<?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="2009-01-17 08:50:15"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C09SLm0037I08-8pDIj/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C09SLm0037I08-8pDIj/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-C09SLm0037I08-8pDIj/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M7871" ref_strand="+" ref_description="SGN-M7871 C2_At3g25400 [cosii_markers]">
      <seq>aacagtcggcgcagtttcaaaattttatgtaaatcacaacagaagaagaagaagatgaagggaaaaacagagaatgatgaagaaggagcaaaaggggttgtgactcttgaagagctgaagaaaaaaatggctgattttgctaaagaaagagagtgggatcagtttcatacaccaagaaatctccttttagctatggtgggtgaagtgggagaattgtctgaaatatttcagtggaaaggtgaggtcccaagaggtctaccagattgggcagaaaaagagaagcagcatttaggtgaagagctatcagatgtattgctttatcttgtcaggctttcagatatttgtggcattgatctaggtaatgctgtactcagaaaactggagcttaatgccattaaataccctgttagtctttgcaaaggttcatcaaaaaagcttactcttttgagcaaaagtacaaccaccaccaccaccacctcaagcagtgaaaatggtgtgattaatgatggtgaatgatctttttttgatttagtaggtggtctatttataggtacttgcaatgacatctaatagtttttttttgtgctaaaaggggatgtagagacatatagtgtttgatttgaagtaacatgtatcaagtcaactaatttcttcctatttctagattgtttggttttttgctttatccatatcccctttgcctacaggttaatactgtagaagtttaagacaaatgt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09SLm0037I08-8pDIj/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C09SLm0037I08.2" temp_strand="-" temp_description="C09SLm0037I08.2  EF647613.2 htgs_phase:2 submitted_to_sgn_as:gb|EF647613| upload_account_name:spain (1 - 88383)">
        <position start="53004" stop="50247"/>
      </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="52704" g_stop="52510" g_length="195"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="195" r_length="195" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="52509" i_stop="51089" i_length="1421">
            <donor d_prob="0.939" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="51088" g_stop="50547" g_length="542"/>
          <reference_exon_boundary r_type="cDNA" r_start="196" r_stop="737" r_length="542" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09SLm0037I08.2" gen_strand="-" ref_id="SGN-M7871" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>737</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09SLm0037I08.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M7871" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="52704" e_stop="52510"/>
          <exon e_start="51088" e_stop="50547"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AACAGTCGGCGCAGTTTCAAAATTTTATGTAAATCACAACAGAAGAAGAAGAAGATGAAGGGAAAAACAGAGAATGATGAAGAAGGAGCAAAAGGGGTTGTGACTCTTGAAGAGCTGAAGAAAAAAATGGCTGATTTTGCTAAAGAAAGAGAGTGGGATCAGTTTCATACACCAAGAAATCTCCTTTTAGCTATGGTTTGTATATACCCATTACCCCTTTTGTAAAAAATGAAGTCTTTTTTGGCTTTCAAGTATGTGGGGTTTGGGTTTGGGTTGGTACATAGTGCAACTTTGTCTTCTGTGGGTTTTTTCTGTTGTCTACATTTATGGGTTTTGTTGTGTATCATGTTTTGAGCCATGAAAATGGTGTCTTTTTCTCTGTGTTTTATGATTTTCTGCTATTCTTGGTGATTTTGCTTTGTTTTCTATTTTTTTTAAGGAAAAGCTGGTGTTTTAATTTTTCTGCTCAATGGGTCAGTCTTTATGCTAGTCTGATTATTTTTTTTGTTTGTTTTGTTTTTCAAGATTGCTACTTTTGTTTATCTCTTAGTAAATGTGTTTTTCCTGTGGAATTAGCAAGATATACACATATACACTCAAACTTGGCTGCAGTTGTTGAAGAATAAGCACTTTAATATTGATAGTGAACGTTTAGATACCTCAACTTATCTTTATTGTGTAGGTTGAACACTCTCAACTTCAAAAAGACTATCTAAATACCTCTAAAATTTATGTATTAGGTGTTCATGACACACAATATCGACAAGTTCGAGCGTTTAGTTGTCACTTGAAATCAAGTTAGCTGATAGTTAGAAGTGTTACTTTTCGGCTGAGGTTAAGTTTAGAAAGTTGGAGTCTTGAAAGATAAAAGAACAATTCTTCTCTAAATTTTCCTTAGACAAAACCATGGAACAAAGAGTTCTGTTTGTTTCATAGAAACTAGAAATGTTTGCCAGTATTGGGTCATTGTGGAGAATTTGGATTTCCAATTTTGTGGAAACCCCAATAAAAAAAAAAGCTTTCTTTTGTTTCCCACCAAAGAAGGCATAGTGCTAATAATCTTTTATATGATTTTATGTTCCCCATTATGTAATTTTAGCTTTGCAGTACTTACATGGAAACTAGTGCAACACTTGCACTAATACTAAAAAATGGACATTATAATAAAAGGCTCATATCAATATTCTTCATTTTATAATGGGCATGTAAAGTTCATATTGAACAAATAAAATTGTACGGAGAGAGTAAATAATACTACTCCTAGTAGTGTAAAAACCACATGTAGTGTCAGTTGTATAGATAAATCATTGGATAAATTACTTGGTGAAGATTAAGAAAAGTGGTATTTTGCTTATTTTGACACACACTTCTAATACGTTATATATGCATTTGTGATGTCGCTCGGACTCTTCAGAAATGTTGGCAAGAGTGTGTCAGATGCTCCTATGCAGGTGTGAATAATTCTGGACTCTTGCCAGATACTCCTACGCAGGTGTGACAATAATTTCGGAGAGTTCGAGCAACATAGTGTATTTGCACAATATTGGCATAAAATGAGTTTATATGGTCAATGAAGATTCATATAGTCGATTCTAAAACTTTATTTTGAATACCAGGTGGGTGAAGTGGGAGAATTGTCTGAAATATTTCAGTGGAAAGGTGAGGTCCCAAGAGGTCTACCAGATTGGGCAGAAAAAGAGAAGCAGCATTTAGGTGAAGAGCTATCAGATGTATTGCTTTATCTTGTCAGGCTTTCAGATATTTGTGGCATTGATCTAGGTAATGCTGTACTCAGAAAACTGGAGCTTAATGCCATTAAATACCCTGTTAGTCTTTGCAAAGGTTCATCAAAAAAGCTTACTCTTTTGAGCAAAAGTACAACCACCACCACCACCACCTCAAGCAGTGAAAATGGTGTGATTAATGATGGTGAATGATCTTTTTTTGATTTAGTAGGTGGTCTATTTATAGGTACTTGCAATGACATCTAATAGTTTTTTTTTGTGCTAAAAGGGGATGTAGAGACATATAGTGTTTGATTTGAAGTAACATGTATCAAGTCAACTAATTTCTTCCTATTTCTAGATTGTTTGGTTTTTTGCTTTATCCATATCCCCTTTGCCTACAGGTTAATACTGTAGAAGTTTAAGACAAATGT</genome_strand>
        <mrna_strand>AACAGTCGGCGCAGTTTCAAAATTTTATGTAAATCACAACAGAAGAAGAAGAAGATGAAGGGAAAAACAGAGAATGATGAAGAAGGAGCAAAAGGGGTTGTGACTCTTGAAGAGCTGAAGAAAAAAATGGCTGATTTTGCTAAAGAAAGAGAGTGGGATCAGTTTCATACACCAAGAAATCTCCTTTTAGCTATG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGGGTGAAGTGGGAGAATTGTCTGAAATATTTCAGTGGAAAGGTGAGGTCCCAAGAGGTCTACCAGATTGGGCAGAAAAAGAGAAGCAGCATTTAGGTGAAGAGCTATCAGATGTATTGCTTTATCTTGTCAGGCTTTCAGATATTTGTGGCATTGATCTAGGTAATGCTGTACTCAGAAAACTGGAGCTTAATGCCATTAAATACCCTGTTAGTCTTTGCAAAGGTTCATCAAAAAAGCTTACTCTTTTGAGCAAAAGTACAACCACCACCACCACCACCTCAAGCAGTGAAAATGGTGTGATTAATGATGGTGAATGATCTTTTTTTGATTTAGTAGGTGGTCTATTTATAGGTACTTGCAATGACATCTAATAGTTTTTTTTTGTGCTAAAAGGGGATGTAGAGACATATAGTGTTTGATTTGAAGTAACATGTATCAAGTCAACTAATTTCTTCCTATTTCTAGATTGTTTGGTTTTTTGCTTTATCCATATCCCCTTTGCCTACAGGTTAATACTGTAGAAGTTTAAGACAAATGT</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-C09SLm0037I08-8pDIj/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M1453" ref_strand="+" ref_description="SGN-M1453 T0521 [cos_markers]">
      <seq>aacagtcggcgcagtttcaaaattttatgtaaatcacaacagaagaagaagaagatgaagggaaaaacagagaatgatgaagaaggagcaaaaggggttgtgactcttgaagagctgaagaaaaaaatggctgattttgctaaagaaagagagtgggatcagtttcatacaccaagaaatctccttttagctatggtgggtgaagtgggagaattgtctgaaatatttcagtggaaaggtgaggtcccaagaggtctaccagattgggcagaaaaagagaagcagcatttaggtgaagagctatcagatgtattgctttatcttgtcaggctttcagatatttgtggcattgatctaggtaatgct</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09SLm0037I08-8pDIj/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C09SLm0037I08.2" temp_strand="-" temp_description="C09SLm0037I08.2  EF647613.2 htgs_phase:2 submitted_to_sgn_as:gb|EF647613| upload_account_name:spain (1 - 88383)">
        <position start="53004" stop="50618"/>
      </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="52704" g_stop="52510" g_length="195"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="195" r_length="195" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="52509" i_stop="51089" i_length="1421">
            <donor d_prob="0.939" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="51088" g_stop="50918" g_length="171"/>
          <reference_exon_boundary r_type="cDNA" r_start="196" r_stop="366" r_length="171" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09SLm0037I08.2" gen_strand="-" ref_id="SGN-M1453" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>366</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09SLm0037I08.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M1453" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="52704" e_stop="52510"/>
          <exon e_start="51088" e_stop="50918"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AACAGTCGGCGCAGTTTCAAAATTTTATGTAAATCACAACAGAAGAAGAAGAAGATGAAGGGAAAAACAGAGAATGATGAAGAAGGAGCAAAAGGGGTTGTGACTCTTGAAGAGCTGAAGAAAAAAATGGCTGATTTTGCTAAAGAAAGAGAGTGGGATCAGTTTCATACACCAAGAAATCTCCTTTTAGCTATGGTTTGTATATACCCATTACCCCTTTTGTAAAAAATGAAGTCTTTTTTGGCTTTCAAGTATGTGGGGTTTGGGTTTGGGTTGGTACATAGTGCAACTTTGTCTTCTGTGGGTTTTTTCTGTTGTCTACATTTATGGGTTTTGTTGTGTATCATGTTTTGAGCCATGAAAATGGTGTCTTTTTCTCTGTGTTTTATGATTTTCTGCTATTCTTGGTGATTTTGCTTTGTTTTCTATTTTTTTTAAGGAAAAGCTGGTGTTTTAATTTTTCTGCTCAATGGGTCAGTCTTTATGCTAGTCTGATTATTTTTTTTGTTTGTTTTGTTTTTCAAGATTGCTACTTTTGTTTATCTCTTAGTAAATGTGTTTTTCCTGTGGAATTAGCAAGATATACACATATACACTCAAACTTGGCTGCAGTTGTTGAAGAATAAGCACTTTAATATTGATAGTGAACGTTTAGATACCTCAACTTATCTTTATTGTGTAGGTTGAACACTCTCAACTTCAAAAAGACTATCTAAATACCTCTAAAATTTATGTATTAGGTGTTCATGACACACAATATCGACAAGTTCGAGCGTTTAGTTGTCACTTGAAATCAAGTTAGCTGATAGTTAGAAGTGTTACTTTTCGGCTGAGGTTAAGTTTAGAAAGTTGGAGTCTTGAAAGATAAAAGAACAATTCTTCTCTAAATTTTCCTTAGACAAAACCATGGAACAAAGAGTTCTGTTTGTTTCATAGAAACTAGAAATGTTTGCCAGTATTGGGTCATTGTGGAGAATTTGGATTTCCAATTTTGTGGAAACCCCAATAAAAAAAAAAGCTTTCTTTTGTTTCCCACCAAAGAAGGCATAGTGCTAATAATCTTTTATATGATTTTATGTTCCCCATTATGTAATTTTAGCTTTGCAGTACTTACATGGAAACTAGTGCAACACTTGCACTAATACTAAAAAATGGACATTATAATAAAAGGCTCATATCAATATTCTTCATTTTATAATGGGCATGTAAAGTTCATATTGAACAAATAAAATTGTACGGAGAGAGTAAATAATACTACTCCTAGTAGTGTAAAAACCACATGTAGTGTCAGTTGTATAGATAAATCATTGGATAAATTACTTGGTGAAGATTAAGAAAAGTGGTATTTTGCTTATTTTGACACACACTTCTAATACGTTATATATGCATTTGTGATGTCGCTCGGACTCTTCAGAAATGTTGGCAAGAGTGTGTCAGATGCTCCTATGCAGGTGTGAATAATTCTGGACTCTTGCCAGATACTCCTACGCAGGTGTGACAATAATTTCGGAGAGTTCGAGCAACATAGTGTATTTGCACAATATTGGCATAAAATGAGTTTATATGGTCAATGAAGATTCATATAGTCGATTCTAAAACTTTATTTTGAATACCAGGTGGGTGAAGTGGGAGAATTGTCTGAAATATTTCAGTGGAAAGGTGAGGTCCCAAGAGGTCTACCAGATTGGGCAGAAAAAGAGAAGCAGCATTTAGGTGAAGAGCTATCAGATGTATTGCTTTATCTTGTCAGGCTTTCAGATATTTGTGGCATTGATCTAGGTAATGCT</genome_strand>
        <mrna_strand>AACAGTCGGCGCAGTTTCAAAATTTTATGTAAATCACAACAGAAGAAGAAGAAGATGAAGGGAAAAACAGAGAATGATGAAGAAGGAGCAAAAGGGGTTGTGACTCTTGAAGAGCTGAAGAAAAAAATGGCTGATTTTGCTAAAGAAAGAGAGTGGGATCAGTTTCATACACCAAGAAATCTCCTTTTAGCTATG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGGGTGAAGTGGGAGAATTGTCTGAAATATTTCAGTGGAAAGGTGAGGTCCCAAGAGGTCTACCAGATTGGGCAGAAAAAGAGAAGCAGCATTTAGGTGAAGAGCTATCAGATGTATTGCTTTATCTTGTCAGGCTTTCAGATATTTGTGGCATTGATCTAGGTAATGCT</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-C09SLm0037I08-8pDIj/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M1440" ref_strand="+" ref_description="SGN-M1440 T0486 [cos_markers]">
      <seq>aatgacgaaagagggaaagaatgtgaaaagaatcaaattgggttcagagggacttgaagtatctgttcaaggacttggttgtctgggtatgtccgatttctacggtccgcccaaacccgaacccgatatgattgaactaatacaccatgccattaactccggcataacatttttcgatacttcaaatagttatgggccttacactaatgaaatcctccttggcaaggctttgaagggaggaatgagggaacgagtcgagttagcaacaaaatttggtatacattttgcagatggaaagatagaagtacgtggagagccataatatgtaagggcagcatgcgaggctagcttaaagcgacttgatgttgattgcatagacttgtactacc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09SLm0037I08-8pDIj/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C09SLm0037I08.2" temp_strand="+" temp_description="C09SLm0037I08.2  EF647613.2 htgs_phase:2 submitted_to_sgn_as:gb|EF647613| upload_account_name:spain (1 - 88383)">
        <position start="60642" stop="61728"/>
      </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="60942" g_stop="61167" g_length="226"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="226" r_length="226" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="61168" i_stop="61265" i_length="98">
            <donor d_prob="0.995" d_score="1.00"/>
            <acceptor a_prob="0.987" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="61266" g_stop="61428" g_length="163"/>
          <reference_exon_boundary r_type="cDNA" r_start="227" r_stop="389" r_length="163" r_score="0.994"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09SLm0037I08.2" gen_strand="+" ref_id="SGN-M1440" ref_strand="+">
        <total_alignment_score>0.997</total_alignment_score>
        <cumulative_length_of_scored_exons>389</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09SLm0037I08.2" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M1440" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="60942" e_stop="61167"/>
          <exon e_start="61266" e_stop="61428"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AATGACGAAAGAGGGAAAGAATGTGAAAAGAATCAAATTGGGTTCAGAGGGACTTGAAGTATCTGTTCAAGGACTTGGTTGTCTGGGTATGTCCGATTTCTACGGTCCGCCCAAACCCGAACCCGATATGATTGAACTAATACACCATGCCATTAACTCCGGCATAACATTTTTCGATACTTCAAATAGTTATGGGCCTTACACTAATGAAATCCTCCTTGGCAAGGTATCAATTTGTCAATTCTTTTAAGTTATGGTTGTACCGAATCGAACATGAAGTAATAAGGTGAAAGTAAATACTGAGCTGCTAAAATTCTAATACAGGCTTTGAAGGGAGGAATGAGGGAACGAGTCGAGTTAGCAACAAAATTTGGTATACATTTTGCAGATGGAAAGATAGAAGTACGTGGAGAGCCAGAATATGTAAGGGCAGCATGCGAGGCTAGCTTAAAGCGACTTGATGTTGATTGCATAGACTTGTACTACC</genome_strand>
        <mrna_strand>AATGACGAAAGAGGGAAAGAATGTGAAAAGAATCAAATTGGGTTCAGAGGGACTTGAAGTATCTGTTCAAGGACTTGGTTGTCTGGGTATGTCCGATTTCTACGGTCCGCCCAAACCCGAACCCGATATGATTGAACTAATACACCATGCCATTAACTCCGGCATAACATTTTTCGATACTTCAAATAGTTATGGGCCTTACACTAATGAAATCCTCCTTGGCAAG..................................................................................................GCTTTGAAGGGAGGAATGAGGGAACGAGTCGAGTTAGCAACAAAATTTGGTATACATTTTGCAGATGGAAAGATAGAAGTACGTGGAGAGCCATAATATGTAAGGGCAGCATGCGAGGCTAGCTTAAAGCGACTTGATGTTGATTGCATAGACTTGTACTACC</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="52704" PGL_stop="50547"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="52704" e_stop="52510"/>
            <exon e_start="51088" e_stop="50547"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.939" acc_prob="0.998" e_score="1.000"/>
          <exon-only e_score="1.000"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="1.000">
            <gDNA_exon_boundary e_start="52704" e_stop="52510" e_length="195"/>
          </exon>
          <intron i_serial="1" don_prob="0.939" acc_prob="0.998">
            <gDNA_intron_boundary i_start="52509" i_stop="51089" i_length="1421"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="51088" e_stop="50547" e_length="542"/>
          </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="52704" stop="52510"/>
              <exon start="51088" stop="50547"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M7871" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="52704" stop="52510"/>
              <exon start="51088" stop="50918"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1453" 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>AACAGTCGGCGCAGTTTCAAAATTTTATGTAAATCACAACAGAAGAAGAAGAAGATGAAGGGAAAAACAGAGAATGATGAAGAAGGAGCAAAAGGGGTTGTGACTCTTGAAGAGCTGAAGAAAAAAATGGCTGATTTTGCTAAAGAAAGAGAGTGGGATCAGTTTCATACACCAAGAAATCTCCTTTTAGCTATG : GTGGGTGAAGTGGGAGAATTGTCTGAAATATTTCAGTGGAAAGGTGAGGTCCCAAGAGGTCTACCAGATTGGGCAGAAAAAGAGAAGCAGCATTTAGGTGAAGAGCTATCAGATGTATTGCTTTATCTTGTCAGGCTTTCAGATATTTGTGGCATTGATCTAGGTAATGCTGTACTCAGAAAACTGGAGCTTAATGCCATTAAATACCCTGTTAGTCTTTGCAAAGGTTCATCAAAAAAGCTTACTCTTTTGAGCAAAAGTACAACCACCACCACCACCACCTCAAGCAGTGAAAATGGTGTGATTAATGATGGTGAATGATCTTTTTTTGATTTAGTAGGTGGTCTATTTATAGGTACTTGCAATGACATCTAATAGTTTTTTTTTGTGCTAAAAGGGGATGTAGAGACATATAGTGTTTGATTTGAAGTAACATGTATCAAGTCAACTAATTTCTTCCTATTTCTAGATTGTTTGGTTTTTTGCTTTATCCATATCCCCTTTGCCTACAGGTTAATACTGTAGAAGTTTAAGACAAATGT</gDNA_template>
            <first_frame> N  S  R  R  S  F  K  I  L  C  K  S  Q  Q  K  K  K  K  M  K  G  K  T  E  N  D  E  E  G  A  K  G  V  V  T  L  E  E  L  K  K  K  M  A  D  F  A  K  E  R  E  W  D  Q  F  H  T  P  R  N  L  L  L  A  M  :  V  G  E  V  G  E  L  S  E  I  F  Q  W  K  G  E  V  P  R  G  L  P  D  W  A  E  K  E  K  Q  H  L  G  E  E  L  S  D  V  L  L  Y  L  V  R  L  S  D  I  C  G  I  D  L  G  N  A  V  L  R  K  L  E  L  N  A  I  K  Y  P  V  S  L  C  K  G  S  S  K  K  L  T  L  L  S  K  S  T  T  T  T  T  T  T  S  S  S  E  N  G  V  I  N  D  G  E  *  S  F  F  D  L  V  G  G  L  F  I  G  T  C  N  D  I  *  *  F  F  F  V  L  K  G  D  V  E  T  Y  S  V  *  F  E  V  T  C  I  K  S  T  N  F  F  L  F  L  D  C  L  V  F  C  F  I  H  I  P  F  A  Y  R  L  I  L  *  K  F  K  T  N   </first_frame>
            <second_frame>  T  V  G  A  V  S  K  F  Y  V  N  H  N  R  R  R  R  R  *  R  E  K  Q  R  M  M  K  K  E  Q  K  G  L  *  L  L  K  S  *  R  K  K  W  L  I  L  L  K  K  E  S  G  I  S  F  I  H  Q  E  I  S  F  *  L  W :   W  V  K  W  E  N  C  L  K  Y  F  S  G  K  V  R  S  Q  E  V  Y  Q  I  G  Q  K  K  R  S  S  I  *  V  K  S  Y  Q  M  Y  C  F  I  L  S  G  F  Q  I  F  V  A  L  I  *  V  M  L  Y  S  E  N  W  S  L  M  P  L  N  T  L  L  V  F  A  K  V  H  Q  K  S  L  L  F  *  A  K  V  Q  P  P  P  P  P  P  Q  A  V  K  M  V  *  L  M  M  V  N  D  L  F  L  I  *  *  V  V  Y  L  *  V  L  A  M  T  S  N  S  F  F  L  C  *  K  G  M  *  R  H  I  V  F  D  L  K  *  H  V  S  S  Q  L  I  S  S  Y  F  *  I  V  W  F  F  A  L  S  I  S  P  L  P  T  G  *  Y  C  R  S  L  R  Q  M  </second_frame>
            <third_frame>   Q  S  A  Q  F  Q  N  F  M  *  I  T  T  E  E  E  E  D  E  G  K  N  R  E  *  *  R  R  S  K  R  G  C  D  S  *  R  A  E  E  K  N  G  *  F  C  *  R  K  R  V  G  S  V  S  Y  T  K  K  S  P  F  S  Y   : G  G  *  S  G  R  I  V  *  N  I  S  V  E  R  *  G  P  K  R  S  T  R  L  G  R  K  R  E  A  A  F  R  *  R  A  I  R  C  I  A  L  S  C  Q  A  F  R  Y  L  W  H  *  S  R  *  C  C  T  Q  K  T  G  A  *  C  H  *  I  P  C  *  S  L  Q  R  F  I  K  K  A  Y  S  F  E  Q  K  Y  N  H  H  H  H  H  L  K  Q  *  K  W  C  D  *  *  W  *  M  I  F  F  *  F  S  R  W  S  I  Y  R  Y  L  Q  *  H  L  I  V  F  F  C  A  K  R  G  C  R  D  I  *  C  L  I  *  S  N  M  Y  Q  V  N  *  F  L  P  I  S  R  L  F  G  F  L  L  Y  P  Y  P  L  C  L  Q  V  N  T  V  E  V  *  D  K  C </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="C09SLm0037I08.2" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="52704" stop="52510"/>
                    <exon start="51088" stop="50768"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>513</number_coding_nucleotides>
                  <number_encoded_amino_acids>171</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>NSRRSFKILCKSQQKKKKMKGKTENDEEGAKGVVTLEELKKKMADFAKEREWDQFHTPRNLLLAMVGEVGELSEIFQWKGEVPRGLPDWAEKEKQHLGEELSDVLLYLVRLSDICGIDLGNAVLRKLELNAIKYPVSLCKGSSKKLTLLSKSTTTTTTTSSSENGVINDGE*</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="60942" PGL_stop="61428"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="60942" e_stop="61167"/>
            <exon e_start="61266" e_stop="61428"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.995" acc_prob="0.987" e_score="1.000"/>
          <exon-only e_score="0.994"/>
        </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="60942" e_stop="61167" e_length="226"/>
          </exon>
          <intron i_serial="1" don_prob="0.995" acc_prob="0.987">
            <gDNA_intron_boundary i_start="61168" i_stop="61265" i_length="98"/>
          </intron>
          <exon e_serial="2" e_score="0.994">
            <gDNA_exon_boundary e_start="61266" e_stop="61428" e_length="163"/>
          </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="60942" stop="61167"/>
              <exon start="61266" stop="61428"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1440" 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>AATGACGAAAGAGGGAAAGAATGTGAAAAGAATCAAATTGGGTTCAGAGGGACTTGAAGTATCTGTTCAAGGACTTGGTTGTCTGGGTATGTCCGATTTCTACGGTCCGCCCAAACCCGAACCCGATATGATTGAACTAATACACCATGCCATTAACTCCGGCATAACATTTTTCGATACTTCAAATAGTTATGGGCCTTACACTAATGAAATCCTCCTTGGCAAG : GCTTTGAAGGGAGGAATGAGGGAACGAGTCGAGTTAGCAACAAAATTTGGTATACATTTTGCAGATGGAAAGATAGAAGTACGTGGAGAGCCAGAATATGTAAGGGCAGCATGCGAGGCTAGCTTAAAGCGACTTGATGTTGATTGCATAGACTTGTACTACC</gDNA_template>
            <first_frame> N  D  E  R  G  K  E  C  E  K  N  Q  I  G  F  R  G  T  *  S  I  C  S  R  T  W  L  S  G  Y  V  R  F  L  R  S  A  Q  T  R  T  R  Y  D  *  T  N  T  P  C  H  *  L  R  H  N  I  F  R  Y  F  K  *  L  W  A  L  H  *  *  N  P  P  W  Q   : G  F  E  G  R  N  E  G  T  S  R  V  S  N  K  I  W  Y  T  F  C  R  W  K  D  R  S  T  W  R  A  R  I  C  K  G  S  M  R  G  *  L  K  A  T  *  C  *  L  H  R  L  V  L   </first_frame>
            <second_frame>  M  T  K  E  G  K  N  V  K  R  I  K  L  G  S  E  G  L  E  V  S  V  Q  G  L  G  C  L  G  M  S  D  F  Y  G  P  P  K  P  E  P  D  M  I  E  L  I  H  H  A  I  N  S  G  I  T  F  F  D  T  S  N  S  Y  G  P  Y  T  N  E  I  L  L  G  K  :  A  L  K  G  G  M  R  E  R  V  E  L  A  T  K  F  G  I  H  F  A  D  G  K  I  E  V  R  G  E  P  E  Y  V  R  A  A  C  E  A  S  L  K  R  L  D  V  D  C  I  D  L  Y  Y  </second_frame>
            <third_frame>   *  R  K  R  E  R  M  *  K  E  S  N  W  V  Q  R  D  L  K  Y  L  F  K  D  L  V  V  W  V  C  P  I  S  T  V  R  P  N  P  N  P  I  *  L  N  *  Y  T  M  P  L  T  P  A  *  H  F  S  I  L  Q  I  V  M  G  L  T  L  M  K  S  S  L  A  R :   L  *  R  E  E  *  G  N  E  S  S  *  Q  Q  N  L  V  Y  I  L  Q  M  E  R  *  K  Y  V  E  S  Q  N  M  *  G  Q  H  A  R  L  A  *  S  D  L  M  L  I  A  *  T  C  T  T </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="C09SLm0037I08.2" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="60943" stop="61167"/>
                    <exon start="61266" stop="61427"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>387</number_coding_nucleotides>
                  <number_encoded_amino_acids>129</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>MTKEGKNVKRIKLGSEGLEVSVQGLGCLGMSDFYGPPKPEPDMIELIHHAINSGITFFDTSNSYGPYTNEILLGKALKGGMRERVELATKFGIHFADGKIEVRGEPEYVRAACEASLKRLDVDCIDLYY</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:
$ 6840 bytes spliced alignments in total
$ 3 spliced alignments have been stored
$ 2280 bytes was the average size of a spliced alignment
$ 6768 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3384 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 12 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-17 08:50:19
-->
