  Q  S  R  L  G  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/">
            <none gDNA_id="C00SLm0081L19.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 115 chains have been computed
$ 
$ memory statistics:
$ 2536 bytes spliced alignments in total
$ 1 spliced alignments have been stored
$ 2536 bytes was the average size of a spliced alignment
$ 5560 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5560 bytes was the average size of a predicted gene location
$ 2 megabytes was the average size of the backtrace matrix
$ 130 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 07:06:09
-->
