<?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="2009-01-15 15:26:41"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C07HBa0308M01-HT6HJ/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C07HBa0308M01-HT6HJ/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-C07HBa0308M01-HT6HJ/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M1811" ref_strand="+" ref_description="SGN-M1811 T1171 [cos_markers]">
      <seq>gaggccattgctaagtactgccccaatgctctggtcaatatgataagcaacccagtgaattccactgtccctattgctgctgaggtgtttaagaaagctggaacttatgatgaaaagaagctctttggagttaccatgcttgatgtggttagggccaagacattttatgctggaaaagctaaagtaaatgttgctgaggtcaatctcccagtagttggtggtcatgctggcataactatcctcccattattttctcaagccactccaaaggcaaatctatcagatgaggaaattgttgcactcacaaagcgaacccaagatggtgggacagaagttgtagaggccaaggctggaaagggttcagccaccctctcaatggcctatgctggggctatttttgccgatgcttgcttgaaggggttgaatggagttcccgatgttgttgaatgtgcttttgtgcagtccaatgtcaccgagcttcccttcttcgcatccaaagtaagacttgggaaaaatggagt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0308M01-HT6HJ/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07HBa0308M01.1" temp_strand="-" temp_description="C07HBa0308M01.1  AC210364.1 htgs_phase:3 submitted_to_sgn_as:C07HBa0308M01 upload_account_name:france">
        <position start="20160" stop="17908"/>
      </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="19862" g_stop="19836" g_length="27"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="27" r_length="27" r_score="0.926"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="19835" i_stop="19727" i_length="109">
            <donor d_prob="0.718" d_score="0.00"/>
            <acceptor a_prob="0.960" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="19726" g_stop="19558" g_length="169"/>
          <reference_exon_boundary r_type="cDNA" r_start="28" r_stop="196" r_length="169" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="19557" i_stop="19441" i_length="117">
            <donor d_prob="0.990" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="19440" g_stop="19379" g_length="62"/>
          <reference_exon_boundary r_type="cDNA" r_start="197" r_stop="258" r_length="62" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="19378" i_stop="19196" i_length="183">
            <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="4">
          <gDNA_exon_boundary g_start="19195" g_stop="19074" g_length="122"/>
          <reference_exon_boundary r_type="cDNA" r_start="259" r_stop="380" r_length="122" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="19073" i_stop="18830" i_length="244">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="0.963" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="18829" g_stop="18712" g_length="118"/>
          <reference_exon_boundary r_type="cDNA" r_start="381" r_stop="498" r_length="118" r_score="0.992"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="18711" i_stop="18231" i_length="481">
            <donor d_prob="1.000" d_score="0.98"/>
            <acceptor a_prob="1.000" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="18230" g_stop="18208" g_length="23"/>
          <reference_exon_boundary r_type="cDNA" r_start="499" r_stop="521" r_length="23" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07HBa0308M01.1" gen_strand="-" ref_id="SGN-M1811" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>521</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0308M01.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M1811" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="19862" e_stop="19836"/>
          <exon e_start="19726" e_stop="19558"/>
          <exon e_start="19440" e_stop="19379"/>
          <exon e_start="19195" e_stop="19074"/>
          <exon e_start="18829" e_stop="18712"/>
          <exon e_start="18230" e_stop="18208"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ACGGCCATTGCTAAGTACTGCCCCAATGTGAGTATGCTTGTGTAATTATCTCTGTATATGGGGGTTATATATAGGAGATTCTAGAAAAAGTTTCTGATTAATTTTCTCATTTGCTGCTTGTTCTGATAACTTAAAGGCTCTGGTCAATATGATAAGCAACCCAGTGAATTCCACTGTCCCTATTGCTGCTGAGGTGTTTAAGAAAGCTGGAACTTATGATGAAAAGAAGCTCTTTGGAGTTACCATGCTTGATGTGGTTAGGGCCAAGACATTTTATGCTGGAAAAGCTAAAGTAAATGTTGCTGGTGCGCGTCTTCTTGTCTAATTCTTTATTTGAATTGATTTTGTTTCGCTTTACATGAAACTGTAAATTCATACAATACTATCTGTCTACTTTACTTACTTTTTGCTTCGTTTTTCAGAGGTCAATCTCCCAGTAGTTGGTGGTCATGCTGGCATAACTATCCTCCCATTATTTTCTCAAGTAATTTTTCTTTTCTTGTCCCTTGTTATAAAGCTTTTTCTTTTTTTAGTATCTATTATTATCTTCTTTATGTTGTAAGTGTTTGATTGAACATTTTTTAGTATGTATTATCTAAATTGTTATTGGTGATTTCCATATTGTGGCATATTGAGTCTTGTTTTTATCACTAAATTTTGGATACAGGCCACTCCAAAGGCAAATCTATCAGATGAGGAAATTGTTGCACTCACAAAGCGAACCCAAGATGGTGGGACAGAAGTTGTAGAGGCCAAGGCTGGAAAGGGTTCAGCCACCCTCTCAATGGCGTACGTTTCCACTTCAATGTTTTTCTTGATTTATTTTTTTTTCCTGAAGGATTTTCACTTTGATTGCAAGATTTTGTTTACGAATAAGTTATGGTGCTGCCCAATGTCACGGTCAAATATTTAGGAATGTAGAGAAACAAACAAAAAAAGAAACTTTTTTGACATATACTGCCCCAAACCACTTCATTTACTGGCCTTTCCTGTTTGCATACTCGGTTCTAAGCAGTTAGTTTTACTTGTGCAGCTATGCTGGGGCTATTTTTGCCGATGCTTGCTTGAAGGGGTTGAATGGAGTTCCCGATGTTGTTGAATGTGCTTTTGTGCAGTCCAATGTCACCGAGCTTCCCTTCTTCGCATCCAAGGTAATAAGCCTTTTCTTTTCCTACAAAGACACTGGACGTCATGTATACTTTTTTCTTTGAACTGTCTGATTCATTTGGTCATTGCCCTCTTATCATGTGGGTATGAAAAGGTCAAAACAAATTATATAGTTCAAGTTTAGGTTTGTTTAAGCATGTCTGAAGCTGTGTCTATTCTGGATGTGTTGAGGGATAGTTTTGACATCATGAGTCATCGATTGATCTTGATTAAGCATGTCTCATGTGGAATGGTTGGTAGCTTTTCAACAGTGCAAGTCGAATGTGTCAAGAACTAAGTTGACATCCTAGGTTATTATTTGTTGTTAGTCACACACGCATCTGAACGTAAATAGCTCGTTAACTTTGAATCATGGGCTAAATTTGTACTTCCTCTTATCAACTGACTTGTGGGTAATTCACTGTATAAGGTCACTATTTTCATTTTGCTTACTTATACATGTCATTCAATTTGATCGCTTTGCAGGTAAGACTTGGGAAAAATGGAGT</genome_strand>
        <mrna_strand>GAGGCCATTGCTAAGTACTGCCCCAAT.............................................................................................................GCTCTGGTCAATATGATAAGCAACCCAGTGAATTCCACTGTCCCTATTGCTGCTGAGGTGTTTAAGAAAGCTGGAACTTATGATGAAAAGAAGCTCTTTGGAGTTACCATGCTTGATGTGGTTAGGGCCAAGACATTTTATGCTGGAAAAGCTAAAGTAAATGTTGCTG.....................................................................................................................AGGTCAATCTCCCAGTAGTTGGTGGTCATGCTGGCATAACTATCCTCCCATTATTTTCTCAA.......................................................................................................................................................................................GCCACTCCAAAGGCAAATCTATCAGATGAGGAAATTGTTGCACTCACAAAGCGAACCCAAGATGGTGGGACAGAAGTTGTAGAGGCCAAGGCTGGAAAGGGTTCAGCCACCCTCTCAATGGC....................................................................................................................................................................................................................................................CTATGCTGGGGCTATTTTTGCCGATGCTTGCTTGAAGGGGTTGAATGGAGTTCCCGATGTTGTTGAATGTGCTTTTGTGCAGTCCAATGTCACCGAGCTTCCCTTCTTCGCATCCAAA.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTAAGACTTGGGAAAAATGGAGT</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-C07HBa0308M01-HT6HJ/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M416-F" ref_strand="-" ref_description="SGN-M416-F CT54-F [rflp_markers_forward]">
      <seq>caacaatctttccgatccaagtgaagcagaaaacaggggggtggtagatggaaatctcgttcccagcagaggtccaggatctaccatggagttcccactgcccattgcagataagtttatgggccccagggaaccattagagctagcaaaggagaccattttttaagtatttaccctttttgccgttatgatccttctttagcatcatatccactttgatataggatggggtaaacttgtagtataataaactttgttataccactgtgcgcttacagctttgtttcggtggtcgttagttaccatgtcgtattgggggggtagtttaaatacaaattatcttcaggtaatgtcaaaaaagtctcaagttttgtgtaccaaaaaataaaaaaaaaaaaaacacaaaaaaaaaaaaaaaag</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0308M01-HT6HJ/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07HBa0308M01.1" temp_strand="-" temp_description="C07HBa0308M01.1  AC210364.1 htgs_phase:3 submitted_to_sgn_as:C07HBa0308M01 upload_account_name:france">
        <position start="50850" stop="49865"/>
      </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="50550" g_stop="50171" g_length="380"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="380" r_length="380" r_score="0.911"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="381" polyA_stop="400"/>
      <MATCH_line gen_id="C07HBa0308M01.1" gen_strand="-" ref_id="SGN-M416-F" ref_strand="-">
        <total_alignment_score>0.911</total_alignment_score>
        <cumulative_length_of_scored_exons>380</cumulative_length_of_scored_exons>
        <coverage percentage="0.905" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0308M01.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M416-F" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="50550" e_stop="50171"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CAACAAACTTTCCGATCCAAGTGAAGCAGAAAACAGGGTGGTGGTAGATGGAAATCTCGTTACCAGCAGAGGACCAGGAACTACCATGGAGTTCGCACTGGCCATTGCAGATAAGTTTATTGGGCACAAGGAAACATTAGAGCTAGCAAAGGAGATGATTTTCTAAGTATTTAACTTTTTTGCCGCTATGATCCGTCTTTAGCATCATATACACTTTGCTATATGATGGTGTAAACTTGTAGTATAATAAACTTTGCTATATCACTCTGCACTTACAGCTTTGTTTCGGTGGTTGTTAGTTATCATGTTGTATTGTGGTGGTAGTTTAAATACAAATTATCTTCAGGTAATGACAAAAAAGTCTCAAGTTTTGTGTAACA</genome_strand>
        <mrna_strand>CAACAATCTTTCCGATCCAAGTGAAGCAGAAAACAGGGGGGTGGTAGATGGAAATCTCGTTCCCAGCAGAGGTCCAGGATCTACCATGGAGTTCCCACTGCCCATTGCAGATAAGTTTATGGGCCCCAGGGAACCATTAGAGCTAGCAAAGGAGACCATTTTTTAAGTATTTACCCTTTTTGCCGTTATGATCCTTCTTTAGCATCATATCCACTTTGATATAGGATGGGGTAAACTTGTAGTATAATAAACTTTGTTATACCACTGTGCGCTTACAGCTTTGTTTCGGTGGTCGTTAGTTACCATGTCGTATTGGGGGGGTAGTTTAAATACAAATTATCTTCAGGTAATGTCAAAAAAGTCTCAAGTTTTGTGTACCA</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-C07HBa0308M01-HT6HJ/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M416-R" ref_strand="+" ref_description="SGN-M416-R CT54-R [rflp_markers_reverse]">
      <seq>tcttgacctattgcaaatggttctgaggaaatggaagctactattattattgatgtacttcggcgagcaaacgctcaagtagttgtggcatctatggaagataaattggagattgttgcttccagaaaagttaaactagttgcagatgtgctccttgatgaagctgctaaacagtcttacgatctcattgtcctaccaggcggtcttggtggtgccgaaacatttgccaaatcagaaaagttggttgacatgctgaagaagcagagggaatcaagcaaaccatatggagcaatgtgtgcatctccagctctagtcctagagccccatgggcttctccaggtaagagacatactcatgctcttcgattttgaaagtaaaactgttttaaagcaagtgaatattacctcaagtactgtaatttgtacattaccttggtttatcaggataaaaaaagccacgacttaaaggtcttgattggccttaaccttgatgagctaggctatattggttcatctaaataggttcaaaaaagcaacagtattatattattaaatatacaaggggcctgttgttccaagtcttgca</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0308M01-HT6HJ/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07HBa0308M01.1" temp_strand="-" temp_description="C07HBa0308M01.1  AC210364.1 htgs_phase:3 submitted_to_sgn_as:C07HBa0308M01 upload_account_name:france">
        <position start="51609" stop="50348"/>
      </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="51309" g_stop="51111" g_length="199"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="198" r_length="198" r_score="0.995"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="51110" i_stop="51035" i_length="76">
            <donor d_prob="0.958" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="51034" g_stop="50648" g_length="387"/>
          <reference_exon_boundary r_type="cDNA" r_start="199" r_stop="585" r_length="387" r_score="0.997"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07HBa0308M01.1" gen_strand="-" ref_id="SGN-M416-R" ref_strand="+">
        <total_alignment_score>0.997</total_alignment_score>
        <cumulative_length_of_scored_exons>586</cumulative_length_of_scored_exons>
        <coverage percentage="1.002" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0308M01.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M416-R" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="51309" e_stop="51111"/>
          <exon e_start="51034" e_stop="50648"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCTTGTACCTATTGCAAATGGTTCTGAGGAAATGGAAGCTACTATTATTATTGATGTACTTCGGCGAGCAAACGCTCAAGTAGTTGTGGCATCTATGGAAGATAAATTGGAGATTGTTGCTTCCAGAAAAGTTAAACTAGTTGCAGATGTGCTCCTTGATGAAGCTGCTAAACAGTCTTACGATCTCATTGTCCTACCAGTGAGTGCAATCCTCTGAAAATCTGCTTCTAAAGCTTCTTGAAGTTCTTGTCTTACTGTAATATATGAATATGCAGGGCGGTCTTGGTGGTGCCGAAACATTTGCCAAATCAGAAAAGTTGGTTGACATGCTGAAGAAGCAGAGGGAATCAAGCAAACCATATGGAGCAATGTGTGCATCTCCAGCTCTAGTCCTAGAGCCCCATGGGCTTCTCCAGGTAAGAGACATACTCATGCTCTTCGATTTTGAAAGTAAAACTATTTTAAAGCAAGTGAATATTACCTCAAGTACTGTAATTTGTACATTACCTTGGTTTATCAGGATAAAAAAAGCCACGACTTAAAGGTCTTGATTGGCCTTAACCTTGATGAGCTAGGCTATATTGGTTCATCTAAATAGGTTCAAAAAAGCAACAGTATTATATTATTAAATATACAAGGGGCCTGTTGTTCCAAGTCTTGCA</genome_strand>
        <mrna_strand>TCTTG-ACCTATTGCAAATGGTTCTGAGGAAATGGAAGCTACTATTATTATTGATGTACTTCGGCGAGCAAACGCTCAAGTAGTTGTGGCATCTATGGAAGATAAATTGGAGATTGTTGCTTCCAGAAAAGTTAAACTAGTTGCAGATGTGCTCCTTGATGAAGCTGCTAAACAGTCTTACGATCTCATTGTCCTACCA............................................................................GGCGGTCTTGGTGGTGCCGAAACATTTGCCAAATCAGAAAAGTTGGTTGACATGCTGAAGAAGCAGAGGGAATCAAGCAAACCATATGGAGCAATGTGTGCATCTCCAGCTCTAGTCCTAGAGCCCCATGGGCTTCTCCAGGTAAGAGACATACTCATGCTCTTCGATTTTGAAAGTAAAACTGTTTTAAAGCAAGTGAATATTACCTCAAGTACTGTAATTTGTACATTACCTTGGTTTATCAGGATAAAAAAAGCCACGACTTAAAGGTCTTGATTGGCCTTAACCTTGATGAGCTAGGCTATATTGGTTCATCTAAATAGGTTCAAAAAAGCAACAGTATTATATTATTAAATATACAAGGGGCCTGTTGTTCCAAGTCTTGCA</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="19862" PGL_stop="18208"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="19862" e_stop="19836"/>
            <exon e_start="19726" e_stop="19558"/>
            <exon e_start="19440" e_stop="19379"/>
            <exon e_start="19195" e_stop="19074"/>
            <exon e_start="18829" e_stop="18712"/>
            <exon e_start="18230" e_stop="18208"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.718" acc_prob="0.960" e_score="0.926"/>
          <exon-intron don_prob="0.990" acc_prob="0.999" e_score="1.000"/>
          <exon-intron don_prob="0.998" acc_prob="1.000" e_score="1.000"/>
          <exon-intron don_prob="0.998" acc_prob="0.963" e_score="1.000"/>
          <exon-intron don_prob="1.000" acc_prob="1.000" e_score="0.992"/>
          <exon-only e_score="1.000"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="0.926">
            <gDNA_exon_boundary e_start="19862" e_stop="19836" e_length="27"/>
          </exon>
          <intron i_serial="1" don_prob="0.718" acc_prob="0.960">
            <gDNA_intron_boundary i_start="19835" i_stop="19727" i_length="109"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="19726" e_stop="19558" e_length="169"/>
          </exon>
          <intron i_serial="2" don_prob="0.990" acc_prob="0.999">
            <gDNA_intron_boundary i_start="19557" i_stop="19441" i_length="117"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="19440" e_stop="19379" e_length="62"/>
          </exon>
          <intron i_serial="3" don_prob="0.998" acc_prob="1.000">
            <gDNA_intron_boundary i_start="19378" i_stop="19196" i_length="183"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="19195" e_stop="19074" e_length="122"/>
          </exon>
          <intron i_serial="4" don_prob="0.998" acc_prob="0.963">
            <gDNA_intron_boundary i_start="19073" i_stop="18830" i_length="244"/>
          </intron>
          <exon e_serial="5" e_score="0.992">
            <gDNA_exon_boundary e_start="18829" e_stop="18712" e_length="118"/>
          </exon>
          <intron i_serial="5" don_prob="1.000" acc_prob="1.000">
            <gDNA_intron_boundary i_start="18711" i_stop="18231" i_length="481"/>
          </intron>
          <exon e_serial="6" e_score="1.000">
            <gDNA_exon_boundary e_start="18230" e_stop="18208" e_length="23"/>
          </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="19862" stop="19836"/>
              <exon start="19726" stop="19558"/>
              <exon start="19440" stop="19379"/>
              <exon start="19195" stop="19074"/>
              <exon start="18829" stop="18712"/>
              <exon start="18230" stop="18208"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1811" 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>ACGGCCATTGCTAAGTACTGCCCCAAT : GCTCTGGTCAATATGATAAGCAACCCAGTGAATTCCACTGTCCCTATTGCTGCTGAGGTGTTTAAGAAAGCTGGAACTTATGATGAAAAGAAGCTCTTTGGAGTTACCATGCTTGATGTGGTTAGGGCCAAGACATTTTATGCTGGAAAAGCTAAAGTAAATGTTGCTG : AGGTCAATCTCCCAGTAGTTGGTGGTCATGCTGGCATAACTATCCTCCCATTATTTTCTCAA : GCCACTCCAAAGGCAAATCTATCAGATGAGGAAATTGTTGCACTCACAAAGCGAACCCAAGATGGTGGGACAGAAGTTGTAGAGGCCAAGGCTGGAAAGGGTTCAGCCACCCTCTCAATGGC : CTATGCTGGGGCTATTTTTGCCGATGCTTGCTTGAAGGGGTTGAATGGAGTTCCCGATGTTGTTGAATGTGCTTTTGTGCAGTCCAATGTCACCGAGCTTCCCTTCTTCGCATCCAAG : GTAAGACTTGGGAAAAATGGAGT</gDNA_template>
            <first_frame> T  A  I  A  K  Y  C  P  N  :  A  L  V  N  M  I  S  N  P  V  N  S  T  V  P  I  A  A  E  V  F  K  K  A  G  T  Y  D  E  K  K  L  F  G  V  T  M  L  D  V  V  R  A  K  T  F  Y  A  G  K  A  K  V  N  V  A   : E  V  N  L  P  V  V  G  G  H  A  G  I  T  I  L  P  L  F  S  Q  :  A  T  P  K  A  N  L  S  D  E  E  I  V  A  L  T  K  R  T  Q  D  G  G  T  E  V  V  E  A  K  A  G  K  G  S  A  T  L  S  M  A :   Y  A  G  A  I  F  A  D  A  C  L  K  G  L  N  G  V  P  D  V  V  E  C  A  F  V  Q  S  N  V  T  E  L  P  F  F  A  S  K  :  V  R  L  G  K  N  G   </first_frame>
            <second_frame>  R  P  L  L  S  T  A  P  M :   L  W  S  I  *  *  A  T  Q  *  I  P  L  S  L  L  L  L  R  C  L  R  K  L  E  L  M  M  K  R  S  S  L  E  L  P  C  L  M  W  L  G  P  R  H  F  M  L  E  K  L  K  *  M  L  L  :  R  S  I  S  Q  *  L  V  V  M  L  A  *  L  S  S  H  Y  F  L  K :   P  L  Q  R  Q  I  Y  Q  M  R  K  L  L  H  S  Q  S  E  P  K  M  V  G  Q  K  L  *  R  P  R  L  E  R  V  Q  P  P  S  Q  W   : P  M  L  G  L  F  L  P  M  L  A  *  R  G  *  M  E  F  P  M  L  L  N  V  L  L  C  S  P  M  S  P  S  F  P  S  S  H  P  R :   *  D  L  G  K  M  E  </second_frame>
            <third_frame>   G  H  C  *  V  L  P  Q   : C  S  G  Q  Y  D  K  Q  P  S  E  F  H  C  P  Y  C  C  *  G  V  *  E  S  W  N  L  *  *  K  E  A  L  W  S  Y  H  A  *  C  G  *  G  Q  D  I  L  C  W  K  S  *  S  K  C  C  * :   G  Q  S  P  S  S  W  W  S  C  W  H  N  Y  P  P  I  I  F  S   : S  H  S  K  G  K  S  I  R  *  G  N  C  C  T  H  K  A  N  P  R  W  W  D  R  S  C  R  G  Q  G  W  K  G  F  S  H  P  L  N  G  :  L  C  W  G  Y  F  C  R  C  L  L  E  G  V  E  W  S  S  R  C  C  *  M  C  F  C  A  V  Q  C  H  R  A  S  L  L  R  I  Q   : G  K  T  W  E  K  W  S </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="C07HBa0308M01.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="19862" stop="19836"/>
                    <exon start="19726" stop="19558"/>
                    <exon start="19440" stop="19379"/>
                    <exon start="19195" stop="19074"/>
                    <exon start="18829" stop="18712"/>
                    <exon start="18230" stop="18210"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>519</number_coding_nucleotides>
                  <number_encoded_amino_acids>173</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>TAIAKYCPNALVNMISNPVNSTVPIAAEVFKKAGTYDEKKLFGVTMLDVVRAKTFYAGKAKVNVAEVNLPVVGGHAGITILPLFSQATPKANLSDEEIVALTKRTQDGGTEVVEAKAGKGSATLSMAYAGAIFADACLKGLNGVPDVVECAFVQSNVTELPFFASKVRLGKNG</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="50550" PGL_stop="50171"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="50550" e_stop="50171"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.911"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="0.911">
            <gDNA_exon_boundary e_start="50550" e_stop="50171" e_length="380"/>
          </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="50550" stop="50171"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M416-F" 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>CAACAAACTTTCCGATCCAAGTGAAGCAGAAAACAGGGTGGTGGTAGATGGAAATCTCGTTACCAGCAGAGGACCAGGAACTACCATGGAGTTCGCACTGGCCATTGCAGATAAGTTTATTGGGCACAAGGAAACATTAGAGCTAGCAAAGGAGATGATTTTCTAAGTATTTAACTTTTTTGCCGCTATGATCCGTCTTTAGCATCATATACACTTTGCTATATGATGGTGTAAACTTGTAGTATAATAAACTTTGCTATATCACTCTGCACTTACAGCTTTGTTTCGGTGGTTGTTAGTTATCATGTTGTATTGTGGTGGTAGTTTAAATACAAATTATCTTCAGGTAATGACAAAAAAGTCTCAAGTTTTGTGTAACA</gDNA_template>
            <first_frame> Q  Q  T  F  R  S  K  *  S  R  K  Q  G  G  G  R  W  K  S  R  Y  Q  Q  R  T  R  N  Y  H  G  V  R  T  G  H  C  R  *  V  Y  W  A  Q  G  N  I  R  A  S  K  G  D  D  F  L  S  I  *  L  F  C  R  Y  D  P  S  L  A  S  Y  T  L  C  Y  M  M  V  *  T  C  S  I  I  N  F  A  I  S  L  C  T  Y  S  F  V  S  V  V  V  S  Y  H  V  V  L  W  W  *  F  K  Y  K  L  S  S  G  N  D  K  K  V  S  S  F  V  *   </first_frame>
            <second_frame>  N  K  L  S  D  P  S  E  A  E  N  R  V  V  V  D  G  N  L  V  T  S  R  G  P  G  T  T  M  E  F  A  L  A  I  A  D  K  F  I  G  H  K  E  T  L  E  L  A  K  E  M  I  F  *  V  F  N  F  F  A  A  M  I  R  L  *  H  H  I  H  F  A  I  *  W  C  K  L  V  V  *  *  T  L  L  Y  H  S  A  L  T  A  L  F  R  W  L  L  V  I  M  L  Y  C  G  G  S  L  N  T  N  Y  L  Q  V  M  T  K  K  S  Q  V  L  C  N  </second_frame>
            <third_frame>   T  N  F  P  I  Q  V  K  Q  K  T  G  W  W  *  M  E  I  S  L  P  A  E  D  Q  E  L  P  W  S  S  H  W  P  L  Q  I  S  L  L  G  T  R  K  H  *  S  *  Q  R  R  *  F  S  K  Y  L  T  F  L  P  L  *  S  V  F  S  I  I  Y  T  L  L  Y  D  G  V  N  L  *  Y  N  K  L  C  Y  I  T  L  H  L  Q  L  C  F  G  G  C  *  L  S  C  C  I  V  V  V  V  *  I  Q  I  I  F  R  *  *  Q  K  S  L  K  F  C  V  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/">
            <none gDNA_id="C07HBa0308M01.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="3" PGL_strand="-" PGL_start="51309" PGL_stop="50648"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="51309" e_stop="51111"/>
            <exon e_start="51034" e_stop="50648"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.958" acc_prob="0.999" e_score="0.995"/>
          <exon-only e_score="0.997"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="0.995">
            <gDNA_exon_boundary e_start="51309" e_stop="51111" e_length="199"/>
          </exon>
          <intron i_serial="1" don_prob="0.958" acc_prob="0.999">
            <gDNA_intron_boundary i_start="51110" i_stop="51035" i_length="76"/>
          </intron>
          <exon e_serial="2" e_score="0.997">
            <gDNA_exon_boundary e_start="51034" e_stop="50648" e_length="387"/>
          </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="51309" stop="51111"/>
              <exon start="51034" stop="50648"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M416-R" 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="3" AGS_serial="1" gDNA_strand="-"/>
          <translation>
            <gDNA_template>TCTTGTACCTATTGCAAATGGTTCTGAGGAAATGGAAGCTACTATTATTATTGATGTACTTCGGCGAGCAAACGCTCAAGTAGTTGTGGCATCTATGGAAGATAAATTGGAGATTGTTGCTTCCAGAAAAGTTAAACTAGTTGCAGATGTGCTCCTTGATGAAGCTGCTAAACAGTCTTACGATCTCATTGTCCTACCA : GGCGGTCTTGGTGGTGCCGAAACATTTGCCAAATCAGAAAAGTTGGTTGACATGCTGAAGAAGCAGAGGGAATCAAGCAAACCATATGGAGCAATGTGTGCATCTCCAGCTCTAGTCCTAGAGCCCCATGGGCTTCTCCAGGTAAGAGACATACTCATGCTCTTCGATTTTGAAAGTAAAACTATTTTAAAGCAAGTGAATATTACCTCAAGTACTGTAATTTGTACATTACCTTGGTTTATCAGGATAAAAAAAGCCACGACTTAAAGGTCTTGATTGGCCTTAACCTTGATGAGCTAGGCTATATTGGTTCATCTAAATAGGTTCAAAAAAGCAACAGTATTATATTATTAAATATACAAGGGGCCTGTTGTTCCAAGTCTTGCA</gDNA_template>
            <first_frame> S  C  T  Y  C  K  W  F  *  G  N  G  S  Y  Y  Y  Y  *  C  T  S  A  S  K  R  S  S  S  C  G  I  Y  G  R  *  I  G  D  C  C  F  Q  K  S  *  T  S  C  R  C  A  P  *  *  S  C  *  T  V  L  R  S  H  C  P  T   : R  R  S  W  W  C  R  N  I  C  Q  I  R  K  V  G  *  H  A  E  E  A  E  G  I  K  Q  T  I  W  S  N  V  C  I  S  S  S  S  P  R  A  P  W  A  S  P  G  K  R  H  T  H  A  L  R  F  *  K  *  N  Y  F  K  A  S  E  Y  Y  L  K  Y  C  N  L  Y  I  T  L  V  Y  Q  D  K  K  S  H  D  L  K  V  L  I  G  L  N  L  D  E  L  G  Y  I  G  S  S  K  *  V  Q  K  S  N  S  I  I  L  L  N  I  Q  G  A  C  C  S  K  S  C  </first_frame>
            <second_frame>  L  V  P  I  A  N  G  S  E  E  M  E  A  T  I  I  I  D  V  L  R  R  A  N  A  Q  V  V  V  A  S  M  E  D  K  L  E  I  V  A  S  R  K  V  K  L  V  A  D  V  L  L  D  E  A  A  K  Q  S  Y  D  L  I  V  L  P  :  G  G  L  G  G  A  E  T  F  A  K  S  E  K  L  V  D  M  L  K  K  Q  R  E  S  S  K  P  Y  G  A  M  C  A  S  P  A  L  V  L  E  P  H  G  L  L  Q  V  R  D  I  L  M  L  F  D  F  E  S  K  T  I  L  K  Q  V  N  I  T  S  S  T  V  I  C  T  L  P  W  F  I  R  I  K  K  A  T  T  *  R  S  *  L  A  L  T  L  M  S  *  A  I  L  V  H  L  N  R  F  K  K  A  T  V  L  Y  Y  *  I  Y  K  G  P  V  V  P  S  L  A </second_frame>
            <third_frame>   L  Y  L  L  Q  M  V  L  R  K  W  K  L  L  L  L  L  M  Y  F  G  E  Q  T  L  K  *  L  W  H  L  W  K  I  N  W  R  L  L  L  P  E  K  L  N  *  L  Q  M  C  S  L  M  K  L  L  N  S  L  T  I  S  L  S  Y  Q :   A  V  L  V  V  P  K  H  L  P  N  Q  K  S  W  L  T  C  *  R  S  R  G  N  Q  A  N  H  M  E  Q  C  V  H  L  Q  L  *  S  *  S  P  M  G  F  S  R  *  E  T  Y  S  C  S  S  I  L  K  V  K  L  F  *  S  K  *  I  L  P  Q  V  L  *  F  V  H  Y  L  G  L  S  G  *  K  K  P  R  L  K  G  L  D  W  P  *  P  *  *  A  R  L  Y  W  F  I  *  I  G  S  K  K  Q  Q  Y  Y  I  I  K  Y  T  R  G  L  L  F  Q  V  L   </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C07HBa0308M01.1" strand="-"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="51308" stop="51111"/>
                    <exon start="51034" stop="50768"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>462</number_coding_nucleotides>
                  <number_encoded_amino_acids>154</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LVPIANGSEEMEATIIIDVLRRANAQVVVASMEDKLEIVASRKVKLVADVLLDEAAKQSYDLIVLPGGLGGAETFAKSEKLVDMLKKQRESSKPYGAMCASPALVLEPHGLLQVRDILMLFDFESKTILKQVNITSSTVICTLPWFIRIKKATT*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 7 chains have been computed
$ 
$ memory statistics:
$ 6344 bytes spliced alignments in total
$ 3 spliced alignments have been stored
$ 2114 bytes was the average size of a spliced alignment
$ 8072 bytes predicted gene locations in total
$ 3 predicted gene locations have been stored
$ 2690 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: 2009-01-15 15:26:44
-->
