<?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="2009-01-15 15:27:25"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C07HBa0012N15-sWHaE/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C07HBa0012N15-sWHaE/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-C07HBa0012N15-sWHaE/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U346572" ref_strand="+" ref_description="SGN-U346572        Tomato 200607 #1 [1 ESTs aligned] genbank/nr: gi|47824972|gb|AAT38745.1| putative polyprotein, 3'-partial [Solanum demissum] (evalue: 2e-31, score=89.7)">
      <seq>agatgatcaaccaggttctttctcatcttagcgggttatctgatcagggccagacacctccagtgtttcctgtaccagcacctcaggttccgggagtacaacatgcagctgttgtggctctccgcatggatgcctcattggaaataggcacatttcctcgattgactacagggcctataatgacgagtgatcaacatgaacttttcactaaattcttgaagttgaaacctctagtcttcaagggtgctgaatctgaggatgcctatgattttcttgttgattgtcatgagctgctacataagatggacatagtagaacggttcggggttgagtttgtgacctatcaatttcagggaaatgtcaaaatgtggtggcggtcgtatgttgagtgtcaaccagcacagcaccacctatgacttgggcatcattctctagcttatttatggaaaagtgtataccccggacgttgagggataggaggagagatgagttcctgagtctatagcaaggcaggatgtctgttactgcttatgaggctaaattttgtgcactatccaggtatgccacccagctttgcttcagtccacaagagcggattcaccgttttgtgaaaggattgaggtcagatttgcagatcccagccctacaggtagct</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0012N15-sWHaE/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C07HBa0012N15.1" temp_strand="+" temp_description="C07HBa0012N15.1  AC210347.1 htgs_phase:2 submitted_to_sgn_as:C07HBa0012N15 upload_account_name:france">
        <position start="106039" stop="107294"/>
      </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="106339" g_stop="106994" g_length="656"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="655" r_length="655" r_score="0.905"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07HBa0012N15.1" gen_strand="+" ref_id="SGN-U346572" ref_strand="+">
        <total_alignment_score>0.905</total_alignment_score>
        <cumulative_length_of_scored_exons>656</cumulative_length_of_scored_exons>
        <coverage percentage="1.002" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0012N15.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U346572" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="106339" e_stop="106994"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGATGATTAAGTAGGTTCTTTCTTATCTTAGCGGGTTATCTGATCAAGGCTAGACACCTCCAGTGTTTTATGCACCAGCACGTTAGGTTTCGGGAGTACAACATGCAAATGTTGTGGCTCCCCGCATGGATGCCTCATTGGAAGTTGGCACGTTTCCTCGGTTGACTACAGGGCCTATAATGACGAGTGATCAGCATGAACTTTTCACTATGTTCTTGAAATTGAATCCTCCAGTCTTCAAGTGTGCTGAATCTAAGGATGCCTATGATTTTTAGGTTGATTGTGATGAGCTGCTACATAATATGGACATAGTAAAATGATTCGGTGTTGAGTTTGTGACCTATCAGTTTCAGGGAAATGCCAAAATGTGGTGGCGATCGTATGTTGAGTGTCAACCAGCACATGCACCACCTATGACTTGGGCATCATTCTCTAGCCTATCTATAGAGAAGTATATACCCCGAACATTAAGGCATAGGAGGAGAGATGAGTTCCTAAGCTTAGAGCAAGGCAGGATGTCTGTTACTGCTTATGAGGCTAAGTTTCGTGCACTATCTAGGTATGCCACCCAGCTTTTCTTCAATCCACAAGAGCGGATTCGCCATTTTGTAAAAGGATTGAGGTCAGATTTGCAGATCCCAGCCTTACAGGTAGCT</genome_strand>
        <mrna_strand>AGATGATCAACCAGGTTCTTTCTCATCTTAGCGGGTTATCTGATCAGGGCCAGACACCTCCAGTGTTTCCTGTACCAGCACCTCAGGTTCCGGGAGTACAACATGCAGCTGTTGTGGCTCTCCGCATGGATGCCTCATTGGAAATAGGCACATTTCCTCGATTGACTACAGGGCCTATAATGACGAGTGATCAACATGAACTTTTCACTAAATTCTTGAAGTTGAAACCTCTAGTCTTCAAGGGTGCTGAATCTGAGGATGCCTATGATTTTCTTGTTGATTGTCATGAGCTGCTACATAAGATGGACATAGTAGAACGGTTCGGGGTTGAGTTTGTGACCTATCAATTTCAGGGAAATGTCAAAATGTGGTGGCGGTCGTATGTTGAGTGTCAACCAGCACA-GCACCACCTATGACTTGGGCATCATTCTCTAGCTTATTTATGGAAAAGTGTATACCCCGGACGTTGAGGGATAGGAGGAGAGATGAGTTCCTGAGTCTATAGCAAGGCAGGATGTCTGTTACTGCTTATGAGGCTAAATTTTGTGCACTATCCAGGTATGCCACCCAGCTTTGCTTCAGTCCACAAGAGCGGATTCACCGTTTTGTGAAAGGATTGAGGTCAGATTTGCAGATCCCAGCCCTACAGGTAGCT</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="106339" PGL_stop="106994"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="106339" e_stop="106994"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.905"/>
        </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="0.905">
            <gDNA_exon_boundary e_start="106339" e_stop="106994" 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="106339" stop="106994"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U346572" 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>AGATGATTAAGTAGGTTCTTTCTTATCTTAGCGGGTTATCTGATCAAGGCTAGACACCTCCAGTGTTTTATGCACCAGCACGTTAGGTTTCGGGAGTACAACATGCAAATGTTGTGGCTCCCCGCATGGATGCCTCATTGGAAGTTGGCACGTTTCCTCGGTTGACTACAGGGCCTATAATGACGAGTGATCAGCATGAACTTTTCACTATGTTCTTGAAATTGAATCCTCCAGTCTTCAAGTGTGCTGAATCTAAGGATGCCTATGATTTTTAGGTTGATTGTGATGAGCTGCTACATAATATGGACATAGTAAAATGATTCGGTGTTGAGTTTGTGACCTATCAGTTTCAGGGAAATGCCAAAATGTGGTGGCGATCGTATGTTGAGTGTCAACCAGCACATGCACCACCTATGACTTGGGCATCATTCTCTAGCCTATCTATAGAGAAGTATATACCCCGAACATTAAGGCATAGGAGGAGAGATGAGTTCCTAAGCTTAGAGCAAGGCAGGATGTCTGTTACTGCTTATGAGGCTAAGTTTCGTGCACTATCTAGGTATGCCACCCAGCTTTTCTTCAATCCACAAGAGCGGATTCGCCATTTTGTAAAAGGATTGAGGTCAGATTTGCAGATCCCAGCCTTACAGGTAGCT</gDNA_template>
            <first_frame> R  *  L  S  R  F  F  L  I  L  A  G  Y  L  I  K  A  R  H  L  Q  C  F  M  H  Q  H  V  R  F  R  E  Y  N  M  Q  M  L  W  L  P  A  W  M  P  H  W  K  L  A  R  F  L  G  *  L  Q  G  L  *  *  R  V  I  S  M  N  F  S  L  C  S  *  N  *  I  L  Q  S  S  S  V  L  N  L  R  M  P  M  I  F  R  L  I  V  M  S  C  Y  I  I  W  T  *  *  N  D  S  V  L  S  L  *  P  I  S  F  R  E  M  P  K  C  G  G  D  R  M  L  S  V  N  Q  H  M  H  H  L  *  L  G  H  H  S  L  A  Y  L  *  R  S  I  Y  P  E  H  *  G  I  G  G  E  M  S  S  *  A  *  S  K  A  G  C  L  L  L  L  M  R  L  S  F  V  H  Y  L  G  M  P  P  S  F  S  S  I  H  K  S  G  F  A  I  L  *  K  D  *  G  Q  I  C  R  S  Q  P  Y  R  *   </first_frame>
            <second_frame>  D  D  *  V  G  S  F  L  S  *  R  V  I  *  S  R  L  D  T  S  S  V  L  C  T  S  T  L  G  F  G  S  T  T  C  K  C  C  G  S  P  H  G  C  L  I  G  S  W  H  V  S  S  V  D  Y  R  A  Y  N  D  E  *  S  A  *  T  F  H  Y  V  L  E  I  E  S  S  S  L  Q  V  C  *  I  *  G  C  L  *  F  L  G  *  L  *  *  A  A  T  *  Y  G  H  S  K  M  I  R  C  *  V  C  D  L  S  V  S  G  K  C  Q  N  V  V  A  I  V  C  *  V  S  T  S  T  C  T  T  Y  D  L  G  I  I  L  *  P  I  Y  R  E  V  Y  T  P  N  I  K  A  *  E  E  R  *  V  P  K  L  R  A  R  Q  D  V  C  Y  C  L  *  G  *  V  S  C  T  I  *  V  C  H  P  A  F  L  Q  S  T  R  A  D  S  P  F  C  K  R  I  E  V  R  F  A  D  P  S  L  T  G  S  </second_frame>
            <third_frame>   M  I  K  *  V  L  S  Y  L  S  G  L  S  D  Q  G  *  T  P  P  V  F  Y  A  P  A  R  *  V  S  G  V  Q  H  A  N  V  V  A  P  R  M  D  A  S  L  E  V  G  T  F  P  R  L  T  T  G  P  I  M  T  S  D  Q  H  E  L  F  T  M  F  L  K  L  N  P  P  V  F  K  C  A  E  S  K  D  A  Y  D  F  *  V  D  C  D  E  L  L  H  N  M  D  I  V  K  *  F  G  V  E  F  V  T  Y  Q  F  Q  G  N  A  K  M  W  W  R  S  Y  V  E  C  Q  P  A  H  A  P  P  M  T  W  A  S  F  S  S  L  S  I  E  K  Y  I  P  R  T  L  R  H  R  R  R  D  E  F  L  S  L  E  Q  G  R  M  S  V  T  A  Y  E  A  K  F  R  A  L  S  R  Y  A  T  Q  L  F  F  N  P  Q  E  R  I  R  H  F  V  K  G  L  R  S  D  L  Q  I  P  A  L  Q  V  A </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="C07HBa0012N15.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="106659" stop="106994"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>336</number_coding_nucleotides>
                  <number_encoded_amino_acids>112</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>FGVEFVTYQFQGNAKMWWRSYVECQPAHAPPMTWASFSSLSIEKYIPRTLRHRRRDEFLSLEQGRMSVTAYEAKFRALSRYATQLFFNPQERIRHFVKGLRSDLQIPALQVA</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 51 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
$ 0 megabytes was the average size of the backtrace matrix
$ 62 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-15 15:27:54
-->
