<?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="2009-01-06 17:22:36"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0068N05-7fT6o/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C04HBa0068N05-7fT6o/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-C04HBa0068N05-7fT6o/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M45-F" ref_strand="-" ref_description="SGN-M45-F CT61-F [rflp_markers_forward]">
      <seq>tgtattcagtggtatcacgcttacaaagcttgtcggtgtcattgttctttgtttctcaaggacagaagtttttgtggtttactactttcaaatgtacctggctttggttcttcttggttttctacatgggctcatatttttacctgtactattaagcatttttggtccgccatcaagatgtgtgcttgtagagaagcaagaggatcgtccatatacatcttcccaattctaatctaatcaggtgttaaaagagtctcctcggtaggaaatatattctttttgttcagaagccacgacttgatgtttgatccatgagataacaagcaggataattggtggtctacctacagcacaattttgatacaagctaatgcattaaaaagagctgtcctttgtagtgatacataatcttttctttttctctagattttgtgggtagtagagggagcccttgaatgttcatggctgcatgtataaccttctgaagaacacatcagaatagttttgttaattgtaaatttatacaattatatttctctgtaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0068N05-7fT6o/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0068N05.1" temp_strand="-" temp_description="C04HBa0068N05.1  CU326379.2 htgs_phase:3 submitted_to_sgn_as:C04HBa0068N05 sequenced_by:sanger upload_account_name:uk">
        <position start="14312" stop="12612"/>
      </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="14012" g_stop="13936" g_length="77"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="76" r_length="76" r_score="0.961"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="13935" i_stop="13857" i_length="79">
            <donor d_prob="0.674" d_score="1.00"/>
            <acceptor a_prob="0.405" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="13856" g_stop="13788" g_length="69"/>
          <reference_exon_boundary r_type="cDNA" r_start="77" r_stop="145" r_length="69" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="13787" i_stop="13319" i_length="469">
            <donor d_prob="0.968" d_score="1.00"/>
            <acceptor a_prob="0.627" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="13318" g_stop="12911" g_length="408"/>
          <reference_exon_boundary r_type="cDNA" r_start="146" r_stop="553" r_length="408" r_score="0.988"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0068N05.1" gen_strand="-" ref_id="SGN-M45-F" ref_strand="-">
        <total_alignment_score>0.986</total_alignment_score>
        <cumulative_length_of_scored_exons>554</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0068N05.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M45-F" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="14012" e_stop="13936"/>
          <exon e_start="13856" e_stop="13788"/>
          <exon e_start="13318" e_stop="12911"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCTTTTGCAGTGGTATCACGCTTACAAAGCTTGTCGGTGTCATTGTTCTTTGTTTCTCAAGGACAGAAGTTTTTGTGGTACGTGTACTTGCATACAAAGTCATAAATGGAGTGAGCTACTTGTTCTGGTTGATTCATCTTAACCTGCATTTTGCAGGTTTACTACTTTCAAATGTACCTGGCTTTGGTTCTTCTTGGTTTTCTACATGGGCTCATATTTTTACCTGTAAGTGACTTAAAGTTATAGCATCCTCTTTTCTTCCGTTGAGAAAATTCTCCTTCACAGCCTTCATAACAAATTATAAACGCTTTTCGTTGTTACCCAAAATCTTTAATCTTATATTGAATATATGTAAAAAGTCTTCTGTGGTGAGTTTCGACTTAGAACAGTCTTTTTCTTCATCGTTATCTAAATATTTCCATCGTTTTTCTTTCAAGTAGCAAATGAAAAGTTAATGGAAAATTAAAATTACCATATGAGTATATCCTTGAGAGATGTAAAATTACCATATGAGTACAAAGAATTTTCCTTAGTTTTACTTAAAAATTCTTAAGTTGACGATTATATTGGTAGCAATGCCAGATCCCTGAGAAATGTACAACTGTGTTGGAAATAATTCAAGGAGGATTTTGAAACATGAAGGAAAACTTGGCTACAACTTCTAAGTACCCCACTTGTACCACCTCCATTTCAGGTACTATTAAGCATTTTTGGTCCGCCATCAAGATGTGTGCTTGTAGAGAAGCAAGAGGATCGTCCATCTACATCTTCCCAATTCTAATCTAATCAGGTGTTAAAAGAGTCTCCTCGGTAGGAAATATATTCTTTTTGTTCAGAAGCCACGACTTGATGTTTGATCCATGAGATAACAAGCAGGATAATTGGTGGTCTACCTACAGCACAATTCTGATACAAGCTAATGCATTAAAAAGAGCTGTCCTTTGTAGTGATACATAATCTTTTCTTTTTCTCTAGATTTTGTGGGTAGTAGAGGGAGCCCTTGAATGTTCATGGCTGCATGTATAACCTTCTGAAGAACACATCAGAATAGTTTTGTTAATTGTAAATTTATACAATTATATTTCTCTGTAAAAGAAGAAAG</genome_strand>
        <mrna_strand>TGTATT-CAGTGGTATCACGCTTACAAAGCTTGTCGGTGTCATTGTTCTTTGTTTCTCAAGGACAGAAGTTTTTGTG...............................................................................GTTTACTACTTTCAAATGTACCTGGCTTTGGTTCTTCTTGGTTTTCTACATGGGCTCATATTTTTACCT.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTACTATTAAGCATTTTTGGTCCGCCATCAAGATGTGTGCTTGTAGAGAAGCAAGAGGATCGTCCATATACATCTTCCCAATTCTAATCTAATCAGGTGTTAAAAGAGTCTCCTCGGTAGGAAATATATTCTTTTTGTTCAGAAGCCACGACTTGATGTTTGATCCATGAGATAACAAGCAGGATAATTGGTGGTCTACCTACAGCACAATTTTGATACAAGCTAATGCATTAAAAAGAGCTGTCCTTTGTAGTGATACATAATCTTTTCTTTTTCTCTAGATTTTGTGGGTAGTAGAGGGAGCCCTTGAATGTTCATGGCTGCATGTATAACCTTCTGAAGAACACATCAGAATAGTTTTGTTAATTGTAAATTTATACAATTATATTTCTCTGTAAAAAAAAAAAA</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-C04HBa0068N05-7fT6o/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M45-R" ref_strand="+" ref_description="SGN-M45-R CT61-R [rflp_markers_reverse]">
      <seq>tctatgaattcagttcaagggtttctgattctctaaagatggaggtcttcccgtatgcagtgttttatatgttctttgagcaatatttaagcatatggaggacagccctaattaacttagcgattgctattggtgccgtatttattgtatgcttagttatcacttgtagtttttggacttcagcaattatcttgctcgtgctgaccatgattgttctggatcttatgggagtaatggcaattctaaaaatccagctcaatgctgtatcagttgttaaccttgtgatggccgatggtattgctgttgaattctgtgtccatataacacatgccttcttggttagcagtggagatagaaaccaacgcatgaaggaggcactgactactatgggcgcttctgtata</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0068N05-7fT6o/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0068N05.1" temp_strand="-" temp_description="C04HBa0068N05.1  CU326379.2 htgs_phase:3 submitted_to_sgn_as:C04HBa0068N05 sequenced_by:sanger upload_account_name:uk">
        <position start="17189" stop="14471"/>
      </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="16890" g_stop="16854" g_length="37"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="38" r_length="38" r_score="0.892"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="16853" i_stop="16025" i_length="829">
            <donor d_prob="0.940" d_score="0.00"/>
            <acceptor a_prob="0.863" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="16024" g_stop="15931" g_length="94"/>
          <reference_exon_boundary r_type="cDNA" r_start="39" r_stop="132" r_length="94" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="15930" i_stop="15730" i_length="201">
            <donor d_prob="0.848" d_score="1.00"/>
            <acceptor a_prob="0.364" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="15729" g_stop="15693" g_length="37"/>
          <reference_exon_boundary r_type="cDNA" r_start="133" r_stop="169" r_length="37" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="15692" i_stop="15569" i_length="124">
            <donor d_prob="0.562" d_score="0.00"/>
            <acceptor a_prob="0.701" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="15568" g_stop="15511" g_length="58"/>
          <reference_exon_boundary r_type="cDNA" r_start="170" r_stop="227" r_length="58" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="15510" i_stop="15422" i_length="89">
            <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="5">
          <gDNA_exon_boundary g_start="15421" g_stop="15311" g_length="111"/>
          <reference_exon_boundary r_type="cDNA" r_start="228" r_stop="338" r_length="111" r_score="0.991"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="15310" i_stop="14835" i_length="476">
            <donor d_prob="0.977" d_score="0.98"/>
            <acceptor a_prob="0.996" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="14834" g_stop="14770" g_length="65"/>
          <reference_exon_boundary r_type="cDNA" r_start="339" r_stop="403" r_length="65" r_score="0.985"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0068N05.1" gen_strand="-" ref_id="SGN-M45-R" ref_strand="+">
        <total_alignment_score>0.994</total_alignment_score>
        <cumulative_length_of_scored_exons>402</cumulative_length_of_scored_exons>
        <coverage percentage="0.998" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0068N05.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M45-R" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="16890" e_stop="16854"/>
          <exon e_start="16024" e_stop="15931"/>
          <exon e_start="15729" e_stop="15693"/>
          <exon e_start="15568" e_stop="15511"/>
          <exon e_start="15421" e_stop="15311"/>
          <exon e_start="14834" e_stop="14770"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ACGA-GAATTCAGTTCAAGGGTTTCTGATTCTCTAAAGGTAATTTCTGAATGCAGCATAATGAAGTATTGCTGTCACTCTCAGGAGCTTAACTGTTTGGCCTGTTTTTGTTGTCTCTACTGATTTTTTTTTAATGACCACTACTGAGATTCTCTCTTTTCTTTTAATTTGTTCATCTATCAGTTATACATTCTGATGATAAACTAATGGTACTGTCCGCAAGCAAGTTCTGATTTTCCATTATAGCTTGCAGAACATTGTCATTAGTGTATTCAACTCCTTTATTTGTGTACTGATAATTACAGTTTATTTAAGAATATTAAGACGTTTATATCAAGATTGTTGCTGCGTCATGAATGTGAAATATGGTAAATTTGATAAGTATAGCAGCAATAAGGTCTTCTATATAGAGTACTTTTACTTCCTTTTATGCCAAATCTGACTGTACCAGAACAGAAGGAAGATAATCTGGAGTAGTGATTATCTGATCCAAAAACCAAAAGGCATGTCATAGTTGTAATATTAAGGTTTTAGAAAGTTTAGGTGAAAAAAAAATCATTGTGGTACTTTCGAGAGATTCTGGAGGTTAGATATTTGTATATCGTGTCTTGTAGATTTTATCTAAGTAGAAAATACTCATCTGTACTTATAAGATTCCAGGTAAAAAGGAAGAACGAATTAGGATAGTGGCATAAATGGAAATTGTGCCCAAGTGCAAGAGAGTTCTACACCCTACAATTTATACCCCATAATAAGTTGCTTCTGATCTGTGATTTGTCCCATTATCTTCTTCTGGCAATTACACACTTGGCATGCATTTCCATAAGTTCTGTGTATTAGCCACGACTTACCTCTTTCGTTTCTGCAGATGGAGGTCTTCCCGTATGCAGTGTTTTATATGTTCTTTGAGCAATATTTAAGCATATGGAGGACAGCCCTAATTAACTTAGCGATTGCTATTGGTCAGTGTCATCTCTCTGTACTTAATTTAATTCACCTTTCAGCTGATGCATGACATATCTTTAATTATGTGGATATTTTGAAAAAAAAAATTCTCTTTTTGTCTGCTGGTTATCATTTCTATTGGAAGCATTGGGTAGTTTTAAAACGACTAAGACCATTGAGAGACATTAACTATGTATTTCTTTTTTCATTTTCAACAGGTGCCGTATTTATTGTATGCTTAGTTATCACTTGTAGGTTAGTATATTATCTCTTGGAATGCTATCCATTCCTATCCTTTCTTGCTTTCTTGAACAAAACACATTTATTTTTTGTATCTATAAGATATAACTCTGTTTTGTTTGACCTTTGCTACATCTAGTTTTTGGACTTCAGCAATTATCTTGCTCGTGCTGACCATGATTGTTCTGGATCTTATGGTATGTTTTCCTCTTTGAACAATTGTTTGAGTTCATATATTACACCTGATTTTCTCTCTCTAGCAGTGACATCTTACATCATTTTGCAGGGAGTAATGGCAATTCTAAAAATCCAGCTCAATGCTGTATCAGTTGTTAACCTTGTGATGGCCGTTGGTATTGCTGTTGAATTCTGTGTCCATATAACACATGCCTTCTTGGTTAGTCTTCTATCAGAGTGATCTATCTGGTCTACTTTTCTGTTTAAAATAATGAGAGAATGAAGATCAACTTGAGTAGGTTAAGTAAGAGAATACTGTATATTAAACAAATATAATTGTCTGCAAATAATTGAGAAGATAATCCTTGTCTGAGTGAGTAGAATGAATGACTAATAGGTTCAAGTAAATCTTTATGCCCCTGAAGTTAACTGTTTGAATGATATCTGTCATTATCAGCAATGAACCATCTGCAGCGAATTACACATGTGCATCAAACCTTAGCTTGGGTGTCAATTATGACCCCACTCTTTCTCAAAAAAAAGAAATACAAATTATGACCCCACTCATGTAATAAGAAGTCAAAATATTTTAGTTGGCTCTAATTCCCTTTGAGCAAGGTTTCATCATTTGTTATCTTTTCTTTGAGGCATTCATCCTATAGTTCTCTCTTTAACATTCTTCTGCACTTTATGCAGGTTAGCAGTGGAGATAGAAACCAACGCATGAAGGAGGCACTGACTACTATGGGCGCTTCTGTATT</genome_strand>
        <mrna_strand>TCTATGAATTCAGTTCAAGGGTTTCTGATTCTCTAAAG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATGGAGGTCTTCCCGTATGCAGTGTTTTATATGTTCTTTGAGCAATATTTAAGCATATGGAGGACAGCCCTAATTAACTTAGCGATTGCTATTG.........................................................................................................................................................................................................GTGCCGTATTTATTGTATGCTTAGTTATCACTTGTAG............................................................................................................................TTTTTGGACTTCAGCAATTATCTTGCTCGTGCTGACCATGATTGTTCTGGATCTTATG.........................................................................................GGAGTAATGGCAATTCTAAAAATCCAGCTCAATGCTGTATCAGTTGTTAACCTTGTGATGGCCGATGGTATTGCTGTTGAATTCTGTGTCCATATAACACATGCCTTCTTG............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTAGCAGTGGAGATAGAAACCAACGCATGAAGGAGGCACTGACTACTATGGGCGCTTCTGTATA</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="14012" PGL_stop="12911"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="14012" e_stop="13936"/>
            <exon e_start="13856" e_stop="13788"/>
            <exon e_start="13318" e_stop="12911"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.674" acc_prob="0.405" e_score="0.961"/>
          <exon-intron don_prob="0.968" acc_prob="0.627" e_score="1.000"/>
          <exon-only e_score="0.988"/>
        </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="0.961">
            <gDNA_exon_boundary e_start="14012" e_stop="13936" e_length="77"/>
          </exon>
          <intron i_serial="1" don_prob="0.674" acc_prob="0.405">
            <gDNA_intron_boundary i_start="13935" i_stop="13857" i_length="79"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="13856" e_stop="13788" e_length="69"/>
          </exon>
          <intron i_serial="2" don_prob="0.968" acc_prob="0.627">
            <gDNA_intron_boundary i_start="13787" i_stop="13319" i_length="469"/>
          </intron>
          <exon e_serial="3" e_score="0.988">
            <gDNA_exon_boundary e_start="13318" e_stop="12911" e_length="408"/>
          </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="14012" stop="13936"/>
              <exon start="13856" stop="13788"/>
              <exon start="13318" stop="12911"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M45-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="1" AGS_serial="1" gDNA_strand="-"/>
          <translation>
            <gDNA_template>TCTTTTGCAGTGGTATCACGCTTACAAAGCTTGTCGGTGTCATTGTTCTTTGTTTCTCAAGGACAGAAGTTTTTGTG : GTTTACTACTTTCAAATGTACCTGGCTTTGGTTCTTCTTGGTTTTCTACATGGGCTCATATTTTTACCT : GTACTATTAAGCATTTTTGGTCCGCCATCAAGATGTGTGCTTGTAGAGAAGCAAGAGGATCGTCCATCTACATCTTCCCAATTCTAATCTAATCAGGTGTTAAAAGAGTCTCCTCGGTAGGAAATATATTCTTTTTGTTCAGAAGCCACGACTTGATGTTTGATCCATGAGATAACAAGCAGGATAATTGGTGGTCTACCTACAGCACAATTCTGATACAAGCTAATGCATTAAAAAGAGCTGTCCTTTGTAGTGATACATAATCTTTTCTTTTTCTCTAGATTTTGTGGGTAGTAGAGGGAGCCCTTGAATGTTCATGGCTGCATGTATAACCTTCTGAAGAACACATCAGAATAGTTTTGTTAATTGTAAATTTATACAATTATATTTCTCTGTAAAAGAAGAAAG</gDNA_template>
            <first_frame> S  F  A  V  V  S  R  L  Q  S  L  S  V  S  L  F  F  V  S  Q  G  Q  K  F  L  W :   F  T  T  F  K  C  T  W  L  W  F  F  L  V  F  Y  M  G  S  Y  F  Y  L :   Y  Y  *  A  F  L  V  R  H  Q  D  V  C  L  *  R  S  K  R  I  V  H  L  H  L  P  N  S  N  L  I  R  C  *  K  S  L  L  G  R  K  Y  I  L  F  V  Q  K  P  R  L  D  V  *  S  M  R  *  Q  A  G  *  L  V  V  Y  L  Q  H  N  S  D  T  S  *  C  I  K  K  S  C  P  L  *  *  Y  I  I  F  S  F  S  L  D  F  V  G  S  R  G  S  P  *  M  F  M  A  A  C  I  T  F  *  R  T  H  Q  N  S  F  V  N  C  K  F  I  Q  L  Y  F  S  V  K  E  E   </first_frame>
            <second_frame>  L  L  Q  W  Y  H  A  Y  K  A  C  R  C  H  C  S  L  F  L  K  D  R  S  F  C   : G  L  L  L  S  N  V  P  G  F  G  S  S  W  F  S  T  W  A  H  I  F  T   : C  T  I  K  H  F  W  S  A  I  K  M  C  A  C  R  E  A  R  G  S  S  I  Y  I  F  P  I  L  I  *  S  G  V  K  R  V  S  S  V  G  N  I  F  F  L  F  R  S  H  D  L  M  F  D  P  *  D  N  K  Q  D  N  W  W  S  T  Y  S  T  I  L  I  Q  A  N  A  L  K  R  A  V  L  C  S  D  T  *  S  F  L  F  L  *  I  L  W  V  V  E  G  A  L  E  C  S  W  L  H  V  *  P  S  E  E  H  I  R  I  V  L  L  I  V  N  L  Y  N  Y  I  S  L  *  K  K  K  </second_frame>
            <third_frame>   F  C  S  G  I  T  L  T  K  L  V  G  V  I  V  L  C  F  S  R  T  E  V  F  V  :  V  Y  Y  F  Q  M  Y  L  A  L  V  L  L  G  F  L  H  G  L  I  F  L  P  :  V  L  L  S  I  F  G  P  P  S  R  C  V  L  V  E  K  Q  E  D  R  P  S  T  S  S  Q  F  *  S  N  Q  V  L  K  E  S  P  R  *  E  I  Y  S  F  C  S  E  A  T  T  *  C  L  I  H  E  I  T  S  R  I  I  G  G  L  P  T  A  Q  F  *  Y  K  L  M  H  *  K  E  L  S  F  V  V  I  H  N  L  F  F  F  S  R  F  C  G  *  *  R  E  P  L  N  V  H  G  C  M  Y  N  L  L  K  N  T  S  E  *  F  C  *  L  *  I  Y  T  I  I  F  L  C  K  R  R  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="C04HBa0068N05.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="14011" stop="13936"/>
                    <exon start="13856" stop="13788"/>
                    <exon start="13318" stop="13227"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>234</number_coding_nucleotides>
                  <number_encoded_amino_acids>78</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LLQWYHAYKACRCHCSLFLKDRSFCGLLLSNVPGFGSSWFSTWAHIFTCTIKHFWSAIKMCACREARGSSIYIFPILI*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0068N05.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="14010" stop="13936"/>
                    <exon start="13856" stop="13788"/>
                    <exon start="13318" stop="13232"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>228</number_coding_nucleotides>
                  <number_encoded_amino_acids>76</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>FCSGITLTKLVGVIVLCFSRTEVFVVYYFQMYLALVLLGFLHGLIFLPVLLSIFGPPSRCVLVEKQEDRPSTSSQF*</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="16890" PGL_stop="14770"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="16890" e_stop="16854"/>
            <exon e_start="16024" e_stop="15931"/>
            <exon e_start="15729" e_stop="15693"/>
            <exon e_start="15568" e_stop="15511"/>
            <exon e_start="15421" e_stop="15311"/>
            <exon e_start="14834" e_stop="14770"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.940" acc_prob="0.863" e_score="0.892"/>
          <exon-intron don_prob="0.848" acc_prob="0.364" e_score="1.000"/>
          <exon-intron don_prob="0.562" acc_prob="0.701" e_score="1.000"/>
          <exon-intron don_prob="0.999" acc_prob="0.992" e_score="1.000"/>
          <exon-intron don_prob="0.977" acc_prob="0.996" e_score="0.991"/>
          <exon-only e_score="0.985"/>
        </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="0.892">
            <gDNA_exon_boundary e_start="16890" e_stop="16854" e_length="37"/>
          </exon>
          <intron i_serial="1" don_prob="0.940" acc_prob="0.863">
            <gDNA_intron_boundary i_start="16853" i_stop="16025" i_length="829"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="16024" e_stop="15931" e_length="94"/>
          </exon>
          <intron i_serial="2" don_prob="0.848" acc_prob="0.364">
            <gDNA_intron_boundary i_start="15930" i_stop="15730" i_length="201"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="15729" e_stop="15693" e_length="37"/>
          </exon>
          <intron i_serial="3" don_prob="0.562" acc_prob="0.701">
            <gDNA_intron_boundary i_start="15692" i_stop="15569" i_length="124"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="15568" e_stop="15511" e_length="58"/>
          </exon>
          <intron i_serial="4" don_prob="0.999" acc_prob="0.992">
            <gDNA_intron_boundary i_start="15510" i_stop="15422" i_length="89"/>
          </intron>
          <exon e_serial="5" e_score="0.991">
            <gDNA_exon_boundary e_start="15421" e_stop="15311" e_length="111"/>
          </exon>
          <intron i_serial="5" don_prob="0.977" acc_prob="0.996">
            <gDNA_intron_boundary i_start="15310" i_stop="14835" i_length="476"/>
          </intron>
          <exon e_serial="6" e_score="0.985">
            <gDNA_exon_boundary e_start="14834" e_stop="14770" e_length="65"/>
          </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="16890" stop="16854"/>
              <exon start="16024" stop="15931"/>
              <exon start="15729" stop="15693"/>
              <exon start="15568" stop="15511"/>
              <exon start="15421" stop="15311"/>
              <exon start="14834" stop="14770"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M45-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="2" AGS_serial="1" gDNA_strand="-"/>
          <translation>
            <gDNA_template>ACGAGAATTCAGTTCAAGGGTTTCTGATTCTCTAAAG : ATGGAGGTCTTCCCGTATGCAGTGTTTTATATGTTCTTTGAGCAATATTTAAGCATATGGAGGACAGCCCTAATTAACTTAGCGATTGCTATTG : GTGCCGTATTTATTGTATGCTTAGTTATCACTTGTAG : TTTTTGGACTTCAGCAATTATCTTGCTCGTGCTGACCATGATTGTTCTGGATCTTATG : GGAGTAATGGCAATTCTAAAAATCCAGCTCAATGCTGTATCAGTTGTTAACCTTGTGATGGCCGTTGGTATTGCTGTTGAATTCTGTGTCCATATAACACATGCCTTCTTG : GTTAGCAGTGGAGATAGAAACCAACGCATGAAGGAGGCACTGACTACTATGGGCGCTTCTGTATT</gDNA_template>
            <first_frame> T  R  I  Q  F  K  G  F  *  F  S  K   : D  G  G  L  P  V  C  S  V  L  Y  V  L  *  A  I  F  K  H  M  E  D  S  P  N  *  L  S  D  C  Y  W :   C  R  I  Y  C  M  L  S  Y  H  L  *  :  F  L  D  F  S  N  Y  L  A  R  A  D  H  D  C  S  G  S  Y   : G  S  N  G  N  S  K  N  P  A  Q  C  C  I  S  C  *  P  C  D  G  R  W  Y  C  C  *  I  L  C  P  Y  N  T  C  L  L   : G  *  Q  W  R  *  K  P  T  H  E  G  G  T  D  Y  Y  G  R  F  C  I </first_frame>
            <second_frame>  R  E  F  S  S  R  V  S  D  S  L  K  :  M  E  V  F  P  Y  A  V  F  Y  M  F  F  E  Q  Y  L  S  I  W  R  T  A  L  I  N  L  A  I  A  I   : G  A  V  F  I  V  C  L  V  I  T  C  S :   F  W  T  S  A  I  I  L  L  V  L  T  M  I  V  L  D  L  M  :  G  V  M  A  I  L  K  I  Q  L  N  A  V  S  V  V  N  L  V  M  A  V  G  I  A  V  E  F  C  V  H  I  T  H  A  F  L  :  V  S  S  G  D  R  N  Q  R  M  K  E  A  L  T  T  M  G  A  S  V   </second_frame>
            <third_frame>   E  N  S  V  Q  G  F  L  I  L  *  R :   W  R  S  S  R  M  Q  C  F  I  C  S  L  S  N  I  *  A  Y  G  G  Q  P  *  L  T  *  R  L  L  L  :  V  P  Y  L  L  Y  A  *  L  S  L  V   : V  F  G  L  Q  Q  L  S  C  S  C  *  P  *  L  F  W  I  L  W :   E  *  W  Q  F  *  K  S  S  S  M  L  Y  Q  L  L  T  L  *  W  P  L  V  L  L  L  N  S  V  S  I  *  H  M  P  S  W :   L  A  V  E  I  E  T  N  A  *  R  R  H  *  L  L  W  A  L  L  Y  </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="C04HBa0068N05.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="16889" stop="16854"/>
                    <exon start="16024" stop="15931"/>
                    <exon start="15729" stop="15693"/>
                    <exon start="15568" stop="15511"/>
                    <exon start="15421" stop="15311"/>
                    <exon start="14834" stop="14772"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>399</number_coding_nucleotides>
                  <number_encoded_amino_acids>133</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>REFSSRVSDSLKMEVFPYAVFYMFFEQYLSIWRTALINLAIAIGAVFIVCLVITCSFWTSAIILLVLTMIVLDLMGVMAILKIQLNAVSVVNLVMAVGIAVEFCVHITHAFLVSSGDRNQRMKEALTTMGASV</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:
$ 4048 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 2024 bytes was the average size of a spliced alignment
$ 6928 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3464 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 8 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-06 17:22:39
-->
