<?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 10:31:26"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C02HBa0320M09-0CleD/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C02HBa0320M09-0CleD/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-C02HBa0320M09-0CleD/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="T1698" ref_strand="+" ref_description="T1698">
      <seq>gcacttttgtatttcaacagccttctttcaagcaaagtatacgaatggctcgttccgctctggatgagatgtcagcaacaggtgcttttgagagaactgcttcaaccttccgtaatatagtctcaagggaacccggctcagtttttccagtcgaatctgggaggtaccacctctacatatcatatgcttgcccatgggcatcaaggtgcctggcttacttgaagattaaaggccttgatcaagccattgatttcacatctgttaaacctgtttgggagaggacgaaggacagcgatgagcacacgggatgggtttttgcttcatcaagcaccgaggaagcaggagctgatcttgatcctcttaatggagccaaaagcatacgggagctgtatgagcttgcaagtacaaactattctgggaaatacactgttccggttctttgggataagaaactgaagacaatcgtgaacaacgagagtgcagaaataatacgcatgtttaatagtgaatttaatgatatagctgagaatgcaactttggacctttatcctcctcatttgcaatccctaatcaatga</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C02HBa0320M09-0CleD/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C02HBa0320M09.4" temp_strand="+" temp_description="C02HBa0320M09.4  AC215438.3 htgs_phase:3 submitted_to_sgn_as:C02HBa0320M09 sequenced_by:kribb upload_account_name:korea">
        <position start="86771" stop="89174"/>
      </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="87070" g_stop="87101" g_length="32"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="32" r_length="32" r_score="0.969"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="87102" i_stop="88156" i_length="1055">
            <donor d_prob="0.996" d_score="0.00"/>
            <acceptor a_prob="0.816" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="88157" g_stop="88381" g_length="225"/>
          <reference_exon_boundary r_type="cDNA" r_start="33" r_stop="257" r_length="225" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="88382" i_stop="88462" i_length="81">
            <donor d_prob="0.966" d_score="1.00"/>
            <acceptor a_prob="0.988" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="88463" g_stop="88639" g_length="177"/>
          <reference_exon_boundary r_type="cDNA" r_start="258" r_stop="434" r_length="177" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="88640" i_stop="88731" i_length="92">
            <donor d_prob="0.896" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="88732" g_stop="88874" g_length="143"/>
          <reference_exon_boundary r_type="cDNA" r_start="435" r_stop="577" r_length="143" r_score="0.993"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C02HBa0320M09.4" gen_strand="+" ref_id="T1698" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>577</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C02HBa0320M09.4" gen_strand="+"/>
        <rDNA rDNA_id="T1698" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="87070" e_stop="87101"/>
          <exon e_start="88157" e_stop="88381"/>
          <exon e_start="88463" e_stop="88639"/>
          <exon e_start="88732" e_stop="88874"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ACACTTTTGTATTTCAACAGCCTTCTTTCAAGGTAAACAACTTTAATTTCAGTTCTTAATCATTTTTCCAGGTACCCCATATGGGGTAGATGTGTTTATATGCACTTCTATATGTTGATTGGAGTTATGGGGGAAGCGGGTGTTTCTGCTTTTCTTCTCTGTGTTTGAGGGTTTTGTGATTTTTGAAACTTTTTATACAAGATGGCTAATTTATGATCTTAAAGGAATTCTTGAGTTTGTGGTTTACTAGTCTAAGATATGTTTGTATGGTGATCAAGAAAATGGAAAAAAGAAGTGATTTTTATGTTCTTTTGTATAACTTGTGATTGTGTTACTTTGAAAAAAAATGTGTGTAGGGGAAGGAGAAATGGGGAGTCGAACTCTCGAGGAGGAAGTTGAGGTAGTCAATCAACTGAGCTACTAAGATTTCCCATTTTGGTTCAGAGCTTTAGCTGATTGTTTATTTTGTTAAGAGTCTGAAAGGGTTTACTGTTTTTGAGTTTCTTAGGTTGATTGCTTAGATGGTCACTCAATTACTAATAGTTATAGTTATTATCTAAGAAAGTGACTTTCTGCGATAACAATTATTAGTTGAGTGACCATTTGAGAAATCAATTCGAATTTCTTGGTGCCCCTTTTCAGCAATTTGAGCAGCGTCTCATAAAGAGAAAAGGATAAGAAAGGGGATGGGATTCTGAATTTATTGTGTTTTGCGAGATTGTAAGTTCATGTGATGAACTATGAATTGTGTCTGTGCAAGAATGAGAAGGAATTTCACTAAACGGAAAAGATAAATACAACAAGCAATGCTGTAACTAATGTACCGAAGCGGAGACTGTATTGTCTATTTTCTGCAGAGTAGGTATATTTCTCTGTACAAACAGGAACATGGAGCATATGTTAGTGTTATTCAATTGGATATATTGACTGCGTCATTTACATTTTATCTGAATATTTTAGTGAACGTATCATGTGCTTTGTTGAAAAAATGTCATCTTCTTTAGATGCAGTATCATGTTCATTTAGGCTTCTGGTAAAAGAGGATGAAAGGTTATACTAACATTCTGCACTTACTGGTTGTTTCCAGCAAAGTATACGAATGGCTCGTTCCGCTCTGGATGAGATGTCAGCAACAGGTGCTTTTGAGAGAACTGCTTCAACCTTCCGTAATATAGTCTCAAGGGAACCCGGCTCAGTTTTTCCAGTCGAATCTGGGAGGTACCACCTCTACATATCATATGCTTGCCCATGGGCATCAAGGTGCCTGGCTTACTTGAAGATTAAAGGCCTTGATCAAGCCATTGATTTCACAGTAAGAAGTTGAATGAACTACTTGTATCTTGGACTCAAGTTTGGACTCCTAACAATCTGTTTCCGTTGTGTTGGCTTGCAGTCTGTTAAACCTGTTTGGGAGAGGACGAAGGACAGCGATGAGCACACGGGATGGGTTTTTGCTTCATCAAGCACCGAGGAAGCAGGAGCTGATCTTGATCCTCTTAATGGAGCCAAAAGCATACGGGAGCTGTATGAGCTTGCAAGTACAAACTATTCTGGGAAATACACTGTTCCGGTATTGTTTATCAATAAATAGAATCTCTAATAACATTTATTTGCTTGGTCTGTTCATATTTTTATTGATTGATGGTCTGGTTTTTGTTATAGGTTCTTTGGGATAAGAAACTGAAGACAATCGTGAACAACGAGAGTGCAGAAATAATACGCATGTTTAATAGTGAATTTAATGATATAGCTGAGAATGCAGCTTTGGACCTTTATCCTCCTCATTTGCAATCCCTAATCAATGA</genome_strand>
        <mrna_strand>GCACTTTTGTATTTCAACAGCCTTCTTTCAAG...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CAAAGTATACGAATGGCTCGTTCCGCTCTGGATGAGATGTCAGCAACAGGTGCTTTTGAGAGAACTGCTTCAACCTTCCGTAATATAGTCTCAAGGGAACCCGGCTCAGTTTTTCCAGTCGAATCTGGGAGGTACCACCTCTACATATCATATGCTTGCCCATGGGCATCAAGGTGCCTGGCTTACTTGAAGATTAAAGGCCTTGATCAAGCCATTGATTTCACA.................................................................................TCTGTTAAACCTGTTTGGGAGAGGACGAAGGACAGCGATGAGCACACGGGATGGGTTTTTGCTTCATCAAGCACCGAGGAAGCAGGAGCTGATCTTGATCCTCTTAATGGAGCCAAAAGCATACGGGAGCTGTATGAGCTTGCAAGTACAAACTATTCTGGGAAATACACTGTTCCG............................................................................................GTTCTTTGGGATAAGAAACTGAAGACAATCGTGAACAACGAGAGTGCAGAAATAATACGCATGTTTAATAGTGAATTTAATGATATAGCTGAGAATGCAACTTTGGACCTTTATCCTCCTCATTTGCAATCCCTAATCAATGA</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="87070" PGL_stop="88874"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="87070" e_stop="87101"/>
            <exon e_start="88157" e_stop="88381"/>
            <exon e_start="88463" e_stop="88639"/>
            <exon e_start="88732" e_stop="88874"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.996" acc_prob="0.816" e_score="0.969"/>
          <exon-intron don_prob="0.966" acc_prob="0.988" e_score="1.000"/>
          <exon-intron don_prob="0.896" acc_prob="1.000" e_score="1.000"/>
          <exon-only e_score="0.993"/>
        </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="0.969">
            <gDNA_exon_boundary e_start="87070" e_stop="87101" e_length="32"/>
          </exon>
          <intron i_serial="1" don_prob="0.996" acc_prob="0.816">
            <gDNA_intron_boundary i_start="87102" i_stop="88156" i_length="1055"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="88157" e_stop="88381" e_length="225"/>
          </exon>
          <intron i_serial="2" don_prob="0.966" acc_prob="0.988">
            <gDNA_intron_boundary i_start="88382" i_stop="88462" i_length="81"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="88463" e_stop="88639" e_length="177"/>
          </exon>
          <intron i_serial="3" don_prob="0.896" acc_prob="1.000">
            <gDNA_intron_boundary i_start="88640" i_stop="88731" i_length="92"/>
          </intron>
          <exon e_serial="4" e_score="0.993">
            <gDNA_exon_boundary e_start="88732" e_stop="88874" e_length="143"/>
          </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="87070" stop="87101"/>
              <exon start="88157" stop="88381"/>
              <exon start="88463" stop="88639"/>
              <exon start="88732" stop="88874"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="T1698" 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>ACACTTTTGTATTTCAACAGCCTTCTTTCAAG : CAAAGTATACGAATGGCTCGTTCCGCTCTGGATGAGATGTCAGCAACAGGTGCTTTTGAGAGAACTGCTTCAACCTTCCGTAATATAGTCTCAAGGGAACCCGGCTCAGTTTTTCCAGTCGAATCTGGGAGGTACCACCTCTACATATCATATGCTTGCCCATGGGCATCAAGGTGCCTGGCTTACTTGAAGATTAAAGGCCTTGATCAAGCCATTGATTTCACA : TCTGTTAAACCTGTTTGGGAGAGGACGAAGGACAGCGATGAGCACACGGGATGGGTTTTTGCTTCATCAAGCACCGAGGAAGCAGGAGCTGATCTTGATCCTCTTAATGGAGCCAAAAGCATACGGGAGCTGTATGAGCTTGCAAGTACAAACTATTCTGGGAAATACACTGTTCCG : GTTCTTTGGGATAAGAAACTGAAGACAATCGTGAACAACGAGAGTGCAGAAATAATACGCATGTTTAATAGTGAATTTAATGATATAGCTGAGAATGCAGCTTTGGACCTTTATCCTCCTCATTTGCAATCCCTAATCAATGA</gDNA_template>
            <first_frame> T  L  L  Y  F  N  S  L  L  S  S :   K  V  Y  E  W  L  V  P  L  W  M  R  C  Q  Q  Q  V  L  L  R  E  L  L  Q  P  S  V  I  *  S  Q  G  N  P  A  Q  F  F  Q  S  N  L  G  G  T  T  S  T  Y  H  M  L  A  H  G  H  Q  G  A  W  L  T  *  R  L  K  A  L  I  K  P  L  I  S  H :   L  L  N  L  F  G  R  G  R  R  T  A  M  S  T  R  D  G  F  L  L  H  Q  A  P  R  K  Q  E  L  I  L  I  L  L  M  E  P  K  A  Y  G  S  C  M  S  L  Q  V  Q  T  I  L  G  N  T  L  F  R :   F  F  G  I  R  N  *  R  Q  S  *  T  T  R  V  Q  K  *  Y  A  C  L  I  V  N  L  M  I  *  L  R  M  Q  L  W  T  F  I  L  L  I  C  N  P  *  S  M  </first_frame>
            <second_frame>  H  F  C  I  S  T  A  F  F  Q   : A  K  Y  T  N  G  S  F  R  S  G  *  D  V  S  N  R  C  F  *  E  N  C  F  N  L  P  *  Y  S  L  K  G  T  R  L  S  F  S  S  R  I  W  E  V  P  P  L  H  I  I  C  L  P  M  G  I  K  V  P  G  L  L  E  D  *  R  P  *  S  S  H  *  F  H   : I  C  *  T  C  L  G  E  D  E  G  Q  R  *  A  H  G  M  G  F  C  F  I  K  H  R  G  S  R  S  *  S  *  S  S  *  W  S  Q  K  H  T  G  A  V  *  A  C  K  Y  K  L  F  W  E  I  H  C  S   : G  S  L  G  *  E  T  E  D  N  R  E  Q  R  E  C  R  N  N  T  H  V  *  *  *  I  *  *  Y  S  *  E  C  S  F  G  P  L  S  S  S  F  A  I  P  N  Q  * </second_frame>
            <third_frame>   T  F  V  F  Q  Q  P  S  F  K  :  Q  S  I  R  M  A  R  S  A  L  D  E  M  S  A  T  G  A  F  E  R  T  A  S  T  F  R  N  I  V  S  R  E  P  G  S  V  F  P  V  E  S  G  R  Y  H  L  Y  I  S  Y  A  C  P  W  A  S  R  C  L  A  Y  L  K  I  K  G  L  D  Q  A  I  D  F  T  :  S  V  K  P  V  W  E  R  T  K  D  S  D  E  H  T  G  W  V  F  A  S  S  S  T  E  E  A  G  A  D  L  D  P  L  N  G  A  K  S  I  R  E  L  Y  E  L  A  S  T  N  Y  S  G  K  Y  T  V  P  :  V  L  W  D  K  K  L  K  T  I  V  N  N  E  S  A  E  I  I  R  M  F  N  S  E  F  N  D  I  A  E  N  A  A  L  D  L  Y  P  P  H  L  Q  S  L  I  N   </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="C02HBa0320M09.4" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="87072" stop="87101"/>
                    <exon start="88157" stop="88381"/>
                    <exon start="88463" stop="88639"/>
                    <exon start="88732" stop="88872"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>573</number_coding_nucleotides>
                  <number_encoded_amino_acids>191</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>TFVFQQPSFKQSIRMARSALDEMSATGAFERTASTFRNIVSREPGSVFPVESGRYHLYISYACPWASRCLAYLKIKGLDQAIDFTSVKPVWERTKDSDEHTGWVFASSSTEEAGADLDPLNGAKSIRELYELASTNYSGKYTVPVLWDKKLKTIVNNESAEIIRMFNSEFNDIAENAALDLYPPHLQSLIN</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 5 chains have been computed
$ 
$ memory statistics:
$ 2280 bytes spliced alignments in total
$ 1 spliced alignments have been stored
$ 2280 bytes was the average size of a spliced alignment
$ 5624 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5624 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 5 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 10:31:29
-->
