<?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 09:52:18"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C02HBa0177F12-Yr9OK/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C02HBa0177F12-Yr9OK/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-C02HBa0177F12-Yr9OK/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="T1323" ref_strand="+" ref_description="T1323">
      <seq>aaggttcagcaggaaaccagctcttgttcgtcttctctctgttgctgctctcttctccattatacttatcgccattcagtcctctttcttcactggtagccgggctcccgttaatttggatattccgatcttgtcccacttccagtctaaccttcagcaatgcgtcgctaaccgagggctgggattgactgctcatataattgatcattgcagtgtcattctcaagtttccccaaggaactaatagcacttggtataatgagcagttcaagatctttgaaccattggagtacaagtacgacgtttgcgaagcaatacttctgtgggagcagtaccgtaacatgacgacagtgttgacaagagaatatttggattctcggcctgatggatggtttgactatgcagcaaaaaggattgcacagctaggagcagacaaatgttacaatcagactctttgcgaagaacatctcaatctaactttaccagctaagcccccgtttcaccctc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C02HBa0177F12-Yr9OK/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C02HBa0177F12.3" temp_strand="-" temp_description="C02HBa0177F12.3  AC215410.1 htgs_phase:3 submitted_to_sgn_as:C02HBa0177F12 sequenced_by:kribb upload_account_name:korea">
        <position start="33040" stop="31489"/>
      </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="32740" g_stop="32646" g_length="95"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="95" r_length="95" r_score="0.989"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="32645" i_stop="32555" i_length="91">
            <donor d_prob="0.997" d_score="0.98"/>
            <acceptor a_prob="0.907" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="32554" g_stop="32484" g_length="71"/>
          <reference_exon_boundary r_type="cDNA" r_start="96" r_stop="166" r_length="71" r_score="0.986"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="32483" i_stop="32407" i_length="77">
            <donor d_prob="0.884" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="32406" g_stop="32320" g_length="87"/>
          <reference_exon_boundary r_type="cDNA" r_start="167" r_stop="253" r_length="87" r_score="0.977"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="32319" i_stop="32237" i_length="83">
            <donor d_prob="0.845" d_score="0.98"/>
            <acceptor a_prob="0.918" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="32236" g_stop="32159" g_length="78"/>
          <reference_exon_boundary r_type="cDNA" r_start="254" r_stop="331" r_length="78" r_score="0.987"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="32158" i_stop="32076" i_length="83">
            <donor d_prob="0.957" d_score="0.98"/>
            <acceptor a_prob="0.990" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="32075" g_stop="31984" g_length="92"/>
          <reference_exon_boundary r_type="cDNA" r_start="332" r_stop="423" r_length="92" r_score="0.989"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="31983" i_stop="31872" i_length="112">
            <donor d_prob="0.995" d_score="0.98"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="31871" g_stop="31789" g_length="83"/>
          <reference_exon_boundary r_type="cDNA" r_start="424" r_stop="506" r_length="83" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C02HBa0177F12.3" gen_strand="-" ref_id="T1323" ref_strand="+">
        <total_alignment_score>0.988</total_alignment_score>
        <cumulative_length_of_scored_exons>506</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C02HBa0177F12.3" gen_strand="-"/>
        <rDNA rDNA_id="T1323" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="32740" e_stop="32646"/>
          <exon e_start="32554" e_stop="32484"/>
          <exon e_start="32406" e_stop="32320"/>
          <exon e_start="32236" e_stop="32159"/>
          <exon e_start="32075" e_stop="31984"/>
          <exon e_start="31871" e_stop="31789"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAGGTTCAGCAGGAAACCAGCTCTTGTTCGTCTTCTCTCTGTTGCTGCTCTCTTCTCCATTATACTAATCGCCATTCAGTCCTCTTTCTTCACTGGTTGGTACTACATATCTTCTTTTCCTTAACCCTAATTGTTTGAAAATCCTCTTCGCTAATTTACTATTTTGAATGAATTTGATGCATCCAGGTAGTCGGGCTCCCGTTAATTTGGATATTCCGATCTTGTCCCACTTCCAGTCTAACCTTCAGCAATGCGTCGTAATTATTTTCTGGATCTCCTATATTTTGTTGAAAACTGCACATGTTAGTTGTTTATTCGAATTTCTGCTTTACAGGCTAATCGAGGGCTGGGATTGACTGCTCATATAATTGATCATTGCAATGTCATTCTCAAGTTTCCCCAAGGAACTAATAGCACTTGGGTTTGTCTCTCATCCGTCTCCTACCTGTTGGTTACCTTCTACAAAACACTGAAATGCATTTCCCCATTCATTTTATCTTACAGTATAATGAGCAGTTCAAGATCTTTGAACCATTGGAGTACAAGTACGACGTTTGCGAAACAATACTTCTGTGGGAGCAGGTTCCTCATACTTGTTATTCATGTTAATTAATCATGTTTCCACAACTAGTACATTAAAATATATTGGATTATCTGAAATGCAGTACCGTAACATGACGACAGTGTTGACAAGAGAATATTTGGATTCTCGGCCTGATGGATGGTTTGACTATGCAGCAAAAAGGATCGCACAGCTGTAAGTTATTGGCTTCATCCTCCATTCACCTTCTTAATCAATTAATGATAGATTTTATGTGATTTGATCTTCATATTTTGTTTCATTGTTTCCTTACTTTTCCTGTTTGCAGAGGAGCAGACAAATGTTACAATCAGACTCTTTGCGAAGAACATCTCAATCTAACTTTACCAGCTAAGCCCCCGTTTCACCCTC</genome_strand>
        <mrna_strand>AAGGTTCAGCAGGAAACCAGCTCTTGTTCGTCTTCTCTCTGTTGCTGCTCTCTTCTCCATTATACTTATCGCCATTCAGTCCTCTTTCTTCACTG...........................................................................................GTAGCCGGGCTCCCGTTAATTTGGATATTCCGATCTTGTCCCACTTCCAGTCTAACCTTCAGCAATGCGTC.............................................................................GCTAACCGAGGGCTGGGATTGACTGCTCATATAATTGATCATTGCAGTGTCATTCTCAAGTTTCCCCAAGGAACTAATAGCACTTGG...................................................................................TATAATGAGCAGTTCAAGATCTTTGAACCATTGGAGTACAAGTACGACGTTTGCGAAGCAATACTTCTGTGGGAGCAG...................................................................................TACCGTAACATGACGACAGTGTTGACAAGAGAATATTTGGATTCTCGGCCTGATGGATGGTTTGACTATGCAGCAAAAAGGATTGCACAGCT................................................................................................................AGGAGCAGACAAATGTTACAATCAGACTCTTTGCGAAGAACATCTCAATCTAACTTTACCAGCTAAGCCCCCGTTTCACCCTC</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-C02HBa0177F12-Yr9OK/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="C2_At3g26730" ref_strand="+" ref_description="C2_At3g26730">
      <seq>ggctaaaaccttaaaagatcaacccaatcaaccccctttgtctaatctaatatcccaggaggaatttcatgtccatctcgccctcccatagcgacaatcatacagcttcctcttcttctttttcttctccaaaccctaactctaatcatggatccaaatccaaacaacagcagcagcaacccgacaacttctcaggaaacatggctaccactgcatctacttctggtggatcctccaaaaaggtgaacaactccggtagcagtcgagaaagttcacgacatcataacagtgatagaatctcactgcacggacaaagaaaatcagctaggaccaatgatccttccagcggaagagaccagtttggctccaacagtccccaaggagttgttacccgctcagctccaagaagaacccagatggttagtggaaaccacttactcaattttcagtatgatcccatttctcgtccacaatctaggttgcctcctcctaggagatacgtcaagaggaagccttacaacaaagacttgtttcttcaagcaaattacaagtttgttctgttggattcaggcaattacacgcctgactcgatggatccagacaaaatgttacactgggaggatattgtttgtgtgagatattccactccatttcatgtgcaatgccccatatgcttagaggatcctctttgtcctcagataacttcgtgtggtcatatcttctgttttccctgtgttatgcaatattttatgatctccgaagaagatgaccataaggatgatttcaagaagaaatgccctttgtgttttatgatgatatcttcacagg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C02HBa0177F12-Yr9OK/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C02HBa0177F12.3" temp_strand="-" temp_description="C02HBa0177F12.3  AC215410.1 htgs_phase:3 submitted_to_sgn_as:C02HBa0177F12 sequenced_by:kribb upload_account_name:korea">
        <position start="47452" stop="45839"/>
      </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="47152" g_stop="46952" g_length="201"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="195" r_length="195" r_score="0.930"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="46951" i_stop="46851" i_length="101">
            <donor d_prob="0.590" d_score="0.94"/>
            <acceptor a_prob="0.998" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="46850" g_stop="46804" g_length="47"/>
          <reference_exon_boundary r_type="cDNA" r_start="196" r_stop="242" r_length="47" r_score="0.979"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="46803" i_stop="46725" i_length="79">
            <donor d_prob="1.000" d_score="0.98"/>
            <acceptor a_prob="0.995" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="46724" g_stop="46139" g_length="586"/>
          <reference_exon_boundary r_type="cDNA" r_start="243" r_stop="828" r_length="586" r_score="0.981"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C02HBa0177F12.3" gen_strand="-" ref_id="C2_At3g26730" ref_strand="+">
        <total_alignment_score>0.968</total_alignment_score>
        <cumulative_length_of_scored_exons>834</cumulative_length_of_scored_exons>
        <coverage percentage="1.007" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C02HBa0177F12.3" gen_strand="-"/>
        <rDNA rDNA_id="C2_At3g26730" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="47152" e_stop="46952"/>
          <exon e_start="46850" e_stop="46804"/>
          <exon e_start="46724" e_stop="46139"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GGCTAAAACCCGAAAAGATCAACCCAACCAACCCCCTTTGTCTAATCTAATCTCCCAGGAGGAATTTCATGTCCATCTTGCCCTCCCATAGCGACAATCATACAACCTCCTCCTCCTCTTCTTCTTCTTCTCCAAACCCTAACTCTAATCATGGATCCAAATCCAAACAACAGCAGCAGCAGCAACCCGACAACTTCTCAGGTTTCCGTCCCGTATACCCTAATTCAACGATGTCATTTTGTCTCGCCTTATTTATTTTAGTTCCTTTTCTTTCCGTCTCATGCTTTTTTTTTCTTTGTCAGGAAACATGGCTACCGCTGCATCTACTTCTGGTGGATCCTCCAAAAAGGTAAATTTTGTGTTGTAACTTCTCTTCTCTTAATAAACCAATTTACTAATGCAGCTCTGCTCTTCACAATATATTGCAGGTGAACAACTCCGGTAGCAGTCGAGAAAGTTCACGACATCATAACAGTGATATAATCTCACTGCACGGACAAGGAAAACCAGCTAGGACCAATGATCCTTCCAGCGGAAGAGACCAGTTTGGCTTTAACAGTCCCCAAGGAGTTGTTACCCGCTCAGCTTCAAGAAGAACCCAGATGGTTAGTGGAAACCACTTGCTCAATTTTCAGTATGATCCCATTTCTCGTCCACAATCTAGGTTGCCTCCTCCTAGGAGATACGTCAAGAGGAAGCCTTACAACAAAGACTTGTTTCTTCAAGCAAATTACAAGTTTGTTCTGTTGGATTCAGGCAATTACACGCCTGACTCGATGGATCCAGACAAAATGTTACAGTGGGAGGATATTGTTTGTGTGAGATATTCCACTCCATTTCATGTGCAATGCCCCATATGCTTAGAGGATCCTCTTTGTCCTCAGATAACTTCGTGTGGTCATATCTTCTGTTTTCCCTGTGTTATGCAATATTTTATGATCTCCGAAGAAGATGACCATAAAAATAATTTCAAGAAGAAATGCCCTTTGTGTTTTATGATGATATCTTCACAGG</genome_strand>
        <mrna_strand>GGCTAAAACCTTAAAAGATCAACCCAATCAACCCCCTTTGTCTAATCTAATATCCCAGGAGGAATTTCATGTCCATCTCGCCCTCCCATAGCGACAATCATAC-AGCT--TCCTCTTCTTCTTTTTCTTCTCCAAACCCTAACTCTAATCATGGATCCAAATCCAAAC-A-A-CAGCAGCAGCAACCCGACAACTTCTCAG.....................................................................................................GAAACATGGCTACCACTGCATCTACTTCTGGTGGATCCTCCAAAAAG...............................................................................GTGAACAACTCCGGTAGCAGTCGAGAAAGTTCACGACATCATAACAGTGATAGAATCTCACTGCACGGACAAAGAAAATCAGCTAGGACCAATGATCCTTCCAGCGGAAGAGACCAGTTTGGCTCCAACAGTCCCCAAGGAGTTGTTACCCGCTCAGCTCCAAGAAGAACCCAGATGGTTAGTGGAAACCACTTACTCAATTTTCAGTATGATCCCATTTCTCGTCCACAATCTAGGTTGCCTCCTCCTAGGAGATACGTCAAGAGGAAGCCTTACAACAAAGACTTGTTTCTTCAAGCAAATTACAAGTTTGTTCTGTTGGATTCAGGCAATTACACGCCTGACTCGATGGATCCAGACAAAATGTTACACTGGGAGGATATTGTTTGTGTGAGATATTCCACTCCATTTCATGTGCAATGCCCCATATGCTTAGAGGATCCTCTTTGTCCTCAGATAACTTCGTGTGGTCATATCTTCTGTTTTCCCTGTGTTATGCAATATTTTATGATCTCCGAAGAAGATGACCATAAGGATGATTTCAAGAAGAAATGCCCTTTGTGTTTTATGATGATATCTTCACAGG</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-C02HBa0177F12-Yr9OK/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="T1554" ref_strand="+" ref_description="T1554">
      <seq>atggatccaaatccaaacaacagcagcagcagcaacccgacaacttttcaggaaacatggctaccgctgcatctacttctggaggatcctccaaaaaggtgaacaactccggcagcagtcgagaaagttcacgacatcataacagtgatataatctgactgcacggacaaggaaaaccagctaggaccaatgatccttccagcggaagagaccagtttggctttaacagtccccaaggagttgttacccgctcagctccaagaagaacccagatggttagtggaaaccacttgctcaattttcagtatgatcccatttctcgtccacaatctaggttgcctcctcctaggagatacgtcaagaggaagccttacaacaaagactcgtttcttcaagcaaattacaagtttgttctgttggattcaggccattacacgcctgactcgatggatccagacaaaatgttacagtgggaggatattgcttgtgtgagatattgcactccatttcatgtgcaaagccccatat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C02HBa0177F12-Yr9OK/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C02HBa0177F12.3" temp_strand="-" temp_description="C02HBa0177F12.3  AC215410.1 htgs_phase:3 submitted_to_sgn_as:C02HBa0177F12 sequenced_by:kribb upload_account_name:korea">
        <position start="47302" stop="45995"/>
      </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="47002" g_stop="46952" g_length="51"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="51" r_length="51" r_score="0.980"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="46951" i_stop="46851" i_length="101">
            <donor d_prob="0.590" d_score="0.98"/>
            <acceptor a_prob="0.998" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="46850" g_stop="46804" g_length="47"/>
          <reference_exon_boundary r_type="cDNA" r_start="52" r_stop="98" r_length="47" r_score="0.979"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="46803" i_stop="46725" i_length="79">
            <donor d_prob="1.000" d_score="0.98"/>
            <acceptor a_prob="0.995" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="46724" g_stop="46295" g_length="430"/>
          <reference_exon_boundary r_type="cDNA" r_start="99" r_stop="528" r_length="430" r_score="0.981"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C02HBa0177F12.3" gen_strand="-" ref_id="T1554" ref_strand="+">
        <total_alignment_score>0.981</total_alignment_score>
        <cumulative_length_of_scored_exons>528</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C02HBa0177F12.3" gen_strand="-"/>
        <rDNA rDNA_id="T1554" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="47002" e_stop="46952"/>
          <exon e_start="46850" e_stop="46804"/>
          <exon e_start="46724" e_stop="46295"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATGGATCCAAATCCAAACAACAGCAGCAGCAGCAACCCGACAACTTCTCAGGTTTCCGTCCCGTATACCCTAATTCAACGATGTCATTTTGTCTCGCCTTATTTATTTTAGTTCCTTTTCTTTCCGTCTCATGCTTTTTTTTTCTTTGTCAGGAAACATGGCTACCGCTGCATCTACTTCTGGTGGATCCTCCAAAAAGGTAAATTTTGTGTTGTAACTTCTCTTCTCTTAATAAACCAATTTACTAATGCAGCTCTGCTCTTCACAATATATTGCAGGTGAACAACTCCGGTAGCAGTCGAGAAAGTTCACGACATCATAACAGTGATATAATCTCACTGCACGGACAAGGAAAACCAGCTAGGACCAATGATCCTTCCAGCGGAAGAGACCAGTTTGGCTTTAACAGTCCCCAAGGAGTTGTTACCCGCTCAGCTTCAAGAAGAACCCAGATGGTTAGTGGAAACCACTTGCTCAATTTTCAGTATGATCCCATTTCTCGTCCACAATCTAGGTTGCCTCCTCCTAGGAGATACGTCAAGAGGAAGCCTTACAACAAAGACTTGTTTCTTCAAGCAAATTACAAGTTTGTTCTGTTGGATTCAGGCAATTACACGCCTGACTCGATGGATCCAGACAAAATGTTACAGTGGGAGGATATTGTTTGTGTGAGATATTCCACTCCATTTCATGTGCAATGCCCCATAT</genome_strand>
        <mrna_strand>ATGGATCCAAATCCAAACAACAGCAGCAGCAGCAACCCGACAACTTTTCAG.....................................................................................................GAAACATGGCTACCGCTGCATCTACTTCTGGAGGATCCTCCAAAAAG...............................................................................GTGAACAACTCCGGCAGCAGTCGAGAAAGTTCACGACATCATAACAGTGATATAATCTGACTGCACGGACAAGGAAAACCAGCTAGGACCAATGATCCTTCCAGCGGAAGAGACCAGTTTGGCTTTAACAGTCCCCAAGGAGTTGTTACCCGCTCAGCTCCAAGAAGAACCCAGATGGTTAGTGGAAACCACTTGCTCAATTTTCAGTATGATCCCATTTCTCGTCCACAATCTAGGTTGCCTCCTCCTAGGAGATACGTCAAGAGGAAGCCTTACAACAAAGACTCGTTTCTTCAAGCAAATTACAAGTTTGTTCTGTTGGATTCAGGCCATTACACGCCTGACTCGATGGATCCAGACAAAATGTTACAGTGGGAGGATATTGCTTGTGTGAGATATTGCACTCCATTTCATGTGCAAAGCCCCATAT</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>3</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="32740" PGL_stop="31789"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="32740" e_stop="32646"/>
            <exon e_start="32554" e_stop="32484"/>
            <exon e_start="32406" e_stop="32320"/>
            <exon e_start="32236" e_stop="32159"/>
            <exon e_start="32075" e_stop="31984"/>
            <exon e_start="31871" e_stop="31789"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.997" acc_prob="0.907" e_score="0.989"/>
          <exon-intron don_prob="0.884" acc_prob="0.998" e_score="0.986"/>
          <exon-intron don_prob="0.845" acc_prob="0.918" e_score="0.977"/>
          <exon-intron don_prob="0.957" acc_prob="0.990" e_score="0.987"/>
          <exon-intron don_prob="0.995" acc_prob="1.000" e_score="0.989"/>
          <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="0.989">
            <gDNA_exon_boundary e_start="32740" e_stop="32646" e_length="95"/>
          </exon>
          <intron i_serial="1" don_prob="0.997" acc_prob="0.907">
            <gDNA_intron_boundary i_start="32645" i_stop="32555" i_length="91"/>
          </intron>
          <exon e_serial="2" e_score="0.986">
            <gDNA_exon_boundary e_start="32554" e_stop="32484" e_length="71"/>
          </exon>
          <intron i_serial="2" don_prob="0.884" acc_prob="0.998">
            <gDNA_intron_boundary i_start="32483" i_stop="32407" i_length="77"/>
          </intron>
          <exon e_serial="3" e_score="0.977">
            <gDNA_exon_boundary e_start="32406" e_stop="32320" e_length="87"/>
          </exon>
          <intron i_serial="3" don_prob="0.845" acc_prob="0.918">
            <gDNA_intron_boundary i_start="32319" i_stop="32237" i_length="83"/>
          </intron>
          <exon e_serial="4" e_score="0.987">
            <gDNA_exon_boundary e_start="32236" e_stop="32159" e_length="78"/>
          </exon>
          <intron i_serial="4" don_prob="0.957" acc_prob="0.990">
            <gDNA_intron_boundary i_start="32158" i_stop="32076" i_length="83"/>
          </intron>
          <exon e_serial="5" e_score="0.989">
            <gDNA_exon_boundary e_start="32075" e_stop="31984" e_length="92"/>
          </exon>
          <intron i_serial="5" don_prob="0.995" acc_prob="1.000">
            <gDNA_intron_boundary i_start="31983" i_stop="31872" i_length="112"/>
          </intron>
          <exon e_serial="6" e_score="1.000">
            <gDNA_exon_boundary e_start="31871" e_stop="31789" e_length="83"/>
          </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="32740" stop="32646"/>
              <exon start="32554" stop="32484"/>
              <exon start="32406" stop="32320"/>
              <exon start="32236" stop="32159"/>
              <exon start="32075" stop="31984"/>
              <exon start="31871" stop="31789"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="T1323" 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>AAGGTTCAGCAGGAAACCAGCTCTTGTTCGTCTTCTCTCTGTTGCTGCTCTCTTCTCCATTATACTAATCGCCATTCAGTCCTCTTTCTTCACTG : GTAGTCGGGCTCCCGTTAATTTGGATATTCCGATCTTGTCCCACTTCCAGTCTAACCTTCAGCAATGCGTC : GCTAATCGAGGGCTGGGATTGACTGCTCATATAATTGATCATTGCAATGTCATTCTCAAGTTTCCCCAAGGAACTAATAGCACTTGG : TATAATGAGCAGTTCAAGATCTTTGAACCATTGGAGTACAAGTACGACGTTTGCGAAACAATACTTCTGTGGGAGCAG : TACCGTAACATGACGACAGTGTTGACAAGAGAATATTTGGATTCTCGGCCTGATGGATGGTTTGACTATGCAGCAAAAAGGATCGCACAGCT : AGGAGCAGACAAATGTTACAATCAGACTCTTTGCGAAGAACATCTCAATCTAACTTTACCAGCTAAGCCCCCGTTTCACCCTC</gDNA_template>
            <first_frame> K  V  Q  Q  E  T  S  S  C  S  S  S  L  C  C  C  S  L  L  H  Y  T  N  R  H  S  V  L  F  L  H  W :   *  S  G  S  R  *  F  G  Y  S  D  L  V  P  L  P  V  *  P  S  A  M  R   : R  *  S  R  A  G  I  D  C  S  Y  N  *  S  L  Q  C  H  S  Q  V  S  P  R  N  *  *  H  L   : V  *  *  A  V  Q  D  L  *  T  I  G  V  Q  V  R  R  L  R  N  N  T  S  V  G  A   : V  P  *  H  D  D  S  V  D  K  R  I  F  G  F  S  A  *  W  M  V  *  L  C  S  K  K  D  R  T  A  :  R  S  R  Q  M  L  Q  S  D  S  L  R  R  T  S  Q  S  N  F  T  S  *  A  P  V  S  P   </first_frame>
            <second_frame>  R  F  S  R  K  P  A  L  V  R  L  L  S  V  A  A  L  F  S  I  I  L  I  A  I  Q  S  S  F  F  T   : G  S  R  A  P  V  N  L  D  I  P  I  L  S  H  F  Q  S  N  L  Q  Q  C  V  :  A  N  R  G  L  G  L  T  A  H  I  I  D  H  C  N  V  I  L  K  F  P  Q  G  T  N  S  T  W  :  Y  N  E  Q  F  K  I  F  E  P  L  E  Y  K  Y  D  V  C  E  T  I  L  L  W  E  Q  :  Y  R  N  M  T  T  V  L  T  R  E  Y  L  D  S  R  P  D  G  W  F  D  Y  A  A  K  R  I  A  Q  L :   G  A  D  K  C  Y  N  Q  T  L  C  E  E  H  L  N  L  T  L  P  A  K  P  P  F  H  P  </second_frame>
            <third_frame>   G  S  A  G  N  Q  L  L  F  V  F  S  L  L  L  L  S  S  P  L  Y  *  S  P  F  S  P  L  S  S  L  :  V  V  G  L  P  L  I  W  I  F  R  S  C  P  T  S  S  L  T  F  S  N  A  S :   L  I  E  G  W  D  *  L  L  I  *  L  I  I  A  M  S  F  S  S  F  P  K  E  L  I  A  L  G :   I  M  S  S  S  R  S  L  N  H  W  S  T  S  T  T  F  A  K  Q  Y  F  C  G  S  S :   T  V  T  *  R  Q  C  *  Q  E  N  I  W  I  L  G  L  M  D  G  L  T  M  Q  Q  K  G  S  H  S   : *  E  Q  T  N  V  T  I  R  L  F  A  K  N  I  S  I  *  L  Y  Q  L  S  P  R  F  T  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="C02HBa0177F12.3" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="32739" stop="32646"/>
                    <exon start="32554" stop="32484"/>
                    <exon start="32406" stop="32320"/>
                    <exon start="32236" stop="32159"/>
                    <exon start="32075" stop="31984"/>
                    <exon start="31871" stop="31790"/>
                  </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>RFSRKPALVRLLSVAALFSIILIAIQSSFFTGSRAPVNLDIPILSHFQSNLQQCVANRGLGLTAHIIDHCNVILKFPQGTNSTWYNEQFKIFEPLEYKYDVCETILLWEQYRNMTTVLTREYLDSRPDGWFDYAAKRIAQLGADKCYNQTLCEEHLNLTLPAKPPFHP</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="47152" PGL_stop="46139"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="47152" e_stop="46952"/>
            <exon e_start="46850" e_stop="46804"/>
            <exon e_start="46724" e_stop="46139"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.590" acc_prob="0.998" e_score="0.930"/>
          <exon-intron don_prob="1.000" acc_prob="0.995" e_score="0.979"/>
          <exon-only e_score="0.981"/>
        </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="0.930">
            <gDNA_exon_boundary e_start="47152" e_stop="46952" e_length="201"/>
          </exon>
          <intron i_serial="1" don_prob="0.590" acc_prob="0.998">
            <gDNA_intron_boundary i_start="46951" i_stop="46851" i_length="101"/>
          </intron>
          <exon e_serial="2" e_score="0.979">
            <gDNA_exon_boundary e_start="46850" e_stop="46804" e_length="47"/>
          </exon>
          <intron i_serial="2" don_prob="1.000" acc_prob="0.995">
            <gDNA_intron_boundary i_start="46803" i_stop="46725" i_length="79"/>
          </intron>
          <exon e_serial="3" e_score="0.981">
            <gDNA_exon_boundary e_start="46724" e_stop="46139" e_length="586"/>
          </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="47152" stop="46952"/>
              <exon start="46850" stop="46804"/>
              <exon start="46724" stop="46139"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="C2_At3g26730" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="47002" stop="46952"/>
              <exon start="46850" stop="46804"/>
              <exon start="46724" stop="46295"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="T1554" 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>GGCTAAAACCCGAAAAGATCAACCCAACCAACCCCCTTTGTCTAATCTAATCTCCCAGGAGGAATTTCATGTCCATCTTGCCCTCCCATAGCGACAATCATACAACCTCCTCCTCCTCTTCTTCTTCTTCTCCAAACCCTAACTCTAATCATGGATCCAAATCCAAACAACAGCAGCAGCAGCAACCCGACAACTTCTCAG : GAAACATGGCTACCGCTGCATCTACTTCTGGTGGATCCTCCAAAAAG : GTGAACAACTCCGGTAGCAGTCGAGAAAGTTCACGACATCATAACAGTGATATAATCTCACTGCACGGACAAGGAAAACCAGCTAGGACCAATGATCCTTCCAGCGGAAGAGACCAGTTTGGCTTTAACAGTCCCCAAGGAGTTGTTACCCGCTCAGCTTCAAGAAGAACCCAGATGGTTAGTGGAAACCACTTGCTCAATTTTCAGTATGATCCCATTTCTCGTCCACAATCTAGGTTGCCTCCTCCTAGGAGATACGTCAAGAGGAAGCCTTACAACAAAGACTTGTTTCTTCAAGCAAATTACAAGTTTGTTCTGTTGGATTCAGGCAATTACACGCCTGACTCGATGGATCCAGACAAAATGTTACAGTGGGAGGATATTGTTTGTGTGAGATATTCCACTCCATTTCATGTGCAATGCCCCATATGCTTAGAGGATCCTCTTTGTCCTCAGATAACTTCGTGTGGTCATATCTTCTGTTTTCCCTGTGTTATGCAATATTTTATGATCTCCGAAGAAGATGACCATAAAAATAATTTCAAGAAGAAATGCCCTTTGTGTTTTATGATGATATCTTCACAGG</gDNA_template>
            <first_frame> G  *  N  P  K  R  S  T  Q  P  T  P  F  V  *  S  N  L  P  G  G  I  S  C  P  S  C  P  P  I  A  T  I  I  Q  P  P  P  P  L  L  L  L  L  Q  T  L  T  L  I  M  D  P  N  P  N  N  S  S  S  S  N  P  T  T  S  Q  :  E  T  W  L  P  L  H  L  L  L  V  D  P  P  K  R :   *  T  T  P  V  A  V  E  K  V  H  D  I  I  T  V  I  *  S  H  C  T  D  K  E  N  Q  L  G  P  M  I  L  P  A  E  E  T  S  L  A  L  T  V  P  K  E  L  L  P  A  Q  L  Q  E  E  P  R  W  L  V  E  T  T  C  S  I  F  S  M  I  P  F  L  V  H  N  L  G  C  L  L  L  G  D  T  S  R  G  S  L  T  T  K  T  C  F  F  K  Q  I  T  S  L  F  C  W  I  Q  A  I  T  R  L  T  R  W  I  Q  T  K  C  Y  S  G  R  I  L  F  V  *  D  I  P  L  H  F  M  C  N  A  P  Y  A  *  R  I  L  F  V  L  R  *  L  R  V  V  I  S  S  V  F  P  V  L  C  N  I  L  *  S  P  K  K  M  T  I  K  I  I  S  R  R  N  A  L  C  V  L  *  *  Y  L  H  R </first_frame>
            <second_frame>  A  K  T  R  K  D  Q  P  N  Q  P  P  L  S  N  L  I  S  Q  E  E  F  H  V  H  L  A  L  P  *  R  Q  S  Y  N  L  L  L  L  F  F  F  F  S  K  P  *  L  *  S  W  I  Q  I  Q  T  T  A  A  A  A  T  R  Q  L  L  R :   K  H  G  Y  R  C  I  Y  F  W  W  I  L  Q  K   : G  E  Q  L  R  *  Q  S  R  K  F  T  T  S  *  Q  *  Y  N  L  T  A  R  T  R  K  T  S  *  D  Q  *  S  F  Q  R  K  R  P  V  W  L  *  Q  S  P  R  S  C  Y  P  L  S  F  K  K  N  P  D  G  *  W  K  P  L  A  Q  F  S  V  *  S  H  F  S  S  T  I  *  V  A  S  S  *  E  I  R  Q  E  E  A  L  Q  Q  R  L  V  S  S  S  K  L  Q  V  C  S  V  G  F  R  Q  L  H  A  *  L  D  G  S  R  Q  N  V  T  V  G  G  Y  C  L  C  E  I  F  H  S  I  S  C  A  M  P  H  M  L  R  G  S  S  L  S  S  D  N  F  V  W  S  Y  L  L  F  S  L  C  Y  A  I  F  Y  D  L  R  R  R  *  P  *  K  *  F  Q  E  E  M  P  F  V  F  Y  D  D  I  F  T   </second_frame>
            <third_frame>   L  K  P  E  K  I  N  P  T  N  P  L  C  L  I  *  S  P  R  R  N  F  M  S  I  L  P  S  H  S  D  N  H  T  T  S  S  S  S  S  S  S  S  P  N  P  N  S  N  H  G  S  K  S  K  Q  Q  Q  Q  Q  Q  P  D  N  F  S   : G  N  M  A  T  A  A  S  T  S  G  G  S  S  K  K  :  V  N  N  S  G  S  S  R  E  S  S  R  H  H  N  S  D  I  I  S  L  H  G  Q  G  K  P  A  R  T  N  D  P  S  S  G  R  D  Q  F  G  F  N  S  P  Q  G  V  V  T  R  S  A  S  R  R  T  Q  M  V  S  G  N  H  L  L  N  F  Q  Y  D  P  I  S  R  P  Q  S  R  L  P  P  P  R  R  Y  V  K  R  K  P  Y  N  K  D  L  F  L  Q  A  N  Y  K  F  V  L  L  D  S  G  N  Y  T  P  D  S  M  D  P  D  K  M  L  Q  W  E  D  I  V  C  V  R  Y  S  T  P  F  H  V  Q  C  P  I  C  L  E  D  P  L  C  P  Q  I  T  S  C  G  H  I  F  C  F  P  C  V  M  Q  Y  F  M  I  S  E  E  D  D  H  K  N  N  F  K  K  K  C  P  L  C  F  M  M  I  S  S  Q  </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="C02HBa0177F12.3" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="47102" stop="46952"/>
                    <exon start="46850" stop="46804"/>
                    <exon start="46724" stop="46140"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>783</number_coding_nucleotides>
                  <number_encoded_amino_acids>261</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>SPRRNFMSILPSHSDNHTTSSSSSSSSPNPNSNHGSKSKQQQQQQPDNFSGNMATAASTSGGSSKKVNNSGSSRESSRHHNSDIISLHGQGKPARTNDPSSGRDQFGFNSPQGVVTRSASRRTQMVSGNHLLNFQYDPISRPQSRLPPPRRYVKRKPYNKDLFLQANYKFVLLDSGNYTPDSMDPDKMLQWEDIVCVRYSTPFHVQCPICLEDPLCPQITSCGHIFCFPCVMQYFMISEEDDHKNNFKKKCPLCFMMISSQ</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 127 chains have been computed
$ 
$ memory statistics:
$ 7096 bytes spliced alignments in total
$ 3 spliced alignments have been stored
$ 2365 bytes was the average size of a spliced alignment
$ 6928 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3464 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 127 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 09:52:24
-->
