<?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="2009-02-20 17:42:43"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04SLm0080H23-xdQmb/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C04SLm0080H23-xdQmb/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-C04SLm0080H23-xdQmb/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M2085" ref_strand="+" ref_description="SGN-M2085 T1546 [cos_markers]">
      <seq>gaagaaggaatgagtatgagagacataaattgctagctttaaatcaacgacaaaagatggttcttcaaagaaagacggaggaggctgctatggcaactaagagactaaaagaattgctagaagcgcgtaaatcttcaggtcgcgagaactcagttactagcaatggccatgtagcaaatggacagagcaatgagaaatcgttgcaacgttggcttgatcatgagcttgaagtgatggtgaatgttcatgaagttcgtcatgagtatgagaagcaaagtcaagtacgagccgcacttggtgaagagctagcagttttgaaacaagttgatgaatttgcttcaaaaagactgagtcctccaaggggtaaaaatggtttctctagggcatcttcaatgtcgccaaatgctagaatggcacgaattgcttctctagagaatatgttaggcatttcatccaattccctagttgcaatggcttcacaactttcagaagcagaagaacgagagc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0080H23-xdQmb/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04SLm0080H23.1" temp_strand="+" temp_description="C04SLm0080H23.1  CU928590.2 htgs_phase:3 submitted_to_sgn_as:C04SLm0080H23 sequenced_by:sanger upload_account_name:uk">
        <position start="29279" stop="31394"/>
      </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="29579" g_stop="29637" g_length="59"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="59" r_length="59" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="29638" i_stop="30138" i_length="501">
            <donor d_prob="0.982" d_score="1.00"/>
            <acceptor a_prob="0.995" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="30139" g_stop="30232" g_length="94"/>
          <reference_exon_boundary r_type="cDNA" r_start="60" r_stop="153" r_length="94" r_score="0.979"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="30233" i_stop="30401" i_length="169">
            <donor d_prob="0.983" d_score="0.98"/>
            <acceptor a_prob="0.999" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="30402" g_stop="30433" g_length="32"/>
          <reference_exon_boundary r_type="cDNA" r_start="154" r_stop="185" r_length="32" r_score="0.969"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="30434" i_stop="30523" i_length="90">
            <donor d_prob="1.000" d_score="0.00"/>
            <acceptor a_prob="0.983" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="30524" g_stop="30621" g_length="98"/>
          <reference_exon_boundary r_type="cDNA" r_start="186" r_stop="283" r_length="98" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="30622" i_stop="30723" i_length="102">
            <donor d_prob="0.994" d_score="1.00"/>
            <acceptor a_prob="0.967" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="30724" g_stop="30822" g_length="99"/>
          <reference_exon_boundary r_type="cDNA" r_start="284" r_stop="382" r_length="99" r_score="0.980"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="30823" i_stop="30969" i_length="147">
            <donor d_prob="0.985" d_score="0.96"/>
            <acceptor a_prob="0.994" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="30970" g_stop="31094" g_length="125"/>
          <reference_exon_boundary r_type="cDNA" r_start="383" r_stop="507" r_length="125" r_score="0.992"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04SLm0080H23.1" gen_strand="+" ref_id="SGN-M2085" ref_strand="+">
        <total_alignment_score>0.989</total_alignment_score>
        <cumulative_length_of_scored_exons>507</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0080H23.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M2085" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="29579" e_stop="29637"/>
          <exon e_start="30139" e_stop="30232"/>
          <exon e_start="30402" e_stop="30433"/>
          <exon e_start="30524" e_stop="30621"/>
          <exon e_start="30724" e_stop="30822"/>
          <exon e_start="30970" e_stop="31094"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GAAGAAGGAATGAGTATGAGAGACATAAATTGCTAGCTTTAAATCAACGACAAAAGATGGTGAGCATTTTAAGTTCCTCTATGTCCTTGTGTTGTCTTTCATTCTTCTCCAACTGTTTTAGTGAAGAAACACTTGACGTACATTCTAGTTGTGACATCCAAAAAATCAATGTCTTTAAATGCTACAATTCTACTTCATGAAATGGATATGTGTAATTGAGCATTTGATTTGATCCTTGAAGAAAAATTCAGCCACTTGAACATCTATTTGTAGCAGAGTAGAAAAAATCCCGTTTCTTGAAATTTTTTACACTTTGATCACAAGTTCAGAACAGATCTTGTATTTCTTGAAGACCTAGCTCAAACAAAATGCAGCGTGTATTAGAGAGGAAACAGTACACCTCCTGCCCAATTGAAGCTATTGTACCTTTGACAGCTTTTGTTAAATGGCTAACATAAATTGATGGCTTACTAGAATAACATGCACAATAGTCAAGCTCGTGCTAGTAGGTGATCACAGTCAATATCTGAATGTTATATGGCATCATGGATTTATTTCAGGTTCTTCAAAGAAAGACGGAGGAGGCTGCTATGGCAACCAAGAGACTAAAAGAATTGCTAGAAGCGCGTAAATCTTCTGGTCGCGAGAACTCAGGTTTGCACTATATTTAGCTTTTATCTGATGCCTTTTTTGTGGATTACTATTTACTGGTGAATTCTATTTCTATTAAAAATATATTCTCTCATAGAAGGTTCCACTGATTTATGCTAGTCTTTGCATTTTAATTTGTTCAACTTACTAAAATGTTCTGTTTATCATGCAGTTACTAGCAACGGCCATGTAGCAAATGGACAGGTACCAATCTTGCTCCTTTTGGACTCTAATGGACTTTTGTCTTTATACCTATTTGATCAAATAATTTAGTCAAGTATCTTTTGTATTCAGAGCAATGAGAAATCGTTGCAACGTTGGCTTGATCATGAGCTTGAAGTGATGGTGAATGTTCATGAAGTTCGTCATGAGTATGAGAAGCAAAGTCAAGTGTATGTAACAAAACTTATTTTACCTAAATTAATCTTCTCTTAATGTGTGCACACTTAACATATTCTGGGTTGCTTTTTTGAAATGGTTTCTTTTCATCTCAGACGAGCCGCACTTGGTGAAGAGCTAGCAGTTTTGAAACAAGTTGATGAATTTGCTTCAAAAGGACTGAGTCCTCCAAGGGGTAAAAATGGCTTCTCTAGGTACATATACTGAATGCATCTCTATTCTATCTGCCAATAATGGATTCAGTATCTCCAAAATGCAGCCTTAAGTAGCACTAAAGAAAACATTTTAAGTGCTAAAGAAAGTTCACTCTAATGGATTTCTATTTGTGGTTATCTGTTCAGGGCATCTTCAATGTCGCCAAATGCTAGAATGGCACGAATTGCTTCTCTAGAGAATATGTTAGGCATTTCATCCAATTCTCTAGTTGCAATGGCTTCACAACTTTCAGAAGCAGAAGAACGAGAGC</genome_strand>
        <mrna_strand>GAAGAAGGAATGAGTATGAGAGACATAAATTGCTAGCTTTAAATCAACGACAAAAGATG.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTCTTCAAAGAAAGACGGAGGAGGCTGCTATGGCAACTAAGAGACTAAAAGAATTGCTAGAAGCGCGTAAATCTTCAGGTCGCGAGAACTCAG.........................................................................................................................................................................TTACTAGCAATGGCCATGTAGCAAATGGACAG..........................................................................................AGCAATGAGAAATCGTTGCAACGTTGGCTTGATCATGAGCTTGAAGTGATGGTGAATGTTCATGAAGTTCGTCATGAGTATGAGAAGCAAAGTCAAGT......................................................................................................ACGAGCCGCACTTGGTGAAGAGCTAGCAGTTTTGAAACAAGTTGATGAATTTGCTTCAAAAAGACTGAGTCCTCCAAGGGGTAAAAATGGTTTCTCTAG...................................................................................................................................................GGCATCTTCAATGTCGCCAAATGCTAGAATGGCACGAATTGCTTCTCTAGAGAATATGTTAGGCATTTCATCCAATTCCCTAGTTGCAATGGCTTCACAACTTTCAGAAGCAGAAGAACGAGAGC</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-C04SLm0080H23-xdQmb/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M1241" ref_strand="+" ref_description="SGN-M1241 SSR568 [est_by_read_no_qc_info]">
      <seq>ctctctcatttttatttctatatcttcattagctactacccctctcttcactctttacaattgccttcttcttcttcttcttcttcttcttctctctgttctatggtattgtaaacatggctggagacttaatgaccagtggttacggaaccgataatttttcatcaaaaatggaggaaaccgccgcacaagaagctgcaaccgccggacttcaaagcgttgagaaagtaatcagattgttgtctaaatctcatcaaaagcaacaacaacagcaaacgaattttcaggattcggcatcgggtaattcctctgtttctgcagattatcaagctgtagctgatgctgctgtaaacaaattcaaaaagttcatttctttacttgataaaaacagaactggtcatgctagattccggcgaggaccaattagttctctttctcctccacttccatcaaagccacaacaattacaacaatccattaagaatcaaaacccccaaattgaagaaatcgaaaaaccccaagcttcaaataccaaaatctactgtccgaccccaattcaaagattgcctcctttacctcataaccatcttcaattagtgaaaaatgggtcgattgaaaggaaagaagcatcaactaccattaattttgcttctccatcgccggcgac</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0080H23-xdQmb/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04SLm0080H23.1" temp_strand="-" temp_description="C04SLm0080H23.1  CU928590.2 htgs_phase:3 submitted_to_sgn_as:C04SLm0080H23 sequenced_by:sanger upload_account_name:uk">
        <position start="58236" stop="56979"/>
      </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="57936" g_stop="57279" g_length="658"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="667" r_length="667" r_score="0.960"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04SLm0080H23.1" gen_strand="-" ref_id="SGN-M1241" ref_strand="+">
        <total_alignment_score>0.960</total_alignment_score>
        <cumulative_length_of_scored_exons>658</cumulative_length_of_scored_exons>
        <coverage percentage="0.987" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0080H23.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M1241" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="57936" e_stop="57279"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTCTCTCATTTTTATTTCTATATCTTCATTAGCTTCTACCCCTCTCTTCACTCTTTACAA------T-TTC--CTTCTTCTTCTTCTTCTTCTCTCTGTTCTATGGTATTGTAAACATGGCTGTAGACTTAATGACCAGTGGTTACAGAACCGATAATTTTTCATCAAAAATGGAGGAAACCGCCGTACAAGAAGCTGCAACCGCCGGACTTCAAAGCGTTGAGAAATTAATCAGATTGTTGTCTAAATCTCATCAAAATCAACAACAACAACAAACGAATTTTCAGGATTCGTCATCGGGTAATTCCTCTGTTTCTGCAGATTATCAAGCTGTAGCTGATGCTGCTGTAAACAAATTCAAAAAGTTCATTTCTTTACTTGATAAAAACAGAACTGGTCATGCTAGATTCCGGCGAGGACCAATTAGTTCTCTTTCTCCTCCACTTCCATCAAAGCCACAACAATTACAACAATCCATTAAGAATCAAAACCCCCAAATTGAAGAAATCGAAAAACCCCAAGCTTCAAATACCAAAATCTACTGTCCGACCCCAATTCAAAGATTGCCTCCTTTACCTCATAACCATCTTCAATTAGTGAAAAATGGGTCGATTGAAAGGAAAGAAGCATCAACTACCATTAATTTTGCTTCTCCATCGCCGGCGAC</genome_strand>
        <mrna_strand>CTCTCTCATTTTTATTTCTATATCTTCATTAGCTACTACCCCTCTCTTCACTCTTTACAATTGCCTTCTTCTTCTTCTTCTTCTTCTTCTTCTCTCTGTTCTATGGTATTGTAAACATGGCTGGAGACTTAATGACCAGTGGTTACGGAACCGATAATTTTTCATCAAAAATGGAGGAAACCGCCGCACAAGAAGCTGCAACCGCCGGACTTCAAAGCGTTGAGAAAGTAATCAGATTGTTGTCTAAATCTCATCAAAAGCAACAACAACAGCAAACGAATTTTCAGGATTCGGCATCGGGTAATTCCTCTGTTTCTGCAGATTATCAAGCTGTAGCTGATGCTGCTGTAAACAAATTCAAAAAGTTCATTTCTTTACTTGATAAAAACAGAACTGGTCATGCTAGATTCCGGCGAGGACCAATTAGTTCTCTTTCTCCTCCACTTCCATCAAAGCCACAACAATTACAACAATCCATTAAGAATCAAAACCCCCAAATTGAAGAAATCGAAAAACCCCAAGCTTCAAATACCAAAATCTACTGTCCGACCCCAATTCAAAGATTGCCTCCTTTACCTCATAACCATCTTCAATTAGTGAAAAATGGGTCGATTGAAAGGAAAGAAGCATCAACTACCATTAATTTTGCTTCTCCATCGCCGGCGAC</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-C04SLm0080H23-xdQmb/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M804" ref_strand="+" ref_description="SGN-M804 SSR131 [est_by_read_no_qc_info]">
      <seq>ctctctcatttttatttctatatcttcattagctactacccctctcttcactctttacaattgccttcttcttcttcttcttcttcttcttctctctgttctatggtattgtaaacatggctggagacttaatgaccagtggttacggaaccgataatttttcatcaaaaatggaggaaaccgccgcacaagaagctgcaaccgccggacttcaaagcgttgagaaagtaatcagattgttgtctaaatctcatcaaaagcaacaacaacagcaaacgaattttcaggattcggcatcgggtaattcctctgtttctgcagattatcaagctgtagctgatgctgctgtaaacaaattcaaaaagttcatttctttacttgataaaaacagaactggtcatgctagattccggcgaggaccaattagttctctttctcctccacttccatcaaagccacaacaattacaacaatccattaagaatcaaaacccccaaattgaagaaatcgaaaaaccccaagcttcaaataccaaaatctactgtccgaccccaattcaaagattgcctcctttacctcataaccatcttcaattagtgaaaaatgggtcgattgaaaggaaagaagcatcaactaccattaattttgcttctccatcgccggcgac</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0080H23-xdQmb/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04SLm0080H23.1" temp_strand="-" temp_description="C04SLm0080H23.1  CU928590.2 htgs_phase:3 submitted_to_sgn_as:C04SLm0080H23 sequenced_by:sanger upload_account_name:uk">
        <position start="58236" stop="56979"/>
      </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="57936" g_stop="57279" g_length="658"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="667" r_length="667" r_score="0.960"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04SLm0080H23.1" gen_strand="-" ref_id="SGN-M804" ref_strand="+">
        <total_alignment_score>0.960</total_alignment_score>
        <cumulative_length_of_scored_exons>658</cumulative_length_of_scored_exons>
        <coverage percentage="0.987" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0080H23.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M804" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="57936" e_stop="57279"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTCTCTCATTTTTATTTCTATATCTTCATTAGCTTCTACCCCTCTCTTCACTCTTTACAA------T-TTC--CTTCTTCTTCTTCTTCTTCTCTCTGTTCTATGGTATTGTAAACATGGCTGTAGACTTAATGACCAGTGGTTACAGAACCGATAATTTTTCATCAAAAATGGAGGAAACCGCCGTACAAGAAGCTGCAACCGCCGGACTTCAAAGCGTTGAGAAATTAATCAGATTGTTGTCTAAATCTCATCAAAATCAACAACAACAACAAACGAATTTTCAGGATTCGTCATCGGGTAATTCCTCTGTTTCTGCAGATTATCAAGCTGTAGCTGATGCTGCTGTAAACAAATTCAAAAAGTTCATTTCTTTACTTGATAAAAACAGAACTGGTCATGCTAGATTCCGGCGAGGACCAATTAGTTCTCTTTCTCCTCCACTTCCATCAAAGCCACAACAATTACAACAATCCATTAAGAATCAAAACCCCCAAATTGAAGAAATCGAAAAACCCCAAGCTTCAAATACCAAAATCTACTGTCCGACCCCAATTCAAAGATTGCCTCCTTTACCTCATAACCATCTTCAATTAGTGAAAAATGGGTCGATTGAAAGGAAAGAAGCATCAACTACCATTAATTTTGCTTCTCCATCGCCGGCGAC</genome_strand>
        <mrna_strand>CTCTCTCATTTTTATTTCTATATCTTCATTAGCTACTACCCCTCTCTTCACTCTTTACAATTGCCTTCTTCTTCTTCTTCTTCTTCTTCTTCTCTCTGTTCTATGGTATTGTAAACATGGCTGGAGACTTAATGACCAGTGGTTACGGAACCGATAATTTTTCATCAAAAATGGAGGAAACCGCCGCACAAGAAGCTGCAACCGCCGGACTTCAAAGCGTTGAGAAAGTAATCAGATTGTTGTCTAAATCTCATCAAAAGCAACAACAACAGCAAACGAATTTTCAGGATTCGGCATCGGGTAATTCCTCTGTTTCTGCAGATTATCAAGCTGTAGCTGATGCTGCTGTAAACAAATTCAAAAAGTTCATTTCTTTACTTGATAAAAACAGAACTGGTCATGCTAGATTCCGGCGAGGACCAATTAGTTCTCTTTCTCCTCCACTTCCATCAAAGCCACAACAATTACAACAATCCATTAAGAATCAAAACCCCCAAATTGAAGAAATCGAAAAACCCCAAGCTTCAAATACCAAAATCTACTGTCCGACCCCAATTCAAAGATTGCCTCCTTTACCTCATAACCATCTTCAATTAGTGAAAAATGGGTCGATTGAAAGGAAAGAAGCATCAACTACCATTAATTTTGCTTCTCCATCGCCGGCGAC</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-C04SLm0080H23-xdQmb/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M1241-2" ref_strand="+" ref_description="SGN-M1241-2 SSR568-2 [est_by_read]">
      <seq>ttgattagaataagaagttcctcccatttttctctctcatttttatttctatatcttcattagctactacccctctcttcactctttacaattgccttcttcttcttcttcttcttcttcttctctctgttctatggtattgtaaacatggctggagacttaatgaccagtggttacggaaccgataatttttcatcaaaaatggaggaaaccgccgcacaagaagctgcaaccgccggacttcaaagcgttgagaaagtaatcagattgttgtctaaatctcatcaaaagcaacaacaacagcaaacgaattttcaggattcggcatcgggtaattcctctgtttctgcagattatcaagctgtagctgatgctgctgtaaacaaattcaaaaagttcatttctttacttgataaaaacagaactggtcatgctagattccggcgaggaccaattagttctctttctcctccacttccatcaaagccacaacaattacaacaatccattaagaatcaaaacccccaaattgaagaaatcgaaaaaccccaagcttcaaataccaaaatctactgtccgaccccaattcaaagattgcctcctttacctcataaccatcttcaattagtgaaaaatgggtcgattgaaaggaaagaagcatcaactaccattaattttgc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0080H23-xdQmb/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04SLm0080H23.1" temp_strand="-" temp_description="C04SLm0080H23.1  CU928590.2 htgs_phase:3 submitted_to_sgn_as:C04SLm0080H23 sequenced_by:sanger upload_account_name:uk">
        <position start="58267" stop="56997"/>
      </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="57967" g_stop="57297" g_length="671"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="680" r_length="680" r_score="0.960"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04SLm0080H23.1" gen_strand="-" ref_id="SGN-M1241-2" ref_strand="+">
        <total_alignment_score>0.960</total_alignment_score>
        <cumulative_length_of_scored_exons>671</cumulative_length_of_scored_exons>
        <coverage percentage="0.987" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0080H23.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M1241-2" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="57967" e_stop="57297"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTGATTAGAATAAGAATTTCCTCCCATTTTTCTCTCTCATTTTTATTTCTATATCTTCATTAGCTTCTACCCCTCTCTTCACTCTTTACAA-T---TTC--CTTCTTCTTCTTCTTC---TTCTCTCTGTTCTATGGTATTGTAAACATGGCTGTAGACTTAATGACCAGTGGTTACAGAACCGATAATTTTTCATCAAAAATGGAGGAAACCGCCGTACAAGAAGCTGCAACCGCCGGACTTCAAAGCGTTGAGAAATTAATCAGATTGTTGTCTAAATCTCATCAAAATCAACAACAACAACAAACGAATTTTCAGGATTCGTCATCGGGTAATTCCTCTGTTTCTGCAGATTATCAAGCTGTAGCTGATGCTGCTGTAAACAAATTCAAAAAGTTCATTTCTTTACTTGATAAAAACAGAACTGGTCATGCTAGATTCCGGCGAGGACCAATTAGTTCTCTTTCTCCTCCACTTCCATCAAAGCCACAACAATTACAACAATCCATTAAGAATCAAAACCCCCAAATTGAAGAAATCGAAAAACCCCAAGCTTCAAATACCAAAATCTACTGTCCGACCCCAATTCAAAGATTGCCTCCTTTACCTCATAACCATCTTCAATTAGTGAAAAATGGGTCGATTGAAAGGAAAGAAGCATCAACTACCATTAATTTTGC</genome_strand>
        <mrna_strand>TTGATTAGAATAAGAAGTTCCTCCCATTTTTCTCTCTCATTTTTATTTCTATATCTTCATTAGCTACTACCCCTCTCTTCACTCTTTACAATTGCCTTCTTCTTCTTCTTCTTCTTCTTCTTCTCTCTGTTCTATGGTATTGTAAACATGGCTGGAGACTTAATGACCAGTGGTTACGGAACCGATAATTTTTCATCAAAAATGGAGGAAACCGCCGCACAAGAAGCTGCAACCGCCGGACTTCAAAGCGTTGAGAAAGTAATCAGATTGTTGTCTAAATCTCATCAAAAGCAACAACAACAGCAAACGAATTTTCAGGATTCGGCATCGGGTAATTCCTCTGTTTCTGCAGATTATCAAGCTGTAGCTGATGCTGCTGTAAACAAATTCAAAAAGTTCATTTCTTTACTTGATAAAAACAGAACTGGTCATGCTAGATTCCGGCGAGGACCAATTAGTTCTCTTTCTCCTCCACTTCCATCAAAGCCACAACAATTACAACAATCCATTAAGAATCAAAACCCCCAAATTGAAGAAATCGAAAAACCCCAAGCTTCAAATACCAAAATCTACTGTCCGACCCCAATTCAAAGATTGCCTCCTTTACCTCATAACCATCTTCAATTAGTGAAAAATGGGTCGATTGAAAGGAAAGAAGCATCAACTACCATTAATTTTGC</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-C04SLm0080H23-xdQmb/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M804-2" ref_strand="+" ref_description="SGN-M804-2 SSR131-2 [est_by_read]">
      <seq>ttgattagaataagaagttcctcccatttttctctctcatttttatttctatatcttcattagctactacccctctcttcactctttacaattgccttcttcttcttcttcttcttcttcttctctctgttctatggtattgtaaacatggctggagacttaatgaccagtggttacggaaccgataatttttcatcaaaaatggaggaaaccgccgcacaagaagctgcaaccgccggacttcaaagcgttgagaaagtaatcagattgttgtctaaatctcatcaaaagcaacaacaacagcaaacgaattttcaggattcggcatcgggtaattcctctgtttctgcagattatcaagctgtagctgatgctgctgtaaacaaattcaaaaagttcatttctttacttgataaaaacagaactggtcatgctagattccggcgaggaccaattagttctctttctcctccacttccatcaaagccacaacaattacaacaatccattaagaatcaaaacccccaaattgaagaaatcgaaaaaccccaagcttcaaataccaaaatctactgtccgaccccaattcaaagattgcctcctttacctcataaccatcttcaattagtgaaaaatgggtcgattgaaaggaaagaagcatcaactaccattaattttgc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0080H23-xdQmb/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04SLm0080H23.1" temp_strand="-" temp_description="C04SLm0080H23.1  CU928590.2 htgs_phase:3 submitted_to_sgn_as:C04SLm0080H23 sequenced_by:sanger upload_account_name:uk">
        <position start="58267" stop="56997"/>
      </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="57967" g_stop="57297" g_length="671"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="680" r_length="680" r_score="0.960"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04SLm0080H23.1" gen_strand="-" ref_id="SGN-M804-2" ref_strand="+">
        <total_alignment_score>0.960</total_alignment_score>
        <cumulative_length_of_scored_exons>671</cumulative_length_of_scored_exons>
        <coverage percentage="0.987" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0080H23.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M804-2" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="57967" e_stop="57297"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTGATTAGAATAAGAATTTCCTCCCATTTTTCTCTCTCATTTTTATTTCTATATCTTCATTAGCTTCTACCCCTCTCTTCACTCTTTACAA-T---TTC--CTTCTTCTTCTTCTTC---TTCTCTCTGTTCTATGGTATTGTAAACATGGCTGTAGACTTAATGACCAGTGGTTACAGAACCGATAATTTTTCATCAAAAATGGAGGAAACCGCCGTACAAGAAGCTGCAACCGCCGGACTTCAAAGCGTTGAGAAATTAATCAGATTGTTGTCTAAATCTCATCAAAATCAACAACAACAACAAACGAATTTTCAGGATTCGTCATCGGGTAATTCCTCTGTTTCTGCAGATTATCAAGCTGTAGCTGATGCTGCTGTAAACAAATTCAAAAAGTTCATTTCTTTACTTGATAAAAACAGAACTGGTCATGCTAGATTCCGGCGAGGACCAATTAGTTCTCTTTCTCCTCCACTTCCATCAAAGCCACAACAATTACAACAATCCATTAAGAATCAAAACCCCCAAATTGAAGAAATCGAAAAACCCCAAGCTTCAAATACCAAAATCTACTGTCCGACCCCAATTCAAAGATTGCCTCCTTTACCTCATAACCATCTTCAATTAGTGAAAAATGGGTCGATTGAAAGGAAAGAAGCATCAACTACCATTAATTTTGC</genome_strand>
        <mrna_strand>TTGATTAGAATAAGAAGTTCCTCCCATTTTTCTCTCTCATTTTTATTTCTATATCTTCATTAGCTACTACCCCTCTCTTCACTCTTTACAATTGCCTTCTTCTTCTTCTTCTTCTTCTTCTTCTCTCTGTTCTATGGTATTGTAAACATGGCTGGAGACTTAATGACCAGTGGTTACGGAACCGATAATTTTTCATCAAAAATGGAGGAAACCGCCGCACAAGAAGCTGCAACCGCCGGACTTCAAAGCGTTGAGAAAGTAATCAGATTGTTGTCTAAATCTCATCAAAAGCAACAACAACAGCAAACGAATTTTCAGGATTCGGCATCGGGTAATTCCTCTGTTTCTGCAGATTATCAAGCTGTAGCTGATGCTGCTGTAAACAAATTCAAAAAGTTCATTTCTTTACTTGATAAAAACAGAACTGGTCATGCTAGATTCCGGCGAGGACCAATTAGTTCTCTTTCTCCTCCACTTCCATCAAAGCCACAACAATTACAACAATCCATTAAGAATCAAAACCCCCAAATTGAAGAAATCGAAAAACCCCAAGCTTCAAATACCAAAATCTACTGTCCGACCCCAATTCAAAGATTGCCTCCTTTACCTCATAACCATCTTCAATTAGTGAAAAATGGGTCGATTGAAAGGAAAGAAGCATCAACTACCATTAATTTTGC</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-C04SLm0080H23-xdQmb/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M3067" ref_strand="+" ref_description="SGN-M3067 cLEC-7-B23 [est_clones]">
      <seq>atggattattggattgtgaggaactcatggggtgcttcctggggagaacacggctacctcaggatgcagcgtaacattgctaacccaaagggtttgtgtggtattgctacagttgtttcttaccctgtcaagacaggccaaaatcccccgaaaccagctccatctcctccatcgccagtcaagccacctactacttgtgatgatatgtacagttgcccatcaggaacaacgtgttgctgtgtctacgagtactatcacatgtgctttgcttggggttgctgccctatggaaggagctacttgctgtaaagaccataacagttgctgcccacatgattatcctgtctgcaatgttaaagccggcacctgctcaatcagcgagaataaccctctttcagtcaaagcaatgtcacacattcttgccaaacctattggatccttcagcaatcanggaatgaaaaacactatctcttgaagtgtctccaatgggaatgc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0080H23-xdQmb/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04SLm0080H23.1" temp_strand="+" temp_description="C04SLm0080H23.1  CU928590.2 htgs_phase:3 submitted_to_sgn_as:C04SLm0080H23 sequenced_by:sanger upload_account_name:uk">
        <position start="73119" stop="74301"/>
      </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="73419" g_stop="73793" g_length="375"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="375" r_length="375" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="73794" i_stop="73882" i_length="89">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.988" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="73883" g_stop="74001" g_length="119"/>
          <reference_exon_boundary r_type="cDNA" r_start="376" r_stop="494" r_length="119" r_score="0.992"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04SLm0080H23.1" gen_strand="+" ref_id="SGN-M3067" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>494</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0080H23.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M3067" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="73419" e_stop="73793"/>
          <exon e_start="73883" e_stop="74001"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATGGATTATTGGATTGTGAGGAACTCATGGGGTGCTTCCTGGGGAGAACACGGCTACCTCAGGATGCAGCGTAACATTGCTAACCCAAAGGGTTTGTGTGGTATTGCTACAGTTGTTTCTTACCCTGTCAAGACAGGCCAAAATCCCCCGAAACCAGCTCCATCTCCTCCATCGCCAGTCAAGCCACCTACTACTTGTGATGATATGTACAGTTGCCCATCAGGAACAACGTGTTGCTGTGTCTACGAGTACTATCACATGTGCTTTGCTTGGGGTTGCTGCCCTATGGAAGGAGCTACTTGCTGTAAAGACCATAACAGTTGCTGCCCACATGATTATCCTGTCTGCAATGTTAAAGCCGGCACCTGCTCAATCGTAAGTGATCCATCCCTACTTTGTAATTGTATGACGCACACAATATAATCATTTCCTTTATTAACGCGATTGTGTTTTTGTCTCTACAGAGCGAGAATAACCCTCTTTCAGTCAAAGCAATGTCACACATTCTTGCCAAACCTATTGGATCCTTCAGCAATCAGGGAATGAAAAACACTATCTCTTGAAGTGTCTCCAATGGGAATGC</genome_strand>
        <mrna_strand>ATGGATTATTGGATTGTGAGGAACTCATGGGGTGCTTCCTGGGGAGAACACGGCTACCTCAGGATGCAGCGTAACATTGCTAACCCAAAGGGTTTGTGTGGTATTGCTACAGTTGTTTCTTACCCTGTCAAGACAGGCCAAAATCCCCCGAAACCAGCTCCATCTCCTCCATCGCCAGTCAAGCCACCTACTACTTGTGATGATATGTACAGTTGCCCATCAGGAACAACGTGTTGCTGTGTCTACGAGTACTATCACATGTGCTTTGCTTGGGGTTGCTGCCCTATGGAAGGAGCTACTTGCTGTAAAGACCATAACAGTTGCTGCCCACATGATTATCCTGTCTGCAATGTTAAAGCCGGCACCTGCTCAATC.........................................................................................AGCGAGAATAACCCTCTTTCAGTCAAAGCAATGTCACACATTCTTGCCAAACCTATTGGATCCTTCAGCAATCANGGAATGAAAAACACTATCTCTTGAAGTGTCTCCAATGGGAATGC</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-C04SLm0080H23-xdQmb/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M605-R" ref_strand="+" ref_description="SGN-M605-R TG345-R [rflp_markers_reverse]">
      <seq>ctcactatagggagacagcttgcatgcctgcagctgagccaattggtcctggtgttgcagggggttctctgagagttatttgccttaaggaactctacaatggacagtgttttggaccgttgattattggatcgaagagtttgcggacgctgaagctgttccgttgttctggagattgggataagattctggaagtgattgctgaacaagtcagtgaacttgttgaaattcatcttgagaggcttcaggtcagtgataccggtcttgctgctatatctaaatgttccattcttgaaattctgcaccttgtgaaaacgcctgaatgcactaataatggtctaaagactgttgctgaaaactgtaagcttctaagaaagcttcacattgatgggtggaagactaacaggataagtgatgatgggttaattgctgtggcaaaacattgccccaatttacaagaattggttttaataggtgtgaatccaacatgtgctagtttggagaagttggctacaaattgcttgaatttagagagattagctctgtgtggaagtgaaactgttggg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0080H23-xdQmb/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04SLm0080H23.1" temp_strand="-" temp_description="C04SLm0080H23.1  CU928590.2 htgs_phase:3 submitted_to_sgn_as:C04SLm0080H23 sequenced_by:sanger upload_account_name:uk">
        <position start="91739" stop="90599"/>
      </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="91437" g_stop="90899" g_length="539"/>
          <reference_exon_boundary r_type="cDNA" r_start="28" r_stop="566" r_length="539" r_score="0.998"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04SLm0080H23.1" gen_strand="-" ref_id="SGN-M605-R" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>539</cumulative_length_of_scored_exons>
        <coverage percentage="0.952" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0080H23.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M605-R" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="91437" e_stop="90899"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTGCAGCTGAGCCAATTGGTCCTGGTGTTGCAGGGGGTTCTCTGAGAGTTATTTGCCTTAAGGAACTCTACAATGGACAGTGTTTTGGACCGTTGATTATTGGATCGAAGAGTTTGCGGACGCTGAAGCTGTTCCGTTGTTCTGGAGATTGGGATAAGATTCTGGAAGTGATTGCTGAACAAGTCAGTGAACTTGTTGAAATTCATCTTGAGAGGCTTCAGGTCAGTGATACCGGTCTTGCTGCTATATCTAAATGTTCCATTCTTGAAATTCTGCACCTTGTGAAAACGCCTGAATGCACTAATAATGGTCTAAAGGCTGTTGCTGAAAACTGTAAGCTTCTAAGAAAGCTTCACATTGATGGGTGGAAGACTAACAGGATAAGTGATGATGGGTTAATTGCTGTGGCAAAACATTGCCCCAATTTACAAGAATTGGTTTTAATAGGTGTGAATCCAACATGTGCTAGTTTGGAGAAGTTGGCTACAAATTGCTTGAATTTAGAGAGATTAGCTCTGTGTGGAAGTGAAACTGTTGGG</genome_strand>
        <mrna_strand>CTGCAGCTGAGCCAATTGGTCCTGGTGTTGCAGGGGGTTCTCTGAGAGTTATTTGCCTTAAGGAACTCTACAATGGACAGTGTTTTGGACCGTTGATTATTGGATCGAAGAGTTTGCGGACGCTGAAGCTGTTCCGTTGTTCTGGAGATTGGGATAAGATTCTGGAAGTGATTGCTGAACAAGTCAGTGAACTTGTTGAAATTCATCTTGAGAGGCTTCAGGTCAGTGATACCGGTCTTGCTGCTATATCTAAATGTTCCATTCTTGAAATTCTGCACCTTGTGAAAACGCCTGAATGCACTAATAATGGTCTAAAGACTGTTGCTGAAAACTGTAAGCTTCTAAGAAAGCTTCACATTGATGGGTGGAAGACTAACAGGATAAGTGATGATGGGTTAATTGCTGTGGCAAAACATTGCCCCAATTTACAAGAATTGGTTTTAATAGGTGTGAATCCAACATGTGCTAGTTTGGAGAAGTTGGCTACAAATTGCTTGAATTTAGAGAGATTAGCTCTGTGTGGAAGTGAAACTGTTGGG</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-C04SLm0080H23-xdQmb/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M605-F" ref_strand="+" ref_description="SGN-M605-F TG345-F [rflp_markers_forward]">
      <seq>ctgagccaattggtcctggtgttgcagggggttctctgagagttatttgccttaaggaactctacaatggacagtgttttggaccgttgattattggatcgaagagtttgcggacgctgaagctgttccgttgttctggagattgggataagattctggaagtgattgctgaacaagtcagtgaacttgttgaaattcatcttgagaggcttcaggtcagtgataccggtcttgctgctatatctaaatgttccattcttgaaattctgcaccttgtgaaaacgcctgaatgcactaataatggtctaaagactgttgctgaaaactgtaagcttctaagaaagcttcacattgatgggtggaagactaacaggataagtgatgatgggttaattgctgtggcaaaacattgccccaatttacaagaattggttttaataggtgtgaatccaacatgtgctagtttggagaagttggctacaaattgcttgaatttagagagattagctctgtgtggaagtgaaactgttg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0080H23-xdQmb/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04SLm0080H23.1" temp_strand="-" temp_description="C04SLm0080H23.1  CU928590.2 htgs_phase:3 submitted_to_sgn_as:C04SLm0080H23 sequenced_by:sanger upload_account_name:uk">
        <position start="91731" stop="90601"/>
      </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="91431" g_stop="90901" g_length="531"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="531" r_length="531" r_score="0.998"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04SLm0080H23.1" gen_strand="-" ref_id="SGN-M605-F" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>531</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0080H23.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M605-F" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="91431" e_stop="90901"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTGAGCCAATTGGTCCTGGTGTTGCAGGGGGTTCTCTGAGAGTTATTTGCCTTAAGGAACTCTACAATGGACAGTGTTTTGGACCGTTGATTATTGGATCGAAGAGTTTGCGGACGCTGAAGCTGTTCCGTTGTTCTGGAGATTGGGATAAGATTCTGGAAGTGATTGCTGAACAAGTCAGTGAACTTGTTGAAATTCATCTTGAGAGGCTTCAGGTCAGTGATACCGGTCTTGCTGCTATATCTAAATGTTCCATTCTTGAAATTCTGCACCTTGTGAAAACGCCTGAATGCACTAATAATGGTCTAAAGGCTGTTGCTGAAAACTGTAAGCTTCTAAGAAAGCTTCACATTGATGGGTGGAAGACTAACAGGATAAGTGATGATGGGTTAATTGCTGTGGCAAAACATTGCCCCAATTTACAAGAATTGGTTTTAATAGGTGTGAATCCAACATGTGCTAGTTTGGAGAAGTTGGCTACAAATTGCTTGAATTTAGAGAGATTAGCTCTGTGTGGAAGTGAAACTGTTG</genome_strand>
        <mrna_strand>CTGAGCCAATTGGTCCTGGTGTTGCAGGGGGTTCTCTGAGAGTTATTTGCCTTAAGGAACTCTACAATGGACAGTGTTTTGGACCGTTGATTATTGGATCGAAGAGTTTGCGGACGCTGAAGCTGTTCCGTTGTTCTGGAGATTGGGATAAGATTCTGGAAGTGATTGCTGAACAAGTCAGTGAACTTGTTGAAATTCATCTTGAGAGGCTTCAGGTCAGTGATACCGGTCTTGCTGCTATATCTAAATGTTCCATTCTTGAAATTCTGCACCTTGTGAAAACGCCTGAATGCACTAATAATGGTCTAAAGACTGTTGCTGAAAACTGTAAGCTTCTAAGAAAGCTTCACATTGATGGGTGGAAGACTAACAGGATAAGTGATGATGGGTTAATTGCTGTGGCAAAACATTGCCCCAATTTACAAGAATTGGTTTTAATAGGTGTGAATCCAACATGTGCTAGTTTGGAGAAGTTGGCTACAAATTGCTTGAATTTAGAGAGATTAGCTCTGTGTGGAAGTGAAACTGTTG</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>8</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="29579" PGL_stop="31094"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="29579" e_stop="29637"/>
            <exon e_start="30139" e_stop="30232"/>
            <exon e_start="30402" e_stop="30433"/>
            <exon e_start="30524" e_stop="30621"/>
            <exon e_start="30724" e_stop="30822"/>
            <exon e_start="30970" e_stop="31094"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.982" acc_prob="0.995" e_score="1.000"/>
          <exon-intron don_prob="0.983" acc_prob="0.999" e_score="0.979"/>
          <exon-intron don_prob="1.000" acc_prob="0.983" e_score="0.969"/>
          <exon-intron don_prob="0.994" acc_prob="0.967" e_score="1.000"/>
          <exon-intron don_prob="0.985" acc_prob="0.994" e_score="0.980"/>
          <exon-only e_score="0.992"/>
        </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="29579" e_stop="29637" e_length="59"/>
          </exon>
          <intron i_serial="1" don_prob="0.982" acc_prob="0.995">
            <gDNA_intron_boundary i_start="29638" i_stop="30138" i_length="501"/>
          </intron>
          <exon e_serial="2" e_score="0.979">
            <gDNA_exon_boundary e_start="30139" e_stop="30232" e_length="94"/>
          </exon>
          <intron i_serial="2" don_prob="0.983" acc_prob="0.999">
            <gDNA_intron_boundary i_start="30233" i_stop="30401" i_length="169"/>
          </intron>
          <exon e_serial="3" e_score="0.969">
            <gDNA_exon_boundary e_start="30402" e_stop="30433" e_length="32"/>
          </exon>
          <intron i_serial="3" don_prob="1.000" acc_prob="0.983">
            <gDNA_intron_boundary i_start="30434" i_stop="30523" i_length="90"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="30524" e_stop="30621" e_length="98"/>
          </exon>
          <intron i_serial="4" don_prob="0.994" acc_prob="0.967">
            <gDNA_intron_boundary i_start="30622" i_stop="30723" i_length="102"/>
          </intron>
          <exon e_serial="5" e_score="0.980">
            <gDNA_exon_boundary e_start="30724" e_stop="30822" e_length="99"/>
          </exon>
          <intron i_serial="5" don_prob="0.985" acc_prob="0.994">
            <gDNA_intron_boundary i_start="30823" i_stop="30969" i_length="147"/>
          </intron>
          <exon e_serial="6" e_score="0.992">
            <gDNA_exon_boundary e_start="30970" e_stop="31094" e_length="125"/>
          </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="29579" stop="29637"/>
              <exon start="30139" stop="30232"/>
              <exon start="30402" stop="30433"/>
              <exon start="30524" stop="30621"/>
              <exon start="30724" stop="30822"/>
              <exon start="30970" stop="31094"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M2085" 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>GAAGAAGGAATGAGTATGAGAGACATAAATTGCTAGCTTTAAATCAACGACAAAAGATG : GTTCTTCAAAGAAAGACGGAGGAGGCTGCTATGGCAACCAAGAGACTAAAAGAATTGCTAGAAGCGCGTAAATCTTCTGGTCGCGAGAACTCAG : TTACTAGCAACGGCCATGTAGCAAATGGACAG : AGCAATGAGAAATCGTTGCAACGTTGGCTTGATCATGAGCTTGAAGTGATGGTGAATGTTCATGAAGTTCGTCATGAGTATGAGAAGCAAAGTCAAGT : ACGAGCCGCACTTGGTGAAGAGCTAGCAGTTTTGAAACAAGTTGATGAATTTGCTTCAAAAGGACTGAGTCCTCCAAGGGGTAAAAATGGCTTCTCTAG : GGCATCTTCAATGTCGCCAAATGCTAGAATGGCACGAATTGCTTCTCTAGAGAATATGTTAGGCATTTCATCCAATTCTCTAGTTGCAATGGCTTCACAACTTTCAGAAGCAGAAGAACGAGAGC</gDNA_template>
            <first_frame> E  E  G  M  S  M  R  D  I  N  C  *  L  *  I  N  D  K  R  W :   F  F  K  E  R  R  R  R  L  L  W  Q  P  R  D  *  K  N  C  *  K  R  V  N  L  L  V  A  R  T  Q  :  L  L  A  T  A  M  *  Q  M  D  R :   A  M  R  N  R  C  N  V  G  L  I  M  S  L  K  *  W  *  M  F  M  K  F  V  M  S  M  R  S  K  V  K   : Y  E  P  H  L  V  K  S  *  Q  F  *  N  K  L  M  N  L  L  Q  K  D  *  V  L  Q  G  V  K  M  A  S  L   : G  H  L  Q  C  R  Q  M  L  E  W  H  E  L  L  L  *  R  I  C  *  A  F  H  P  I  L  *  L  Q  W  L  H  N  F  Q  K  Q  K  N  E  S </first_frame>
            <second_frame>  K  K  E  *  V  *  E  T  *  I  A  S  F  K  S  T  T  K  D   : G  S  S  K  K  D  G  G  G  C  Y  G  N  Q  E  T  K  R  I  A  R  S  A  *  I  F  W  S  R  E  L  S :   Y  *  Q  R  P  C  S  K  W  T   : E  Q  *  E  I  V  A  T  L  A  *  S  *  A  *  S  D  G  E  C  S  *  S  S  S  *  V  *  E  A  K  S  S  :  T  S  R  T  W  *  R  A  S  S  F  E  T  S  *  *  I  C  F  K  R  T  E  S  S  K  G  *  K  W  L  L  *  :  G  I  F  N  V  A  K  C  *  N  G  T  N  C  F  S  R  E  Y  V  R  H  F  I  Q  F  S  S  C  N  G  F  T  T  F  R  S  R  R  T  R   </second_frame>
            <third_frame>   R  R  N  E  Y  E  R  H  K  L  L  A  L  N  Q  R  Q  K  M  :  V  L  Q  R  K  T  E  E  A  A  M  A  T  K  R  L  K  E  L  L  E  A  R  K  S  S  G  R  E  N  S   : V  T  S  N  G  H  V  A  N  G  Q  :  S  N  E  K  S  L  Q  R  W  L  D  H  E  L  E  V  M  V  N  V  H  E  V  R  H  E  Y  E  K  Q  S  Q  V :   R  A  A  L  G  E  E  L  A  V  L  K  Q  V  D  E  F  A  S  K  G  L  S  P  P  R  G  K  N  G  F  S  R :   A  S  S  M  S  P  N  A  R  M  A  R  I  A  S  L  E  N  M  L  G  I  S  S  N  S  L  V  A  M  A  S  Q  L  S  E  A  E  E  R  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="C04SLm0080H23.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="29581" stop="29637"/>
                    <exon start="30139" stop="30232"/>
                    <exon start="30402" stop="30433"/>
                    <exon start="30524" stop="30621"/>
                    <exon start="30724" stop="30822"/>
                    <exon start="30970" stop="31093"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>504</number_coding_nucleotides>
                  <number_encoded_amino_acids>168</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>RRNEYERHKLLALNQRQKMVLQRKTEEAAMATKRLKELLEARKSSGRENSVTSNGHVANGQSNEKSLQRWLDHELEVMVNVHEVRHEYEKQSQVRAALGEELAVLKQVDEFASKGLSPPRGKNGFSRASSMSPNARMARIASLENMLGISSNSLVAMASQLSEAEERE</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="57967" PGL_stop="57279"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="57967" e_stop="57279"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.960"/>
        </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="0.960">
            <gDNA_exon_boundary e_start="57967" e_stop="57279" e_length="689"/>
          </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="57967" stop="57297"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1241-2" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="57967" stop="57297"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M804-2" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="57936" stop="57279"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1241" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="57936" stop="57279"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M804" 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>TTGATTAGAATAAGAATTTCCTCCCATTTTTCTCTCTCATTTTTATTTCTATATCTTCATTAGCTTCTACCCCTCTCTTCACTCTTTACAATTTCCTTCTTCTTCTTCTTCTTCTCTCTGTTCTATGGTATTGTAAACATGGCTGTAGACTTAATGACCAGTGGTTACAGAACCGATAATTTTTCATCAAAAATGGAGGAAACCGCCGTACAAGAAGCTGCAACCGCCGGACTTCAAAGCGTTGAGAAATTAATCAGATTGTTGTCTAAATCTCATCAAAATCAACAACAACAACAAACGAATTTTCAGGATTCGTCATCGGGTAATTCCTCTGTTTCTGCAGATTATCAAGCTGTAGCTGATGCTGCTGTAAACAAATTCAAAAAGTTCATTTCTTTACTTGATAAAAACAGAACTGGTCATGCTAGATTCCGGCGAGGACCAATTAGTTCTCTTTCTCCTCCACTTCCATCAAAGCCACAACAATTACAACAATCCATTAAGAATCAAAACCCCCAAATTGAAGAAATCGAAAAACCCCAAGCTTCAAATACCAAAATCTACTGTCCGACCCCAATTCAAAGATTGCCTCCTTTACCTCATAACCATCTTCAATTAGTGAAAAATGGGTCGATTGAAAGGAAAGAAGCATCAACTACCATTAATTTTGCTTCTCCATCGCCGGCGAC</gDNA_template>
            <first_frame> L  I  R  I  R  I  S  S  H  F  S  L  S  F  L  F  L  Y  L  H  *  L  L  P  L  S  S  L  F  T  I  S  F  F  F  F  F  F  S  L  F  Y  G  I  V  N  M  A  V  D  L  M  T  S  G  Y  R  T  D  N  F  S  S  K  M  E  E  T  A  V  Q  E  A  A  T  A  G  L  Q  S  V  E  K  L  I  R  L  L  S  K  S  H  Q  N  Q  Q  Q  Q  Q  T  N  F  Q  D  S  S  S  G  N  S  S  V  S  A  D  Y  Q  A  V  A  D  A  A  V  N  K  F  K  K  F  I  S  L  L  D  K  N  R  T  G  H  A  R  F  R  R  G  P  I  S  S  L  S  P  P  L  P  S  K  P  Q  Q  L  Q  Q  S  I  K  N  Q  N  P  Q  I  E  E  I  E  K  P  Q  A  S  N  T  K  I  Y  C  P  T  P  I  Q  R  L  P  P  L  P  H  N  H  L  Q  L  V  K  N  G  S  I  E  R  K  E  A  S  T  T  I  N  F  A  S  P  S  P  A   </first_frame>
            <second_frame>  *  L  E  *  E  F  P  P  I  F  L  S  H  F  Y  F  Y  I  F  I  S  F  Y  P  S  L  H  S  L  Q  F  P  S  S  S  S  S  S  L  C  S  M  V  L  *  T  W  L  *  T  *  *  P  V  V  T  E  P  I  I  F  H  Q  K  W  R  K  P  P  Y  K  K  L  Q  P  P  D  F  K  A  L  R  N  *  S  D  C  C  L  N  L  I  K  I  N  N  N  N  K  R  I  F  R  I  R  H  R  V  I  P  L  F  L  Q  I  I  K  L  *  L  M  L  L  *  T  N  S  K  S  S  F  L  Y  L  I  K  T  E  L  V  M  L  D  S  G  E  D  Q  L  V  L  F  L  L  H  F  H  Q  S  H  N  N  Y  N  N  P  L  R  I  K  T  P  K  L  K  K  S  K  N  P  K  L  Q  I  P  K  S  T  V  R  P  Q  F  K  D  C  L  L  Y  L  I  T  I  F  N  *  *  K  M  G  R  L  K  G  K  K  H  Q  L  P  L  I  L  L  L  H  R  R  R  </second_frame>
            <third_frame>   D  *  N  K  N  F  L  P  F  F  S  L  I  F  I  S  I  S  S  L  A  S  T  P  L  F  T  L  Y  N  F  L  L  L  L  L  L  L  S  V  L  W  Y  C  K  H  G  C  R  L  N  D  Q  W  L  Q  N  R  *  F  F  I  K  N  G  G  N  R  R  T  R  S  C  N  R  R  T  S  K  R  *  E  I  N  Q  I  V  V  *  I  S  S  K  S  T  T  T  T  N  E  F  S  G  F  V  I  G  *  F  L  C  F  C  R  L  S  S  C  S  *  C  C  C  K  Q  I  Q  K  V  H  F  F  T  *  *  K  Q  N  W  S  C  *  I  P  A  R  T  N  *  F  S  F  S  S  T  S  I  K  A  T  T  I  T  T  I  H  *  E  S  K  P  P  N  *  R  N  R  K  T  P  S  F  K  Y  Q  N  L  L  S  D  P  N  S  K  I  A  S  F  T  S  *  P  S  S  I  S  E  K  W  V  D  *  K  E  R  S  I  N  Y  H  *  F  C  F  S  I  A  G  D </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="C04SLm0080H23.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="57904" stop="57281"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>624</number_coding_nucleotides>
                  <number_encoded_amino_acids>208</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LLPLSSLFTISFFFFFFSLFYGIVNMAVDLMTSGYRTDNFSSKMEETAVQEAATAGLQSVEKLIRLLSKSHQNQQQQQTNFQDSSSGNSSVSADYQAVADAAVNKFKKFISLLDKNRTGHARFRRGPISSLSPPLPSKPQQLQQSIKNQNPQIEEIEKPQASNTKIYCPTPIQRLPPLPHNHLQLVKNGSIERKEASTTINFASPSPA</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="73419" PGL_stop="74001"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="73419" e_stop="73793"/>
            <exon e_start="73883" e_stop="74001"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.999" acc_prob="0.988" e_score="1.000"/>
          <exon-only e_score="0.992"/>
        </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="73419" e_stop="73793" e_length="375"/>
          </exon>
          <intron i_serial="1" don_prob="0.999" acc_prob="0.988">
            <gDNA_intron_boundary i_start="73794" i_stop="73882" i_length="89"/>
          </intron>
          <exon e_serial="2" e_score="0.992">
            <gDNA_exon_boundary e_start="73883" e_stop="74001" e_length="119"/>
          </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="73419" stop="73793"/>
              <exon start="73883" stop="74001"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M3067" 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>ATGGATTATTGGATTGTGAGGAACTCATGGGGTGCTTCCTGGGGAGAACACGGCTACCTCAGGATGCAGCGTAACATTGCTAACCCAAAGGGTTTGTGTGGTATTGCTACAGTTGTTTCTTACCCTGTCAAGACAGGCCAAAATCCCCCGAAACCAGCTCCATCTCCTCCATCGCCAGTCAAGCCACCTACTACTTGTGATGATATGTACAGTTGCCCATCAGGAACAACGTGTTGCTGTGTCTACGAGTACTATCACATGTGCTTTGCTTGGGGTTGCTGCCCTATGGAAGGAGCTACTTGCTGTAAAGACCATAACAGTTGCTGCCCACATGATTATCCTGTCTGCAATGTTAAAGCCGGCACCTGCTCAATC : AGCGAGAATAACCCTCTTTCAGTCAAAGCAATGTCACACATTCTTGCCAAACCTATTGGATCCTTCAGCAATCAGGGAATGAAAAACACTATCTCTTGAAGTGTCTCCAATGGGAATGC</gDNA_template>
            <first_frame> M  D  Y  W  I  V  R  N  S  W  G  A  S  W  G  E  H  G  Y  L  R  M  Q  R  N  I  A  N  P  K  G  L  C  G  I  A  T  V  V  S  Y  P  V  K  T  G  Q  N  P  P  K  P  A  P  S  P  P  S  P  V  K  P  P  T  T  C  D  D  M  Y  S  C  P  S  G  T  T  C  C  C  V  Y  E  Y  Y  H  M  C  F  A  W  G  C  C  P  M  E  G  A  T  C  C  K  D  H  N  S  C  C  P  H  D  Y  P  V  C  N  V  K  A  G  T  C  S  I  :  S  E  N  N  P  L  S  V  K  A  M  S  H  I  L  A  K  P  I  G  S  F  S  N  Q  G  M  K  N  T  I  S  *  S  V  S  N  G  N   </first_frame>
            <second_frame>  W  I  I  G  L  *  G  T  H  G  V  L  P  G  E  N  T  A  T  S  G  C  S  V  T  L  L  T  Q  R  V  C  V  V  L  L  Q  L  F  L  T  L  S  R  Q  A  K  I  P  R  N  Q  L  H  L  L  H  R  Q  S  S  H  L  L  L  V  M  I  C  T  V  A  H  Q  E  Q  R  V  A  V  S  T  S  T  I  T  C  A  L  L  G  V  A  A  L  W  K  E  L  L  A  V  K  T  I  T  V  A  A  H  M  I  I  L  S  A  M  L  K  P  A  P  A  Q  S :   A  R  I  T  L  F  Q  S  K  Q  C  H  T  F  L  P  N  L  L  D  P  S  A  I  R  E  *  K  T  L  S  L  E  V  S  P  M  G  M  </second_frame>
            <third_frame>   G  L  L  D  C  E  E  L  M  G  C  F  L  G  R  T  R  L  P  Q  D  A  A  *  H  C  *  P  K  G  F  V  W  Y  C  Y  S  C  F  L  P  C  Q  D  R  P  K  S  P  E  T  S  S  I  S  S  I  A  S  Q  A  T  Y  Y  L  *  *  Y  V  Q  L  P  I  R  N  N  V  L  L  C  L  R  V  L  S  H  V  L  C  L  G  L  L  P  Y  G  R  S  Y  L  L  *  R  P  *  Q  L  L  P  T  *  L  S  C  L  Q  C  *  S  R  H  L  L  N   : Q  R  E  *  P  S  F  S  Q  S  N  V  T  H  S  C  Q  T  Y  W  I  L  Q  Q  S  G  N  E  K  H  Y  L  L  K  C  L  Q  W  E  C </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C04SLm0080H23.1" strand="+"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="73419" stop="73793"/>
                    <exon start="73883" stop="73981"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>471</number_coding_nucleotides>
                  <number_encoded_amino_acids>157</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>MDYWIVRNSWGASWGEHGYLRMQRNIANPKGLCGIATVVSYPVKTGQNPPKPAPSPPSPVKPPTTCDDMYSCPSGTTCCCVYEYYHMCFAWGCCPMEGATCCKDHNSCCPHDYPVCNVKAGTCSISENNPLSVKAMSHILAKPIGSFSNQGMKNTIS*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C04SLm0080H23.1" strand="+"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="73438" stop="73793"/>
                    <exon start="73883" stop="73964"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>435</number_coding_nucleotides>
                  <number_encoded_amino_acids>145</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>GTHGVLPGENTATSGCSVTLLTQRVCVVLLQLFLTLSRQAKIPRNQLHLLHRQSSHLLLVMICTVAHQEQRVAVSTSTITCALLGVAALWKELLAVKTITVAAHMIILSAMLKPAPAQSARITLFQSKQCHTFLPNLLDPSAIRE*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="4" PGL_strand="-" PGL_start="91437" PGL_stop="90899"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="91437" e_stop="90899"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.998"/>
        </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="0.998">
            <gDNA_exon_boundary e_start="91437" e_stop="90899" e_length="539"/>
          </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="91437" stop="90899"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M605-R" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="91431" stop="90901"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M605-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="4" AGS_serial="1" gDNA_strand="-"/>
          <translation>
            <gDNA_template>CTGCAGCTGAGCCAATTGGTCCTGGTGTTGCAGGGGGTTCTCTGAGAGTTATTTGCCTTAAGGAACTCTACAATGGACAGTGTTTTGGACCGTTGATTATTGGATCGAAGAGTTTGCGGACGCTGAAGCTGTTCCGTTGTTCTGGAGATTGGGATAAGATTCTGGAAGTGATTGCTGAACAAGTCAGTGAACTTGTTGAAATTCATCTTGAGAGGCTTCAGGTCAGTGATACCGGTCTTGCTGCTATATCTAAATGTTCCATTCTTGAAATTCTGCACCTTGTGAAAACGCCTGAATGCACTAATAATGGTCTAAAGGCTGTTGCTGAAAACTGTAAGCTTCTAAGAAAGCTTCACATTGATGGGTGGAAGACTAACAGGATAAGTGATGATGGGTTAATTGCTGTGGCAAAACATTGCCCCAATTTACAAGAATTGGTTTTAATAGGTGTGAATCCAACATGTGCTAGTTTGGAGAAGTTGGCTACAAATTGCTTGAATTTAGAGAGATTAGCTCTGTGTGGAAGTGAAACTGTTGGG</gDNA_template>
            <first_frame> L  Q  L  S  Q  L  V  L  V  L  Q  G  V  L  *  E  L  F  A  L  R  N  S  T  M  D  S  V  L  D  R  *  L  L  D  R  R  V  C  G  R  *  S  C  S  V  V  L  E  I  G  I  R  F  W  K  *  L  L  N  K  S  V  N  L  L  K  F  I  L  R  G  F  R  S  V  I  P  V  L  L  L  Y  L  N  V  P  F  L  K  F  C  T  L  *  K  R  L  N  A  L  I  M  V  *  R  L  L  L  K  T  V  S  F  *  E  S  F  T  L  M  G  G  R  L  T  G  *  V  M  M  G  *  L  L  W  Q  N  I  A  P  I  Y  K  N  W  F  *  *  V  *  I  Q  H  V  L  V  W  R  S  W  L  Q  I  A  *  I  *  R  D  *  L  C  V  E  V  K  L  L   </first_frame>
            <second_frame>  C  S  *  A  N  W  S  W  C  C  R  G  F  S  E  S  Y  L  P  *  G  T  L  Q  W  T  V  F  W  T  V  D  Y  W  I  E  E  F  A  D  A  E  A  V  P  L  F  W  R  L  G  *  D  S  G  S  D  C  *  T  S  Q  *  T  C  *  N  S  S  *  E  A  S  G  Q  *  Y  R  S  C  C  Y  I  *  M  F  H  S  *  N  S  A  P  C  E  N  A  *  M  H  *  *  W  S  K  G  C  C  *  K  L  *  A  S  K  K  A  S  H  *  W  V  E  D  *  Q  D  K  *  *  W  V  N  C  C  G  K  T  L  P  Q  F  T  R  I  G  F  N  R  C  E  S  N  M  C  *  F  G  E  V  G  Y  K  L  L  E  F  R  E  I  S  S  V  W  K  *  N  C  W  </second_frame>
            <third_frame>   A  A  E  P  I  G  P  G  V  A  G  G  S  L  R  V  I  C  L  K  E  L  Y  N  G  Q  C  F  G  P  L  I  I  G  S  K  S  L  R  T  L  K  L  F  R  C  S  G  D  W  D  K  I  L  E  V  I  A  E  Q  V  S  E  L  V  E  I  H  L  E  R  L  Q  V  S  D  T  G  L  A  A  I  S  K  C  S  I  L  E  I  L  H  L  V  K  T  P  E  C  T  N  N  G  L  K  A  V  A  E  N  C  K  L  L  R  K  L  H  I  D  G  W  K  T  N  R  I  S  D  D  G  L  I  A  V  A  K  H  C  P  N  L  Q  E  L  V  L  I  G  V  N  P  T  C  A  S  L  E  K  L  A  T  N  C  L  N  L  E  R  L  A  L  C  G  S  E  T  V  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="C04SLm0080H23.1" strand="-"/>
                <serials PGL_serial="4" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="91435" stop="90899"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>537</number_coding_nucleotides>
                  <number_encoded_amino_acids>179</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>AAEPIGPGVAGGSLRVICLKELYNGQCFGPLIIGSKSLRTLKLFRCSGDWDKILEVIAEQVSELVEIHLERLQVSDTGLAAISKCSILEILHLVKTPECTNNGLKAVAENCKLLRKLHIDGWKTNRISDDGLIAVAKHCPNLQELVLIGVNPTCASLEKLATNCLNLERLALCGSETVG</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 32 chains have been computed
$ 
$ memory statistics:
$ 16288 bytes spliced alignments in total
$ 8 spliced alignments have been stored
$ 2036 bytes was the average size of a spliced alignment
$ 9248 bytes predicted gene locations in total
$ 4 predicted gene locations have been stored
$ 2312 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 32 backtrace matrices have been allocated
$ 
$ date finished: 2009-02-20 17:42:48
-->
