<?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 09:42:19"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C02HBa0167J21-kGm3T/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C02HBa0167J21-kGm3T/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-C02HBa0167J21-kGm3T/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="T0562" ref_strand="+" ref_description="T0562">
      <seq>agacaaaacccaatctttatccctgccacttcactctttggagcagccacattcctgagctaaaagaaaaaacatgtcttgttcaaatttgacaatgttggtgtcctcaaaaccatctctttctgaatcctctgccctttctttccgctctgctgtcagctcttttcagcttcctaaccacaacctatcaggcccttcaaacccctcaagatcatcatcagttatccctgtccgatgtggtctccgtgatctgcgtgatcgaattgactctgtcaagaacacacacaagattactgaggctatgaagcttgtggctgctgctaaagtcagaagagcacaaaaagctgttgtgggtgcgaggcctttctctgagactttggttgaggtactttacaacatcaatgagcagctccagacagatgacattgatgttccactcaccaaagtaagacctgtcaagaaagtggcgttggtggttgtcaccggtgaccggagtctttgtggtgggtttaacaactatatcatcaaaaaagctgaagccaggattagaaatttgaaagctct</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C02HBa0167J21-kGm3T/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C02HBa0167J21.2" temp_strand="+" temp_description="C02HBa0167J21.2  AC215407.2 htgs_phase:3 submitted_to_sgn_as:C02HBa0167J21 sequenced_by:kribb upload_account_name:korea">
        <position start="6575" stop="7736"/>
      </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="6873" g_stop="7436" g_length="564"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="564" r_length="564" r_score="0.984"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C02HBa0167J21.2" gen_strand="+" ref_id="T0562" ref_strand="+">
        <total_alignment_score>0.984</total_alignment_score>
        <cumulative_length_of_scored_exons>564</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C02HBa0167J21.2" gen_strand="+"/>
        <rDNA rDNA_id="T0562" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="6873" e_stop="7436"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAACAAAACCCAATCTTTATCCCTCCCACTTCACTCTTTGGAGCAGCCACATTCCTGAGCTAAAAGAAAAAACATGTCTTGTTCAAATTTGACAATGTTGGTGTCCTCAAAACCATCTCTTTCTGAATCCTCTGCCCTTTCTTTCCGCTCTGCTGTCAGCTCTTTTCAGCTTCCTAACCACAACCTATCAGGCCCTTCAAACCCCTCAAGATCATCATCAGTTATCCCTGTCCGATGTGGTCTCCGTGATCTGCGTGATCGAATTGACTCTGTCAAGAACACACAGAAGATTACTGAGGCTATGAAGCTTGTGGCTGCTGCTAAAGTCAGAAGAGCACAAGAAGCTGTTGTGGGTGCGAGGCCTTTCTCTGAGACTTTGGTTGAGGTACTTTACAACATCAATGAGCAGCTCCAGACAGATGACATTGATGTACCACTCACCAAAGTAAGACCTGTCAAGAAAGTGGCGTTGGTGGTTGTCACCGGTGACCGGGGTCTTTGTGGTGGTTTTAACAACTATATCATCAAAAAAGCTGAGGCCAGGATTAGAGATTTGAAAGCTCT</genome_strand>
        <mrna_strand>AGACAAAACCCAATCTTTATCCCTGCCACTTCACTCTTTGGAGCAGCCACATTCCTGAGCTAAAAGAAAAAACATGTCTTGTTCAAATTTGACAATGTTGGTGTCCTCAAAACCATCTCTTTCTGAATCCTCTGCCCTTTCTTTCCGCTCTGCTGTCAGCTCTTTTCAGCTTCCTAACCACAACCTATCAGGCCCTTCAAACCCCTCAAGATCATCATCAGTTATCCCTGTCCGATGTGGTCTCCGTGATCTGCGTGATCGAATTGACTCTGTCAAGAACACACACAAGATTACTGAGGCTATGAAGCTTGTGGCTGCTGCTAAAGTCAGAAGAGCACAAAAAGCTGTTGTGGGTGCGAGGCCTTTCTCTGAGACTTTGGTTGAGGTACTTTACAACATCAATGAGCAGCTCCAGACAGATGACATTGATGTTCCACTCACCAAAGTAAGACCTGTCAAGAAAGTGGCGTTGGTGGTTGTCACCGGTGACCGGAGTCTTTGTGGTGGGTTTAACAACTATATCATCAAAAAAGCTGAAGCCAGGATTAGAAATTTGAAAGCTCT</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C02HBa0167J21-kGm3T/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="cLEX-4-I9" ref_strand="+" ref_description="cLEX-4-I9">
      <seq>gactgatctcactctctctcaatctgaacatggcggaagcaagtgcaccagctgtaccaagtactgagttgttggagtggccaaagaaagataagcgcagaatgttgcatgctgtatatcgtgtcggtgaccttgaacgtaccatcaagttttacacagaatgttttgggatgaaattgttgaggcagagagatattccagaggagaagtattcgaatgcttttcttggttttggccctgaagagtctcactttgtggttgagttgacatataattatggagttgataagtatgacatcggaaccggctttgggcattttgctattgccacaccagatgtttacaaactggttgaggagataaaggccaagggtggaactgtcacaagggagcctggtcctgtcaagggtggatctagtgttattgcttttgttcaaagatcctgatggctacctatttgaaatcatccagagagagtctactcctgaaccactttgccaagtgatgcttcgtgtgggggatcttgaacgtgcgatcaaattctacgaaaaggcacttggga</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C02HBa0167J21-kGm3T/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C02HBa0167J21.2" temp_strand="-" temp_description="C02HBa0167J21.2  AC215407.2 htgs_phase:3 submitted_to_sgn_as:C02HBa0167J21 sequenced_by:kribb upload_account_name:korea">
        <position start="79424" stop="76128"/>
      </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="79124" g_stop="79099" g_length="26"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="26" r_length="26" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="79098" i_stop="78861" i_length="238">
            <donor d_prob="1.000" d_score="0.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="78860" g_stop="78739" g_length="122"/>
          <reference_exon_boundary r_type="cDNA" r_start="27" r_stop="148" r_length="122" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="78738" i_stop="78663" i_length="76">
            <donor d_prob="0.804" d_score="1.00"/>
            <acceptor a_prob="0.840" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="78662" g_stop="78538" g_length="125"/>
          <reference_exon_boundary r_type="cDNA" r_start="149" r_stop="273" r_length="125" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="78537" i_stop="76783" i_length="1755">
            <donor d_prob="0.967" d_score="1.00"/>
            <acceptor a_prob="0.916" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="76782" g_stop="76718" g_length="65"/>
          <reference_exon_boundary r_type="cDNA" r_start="274" r_stop="338" r_length="65" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="76717" i_stop="76642" i_length="76">
            <donor d_prob="0.996" d_score="1.00"/>
            <acceptor a_prob="0.934" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="76641" g_stop="76429" g_length="213"/>
          <reference_exon_boundary r_type="cDNA" r_start="339" r_stop="552" r_length="214" r_score="0.991"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C02HBa0167J21.2" gen_strand="-" ref_id="cLEX-4-I9" ref_strand="+">
        <total_alignment_score>0.996</total_alignment_score>
        <cumulative_length_of_scored_exons>551</cumulative_length_of_scored_exons>
        <coverage percentage="0.980" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C02HBa0167J21.2" gen_strand="-"/>
        <rDNA rDNA_id="cLEX-4-I9" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="79124" e_stop="79099"/>
          <exon e_start="78860" e_stop="78739"/>
          <exon e_start="78662" e_stop="78538"/>
          <exon e_start="76782" e_stop="76718"/>
          <exon e_start="76641" e_stop="76429"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GACTGATCTCACTCTCTCTCAATCTGGTAACACTTTCCTCTCTCTACATATTTTTTTTCTTTAATTTAGGGTTTTACTCTGTTCTTCAATTCTTGATGGCATTGTAAAGAGTTTCTAGTAAATGCTTTGAGTAATTTTTCATCTTGGAAGATTTGTAGGGATTTTGTGATAAAAATTAGTGATACTTCTGTATGATTTGTGTTCTTTGTTGTTTGTTTTGAGATTTCTTTCTTTCTTAGAATCTACAATTTTTATTTGTAGTAGAACATGGCGGAAGCAAGTGCACCAGCTGTACCAAGTACTGAGTTGTTGGAGTGGCCAAAGAAAGATAAGCGCAGAATGTTGCATGCTGTATATCGTGTCGGTGACCTTGAACGTACCATCAAGTAGGTGGTTAGATGTTACAAGTGTTGATCTTGTTTTCTTGGTTAGATAGTAATAGTATCTTCTTATTGTTGTTAGGTTTTACACAGAATGTTTTGGGATGAAATTGTTGAGGCAGAGAGATATTCCAGAGGAGAAGTATTCGAATGCTTTTCTTGGTTTTGGCCCTGAAGAGTCTCACTTTGTGGTTGAGTTGACATATAGTAAGTTTAAAGCTTTTATATGTCTGTTACAACTTACACATTTTGATTCTCAATTCTAGAAAGCTCCCTTATCAATTCCATGAAAGAAAAGGATTTTGGTCATCTCTCTATGGAGTTCATGCCGTGTGATAAGCCTCTAAAGAAGGTGCGAGCGTTGAGATTTAGCCTATTGTCTTAGAACTCCTTTGCCTTAAAATTACATGGATTTGTTAAGAACAGGTTCAAAGTCGCGATCAATTCCTTTTTCAAATCCTGCTGCAGCTGCACGAGCCCTTCCTGCGTGCCACAAATGACCTACAAAGAAGAAGAATCCTAGAACAAAATGAGAGGTAGCTAACCAACTTCTAGGAGAGACATAATTGACTGCATTGATCTCGGTAGCTACACCACCCACGGAATTTAAAGAACCTAAAGGAGCATGAGTCATATATTCCGCGGAACGCCGTTCCTGCCAAGGTTGTATGTCTTTTTTCAACCTACTCAAGTCTAACCCATTTGGACCCCTTAGAGGCTCTAACCATGGAGCACGCAGATCCCAAAAACGCATAGTTTCTCCTCCAAAAATGACTTCTCTGGTTGGGGAACGCATTAGATATTTACCTAAACCAGTAGGTCCTTGAGCGGATCCGACGTTAGTCCCAAGACGTTGGTCTCTAACTAGAAAAGTAAATGCTTGAGCTTGAGAAGCTTCTGGTCCAGCTCTGCGAAGGCCTTTCGGAGATTGACCTTTCTTTCTCTTCTTTCGGGTCTGATCGGTCGAGCTCTCGTAATCGATCGCTCATATGTCCATTTCGTTCTGGCTAGCGAAGTCGGGATATTCTACGTTTAATGATAAATAGTAAAGTTATGAACTCAAGCTAGCAAAAAACAAGACTGAGGTCGATAGGGGCATTACTGGTAATTGCTAAGGTGCTTTCTGAAGTCTTAACCATTGGCTAGCGCTCATCTCCAGCTCTGTTTCCAACCTGTCATTTCATATATCATTCCCGTATGCAATACCTCTTATTTAATCTTGCTATACGTCCAAGCCTTCTCCCATCGGTAGTTGGAAGCAGAACTGAAACTGGATATAACTGAAGGAAAGGCTATATAGGTACGATAGGAGGGTACGGTTAAGCAGGTAAGCGAAGGCGCTCTCTCTCGCTCTGTGGTCTTGTGTAAAGCCTTTCCGCCTATCTATTCTTTTTTTTCTCTTTATTCAAAGTAAGCAGATCGAAAGCACGAAAAGGAATGTCTCAGCGTGCCCTTACTCTAATTCGAAATACGTCTCTTTGACCTCATTGAATGATTGTTTTCCCTTGTCTCTGCGAAAGAACTCCCTTGTTTCATCGGTGCAGCTGCTATTTGGTGAGAAAACTCCTTGCTTGTCGATAAGAGGAAATAAGCAGCTGTAGTAAGCGAGTAAGGAAGCGAAACTAGTCTTAGATGTCGCTAATCCGCTGCTTCTTCCTTCCTCTTAGCTCTTAGAAGTTGTTCTTGGTTTGTTCTCTGGGTTCTCTTTGGGTGGTGGAGAGAGAGTTGGAGAATGAAGCATGCATAACATTGTTAGGATACTCAGTATATGGTCCAATAGAGAGCCACGTGGAGAAGGGGATGCCAGGAGGTGACTTGATTTTACTGAACCAAAGGCACATCATTTAGTTAAGGAGCATAGATTTTAATAAATAGTTTACCTATTATCCAACACCAATAAATGAATTATATACTGTACCTTGAAGCGTAAATTTCAAATCTTACATAGATACCATTGTACAGATTATGGAGTTGATAAGTATGACATCGGAACCGGCTTTGGGCATTTTGCTATTGCCACACCAGATGTAAGTAAATTTTGTAAGCAAAATTATGCGCACCATTTGTTTCTTCTAAATGAGCTTTGTTCCTCCTTTTCTCAAGGTTTACAAACTGGTTGAGGAGATAAAGGCCAAGGGTGGAACTGTCACAAGGGAGCCTGGTCCTGTCAAGGGTGGATCTAGTGTTATTGCTTTTG-TCAAAGATCCTGATGGCTACCTATTTGAAATCATCCAGAGAGAGTCTACTCCTGAACCACTTTGCCAAGTGATGCTTCGTGTGGGGGATCTTGAACGTGCGATCAAATTCTACGAAAAG</genome_strand>
        <mrna_strand>GACTGATCTCACTCTCTCTCAATCTG..............................................................................................................................................................................................................................................AACATGGCGGAAGCAAGTGCACCAGCTGTACCAAGTACTGAGTTGTTGGAGTGGCCAAAGAAAGATAAGCGCAGAATGTTGCATGCTGTATATCGTGTCGGTGACCTTGAACGTACCATCAA............................................................................GTTTTACACAGAATGTTTTGGGATGAAATTGTTGAGGCAGAGAGATATTCCAGAGGAGAAGTATTCGAATGCTTTTCTTGGTTTTGGCCCTGAAGAGTCTCACTTTGTGGTTGAGTTGACATATA...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATTATGGAGTTGATAAGTATGACATCGGAACCGGCTTTGGGCATTTTGCTATTGCCACACCAGAT............................................................................GTTTACAAACTGGTTGAGGAGATAAAGGCCAAGGGTGGAACTGTCACAAGGGAGCCTGGTCCTGTCAAGGGTGGATCTAGTGTTATTGCTTTTGTTCAAAGATCCTGATGGCTACCTATTTGAAATCATCCAGAGAGAGTCTACTCCTGAACCACTTTGCCAAGTGATGCTTCGTGTGGGGGATCTTGAACGTGCGATCAAATTCTACGAAAAG</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>2</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="6873" PGL_stop="7436"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="6873" e_stop="7436"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.984"/>
        </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="0.984">
            <gDNA_exon_boundary e_start="6873" e_stop="7436" e_length="564"/>
          </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="6873" stop="7436"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="T0562" 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>AAACAAAACCCAATCTTTATCCCTCCCACTTCACTCTTTGGAGCAGCCACATTCCTGAGCTAAAAGAAAAAACATGTCTTGTTCAAATTTGACAATGTTGGTGTCCTCAAAACCATCTCTTTCTGAATCCTCTGCCCTTTCTTTCCGCTCTGCTGTCAGCTCTTTTCAGCTTCCTAACCACAACCTATCAGGCCCTTCAAACCCCTCAAGATCATCATCAGTTATCCCTGTCCGATGTGGTCTCCGTGATCTGCGTGATCGAATTGACTCTGTCAAGAACACACAGAAGATTACTGAGGCTATGAAGCTTGTGGCTGCTGCTAAAGTCAGAAGAGCACAAGAAGCTGTTGTGGGTGCGAGGCCTTTCTCTGAGACTTTGGTTGAGGTACTTTACAACATCAATGAGCAGCTCCAGACAGATGACATTGATGTACCACTCACCAAAGTAAGACCTGTCAAGAAAGTGGCGTTGGTGGTTGTCACCGGTGACCGGGGTCTTTGTGGTGGTTTTAACAACTATATCATCAAAAAAGCTGAGGCCAGGATTAGAGATTTGAAAGCTCT</gDNA_template>
            <first_frame> K  Q  N  P  I  F  I  P  P  T  S  L  F  G  A  A  T  F  L  S  *  K  K  K  H  V  L  F  K  F  D  N  V  G  V  L  K  T  I  S  F  *  I  L  C  P  F  F  P  L  C  C  Q  L  F  S  A  S  *  P  Q  P  I  R  P  F  K  P  L  K  I  I  I  S  Y  P  C  P  M  W  S  P  *  S  A  *  S  N  *  L  C  Q  E  H  T  E  D  Y  *  G  Y  E  A  C  G  C  C  *  S  Q  K  S  T  R  S  C  C  G  C  E  A  F  L  *  D  F  G  *  G  T  L  Q  H  Q  *  A  A  P  D  R  *  H  *  C  T  T  H  Q  S  K  T  C  Q  E  S  G  V  G  G  C  H  R  *  P  G  S  L  W  W  F  *  Q  L  Y  H  Q  K  S  *  G  Q  D  *  R  F  E  S  S </first_frame>
            <second_frame>  N  K  T  Q  S  L  S  L  P  L  H  S  L  E  Q  P  H  S  *  A  K  R  K  N  M  S  C  S  N  L  T  M  L  V  S  S  K  P  S  L  S  E  S  S  A  L  S  F  R  S  A  V  S  S  F  Q  L  P  N  H  N  L  S  G  P  S  N  P  S  R  S  S  S  V  I  P  V  R  C  G  L  R  D  L  R  D  R  I  D  S  V  K  N  T  Q  K  I  T  E  A  M  K  L  V  A  A  A  K  V  R  R  A  Q  E  A  V  V  G  A  R  P  F  S  E  T  L  V  E  V  L  Y  N  I  N  E  Q  L  Q  T  D  D  I  D  V  P  L  T  K  V  R  P  V  K  K  V  A  L  V  V  V  T  G  D  R  G  L  C  G  G  F  N  N  Y  I  I  K  K  A  E  A  R  I  R  D  L  K  A   </second_frame>
            <third_frame>   T  K  P  N  L  Y  P  S  H  F  T  L  W  S  S  H  I  P  E  L  K  E  K  T  C  L  V  Q  I  *  Q  C  W  C  P  Q  N  H  L  F  L  N  P  L  P  F  L  S  A  L  L  S  A  L  F  S  F  L  T  T  T  Y  Q  A  L  Q  T  P  Q  D  H  H  Q  L  S  L  S  D  V  V  S  V  I  C  V  I  E  L  T  L  S  R  T  H  R  R  L  L  R  L  *  S  L  W  L  L  L  K  S  E  E  H  K  K  L  L  W  V  R  G  L  S  L  R  L  W  L  R  Y  F  T  T  S  M  S  S  S  R  Q  M  T  L  M  Y  H  S  P  K  *  D  L  S  R  K  W  R  W  W  L  S  P  V  T  G  V  F  V  V  V  L  T  T  I  S  S  K  K  L  R  P  G  L  E  I  *  K  L  </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="C02HBa0167J21.2" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="6931" stop="7434"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>504</number_coding_nucleotides>
                  <number_encoded_amino_acids>168</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>AKRKNMSCSNLTMLVSSKPSLSESSALSFRSAVSSFQLPNHNLSGPSNPSRSSSVIPVRCGLRDLRDRIDSVKNTQKITEAMKLVAAAKVRRAQEAVVGARPFSETLVEVLYNINEQLQTDDIDVPLTKVRPVKKVALVVVTGDRGLCGGFNNYIIKKAEARIRDLKA</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="2" PGL_strand="-" PGL_start="79124" PGL_stop="76429"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="79124" e_stop="79099"/>
            <exon e_start="78860" e_stop="78739"/>
            <exon e_start="78662" e_stop="78538"/>
            <exon e_start="76782" e_stop="76718"/>
            <exon e_start="76641" e_stop="76429"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="1.000" acc_prob="0.999" e_score="1.000"/>
          <exon-intron don_prob="0.804" acc_prob="0.840" e_score="1.000"/>
          <exon-intron don_prob="0.967" acc_prob="0.916" e_score="1.000"/>
          <exon-intron don_prob="0.996" acc_prob="0.934" e_score="1.000"/>
          <exon-only e_score="0.991"/>
        </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="1.000">
            <gDNA_exon_boundary e_start="79124" e_stop="79099" e_length="26"/>
          </exon>
          <intron i_serial="1" don_prob="1.000" acc_prob="0.999">
            <gDNA_intron_boundary i_start="79098" i_stop="78861" i_length="238"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="78860" e_stop="78739" e_length="122"/>
          </exon>
          <intron i_serial="2" don_prob="0.804" acc_prob="0.840">
            <gDNA_intron_boundary i_start="78738" i_stop="78663" i_length="76"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="78662" e_stop="78538" e_length="125"/>
          </exon>
          <intron i_serial="3" don_prob="0.967" acc_prob="0.916">
            <gDNA_intron_boundary i_start="78537" i_stop="76783" i_length="1755"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="76782" e_stop="76718" e_length="65"/>
          </exon>
          <intron i_serial="4" don_prob="0.996" acc_prob="0.934">
            <gDNA_intron_boundary i_start="76717" i_stop="76642" i_length="76"/>
          </intron>
          <exon e_serial="5" e_score="0.991">
            <gDNA_exon_boundary e_start="76641" e_stop="76429" e_length="213"/>
          </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="79124" stop="79099"/>
              <exon start="78860" stop="78739"/>
              <exon start="78662" stop="78538"/>
              <exon start="76782" stop="76718"/>
              <exon start="76641" stop="76429"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="cLEX-4-I9" 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="2" AGS_serial="1" gDNA_strand="-"/>
          <translation>
            <gDNA_template>GACTGATCTCACTCTCTCTCAATCTG : AACATGGCGGAAGCAAGTGCACCAGCTGTACCAAGTACTGAGTTGTTGGAGTGGCCAAAGAAAGATAAGCGCAGAATGTTGCATGCTGTATATCGTGTCGGTGACCTTGAACGTACCATCAA : GTTTTACACAGAATGTTTTGGGATGAAATTGTTGAGGCAGAGAGATATTCCAGAGGAGAAGTATTCGAATGCTTTTCTTGGTTTTGGCCCTGAAGAGTCTCACTTTGTGGTTGAGTTGACATATA : ATTATGGAGTTGATAAGTATGACATCGGAACCGGCTTTGGGCATTTTGCTATTGCCACACCAGAT : GTTTACAAACTGGTTGAGGAGATAAAGGCCAAGGGTGGAACTGTCACAAGGGAGCCTGGTCCTGTCAAGGGTGGATCTAGTGTTATTGCTTTTGTCAAAGATCCTGATGGCTACCTATTTGAAATCATCCAGAGAGAGTCTACTCCTGAACCACTTTGCCAAGTGATGCTTCGTGTGGGGGATCTTGAACGTGCGATCAAATTCTACGAAAAG</gDNA_template>
            <first_frame> D  *  S  H  S  L  S  I  * :   T  W  R  K  Q  V  H  Q  L  Y  Q  V  L  S  C  W  S  G  Q  R  K  I  S  A  E  C  C  M  L  Y  I  V  S  V  T  L  N  V  P  S   : S  F  T  Q  N  V  L  G  *  N  C  *  G  R  E  I  F  Q  R  R  S  I  R  M  L  F  L  V  L  A  L  K  S  L  T  L  W  L  S  *  H  I  :  I  M  E  L  I  S  M  T  S  E  P  A  L  G  I  L  L  L  P  H  Q  M :   F  T  N  W  L  R  R  *  R  P  R  V  E  L  S  Q  G  S  L  V  L  S  R  V  D  L  V  L  L  L  L  S  K  I  L  M  A  T  Y  L  K  S  S  R  E  S  L  L  L  N  H  F  A  K  *  C  F  V  W  G  I  L  N  V  R  S  N  S  T  K   </first_frame>
            <second_frame>  T  D  L  T  L  S  Q  S   : E  H  G  G  S  K  C  T  S  C  T  K  Y  *  V  V  G  V  A  K  E  R  *  A  Q  N  V  A  C  C  I  S  C  R  *  P  *  T  Y  H  Q  :  V  L  H  R  M  F  W  D  E  I  V  E  A  E  R  Y  S  R  G  E  V  F  E  C  F  S  W  F  W  P  *  R  V  S  L  C  G  *  V  D  I  * :   L  W  S  *  *  V  *  H  R  N  R  L  W  A  F  C  Y  C  H  T  R   : C  L  Q  T  G  *  G  D  K  G  Q  G  W  N  C  H  K  G  A  W  S  C  Q  G  W  I  *  C  Y  C  F  C  Q  R  S  *  W  L  P  I  *  N  H  P  E  R  V  Y  S  *  T  T  L  P  S  D  A  S  C  G  G  S  *  T  C  D  Q  I  L  R  K  </second_frame>
            <third_frame>   L  I  S  L  S  L  N  L  :  N  M  A  E  A  S  A  P  A  V  P  S  T  E  L  L  E  W  P  K  K  D  K  R  R  M  L  H  A  V  Y  R  V  G  D  L  E  R  T  I  K :   F  Y  T  E  C  F  G  M  K  L  L  R  Q  R  D  I  P  E  E  K  Y  S  N  A  F  L  G  F  G  P  E  E  S  H  F  V  V  E  L  T  Y   : N  Y  G  V  D  K  Y  D  I  G  T  G  F  G  H  F  A  I  A  T  P  D  :  V  Y  K  L  V  E  E  I  K  A  K  G  G  T  V  T  R  E  P  G  P  V  K  G  G  S  S  V  I  A  F  V  K  D  P  D  G  Y  L  F  E  I  I  Q  R  E  S  T  P  E  P  L  C  Q  V  M  L  R  V  G  D  L  E  R  A  I  K  F  Y  E  K </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="C02HBa0167J21.2" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="79122" stop="79099"/>
                    <exon start="78860" stop="78739"/>
                    <exon start="78662" stop="78538"/>
                    <exon start="76782" stop="76718"/>
                    <exon start="76641" stop="76429"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>549</number_coding_nucleotides>
                  <number_encoded_amino_acids>183</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LISLSLNLNMAEASAPAVPSTELLEWPKKDKRRMLHAVYRVGDLERTIKFYTECFGMKLLRQRDIPEEKYSNAFLGFGPEESHFVVELTYNYGVDKYDIGTGFGHFAIATPDVYKLVEEIKAKGGTVTREPGPVKGGSSVIAFVKDPDGYLFEIIQRESTPEPLCQVMLRVGDLERAIKFYEK</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 6 chains have been computed
$ 
$ memory statistics:
$ 3808 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 1904 bytes was the average size of a spliced alignment
$ 6832 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3416 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 6 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 09:42:22
-->
