<?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="2009-12-03 20:36:26"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C01HBa0023H04-y1rEj/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C01HBa0023H04-y1rEj/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" 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-C01HBa0023H04-y1rEj/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="T1524" ref_strand="+" ref_description="T1524">
      <seq>gcgttcgacccgagggtgaagctagggtcacatggtctagaagtttccaggatcgggctgggctgtatgagtatgtccggtaactacggccctcccaagcccgaggccgaaatgatcaagctacttcatcacgctattgatactggagtcaccttactcgatacttctgatgtctatggccctcttactaatgaaatactcatcggcaaggctattaaagggataagagagagagtgcaaatagctaccaagtttggtatacgttttgaagatggaaacaggggcatttgtggtgaacctgcgtatgtaagggcttgttgtgaggccagcttgaagagacttgatatcgactgcattgatctctattatgttcatcgcatcgatactcagttgccaattgaagtcacgatgggagaactaaaaaaactcgttgaagagggcaaaataaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C01HBa0023H04-y1rEj/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C01HBa0023H04.2" temp_strand="-" temp_description="C01HBa0023H04.2  AC238505.4 htgs_phase:2 submitted_to_sgn_as:C01HBa0023H04 upload_account_name:manual">
        <position start="29956" stop="28081"/>
      </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="29664" g_stop="29452" g_length="213"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="210" r_length="210" r_score="0.958"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="29451" i_stop="29209" i_length="243">
            <donor d_prob="0.989" d_score="1.00"/>
            <acceptor a_prob="0.996" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="29208" g_stop="29011" g_length="198"/>
          <reference_exon_boundary r_type="cDNA" r_start="211" r_stop="408" r_length="198" r_score="0.975"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="29010" i_stop="28422" i_length="589">
            <donor d_prob="0.961" d_score="1.00"/>
            <acceptor a_prob="0.530" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="28421" g_stop="28392" g_length="30"/>
          <reference_exon_boundary r_type="cDNA" r_start="409" r_stop="438" r_length="30" r_score="0.933"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C01HBa0023H04.2" gen_strand="-" ref_id="T1524" ref_strand="+">
        <total_alignment_score>0.966</total_alignment_score>
        <cumulative_length_of_scored_exons>441</cumulative_length_of_scored_exons>
        <coverage percentage="0.980" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C01HBa0023H04.2" gen_strand="-"/>
        <rDNA rDNA_id="T1524" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="29664" e_stop="29452"/>
          <exon e_start="29208" e_stop="29011"/>
          <exon e_start="28421" e_stop="28392"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CCGTTCGACGTTCCGAGGATAAAGCTAGGTTCACAAGGTCTAGAAGTTTCCAGGATCGGGCTGGGCTGTATGAGTATGTCCGGTAACTACGGCCCGCCCAAGCCCGAGGCCGAAATGATCAAGCTACTTCATCACGCTATTGATACTGGAGTCACCTTACTCGATACTTCTGATGTCTATGGCCCTCTTACTAATGAAATACTCATCGGCAAGGTGAAGATGTCTTTTTTTTCAAACAAGTAATTGCAAAGTGCTGCAGGAATTAGTTGTACTTCCTTTTTACTTTGTTGTACATGTCTGATCCTGTAGTTTTTCAATTGTTCACTGAGAAAAAAAAATGAAATTTCAGGATTAAATCTTCCAGAGAGTCGAATCTGTATCCTATAGATTTACGTTTTCTACCTGAGTTTTATAGATATGTTATATGTTCATGTTAATCTACCTGATTTTATGTAGGCTATTAAAGGAATAAGAGAGAAAGTACAAATAGCTACCAAGTTTGGTATCCGTTTTGAAGATGGAAATAGGGGCATTTGTGGTGAACCTGCGTATGTAAGGGCTTGTTGTGAGGCCAGCTTGAAGAGACTTGATATCGACTGCATTGATCTCTATTATGTTCATCGCATCGATACTCAGTTGCCAATTGAAGTCACGGTTTGACATCTTTGCTCCAAATTTCTATTTTTGCAGTGTACTTCATCACTCTTTAAGTTTTAAGAAGTAGTTGCATTATATGATTTGCGTGTCTAATTAGGTAAATCCTATTTCATTGATCATAGCCTATAGAGTCAATTTTTTTCCAAGTTGTTATCCAAAAGTACTACTTGTACTTGGTTTGATTGGTATATCAGTCTATTTTTGTTAAGTCTATGCTACTCTTCCATTTTTGCTTCTCTTCATTTTACGATTTTATTGATGTGTCATTTTACAAACTTCTTCAATTTATGATAAACATGTTCATAACAAGATATTTCTGAAATACTTAAAATTGGAAATGAATTCTCGAGACAAAAGGTTCTCCCAGCATTTGTGAATTCCGTCATACCTAGTTATTAAGTGATGTCGTTTCATAAACTAGTTTCTCGCAATAAGGTTTTTGTGTTGCCATTCAGATTCTATGATTTATGCGTTTGTCTGAAGGTCTATGTGACACACATTCAACTGCGGAATCTGTAGTATCATTACTATATTCAAAATTGTGCTATATATGTTCTAATACTGCTTGCATAAATACTGTTTTAAGATGGGAGAACTGAAGAAACTCGTTGAAGAG</genome_strand>
        <mrna_strand>GCGTTCGAC---CCGAGGGTGAAGCTAGGGTCACATGGTCTAGAAGTTTCCAGGATCGGGCTGGGCTGTATGAGTATGTCCGGTAACTACGGCCCTCCCAAGCCCGAGGCCGAAATGATCAAGCTACTTCATCACGCTATTGATACTGGAGTCACCTTACTCGATACTTCTGATGTCTATGGCCCTCTTACTAATGAAATACTCATCGGCAAG...................................................................................................................................................................................................................................................GCTATTAAAGGGATAAGAGAGAGAGTGCAAATAGCTACCAAGTTTGGTATACGTTTTGAAGATGGAAACAGGGGCATTTGTGGTGAACCTGCGTATGTAAGGGCTTGTTGTGAGGCCAGCTTGAAGAGACTTGATATCGACTGCATTGATCTCTATTATGTTCATCGCATCGATACTCAGTTGCCAATTGAAGTCACG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATGGGAGAACTAAAAAAACTCGTTGAAGAG</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="29664" PGL_stop="28392"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="29664" e_stop="29452"/>
            <exon e_start="29208" e_stop="29011"/>
            <exon e_start="28421" e_stop="28392"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.989" acc_prob="0.996" e_score="0.958"/>
          <exon-intron don_prob="0.961" acc_prob="0.530" e_score="0.975"/>
          <exon-only e_score="0.933"/>
        </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="0.958">
            <gDNA_exon_boundary e_start="29664" e_stop="29452" e_length="213"/>
          </exon>
          <intron i_serial="1" don_prob="0.989" acc_prob="0.996">
            <gDNA_intron_boundary i_start="29451" i_stop="29209" i_length="243"/>
          </intron>
          <exon e_serial="2" e_score="0.975">
            <gDNA_exon_boundary e_start="29208" e_stop="29011" e_length="198"/>
          </exon>
          <intron i_serial="2" don_prob="0.961" acc_prob="0.530">
            <gDNA_intron_boundary i_start="29010" i_stop="28422" i_length="589"/>
          </intron>
          <exon e_serial="3" e_score="0.933">
            <gDNA_exon_boundary e_start="28421" e_stop="28392" e_length="30"/>
          </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="29664" stop="29452"/>
              <exon start="29208" stop="29011"/>
              <exon start="28421" stop="28392"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="T1524" 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>CCGTTCGACGTTCCGAGGATAAAGCTAGGTTCACAAGGTCTAGAAGTTTCCAGGATCGGGCTGGGCTGTATGAGTATGTCCGGTAACTACGGCCCGCCCAAGCCCGAGGCCGAAATGATCAAGCTACTTCATCACGCTATTGATACTGGAGTCACCTTACTCGATACTTCTGATGTCTATGGCCCTCTTACTAATGAAATACTCATCGGCAAG : GCTATTAAAGGAATAAGAGAGAAAGTACAAATAGCTACCAAGTTTGGTATCCGTTTTGAAGATGGAAATAGGGGCATTTGTGGTGAACCTGCGTATGTAAGGGCTTGTTGTGAGGCCAGCTTGAAGAGACTTGATATCGACTGCATTGATCTCTATTATGTTCATCGCATCGATACTCAGTTGCCAATTGAAGTCACG : ATGGGAGAACTGAAGAAACTCGTTGAAGAG</gDNA_template>
            <first_frame> P  F  D  V  P  R  I  K  L  G  S  Q  G  L  E  V  S  R  I  G  L  G  C  M  S  M  S  G  N  Y  G  P  P  K  P  E  A  E  M  I  K  L  L  H  H  A  I  D  T  G  V  T  L  L  D  T  S  D  V  Y  G  P  L  T  N  E  I  L  I  G  K  :  A  I  K  G  I  R  E  K  V  Q  I  A  T  K  F  G  I  R  F  E  D  G  N  R  G  I  C  G  E  P  A  Y  V  R  A  C  C  E  A  S  L  K  R  L  D  I  D  C  I  D  L  Y  Y  V  H  R  I  D  T  Q  L  P  I  E  V  T  :  M  G  E  L  K  K  L  V  E  E </first_frame>
            <second_frame>  R  S  T  F  R  G  *  S  *  V  H  K  V  *  K  F  P  G  S  G  W  A  V  *  V  C  P  V  T  T  A  R  P  S  P  R  P  K  *  S  S  Y  F  I  T  L  L  I  L  E  S  P  Y  S  I  L  L  M  S  M  A  L  L  L  M  K  Y  S  S  A  R :   L  L  K  E  *  E  R  K  Y  K  *  L  P  S  L  V  S  V  L  K  M  E  I  G  A  F  V  V  N  L  R  M  *  G  L  V  V  R  P  A  *  R  D  L  I  S  T  A  L  I  S  I  M  F  I  A  S  I  L  S  C  Q  L  K  S  R :   W  E  N  *  R  N  S  L  K   </second_frame>
            <third_frame>   V  R  R  S  E  D  K  A  R  F  T  R  S  R  S  F  Q  D  R  A  G  L  Y  E  Y  V  R  *  L  R  P  A  Q  A  R  G  R  N  D  Q  A  T  S  S  R  Y  *  Y  W  S  H  L  T  R  Y  F  *  C  L  W  P  S  Y  *  *  N  T  H  R  Q   : G  Y  *  R  N  K  R  E  S  T  N  S  Y  Q  V  W  Y  P  F  *  R  W  K  *  G  H  L  W  *  T  C  V  C  K  G  L  L  *  G  Q  L  E  E  T  *  Y  R  L  H  *  S  L  L  C  S  S  H  R  Y  S  V  A  N  *  S  H   : D  G  R  T  E  E  T  R  *  R  </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="C01HBa0023H04.2" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="29664" stop="29452"/>
                    <exon start="29208" stop="29011"/>
                    <exon start="28421" stop="28392"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>441</number_coding_nucleotides>
                  <number_encoded_amino_acids>147</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>PFDVPRIKLGSQGLEVSRIGLGCMSMSGNYGPPKPEAEMIKLLHHAIDTGVTLLDTSDVYGPLTNEILIGKAIKGIREKVQIATKFGIRFEDGNRGICGEPAYVRACCEASLKRLDIDCIDLYYVHRIDTQLPIEVTMGELKKLVEE</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 2 chains have been computed
$ 
$ memory statistics:
$ 1768 bytes spliced alignments in total
$ 1 spliced alignments have been stored
$ 1768 bytes was the average size of a spliced alignment
$ 5592 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5592 bytes was the average size of a predicted gene location
$ 5 megabytes was the average size of the backtrace matrix
$ 2 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-03 20:36:32
-->
