<?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 13:47:22"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C00HBa0027O01-UWVKi/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C00HBa0027O01-UWVKi/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" 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-C00HBa0027O01-UWVKi/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E577888" ref_strand="+" ref_description="SGN-E577888 [LE08BA01]">
      <seq>ctacatctcctaccatacaatgcttcaaatggagccatatcaatgcttgattgatagctattattgtatgaaaactccgctaagggtaggaagctatcccaatgaccaccaaactctatcacacacgcacgaagcatattctccaacacttgaatcgttcgctcagactgaccatcgggagaactagt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0027O01-UWVKi/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00HBa0027O01.2" temp_strand="-" temp_description="C00HBa0027O01.2  CU927992.4 htgs_phase:3 submitted_to_sgn_as:C04HBa0027O01 sequenced_by:sanger upload_account_name:uk">
        <position start="14076" stop="13299"/>
      </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="13776" g_stop="13600" g_length="177"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="177" r_length="177" r_score="0.904"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0027O01.2" gen_strand="-" ref_id="SGN-E577888" ref_strand="+">
        <total_alignment_score>0.904</total_alignment_score>
        <cumulative_length_of_scored_exons>177</cumulative_length_of_scored_exons>
        <coverage percentage="0.941" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0027O01.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E577888" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="13776" e_stop="13600"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTACATCTTCTCCCGTACAATGCCTCGAATGGGGCCATATCAATACTTGAGTGATAGCTATTATTGTATGAGAACTCTGCTAAGAGTAAGAATTTATCCCAATGACCACCAAATTCTATCACACATGCACGAAGCATATCCTCCAACACTTGAATCGTTCGCTCAGACTGACCATCG</genome_strand>
        <mrna_strand>CTACATCTCCTACCATACAATGCTTCAAATGGAGCCATATCAATGCTTGATTGATAGCTATTATTGTATGAAAACTCCGCTAAGGGTAGGAAGCTATCCCAATGACCACCAAACTCTATCACACACGCACGAAGCATATTCTCCAACACTTGAATCGTTCGCTCAGACTGACCATCG</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="13776" PGL_stop="13600"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="13776" e_stop="13600"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.904"/>
        </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="0.904">
            <gDNA_exon_boundary e_start="13776" e_stop="13600" e_length="177"/>
          </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="13776" stop="13600"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E577888" 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>CTACATCTTCTCCCGTACAATGCCTCGAATGGGGCCATATCAATACTTGAGTGATAGCTATTATTGTATGAGAACTCTGCTAAGAGTAAGAATTTATCCCAATGACCACCAAATTCTATCACACATGCACGAAGCATATCCTCCAACACTTGAATCGTTCGCTCAGACTGACCATCG</gDNA_template>
            <first_frame> L  H  L  L  P  Y  N  A  S  N  G  A  I  S  I  L  E  *  *  L  L  L  Y  E  N  S  A  K  S  K  N  L  S  Q  *  P  P  N  S  I  T  H  A  R  S  I  S  S  N  T  *  I  V  R  S  D  *  P  S </first_frame>
            <second_frame>  Y  I  F  S  R  T  M  P  R  M  G  P  Y  Q  Y  L  S  D  S  Y  Y  C  M  R  T  L  L  R  V  R  I  Y  P  N  D  H  Q  I  L  S  H  M  H  E  A  Y  P  P  T  L  E  S  F  A  Q  T  D  H   </second_frame>
            <third_frame>   T  S  S  P  V  Q  C  L  E  W  G  H  I  N  T  *  V  I  A  I  I  V  *  E  L  C  *  E  *  E  F  I  P  M  T  T  K  F  Y  H  T  C  T  K  H  I  L  Q  H  L  N  R  S  L  R  L  T  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="C00HBa0027O01.2"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 152 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
$ 0 megabytes was the average size of the backtrace matrix
$ 186 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 13:49:52
-->
