<?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="2009-01-16 03:01:16"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C09HBa0130D14-DqTIN/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C09HBa0130D14-DqTIN/gth_cdna_fileCXGN::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-C09HBa0130D14-DqTIN/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M8952-2" ref_strand="+" ref_description="SGN-M8952-2 C2_At5g43940-2 [cosii_markers]">
      <seq>tagagtcatcctcaaaaacactatttttattttctttgattctgtggtctgtaaatcatggctacacaaggtcaagtcatcacctgcaaagctgcggtggcctgggaacccaacaagcctttggtgattgaggatgtgcaggtggctccaccgcaagccggtgaagtccgggttaaagttttgtatactgctctctgccacaccgatgcttatacctggagtggcaaggatcctgagggtctcttcccatgtgttcttggtcatgaggctgcggggatagtagaaagtgttggtgagggagtgactgaggttcagccaggagaccatgttataccttgctaccaggcagaatgcagagaatgcaagttctgcaaatcaggaaagaccaatctttgtggtaaagtaagggctgctactggagtgggagttatgatgaacgaccgtaagagtcgattttctatcaatggaaaaccgatctatcatttcatgggaacttcaaccttcagtcagtacactgttgtccatgatgttagtgttgcaaagattgacccagtagctcctctggagaaagtctgccttcttggatgtggtgttccaactggccttggagctgtttggaacactgcaaaagttgaaccaggttccattgttgccgtctttggcctgggaacagttggtcttgctgtggcggagggtgcaaaagctgctggtgcttcacgaattattggaattgatattgacagcaaaaagtttgatagagccaaaaattttggtgtgactgaattcattaatcccaaggagcatgagaaacccattcagcaagtcattgtggatcttacagatggtggtgttgattacagttttgagtgcataggaaatgtctctgttatgaggtctgctttagagtgttgtcacaagggttggggaacctcagtgattgtaggtgttgctgcttctggtcaggagatatctacacgtccatttcagctggtgactggtcgtgtttggaagggaactgcttttggtggtttcaaaagccgatcacaagttccttccctcgtggacaagtatttaaagaaggaaatcaaggtggatgaatacatcactcataacatgacacttgcggacataaacaaagctttcgacctgatgcatgacggggactgcctccgtgttgtcctggatatgtttgtttgaatgaagtctgtaggctctttatgtttttgtgctatttctcatacactatttacctttccccttcctaattatgtgttgaataaaaagaaagtgagaaaaaaaggatcaagatgacagatgaactctttttaaatggatggtagtttattatcttttcaaaaaaaaaaaaaaagttcttactttgaaggctaaaaccatcattactggttttagagtttggcataaaccattgccatgtttgcataaatggaatcctccccttttccaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09HBa0130D14-DqTIN/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C09HBa0130D14.1" temp_strand="-" temp_description="C09HBa0130D14.1  AC217143.1 htgs_phase:3 submitted_to_sgn_as:C09HBa0130D14 upload_account_name:spain">
        <position start="6852" stop="1699"/>
      </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="6552" g_stop="6462" g_length="91"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="91" r_length="91" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="6461" i_stop="6326" i_length="136">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="6325" g_stop="6189" g_length="137"/>
          <reference_exon_boundary r_type="cDNA" r_start="92" r_stop="228" r_length="137" r_score="0.993"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="6188" i_stop="5747" i_length="442">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.992" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="5746" g_stop="5700" g_length="47"/>
          <reference_exon_boundary r_type="cDNA" r_start="229" r_stop="275" r_length="47" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="5699" i_stop="5576" i_length="124">
            <donor d_prob="0.961" d_score="1.00"/>
            <acceptor a_prob="0.995" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="5575" g_stop="5250" g_length="326"/>
          <reference_exon_boundary r_type="cDNA" r_start="276" r_stop="601" r_length="326" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="5249" i_stop="4498" i_length="752">
            <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="4497" g_stop="4415" g_length="83"/>
          <reference_exon_boundary r_type="cDNA" r_start="602" r_stop="684" r_length="83" r_score="1.000"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="4414" i_stop="4333" i_length="82">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="4332" g_stop="4257" g_length="76"/>
          <reference_exon_boundary r_type="cDNA" r_start="685" r_stop="760" r_length="76" r_score="1.000"/>
        </exon>
        <intron i_serial="6">
          <gDNA_intron_boundary i_start="4256" i_stop="3027" i_length="1230">
            <donor d_prob="0.937" d_score="1.00"/>
            <acceptor a_prob="0.967" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="7">
          <gDNA_exon_boundary g_start="3026" g_stop="2869" g_length="158"/>
          <reference_exon_boundary r_type="cDNA" r_start="761" r_stop="918" r_length="158" r_score="0.987"/>
        </exon>
        <intron i_serial="7">
          <gDNA_intron_boundary i_start="2868" i_stop="2643" i_length="226">
            <donor d_prob="0.975" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="8">
          <gDNA_exon_boundary g_start="2642" g_stop="2481" g_length="162"/>
          <reference_exon_boundary r_type="cDNA" r_start="919" r_stop="1080" r_length="162" r_score="1.000"/>
        </exon>
        <intron i_serial="8">
          <gDNA_intron_boundary i_start="2480" i_stop="2392" i_length="89">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="0.965" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="9">
          <gDNA_exon_boundary g_start="2391" g_stop="1995" g_length="397"/>
          <reference_exon_boundary r_type="cDNA" r_start="1081" r_stop="1470" r_length="390" r_score="0.904"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09HBa0130D14.1" gen_strand="-" ref_id="SGN-M8952-2" ref_strand="+">
        <total_alignment_score>0.971</total_alignment_score>
        <cumulative_length_of_scored_exons>1477</cumulative_length_of_scored_exons>
        <coverage percentage="1.005" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09HBa0130D14.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M8952-2" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="6552" e_stop="6462"/>
          <exon e_start="6325" e_stop="6189"/>
          <exon e_start="5746" e_stop="5700"/>
          <exon e_start="5575" e_stop="5250"/>
          <exon e_start="4497" e_stop="4415"/>
          <exon e_start="4332" e_stop="4257"/>
          <exon e_start="3026" e_stop="2869"/>
          <exon e_start="2642" e_stop="2481"/>
          <exon e_start="2391" e_stop="1995"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TAGAGTCATCCTCAAAAACACTATTTTTATTTTCTTTGATTCTGTGGTCTGTAAATCATGGCTACACAAGGTCAAGTCATCACCTGCAAAGGTACTTTTTTTTTTTTTTACTCTCTCTGCATCTTCATCTTACTATATATGTGTGTCACTTGCACGTTTTTTGCTTTCTATAAACCCTAAATGTTGTAGCTTAATGTATGATTATGGATTTTGAAAATGGTGTATAGCTGCGGTGGCCTGGGAACCCAACAAGCCCTTGGTGATTGAGGATGTGCAGGTGGCTCCACCGCAAGCCGGTGAAGTCCGGGTTAAAGTTTTGTATACTGCTCTCTGCCACACCGATGCTTATACCTGGAGTGGCAAGGTAATCTAATCCATACATCTTTCTCCGTTTTATTAGTAATTGCAAATTTTTGGTATGAGTTAAATTTGATGAAAATCTAAGTGATTTGGGATTGATGAATAGTTGAAATTTAGAGAACGGAGTTGAAGCTTTTTGCATTTCTGCAACAATGTTAATTTGTTTTGGATGGCTAATGTTGTGACATATGGAATTTCATTGAAACATGCATACCCAGATTTTAGGTTCTTCAAACCATTTATGCTCAAGGGTATTTGCAGAATGGCAAGAATTTTTAGTTCTTTCCTTCTTTTATGAAAAATTTCTTGCATTTCATTTGTGGTTTTCTGGAAATTGGAGAAAGATAAGTCTGGAGTCAATGGTTTAAGATCATTAGTTTATTGAACTATTTCTTGTTGTTTGGTATTGCACTAACAATCTAACACATGTTTCTTTTTCCTTGAAGGATCCTGAGGGTCTCTTCCCATGTGTTCTTGGTCATGAGGCTGCGGGGTACGTGCTCTCTTTGTGTCATAGTGTTTTGATTGAATGTACTAGCTTCGATTGAAGCTAAACAAGATTTTTTCTGGATGCCATTTTTCTTGGTCTTAGGCTCTTAGCTATCTAAAATTTGCAGGATAGTAGAAAGTGTTGGTGAGGGAGTGACTGAGGTTCAGCCAGGAGACCATGTTATACCTTGCTACCAGGCAGAATGCAGAGAATGCAAGTTCTGCAAATCAGGAAAGACCAATCTTTGTGGTAAAGTAAGGGCTGCTACTGGAGTGGGAGTTATGATGAACGACCGTAAGAGTCGATTTTCTATCAATGGAAAACCGATCTATCATTTCATGGGAACTTCAACCTTCAGTCAGTACACTGTTGTCCATGATGTTAGTGTTGCAAAGATTGACCCAGTAGCTCCTCTGGAGAAAGTCTGCCTTCTTGGATGTGGTGTTCCAACTGGTAAATTGACTTTCAGACCTAATATGTGATTGAACTAAAATCTTGTGATTTTCTTCAGGCTAATTCATGAAACGTATTCTGTAGCATCTCTGATTTAGTGCTGTCCATTAACTCCTTTTCTAATCCATTATTTATCAATAATATAGGTGTAATAAACTGTTGTGTTGGTTCTCGAAGTACTTGCTTTCAATTTTCATGTGACTTCATCATCTTTTTATTAGTTGTTCTTTTTGATTTGTTAAATCTCTCAAATTTTGGTCAAAATTACTGCAACACCTGACACCTGTCAAAATTGAGAGCACTTCTGAGATAATATGATGTATGTAAAGGGAAGACAGGATTTTGAGAGAATATACCCCAAGATAAAAGCTAAAAGAGAGAAGTAAAAAAGGAAATTTAAAACCAAGTTATCGTATAAATGATTGATTGCGCAAGGATGGAAATATATTTGAGTATATTGTCTAGGGAGCATGTCATCATAGTAATTTGATCTTTATGAGTTTAGTAGATAGTGTCTTTTGGTTGGTTTATCCAGGTGTCCATCTTATTTATCATTTTGCATCACTTCATGCTGGTTTATTCCCCTAGATTAGAAGTTGAGGAAGAAATAAAACATAGAATGCCCATCTAACTATATCCCTTTTGTTTCCTTCCAAATCCAATACACTGTGTTTTCTTTAGTTTTAGATAATGCTAATTACATTCTTACTATACACTCCTTGCGTTTTACATTGTGTATTTGCTGTCTTTAGGCCTTGGAGCTGTTTGGAACACTGCAAAAGTTGAACCAGGTTCCATTGTTGCCGTCTTTGGCCTGGGAACAGTTGGTCTTGCTGTAAGTATCTAACAATTTGATTGTGTGTCAAATAATTAAGCTCCTTTAATATATGTATGCAATCTATCTATTTGTTTGTTAGGTGGCGGAGGGTGCAAAAGCTGCTGGTGCTTCACGAATTATTGGAATTGATATTGACAGCAAAAAGTTTGATAGAGGTACAGCTTTGTCCAATTTGTCTAAGATTGTGAACTATGAACTTTTAGGAATAGTAAAGTATATGATTAGGTTCCAATTATATTTTACATCAGATTTGTCAGAACTTGCTACTCCTAAGTCCTAAGATCAATTTCTTGGTAGACTTCAAATACTAGTTACTAATCTCTAATGTTCAATCAAAAGCTAAAGCCCCTAGGGCTTTGGTTCAATGGTAAGAGTGTCTCGTGATGTGTGATTAGGTGCATGTCATGAATTTGTACCCTGTTGCAAACAAAAGCCTTGTATTTAATTGGGGAAGGGTAGAAGGATGGGCCCGTTACCACCGAGTTTCAAATCATGGGCCAGTTGGTCCTCAGGGATTCTAGATTATTAAGTATATGTTTGTTAAAAGCAGATAAATGATTTCAAAGTTAGATGTATATCTGTAGGGTTTCTTGTAGATATATGTTTTGCATGTGCTTAGATGGTTTTTTCTACATCATCGCTATGTCATAGTGGTAGTATGTGTAGAGAACTTCCTTATGGAATGGAGTATGTAATGGTAATGGAAAAGAAAAAGAAGCCTAATAATAATTTGTTGTCTTCATGCCCTCATCCTTTCTACCAAATCAAATGCAACAGCCATTTATCCAACAAAGAATGAGACAGAGATCTCTTCTAAAAATGATGCTGAACATTGCCTTGCCCTTTAGGTCTTAAAACTTTGGTTTCAATCAGTCAACGCCTATAGGTGCATTTTCCCCTCTTCAGTTTTCTGTCGATTTCTCAAGCTCAAGCTATTATTTCCTGACCTCTTTCCAGCTAATTCCATATCATTTCAAGCTTTGAAATTTTGAAAGCAAGAGATGATATTTTTCGCCGAATCATTTTAAAACTTTCAGATTAGATGTCATGATTTAATCAGTCATATATCTTGATTATCATCTGTATATTTCTGTATGATAAGCAGTAGATTGCTCTTATGAAAGTCTAATGTATAAATATCTTGTTTGATCTCATGCTGATCATAGGAGGAAACAAGTTGTTAACAAAATAATTTTGAAGCTTATGTCAGATTGAAGTGGCGGTGAAAGTATGTCTGGTTAAGTTAATCAGACTTATTCAAGAAATAGCATTTGAAACAAACTTGAGCAGCACAACAGTTTTCATGCTCTAGTGTCCTTAATTATTCTGTTGTATGGCACATAAGTTGTCACATCATCTGATCCATATATCTAACTGTTATGCAGCCAAAAATTTTGGTGTGACTGAATTCATTAATCCCAAGGAGCATGAGCAACCCATTCAGCAAGTCATTGTGGATCTTACTGATGGTGGTGTTGATTACAGTTTTGAGTGCATAGGAAATGTCTCTGTTATGAGGTCTGCTTTAGAGTGTTGTCACAAGGTAAATATGCTAGTATCTAATCAATAAAATTGTAATTTCAGTTTCCCCACCACGTCTTCACTCCGCTTGAAATTGCTGAGCTTCCCATCAGACGTTCCCCTTTATCTTTCAATATTTTTATTTTCATTTCTCTTCGGGATGCTATTAATGTCTCCACCTTATGAAAAAATTAATCTATTGTACAAGATACTAATGCTGAACATGTCCAATCTTATTGGAATTGCAGGGTTGGGGAACCTCAGTGATTGTAGGTGTTGCTGCTTCTGGTCAGGAGATATCTACACGTCCATTTCAGCTGGTGACTGGTCGTGTTTGGAAGGGAACTGCTTTTGGTGGTTTCAAAAGCCGATCACAAGTTCCTTCCCTCGTGGACAAGTATTTAAAGAAGGTCTGTTATTTCCCTTTTCGATATTTTCTTCTTCCCTTATTATACCATTTAGTCACTATTCATTTATCCAACACTTCCACTACTAATAGGAAATCAAGGTGGATGAATACATCACTCATAACATGACACTTGCGGACATAAACAAAGCTTTCGACCTGATGCATGACGGGGACTGCCTCCGTGTTGTCCTGGATATGTTTGTATGAATGAAGTCTGTAGGCTCTTTATGTTGCTTACTTTCTGTTTTTGTGCTATTTCTCAGAGACTATTTACCTTTCCCCTTGCTAATTATGTGTTGAATAAAAAGAAAGTGAGAAAAAAAGGATCAAGATGACAGATGAACTCTTTTTAAATGGATGGTAGTTTATTATCTTTTC------AAGTAAAATGTTCTTACTTTGAAGGCTAAAACCATCATTACTGGTTTTAGAGTTTGGCATAAACCATTGCCATGTTTGCATAAATGGAATCCT-CCCTTTTCCAAAGTAG</genome_strand>
        <mrna_strand>TAGAGTCATCCTCAAAAACACTATTTTTATTTTCTTTGATTCTGTGGTCTGTAAATCATGGCTACACAAGGTCAAGTCATCACCTGCAAAG........................................................................................................................................CTGCGGTGGCCTGGGAACCCAACAAGCCTTTGGTGATTGAGGATGTGCAGGTGGCTCCACCGCAAGCCGGTGAAGTCCGGGTTAAAGTTTTGTATACTGCTCTCTGCCACACCGATGCTTATACCTGGAGTGGCAAG..........................................................................................................................................................................................................................................................................................................................................................................................................................................................GATCCTGAGGGTCTCTTCCCATGTGTTCTTGGTCATGAGGCTGCGGG............................................................................................................................GATAGTAGAAAGTGTTGGTGAGGGAGTGACTGAGGTTCAGCCAGGAGACCATGTTATACCTTGCTACCAGGCAGAATGCAGAGAATGCAAGTTCTGCAAATCAGGAAAGACCAATCTTTGTGGTAAAGTAAGGGCTGCTACTGGAGTGGGAGTTATGATGAACGACCGTAAGAGTCGATTTTCTATCAATGGAAAACCGATCTATCATTTCATGGGAACTTCAACCTTCAGTCAGTACACTGTTGTCCATGATGTTAGTGTTGCAAAGATTGACCCAGTAGCTCCTCTGGAGAAAGTCTGCCTTCTTGGATGTGGTGTTCCAACTG................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCCTTGGAGCTGTTTGGAACACTGCAAAAGTTGAACCAGGTTCCATTGTTGCCGTCTTTGGCCTGGGAACAGTTGGTCTTGCT..................................................................................GTGGCGGAGGGTGCAAAAGCTGCTGGTGCTTCACGAATTATTGGAATTGATATTGACAGCAAAAAGTTTGATAGAG..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CCAAAAATTTTGGTGTGACTGAATTCATTAATCCCAAGGAGCATGAGAAACCCATTCAGCAAGTCATTGTGGATCTTACAGATGGTGGTGTTGATTACAGTTTTGAGTGCATAGGAAATGTCTCTGTTATGAGGTCTGCTTTAGAGTGTTGTCACAAG..................................................................................................................................................................................................................................GGTTGGGGAACCTCAGTGATTGTAGGTGTTGCTGCTTCTGGTCAGGAGATATCTACACGTCCATTTCAGCTGGTGACTGGTCGTGTTTGGAAGGGAACTGCTTTTGGTGGTTTCAAAAGCCGATCACAAGTTCCTTCCCTCGTGGACAAGTATTTAAAGAAG.........................................................................................GAAATCAAGGTGGATGAATACATCACTCATAACATGACACTTGCGGACATAAACAAAGCTTTCGACCTGATGCATGACGGGGACTGCCTCCGTGTTGTCCTGGATATGTTTGTTTGAATGAAGTCTGTAGGCTC-------T--TTA-----TGTTTTTGTGCTATTTCTCATACACTATTTACCTTTCCCCTTCCTAATTATGTGTTGAATAAAAAGAAAGTGAGAAAAAAAGGATCAAGATGACAGATGAACTCTTTTTAAATGGATGGTAGTTTATTATCTTTTCAAAAAAAAAAAAAAAGTTCTTACTTTGAAGGCTAAAACCATCATTACTGGTTTTAGAGTTTGGCATAAACCATTGCCATGTTTGCATAAATGGAATCCTCCCCTTTTCCAAAAAAA</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-C09HBa0130D14-DqTIN/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M8952-3" ref_strand="+" ref_description="SGN-M8952-3 C2_At5g43940-3 [cosii_markers]">
      <seq>ttgcatttagctgtagactcatcttctttaaagcactattttattttctttgattctgtggtctgtaaatcatggctacacaaggtcaagtcatcacctgcaaagctgcggtggcctgggaacccaacaagcctttggtgattgaggatgtgcaggtggctccaccgcaagccggtgaagttcgggttaaagttttgtatactgctctctgccataccgatgcttatacctggagtggcaaggatcctgagggtctctttccatgtgttcttggtcatgaggctgcagggatagtagaaagtgttggtgagggagtgactgaggttcagccaggagaccatgttataccttgctaccaggcagaatgcagagaatgcaagttctgcaaatcaggaaagaccaatctttgtggtaaagtaagggctgctactggagtgggagttatgatgaacgaccgcaagagtcgattttctatcaatggaaaaccgatctatcatttcatgggaacttcaaccttcagtcagtacactgttgtccatgatgttagtgttgcaaagattgacccagcagctcctctggagaaagtctgccttctcgggtgtggtgttccaactggccttggagctgtttggaacactgcaaaagttgaacccggttccattgttgccgtctttggcctgggaacagttggtcttgctgtggcggagggtgcaaaagctgctggtgcttcacgaattattggaattgatattgacagcaaaaagttcgatagagccaaaaattttggtgtgactgaattcatcaatcccaaggagcatgagcaacccattcagcaagtcattgtggatcttacagatggtggtgttgattacagttttgagtgcataggaaatgtctctgttatgagggctgctttagagtgttgtcacaagggttggggaacctcagtgattgtaggtgttgctgcttctggtcaggagatatctacacgtccatttcagctggtaactggtcgtgtttggaagggaactgcttttggtggtttcaaaagccgatcacaagttccttccctcgtggacaagtatttaaagaaggaaatcaaggtggatgaatacatcactcataacatgacacttgcggacataaacaaagcttttgacctgatgcatgacggggactgcctccgtgttgtcctggatatgtttgtatgaacgaagtctggaggcactttatgttgctgactttctgtttttgtgctatttatcggacactatttccctttccccttccccttcctaattgtatgtgtggaataaaaagaaagtaagaaaaaaaggatccatgggacggatgaactctttttaaatggatgctattttattatcttttcaactaaaaaaaaaaaaaaaaaaaactcgagac</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09HBa0130D14-DqTIN/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C09HBa0130D14.1" temp_strand="-" temp_description="C09HBa0130D14.1  AC217143.1 htgs_phase:3 submitted_to_sgn_as:C09HBa0130D14 upload_account_name:spain">
        <position start="6847" stop="1796"/>
      </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="6565" g_stop="6462" g_length="104"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="105" r_length="105" r_score="0.875"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="6461" i_stop="6326" i_length="136">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="6325" g_stop="6189" g_length="137"/>
          <reference_exon_boundary r_type="cDNA" r_start="106" r_stop="242" r_length="137" r_score="0.978"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="6188" i_stop="5747" i_length="442">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.992" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="5746" g_stop="5700" g_length="47"/>
          <reference_exon_boundary r_type="cDNA" r_start="243" r_stop="289" r_length="47" r_score="0.957"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="5699" i_stop="5576" i_length="124">
            <donor d_prob="0.961" d_score="0.96"/>
            <acceptor a_prob="0.995" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="5575" g_stop="5250" g_length="326"/>
          <reference_exon_boundary r_type="cDNA" r_start="290" r_stop="615" r_length="326" r_score="0.988"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="5249" i_stop="4498" i_length="752">
            <donor d_prob="0.990" d_score="0.94"/>
            <acceptor a_prob="0.995" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="4497" g_stop="4415" g_length="83"/>
          <reference_exon_boundary r_type="cDNA" r_start="616" r_stop="698" r_length="83" r_score="0.988"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="4414" i_stop="4333" i_length="82">
            <donor d_prob="0.998" 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="4332" g_stop="4257" g_length="76"/>
          <reference_exon_boundary r_type="cDNA" r_start="699" r_stop="774" r_length="76" r_score="0.987"/>
        </exon>
        <intron i_serial="6">
          <gDNA_intron_boundary i_start="4256" i_stop="3027" i_length="1230">
            <donor d_prob="0.937" d_score="0.98"/>
            <acceptor a_prob="0.967" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="7">
          <gDNA_exon_boundary g_start="3026" g_stop="2869" g_length="158"/>
          <reference_exon_boundary r_type="cDNA" r_start="775" r_stop="932" r_length="158" r_score="0.981"/>
        </exon>
        <intron i_serial="7">
          <gDNA_intron_boundary i_start="2868" i_stop="2643" i_length="226">
            <donor d_prob="0.975" d_score="0.98"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="8">
          <gDNA_exon_boundary g_start="2642" g_stop="2481" g_length="162"/>
          <reference_exon_boundary r_type="cDNA" r_start="933" r_stop="1094" r_length="162" r_score="0.994"/>
        </exon>
        <intron i_serial="8">
          <gDNA_intron_boundary i_start="2480" i_stop="2392" i_length="89">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="0.965" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="9">
          <gDNA_exon_boundary g_start="2391" g_stop="2097" g_length="295"/>
          <reference_exon_boundary r_type="cDNA" r_start="1095" r_stop="1397" r_length="303" r_score="0.878"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="1398" polyA_stop="1415"/>
      <MATCH_line gen_id="C09HBa0130D14.1" gen_strand="-" ref_id="SGN-M8952-3" ref_strand="+">
        <total_alignment_score>0.954</total_alignment_score>
        <cumulative_length_of_scored_exons>1388</cumulative_length_of_scored_exons>
        <coverage percentage="0.976" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09HBa0130D14.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M8952-3" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="6565" e_stop="6462"/>
          <exon e_start="6325" e_stop="6189"/>
          <exon e_start="5746" e_stop="5700"/>
          <exon e_start="5575" e_stop="5250"/>
          <exon e_start="4497" e_stop="4415"/>
          <exon e_start="4332" e_stop="4257"/>
          <exon e_start="3026" e_stop="2869"/>
          <exon e_start="2642" e_stop="2481"/>
          <exon e_start="2391" e_stop="2097"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTGGATCTATTTGTAGAGTCATCCTC-AAAAA-CACTATTTTTATTTTCTTTGATTCTGTGGTCTGTAAATCATGGCTACACAAGGTCAAGTCATCACCTGCAAAGGTACTTTTTTTTTTTTTTACTCTCTCTGCATCTTCATCTTACTATATATGTGTGTCACTTGCACGTTTTTTGCTTTCTATAAACCCTAAATGTTGTAGCTTAATGTATGATTATGGATTTTGAAAATGGTGTATAGCTGCGGTGGCCTGGGAACCCAACAAGCCCTTGGTGATTGAGGATGTGCAGGTGGCTCCACCGCAAGCCGGTGAAGTCCGGGTTAAAGTTTTGTATACTGCTCTCTGCCACACCGATGCTTATACCTGGAGTGGCAAGGTAATCTAATCCATACATCTTTCTCCGTTTTATTAGTAATTGCAAATTTTTGGTATGAGTTAAATTTGATGAAAATCTAAGTGATTTGGGATTGATGAATAGTTGAAATTTAGAGAACGGAGTTGAAGCTTTTTGCATTTCTGCAACAATGTTAATTTGTTTTGGATGGCTAATGTTGTGACATATGGAATTTCATTGAAACATGCATACCCAGATTTTAGGTTCTTCAAACCATTTATGCTCAAGGGTATTTGCAGAATGGCAAGAATTTTTAGTTCTTTCCTTCTTTTATGAAAAATTTCTTGCATTTCATTTGTGGTTTTCTGGAAATTGGAGAAAGATAAGTCTGGAGTCAATGGTTTAAGATCATTAGTTTATTGAACTATTTCTTGTTGTTTGGTATTGCACTAACAATCTAACACATGTTTCTTTTTCCTTGAAGGATCCTGAGGGTCTCTTCCCATGTGTTCTTGGTCATGAGGCTGCGGGGTACGTGCTCTCTTTGTGTCATAGTGTTTTGATTGAATGTACTAGCTTCGATTGAAGCTAAACAAGATTTTTTCTGGATGCCATTTTTCTTGGTCTTAGGCTCTTAGCTATCTAAAATTTGCAGGATAGTAGAAAGTGTTGGTGAGGGAGTGACTGAGGTTCAGCCAGGAGACCATGTTATACCTTGCTACCAGGCAGAATGCAGAGAATGCAAGTTCTGCAAATCAGGAAAGACCAATCTTTGTGGTAAAGTAAGGGCTGCTACTGGAGTGGGAGTTATGATGAACGACCGTAAGAGTCGATTTTCTATCAATGGAAAACCGATCTATCATTTCATGGGAACTTCAACCTTCAGTCAGTACACTGTTGTCCATGATGTTAGTGTTGCAAAGATTGACCCAGTAGCTCCTCTGGAGAAAGTCTGCCTTCTTGGATGTGGTGTTCCAACTGGTAAATTGACTTTCAGACCTAATATGTGATTGAACTAAAATCTTGTGATTTTCTTCAGGCTAATTCATGAAACGTATTCTGTAGCATCTCTGATTTAGTGCTGTCCATTAACTCCTTTTCTAATCCATTATTTATCAATAATATAGGTGTAATAAACTGTTGTGTTGGTTCTCGAAGTACTTGCTTTCAATTTTCATGTGACTTCATCATCTTTTTATTAGTTGTTCTTTTTGATTTGTTAAATCTCTCAAATTTTGGTCAAAATTACTGCAACACCTGACACCTGTCAAAATTGAGAGCACTTCTGAGATAATATGATGTATGTAAAGGGAAGACAGGATTTTGAGAGAATATACCCCAAGATAAAAGCTAAAAGAGAGAAGTAAAAAAGGAAATTTAAAACCAAGTTATCGTATAAATGATTGATTGCGCAAGGATGGAAATATATTTGAGTATATTGTCTAGGGAGCATGTCATCATAGTAATTTGATCTTTATGAGTTTAGTAGATAGTGTCTTTTGGTTGGTTTATCCAGGTGTCCATCTTATTTATCATTTTGCATCACTTCATGCTGGTTTATTCCCCTAGATTAGAAGTTGAGGAAGAAATAAAACATAGAATGCCCATCTAACTATATCCCTTTTGTTTCCTTCCAAATCCAATACACTGTGTTTTCTTTAGTTTTAGATAATGCTAATTACATTCTTACTATACACTCCTTGCGTTTTACATTGTGTATTTGCTGTCTTTAGGCCTTGGAGCTGTTTGGAACACTGCAAAAGTTGAACCAGGTTCCATTGTTGCCGTCTTTGGCCTGGGAACAGTTGGTCTTGCTGTAAGTATCTAACAATTTGATTGTGTGTCAAATAATTAAGCTCCTTTAATATATGTATGCAATCTATCTATTTGTTTGTTAGGTGGCGGAGGGTGCAAAAGCTGCTGGTGCTTCACGAATTATTGGAATTGATATTGACAGCAAAAAGTTTGATAGAGGTACAGCTTTGTCCAATTTGTCTAAGATTGTGAACTATGAACTTTTAGGAATAGTAAAGTATATGATTAGGTTCCAATTATATTTTACATCAGATTTGTCAGAACTTGCTACTCCTAAGTCCTAAGATCAATTTCTTGGTAGACTTCAAATACTAGTTACTAATCTCTAATGTTCAATCAAAAGCTAAAGCCCCTAGGGCTTTGGTTCAATGGTAAGAGTGTCTCGTGATGTGTGATTAGGTGCATGTCATGAATTTGTACCCTGTTGCAAACAAAAGCCTTGTATTTAATTGGGGAAGGGTAGAAGGATGGGCCCGTTACCACCGAGTTTCAAATCATGGGCCAGTTGGTCCTCAGGGATTCTAGATTATTAAGTATATGTTTGTTAAAAGCAGATAAATGATTTCAAAGTTAGATGTATATCTGTAGGGTTTCTTGTAGATATATGTTTTGCATGTGCTTAGATGGTTTTTTCTACATCATCGCTATGTCATAGTGGTAGTATGTGTAGAGAACTTCCTTATGGAATGGAGTATGTAATGGTAATGGAAAAGAAAAAGAAGCCTAATAATAATTTGTTGTCTTCATGCCCTCATCCTTTCTACCAAATCAAATGCAACAGCCATTTATCCAACAAAGAATGAGACAGAGATCTCTTCTAAAAATGATGCTGAACATTGCCTTGCCCTTTAGGTCTTAAAACTTTGGTTTCAATCAGTCAACGCCTATAGGTGCATTTTCCCCTCTTCAGTTTTCTGTCGATTTCTCAAGCTCAAGCTATTATTTCCTGACCTCTTTCCAGCTAATTCCATATCATTTCAAGCTTTGAAATTTTGAAAGCAAGAGATGATATTTTTCGCCGAATCATTTTAAAACTTTCAGATTAGATGTCATGATTTAATCAGTCATATATCTTGATTATCATCTGTATATTTCTGTATGATAAGCAGTAGATTGCTCTTATGAAAGTCTAATGTATAAATATCTTGTTTGATCTCATGCTGATCATAGGAGGAAACAAGTTGTTAACAAAATAATTTTGAAGCTTATGTCAGATTGAAGTGGCGGTGAAAGTATGTCTGGTTAAGTTAATCAGACTTATTCAAGAAATAGCATTTGAAACAAACTTGAGCAGCACAACAGTTTTCATGCTCTAGTGTCCTTAATTATTCTGTTGTATGGCACATAAGTTGTCACATCATCTGATCCATATATCTAACTGTTATGCAGCCAAAAATTTTGGTGTGACTGAATTCATTAATCCCAAGGAGCATGAGCAACCCATTCAGCAAGTCATTGTGGATCTTACTGATGGTGGTGTTGATTACAGTTTTGAGTGCATAGGAAATGTCTCTGTTATGAGGTCTGCTTTAGAGTGTTGTCACAAGGTAAATATGCTAGTATCTAATCAATAAAATTGTAATTTCAGTTTCCCCACCACGTCTTCACTCCGCTTGAAATTGCTGAGCTTCCCATCAGACGTTCCCCTTTATCTTTCAATATTTTTATTTTCATTTCTCTTCGGGATGCTATTAATGTCTCCACCTTATGAAAAAATTAATCTATTGTACAAGATACTAATGCTGAACATGTCCAATCTTATTGGAATTGCAGGGTTGGGGAACCTCAGTGATTGTAGGTGTTGCTGCTTCTGGTCAGGAGATATCTACACGTCCATTTCAGCTGGTGACTGGTCGTGTTTGGAAGGGAACTGCTTTTGGTGGTTTCAAAAGCCGATCACAAGTTCCTTCCCTCGTGGACAAGTATTTAAAGAAGGTCTGTTATTTCCCTTTTCGATATTTTCTTCTTCCCTTATTATACCATTTAGTCACTATTCATTTATCCAACACTTCCACTACTAATAGGAAATCAAGGTGGATGAATACATCACTCATAACATGACACTTGCGGACATAAACAAAGCTTTCGACCTGATGCATGACGGGGACTGCCTCCGTGTTGTCCTGGATATGTTTGTATGAATGAAGTCTGTAGGCTCTTTATGTTGCTTACTTTCTGTTTTTGTGCTATTTCTCAGAGACTATTTACC--T----TTCCCCTTGCTAA-T-TATGTGTTGAATAAAAAGAAAGTGAGAAAAAAAGGATCAAGATGACAGATGAACTCTTTTTAAATGGATGGTAGTTTATTATCTTTTCAAGTAAA</genome_strand>
        <mrna_strand>TTGCATTTAGCTGTAGACTCATCTTCTTTAAAGCACTATTT-TATTTTCTTTGATTCTGTGGTCTGTAAATCATGGCTACACAAGGTCAAGTCATCACCTGCAAAG........................................................................................................................................CTGCGGTGGCCTGGGAACCCAACAAGCCTTTGGTGATTGAGGATGTGCAGGTGGCTCCACCGCAAGCCGGTGAAGTTCGGGTTAAAGTTTTGTATACTGCTCTCTGCCATACCGATGCTTATACCTGGAGTGGCAAG..........................................................................................................................................................................................................................................................................................................................................................................................................................................................GATCCTGAGGGTCTCTTTCCATGTGTTCTTGGTCATGAGGCTGCAGG............................................................................................................................GATAGTAGAAAGTGTTGGTGAGGGAGTGACTGAGGTTCAGCCAGGAGACCATGTTATACCTTGCTACCAGGCAGAATGCAGAGAATGCAAGTTCTGCAAATCAGGAAAGACCAATCTTTGTGGTAAAGTAAGGGCTGCTACTGGAGTGGGAGTTATGATGAACGACCGCAAGAGTCGATTTTCTATCAATGGAAAACCGATCTATCATTTCATGGGAACTTCAACCTTCAGTCAGTACACTGTTGTCCATGATGTTAGTGTTGCAAAGATTGACCCAGCAGCTCCTCTGGAGAAAGTCTGCCTTCTCGGGTGTGGTGTTCCAACTG................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCCTTGGAGCTGTTTGGAACACTGCAAAAGTTGAACCCGGTTCCATTGTTGCCGTCTTTGGCCTGGGAACAGTTGGTCTTGCT..................................................................................GTGGCGGAGGGTGCAAAAGCTGCTGGTGCTTCACGAATTATTGGAATTGATATTGACAGCAAAAAGTTCGATAGAG..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CCAAAAATTTTGGTGTGACTGAATTCATCAATCCCAAGGAGCATGAGCAACCCATTCAGCAAGTCATTGTGGATCTTACAGATGGTGGTGTTGATTACAGTTTTGAGTGCATAGGAAATGTCTCTGTTATGAGGGCTGCTTTAGAGTGTTGTCACAAG..................................................................................................................................................................................................................................GGTTGGGGAACCTCAGTGATTGTAGGTGTTGCTGCTTCTGGTCAGGAGATATCTACACGTCCATTTCAGCTGGTAACTGGTCGTGTTTGGAAGGGAACTGCTTTTGGTGGTTTCAAAAGCCGATCACAAGTTCCTTCCCTCGTGGACAAGTATTTAAAGAAG.........................................................................................GAAATCAAGGTGGATGAATACATCACTCATAACATGACACTTGCGGACATAAACAAAGCTTTTGACCTGATGCATGACGGGGACTGCCTCCGTGTTGTCCTGGATATGTTTGTATGAACGAAGTCTGGAGGCACTTTATGTTGCTGACTTTCTGTTTTTGTGCTATTTATCGGACACTATTTCCCTTTCCCCTTCCCCTTCCTAATTGTATGTGTGGAATAAAAAGAAAGTAAGAAAAAAAGGATCCATGGGACGGATGAACTCTTTTTAAATGGATGCTATTTTATTATCTTTTCAACTAAA</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="6565" PGL_stop="1995"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="6565" e_stop="6462"/>
            <exon e_start="6325" e_stop="6189"/>
            <exon e_start="5746" e_stop="5700"/>
            <exon e_start="5575" e_stop="5250"/>
            <exon e_start="4497" e_stop="4415"/>
            <exon e_start="4332" e_stop="4257"/>
            <exon e_start="3026" e_stop="2869"/>
            <exon e_start="2642" e_stop="2481"/>
            <exon e_start="2391" e_stop="1995"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="1.000" acc_prob="0.999" e_score="1.000"/>
          <exon-intron don_prob="0.999" acc_prob="0.992" e_score="0.993"/>
          <exon-intron don_prob="0.961" acc_prob="0.995" e_score="1.000"/>
          <exon-intron don_prob="0.990" acc_prob="0.995" e_score="1.000"/>
          <exon-intron don_prob="0.998" acc_prob="1.000" e_score="1.000"/>
          <exon-intron don_prob="0.937" acc_prob="0.967" e_score="1.000"/>
          <exon-intron don_prob="0.975" acc_prob="1.000" e_score="0.987"/>
          <exon-intron don_prob="0.998" acc_prob="0.965" e_score="1.000"/>
          <exon-only e_score="0.904"/>
        </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="6565" e_stop="6462" e_length="104"/>
          </exon>
          <intron i_serial="1" don_prob="1.000" acc_prob="0.999">
            <gDNA_intron_boundary i_start="6461" i_stop="6326" i_length="136"/>
          </intron>
          <exon e_serial="2" e_score="0.993">
            <gDNA_exon_boundary e_start="6325" e_stop="6189" e_length="137"/>
          </exon>
          <intron i_serial="2" don_prob="0.999" acc_prob="0.992">
            <gDNA_intron_boundary i_start="6188" i_stop="5747" i_length="442"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="5746" e_stop="5700" e_length="47"/>
          </exon>
          <intron i_serial="3" don_prob="0.961" acc_prob="0.995">
            <gDNA_intron_boundary i_start="5699" i_stop="5576" i_length="124"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="5575" e_stop="5250" e_length="326"/>
          </exon>
          <intron i_serial="4" don_prob="0.990" acc_prob="0.995">
            <gDNA_intron_boundary i_start="5249" i_stop="4498" i_length="752"/>
          </intron>
          <exon e_serial="5" e_score="1.000">
            <gDNA_exon_boundary e_start="4497" e_stop="4415" e_length="83"/>
          </exon>
          <intron i_serial="5" don_prob="0.998" acc_prob="1.000">
            <gDNA_intron_boundary i_start="4414" i_stop="4333" i_length="82"/>
          </intron>
          <exon e_serial="6" e_score="1.000">
            <gDNA_exon_boundary e_start="4332" e_stop="4257" e_length="76"/>
          </exon>
          <intron i_serial="6" don_prob="0.937" acc_prob="0.967">
            <gDNA_intron_boundary i_start="4256" i_stop="3027" i_length="1230"/>
          </intron>
          <exon e_serial="7" e_score="0.987">
            <gDNA_exon_boundary e_start="3026" e_stop="2869" e_length="158"/>
          </exon>
          <intron i_serial="7" don_prob="0.975" acc_prob="1.000">
            <gDNA_intron_boundary i_start="2868" i_stop="2643" i_length="226"/>
          </intron>
          <exon e_serial="8" e_score="1.000">
            <gDNA_exon_boundary e_start="2642" e_stop="2481" e_length="162"/>
          </exon>
          <intron i_serial="8" don_prob="0.998" acc_prob="0.965">
            <gDNA_intron_boundary i_start="2480" i_stop="2392" i_length="89"/>
          </intron>
          <exon e_serial="9" e_score="0.904">
            <gDNA_exon_boundary e_start="2391" e_stop="1995" e_length="397"/>
          </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="6565" stop="6462"/>
              <exon start="6325" stop="6189"/>
              <exon start="5746" stop="5700"/>
              <exon start="5575" stop="5250"/>
              <exon start="4497" stop="4415"/>
              <exon start="4332" stop="4257"/>
              <exon start="3026" stop="2869"/>
              <exon start="2642" stop="2481"/>
              <exon start="2391" stop="2097"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M8952-3" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="6552" stop="6462"/>
              <exon start="6325" stop="6189"/>
              <exon start="5746" stop="5700"/>
              <exon start="5575" stop="5250"/>
              <exon start="4497" stop="4415"/>
              <exon start="4332" stop="4257"/>
              <exon start="3026" stop="2869"/>
              <exon start="2642" stop="2481"/>
              <exon start="2391" stop="1995"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M8952-2" 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>TTGGATCTATTTGTAGAGTCATCCTCAAAAACACTATTTTTATTTTCTTTGATTCTGTGGTCTGTAAATCATGGCTACACAAGGTCAAGTCATCACCTGCAAAG : CTGCGGTGGCCTGGGAACCCAACAAGCCCTTGGTGATTGAGGATGTGCAGGTGGCTCCACCGCAAGCCGGTGAAGTCCGGGTTAAAGTTTTGTATACTGCTCTCTGCCACACCGATGCTTATACCTGGAGTGGCAAG : GATCCTGAGGGTCTCTTCCCATGTGTTCTTGGTCATGAGGCTGCGGG : GATAGTAGAAAGTGTTGGTGAGGGAGTGACTGAGGTTCAGCCAGGAGACCATGTTATACCTTGCTACCAGGCAGAATGCAGAGAATGCAAGTTCTGCAAATCAGGAAAGACCAATCTTTGTGGTAAAGTAAGGGCTGCTACTGGAGTGGGAGTTATGATGAACGACCGTAAGAGTCGATTTTCTATCAATGGAAAACCGATCTATCATTTCATGGGAACTTCAACCTTCAGTCAGTACACTGTTGTCCATGATGTTAGTGTTGCAAAGATTGACCCAGTAGCTCCTCTGGAGAAAGTCTGCCTTCTTGGATGTGGTGTTCCAACTG : GCCTTGGAGCTGTTTGGAACACTGCAAAAGTTGAACCAGGTTCCATTGTTGCCGTCTTTGGCCTGGGAACAGTTGGTCTTGCT : GTGGCGGAGGGTGCAAAAGCTGCTGGTGCTTCACGAATTATTGGAATTGATATTGACAGCAAAAAGTTTGATAGAG : CCAAAAATTTTGGTGTGACTGAATTCATTAATCCCAAGGAGCATGAGCAACCCATTCAGCAAGTCATTGTGGATCTTACTGATGGTGGTGTTGATTACAGTTTTGAGTGCATAGGAAATGTCTCTGTTATGAGGTCTGCTTTAGAGTGTTGTCACAAG : GGTTGGGGAACCTCAGTGATTGTAGGTGTTGCTGCTTCTGGTCAGGAGATATCTACACGTCCATTTCAGCTGGTGACTGGTCGTGTTTGGAAGGGAACTGCTTTTGGTGGTTTCAAAAGCCGATCACAAGTTCCTTCCCTCGTGGACAAGTATTTAAAGAAG : GAAATCAAGGTGGATGAATACATCACTCATAACATGACACTTGCGGACATAAACAAAGCTTTCGACCTGATGCATGACGGGGACTGCCTCCGTGTTGTCCTGGATATGTTTGTATGAATGAAGTCTGTAGGCTCTTTATGTTGCTTACTTTCTGTTTTTGTGCTATTTCTCAGAGACTATTTACCTTTCCCCTTGCTAATTATGTGTTGAATAAAAAGAAAGTGAGAAAAAAAGGATCAAGATGACAGATGAACTCTTTTTAAATGGATGGTAGTTTATTATCTTTTCAAGTAAAATGTTCTTACTTTGAAGGCTAAAACCATCATTACTGGTTTTAGAGTTTGGCATAAACCATTGCCATGTTTGCATAAATGGAATCCTCCCTTTTCCAAAGTAG</gDNA_template>
            <first_frame> L  D  L  F  V  E  S  S  S  K  T  L  F  L  F  S  L  I  L  W  S  V  N  H  G  Y  T  R  S  S  H  H  L  Q  S :   C  G  G  L  G  T  Q  Q  A  L  G  D  *  G  C  A  G  G  S  T  A  S  R  *  S  P  G  *  S  F  V  Y  C  S  L  P  H  R  C  L  Y  L  E  W  Q   : G  S  *  G  S  L  P  M  C  S  W  S  *  G  C  G  :  D  S  R  K  C  W  *  G  S  D  *  G  S  A  R  R  P  C  Y  T  L  L  P  G  R  M  Q  R  M  Q  V  L  Q  I  R  K  D  Q  S  L  W  *  S  K  G  C  Y  W  S  G  S  Y  D  E  R  P  *  E  S  I  F  Y  Q  W  K  T  D  L  S  F  H  G  N  F  N  L  Q  S  V  H  C  C  P  *  C  *  C  C  K  D  *  P  S  S  S  S  G  E  S  L  P  S  W  M  W  C  S  N  W :   P  W  S  C  L  E  H  C  K  S  *  T  R  F  H  C  C  R  L  W  P  G  N  S  W  S  C   : C  G  G  G  C  K  S  C  W  C  F  T  N  Y  W  N  *  Y  *  Q  Q  K  V  *  *  S :   Q  K  F  W  C  D  *  I  H  *  S  Q  G  A  *  A  T  H  S  A  S  H  C  G  S  Y  *  W  W  C  *  L  Q  F  *  V  H  R  K  C  L  C  Y  E  V  C  F  R  V  L  S  Q   : G  L  G  N  L  S  D  C  R  C  C  C  F  W  S  G  D  I  Y  T  S  I  S  A  G  D  W  S  C  L  E  G  N  C  F  W  W  F  Q  K  P  I  T  S  S  F  P  R  G  Q  V  F  K  E   : G  N  Q  G  G  *  I  H  H  S  *  H  D  T  C  G  H  K  Q  S  F  R  P  D  A  *  R  G  L  P  P  C  C  P  G  Y  V  C  M  N  E  V  C  R  L  F  M  L  L  T  F  C  F  C  A  I  S  Q  R  L  F  T  F  P  L  A  N  Y  V  L  N  K  K  K  V  R  K  K  G  S  R  *  Q  M  N  S  F  *  M  D  G  S  L  L  S  F  Q  V  K  C  S  Y  F  E  G  *  N  H  H  Y  W  F  *  S  L  A  *  T  I  A  M  F  A  *  M  E  S  S  L  F  Q  S   </first_frame>
            <second_frame>  W  I  Y  L  *  S  H  P  Q  K  H  Y  F  Y  F  L  *  F  C  G  L  *  I  M  A  T  Q  G  Q  V  I  T  C  K   : A  A  V  A  W  E  P  N  K  P  L  V  I  E  D  V  Q  V  A  P  P  Q  A  G  E  V  R  V  K  V  L  Y  T  A  L  C  H  T  D  A  Y  T  W  S  G  K  :  D  P  E  G  L  F  P  C  V  L  G  H  E  A  A  G :   I  V  E  S  V  G  E  G  V  T  E  V  Q  P  G  D  H  V  I  P  C  Y  Q  A  E  C  R  E  C  K  F  C  K  S  G  K  T  N  L  C  G  K  V  R  A  A  T  G  V  G  V  M  M  N  D  R  K  S  R  F  S  I  N  G  K  P  I  Y  H  F  M  G  T  S  T  F  S  Q  Y  T  V  V  H  D  V  S  V  A  K  I  D  P  V  A  P  L  E  K  V  C  L  L  G  C  G  V  P  T   : G  L  G  A  V  W  N  T  A  K  V  E  P  G  S  I  V  A  V  F  G  L  G  T  V  G  L  A  :  V  A  E  G  A  K  A  A  G  A  S  R  I  I  G  I  D  I  D  S  K  K  F  D  R   : A  K  N  F  G  V  T  E  F  I  N  P  K  E  H  E  Q  P  I  Q  Q  V  I  V  D  L  T  D  G  G  V  D  Y  S  F  E  C  I  G  N  V  S  V  M  R  S  A  L  E  C  C  H  K  :  G  W  G  T  S  V  I  V  G  V  A  A  S  G  Q  E  I  S  T  R  P  F  Q  L  V  T  G  R  V  W  K  G  T  A  F  G  G  F  K  S  R  S  Q  V  P  S  L  V  D  K  Y  L  K  K  :  E  I  K  V  D  E  Y  I  T  H  N  M  T  L  A  D  I  N  K  A  F  D  L  M  H  D  G  D  C  L  R  V  V  L  D  M  F  V  *  M  K  S  V  G  S  L  C  C  L  L  S  V  F  V  L  F  L  R  D  Y  L  P  F  P  L  L  I  M  C  *  I  K  R  K  *  E  K  K  D  Q  D  D  R  *  T  L  F  K  W  M  V  V  Y  Y  L  F  K  *  N  V  L  T  L  K  A  K  T  I  I  T  G  F  R  V  W  H  K  P  L  P  C  L  H  K  W  N  P  P  F  S  K  V  </second_frame>
            <third_frame>   G  S  I  C  R  V  I  L  K  N  T  I  F  I  F  F  D  S  V  V  C  K  S  W  L  H  K  V  K  S  S  P  A  K  :  L  R  W  P  G  N  P  T  S  P  W  *  L  R  M  C  R  W  L  H  R  K  P  V  K  S  G  L  K  F  C  I  L  L  S  A  T  P  M  L  I  P  G  V  A  R :   I  L  R  V  S  S  H  V  F  L  V  M  R  L  R   : G  *  *  K  V  L  V  R  E  *  L  R  F  S  Q  E  T  M  L  Y  L  A  T  R  Q  N  A  E  N  A  S  S  A  N  Q  E  R  P  I  F  V  V  K  *  G  L  L  L  E  W  E  L  *  *  T  T  V  R  V  D  F  L  S  M  E  N  R  S  I  I  S  W  E  L  Q  P  S  V  S  T  L  L  S  M  M  L  V  L  Q  R  L  T  Q  *  L  L  W  R  K  S  A  F  L  D  V  V  F  Q  L  :  A  L  E  L  F  G  T  L  Q  K  L  N  Q  V  P  L  L  P  S  L  A  W  E  Q  L  V  L  L :   W  R  R  V  Q  K  L  L  V  L  H  E  L  L  E  L  I  L  T  A  K  S  L  I  E  :  P  K  I  L  V  *  L  N  S  L  I  P  R  S  M  S  N  P  F  S  K  S  L  W  I  L  L  M  V  V  L  I  T  V  L  S  A  *  E  M  S  L  L  *  G  L  L  *  S  V  V  T  R :   V  G  E  P  Q  *  L  *  V  L  L  L  L  V  R  R  Y  L  H  V  H  F  S  W  *  L  V  V  F  G  R  E  L  L  L  V  V  S  K  A  D  H  K  F  L  P  S  W  T  S  I  *  R  R :   K  S  R  W  M  N  T  S  L  I  T  *  H  L  R  T  *  T  K  L  S  T  *  C  M  T  G  T  A  S  V  L  S  W  I  C  L  Y  E  *  S  L  *  A  L  Y  V  A  Y  F  L  F  L  C  Y  F  S  E  T  I  Y  L  S  P  C  *  L  C  V  E  *  K  E  S  E  K  K  R  I  K  M  T  D  E  L  F  L  N  G  W  *  F  I  I  F  S  S  K  M  F  L  L  *  R  L  K  P  S  L  L  V  L  E  F  G  I  N  H  C  H  V  C  I  N  G  I  L  P  F  P  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="C09HBa0130D14.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="6498" stop="6462"/>
                    <exon start="6325" stop="6189"/>
                    <exon start="5746" stop="5700"/>
                    <exon start="5575" stop="5250"/>
                    <exon start="4497" stop="4415"/>
                    <exon start="4332" stop="4257"/>
                    <exon start="3026" stop="2869"/>
                    <exon start="2642" stop="2481"/>
                    <exon start="2391" stop="2275"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>1140</number_coding_nucleotides>
                  <number_encoded_amino_acids>380</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>IMATQGQVITCKAAVAWEPNKPLVIEDVQVAPPQAGEVRVKVLYTALCHTDAYTWSGKDPEGLFPCVLGHEAAGIVESVGEGVTEVQPGDHVIPCYQAECRECKFCKSGKTNLCGKVRAATGVGVMMNDRKSRFSINGKPIYHFMGTSTFSQYTVVHDVSVAKIDPVAPLEKVCLLGCGVPTGLGAVWNTAKVEPGSIVAVFGLGTVGLAVAEGAKAAGASRIIGIDIDSKKFDRAKNFGVTEFINPKEHEQPIQQVIVDLTDGGVDYSFECIGNVSVMRSALECCHKGWGTSVIVGVAASGQEISTRPFQLVTGRVWKGTAFGGFKSRSQVPSLVDKYLKKEIKVDEYITHNMTLADINKAFDLMHDGDCLRVVLDMFV*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 12 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
$ 5784 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5784 bytes was the average size of a predicted gene location
$ 2 megabytes was the average size of the backtrace matrix
$ 14 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-16 03:01:25
-->
