<?xml version="1.0" encoding="ISO-8859-1"?>
<GTH_output xmlns="http://www.genomethreader.org/GTH_output/" GTH_XML_version="1.1">
  <header xmlns="http://www.genomethreader.org/GTH_output/header/">
    <source program="GenomeThreader" version="0.9.54" build_date="2006-07-28 11:55:15" run_date="2009-12-03 21:35:52"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C10HBa0306E10-JCcni/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C10HBa0306E10-JCcni/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-C10HBa0306E10-JCcni/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="C2_At4g34150" ref_strand="+" ref_description="C2_At4g34150">
      <seq>tcatcgttgtcttctttcttcttctactttccatgtcgatagcatatggcatccaaggccaactccttgaagtaactgttgttgcttgtaataaactgaaggatactgaatggatttcaaggcaagatccgtatgtttgccttgaatacggaagttctaaattccgtactcgtacatgtacagatggcggtaaaaaccctacgtttcaagagaaatttgtgtttaagctaattgaagggttgcgagagatcaatgttgttgtgtggaatagcaatactgttaattcagatgattttatagggagtggaaaggttcaactacagaaggttctctcacagggatttgatgatactgcttggccacttcagaggaagaacggcaggcatgcaggagaagttcgactaataatgcactatgcaaataccaataagccagcaacaagccatgctcaatcaggccctccatttgttacaccaactcctggatcatatccatattcagtagctccaccacatgtagcttctcacccaacaccttctggctatccagcaccatctccttattccacagcctcgcctccttcagcattttatccagcttctccttattccacagtcccaccacctccagcagcatatcattcaacatctctttatccccctccatcggctgcttatccttcaccttactcatcatctgcgtatccgcctcagccttatccaccacagggttactcttatcccccangtcaataccctggagtctatcctccacgatcgtattgatgctat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C10HBa0306E10-JCcni/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C10HBa0306E10.1" temp_strand="-" temp_description="C10HBa0306E10.1  AC238925.7 htgs_phase:2 submitted_to_sgn_as:C10HBa0306E10 upload_account_name:manual">
        <position start="71091" stop="68448"/>
      </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="70791" g_stop="70714" g_length="78"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="78" r_length="78" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="70713" i_stop="70629" i_length="85">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.974" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="70628" g_stop="70524" g_length="105"/>
          <reference_exon_boundary r_type="cDNA" r_start="79" r_stop="183" r_length="105" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="70523" i_stop="70443" i_length="81">
            <donor d_prob="0.958" d_score="1.00"/>
            <acceptor a_prob="0.997" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="70442" g_stop="70316" g_length="127"/>
          <reference_exon_boundary r_type="cDNA" r_start="184" r_stop="310" r_length="127" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="70315" i_stop="70201" i_length="115">
            <donor d_prob="0.975" d_score="1.00"/>
            <acceptor a_prob="0.983" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="70200" g_stop="70129" g_length="72"/>
          <reference_exon_boundary r_type="cDNA" r_start="311" r_stop="382" r_length="72" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="70128" i_stop="69333" i_length="796">
            <donor d_prob="0.990" d_score="1.00"/>
            <acceptor a_prob="0.995" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="69332" g_stop="69287" g_length="46"/>
          <reference_exon_boundary r_type="cDNA" r_start="383" r_stop="428" r_length="46" r_score="1.000"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="69286" i_stop="69193" i_length="94">
            <donor d_prob="0.806" d_score="1.00"/>
            <acceptor a_prob="0.972" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="69192" g_stop="68874" g_length="319"/>
          <reference_exon_boundary r_type="cDNA" r_start="429" r_stop="747" r_length="319" r_score="0.991"/>
        </exon>
        <intron i_serial="6">
          <gDNA_intron_boundary i_start="68873" i_stop="68792" i_length="82">
            <donor d_prob="0.997" d_score="0.96"/>
            <acceptor a_prob="0.991" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="7">
          <gDNA_exon_boundary g_start="68791" g_stop="68748" g_length="44"/>
          <reference_exon_boundary r_type="cDNA" r_start="748" r_stop="791" r_length="44" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C10HBa0306E10.1" gen_strand="-" ref_id="C2_At4g34150" ref_strand="+">
        <total_alignment_score>0.996</total_alignment_score>
        <cumulative_length_of_scored_exons>791</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C10HBa0306E10.1" gen_strand="-"/>
        <rDNA rDNA_id="C2_At4g34150" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="70791" e_stop="70714"/>
          <exon e_start="70628" e_stop="70524"/>
          <exon e_start="70442" e_stop="70316"/>
          <exon e_start="70200" e_stop="70129"/>
          <exon e_start="69332" e_stop="69287"/>
          <exon e_start="69192" e_stop="68874"/>
          <exon e_start="68791" e_stop="68748"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCATCGTTGTCTTCTTTCTTCTTCTACTTTCCATGTCGATAGCATATGGCATCCAAGGCCAACTCCTTGAAGTAACTGGTACGAACTTCATTCAACTACAGCTAAAATACTGAGATTTTATGAATTACTTTTCATTATTTACTTTGAATTTTCGTTTTTGTAGTTGTTGCTTGTAATAAACTGAAGGATACTGAATGGATTTCAAGGCAAGATCCGTATGTTTGCCTTGAATACGGAAGTTCTAAATTCCGTACTCGTACATGTACAGGTACAAATTGAATGGATTTATATCTGTTAACTATCATTTTTGGTGAATTTTGATGAGATTCATGCTTTTGTTTGTATGTAGATGGCGGTAAAAACCCTACGTTTCAAGAGAAATTTGTGTTTAAGCTAATTGAAGGGTTGCGAGAGATCAATGTTGTTGTGTGGAATAGCAATACTGTTAATTCAGATGATTTTATAGGGAGTGGAAAGTAAGTCTCAATTTGTTTTCTCTTGACTGATTTGGATTTGTTGTTGAGTTGATTGAATGATCTATTTAGTTTGTTAGTTGAGTGTTAATGATTAAATTATTTAATTTAATTCTAGGGTTCAACTACAGAAGGTTCTCTCACAGGGATTTGATGATACTGCTTGGCCACTTCAGAGGAAGAACGGCAGGTATATTGATAAAAACAACTGCTATTTCTTGATGAATTTTGCTATGGTCTTTCTTTTACGGCGAGAATTGTGTTTATAGTCCTTCTAAGTTTGAATTTGTATCTTTTTTTGTTTGTTTTCTTTGACAAAATGTTCTACATTGTGATTCCACTCTTTCATGTGACATTAATATGACAATTTGCGACACCAAGGTCTGGGATGTATGGATATGATGTGATTCTTTTCATTCATCACTGAAGTTCTTCATTTCATCATTATTGATTAACATAGACCTGTCTATAACTAGCCATCAACTTACTTCCGGACAGTGATGCAGGTGGAACTTAAGCTTTCATAAGCTATTTGTATTCTGTAAAAGTGTTGAATTTTTTTTTGTTCAACTTTCTCCCTGTTAATTGTCTACTTCTGGTAGTCAAAGGGGTCATGGATCAGCTCTTTCTACAAAGAGCCTTATAGACCTTTAGGCATACTAGACACAATTGGGTCACATGTTGGCTTCAAGTTTGGTGAAGAATTAGGGGTAGTTGAGGTTCAATATACTAGATATGAGGCGAGGAATTATTGATTACCTTGCAGGATATAAGTTGAGTCAACAGGAGGTGTAATTTGTTTTCTCACATAAAAGGTATTTAGTCAGCACACCAAGTACTGATACTGGTGGATTCATGGGGGCTATAAAGATTTTTTCTTGATAGTATTTGTGAGGTCATTGGAGACGAATGAAGAGAGCAGCTTTTTCAACACTTGTGTATTCCTAATGAAATCACAGTGTAACAGAAGTATATTTCTTTTACAGGCATGCAGGAGAAGTTCGACTAATAATGCACTATGCAAATACCAATGTAAGTGCCGCCGTCTTTTCTTAGAATTTCCTTCTTGCTTCCCACCCCAAAAATCTTTTAATGTCTTTAACATGAATTTCTCTTTTACTTCCAGAAGCCAGCAACAAGCCATGCTCAATCAGGCCCTCCATTTGTTACACCAACTCCTGGATCATATCCATATTCAGTAGCTCCACCACATGTAGCTTCTCACCCAACACCTTCTGGCTATCCAGCACCATCTCCTTATTCCACAGCCTCGCCTCCTTCAGCATTTTATCCAGCTTCTCCTTATTCCACAGTCCCACCACCTCCAGCAGCATATCATTCAACATCTCTTTATCCCCCTCAATCGGCTGCTTATCCTTCACCTTACTCATCATCTGCGTATCTGCCTCAGCCTTATCCACCACAGGGTTACTCTTATCCCCCAGGTAAATCTTGTAAGATGTGAATTTCTTACTCTCCCCTGGTATGTCAATTACGGTTAACTATTTATTTTTGTTGTCTTGCCAGGTCAATACCCTGGAGTCTATCCTCCACGATCGTATTGATGCTAT</genome_strand>
        <mrna_strand>TCATCGTTGTCTTCTTTCTTCTTCTACTTTCCATGTCGATAGCATATGGCATCCAAGGCCAACTCCTTGAAGTAACTG.....................................................................................TTGTTGCTTGTAATAAACTGAAGGATACTGAATGGATTTCAAGGCAAGATCCGTATGTTTGCCTTGAATACGGAAGTTCTAAATTCCGTACTCGTACATGTACAG.................................................................................ATGGCGGTAAAAACCCTACGTTTCAAGAGAAATTTGTGTTTAAGCTAATTGAAGGGTTGCGAGAGATCAATGTTGTTGTGTGGAATAGCAATACTGTTAATTCAGATGATTTTATAGGGAGTGGAAA...................................................................................................................GGTTCAACTACAGAAGGTTCTCTCACAGGGATTTGATGATACTGCTTGGCCACTTCAGAGGAAGAACGGCAG............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCATGCAGGAGAAGTTCGACTAATAATGCACTATGCAAATACCAAT..............................................................................................AAGCCAGCAACAAGCCATGCTCAATCAGGCCCTCCATTTGTTACACCAACTCCTGGATCATATCCATATTCAGTAGCTCCACCACATGTAGCTTCTCACCCAACACCTTCTGGCTATCCAGCACCATCTCCTTATTCCACAGCCTCGCCTCCTTCAGCATTTTATCCAGCTTCTCCTTATTCCACAGTCCCACCACCTCCAGCAGCATATCATTCAACATCTCTTTATCCCCCTCCATCGGCTGCTTATCCTTCACCTTACTCATCATCTGCGTATCCGCCTCAGCCTTATCCACCACAGGGTTACTCTTATCCCCCAN..................................................................................GTCAATACCCTGGAGTCTATCCTCCACGATCGTATTGATGCTAT</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-C10HBa0306E10-JCcni/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="T1681" ref_strand="+" ref_description="T1681">
      <seq>ggtcatcgttgtcttctttcttcttctactttccatgtcgatagcatatggcatccaaggccaactccttgaagtaactgttgttgcttgtaataaactgaaggatactgaatggatttcaaggcaagatccgtatgtttgccttgaatacggaagttctaaattccgtactcgtacatgtacagatggcggtaaaaaccctacgtttcaagagaaatttgtgtttaagctaattgaagggttgcgagagatcaatgttgttgtgtggaatagcaatactgttaattcagatgattttatagggagtggaaaggttcaactacagaaggttctctcacagggatttgatgatactgcttggccacttcagaggaagaacggcaggcatgcaggagaagttcgactaataatgcactatgcaaataccaataagccagcaacaagccatgctcaatcaggccctccatttgttacaccaactcctggatcatatccatattcagtagctccaccacatgtagcttctcacccaacaccttctggctatccagcaccatctccttattccacagcctcgcctccttcagcattttatccagcttctccttattccacagtcccaccacctccagcagcatatcattcaacatc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C10HBa0306E10-JCcni/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C10HBa0306E10.1" temp_strand="-" temp_description="C10HBa0306E10.1  AC238925.7 htgs_phase:2 submitted_to_sgn_as:C10HBa0306E10 upload_account_name:manual">
        <position start="71092" stop="68672"/>
      </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="70793" g_stop="70714" g_length="80"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="80" r_length="80" r_score="0.988"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="70713" i_stop="70629" i_length="85">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.974" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="70628" g_stop="70524" g_length="105"/>
          <reference_exon_boundary r_type="cDNA" r_start="81" r_stop="185" r_length="105" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="70523" i_stop="70443" i_length="81">
            <donor d_prob="0.958" d_score="1.00"/>
            <acceptor a_prob="0.997" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="70442" g_stop="70316" g_length="127"/>
          <reference_exon_boundary r_type="cDNA" r_start="186" r_stop="312" r_length="127" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="70315" i_stop="70201" i_length="115">
            <donor d_prob="0.975" d_score="1.00"/>
            <acceptor a_prob="0.983" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="70200" g_stop="70129" g_length="72"/>
          <reference_exon_boundary r_type="cDNA" r_start="313" r_stop="384" r_length="72" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="70128" i_stop="69333" i_length="796">
            <donor d_prob="0.990" d_score="1.00"/>
            <acceptor a_prob="0.995" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="69332" g_stop="69287" g_length="46"/>
          <reference_exon_boundary r_type="cDNA" r_start="385" r_stop="430" r_length="46" r_score="1.000"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="69286" i_stop="69193" i_length="94">
            <donor d_prob="0.806" d_score="1.00"/>
            <acceptor a_prob="0.972" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="69192" g_stop="68972" g_length="221"/>
          <reference_exon_boundary r_type="cDNA" r_start="431" r_stop="651" r_length="221" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C10HBa0306E10.1" gen_strand="-" ref_id="T1681" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>651</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C10HBa0306E10.1" gen_strand="-"/>
        <rDNA rDNA_id="T1681" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="70793" e_stop="70714"/>
          <exon e_start="70628" e_stop="70524"/>
          <exon e_start="70442" e_stop="70316"/>
          <exon e_start="70200" e_stop="70129"/>
          <exon e_start="69332" e_stop="69287"/>
          <exon e_start="69192" e_stop="68972"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CGTCATCGTTGTCTTCTTTCTTCTTCTACTTTCCATGTCGATAGCATATGGCATCCAAGGCCAACTCCTTGAAGTAACTGGTACGAACTTCATTCAACTACAGCTAAAATACTGAGATTTTATGAATTACTTTTCATTATTTACTTTGAATTTTCGTTTTTGTAGTTGTTGCTTGTAATAAACTGAAGGATACTGAATGGATTTCAAGGCAAGATCCGTATGTTTGCCTTGAATACGGAAGTTCTAAATTCCGTACTCGTACATGTACAGGTACAAATTGAATGGATTTATATCTGTTAACTATCATTTTTGGTGAATTTTGATGAGATTCATGCTTTTGTTTGTATGTAGATGGCGGTAAAAACCCTACGTTTCAAGAGAAATTTGTGTTTAAGCTAATTGAAGGGTTGCGAGAGATCAATGTTGTTGTGTGGAATAGCAATACTGTTAATTCAGATGATTTTATAGGGAGTGGAAAGTAAGTCTCAATTTGTTTTCTCTTGACTGATTTGGATTTGTTGTTGAGTTGATTGAATGATCTATTTAGTTTGTTAGTTGAGTGTTAATGATTAAATTATTTAATTTAATTCTAGGGTTCAACTACAGAAGGTTCTCTCACAGGGATTTGATGATACTGCTTGGCCACTTCAGAGGAAGAACGGCAGGTATATTGATAAAAACAACTGCTATTTCTTGATGAATTTTGCTATGGTCTTTCTTTTACGGCGAGAATTGTGTTTATAGTCCTTCTAAGTTTGAATTTGTATCTTTTTTTGTTTGTTTTCTTTGACAAAATGTTCTACATTGTGATTCCACTCTTTCATGTGACATTAATATGACAATTTGCGACACCAAGGTCTGGGATGTATGGATATGATGTGATTCTTTTCATTCATCACTGAAGTTCTTCATTTCATCATTATTGATTAACATAGACCTGTCTATAACTAGCCATCAACTTACTTCCGGACAGTGATGCAGGTGGAACTTAAGCTTTCATAAGCTATTTGTATTCTGTAAAAGTGTTGAATTTTTTTTTGTTCAACTTTCTCCCTGTTAATTGTCTACTTCTGGTAGTCAAAGGGGTCATGGATCAGCTCTTTCTACAAAGAGCCTTATAGACCTTTAGGCATACTAGACACAATTGGGTCACATGTTGGCTTCAAGTTTGGTGAAGAATTAGGGGTAGTTGAGGTTCAATATACTAGATATGAGGCGAGGAATTATTGATTACCTTGCAGGATATAAGTTGAGTCAACAGGAGGTGTAATTTGTTTTCTCACATAAAAGGTATTTAGTCAGCACACCAAGTACTGATACTGGTGGATTCATGGGGGCTATAAAGATTTTTTCTTGATAGTATTTGTGAGGTCATTGGAGACGAATGAAGAGAGCAGCTTTTTCAACACTTGTGTATTCCTAATGAAATCACAGTGTAACAGAAGTATATTTCTTTTACAGGCATGCAGGAGAAGTTCGACTAATAATGCACTATGCAAATACCAATGTAAGTGCCGCCGTCTTTTCTTAGAATTTCCTTCTTGCTTCCCACCCCAAAAATCTTTTAATGTCTTTAACATGAATTTCTCTTTTACTTCCAGAAGCCAGCAACAAGCCATGCTCAATCAGGCCCTCCATTTGTTACACCAACTCCTGGATCATATCCATATTCAGTAGCTCCACCACATGTAGCTTCTCACCCAACACCTTCTGGCTATCCAGCACCATCTCCTTATTCCACAGCCTCGCCTCCTTCAGCATTTTATCCAGCTTCTCCTTATTCCACAGTCCCACCACCTCCAGCAGCATATCATTCAACATC</genome_strand>
        <mrna_strand>GGTCATCGTTGTCTTCTTTCTTCTTCTACTTTCCATGTCGATAGCATATGGCATCCAAGGCCAACTCCTTGAAGTAACTG.....................................................................................TTGTTGCTTGTAATAAACTGAAGGATACTGAATGGATTTCAAGGCAAGATCCGTATGTTTGCCTTGAATACGGAAGTTCTAAATTCCGTACTCGTACATGTACAG.................................................................................ATGGCGGTAAAAACCCTACGTTTCAAGAGAAATTTGTGTTTAAGCTAATTGAAGGGTTGCGAGAGATCAATGTTGTTGTGTGGAATAGCAATACTGTTAATTCAGATGATTTTATAGGGAGTGGAAA...................................................................................................................GGTTCAACTACAGAAGGTTCTCTCACAGGGATTTGATGATACTGCTTGGCCACTTCAGAGGAAGAACGGCAG............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCATGCAGGAGAAGTTCGACTAATAATGCACTATGCAAATACCAAT..............................................................................................AAGCCAGCAACAAGCCATGCTCAATCAGGCCCTCCATTTGTTACACCAACTCCTGGATCATATCCATATTCAGTAGCTCCACCACATGTAGCTTCTCACCCAACACCTTCTGGCTATCCAGCACCATCTCCTTATTCCACAGCCTCGCCTCCTTCAGCATTTTATCCAGCTTCTCCTTATTCCACAGTCCCACCACCTCCAGCAGCATATCATTCAACATC</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="70793" PGL_stop="68748"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="70793" e_stop="70714"/>
            <exon e_start="70628" e_stop="70524"/>
            <exon e_start="70442" e_stop="70316"/>
            <exon e_start="70200" e_stop="70129"/>
            <exon e_start="69332" e_stop="69287"/>
            <exon e_start="69192" e_stop="68874"/>
            <exon e_start="68791" e_stop="68748"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.999" acc_prob="0.974" e_score="1.000"/>
          <exon-intron don_prob="0.958" acc_prob="0.997" e_score="1.000"/>
          <exon-intron don_prob="0.975" acc_prob="0.983" e_score="1.000"/>
          <exon-intron don_prob="0.990" acc_prob="0.995" e_score="1.000"/>
          <exon-intron don_prob="0.806" acc_prob="0.972" e_score="1.000"/>
          <exon-intron don_prob="0.997" acc_prob="0.991" e_score="0.991"/>
          <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="1.000">
            <gDNA_exon_boundary e_start="70793" e_stop="70714" e_length="80"/>
          </exon>
          <intron i_serial="1" don_prob="0.999" acc_prob="0.974">
            <gDNA_intron_boundary i_start="70713" i_stop="70629" i_length="85"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="70628" e_stop="70524" e_length="105"/>
          </exon>
          <intron i_serial="2" don_prob="0.958" acc_prob="0.997">
            <gDNA_intron_boundary i_start="70523" i_stop="70443" i_length="81"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="70442" e_stop="70316" e_length="127"/>
          </exon>
          <intron i_serial="3" don_prob="0.975" acc_prob="0.983">
            <gDNA_intron_boundary i_start="70315" i_stop="70201" i_length="115"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="70200" e_stop="70129" e_length="72"/>
          </exon>
          <intron i_serial="4" don_prob="0.990" acc_prob="0.995">
            <gDNA_intron_boundary i_start="70128" i_stop="69333" i_length="796"/>
          </intron>
          <exon e_serial="5" e_score="1.000">
            <gDNA_exon_boundary e_start="69332" e_stop="69287" e_length="46"/>
          </exon>
          <intron i_serial="5" don_prob="0.806" acc_prob="0.972">
            <gDNA_intron_boundary i_start="69286" i_stop="69193" i_length="94"/>
          </intron>
          <exon e_serial="6" e_score="0.991">
            <gDNA_exon_boundary e_start="69192" e_stop="68874" e_length="319"/>
          </exon>
          <intron i_serial="6" don_prob="0.997" acc_prob="0.991">
            <gDNA_intron_boundary i_start="68873" i_stop="68792" i_length="82"/>
          </intron>
          <exon e_serial="7" e_score="1.000">
            <gDNA_exon_boundary e_start="68791" e_stop="68748" e_length="44"/>
          </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="70793" stop="70714"/>
              <exon start="70628" stop="70524"/>
              <exon start="70442" stop="70316"/>
              <exon start="70200" stop="70129"/>
              <exon start="69332" stop="69287"/>
              <exon start="69192" stop="68972"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="T1681" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="70791" stop="70714"/>
              <exon start="70628" stop="70524"/>
              <exon start="70442" stop="70316"/>
              <exon start="70200" stop="70129"/>
              <exon start="69332" stop="69287"/>
              <exon start="69192" stop="68874"/>
              <exon start="68791" stop="68748"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="C2_At4g34150" 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>CGTCATCGTTGTCTTCTTTCTTCTTCTACTTTCCATGTCGATAGCATATGGCATCCAAGGCCAACTCCTTGAAGTAACTG : TTGTTGCTTGTAATAAACTGAAGGATACTGAATGGATTTCAAGGCAAGATCCGTATGTTTGCCTTGAATACGGAAGTTCTAAATTCCGTACTCGTACATGTACAG : ATGGCGGTAAAAACCCTACGTTTCAAGAGAAATTTGTGTTTAAGCTAATTGAAGGGTTGCGAGAGATCAATGTTGTTGTGTGGAATAGCAATACTGTTAATTCAGATGATTTTATAGGGAGTGGAAA : GGTTCAACTACAGAAGGTTCTCTCACAGGGATTTGATGATACTGCTTGGCCACTTCAGAGGAAGAACGGCAG : GCATGCAGGAGAAGTTCGACTAATAATGCACTATGCAAATACCAAT : AAGCCAGCAACAAGCCATGCTCAATCAGGCCCTCCATTTGTTACACCAACTCCTGGATCATATCCATATTCAGTAGCTCCACCACATGTAGCTTCTCACCCAACACCTTCTGGCTATCCAGCACCATCTCCTTATTCCACAGCCTCGCCTCCTTCAGCATTTTATCCAGCTTCTCCTTATTCCACAGTCCCACCACCTCCAGCAGCATATCATTCAACATCTCTTTATCCCCCTCAATCGGCTGCTTATCCTTCACCTTACTCATCATCTGCGTATCTGCCTCAGCCTTATCCACCACAGGGTTACTCTTATCCCCCAG : GTCAATACCCTGGAGTCTATCCTCCACGATCGTATTGATGCTAT</gDNA_template>
            <first_frame> R  H  R  C  L  L  S  S  S  T  F  H  V  D  S  I  W  H  P  R  P  T  P  *  S  N  C :   C  C  L  *  *  T  E  G  Y  *  M  D  F  K  A  R  S  V  C  L  P  *  I  R  K  F  *  I  P  Y  S  Y  M  Y  R :   W  R  *  K  P  Y  V  S  R  E  I  C  V  *  A  N  *  R  V  A  R  D  Q  C  C  C  V  E  *  Q  Y  C  *  F  R  *  F  Y  R  E  W  K  :  G  S  T  T  E  G  S  L  T  G  I  *  *  Y  C  L  A  T  S  E  E  E  R  Q  :  A  C  R  R  S  S  T  N  N  A  L  C  K  Y  Q   : *  A  S  N  K  P  C  S  I  R  P  S  I  C  Y  T  N  S  W  I  I  S  I  F  S  S  S  T  T  C  S  F  S  P  N  T  F  W  L  S  S  T  I  S  L  F  H  S  L  A  S  F  S  I  L  S  S  F  S  L  F  H  S  P  T  T  S  S  S  I  S  F  N  I  S  L  S  P  S  I  G  C  L  S  F  T  L  L  I  I  C  V  S  A  S  A  L  S  T  T  G  L  L  L  S  P  R :   S  I  P  W  S  L  S  S  T  I  V  L  M  L  </first_frame>
            <second_frame>  V  I  V  V  F  F  L  L  L  L  S  M  S  I  A  Y  G  I  Q  G  Q  L  L  E  V  T   : V  V  A  C  N  K  L  K  D  T  E  W  I  S  R  Q  D  P  Y  V  C  L  E  Y  G  S  S  K  F  R  T  R  T  C  T   : D  G  G  K  N  P  T  F  Q  E  K  F  V  F  K  L  I  E  G  L  R  E  I  N  V  V  V  W  N  S  N  T  V  N  S  D  D  F  I  G  S  G  K :   V  Q  L  Q  K  V  L  S  Q  G  F  D  D  T  A  W  P  L  Q  R  K  N  G  R :   H  A  G  E  V  R  L  I  M  H  Y  A  N  T  N  :  K  P  A  T  S  H  A  Q  S  G  P  P  F  V  T  P  T  P  G  S  Y  P  Y  S  V  A  P  P  H  V  A  S  H  P  T  P  S  G  Y  P  A  P  S  P  Y  S  T  A  S  P  P  S  A  F  Y  P  A  S  P  Y  S  T  V  P  P  P  P  A  A  Y  H  S  T  S  L  Y  P  P  Q  S  A  A  Y  P  S  P  Y  S  S  S  A  Y  L  P  Q  P  Y  P  P  Q  G  Y  S  Y  P  P   : G  Q  Y  P  G  V  Y  P  P  R  S  Y  *  C  Y </second_frame>
            <third_frame>   S  S  L  S  S  F  F  F  Y  F  P  C  R  *  H  M  A  S  K  A  N  S  L  K  *  L  :  L  L  L  V  I  N  *  R  I  L  N  G  F  Q  G  K  I  R  M  F  A  L  N  T  E  V  L  N  S  V  L  V  H  V  Q  :  M  A  V  K  T  L  R  F  K  R  N  L  C  L  S  *  L  K  G  C  E  R  S  M  L  L  C  G  I  A  I  L  L  I  Q  M  I  L  *  G  V  E   : R  F  N  Y  R  R  F  S  H  R  D  L  M  I  L  L  G  H  F  R  G  R  T  A   : G  M  Q  E  K  F  D  *  *  C  T  M  Q  I  P  I :   S  Q  Q  Q  A  M  L  N  Q  A  L  H  L  L  H  Q  L  L  D  H  I  H  I  Q  *  L  H  H  M  *  L  L  T  Q  H  L  L  A  I  Q  H  H  L  L  I  P  Q  P  R  L  L  Q  H  F  I  Q  L  L  L  I  P  Q  S  H  H  L  Q  Q  H  I  I  Q  H  L  F  I  P  L  N  R  L  L  I  L  H  L  T  H  H  L  R  I  C  L  S  L  I  H  H  R  V  T  L  I  P  Q  :  V  N  T  L  E  S  I  L  H  D  R  I  D  A   </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="C10HBa0306E10.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="70792" stop="70714"/>
                    <exon start="70628" stop="70524"/>
                    <exon start="70442" stop="70316"/>
                    <exon start="70200" stop="70129"/>
                    <exon start="69332" stop="69287"/>
                    <exon start="69192" stop="68874"/>
                    <exon start="68791" stop="68754"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>783</number_coding_nucleotides>
                  <number_encoded_amino_acids>261</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>VIVVFFLLLLSMSIAYGIQGQLLEVTVVACNKLKDTEWISRQDPYVCLEYGSSKFRTRTCTDGGKNPTFQEKFVFKLIEGLREINVVVWNSNTVNSDDFIGSGKVQLQKVLSQGFDDTAWPLQRKNGRHAGEVRLIMHYANTNKPATSHAQSGPPFVTPTPGSYPYSVAPPHVASHPTPSGYPAPSPYSTASPPSAFYPASPYSTVPPPPAAYHSTSLYPPQSAAYPSPYSSSAYLPQPYPPQGYSYPPGQYPGVYPPRSY*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 8 chains have been computed
$ 
$ memory statistics:
$ 4560 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 2280 bytes was the average size of a spliced alignment
$ 5720 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5720 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 8 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-03 21:35:55
-->
