<?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="2009-01-18 08:33:44"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C09SLm0058A04-I962s/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C09SLm0058A04-I962s/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-C09SLm0058A04-I962s/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M8161" ref_strand="-" ref_description="SGN-M8161 C2_At4g02260 [cosii_markers]">
      <seq>ggaaacataataagtgcatgccagcataccaaatttgaaggccacaggggagacattgtcaccaaggaaatggtgttggcgaaatgataccttgctaacataccaaggtaccagggatgttctgcctggattagacggctggatggctagcaaagttgcaacttggcaaaacctggaagggcactctgttcagtggttttgtgttgtcagcatagatcgaaaaggcatgatggccgatattacttcagcattggcagctgtaggcgtcatcatatgttcttgtgcggctgagacggatagagggaagggaatcggtgtcgcgctatttcatattgaagccaacctagagagcttggttggtgcaagttcgaggattgacatgatcctgggtgttttgggatggtccacgggctgcagttggtcagagaacaaacagtttctagaatgctaatttagtggcctggtgaagagtagttgcccagctgttgaatgcttggggaagaaagttttgttcagtgaaacctgagttctgtttgacaagtatagaagcaagcaatataggttatatggtgtagggcgactgtatataaaggaagagtagcaaccagttatacttgtaaaggaattttcaactatacgaactccaacaaaagtatgttacagttatacaaaataaatatattaaattatttgtcaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09SLm0058A04-I962s/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C09SLm0058A04.1" temp_strand="-" temp_description="C09SLm0058A04.1  EU139074.1 htgs_phase:1 submitted_to_sgn_as:gb|EU139074.1| upload_account_name:spain (1 - 96875)">
        <position start="20440" stop="17677"/>
      </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="20140" g_stop="19922" g_length="219"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="224" r_length="224" r_score="0.954"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="19921" i_stop="19236" i_length="686">
            <donor d_prob="0.851" d_score="1.00"/>
            <acceptor a_prob="0.782" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="19235" g_stop="19174" g_length="62"/>
          <reference_exon_boundary r_type="cDNA" r_start="225" r_stop="286" r_length="62" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="19173" i_stop="18471" i_length="703">
            <donor d_prob="0.883" d_score="1.00"/>
            <acceptor a_prob="0.979" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="18470" g_stop="18402" g_length="69"/>
          <reference_exon_boundary r_type="cDNA" r_start="287" r_stop="355" r_length="69" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="18401" i_stop="18320" i_length="82">
            <donor d_prob="0.976" d_score="1.00"/>
            <acceptor a_prob="0.755" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="18319" g_stop="17978" g_length="342"/>
          <reference_exon_boundary r_type="cDNA" r_start="356" r_stop="697" r_length="342" r_score="0.997"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="698" polyA_stop="712"/>
      <MATCH_line gen_id="C09SLm0058A04.1" gen_strand="-" ref_id="SGN-M8161" ref_strand="-">
        <total_alignment_score>0.984</total_alignment_score>
        <cumulative_length_of_scored_exons>692</cumulative_length_of_scored_exons>
        <coverage percentage="0.972" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09SLm0058A04.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M8161" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="20140" e_stop="19922"/>
          <exon e_start="19235" e_stop="19174"/>
          <exon e_start="18470" e_stop="18402"/>
          <exon e_start="18319" e_stop="17978"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GGAAACATAATAAGTGCATG-CAGCATA-CAAATTTGAAGGCCACAGGGGAGACATTGTCA-CAAGGAAATGGTGTTGGCGAAATGATA-CTTGCTAACATACCAAGGTA-CAGGGATGTTCTGCCTGGATTAGACGGCTGGATGGCTAGCAAAGTTGCAACTTGGCAAAACCTGGAAGGGCACTCTGTTCAGTGGTTTTGTGTTGTCAGCATAGATCGAAAAGGTAATGTTTGGTTCAGAGGCTACTTATTGCAGATGAGCATCAAACTGGATAAGGCATCACCGCTCATCTATATTAGATGCATTTGCGAACTCTGCTATGTATTGGTGGTTCTAAGTCCTTTGAAAAATCATTACCACTAGCACTGCTAGTATTTGTTTTTCGCCTTTTGCTTAGGCATTTGGTAGCCGAAACCTACTGCTAGGCCTGAAATGTTCCCAACCAACAGGTTCTAACATTCCTAGGGATCTAATCCAAGACCTTTAGTTAAGTGTGGAAAGATCTTAGCCCACTACATCACACCCCTTGTGAGAGAGGTTTGTCAGAATTACGTATTTAATATCTTGACTTCCTCGAAGGAGCAAATTTTCAAGTTCAAAAGAATGACATCAAAGTTTTGAATAACCAGAGAAGTGTGTGAGAGTATGTCGGGGTGGGGGTGGGGGGGGGGGGAGGCGGGATTCCATCGATGTAGAAGATCTAACTTTCTGTTCTTTTTTGTCTTTGATGTATTTTGTATAGTTCTGACTACATGTTTCCAGTTTATTAACCTTATATGTTCATTTGCATATGCACATTATGTATGACCTGGTTATTGGTTGACTAGTAGCAATATTAATATGTAGCCAACATTTTTCATGGTTTACTACTTGTCATGGCTGACATCTCAAACCACTACAATTATTTAGGCATGATGGCCGATATTACTTCAGCATTGGCAGCTGTAGGCGTCATCATATGTTCTTGTGCGGTGAGTTGGAACATTTATCATATCATTTTTCATCTAGGCTCGAACTCCTGAGCTATTCATATTGATAAATTTTAATATGGTCTGGGTTGACTGTGAAACTGTCTACATTGAGATCTGAACCTAGCTTACATTTGTGAAAATTTTCAATATTTGTTTAATATTAAATAACGGAACCTTGATTCACACCTTTCTTAGCTAGCTATATTAGGCAGTTTGTGACAAAGTATGTGACACTGTTAGCTCTTTAATCTTTATATTACTTCAGCAATAACCAGCAGGAGGTAACAATGAGAACTGTGTCGAAAGAGGATCTTACAAGTTAAGTTAGTCAATTTGCTCTACTACTTGCGTCTTGGTGCAGTGGGAGAGCATACATAGCTTCTTTTTTTCTTGATATGCTGATGGCGAAATAAGAAGAAGATGAATGTCATACCTGGAGTGATTGAGAACATTGTGGAAGGGAAAGAAGTGCTTAGGATAAAAATAAGGAAATTCATGCTAACTGTTACTATGAGAGGACTGAAACAATTCTATCTATTACATTGCATTCTTCTTTTGAGATATTACCTTTTGAGTATTCATTCTGAAAAATGCACAAAGATCTAAGCAATTAAATAGTCATATTCTCCTCCTGTTTCAATTATGTTAGAATTCTCAATTGTGAGGTGACTGCATTGTTACTTGAAAAAAAAAAAAACTGCAGGCTGAGACGGATAGAGGGAAGGGAATCGGTGTCGCGCTATTTCATATTGAAGCCAACCTAGAGAGCTTGGTATGTCTTCTGAACATGCTTCACTAATCTCTCTCTCTCTCTCTCTCTCTCTCTCTATTTTATGAATTCTCAGCTCCCACAGGTTGGTGCAAGTTCGAGGATTGACATGATCCTGGGTGTTTTGGGATGGTCCACGGGCTGCAGTTGGTCAGAGAACAAACAGTTTCTAGAATGCTAATTTAGTGGCCTGGTGAAGAGTAGTTGCCCAGCTGTTGAATGCTTGGGGAAGAAAGTTTTGTTCAGTGAAACCTGAGTTCTGTTTGACAAGTATAGAAGCAAGCAATATAGGTTATATGGTGTAGGGCGACTGTATATAAAGGAAGAGTAGCAACCAGTTATACTTGTAAAGGAATTTTCAACTATACGAACTCCAACAAAAGTATGTTACAGTTATACAAAATAAATATATTAAATTATTTGTCAC</genome_strand>
        <mrna_strand>GGAAACATAATAAGTGCATGCCAGCATACCAAATTTGAAGGCCACAGGGGAGACATTGTCACCAAGGAAATGGTGTTGGCGAAATGATACCTTGCTAACATACCAAGGTACCAGGGATGTTCTGCCTGGATTAGACGGCTGGATGGCTAGCAAAGTTGCAACTTGGCAAAACCTGGAAGGGCACTCTGTTCAGTGGTTTTGTGTTGTCAGCATAGATCGAAAAG..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCATGATGGCCGATATTACTTCAGCATTGGCAGCTGTAGGCGTCATCATATGTTCTTGTGCG...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCTGAGACGGATAGAGGGAAGGGAATCGGTGTCGCGCTATTTCATATTGAAGCCAACCTAGAGAGCTTG..................................................................................GTTGGTGCAAGTTCGAGGATTGACATGATCCTGGGTGTTTTGGGATGGTCCACGGGCTGCAGTTGGTCAGAGAACAAACAGTTTCTAGAATGCTAATTTAGTGGCCTGGTGAAGAGTAGTTGCCCAGCTGTTGAATGCTTGGGGAAGAAAGTTTTGTTCAGTGAAACCTGAGTTCTGTTTGACAAGTATAGAAGCAAGCAATATAGGTTATATGGTGTAGGGCGACTGTATATAAAGGAAGAGTAGCAACCAGTTATACTTGTAAAGGAATTTTCAACTATACGAACTCCAACAAAAGTATGTTACAGTTATACAAAATAAATATATTAAATTATTTGTCAA</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-C09SLm0058A04-I962s/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M1736" ref_strand="+" ref_description="SGN-M1736 T1065 [cos_markers]">
      <seq>ttcattctctcttctattctattcactttctactaagaaaatgaagatgaggatgattatgattttgtttctgttggtaatcattgggggttttgttcatggagatgagaatgagtcattcaggaagcaacccacactagtgaagacggtgaagggtaccaagatgtgtgtgaaggattgggagtgcaacaaattgtctaaattttgttgtaatttgacaattactgattatctggatgttgaccaatttgagctccttttcactaagaggaactcacccgtagctcatgctgttggattctgggattatggatctttcattagggctgcagcactttaccagcctcttggatttggtaccaccggtggtaagaaaatgcagatgaaggagattgctgctttttttggacatgtcggtagcaaaacttcttgtggttatggtgtcgccactggcggaccactcgcttatggtctatgctataacaaagaaatgagtcccagccaagattactgtgatgaatacttcaaattaacctacccatgcactcctggag</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09SLm0058A04-I962s/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C09SLm0058A04.1" temp_strand="+" temp_description="C09SLm0058A04.1  EU139074.1 htgs_phase:1 submitted_to_sgn_as:gb|EU139074.1| upload_account_name:spain (1 - 96875)">
        <position start="55510" stop="56743"/>
      </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="55810" g_stop="56240" g_length="431"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="431" r_length="431" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="56241" i_stop="56320" i_length="80">
            <donor d_prob="0.989" d_score="1.00"/>
            <acceptor a_prob="0.993" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="56321" g_stop="56443" g_length="123"/>
          <reference_exon_boundary r_type="cDNA" r_start="432" r_stop="554" r_length="123" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09SLm0058A04.1" gen_strand="+" ref_id="SGN-M1736" ref_strand="+">
        <total_alignment_score>1.000</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="C09SLm0058A04.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M1736" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="55810" e_stop="56240"/>
          <exon e_start="56321" e_stop="56443"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTCATTCTCTCTTCTATTCTATTCACTTTCTACTAAGAAAATGAAGATGAGGATGATTATGATTTTGTTTCTGTTGGTAATCATTGGGGGTTTTGTTCATGGAGATGAGAATGAGTCATTCAGGAAGCAACCCACACTAGTGAAGACGGTGAAGGGTACCAAGATGTGTGTGAAGGATTGGGAGTGCAACAAATTGTCTAAATTTTGTTGTAATTTGACAATTACTGATTATCTGGATGTTGACCAATTTGAGCTCCTTTTCACTAAGAGGAACTCACCCGTAGCTCATGCTGTTGGATTCTGGGATTATGGATCTTTCATTAGGGCTGCAGCACTTTACCAGCCTCTTGGATTTGGTACCACCGGTGGTAAGAAAATGCAGATGAAGGAGATTGCTGCTTTTTTTGGACATGTCGGTAGCAAAACTTCTTGTAAGTTCATTCATTTGTTGTTGTTGTTATTATGATGATTATTATTATTATTAGATTAAGAGTATTAATTACAAATCCAGGTGGTTATGGTGTCGCCACTGGCGGACCACTCGCTTATGGTCTATGCTATAACAAAGAAATGAGTCCCAGCCAAGATTACTGTGATGAATACTTCAAATTAACCTACCCATGCACTCCTGGAG</genome_strand>
        <mrna_strand>TTCATTCTCTCTTCTATTCTATTCACTTTCTACTAAGAAAATGAAGATGAGGATGATTATGATTTTGTTTCTGTTGGTAATCATTGGGGGTTTTGTTCATGGAGATGAGAATGAGTCATTCAGGAAGCAACCCACACTAGTGAAGACGGTGAAGGGTACCAAGATGTGTGTGAAGGATTGGGAGTGCAACAAATTGTCTAAATTTTGTTGTAATTTGACAATTACTGATTATCTGGATGTTGACCAATTTGAGCTCCTTTTCACTAAGAGGAACTCACCCGTAGCTCATGCTGTTGGATTCTGGGATTATGGATCTTTCATTAGGGCTGCAGCACTTTACCAGCCTCTTGGATTTGGTACCACCGGTGGTAAGAAAATGCAGATGAAGGAGATTGCTGCTTTTTTTGGACATGTCGGTAGCAAAACTTCTT................................................................................GTGGTTATGGTGTCGCCACTGGCGGACCACTCGCTTATGGTCTATGCTATAACAAAGAAATGAGTCCCAGCCAAGATTACTGTGATGAATACTTCAAATTAACCTACCCATGCACTCCTGGAG</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="20140" PGL_stop="17978"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="20140" e_stop="19922"/>
            <exon e_start="19235" e_stop="19174"/>
            <exon e_start="18470" e_stop="18402"/>
            <exon e_start="18319" e_stop="17978"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.851" acc_prob="0.782" e_score="0.954"/>
          <exon-intron don_prob="0.883" acc_prob="0.979" e_score="1.000"/>
          <exon-intron don_prob="0.976" acc_prob="0.755" e_score="1.000"/>
          <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="0.954">
            <gDNA_exon_boundary e_start="20140" e_stop="19922" e_length="219"/>
          </exon>
          <intron i_serial="1" don_prob="0.851" acc_prob="0.782">
            <gDNA_intron_boundary i_start="19921" i_stop="19236" i_length="686"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="19235" e_stop="19174" e_length="62"/>
          </exon>
          <intron i_serial="2" don_prob="0.883" acc_prob="0.979">
            <gDNA_intron_boundary i_start="19173" i_stop="18471" i_length="703"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="18470" e_stop="18402" e_length="69"/>
          </exon>
          <intron i_serial="3" don_prob="0.976" acc_prob="0.755">
            <gDNA_intron_boundary i_start="18401" i_stop="18320" i_length="82"/>
          </intron>
          <exon e_serial="4" e_score="0.997">
            <gDNA_exon_boundary e_start="18319" e_stop="17978" e_length="342"/>
          </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="20140" stop="19922"/>
              <exon start="19235" stop="19174"/>
              <exon start="18470" stop="18402"/>
              <exon start="18319" stop="17978"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M8161" 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>GGAAACATAATAAGTGCATGCAGCATACAAATTTGAAGGCCACAGGGGAGACATTGTCACAAGGAAATGGTGTTGGCGAAATGATACTTGCTAACATACCAAGGTACAGGGATGTTCTGCCTGGATTAGACGGCTGGATGGCTAGCAAAGTTGCAACTTGGCAAAACCTGGAAGGGCACTCTGTTCAGTGGTTTTGTGTTGTCAGCATAGATCGAAAAG : GCATGATGGCCGATATTACTTCAGCATTGGCAGCTGTAGGCGTCATCATATGTTCTTGTGCG : GCTGAGACGGATAGAGGGAAGGGAATCGGTGTCGCGCTATTTCATATTGAAGCCAACCTAGAGAGCTTG : GTTGGTGCAAGTTCGAGGATTGACATGATCCTGGGTGTTTTGGGATGGTCCACGGGCTGCAGTTGGTCAGAGAACAAACAGTTTCTAGAATGCTAATTTAGTGGCCTGGTGAAGAGTAGTTGCCCAGCTGTTGAATGCTTGGGGAAGAAAGTTTTGTTCAGTGAAACCTGAGTTCTGTTTGACAAGTATAGAAGCAAGCAATATAGGTTATATGGTGTAGGGCGACTGTATATAAAGGAAGAGTAGCAACCAGTTATACTTGTAAAGGAATTTTCAACTATACGAACTCCAACAAAAGTATGTTACAGTTATACAAAATAAATATATTAAATTATTTGTCAC</gDNA_template>
            <first_frame> G  N  I  I  S  A  C  S  I  Q  I  *  R  P  Q  G  R  H  C  H  K  E  M  V  L  A  K  *  Y  L  L  T  Y  Q  G  T  G  M  F  C  L  D  *  T  A  G  W  L  A  K  L  Q  L  G  K  T  W  K  G  T  L  F  S  G  F  V  L  S  A  *  I  E  K  :  A  *  W  P  I  L  L  Q  H  W  Q  L  *  A  S  S  Y  V  L  V  R :   L  R  R  I  E  G  R  E  S  V  S  R  Y  F  I  L  K  P  T  *  R  A  W :   L  V  Q  V  R  G  L  T  *  S  W  V  F  W  D  G  P  R  A  A  V  G  Q  R  T  N  S  F  *  N  A  N  L  V  A  W  *  R  V  V  A  Q  L  L  N  A  W  G  R  K  F  C  S  V  K  P  E  F  C  L  T  S  I  E  A  S  N  I  G  Y  M  V  *  G  D  C  I  *  R  K  S  S  N  Q  L  Y  L  *  R  N  F  Q  L  Y  E  L  Q  Q  K  Y  V  T  V  I  Q  N  K  Y  I  K  L  F  V   </first_frame>
            <second_frame>  E  T  *  *  V  H  A  A  Y  K  F  E  G  H  R  G  D  I  V  T  R  K  W  C  W  R  N  D  T  C  *  H  T  K  V  Q  G  C  S  A  W  I  R  R  L  D  G  *  Q  S  C  N  L  A  K  P  G  R  A  L  C  S  V  V  L  C  C  Q  H  R  S  K  R :   H  D  G  R  Y  Y  F  S  I  G  S  C  R  R  H  H  M  F  L  C   : G  *  D  G  *  R  E  G  N  R  C  R  A  I  S  Y  *  S  Q  P  R  E  L   : G  W  C  K  F  E  D  *  H  D  P  G  C  F  G  M  V  H  G  L  Q  L  V  R  E  Q  T  V  S  R  M  L  I  *  W  P  G  E  E  *  L  P  S  C  *  M  L  G  E  E  S  F  V  Q  *  N  L  S  S  V  *  Q  V  *  K  Q  A  I  *  V  I  W  C  R  A  T  V  Y  K  G  R  V  A  T  S  Y  T  C  K  G  I  F  N  Y  T  N  S  N  K  S  M  L  Q  L  Y  K  I  N  I  L  N  Y  L  S  </second_frame>
            <third_frame>   K  H  N  K  C  M  Q  H  T  N  L  K  A  T  G  E  T  L  S  Q  G  N  G  V  G  E  M  I  L  A  N  I  P  R  Y  R  D  V  L  P  G  L  D  G  W  M  A  S  K  V  A  T  W  Q  N  L  E  G  H  S  V  Q  W  F  C  V  V  S  I  D  R  K   : G  M  M  A  D  I  T  S  A  L  A  A  V  G  V  I  I  C  S  C  A  :  A  E  T  D  R  G  K  G  I  G  V  A  L  F  H  I  E  A  N  L  E  S  L  :  V  G  A  S  S  R  I  D  M  I  L  G  V  L  G  W  S  T  G  C  S  W  S  E  N  K  Q  F  L  E  C  *  F  S  G  L  V  K  S  S  C  P  A  V  E  C  L  G  K  K  V  L  F  S  E  T  *  V  L  F  D  K  Y  R  S  K  Q  Y  R  L  Y  G  V  G  R  L  Y  I  K  E  E  *  Q  P  V  I  L  V  K  E  F  S  T  I  R  T  P  T  K  V  C  Y  S  Y  T  K  *  I  Y  *  I  I  C  H </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="C09SLm0058A04.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="20138" stop="19922"/>
                    <exon start="19235" stop="19174"/>
                    <exon start="18470" stop="18402"/>
                    <exon start="18319" stop="18224"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>441</number_coding_nucleotides>
                  <number_encoded_amino_acids>147</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>KHNKCMQHTNLKATGETLSQGNGVGEMILANIPRYRDVLPGLDGWMASKVATWQNLEGHSVQWFCVVSIDRKGMMADITSALAAVGVIICSCAAETDRGKGIGVALFHIEANLESLVGASSRIDMILGVLGWSTGCSWSENKQFLEC*</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="55810" PGL_stop="56443"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="55810" e_stop="56240"/>
            <exon e_start="56321" e_stop="56443"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.989" acc_prob="0.993" 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="55810" e_stop="56240" e_length="431"/>
          </exon>
          <intron i_serial="1" don_prob="0.989" acc_prob="0.993">
            <gDNA_intron_boundary i_start="56241" i_stop="56320" i_length="80"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="56321" e_stop="56443" e_length="123"/>
          </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="55810" stop="56240"/>
              <exon start="56321" stop="56443"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1736" 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>TTCATTCTCTCTTCTATTCTATTCACTTTCTACTAAGAAAATGAAGATGAGGATGATTATGATTTTGTTTCTGTTGGTAATCATTGGGGGTTTTGTTCATGGAGATGAGAATGAGTCATTCAGGAAGCAACCCACACTAGTGAAGACGGTGAAGGGTACCAAGATGTGTGTGAAGGATTGGGAGTGCAACAAATTGTCTAAATTTTGTTGTAATTTGACAATTACTGATTATCTGGATGTTGACCAATTTGAGCTCCTTTTCACTAAGAGGAACTCACCCGTAGCTCATGCTGTTGGATTCTGGGATTATGGATCTTTCATTAGGGCTGCAGCACTTTACCAGCCTCTTGGATTTGGTACCACCGGTGGTAAGAAAATGCAGATGAAGGAGATTGCTGCTTTTTTTGGACATGTCGGTAGCAAAACTTCTT : GTGGTTATGGTGTCGCCACTGGCGGACCACTCGCTTATGGTCTATGCTATAACAAAGAAATGAGTCCCAGCCAAGATTACTGTGATGAATACTTCAAATTAACCTACCCATGCACTCCTGGAG</gDNA_template>
            <first_frame> F  I  L  S  S  I  L  F  T  F  Y  *  E  N  E  D  E  D  D  Y  D  F  V  S  V  G  N  H  W  G  F  C  S  W  R  *  E  *  V  I  Q  E  A  T  H  T  S  E  D  G  E  G  Y  Q  D  V  C  E  G  L  G  V  Q  Q  I  V  *  I  L  L  *  F  D  N  Y  *  L  S  G  C  *  P  I  *  A  P  F  H  *  E  E  L  T  R  S  S  C  C  W  I  L  G  L  W  I  F  H  *  G  C  S  T  L  P  A  S  W  I  W  Y  H  R  W  *  E  N  A  D  E  G  D  C  C  F  F  W  T  C  R  *  Q  N  F  L :   W  L  W  C  R  H  W  R  T  T  R  L  W  S  M  L  *  Q  R  N  E  S  Q  P  R  L  L  *  *  I  L  Q  I  N  L  P  M  H  S  W   </first_frame>
            <second_frame>  S  F  S  L  L  F  Y  S  L  S  T  K  K  M  K  M  R  M  I  M  I  L  F  L  L  V  I  I  G  G  F  V  H  G  D  E  N  E  S  F  R  K  Q  P  T  L  V  K  T  V  K  G  T  K  M  C  V  K  D  W  E  C  N  K  L  S  K  F  C  C  N  L  T  I  T  D  Y  L  D  V  D  Q  F  E  L  L  F  T  K  R  N  S  P  V  A  H  A  V  G  F  W  D  Y  G  S  F  I  R  A  A  A  L  Y  Q  P  L  G  F  G  T  T  G  G  K  K  M  Q  M  K  E  I  A  A  F  F  G  H  V  G  S  K  T  S   : C  G  Y  G  V  A  T  G  G  P  L  A  Y  G  L  C  Y  N  K  E  M  S  P  S  Q  D  Y  C  D  E  Y  F  K  L  T  Y  P  C  T  P  G  </second_frame>
            <third_frame>   H  S  L  F  Y  S  I  H  F  L  L  R  K  *  R  *  G  *  L  *  F  C  F  C  W  *  S  L  G  V  L  F  M  E  M  R  M  S  H  S  G  S  N  P  H  *  *  R  R  *  R  V  P  R  C  V  *  R  I  G  S  A  T  N  C  L  N  F  V  V  I  *  Q  L  L  I  I  W  M  L  T  N  L  S  S  F  S  L  R  G  T  H  P  *  L  M  L  L  D  S  G  I  M  D  L  S  L  G  L  Q  H  F  T  S  L  L  D  L  V  P  P  V  V  R  K  C  R  *  R  R  L  L  L  F  L  D  M  S  V  A  K  L  L  :  V  V  M  V  S  P  L  A  D  H  S  L  M  V  Y  A  I  T  K  K  *  V  P  A  K  I  T  V  M  N  T  S  N  *  P  T  H  A  L  L  E </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="C09SLm0058A04.1" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="55811" stop="56240"/>
                    <exon start="56321" stop="56442"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>552</number_coding_nucleotides>
                  <number_encoded_amino_acids>184</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>SFSLLFYSLSTKKMKMRMIMILFLLVIIGGFVHGDENESFRKQPTLVKTVKGTKMCVKDWECNKLSKFCCNLTITDYLDVDQFELLFTKRNSPVAHAVGFWDYGSFIRAAALYQPLGFGTTGGKKMQMKEIAAFFGHVGSKTSCGYGVATGGPLAYGLCYNKEMSPSQDYCDEYFKLTYPCTPG</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 9 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
$ 6832 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3416 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 10 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-18 08:33:48
-->
