<?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 05:59:40"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C00HBa0205L07-2MrjM/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C00HBa0205L07-2MrjM/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-C00HBa0205L07-2MrjM/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" ref_id="SGN-U599792" ref_strand="+" ref_description="SGN-U599792 Tomato 200607#2 [1 ESTs aligned] ">
      <seq>tattgtaanccctactatatgcttaattgtatgtttgcntgantatgattatgtgattgtgataagataaacatgatgaaaatattgaatcccaaatcttgaaaggaaactttaatatacnttattaatgatgatgccttggtata</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0205L07-2MrjM/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C00HBa0205L07.1" temp_strand="+" temp_description="C00HBa0205L07.1  CU468225.4 htgs_phase:3 submitted_to_sgn_as:C04HBa0205L07 upload_account_name:france">
        <position start="62419" stop="63164"/>
      </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="62719" g_stop="62864" g_length="146"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="146" r_length="146" r_score="0.945"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0205L07.1" gen_strand="+" ref_id="SGN-U599792" ref_strand="+">
        <total_alignment_score>0.945</total_alignment_score>
        <cumulative_length_of_scored_exons>146</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0205L07.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U599792" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="62719" e_stop="62864"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TATTGTAAACCCTACTATATGCTTAATTGTATGTTTGCATGAATATGATTATGTGATTGTGATAAGATAAGCATGATAAAAATATTGAATCCCAAATCTTGAAAAGAAACTTTAAAATACATTATTAATGATGATGCCTTGGTATA</genome_strand>
        <mrna_strand>TATTGTAANCCCTACTATATGCTTAATTGTATGTTTGCNTGANTATGATTATGTGATTGTGATAAGATAAACATGATGAAAATATTGAATCCCAAATCTTGAAAGGAAACTTTAATATACNTTATTAATGATGATGCCTTGGTATA</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="62719" PGL_stop="62864"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="62719" e_stop="62864"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.945"/>
        </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="0.945">
            <gDNA_exon_boundary e_start="62719" e_stop="62864" e_length="146"/>
          </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="62719" stop="62864"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U599792" 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>TATTGTAAACCCTACTATATGCTTAATTGTATGTTTGCATGAATATGATTATGTGATTGTGATAAGATAAGCATGATAAAAATATTGAATCCCAAATCTTGAAAAGAAACTTTAAAATACATTATTAATGATGATGCCTTGGTATA</gDNA_template>
            <first_frame> Y  C  K  P  Y  Y  M  L  N  C  M  F  A  *  I  *  L  C  D  C  D  K  I  S  M  I  K  I  L  N  P  K  S  *  K  E  T  L  K  Y  I  I  N  D  D  A  L  V   </first_frame>
            <second_frame>  I  V  N  P  T  I  C  L  I  V  C  L  H  E  Y  D  Y  V  I  V  I  R  *  A  *  *  K  Y  *  I  P  N  L  E  K  K  L  *  N  T  L  L  M  M  M  P  W  Y  </second_frame>
            <third_frame>   L  *  T  L  L  Y  A  *  L  Y  V  C  M  N  M  I  M  *  L  *  *  D  K  H  D  K  N  I  E  S  Q  I  L  K  R  N  F  K  I  H  Y  *  *  *  C  L  G  I </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="C00HBa0205L07.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 52 chains have been computed
$ 
$ memory statistics:
$ 2040 bytes spliced alignments in total
$ 1 spliced alignments have been stored
$ 2040 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
$ 68 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 06:00:11
-->
