<?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 17:27:03"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0070F01-3skQA/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C04HBa0070F01-3skQA/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-C04HBa0070F01-3skQA/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M27-R" ref_strand="+" ref_description="SGN-M27-R TG339-R [rflp_markers_reverse]">
      <seq>agaatactctttcggcctacaagtctgctcaggtatttagactttcattctttataaaatgtggaggaaaatctcatatgagttctgcgaacgggaatgttctatgtgtgttaaattaggaaattgcataaacaagtactgcaagtcaccatttttatttagaagagtaaccaaaatccattagaattcgtcgtccaagggaaaaaaatgtttcccgtggtgaaccatgtagtattatttaatcgaagcatgaacatgacgtctctctctttttcaggatatcgctaatggcgaattggccccaacacatccaatccgattgggtctagctctcaatttctcagtgttttactatgagatattgaattctcctgatcgtgcttgtaatctcgccaaacaggtaacaaatttattgtattccttgtttcttaattgagcatccagggtgattttggaaagaaaaatagatgtttgtgtctattcaatgatgtttatggtttgtatggttgtgtaatatgcctttgatgaggcaattgcggagcttgacaccctgggagaggagtcctacaaggatagcactttgattatgcaacttctgcg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0070F01-3skQA/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0070F01.1" temp_strand="+" temp_description="C04HBa0070F01.1  CU856251.8 htgs_phase:3 submitted_to_sgn_as:C04HBa0070F01 sequenced_by:sanger upload_account_name:uk">
        <position start="110" stop="1308"/>
      </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="410" g_stop="1008" g_length="599"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="600" r_length="600" r_score="0.995"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0070F01.1" gen_strand="+" ref_id="SGN-M27-R" ref_strand="+">
        <total_alignment_score>0.995</total_alignment_score>
        <cumulative_length_of_scored_exons>599</cumulative_length_of_scored_exons>
        <coverage percentage="0.998" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0070F01.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M27-R" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="410" e_stop="1008"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGAATACTCTTTCGGCCTACAAGTCTGCTCAGGTATTTAGACTTTCATTCTTTATAAAATGTGGAGGAAAATCTCATATGAGTTCTGCGAACGGGAATGTTCTATGTGTGTTAAATTAGGAAATTGCATAAACAAGTACTGCAAGTCACCATTTTTATTTAGAAGAGTAACCAAAATCCATTAGAATTCGTCGTCCAAGGG-AAAAAATGTTTCCCGTGGTGAACCATGTAGTATTATTTAATCGAAGCATGAACATGACGTCTCTCTCTTTTTCAGGATATCGCTAATGGCGAATTGGCCCCAACACATCCAATCCGATTGGGTCTAGCTCTCAATTTCTCAGTGTTTTACTATGAGATATTGAATTCTCCTGATCGTGCTTGTAATCTCGCCAAACAGGTAACAAATTTATTGTATTCCTTGTTTCTTAATTGAGCATCCAGGGTGATTTTGGAAAGAAAAATAGATGTTTGTGTCTATTCAATGATGTTTATGGTTTGTATGGTTGTGTAATAGGCCTTTGATGAGGCAATTGCGGAGCTTGACACCCTGGGAGAGGAGTCCTACAAGGATAGCACTTTGATTATGCAACTTCTGCG</genome_strand>
        <mrna_strand>AGAATACTCTTTCGGCCTACAAGTCTGCTCAGGTATTTAGACTTTCATTCTTTATAAAATGTGGAGGAAAATCTCATATGAGTTCTGCGAACGGGAATGTTCTATGTGTGTTAAATTAGGAAATTGCATAAACAAGTACTGCAAGTCACCATTTTTATTTAGAAGAGTAACCAAAATCCATTAGAATTCGTCGTCCAAGGGAAAAAAATGTTTCCCGTGGTGAACCATGTAGTATTATTTAATCGAAGCATGAACATGACGTCTCTCTCTTTTTCAGGATATCGCTAATGGCGAATTGGCCCCAACACATCCAATCCGATTGGGTCTAGCTCTCAATTTCTCAGTGTTTTACTATGAGATATTGAATTCTCCTGATCGTGCTTGTAATCTCGCCAAACAGGTAACAAATTTATTGTATTCCTTGTTTCTTAATTGAGCATCCAGGGTGATTTTGGAAAGAAAAATAGATGTTTGTGTCTATTCAATGATGTTTATGGTTTGTATGGTTGTGTAATATGCCTTTGATGAGGCAATTGCGGAGCTTGACACCCTGGGAGAGGAGTCCTACAAGGATAGCACTTTGATTATGCAACTTCTGCG</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-C04HBa0070F01-3skQA/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M27-F" ref_strand="+" ref_description="SGN-M27-F TG339-F [rflp_markers_forward]">
      <seq>cattattcagcagaaacaacaacatagtagcgtaatcccacagtttatacagaaaccttacccctctaactactgaggtaaacatagatctatcatatgctttgtaaatgcctaccaaaaaaagggcctctattaaaacagatggaatattaagtcatattcttctttaaaaacccaagctaaaggtatggatggatatgtacttactgccttcaataaagtttaatcttgacttgatacaaaattaatagacacatatccaagtgaacaaaatggagtagacaatcaaaatgcagaatatgaaggaagatcaatccacaatgctctacttcttcgagaaaaaggaaataaaaagtactacttgcttcgtgaaaataaatattcatttccacgaaataagagagcttcatcagagcatccaaatacaagagaaatacgtagacaaaaggtaatctttgatgaaaacaacaaatggcaagaaacagcgcctttaggtaataggtattacaaatcacaggataaggactacaaacagccaattttgatcaatgagtaaaattacatcatcggttgtcaattctaagcaaagaagtttcactcacgatgttactactcattatcagcttttgatggttctttgatctcatcagttccatcatcct</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0070F01-3skQA/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0070F01.1" temp_strand="-" temp_description="C04HBa0070F01.1  CU856251.8 htgs_phase:3 submitted_to_sgn_as:C04HBa0070F01 sequenced_by:sanger upload_account_name:uk">
        <position start="2083" stop="829"/>
      </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="1790" g_stop="1129" g_length="662"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="662" r_length="662" r_score="0.989"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0070F01.1" gen_strand="-" ref_id="SGN-M27-F" ref_strand="+">
        <total_alignment_score>0.989</total_alignment_score>
        <cumulative_length_of_scored_exons>662</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0070F01.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M27-F" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1790" e_stop="1129"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GCTGCAGCAGCAGAAACAACAACATAGTAGCGTAATCCCACAGTTTATACAGAAACCTTACCCCTCTAACTACTGAGGTAAACATAGATCTATCATATGCTTTGTAAATGCCTACCAAAAAAAGGGCCTCTATTAAAACAGATGGAATATTAAGTCATATTCTTCTTTAAAAACCCAAGCTAAAGGTATGGATGGATATGTACTTACTGCCTTCAATAAAGTTTAATCTTGACTTGATTCAAAATTAATAGACACATATCCAAGTGAACAAAATGGAGTAGACAATCAAAATGCAGAATATGAAGGAAGATCAATCCACAATGCTCTACTTCTTCGAGAAAAAGGAAATAAAAAGTACTACTTGCTTCGTGAAAATAAATATTCATTTCCACGAAATAAGAGAGCTTCATCAGAGCATCCAAATACAAGAGAAATACGTAGACAAAAGGTAATCTTTGATGAAAACAACAAATGGCAAGAAACAGCGCCTTTAGGTAATAGGTATTACAAATCACAGGATAAGGACTACAAACAGCCAATTTTGATCAATGAGTAAAATTACATCATCGGTTGTCAATTCTAAGCAAAGAAGTTTCACTCACGATGTTACTACTCATTATCAGCTTTTGATGGTTCTTTGATCTCATCAGTTCCATCATCCT</genome_strand>
        <mrna_strand>CATTATTCAGCAGAAACAACAACATAGTAGCGTAATCCCACAGTTTATACAGAAACCTTACCCCTCTAACTACTGAGGTAAACATAGATCTATCATATGCTTTGTAAATGCCTACCAAAAAAAGGGCCTCTATTAAAACAGATGGAATATTAAGTCATATTCTTCTTTAAAAACCCAAGCTAAAGGTATGGATGGATATGTACTTACTGCCTTCAATAAAGTTTAATCTTGACTTGATACAAAATTAATAGACACATATCCAAGTGAACAAAATGGAGTAGACAATCAAAATGCAGAATATGAAGGAAGATCAATCCACAATGCTCTACTTCTTCGAGAAAAAGGAAATAAAAAGTACTACTTGCTTCGTGAAAATAAATATTCATTTCCACGAAATAAGAGAGCTTCATCAGAGCATCCAAATACAAGAGAAATACGTAGACAAAAGGTAATCTTTGATGAAAACAACAAATGGCAAGAAACAGCGCCTTTAGGTAATAGGTATTACAAATCACAGGATAAGGACTACAAACAGCCAATTTTGATCAATGAGTAAAATTACATCATCGGTTGTCAATTCTAAGCAAAGAAGTTTCACTCACGATGTTACTACTCATTATCAGCTTTTGATGGTTCTTTGATCTCATCAGTTCCATCATCCT</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-C04HBa0070F01-3skQA/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M1739" ref_strand="+" ref_description="SGN-M1739 T1068 [cos_markers]">
      <seq>tttttatggagagagtccaaagcaatgggcaatggtctttattttgtccaagtgaggctcctggattggcagattgctggggtgatgattttgagaagctgtattcgaagtatgaaagagagggtaaggctaagaaggttgtgcaagcacaaaatctctggtttgagatcttgaagtctcagatagaaactgggaccccatacatgctatataaggatacttgtaacagaaaaagcaaccagcagaatcttggcacaatcaagtcttctaacttgtgtactgaaattattgaatacacaagtcctactgaaactgctgtgtgcaatcttgcctcaattgctcttccacgatatgttagagagaaggaggttcctagtgaatcacaaccatctaagcttgttgggagcagaggcgctaaaaaccggtactttgattttgacaaactggcagaggtcactgcattggtgactacaaacctgaacaaaattattgatgtcaactactaccctgttgaaactgcaaaaaggtctaatttacgacatagacctattggacttgggg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0070F01-3skQA/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0070F01.1" temp_strand="+" temp_description="C04HBa0070F01.1  CU856251.8 htgs_phase:3 submitted_to_sgn_as:C04HBa0070F01 sequenced_by:sanger upload_account_name:uk">
        <position start="42316" stop="43863"/>
      </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="42616" g_stop="42737" g_length="122"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="122" r_length="122" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="42738" i_stop="42846" i_length="109">
            <donor d_prob="0.831" d_score="1.00"/>
            <acceptor a_prob="0.991" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="42847" g_stop="42939" g_length="93"/>
          <reference_exon_boundary r_type="cDNA" r_start="123" r_stop="215" r_length="93" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="42940" i_stop="43027" i_length="88">
            <donor d_prob="0.992" 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="43028" g_stop="43177" g_length="150"/>
          <reference_exon_boundary r_type="cDNA" r_start="216" r_stop="365" r_length="150" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="43178" i_stop="43264" i_length="87">
            <donor d_prob="0.979" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="43265" g_stop="43351" g_length="87"/>
          <reference_exon_boundary r_type="cDNA" r_start="366" r_stop="452" r_length="87" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="43352" i_stop="43454" i_length="103">
            <donor d_prob="0.992" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="43455" g_stop="43563" g_length="109"/>
          <reference_exon_boundary r_type="cDNA" r_start="453" r_stop="561" r_length="109" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0070F01.1" gen_strand="+" ref_id="SGN-M1739" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>561</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0070F01.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M1739" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="42616" e_stop="42737"/>
          <exon e_start="42847" e_stop="42939"/>
          <exon e_start="43028" e_stop="43177"/>
          <exon e_start="43265" e_stop="43351"/>
          <exon e_start="43455" e_stop="43563"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTTTTATGGAGAGAGTCCAAAGCAATGGGCAATGGTCTTTATTTTGTCCAAGTGAGGCTCCTGGATTGGCAGATTGCTGGGGTGATGATTTTGAGAAGCTGTATTCGAAGTATGAAAGAGAGGTAAAAGCAAGTCAACTATTGTGCTTAATTGCTTGCCGAGCTTGGAATCCTTAGATTACTTGATGTTTGTCAGCATATGATATATAATGATCCCATTTTGTCAATTCAGGGTAAGGCTAAGAAGGTTGTGCAAGCACAAAATCTCTGGTTTGAGATCTTGAAGTCTCAGATAGAAACTGGGACCCCATACATGCTATATAAGGTGACTTTTATATGGTTTATCTTGTTATTTTTGTTATTTGGATGCATTGTTCTTTCTTTTTAATCCTTTCTTCTGTTTGTTATCATAGGATACTTGTAACAGAAAAAGCAACCAGCAGAATCTTGGCACAATCAAGTCTTCTAACTTGTGTACTGAAATTATTGAATACACAAGTCCTACTGAAACTGCTGTGTGCAATCTTGCCTCAATTGCTCTTCCACGATATGTTAGAGAGAAGGTAGTTACAAATGCCATACACTTGAAAATATTGCTTGGTTTTAAGTTCTTTGTCCTGTTTTTAAGTACCTTTTTTTATATCTTGTAGGAGGTTCCTAGTGAATCACAACCATCTAAGCTTGTTGGGAGCAGAGGCGCTAAAAACCGGTACTTTGATTTTGACAAACTGGCAGAGGTTAGATTTTGTTCTGTCAAATTGGCCTTGTCAACTTCTGATGTTTCTTAGTTATTTATTTTGGATATCTATCTTACTGTGTTGTATTTTTCATGTGAGACAGGTCACTGCATTGGTGACTACAAACCTGAACAAAATTATTGATGTCAACTACTACCCTGTTGAAACTGCAAAAAGGTCTAATTTACGACATAGACCTATTGGACTTGGGG</genome_strand>
        <mrna_strand>TTTTTATGGAGAGAGTCCAAAGCAATGGGCAATGGTCTTTATTTTGTCCAAGTGAGGCTCCTGGATTGGCAGATTGCTGGGGTGATGATTTTGAGAAGCTGTATTCGAAGTATGAAAGAGAG.............................................................................................................GGTAAGGCTAAGAAGGTTGTGCAAGCACAAAATCTCTGGTTTGAGATCTTGAAGTCTCAGATAGAAACTGGGACCCCATACATGCTATATAAG........................................................................................GATACTTGTAACAGAAAAAGCAACCAGCAGAATCTTGGCACAATCAAGTCTTCTAACTTGTGTACTGAAATTATTGAATACACAAGTCCTACTGAAACTGCTGTGTGCAATCTTGCCTCAATTGCTCTTCCACGATATGTTAGAGAGAAG.......................................................................................GAGGTTCCTAGTGAATCACAACCATCTAAGCTTGTTGGGAGCAGAGGCGCTAAAAACCGGTACTTTGATTTTGACAAACTGGCAGAG.......................................................................................................GTCACTGCATTGGTGACTACAAACCTGAACAAAATTATTGATGTCAACTACTACCCTGTTGAAACTGCAAAAAGGTCTAATTTACGACATAGACCTATTGGACTTGGGG</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="410" PGL_stop="1008"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="410" e_stop="1008"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.995"/>
        </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="410" e_stop="1008" e_length="599"/>
          </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="410" stop="1008"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M27-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="1" AGS_serial="1" gDNA_strand="+"/>
          <translation>
            <gDNA_template>AGAATACTCTTTCGGCCTACAAGTCTGCTCAGGTATTTAGACTTTCATTCTTTATAAAATGTGGAGGAAAATCTCATATGAGTTCTGCGAACGGGAATGTTCTATGTGTGTTAAATTAGGAAATTGCATAAACAAGTACTGCAAGTCACCATTTTTATTTAGAAGAGTAACCAAAATCCATTAGAATTCGTCGTCCAAGGGAAAAAATGTTTCCCGTGGTGAACCATGTAGTATTATTTAATCGAAGCATGAACATGACGTCTCTCTCTTTTTCAGGATATCGCTAATGGCGAATTGGCCCCAACACATCCAATCCGATTGGGTCTAGCTCTCAATTTCTCAGTGTTTTACTATGAGATATTGAATTCTCCTGATCGTGCTTGTAATCTCGCCAAACAGGTAACAAATTTATTGTATTCCTTGTTTCTTAATTGAGCATCCAGGGTGATTTTGGAAAGAAAAATAGATGTTTGTGTCTATTCAATGATGTTTATGGTTTGTATGGTTGTGTAATAGGCCTTTGATGAGGCAATTGCGGAGCTTGACACCCTGGGAGAGGAGTCCTACAAGGATAGCACTTTGATTATGCAACTTCTGCG</gDNA_template>
            <first_frame> R  I  L  F  R  P  T  S  L  L  R  Y  L  D  F  H  S  L  *  N  V  E  E  N  L  I  *  V  L  R  T  G  M  F  Y  V  C  *  I  R  K  L  H  K  Q  V  L  Q  V  T  I  F  I  *  K  S  N  Q  N  P  L  E  F  V  V  Q  G  K  K  C  F  P  W  *  T  M  *  Y  Y  L  I  E  A  *  T  *  R  L  S  L  F  Q  D  I  A  N  G  E  L  A  P  T  H  P  I  R  L  G  L  A  L  N  F  S  V  F  Y  Y  E  I  L  N  S  P  D  R  A  C  N  L  A  K  Q  V  T  N  L  L  Y  S  L  F  L  N  *  A  S  R  V  I  L  E  R  K  I  D  V  C  V  Y  S  M  M  F  M  V  C  M  V  V  *  *  A  F  D  E  A  I  A  E  L  D  T  L  G  E  E  S  Y  K  D  S  T  L  I  M  Q  L  L   </first_frame>
            <second_frame>  E  Y  S  F  G  L  Q  V  C  S  G  I  *  T  F  I  L  Y  K  M  W  R  K  I  S  Y  E  F  C  E  R  E  C  S  M  C  V  K  L  G  N  C  I  N  K  Y  C  K  S  P  F  L  F  R  R  V  T  K  I  H  *  N  S  S  S  K  G  K  N  V  S  R  G  E  P  C  S  I  I  *  S  K  H  E  H  D  V  S  L  F  F  R  I  S  L  M  A  N  W  P  Q  H  I  Q  S  D  W  V  *  L  S  I  S  Q  C  F  T  M  R  Y  *  I  L  L  I  V  L  V  I  S  P  N  R  *  Q  I  Y  C  I  P  C  F  L  I  E  H  P  G  *  F  W  K  E  K  *  M  F  V  S  I  Q  *  C  L  W  F  V  W  L  C  N  R  P  L  M  R  Q  L  R  S  L  T  P  W  E  R  S  P  T  R  I  A  L  *  L  C  N  F  C  </second_frame>
            <third_frame>   N  T  L  S  A  Y  K  S  A  Q  V  F  R  L  S  F  F  I  K  C  G  G  K  S  H  M  S  S  A  N  G  N  V  L  C  V  L  N  *  E  I  A  *  T  S  T  A  S  H  H  F  Y  L  E  E  *  P  K  S  I  R  I  R  R  P  R  E  K  M  F  P  V  V  N  H  V  V  L  F  N  R  S  M  N  M  T  S  L  S  F  S  G  Y  R  *  W  R  I  G  P  N  T  S  N  P  I  G  S  S  S  Q  F  L  S  V  L  L  *  D  I  E  F  S  *  S  C  L  *  S  R  Q  T  G  N  K  F  I  V  F  L  V  S  *  L  S  I  Q  G  D  F  G  K  K  N  R  C  L  C  L  F  N  D  V  Y  G  L  Y  G  C  V  I  G  L  *  *  G  N  C  G  A  *  H  P  G  R  G  V  L  Q  G  *  H  F  D  Y  A  T  S  A </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="C04HBa0070F01.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="2" PGL_strand="-" PGL_start="1790" PGL_stop="1129"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="1790" e_stop="1129"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.989"/>
        </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="0.989">
            <gDNA_exon_boundary e_start="1790" e_stop="1129" e_length="662"/>
          </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="1790" stop="1129"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M27-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>GCTGCAGCAGCAGAAACAACAACATAGTAGCGTAATCCCACAGTTTATACAGAAACCTTACCCCTCTAACTACTGAGGTAAACATAGATCTATCATATGCTTTGTAAATGCCTACCAAAAAAAGGGCCTCTATTAAAACAGATGGAATATTAAGTCATATTCTTCTTTAAAAACCCAAGCTAAAGGTATGGATGGATATGTACTTACTGCCTTCAATAAAGTTTAATCTTGACTTGATTCAAAATTAATAGACACATATCCAAGTGAACAAAATGGAGTAGACAATCAAAATGCAGAATATGAAGGAAGATCAATCCACAATGCTCTACTTCTTCGAGAAAAAGGAAATAAAAAGTACTACTTGCTTCGTGAAAATAAATATTCATTTCCACGAAATAAGAGAGCTTCATCAGAGCATCCAAATACAAGAGAAATACGTAGACAAAAGGTAATCTTTGATGAAAACAACAAATGGCAAGAAACAGCGCCTTTAGGTAATAGGTATTACAAATCACAGGATAAGGACTACAAACAGCCAATTTTGATCAATGAGTAAAATTACATCATCGGTTGTCAATTCTAAGCAAAGAAGTTTCACTCACGATGTTACTACTCATTATCAGCTTTTGATGGTTCTTTGATCTCATCAGTTCCATCATCCT</gDNA_template>
            <first_frame> A  A  A  A  E  T  T  T  *  *  R  N  P  T  V  Y  T  E  T  L  P  L  *  L  L  R  *  T  *  I  Y  H  M  L  C  K  C  L  P  K  K  G  P  L  L  K  Q  M  E  Y  *  V  I  F  F  F  K  N  P  S  *  R  Y  G  W  I  C  T  Y  C  L  Q  *  S  L  I  L  T  *  F  K  I  N  R  H  I  S  K  *  T  K  W  S  R  Q  S  K  C  R  I  *  R  K  I  N  P  Q  C  S  T  S  S  R  K  R  K  *  K  V  L  L  A  S  *  K  *  I  F  I  S  T  K  *  E  S  F  I  R  A  S  K  Y  K  R  N  T  *  T  K  G  N  L  *  *  K  Q  Q  M  A  R  N  S  A  F  R  *  *  V  L  Q  I  T  G  *  G  L  Q  T  A  N  F  D  Q  *  V  K  L  H  H  R  L  S  I  L  S  K  E  V  S  L  T  M  L  L  L  I  I  S  F  *  W  F  F  D  L  I  S  S  I  I   </first_frame>
            <second_frame>  L  Q  Q  Q  K  Q  Q  H  S  S  V  I  P  Q  F  I  Q  K  P  Y  P  S  N  Y  *  G  K  H  R  S  I  I  C  F  V  N  A  Y  Q  K  K  G  L  Y  *  N  R  W  N  I  K  S  Y  S  S  L  K  T  Q  A  K  G  M  D  G  Y  V  L  T  A  F  N  K  V  *  S  *  L  D  S  K  L  I  D  T  Y  P  S  E  Q  N  G  V  D  N  Q  N  A  E  Y  E  G  R  S  I  H  N  A  L  L  L  R  E  K  G  N  K  K  Y  Y  L  L  R  E  N  K  Y  S  F  P  R  N  K  R  A  S  S  E  H  P  N  T  R  E  I  R  R  Q  K  V  I  F  D  E  N  N  K  W  Q  E  T  A  P  L  G  N  R  Y  Y  K  S  Q  D  K  D  Y  K  Q  P  I  L  I  N  E  *  N  Y  I  I  G  C  Q  F  *  A  K  K  F  H  S  R  C  Y  Y  S  L  S  A  F  D  G  S  L  I  S  S  V  P  S  S  </second_frame>
            <third_frame>   C  S  S  R  N  N  N  I  V  A  *  S  H  S  L  Y  R  N  L  T  P  L  T  T  E  V  N  I  D  L  S  Y  A  L  *  M  P  T  K  K  R  A  S  I  K  T  D  G  I  L  S  H  I  L  L  *  K  P  K  L  K  V  W  M  D  M  Y  L  L  P  S  I  K  F  N  L  D  L  I  Q  N  *  *  T  H  I  Q  V  N  K  M  E  *  T  I  K  M  Q  N  M  K  E  D  Q  S  T  M  L  Y  F  F  E  K  K  E  I  K  S  T  T  C  F  V  K  I  N  I  H  F  H  E  I  R  E  L  H  Q  S  I  Q  I  Q  E  K  Y  V  D  K  R  *  S  L  M  K  T  T  N  G  K  K  Q  R  L  *  V  I  G  I  T  N  H  R  I  R  T  T  N  S  Q  F  *  S  M  S  K  I  T  S  S  V  V  N  S  K  Q  R  S  F  T  H  D  V  T  T  H  Y  Q  L  L  M  V  L  *  S  H  Q  F  H  H  P </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="C04HBa0070F01.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="1558" stop="1235"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>321</number_coding_nucleotides>
                  <number_encoded_amino_acids>107</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LDSKLIDTYPSEQNGVDNQNAEYEGRSIHNALLLREKGNKKYYLLRENKYSFPRNKRASSEHPNTREIRRQKVIFDENNKWQETAPLGNRYYKSQDKDYKQPILINE*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="3" PGL_strand="+" PGL_start="42616" PGL_stop="43563"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="42616" e_stop="42737"/>
            <exon e_start="42847" e_stop="42939"/>
            <exon e_start="43028" e_stop="43177"/>
            <exon e_start="43265" e_stop="43351"/>
            <exon e_start="43455" e_stop="43563"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.831" acc_prob="0.991" e_score="1.000"/>
          <exon-intron don_prob="0.992" acc_prob="0.999" e_score="1.000"/>
          <exon-intron don_prob="0.979" acc_prob="0.999" e_score="1.000"/>
          <exon-intron don_prob="0.992" acc_prob="0.998" e_score="1.000"/>
          <exon-only e_score="1.000"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="1.000">
            <gDNA_exon_boundary e_start="42616" e_stop="42737" e_length="122"/>
          </exon>
          <intron i_serial="1" don_prob="0.831" acc_prob="0.991">
            <gDNA_intron_boundary i_start="42738" i_stop="42846" i_length="109"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="42847" e_stop="42939" e_length="93"/>
          </exon>
          <intron i_serial="2" don_prob="0.992" acc_prob="0.999">
            <gDNA_intron_boundary i_start="42940" i_stop="43027" i_length="88"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="43028" e_stop="43177" e_length="150"/>
          </exon>
          <intron i_serial="3" don_prob="0.979" acc_prob="0.999">
            <gDNA_intron_boundary i_start="43178" i_stop="43264" i_length="87"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="43265" e_stop="43351" e_length="87"/>
          </exon>
          <intron i_serial="4" don_prob="0.992" acc_prob="0.998">
            <gDNA_intron_boundary i_start="43352" i_stop="43454" i_length="103"/>
          </intron>
          <exon e_serial="5" e_score="1.000">
            <gDNA_exon_boundary e_start="43455" e_stop="43563" e_length="109"/>
          </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="42616" stop="42737"/>
              <exon start="42847" stop="42939"/>
              <exon start="43028" stop="43177"/>
              <exon start="43265" stop="43351"/>
              <exon start="43455" stop="43563"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1739" 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>TTTTTATGGAGAGAGTCCAAAGCAATGGGCAATGGTCTTTATTTTGTCCAAGTGAGGCTCCTGGATTGGCAGATTGCTGGGGTGATGATTTTGAGAAGCTGTATTCGAAGTATGAAAGAGAG : GGTAAGGCTAAGAAGGTTGTGCAAGCACAAAATCTCTGGTTTGAGATCTTGAAGTCTCAGATAGAAACTGGGACCCCATACATGCTATATAAG : GATACTTGTAACAGAAAAAGCAACCAGCAGAATCTTGGCACAATCAAGTCTTCTAACTTGTGTACTGAAATTATTGAATACACAAGTCCTACTGAAACTGCTGTGTGCAATCTTGCCTCAATTGCTCTTCCACGATATGTTAGAGAGAAG : GAGGTTCCTAGTGAATCACAACCATCTAAGCTTGTTGGGAGCAGAGGCGCTAAAAACCGGTACTTTGATTTTGACAAACTGGCAGAG : GTCACTGCATTGGTGACTACAAACCTGAACAAAATTATTGATGTCAACTACTACCCTGTTGAAACTGCAAAAAGGTCTAATTTACGACATAGACCTATTGGACTTGGGG</gDNA_template>
            <first_frame> F  L  W  R  E  S  K  A  M  G  N  G  L  Y  F  V  Q  V  R  L  L  D  W  Q  I  A  G  V  M  I  L  R  S  C  I  R  S  M  K  E  R :   V  R  L  R  R  L  C  K  H  K  I  S  G  L  R  S  *  S  L  R  *  K  L  G  P  H  T  C  Y  I  R :   I  L  V  T  E  K  A  T  S  R  I  L  A  Q  S  S  L  L  T  C  V  L  K  L  L  N  T  Q  V  L  L  K  L  L  C  A  I  L  P  Q  L  L  F  H  D  M  L  E  R  R :   R  F  L  V  N  H  N  H  L  S  L  L  G  A  E  A  L  K  T  G  T  L  I  L  T  N  W  Q  R :   S  L  H  W  *  L  Q  T  *  T  K  L  L  M  S  T  T  T  L  L  K  L  Q  K  G  L  I  Y  D  I  D  L  L  D  L  G </first_frame>
            <second_frame>  F  Y  G  E  S  P  K  Q  W  A  M  V  F  I  L  S  K  *  G  S  W  I  G  R  L  L  G  *  *  F  *  E  A  V  F  E  V  *  K  R   : G  *  G  *  E  G  C  A  S  T  K  S  L  V  *  D  L  E  V  S  D  R  N  W  D  P  I  H  A  I  *   : G  Y  L  *  Q  K  K  Q  P  A  E  S  W  H  N  Q  V  F  *  L  V  Y  *  N  Y  *  I  H  K  S  Y  *  N  C  C  V  Q  S  C  L  N  C  S  S  T  I  C  *  R  E   : G  G  S  *  *  I  T  T  I  *  A  C  W  E  Q  R  R  *  K  P  V  L  *  F  *  Q  T  G  R   : G  H  C  I  G  D  Y  K  P  E  Q  N  Y  *  C  Q  L  L  P  C  *  N  C  K  K  V  *  F  T  T  *  T  Y  W  T  W   </second_frame>
            <third_frame>   F  M  E  R  V  Q  S  N  G  Q  W  S  L  F  C  P  S  E  A  P  G  L  A  D  C  W  G  D  D  F  E  K  L  Y  S  K  Y  E  R  E  :  G  K  A  K  K  V  V  Q  A  Q  N  L  W  F  E  I  L  K  S  Q  I  E  T  G  T  P  Y  M  L  Y  K  :  D  T  C  N  R  K  S  N  Q  Q  N  L  G  T  I  K  S  S  N  L  C  T  E  I  I  E  Y  T  S  P  T  E  T  A  V  C  N  L  A  S  I  A  L  P  R  Y  V  R  E  K  :  E  V  P  S  E  S  Q  P  S  K  L  V  G  S  R  G  A  K  N  R  Y  F  D  F  D  K  L  A  E  :  V  T  A  L  V  T  T  N  L  N  K  I  I  D  V  N  Y  Y  P  V  E  T  A  K  R  S  N  L  R  H  R  P  I  G  L  G  </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="C04HBa0070F01.1" strand="+"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="42618" stop="42737"/>
                    <exon start="42847" stop="42939"/>
                    <exon start="43028" stop="43177"/>
                    <exon start="43265" stop="43351"/>
                    <exon start="43455" stop="43562"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>558</number_coding_nucleotides>
                  <number_encoded_amino_acids>186</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>FMERVQSNGQWSLFCPSEAPGLADCWGDDFEKLYSKYEREGKAKKVVQAQNLWFEILKSQIETGTPYMLYKDTCNRKSNQQNLGTIKSSNLCTEIIEYTSPTETAVCNLASIALPRYVREKEVPSESQPSKLVGSRGAKNRYFDFDKLAEVTALVTTNLNKIIDVNYYPVETAKRSNLRHRPIGLG</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:
$ 6360 bytes spliced alignments in total
$ 3 spliced alignments have been stored
$ 2120 bytes was the average size of a spliced alignment
$ 8008 bytes predicted gene locations in total
$ 3 predicted gene locations have been stored
$ 2669 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 9 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-15 17:27:06
-->
