<?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 09:38:40"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C02HBa0155E05-W6Lay/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C02HBa0155E05-W6Lay/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-C02HBa0155E05-W6Lay/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="T1616" ref_strand="+" ref_description="T1616">
      <seq>gattcccctttaaatcagttgcaatatgtttaccaaaatgtaaggtgaagtctgttcatattccatcagtttctgaagcttcttctatttcatctactaatttggaagaagaggaggacgacgatcccactgctgaacttgtttatcttgaccctgaaattgatcctgagagcttatctgagtgggaattggatttttgttcaagaccaattcttgatattagagggaaaaaattatgggagcttcttgtttgtgatgattccctctctcttcagtataccaaatattttcctaataatcttatcaatagtatcactttgaaagatgctttactatctatatctaatgacttaggtatcccattacccgataaaatcagattcttcaggtcacaaatgcaaactattattacaagagcttgcaacgaacttgccatcaaacctgttcctagcaaacggtgcttatcacttgtcctttggcttgaagaccgctatgaaactgtttatactcgccatcctggttttcaaaaaggagccaagccacttcttgcacttgacaatccttttccaatggaacttcctgagaatctgtatggagaaaagtgggcttttgtccagttgcccgtttcagctgttcgtaaggaagtatctaacctggagactaggttggtttttggct</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C02HBa0155E05-W6Lay/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C02HBa0155E05.3" temp_strand="+" temp_description="C02HBa0155E05.3  AC215399.2 htgs_phase:3 submitted_to_sgn_as:C02HBa0155E05 sequenced_by:kribb upload_account_name:korea">
        <position start="31241" stop="33419"/>
      </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="31540" g_stop="31927" g_length="388"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="388" r_length="388" r_score="0.997"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="31928" i_stop="31998" i_length="71">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.986" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="31999" g_stop="32068" g_length="70"/>
          <reference_exon_boundary r_type="cDNA" r_start="389" r_stop="458" r_length="70" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="32069" i_stop="32688" i_length="620">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="0.879" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="32689" g_stop="32860" g_length="172"/>
          <reference_exon_boundary r_type="cDNA" r_start="459" r_stop="630" r_length="172" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="32861" i_stop="33071" i_length="211">
            <donor d_prob="0.995" d_score="1.00"/>
            <acceptor a_prob="0.991" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="33072" g_stop="33119" g_length="48"/>
          <reference_exon_boundary r_type="cDNA" r_start="631" r_stop="678" r_length="48" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C02HBa0155E05.3" gen_strand="+" ref_id="T1616" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>678</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C02HBa0155E05.3" gen_strand="+"/>
        <rDNA rDNA_id="T1616" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="31540" e_stop="31927"/>
          <exon e_start="31999" e_stop="32068"/>
          <exon e_start="32689" e_stop="32860"/>
          <exon e_start="33072" e_stop="33119"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TATTCCCCTTTAAATCAGTTGCAATATGTTTACCAAAATGTAAGGTGAAGTCTGTTCATATTCCATCAGTTTCTGAAGCTTCTTCTATTTCATCTACTAATTTGGAAGAAGAGGAGGACGACGATCCCACTGCTGAACTTGTTTATCTTGACCCTGAAATTGATCCTGAGAGCTTATCTGAGTGGGAATTGGATTTTTGTTCAAGACCAATTCTTGATATTAGAGGGAAAAAATTATGGGAGCTTCTTGTTTGTGATGATTCCCTCTCTCTTCAGTATACCAAATATTTTCCTAATAATCTTATCAATAGTATCACTTTGAAAGATGCTTTACTATCTATATCTAATGACTTAGGTATCCCATTACCCGATAAAATCAGATTCTTCAGGTACTCTTAACTTACATCCTCTCAACTGTTTTACATTTTCAATTCTCTCATCAATTGTTTTCCATTTTTAGGTCACAAATGCAAACTATTATTACAAGAGCTTGCAACGAACTTGCCATCAAACCTGTTCCTAGCAAACGGGTATTTTCACCAATTTTATTATCCCTATATATACAACATTTCAATCCAATTTTCTAGCACGGATCTATATTTACCGTTCCCCCGATAATTTTTTGTATATCTATAGAGGAAATTAAAAAGCAGATACTAAATAATCACAAAAAAAGTTAGTTGCTGCTTTGGTTCTGGCGTGTAGATGCTGCTAGTCACGAATTCAAATCTTTCTCTACCTGCAATTTTATGTTAAAAGAAAGTGAGCACCCACGACCCTCAAATGTTGGAGACAAGTTGTGTTTGATTTTTCCATCCCTAAGTTCATCCTACCTATTTTGCTGGTAAAGCACATATAGCATTCATTCAAAATTAGCTCTCCCTTTCTTTCCTGGTAAATTCTCCCCCCAAGTCAAGCTTTAGTTTGATATACAATGCATTGCTTCATTTCCATATTTTTATATGATCTGAAAATGAATAGCTCATTTATGTGTATACACAAGACTTCAGTAATGCCTAAATGATCTTTGATCCATGACATAACAAAAGGTCTTTTCTAATATAAAAATAATAACCAAGATACTGCAATATTTTGCTATTTTATGCACAATTGTTTAAAAACAGATTTCTTGTATGCTGCTATATTTCAGTGCTTATCACTTGTCCTTTGGCTTGAAGACCGCTATGAAACTGTTTATACTCGCCATCCTGGTTTTCAAAAAGGAGCCAAGCCACTTCTTGCACTTGACAATCCTTTTCCAATGGAACTTCCTGAGAATCTGTATGGAGAAAAGTGGGCTTTTGTCCAGTTGCCCGTTTCAGGTACATTTAATTCTAACACTCTGGAACAACTAATCTAGTTTAGCTCTTGATGATTTGTAAGAAGAATAGAATTCCTATTCTGTACTATAACTTGCCATATTTCTCATTTTGAGAAGATAAACTTGGATTAGAACCGATATCAAGTTGGACATGAATTTCTAATATTATTGTACCTTTAAAATTATGGACTTACAATTTATCTTGTTTGTAGCTGTTCGTAAGGAAGTATCTAACCTGGAGACTAGGTTGGTTTTTGGCT</genome_strand>
        <mrna_strand>GATTCCCCTTTAAATCAGTTGCAATATGTTTACCAAAATGTAAGGTGAAGTCTGTTCATATTCCATCAGTTTCTGAAGCTTCTTCTATTTCATCTACTAATTTGGAAGAAGAGGAGGACGACGATCCCACTGCTGAACTTGTTTATCTTGACCCTGAAATTGATCCTGAGAGCTTATCTGAGTGGGAATTGGATTTTTGTTCAAGACCAATTCTTGATATTAGAGGGAAAAAATTATGGGAGCTTCTTGTTTGTGATGATTCCCTCTCTCTTCAGTATACCAAATATTTTCCTAATAATCTTATCAATAGTATCACTTTGAAAGATGCTTTACTATCTATATCTAATGACTTAGGTATCCCATTACCCGATAAAATCAGATTCTTCAG.......................................................................GTCACAAATGCAAACTATTATTACAAGAGCTTGCAACGAACTTGCCATCAAACCTGTTCCTAGCAAACGG............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGCTTATCACTTGTCCTTTGGCTTGAAGACCGCTATGAAACTGTTTATACTCGCCATCCTGGTTTTCAAAAAGGAGCCAAGCCACTTCTTGCACTTGACAATCCTTTTCCAATGGAACTTCCTGAGAATCTGTATGGAGAAAAGTGGGCTTTTGTCCAGTTGCCCGTTTCAG...................................................................................................................................................................................................................CTGTTCGTAAGGAAGTATCTAACCTGGAGACTAGGTTGGTTTTTGGCT</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="31540" PGL_stop="33119"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="31540" e_stop="31927"/>
            <exon e_start="31999" e_stop="32068"/>
            <exon e_start="32689" e_stop="32860"/>
            <exon e_start="33072" e_stop="33119"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.999" acc_prob="0.986" e_score="0.997"/>
          <exon-intron don_prob="0.998" acc_prob="0.879" e_score="1.000"/>
          <exon-intron don_prob="0.995" acc_prob="0.991" e_score="1.000"/>
          <exon-only e_score="1.000"/>
        </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="0.997">
            <gDNA_exon_boundary e_start="31540" e_stop="31927" e_length="388"/>
          </exon>
          <intron i_serial="1" don_prob="0.999" acc_prob="0.986">
            <gDNA_intron_boundary i_start="31928" i_stop="31998" i_length="71"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="31999" e_stop="32068" e_length="70"/>
          </exon>
          <intron i_serial="2" don_prob="0.998" acc_prob="0.879">
            <gDNA_intron_boundary i_start="32069" i_stop="32688" i_length="620"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="32689" e_stop="32860" e_length="172"/>
          </exon>
          <intron i_serial="3" don_prob="0.995" acc_prob="0.991">
            <gDNA_intron_boundary i_start="32861" i_stop="33071" i_length="211"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="33072" e_stop="33119" e_length="48"/>
          </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="31540" stop="31927"/>
              <exon start="31999" stop="32068"/>
              <exon start="32689" stop="32860"/>
              <exon start="33072" stop="33119"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="T1616" 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>TATTCCCCTTTAAATCAGTTGCAATATGTTTACCAAAATGTAAGGTGAAGTCTGTTCATATTCCATCAGTTTCTGAAGCTTCTTCTATTTCATCTACTAATTTGGAAGAAGAGGAGGACGACGATCCCACTGCTGAACTTGTTTATCTTGACCCTGAAATTGATCCTGAGAGCTTATCTGAGTGGGAATTGGATTTTTGTTCAAGACCAATTCTTGATATTAGAGGGAAAAAATTATGGGAGCTTCTTGTTTGTGATGATTCCCTCTCTCTTCAGTATACCAAATATTTTCCTAATAATCTTATCAATAGTATCACTTTGAAAGATGCTTTACTATCTATATCTAATGACTTAGGTATCCCATTACCCGATAAAATCAGATTCTTCAG : GTCACAAATGCAAACTATTATTACAAGAGCTTGCAACGAACTTGCCATCAAACCTGTTCCTAGCAAACGG : TGCTTATCACTTGTCCTTTGGCTTGAAGACCGCTATGAAACTGTTTATACTCGCCATCCTGGTTTTCAAAAAGGAGCCAAGCCACTTCTTGCACTTGACAATCCTTTTCCAATGGAACTTCCTGAGAATCTGTATGGAGAAAAGTGGGCTTTTGTCCAGTTGCCCGTTTCAG : CTGTTCGTAAGGAAGTATCTAACCTGGAGACTAGGTTGGTTTTTGGCT</gDNA_template>
            <first_frame> Y  S  P  L  N  Q  L  Q  Y  V  Y  Q  N  V  R  *  S  L  F  I  F  H  Q  F  L  K  L  L  L  F  H  L  L  I  W  K  K  R  R  T  T  I  P  L  L  N  L  F  I  L  T  L  K  L  I  L  R  A  Y  L  S  G  N  W  I  F  V  Q  D  Q  F  L  I  L  E  G  K  N  Y  G  S  F  L  F  V  M  I  P  S  L  F  S  I  P  N  I  F  L  I  I  L  S  I  V  S  L  *  K  M  L  Y  Y  L  Y  L  M  T  *  V  S  H  Y  P  I  K  S  D  S  S   : G  H  K  C  K  L  L  L  Q  E  L  A  T  N  L  P  S  N  L  F  L  A  N  G :   A  Y  H  L  S  F  G  L  K  T  A  M  K  L  F  I  L  A  I  L  V  F  K  K  E  P  S  H  F  L  H  L  T  I  L  F  Q  W  N  F  L  R  I  C  M  E  K  S  G  L  L  S  S  C  P  F  Q  :  L  F  V  R  K  Y  L  T  W  R  L  G  W  F  L  A </first_frame>
            <second_frame>  I  P  L  *  I  S  C  N  M  F  T  K  M  *  G  E  V  C  S  Y  S  I  S  F  *  S  F  F  Y  F  I  Y  *  F  G  R  R  G  G  R  R  S  H  C  *  T  C  L  S  *  P  *  N  *  S  *  E  L  I  *  V  G  I  G  F  L  F  K  T  N  S  *  Y  *  R  E  K  I  M  G  A  S  C  L  *  *  F  P  L  S  S  V  Y  Q  I  F  S  *  *  S  Y  Q  *  Y  H  F  E  R  C  F  T  I  Y  I  *  *  L  R  Y  P  I  T  R  *  N  Q  I  L  Q  :  V  T  N  A  N  Y  Y  Y  K  S  L  Q  R  T  C  H  Q  T  C  S  *  Q  T   : V  L  I  T  C  P  L  A  *  R  P  L  *  N  C  L  Y  S  P  S  W  F  S  K  R  S  Q  A  T  S  C  T  *  Q  S  F  S  N  G  T  S  *  E  S  V  W  R  K  V  G  F  C  P  V  A  R  F  S :   C  S  *  G  S  I  *  P  G  D  *  V  G  F  W   </second_frame>
            <third_frame>   F  P  F  K  S  V  A  I  C  L  P  K  C  K  V  K  S  V  H  I  P  S  V  S  E  A  S  S  I  S  S  T  N  L  E  E  E  E  D  D  D  P  T  A  E  L  V  Y  L  D  P  E  I  D  P  E  S  L  S  E  W  E  L  D  F  C  S  R  P  I  L  D  I  R  G  K  K  L  W  E  L  L  V  C  D  D  S  L  S  L  Q  Y  T  K  Y  F  P  N  N  L  I  N  S  I  T  L  K  D  A  L  L  S  I  S  N  D  L  G  I  P  L  P  D  K  I  R  F  F  R :   S  Q  M  Q  T  I  I  T  R  A  C  N  E  L  A  I  K  P  V  P  S  K  R  :  C  L  S  L  V  L  W  L  E  D  R  Y  E  T  V  Y  T  R  H  P  G  F  Q  K  G  A  K  P  L  L  A  L  D  N  P  F  P  M  E  L  P  E  N  L  Y  G  E  K  W  A  F  V  Q  L  P  V  S   : A  V  R  K  E  V  S  N  L  E  T  R  L  V  F  G  </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="C02HBa0155E05.3" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="31542" stop="31927"/>
                    <exon start="31999" stop="32068"/>
                    <exon start="32689" stop="32860"/>
                    <exon start="33072" stop="33118"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>675</number_coding_nucleotides>
                  <number_encoded_amino_acids>225</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>FPFKSVAICLPKCKVKSVHIPSVSEASSISSTNLEEEEDDDPTAELVYLDPEIDPESLSEWELDFCSRPILDIRGKKLWELLVCDDSLSLQYTKYFPNNLINSITLKDALLSISNDLGIPLPDKIRFFRSQMQTIITRACNELAIKPVPSKRCLSLVLWLEDRYETVYTRHPGFQKGAKPLLALDNPFPMELPENLYGEKWAFVQLPVSAVRKEVSNLETRLVFG</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 236 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
$ 236 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 09:38:46
-->
