<?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="2008-02-20 05:31:01"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0114C15-WzPJH/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/cxgn-bacpublish-resources-Epacxy/sgn_marker_seqs" 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/cxgn-bacpublish-resources-Epacxy/sgn_marker_seqs" ref_id="SGN-M1512" ref_strand="+" ref_description="SGN-M1512 T0635 [cos_markers]">
      <seq>gaaccggaagaccaaaactttgtcaggaaacatgcactagaacaggcaaaaacactcggaattgatggtcgtgaagcagctactagggtcttctcaaacgcttcgggttcttactcttccaacatcaacctagctgttgagaactcatcatggaacgacgagaagcaacttcaagacatgtacttgggccggaagtcatttgcatttgactgtgatgctcctggtgctggcatgatggagaagaagaaagattttgagatggctctaagcacagctgatgccacgttccataacctcgactcatc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0114C15-WzPJH/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0114C15.1" temp_strand="-" temp_description="C04HBa0114C15.1  CT990488.10 htgs_phase:3 submitted_to_sgn_as:C04HBa0114C15 sequenced_by:sanger upload_account_name:uk">
        <position start="74364" stop="73460"/>
      </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="74064" g_stop="73760" g_length="305"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="305" r_length="305" r_score="0.980"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0114C15.1" gen_strand="-" ref_id="SGN-M1512" ref_strand="+">
        <total_alignment_score>0.980</total_alignment_score>
        <cumulative_length_of_scored_exons>305</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0114C15.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M1512" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="74064" e_stop="73760"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GAACCGGAAGACCAAAACTTTGTCAGGAAACATGCACTAGAACAGGCAAAAACACTCGGAATTGATGTTCGTGAAGCAGCTACTAGGGTCTTCTCAAACGCTTCGGGTTCTTACTCTTCCAACATCAACCTAGCTGTTGAGAACTCATCATGGAACGACGAGAAGCAACTTCAAGACATGTACTTGAGCCGAAAGTCATTTGCATTTGACTGTGATGCTCCTGGTGCTGGCATGATGGAGAAGAGGAAAGTTTTTGAGATGGCTCTAAGCACAGCTGATGCCACGTTCCAGAACCTCGACTCATC</genome_strand>
        <mrna_strand>GAACCGGAAGACCAAAACTTTGTCAGGAAACATGCACTAGAACAGGCAAAAACACTCGGAATTGATGGTCGTGAAGCAGCTACTAGGGTCTTCTCAAACGCTTCGGGTTCTTACTCTTCCAACATCAACCTAGCTGTTGAGAACTCATCATGGAACGACGAGAAGCAACTTCAAGACATGTACTTGGGCCGGAAGTCATTTGCATTTGACTGTGATGCTCCTGGTGCTGGCATGATGGAGAAGAAGAAAGATTTTGAGATGGCTCTAAGCACAGCTGATGCCACGTTCCATAACCTCGACTCATC</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/cxgn-bacpublish-resources-Epacxy/sgn_marker_seqs" ref_id="SGN-M7486" ref_strand="-" ref_description="SGN-M7486 C2_At2g41760 [cosii_markers]">
      <seq>aaaaatgtcttcaaatttggaattggaagtgaggtcttcagctacagttccttctctgcaagttccaacctttcatcataccccttattattgtgaggaaaacatctacctgctatgcaaaaagctatgtgatgacggactggcagatcctaatggttctgatctgtttgttattttcatttccaatgagaagaagcagattcctctgtggcatcagaaggctagccagcgagcagagggagttattctgtgggactatcatgtcatctgtgtacagaagaagagaaatgagaactcttcgtcactagtgtgggatttagattcaagtcttccgtttccatcatctcttggcacttatgtcgctgacagcattcgtccatcaattcagatattttctgaattcaaaaggttttttcgagttgtgcatgcccctatattcctccgacacttcgcatcagatagaagacatatgaaggattctgctggaaactggactgcagacccgccatcatatgaagctattgttgctgaaggagctgtacacaacctgaacgagtacattacagtctctcccgatgatgtagtgaagaatgtggaagctgataccgtcaatgttgttctctccgagaaacttggtgtagtaattggtgaagatgatttgttgggatttttctctttgatttcctgatgagagttgagaaaaaacttgctagcttgaaagatgaaatgatgatcttggatttttacatgtaaaaagaaaaagaaagtgtcttgtgagagtttttgcaaatggaatggaaaatattcttgtgttaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0114C15-WzPJH/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0114C15.1" temp_strand="-" temp_description="C04HBa0114C15.1  CT990488.10 htgs_phase:3 submitted_to_sgn_as:C04HBa0114C15 sequenced_by:sanger upload_account_name:uk">
        <position start="90402" stop="84538"/>
      </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="90102" g_stop="90010" g_length="93"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="93" r_length="93" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="90009" i_stop="87341" i_length="2669">
            <donor d_prob="0.969" 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="87340" g_stop="87235" g_length="106"/>
          <reference_exon_boundary r_type="cDNA" r_start="94" r_stop="199" r_length="106" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="87234" i_stop="86673" i_length="562">
            <donor d_prob="0.996" d_score="1.00"/>
            <acceptor a_prob="0.996" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="86672" g_stop="86595" g_length="78"/>
          <reference_exon_boundary r_type="cDNA" r_start="200" r_stop="277" r_length="78" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="86594" i_stop="86473" i_length="122">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.940" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="86472" g_stop="86342" g_length="131"/>
          <reference_exon_boundary r_type="cDNA" r_start="278" r_stop="408" r_length="131" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="86341" i_stop="85877" i_length="465">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.292" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="85876" g_stop="85752" g_length="125"/>
          <reference_exon_boundary r_type="cDNA" r_start="409" r_stop="531" r_length="123" r_score="0.984"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="85751" i_stop="85128" i_length="624">
            <donor d_prob="0.994" d_score="0.96"/>
            <acceptor a_prob="0.909" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="85127" g_stop="84857" g_length="271"/>
          <reference_exon_boundary r_type="cDNA" r_start="532" r_stop="801" r_length="270" r_score="0.996"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="815" polyA_stop="832"/>
      <MATCH_line gen_id="C04HBa0114C15.1" gen_strand="-" ref_id="SGN-M7486" ref_strand="-">
        <total_alignment_score>0.996</total_alignment_score>
        <cumulative_length_of_scored_exons>804</cumulative_length_of_scored_exons>
        <coverage percentage="0.966" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0114C15.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M7486" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="90102" e_stop="90010"/>
          <exon e_start="87340" e_stop="87235"/>
          <exon e_start="86672" e_stop="86595"/>
          <exon e_start="86472" e_stop="86342"/>
          <exon e_start="85876" e_stop="85752"/>
          <exon e_start="85127" e_stop="84857"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAAAATGTCTTCAAATTTGGAATTGGAAGTGAGGTCTTCAGCTACAGTTCCTTCTCTGCAAGTTCCAACCTTTCATCATACCCCTTATTATTGGTACATTCTCTCTCTCTCTCTCTCTGTGCTTTTTTGGGGGTGGAGGGGTATGTGTGTGTATAGATTCTTGAATGATAGACATAGCTGATGATGATTACTGTTTGTTTATGAAATTTGATGCATAATTGAGGATACCCGTTTCATTTGAAGACCTAATTAAGTTAGAATTGGTACTCTGTGTGTGTGTGTGTTTGCCTTTTTAAGGGGTGGGGCGTGTAAAAATGCATTCTTGAAATACAGATACAGCTGGTGATTACTGTTGTTTGGGGTGGGGTGGGGGGAGGTGGGGGTGTGTAAAAATGCATTCTTGAAAATACAGACATTGCTGGTGATTGGGCGGTGGGGGTGGGGCCGTGGGGGTGTGTAAAAATGCGTTCTTGAAATACAGACACAACTGGTAATTATTGTCGTTTGGGAGGGAGGTGGGTGGTGCTGTTTAAAAATGCGTTCTTGAAATATAGACATAGCTGGTGATTACTGATGTGTAACACCAGTACATTTGGAATTGGTAGTCAGTCCTATTTCCGGTAGGGGCAGTTGTCAATTGAATCAGATTTTGACCATTATTTTGATGTATGTAATAGTGCGAAAAGTAGAGCCAGCTCCAAGTTGTTCCGTTGAGTTTCTCGACCCTTTGGCTGAGGATGAGTCAGTTCTATTTCTCGATGTGGCAGGGAAGGGATATTTGTTTTGGGGTGCGGATGTGTAAATGCATTCTTGAAATACAGACATAGCTGGTGACTACTGTTATTTGGAGAGAGGTGTGGGGGAGGAGGTGGGACATAGTTGGTGATTACTGTTTGATTATGAAATCTGATGTACAAATGCTGATACCCTTTTCGTTTAAAGACATAATTTAAGCAAATTCTACAGCTGACCAGTTTTAGATCCACAATCACTACAACATACCGTATGAAATCCCACAAGTGGGGTCTAGGGAGGATAGAGTGTACCAGTCCTTACTCCTACCTCGTGTAGGTAGAGATGTTGCTTTTGAAAGACCCTCTGCTCAAGTGTAGCAATTCAAACTATTTATGGAAAGAAAAAAAGCTATAGGGAAGAAAACATGGCAACTAAAAAGGAAAGAAGTGCAGAGCATACAAGAAAAGAACAGTAACAACAATAGGATAGTGCGATAAGCAAAACACAATAAACAACTGTTGATGATAGATATCAAAAGCAAGCAACTACAAGCTTACAATTAATACTACAATAGACACCGCCAAGCCTAAACCTGTCGAAAAGCAAGACAATGCTCCACAACATACTCTTTTGTTATGTAGTATGAAAATATACATGAAATTTGGTGCAGGAAAGATTGTACGGGCGCCATTTTGTACAAAAAATGTTTGTGGAGTTTGTAGTTGAGCCAAATTTTTTTTGGTAAATGTCAATTAATGAAAGGATTTAGTCTTCGTTTGCTTCAGTAAGGTGTTACTTTGGTAGGCTGAACTGATTTAGCTGATGGCTTTTGTTCGGGGAAAGGGAGAGCTTTATTAAGTAATTTCATGATTTTTACAAATATCTGGTAATTTTGAACTGAACTTATCTAATGAGAATTCAAGATATGAATTTGGAACTTGTTAATTGTTTATTTGGTAAAAGCAATACTGAATGAGTAAAGAGAAAAAGAACTTGGCAATCTATGATTCATAGTATTTTTTTCCTTATTGATCTTTTTGAATTCCATATTCGAAGTTGCGATCAGATCTATAACAAAAAGAATCAGTTCAATATATTTCGTATGTATTCATAGGTAATATATTGGATTTGTATCAAATTTCGGATCAATCTATGTTGAGTGATTGCCTTCATTATGTAGTTGCTACCAAGTACCACTATTTTGGTTTTGGATCTTCAAATCCTTCGCGTAGGAGATCCAAACCCATTTTTTAATCCTTTGAGAAAAATATTCATTCTCTTCCTAAAAGTAGGACGTAGAAGCAACAAAGATTTTTTTTTCTATTCATCCTTGACCTCACTCAAGAATTGTTTTTATCCAATCCGCAGGAATTGATAGAAAAGGCAAATCATGTATAATACACCGGATCCGGCTCAGTTATTAATAGAGTGAATAGATATTGAAAACTTTCTTCTGATTCAAAATCATAGTGTAACGTGTATCCTCCCCTGTAACAAAAAATTGATTTTTGTTCAAGAATGAAATCTTATTGGAACTATCCACATCTAGTTCATCCTTTGGAACCATATCACATCCTGGAAATGATGAAATAGGATGATTGAGACGGTATTTTGTAAATATGTAATTATCTTGAATATATTAACCATTTCTTTATTTTGGGATCGCCTGGAAGGGACAAAAGAAAGATCTTGTTGTTTCTTTAACTTGGAGTATCTCTATGAGCATATTCCTGCAGAAATGCTTCGCCTGTGACCTGTCCTAAAGATAAATGTTCATAAAGAAAAGGGAACTTTTGAAATGAATCTATTTATGTAGAATTATTCAACTTAAGTACTTCCCTTTTCAAATTTGACATGTCTGTTTTTATTTCCATTCACATTAAGCTTGCTTACTGAATATATAGAGGGTTCATATATTTGACTCGGGTTGATCTTGATTTGAGGCATAGTTGATTGATTGAGAAAAATTACTTGCACTAACAATAAGTATTCTTCTGTTTGCTTTCTGTATTTACTTTCTATTACAGTGAGGAAAACATCTACCTGCTATGCAAAAAGCTATGTGATGACGGACTGGCAGATCCTAATGGTTCTGATCTGTTTGTTATTTTCATTTCCAATGAGAAGAAGCAGGCAACTACTCTTTGCTCTTCCTTTGGTTACTGTCTTAAGAAGTTCATTCATTGCATTGATACTTCATCTCAATGAAAATGATAGTAGTATAATATCTGTTCCTCTACTAGTAATGGTAATGCCGTAATGTATTGCGTTAAACTAACAAATGGTTAGATGGATAACAAAATAATGTGAACTGCAAGCCTTTGTTTGCAAACGGGATGTACTAACGTTTAGAACTTAATCTTTCAAATTTTGTTTACCATTTGATAATTCTTTGTAATGCATTAATCAGTTCAGTTTTATCTCCCTGTCCCCAATACAGCAAAGTAAAAGGATGAAGGGAAGTTCATGTTTGAATGGATCTGAAAATGGTCCAGGACACTTAAATAAGTTAAAGATAAATTGGACGTGAACAGTCTTCAAAACTAAATCGATTCAATACTATGAGTCCGTTTCTAGTGTATAATGATTTTCTAACTTAGTTGTTTGAATAAGGAGAGCGACAGAATGGCTGACAGTTAAGTTGTACCTAGCATAATGTTTTTGGGGATGTTAATTTATAATTATATGCTTTCAGATTCCTCTGTGGCATCAGAAGGCTAGCCAGCGAGCAGAGGGAGTTATTCTGTGGGACTATCATGTCATCTGTGTACAGGTTAGATTAACCTACTGTTGTCTAGTATAAACTGAAAATGGTTAACTATATGGTTTTTATTTTTCTCTACTATAGCTATTGGGATTTCATGTCCTTGAGAAAATCTGTTTGGATGCTTGCAGAAGAAGAGAAATGAGAACTCTTCGTCACTAGTGTGGGATTTAGATTCAAGTCTTCCGTTTCCATCATCTCTTGGCACTTATGTCGCTGACAGCATTCGTCCATCAATTCAGATATTTTCTGAATTCAAAAGGTAATAACTGTTCTAGCCCCAAAAAAGAAACATGATTTCTTGAATTTTTTGCTCTTAAACGATGAAGAACTGTTATTTCATTTTCTTTTATAGAAGCTAGATATTTCATTTTTGCTCAAATTATAAGATTCTTGATATAGTGATACAAAAGTAGTTCTATTGCTCTTCTGTGTATTGTTTTTCTCCATTCCTTCCTGAAGTCAACCCAACCTTAAAATGTTTCTAACTTTTCGTAAAATTTATGCTCTACCTAGTGAATCTCATTTTTTGTTTATCTTTAAAAATTGATTTCACAAGTCCACCCTAAAGGGGTGGTCTCATTAAAGAAATGCTCTTTCACTGACCTTTTTCTGAAGAAGAAACCAGAGTATGTTTTTCTTCTGGTGCTAAGCAATGTTGCCAACCTTGTGCTTGGAATAATAAGCTTACTGCAACCACATGAAAGAACAACTTTGGCCATTTCAGGTTTTTTCGAGTTGTGCATGCCCCTATATTCCTCCGACACTTCGCATCAGATAGAAGACATATGAAGGATTCTGCTGGAAACTGGACTGCAGACCCGCCATCATATGAAGCTATTGTTGCTGAAGGTAAATGCAGGAAATAAAAGTTTGCAAGATTATGCTTTTGTCATTTGTTGGTACATTTGGTATATAAAGATAACTTTGTTCCTTCGATTAATATTTTTATCCCGTAACTACTCAAATGCCGTCTCTAATTTGATTATTCTTTTGTTATTTTTGCCAAAGTTCATCAATTTCATGATAAATATCTCGATAAGGAATGACATTTTTGCTTGATAGTCAATTAGTTTGCTCTATATAACCTTTTGATTTGTACACTTAAACAAATTTAGAGGTGGATATCGGTGCATCAAAAATTGAAATACGTGGTTGTATGCCATACCAAACTGACTCGAAGTTCGAATCTCCCCTGCTGGTTTTATTTCCAATTATCTGATCTCATTTTATGTAGTGTCACTTTTCATAGTTAACTTATGGAATAGAACATATAGGAACCAGTAGAACTAAGCCTTTTGAATATATTTTCATTCGTTAAAATTGAATCGAGGAGCACATTTGCATTACCTAATGATATCTGATAGGTGTTTTGTATGATTTTGGGTCATTTGGTACAATTAGTGAGAAAATATGAAACCCTCTCGCTTGCTCTAGTTACGATTTTTGTTTTCATTCTGCCTTTTGCTTGTACAGATGGAGCTGTACACAACCTGAACGAGTACATTACAGTCTCTCCCGATGATGTAGTGAAGAATGTGGAAGCTGATACCGTCAATGTTGTTCTCTCCGAGAAACTTGGTGTAGTAATTGGTGAAGATGATTTGTTGGGATTTTTCTCTTTGATTTCCTGATGAGAGTTGAGAAAAAACTTGCTAGCTTGAAAGATGAAATGATGATCTTGGATTTTTACATGTAAAAAGAAAAAGAAAGTGTCTTGTGAGAGTTTTTGCAAATGGAATGGAAA</genome_strand>
        <mrna_strand>AAAAATGTCTTCAAATTTGGAATTGGAAGTGAGGTCTTCAGCTACAGTTCCTTCTCTGCAAGTTCCAACCTTTCATCATACCCCTTATTATTG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGAGGAAAACATCTACCTGCTATGCAAAAAGCTATGTGATGACGGACTGGCAGATCCTAATGGTTCTGATCTGTTTGTTATTTTCATTTCCAATGAGAAGAAGCAG..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATTCCTCTGTGGCATCAGAAGGCTAGCCAGCGAGCAGAGGGAGTTATTCTGTGGGACTATCATGTCATCTGTGTACAG..........................................................................................................................AAGAAGAGAAATGAGAACTCTTCGTCACTAGTGTGGGATTTAGATTCAAGTCTTCCGTTTCCATCATCTCTTGGCACTTATGTCGCTGACAGCATTCGTCCATCAATTCAGATATTTTCTGAATTCAAAAG.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTTTTTCGAGTTGTGCATGCCCCTATATTCCTCCGACACTTCGCATCAGATAGAAGACATATGAAGGATTCTGCTGGAAACTGGACTGCAGACCCGCCATCATATGAAGCTATTGTTGCTG-A-................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................A-GGAGCTGTACACAACCTGAACGAGTACATTACAGTCTCTCCCGATGATGTAGTGAAGAATGTGGAAGCTGATACCGTCAATGTTGTTCTCTCCGAGAAACTTGGTGTAGTAATTGGTGAAGATGATTTGTTGGGATTTTTCTCTTTGATTTCCTGATGAGAGTTGAGAAAAAACTTGCTAGCTTGAAAGATGAAATGATGATCTTGGATTTTTACATGTAAAAAGAAAAAGAAAGTGTCTTGTGAGAGTTTTTGCAAATGGAATGGAAA</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/cxgn-bacpublish-resources-Epacxy/sgn_marker_seqs" ref_id="SGN-M246-R" ref_strand="+" ref_description="SGN-M246-R TG506-R [rflp_markers_reverse]">
      <seq>ggagacagcttgcatgccagcagtccagtttccagcagaatccttcatatgtcttctatctgatgcgaagtgtcggaggaatataggggcatgcacaactcgaaaaaacctgaaatggccaaagttgttctttcatgtggttgcagtaagcttattattccaagcacaaggttggcaacattgcttagcaccagaagaaaaacacactctggtttcttcttcagaaaaaggtcagtgaaagagcatttctttaatgagaccacccctttagggtggacttgtgaaatcaatttttaaagataaacaaaaaatgagattcactaggtagagcataaattttacgaaaagttagaaacattttaaggttgggttgacttcaggaaggaatggagaaaaacaatacacagaagagcaatagaactacttttgtatcactatatcaagaatcttataatttgagcaaaaatgaaatatctagcttctataaaag</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0114C15-WzPJH/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0114C15.1" temp_strand="+" temp_description="C04HBa0114C15.1  CT990488.10 htgs_phase:3 submitted_to_sgn_as:C04HBa0114C15 sequenced_by:sanger upload_account_name:uk">
        <position start="85471" stop="86557"/>
      </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="85791" g_stop="86257" g_length="467"/>
          <reference_exon_boundary r_type="cDNA" r_start="24" r_stop="490" r_length="467" r_score="0.998"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0114C15.1" gen_strand="+" ref_id="SGN-M246-R" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>467</cumulative_length_of_scored_exons>
        <coverage percentage="0.953" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0114C15.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M246-R" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="85791" e_stop="86257"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCCAGTTTCCAGCAGAATCCTTCATATGTCTTCTATCTGATGCGAAGTGTCGGAGGAATATAGGGGCATGCACAACTCGAAAAAACCTGAAATGGCCAAAGTTGTTCTTTCATGTGGTTGCAGTAAGCTTATTATTCCAAGCACAAGGTTGGCAACATTGCTTAGCACCAGAAGAAAAACATACTCTGGTTTCTTCTTCAGAAAAAGGTCAGTGAAAGAGCATTTCTTTAATGAGACCACCCCTTTAGGGTGGACTTGTGAAATCAATTTTTAAAGATAAACAAAAAATGAGATTCACTAGGTAGAGCATAAATTTTACGAAAAGTTAGAAACATTTTAAGGTTGGGTTGACTTCAGGAAGGAATGGAGAAAAACAATACACAGAAGAGCAATAGAACTACTTTTGTATCACTATATCAAGAATCTTATAATTTGAGCAAAAATGAAATATCTAGCTTCTATAAAAG</genome_strand>
        <mrna_strand>TCCAGTTTCCAGCAGAATCCTTCATATGTCTTCTATCTGATGCGAAGTGTCGGAGGAATATAGGGGCATGCACAACTCGAAAAAACCTGAAATGGCCAAAGTTGTTCTTTCATGTGGTTGCAGTAAGCTTATTATTCCAAGCACAAGGTTGGCAACATTGCTTAGCACCAGAAGAAAAACACACTCTGGTTTCTTCTTCAGAAAAAGGTCAGTGAAAGAGCATTTCTTTAATGAGACCACCCCTTTAGGGTGGACTTGTGAAATCAATTTTTAAAGATAAACAAAAAATGAGATTCACTAGGTAGAGCATAAATTTTACGAAAAGTTAGAAACATTTTAAGGTTGGGTTGACTTCAGGAAGGAATGGAGAAAAACAATACACAGAAGAGCAATAGAACTACTTTTGTATCACTATATCAAGAATCTTATAATTTGAGCAAAAATGAAATATCTAGCTTCTATAAAAG</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/cxgn-bacpublish-resources-Epacxy/sgn_marker_seqs" ref_id="SGN-M246-F" ref_strand="+" ref_description="SGN-M246-F TG506-F [rflp_markers_forward]">
      <seq>aaatgcttcgcctgtgacctgtcctaaagataaatgttcataaagaaaagggaacttttgaaatgaatctatttatgtagaattattcaacttaagtacttcccttttcaaatttgacatgtctgtttttatttccattcacattaagcttgcttactgaatatatagagggttcatatatttgactcgggttgatcttgatttgaggcatagttgattgattgagaaaaattacttgcactaacaataagtattcttctgtttgctttctgtatttactttctattacagtgaggaaaacatctacctgctatgcaaaaagctatgtgatgacggactggcagatcctaatggttctgatctgtttgttattttcatttccaatgagaagaagcaggcaactactctttgctcttcctttggttactgtcttaagaagttcattcattgcattgatactt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0114C15-WzPJH/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0114C15.1" temp_strand="-" temp_description="C04HBa0114C15.1  CT990488.10 htgs_phase:3 submitted_to_sgn_as:C04HBa0114C15 sequenced_by:sanger upload_account_name:uk">
        <position start="87931" stop="86871"/>
      </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="87631" g_stop="87171" g_length="461"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="461" r_length="461" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0114C15.1" gen_strand="-" ref_id="SGN-M246-F" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>461</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0114C15.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M246-F" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="87631" e_stop="87171"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAATGCTTCGCCTGTGACCTGTCCTAAAGATAAATGTTCATAAAGAAAAGGGAACTTTTGAAATGAATCTATTTATGTAGAATTATTCAACTTAAGTACTTCCCTTTTCAAATTTGACATGTCTGTTTTTATTTCCATTCACATTAAGCTTGCTTACTGAATATATAGAGGGTTCATATATTTGACTCGGGTTGATCTTGATTTGAGGCATAGTTGATTGATTGAGAAAAATTACTTGCACTAACAATAAGTATTCTTCTGTTTGCTTTCTGTATTTACTTTCTATTACAGTGAGGAAAACATCTACCTGCTATGCAAAAAGCTATGTGATGACGGACTGGCAGATCCTAATGGTTCTGATCTGTTTGTTATTTTCATTTCCAATGAGAAGAAGCAGGCAACTACTCTTTGCTCTTCCTTTGGTTACTGTCTTAAGAAGTTCATTCATTGCATTGATACTT</genome_strand>
        <mrna_strand>AAATGCTTCGCCTGTGACCTGTCCTAAAGATAAATGTTCATAAAGAAAAGGGAACTTTTGAAATGAATCTATTTATGTAGAATTATTCAACTTAAGTACTTCCCTTTTCAAATTTGACATGTCTGTTTTTATTTCCATTCACATTAAGCTTGCTTACTGAATATATAGAGGGTTCATATATTTGACTCGGGTTGATCTTGATTTGAGGCATAGTTGATTGATTGAGAAAAATTACTTGCACTAACAATAAGTATTCTTCTGTTTGCTTTCTGTATTTACTTTCTATTACAGTGAGGAAAACATCTACCTGCTATGCAAAAAGCTATGTGATGACGGACTGGCAGATCCTAATGGTTCTGATCTGTTTGTTATTTTCATTTCCAATGAGAAGAAGCAGGCAACTACTCTTTGCTCTTCCTTTGGTTACTGTCTTAAGAAGTTCATTCATTGCATTGATACTT</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>4</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="74064" PGL_stop="73760"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="74064" e_stop="73760"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.980"/>
        </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="0.980">
            <gDNA_exon_boundary e_start="74064" e_stop="73760" e_length="305"/>
          </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="74064" stop="73760"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1512" 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>GAACCGGAAGACCAAAACTTTGTCAGGAAACATGCACTAGAACAGGCAAAAACACTCGGAATTGATGTTCGTGAAGCAGCTACTAGGGTCTTCTCAAACGCTTCGGGTTCTTACTCTTCCAACATCAACCTAGCTGTTGAGAACTCATCATGGAACGACGAGAAGCAACTTCAAGACATGTACTTGAGCCGAAAGTCATTTGCATTTGACTGTGATGCTCCTGGTGCTGGCATGATGGAGAAGAGGAAAGTTTTTGAGATGGCTCTAAGCACAGCTGATGCCACGTTCCAGAACCTCGACTCATC</gDNA_template>
            <first_frame> E  P  E  D  Q  N  F  V  R  K  H  A  L  E  Q  A  K  T  L  G  I  D  V  R  E  A  A  T  R  V  F  S  N  A  S  G  S  Y  S  S  N  I  N  L  A  V  E  N  S  S  W  N  D  E  K  Q  L  Q  D  M  Y  L  S  R  K  S  F  A  F  D  C  D  A  P  G  A  G  M  M  E  K  R  K  V  F  E  M  A  L  S  T  A  D  A  T  F  Q  N  L  D  S   </first_frame>
            <second_frame>  N  R  K  T  K  T  L  S  G  N  M  H  *  N  R  Q  K  H  S  E  L  M  F  V  K  Q  L  L  G  S  S  Q  T  L  R  V  L  T  L  P  T  S  T  *  L  L  R  T  H  H  G  T  T  R  S  N  F  K  T  C  T  *  A  E  S  H  L  H  L  T  V  M  L  L  V  L  A  *  W  R  R  G  K  F  L  R  W  L  *  A  Q  L  M  P  R  S  R  T  S  T  H  </second_frame>
            <third_frame>   T  G  R  P  K  L  C  Q  E  T  C  T  R  T  G  K  N  T  R  N  *  C  S  *  S  S  Y  *  G  L  L  K  R  F  G  F  L  L  F  Q  H  Q  P  S  C  *  E  L  I  M  E  R  R  E  A  T  S  R  H  V  L  E  P  K  V  I  C  I  *  L  *  C  S  W  C  W  H  D  G  E  E  E  S  F  *  D  G  S  K  H  S  *  C  H  V  P  E  P  R  L  I </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="C04HBa0114C15.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="74064" stop="73762"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>303</number_coding_nucleotides>
                  <number_encoded_amino_acids>101</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>EPEDQNFVRKHALEQAKTLGIDVREAATRVFSNASGSYSSNINLAVENSSWNDEKQLQDMYLSRKSFAFDCDAPGAGMMEKRKVFEMALSTADATFQNLDS</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="90102" PGL_stop="84857"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="90102" e_stop="90010"/>
            <exon e_start="87340" e_stop="87235"/>
            <exon e_start="86672" e_stop="86595"/>
            <exon e_start="86472" e_stop="86342"/>
            <exon e_start="85876" e_stop="85752"/>
            <exon e_start="85127" e_stop="84857"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.969" acc_prob="0.988" e_score="1.000"/>
          <exon-intron don_prob="0.996" acc_prob="0.996" e_score="1.000"/>
          <exon-intron don_prob="0.997" acc_prob="0.940" e_score="1.000"/>
          <exon-intron don_prob="0.997" acc_prob="0.292" e_score="1.000"/>
          <exon-intron don_prob="0.994" acc_prob="0.909" e_score="0.984"/>
          <exon-only e_score="0.996"/>
        </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="90102" e_stop="90010" e_length="93"/>
          </exon>
          <intron i_serial="1" don_prob="0.969" acc_prob="0.988">
            <gDNA_intron_boundary i_start="90009" i_stop="87341" i_length="2669"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="87340" e_stop="87235" e_length="106"/>
          </exon>
          <intron i_serial="2" don_prob="0.996" acc_prob="0.996">
            <gDNA_intron_boundary i_start="87234" i_stop="86673" i_length="562"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="86672" e_stop="86595" e_length="78"/>
          </exon>
          <intron i_serial="3" don_prob="0.997" acc_prob="0.940">
            <gDNA_intron_boundary i_start="86594" i_stop="86473" i_length="122"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="86472" e_stop="86342" e_length="131"/>
          </exon>
          <intron i_serial="4" don_prob="0.997" acc_prob="0.292">
            <gDNA_intron_boundary i_start="86341" i_stop="85877" i_length="465"/>
          </intron>
          <exon e_serial="5" e_score="0.984">
            <gDNA_exon_boundary e_start="85876" e_stop="85752" e_length="125"/>
          </exon>
          <intron i_serial="5" don_prob="0.994" acc_prob="0.909">
            <gDNA_intron_boundary i_start="85751" i_stop="85128" i_length="624"/>
          </intron>
          <exon e_serial="6" e_score="0.996">
            <gDNA_exon_boundary e_start="85127" e_stop="84857" e_length="271"/>
          </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="90102" stop="90010"/>
              <exon start="87340" stop="87235"/>
              <exon start="86672" stop="86595"/>
              <exon start="86472" stop="86342"/>
              <exon start="85876" stop="85752"/>
              <exon start="85127" stop="84857"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M7486" 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>AAAAATGTCTTCAAATTTGGAATTGGAAGTGAGGTCTTCAGCTACAGTTCCTTCTCTGCAAGTTCCAACCTTTCATCATACCCCTTATTATTG : TGAGGAAAACATCTACCTGCTATGCAAAAAGCTATGTGATGACGGACTGGCAGATCCTAATGGTTCTGATCTGTTTGTTATTTTCATTTCCAATGAGAAGAAGCAG : ATTCCTCTGTGGCATCAGAAGGCTAGCCAGCGAGCAGAGGGAGTTATTCTGTGGGACTATCATGTCATCTGTGTACAG : AAGAAGAGAAATGAGAACTCTTCGTCACTAGTGTGGGATTTAGATTCAAGTCTTCCGTTTCCATCATCTCTTGGCACTTATGTCGCTGACAGCATTCGTCCATCAATTCAGATATTTTCTGAATTCAAAAG : GTTTTTTCGAGTTGTGCATGCCCCTATATTCCTCCGACACTTCGCATCAGATAGAAGACATATGAAGGATTCTGCTGGAAACTGGACTGCAGACCCGCCATCATATGAAGCTATTGTTGCTGAAG : ATGGAGCTGTACACAACCTGAACGAGTACATTACAGTCTCTCCCGATGATGTAGTGAAGAATGTGGAAGCTGATACCGTCAATGTTGTTCTCTCCGAGAAACTTGGTGTAGTAATTGGTGAAGATGATTTGTTGGGATTTTTCTCTTTGATTTCCTGATGAGAGTTGAGAAAAAACTTGCTAGCTTGAAAGATGAAATGATGATCTTGGATTTTTACATGTAAAAAGAAAAAGAAAGTGTCTTGTGAGAGTTTTTGCAAATGGAATGGAAA</gDNA_template>
            <first_frame> K  N  V  F  K  F  G  I  G  S  E  V  F  S  Y  S  S  F  S  A  S  S  N  L  S  S  Y  P  L  L  L  :  *  G  K  H  L  P  A  M  Q  K  A  M  *  *  R  T  G  R  S  *  W  F  *  S  V  C  Y  F  H  F  Q  *  E  E  A   : D  S  S  V  A  S  E  G  *  P  A  S  R  G  S  Y  S  V  G  L  S  C  H  L  C  T   : E  E  E  K  *  E  L  F  V  T  S  V  G  F  R  F  K  S  S  V  S  I  I  S  W  H  L  C  R  *  Q  H  S  S  I  N  S  D  I  F  *  I  Q  K  :  V  F  S  S  C  A  C  P  Y  I  P  P  T  L  R  I  R  *  K  T  Y  E  G  F  C  W  K  L  D  C  R  P  A  I  I  *  S  Y  C  C  *  R :   W  S  C  T  Q  P  E  R  V  H  Y  S  L  S  R  *  C  S  E  E  C  G  S  *  Y  R  Q  C  C  S  L  R  E  T  W  C  S  N  W  *  R  *  F  V  G  I  F  L  F  D  F  L  M  R  V  E  K  K  L  A  S  L  K  D  E  M  M  I  L  D  F  Y  M  *  K  E  K  E  S  V  L  *  E  F  L  Q  M  E  W  K </first_frame>
            <second_frame>  K  M  S  S  N  L  E  L  E  V  R  S  S  A  T  V  P  S  L  Q  V  P  T  F  H  H  T  P  Y  Y  C :   E  E  N  I  Y  L  L  C  K  K  L  C  D  D  G  L  A  D  P  N  G  S  D  L  F  V  I  F  I  S  N  E  K  K  Q  :  I  P  L  W  H  Q  K  A  S  Q  R  A  E  G  V  I  L  W  D  Y  H  V  I  C  V  Q  :  K  K  R  N  E  N  S  S  S  L  V  W  D  L  D  S  S  L  P  F  P  S  S  L  G  T  Y  V  A  D  S  I  R  P  S  I  Q  I  F  S  E  F  K  R :   F  F  R  V  V  H  A  P  I  F  L  R  H  F  A  S  D  R  R  H  M  K  D  S  A  G  N  W  T  A  D  P  P  S  Y  E  A  I  V  A  E   : D  G  A  V  H  N  L  N  E  Y  I  T  V  S  P  D  D  V  V  K  N  V  E  A  D  T  V  N  V  V  L  S  E  K  L  G  V  V  I  G  E  D  D  L  L  G  F  F  S  L  I  S  *  *  E  L  R  K  N  L  L  A  *  K  M  K  *  *  S  W  I  F  T  C  K  K  K  K  K  V  S  C  E  S  F  C  K  W  N  G   </second_frame>
            <third_frame>   K  C  L  Q  I  W  N  W  K  *  G  L  Q  L  Q  F  L  L  C  K  F  Q  P  F  I  I  P  L  I  I   : V  R  K  T  S  T  C  Y  A  K  S  Y  V  M  T  D  W  Q  I  L  M  V  L  I  C  L  L  F  S  F  P  M  R  R  S  R :   F  L  C  G  I  R  R  L  A  S  E  Q  R  E  L  F  C  G  T  I  M  S  S  V  Y  R :   R  R  E  M  R  T  L  R  H  *  C  G  I  *  I  Q  V  F  R  F  H  H  L  L  A  L  M  S  L  T  A  F  V  H  Q  F  R  Y  F  L  N  S  K   : G  F  F  E  L  C  M  P  L  Y  S  S  D  T  S  H  Q  I  E  D  I  *  R  I  L  L  E  T  G  L  Q  T  R  H  H  M  K  L  L  L  L  K  :  M  E  L  Y  T  T  *  T  S  T  L  Q  S  L  P  M  M  *  *  R  M  W  K  L  I  P  S  M  L  F  S  P  R  N  L  V  *  *  L  V  K  M  I  C  W  D  F  S  L  *  F  P  D  E  S  *  E  K  T  C  *  L  E  R  *  N  D  D  L  G  F  L  H  V  K  R  K  R  K  C  L  V  R  V  F  A  N  G  M  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="C04HBa0114C15.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="90101" stop="90010"/>
                    <exon start="87340" stop="87235"/>
                    <exon start="86672" stop="86595"/>
                    <exon start="86472" stop="86342"/>
                    <exon start="85876" stop="85752"/>
                    <exon start="85127" stop="84970"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>687</number_coding_nucleotides>
                  <number_encoded_amino_acids>229</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>KMSSNLELEVRSSATVPSLQVPTFHHTPYYCEENIYLLCKKLCDDGLADPNGSDLFVIFISNEKKQIPLWHQKASQRAEGVILWDYHVICVQKKRNENSSSLVWDLDSSLPFPSSLGTYVADSIRPSIQIFSEFKRFFRVVHAPIFLRHFASDRRHMKDSAGNWTADPPSYEAIVAEDGAVHNLNEYITVSPDDVVKNVEADTVNVVLSEKLGVVIGEDDLLGFFSLIS*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
      <AGS_information>
        <AGS_line AGS_serial="2">
          <exon_coordinates>
            <exon e_start="87631" e_stop="87171"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <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="87631" e_stop="87171" e_length="461"/>
          </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="87631" stop="87171"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M246-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="2" gDNA_strand="-"/>
          <translation>
            <gDNA_template>AAATGCTTCGCCTGTGACCTGTCCTAAAGATAAATGTTCATAAAGAAAAGGGAACTTTTGAAATGAATCTATTTATGTAGAATTATTCAACTTAAGTACTTCCCTTTTCAAATTTGACATGTCTGTTTTTATTTCCATTCACATTAAGCTTGCTTACTGAATATATAGAGGGTTCATATATTTGACTCGGGTTGATCTTGATTTGAGGCATAGTTGATTGATTGAGAAAAATTACTTGCACTAACAATAAGTATTCTTCTGTTTGCTTTCTGTATTTACTTTCTATTACAGTGAGGAAAACATCTACCTGCTATGCAAAAAGCTATGTGATGACGGACTGGCAGATCCTAATGGTTCTGATCTGTTTGTTATTTTCATTTCCAATGAGAAGAAGCAGGCAACTACTCTTTGCTCTTCCTTTGGTTACTGTCTTAAGAAGTTCATTCATTGCATTGATACTT</gDNA_template>
            <first_frame> K  C  F  A  C  D  L  S  *  R  *  M  F  I  K  K  R  E  L  L  K  *  I  Y  L  C  R  I  I  Q  L  K  Y  F  P  F  Q  I  *  H  V  C  F  Y  F  H  S  H  *  A  C  L  L  N  I  *  R  V  H  I  F  D  S  G  *  S  *  F  E  A  *  L  I  D  *  E  K  L  L  A  L  T  I  S  I  L  L  F  A  F  C  I  Y  F  L  L  Q  *  G  K  H  L  P  A  M  Q  K  A  M  *  *  R  T  G  R  S  *  W  F  *  S  V  C  Y  F  H  F  Q  *  E  E  A  G  N  Y  S  L  L  F  L  W  L  L  S  *  E  V  H  S  L  H  *  Y   </first_frame>
            <second_frame>  N  A  S  P  V  T  C  P  K  D  K  C  S  *  R  K  G  N  F  *  N  E  S  I  Y  V  E  L  F  N  L  S  T  S  L  F  K  F  D  M  S  V  F  I  S  I  H  I  K  L  A  Y  *  I  Y  R  G  F  I  Y  L  T  R  V  D  L  D  L  R  H  S  *  L  I  E  K  N  Y  L  H  *  Q  *  V  F  F  C  L  L  S  V  F  T  F  Y  Y  S  E  E  N  I  Y  L  L  C  K  K  L  C  D  D  G  L  A  D  P  N  G  S  D  L  F  V  I  F  I  S  N  E  K  K  Q  A  T  T  L  C  S  S  F  G  Y  C  L  K  K  F  I  H  C  I  D  T  </second_frame>
            <third_frame>   M  L  R  L  *  P  V  L  K  I  N  V  H  K  E  K  G  T  F  E  M  N  L  F  M  *  N  Y  S  T  *  V  L  P  F  S  N  L  T  C  L  F  L  F  P  F  T  L  S  L  L  T  E  Y  I  E  G  S  Y  I  *  L  G  L  I  L  I  *  G  I  V  D  *  L  R  K  I  T  C  T  N  N  K  Y  S  S  V  C  F  L  Y  L  L  S  I  T  V  R  K  T  S  T  C  Y  A  K  S  Y  V  M  T  D  W  Q  I  L  M  V  L  I  C  L  L  F  S  F  P  M  R  R  S  R  Q  L  L  F  A  L  P  L  V  T  V  L  R  S  S  F  I  A  L  I  L </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0114C15.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="2" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="87410" stop="87171"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>240</number_coding_nucleotides>
                  <number_encoded_amino_acids>80</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LRKITCTNNKYSSVCFLYLLSITVRKTSTCYAKSYVMTDWQILMVLICLLFSFPMRRSRQLLFALPLVTVLRSSFIALIL</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0114C15.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="2" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="87381" stop="87172"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>210</number_coding_nucleotides>
                  <number_encoded_amino_acids>70</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>VFFCLLSVFTFYYSEENIYLLCKKLCDDGLADPNGSDLFVIFISNEKKQATTLCSSFGYCLKKFIHCIDT</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="85791" PGL_stop="86257"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="85791" e_stop="86257"/>
          </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="85791" e_stop="86257" e_length="467"/>
          </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="85791" stop="86257"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M246-R" strand="+"/>
          </PGS_line>
        </supporting_evidence>
        <three_phase_translation xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/">
          <description PGL_serial="3" AGS_serial="1" gDNA_strand="+"/>
          <translation>
            <gDNA_template>TCCAGTTTCCAGCAGAATCCTTCATATGTCTTCTATCTGATGCGAAGTGTCGGAGGAATATAGGGGCATGCACAACTCGAAAAAACCTGAAATGGCCAAAGTTGTTCTTTCATGTGGTTGCAGTAAGCTTATTATTCCAAGCACAAGGTTGGCAACATTGCTTAGCACCAGAAGAAAAACATACTCTGGTTTCTTCTTCAGAAAAAGGTCAGTGAAAGAGCATTTCTTTAATGAGACCACCCCTTTAGGGTGGACTTGTGAAATCAATTTTTAAAGATAAACAAAAAATGAGATTCACTAGGTAGAGCATAAATTTTACGAAAAGTTAGAAACATTTTAAGGTTGGGTTGACTTCAGGAAGGAATGGAGAAAAACAATACACAGAAGAGCAATAGAACTACTTTTGTATCACTATATCAAGAATCTTATAATTTGAGCAAAAATGAAATATCTAGCTTCTATAAAAG</gDNA_template>
            <first_frame> S  S  F  Q  Q  N  P  S  Y  V  F  Y  L  M  R  S  V  G  G  I  *  G  H  A  Q  L  E  K  T  *  N  G  Q  S  C  S  F  M  W  L  Q  *  A  Y  Y  S  K  H  K  V  G  N  I  A  *  H  Q  K  K  N  I  L  W  F  L  L  Q  K  K  V  S  E  R  A  F  L  *  *  D  H  P  F  R  V  D  L  *  N  Q  F  L  K  I  N  K  K  *  D  S  L  G  R  A  *  I  L  R  K  V  R  N  I  L  R  L  G  *  L  Q  E  G  M  E  K  N  N  T  Q  K  S  N  R  T  T  F  V  S  L  Y  Q  E  S  Y  N  L  S  K  N  E  I  S  S  F  Y  K   </first_frame>
            <second_frame>  P  V  S  S  R  I  L  H  M  S  S  I  *  C  E  V  S  E  E  Y  R  G  M  H  N  S  K  K  P  E  M  A  K  V  V  L  S  C  G  C  S  K  L  I  I  P  S  T  R  L  A  T  L  L  S  T  R  R  K  T  Y  S  G  F  F  F  R  K  R  S  V  K  E  H  F  F  N  E  T  T  P  L  G  W  T  C  E  I  N  F  *  R  *  T  K  N  E  I  H  *  V  E  H  K  F  Y  E  K  L  E  T  F  *  G  W  V  D  F  R  K  E  W  R  K  T  I  H  R  R  A  I  E  L  L  L  Y  H  Y  I  K  N  L  I  I  *  A  K  M  K  Y  L  A  S  I  K  </second_frame>
            <third_frame>   Q  F  P  A  E  S  F  I  C  L  L  S  D  A  K  C  R  R  N  I  G  A  C  T  T  R  K  N  L  K  W  P  K  L  F  F  H  V  V  A  V  S  L  L  F  Q  A  Q  G  W  Q  H  C  L  A  P  E  E  K  H  T  L  V  S  S  S  E  K  G  Q  *  K  S  I  S  L  M  R  P  P  L  *  G  G  L  V  K  S  I  F  K  D  K  Q  K  M  R  F  T  R  *  S  I  N  F  T  K  S  *  K  H  F  K  V  G  L  T  S  G  R  N  G  E  K  Q  Y  T  E  E  Q  *  N  Y  F  C  I  T  I  S  R  I  L  *  F  E  Q  K  *  N  I  *  L  L  *  K </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0114C15.1" strand="+"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="85831" stop="86064"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>231</number_coding_nucleotides>
                  <number_encoded_amino_acids>77</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>CEVSEEYRGMHNSKKPEMAKVVLSCGCSKLIIPSTRLATLLSTRRKTYSGFFFRKRSVKEHFFNETTPLGWTCEINF*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0114C15.1" strand="+"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="85793" stop="86005"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>210</number_coding_nucleotides>
                  <number_encoded_amino_acids>70</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>QFPAESFICLLSDAKCRRNIGACTTRKNLKWPKLFFHVVAVSLLFQAQGWQHCLAPEEKHTLVSSSEKGQ*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 12 chains have been computed
$ 
$ memory statistics:
$ 7376 bytes spliced alignments in total
$ 4 spliced alignments have been stored
$ 1844 bytes was the average size of a spliced alignment
$ 8128 bytes predicted gene locations in total
$ 3 predicted gene locations have been stored
$ 2709 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 13 backtrace matrices have been allocated
$ 
$ date finished: 2008-02-20 05:31:06
-->
