<?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="2008-04-10 05:52:18"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0094K06-flbfK/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/cxgn-bacpublish-resources-m4uMJa/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-m4uMJa/sgn_marker_seqs" ref_id="SGN-M6802-2" ref_strand="+" ref_description="SGN-M6802-2 C2_At1g43620-2 [cosii_markers]">
      <seq>cctttttaagtcttggattgagcagaaaagaagacttttttcatcagtttttcaagaatatttagtgtgaagtgattagcattctctttgataatcttaatgagttttgatgcacaggattgtttatgaattctttggttgctgaatttgcaagttttttatgttagttgctgaatctggagtttagttgaatttgagttctcttacagttgtttgcgaagcttgaaattttagaagagtaggtgttcagtttggtgaatttaagtggttttggagttcatcatttgaaatggatagtagtgggcttaatggaaatcagagtacaagggattcagaagtaccgaacaatgctgatgaacggtgtgatgctaccttttccgatgaattagatggctggagaacaagttcttcatcacttaaggacattaggtcttcagatgagcatactgatgagtgtttgactccagaaatgaaatacgagagcacacatcggagttctagtcctccgcctcaagctcggagaggtttggagcactgcattactgcacctgtgactattggcggaggtcttttccctgaaggccaggatatggcattttcaagatctttgactgagaggagggttagtccaagacataatgtaatattggatagactttctgaacgtggaaagcaaaagctcatcgcagagctggtaaagatccaaggggatggaacagtagaggttgaccttactaagagtacgcctgaaacttctgaattgttggagctgcgatctgttgaagaacccactcttactgtagacaggattatcacagattttaataagtcagttccaaagttgaaaatcgtggtgcttattgttggaaccaggggagatgttcaaccatttttggctatggccaagagacttcaggcgtttggtcatcatgtcaggctggcaactcattctaacttccgtgattttgtcaaatcaggaggcatagactactacccattgggtggtgatcctcgggtattggcaggatatatggccaggaacaaaggtctcattccttctggaccaggagagatatctgtacaacgaaagcagctaaaggctataattgaatctcttcttccggcttgcactgagccagatattgaaactggtgaacctttcagagcacaagcgattattgcaaatcctcctgcttatggacatgcacacgttgctgaagctcttggggtacccctccacatcttcttcacaatgccctggacgccaacttctgaatttcctcacccgatggctcgtgtacctcaacctgctgcgtattggctttcctacatactcgtggatttacttgtctggtggggcataagaggctacatcaacgattttaggaaaaagaagttaaaccttcctcctatcgcctacttcagtacataccacggatcaatttctcacttcccaactggctacatgtggagtccacatgttgtgccaaagcctaaagattggggctctttggttgatattgttggctattgtttct</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0094K06-flbfK/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0094K06.1" temp_strand="+" temp_description="C04HBa0094K06.1  CU468249.6 htgs_phase:3 submitted_to_sgn_as:C04HBa0094K06 sequenced_by:sanger upload_account_name:uk">
        <position start="39543" stop="49356"/>
      </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="39843" g_stop="39945" g_length="103"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="103" r_length="103" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="39946" i_stop="40595" i_length="650">
            <donor d_prob="0.928" d_score="1.00"/>
            <acceptor a_prob="0.083" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="40596" g_stop="41016" g_length="421"/>
          <reference_exon_boundary r_type="cDNA" r_start="104" r_stop="524" r_length="421" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="41017" i_stop="42829" i_length="1813">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="42830" g_stop="42978" g_length="149"/>
          <reference_exon_boundary r_type="cDNA" r_start="525" r_stop="673" r_length="149" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="42979" i_stop="43916" i_length="938">
            <donor d_prob="0.657" d_score="1.00"/>
            <acceptor a_prob="0.984" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="43917" g_stop="44159" g_length="243"/>
          <reference_exon_boundary r_type="cDNA" r_start="674" r_stop="916" r_length="243" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="44160" i_stop="44996" i_length="837">
            <donor d_prob="0.995" d_score="1.00"/>
            <acceptor a_prob="0.985" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="44997" g_stop="45108" g_length="112"/>
          <reference_exon_boundary r_type="cDNA" r_start="917" r_stop="1028" r_length="112" r_score="1.000"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="45109" i_stop="46136" i_length="1028">
            <donor d_prob="0.821" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="46137" g_stop="46307" g_length="171"/>
          <reference_exon_boundary r_type="cDNA" r_start="1029" r_stop="1199" r_length="171" r_score="1.000"/>
        </exon>
        <intron i_serial="6">
          <gDNA_intron_boundary i_start="46308" i_stop="47488" i_length="1181">
            <donor d_prob="0.990" d_score="1.00"/>
            <acceptor a_prob="0.995" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="7">
          <gDNA_exon_boundary g_start="47489" g_stop="47552" g_length="64"/>
          <reference_exon_boundary r_type="cDNA" r_start="1200" r_stop="1263" r_length="64" r_score="1.000"/>
        </exon>
        <intron i_serial="7">
          <gDNA_intron_boundary i_start="47553" i_stop="48382" i_length="830">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.839" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="8">
          <gDNA_exon_boundary g_start="48383" g_stop="48440" g_length="58"/>
          <reference_exon_boundary r_type="cDNA" r_start="1264" r_stop="1321" r_length="58" r_score="1.000"/>
        </exon>
        <intron i_serial="8">
          <gDNA_intron_boundary i_start="48441" i_stop="48530" i_length="90">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.945" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="9">
          <gDNA_exon_boundary g_start="48531" g_stop="48708" g_length="178"/>
          <reference_exon_boundary r_type="cDNA" r_start="1322" r_stop="1499" r_length="178" r_score="1.000"/>
        </exon>
        <intron i_serial="9">
          <gDNA_intron_boundary i_start="48709" i_stop="49017" i_length="309">
            <donor d_prob="0.985" d_score="1.00"/>
            <acceptor a_prob="0.872" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="10">
          <gDNA_exon_boundary g_start="49018" g_stop="49056" g_length="39"/>
          <reference_exon_boundary r_type="cDNA" r_start="1500" r_stop="1538" r_length="39" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0094K06.1" gen_strand="+" ref_id="SGN-M6802-2" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>1538</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0094K06.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M6802-2" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="39843" e_stop="39945"/>
          <exon e_start="40596" e_stop="41016"/>
          <exon e_start="42830" e_stop="42978"/>
          <exon e_start="43917" e_stop="44159"/>
          <exon e_start="44997" e_stop="45108"/>
          <exon e_start="46137" e_stop="46307"/>
          <exon e_start="47489" e_stop="47552"/>
          <exon e_start="48383" e_stop="48440"/>
          <exon e_start="48531" e_stop="48708"/>
          <exon e_start="49018" e_stop="49056"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CCTTTTTAAGTCTTGGATTGAGCAGAAAAGAAGACTTTTTTCATCAGTTTTTCAAGAATATTTAGTGTGAAGTGATTAGCATTCTCTTTGATAATCTTAATGAGTAAGTGTTCCTCTACAACCCAACAAAGGAATGAAGCTTCTTTTATCAAAAACTGCACACTATCTTGGTGTTTTTTTTTTCTAGCTTCCCTCCATTTTCATCCATAAGAAAACCAATTATTGATGATAATAATCTCCAACTTTGAATGAGTTTTTTCAATCTATAAGACGAAAATGATAAAGTTGCTTTCTTGGTAATTACATGTTGGACACCTGGTAGTTGAGTATTCACTTTCTTTAATGATTGAATCGCCAAAAGGATTAGTCTTTTTGGTATCTTCTGTTATGTGGGGTTTTCCTTTTATGCAACTTCTTAAACATATTTGTTGTTTGTAGTGTTCCTGGTGTGCTCTATTTGATAATATGATGTATTTTGTGAGTTTCCTGTAGATGTTGTTATAATTACTATTCTTTTTGAAGTTTGTGCTGATTTTATACAATGCGATGCTGTTGACTGTTTGGTTGTGTTTCTTTCTTCTTTCTAATTGGTTGTTGCAGAGGGTAGATTAGCTTTTAACATTGCTTGTGGTGTAGTTTGGAAAGTTTTAGCTTTAAATCAAGATTTGTTTTTTCATTGTGGGGTTGCTGAATTTTGGTGAATGGAAGTGTTCTGCATTTTGGGGTTGCTGATATTTTCTCATTTCTTAGCAGGTTTTGATGCACAGGATTGTTTATGAATTCTTTGGTTGCTGAATTTGCAAGTTTTTTATGTTAGTTGCTGAATCTGGAGTTTAGTTGAATTTGAGTTCTCTTACAGTTGTTTGCGAAGCTTGAAATTTTAGAAGAGTAGGTGTTCAGTTTGGTGAATTTAAGTGGTTTTGGAGTTCATCATTTGAAATGGATAGTAGTGGGCTTAATGGAAATCAGAGTACAAGGGATTCAGAAGTACCGAACAATGCTGATGAACGGTGTGATGCTACCTTTTCCGATGAATTAGATGGCTGGAGAACAAGTTCTTCATCACTTAAGGACATTAGGTCTTCAGATGAGCATACTGATGAGTGTTTGACTCCAGAAATGAAATACGAGAGCACACATCGGAGTTCTAGTCCTCCGCCTCAAGCTCGGAGAGGTTAGTGCTTCATCTTCCTAAGCTTTTCTCTGTTGATAAATAATGAATTTGAGAAAACCTGCTACAGATTCTTCCTTGTGCATTTAGTTTAGTCTTCTCTCAATAAATTTAGAATAAGAGTCATGATCTTGGCAAAATGTTATATTGACAAGGATGTAAATGATAGTTAGAGGGGAGAAGTATGAGCGAGTGCCAAGTTACTGGGATAGTAGGACTTCAGAATGATCCTGTGGTTTTTTCTAAAAAAAAACTTTTTTGCTTTTTGTTTCATAATGCTGTTCACTAGGGTGTAATTTGTCTTTGTGGGACGAGTATACTAATAAGTATAATTCTTCTTTGATTGATAGTAAAACTATTTCTTGTGTTGTATCTTTATTCTATTTAATATAAAGTGAATCATGTATGTGTTTTTGTTCTATGTTGGATGACAAAATGGTCTAGGAAACTATCTTATTTATGATGTTAAGCATCATTGTTGTCCTCTGGCTAACAGTTTGATGAATGGAACTATTATTTTCTGTCCCACCAAACGGGCTGGTTCCTTTTCCTTTATTATTCTCTCTCATTACTACTTGTCATCTATGAAATCAATCTAGAAGGAGTTCAAATAATCCTATCTAGATCGACATGTAAGCTTAGTTGTGAATTTCAGACTATTAAGGCTTGTCCTATATTACTCAGCAAGCATTATAGAAAAGATGAGAGTAACTTTTCCTGTCATAGACCTGTATAAATAAATAAAAGTGTTCTGGCTCTAAGTTTTAAGTATATAACTGTGCCTCATCTTACAACTCTGTTCTAAAAGGAGGGTTCATTGACATTTTTCATCTCAAGGTCAAATTATGCCCTTGTCATCCTTTTCTGTCTCTGGAATTCCTTGAGCTAATACACCTCTGTACAGCTATCTGTCGAAAGTCTTGCTTCCTTATAATTGACCATCTGGTTGTTGATTTTGGTTCAAGTTACTTTAAGGGTCACATATTCTATGAAGAGACTGAACTTTTTTTGGGGCTGCAGTGTCTTGCTCGAGTTTCATGAGCTAAATTATATTCACCTGCTTGTTTGGTCCAAATGTGAAGAATTCTTTCCAGTGCTCTATATTCCAAGTTTCACCGCTACCCCTACAAAGGAAAACCAATGCATCAACGAAATTAATGACAAGCAAAACTAACATCATTTGTGGAGGACAGGGTTTGACAGACAACGATGTCAAACCAAGTTACTAAAAGATGGAACCTTGATTTAAAACCAAACATGAAAAATATCAAATACCCAAAAGTCTCCAGAGAACTAACTTTAACTGCTCCGTCTCCTTACAAGAGAAAAATGCTTTTGCTCACGGTTTCTTCTATGCTTCCCTCAAAGCTAAGGTACATTATAGACTTCCTCCTTTGTCACTTCTCACATCAGCTCCACTTTCCTCCCTCCAAAGCAAAAGCTATCTCCTGTATCACATTTAGGATATTCTGCCAGTATGCCGTATTGCTGACAATGATTTCATGTATAGAGTGGCAAAATACTCATGAATTAAACTTGGGAACCTCTTAGCATTGTCTTTCTGAAAATTTAGTAGTAAGAAAATATTGATTTGGTCTTCTATAAGCAATTGAAGCAAATCGTTGCTGCATATGATTCTTTGTTTTTTCTTTTCTTTGCTTTTTCTCTTCTCTTTTGCGTACTTGCTTCAGAAGGGCTTAGACATTTATATCTATGTTGATTGGATAAAGCTGACTATTGTGGTTTACTGGATTAGATGTATTTCTTTCTCATACAGGACTTTTGCATTTTTTTTTTTTTTTTGTTTAACTTGTAGGTTTGGAGCACTGCATTACTGCACCTGTGACTATTGGCGGAGGTCTTTTCCCTGAAGGCCAGGATATGGCATTTTCAAGATCTTTGACTGAGAGGAGGGTTAGTCCAAGACATAATGTAATATTGGATAGACTTTCTGAACGTGGAAAGGTAATTTTGTTATTGACGTCTCCAGCTTTGAGATGCCTATTATCCGACAACCAATTGTGTAGTGCTTTGCTGTGAGATTCTATAATAGTCAACATGGCGTAGGAGTTGAATAGATTTACTAGTCTTGGTTACGATATGCATGTAAATGTGTCAAAAGTTGTTGCAATTTGTTAGAGTTTAATATTTTGTCCTTGACACTAGTTTTGGCTTGAATTTGTTTGATTTGATTGTAAACTTGAAGCATGGAAAGATCCTTTAATGTTGGAGAGTGATAAGGAGTAGAAAAGCTGATATGGGAAGTGCTAAGTGCATGAATAACGAGACTGCTTGTTATCTGAATAAATATGATTTACCTGAACCAATAAAACTTAAAAGAATCCTAGAATGCTGAGCATTATTTTTTCAAATGATGCTTAGACCATGTGAAGCTGGCAATTTGTATTGACCAAGTACTTATTTAGACTTACTGATACAAAATTTACTTTGACCATTTGGTTTTTGAGCTATTTTTTTGCTTTTAACTGATGGAGTTGATATGTATGTTGTAGGGCTCCGCTGAGTCAAGTTGCTATTTAATAAGTGGCTGAAACAAAACCACCCTCTTTAACAAAGTCAATTTTTTCTGCACATAATCACATGTATCCGGCCTGAATCACCGCTTCATACATTAGGTTGTCCATGCCTGTATATGTAAAAATAGCAGCTAATCAAACAGGTTAAGAATTCTTGCTATTTGCCTATGTAAGTATGGATTATGGAGACCCAGGACTGCCCCTCTGCAGCGTCTGAAAGAACCACCACAAATTACTTACATGTGTTTTTTTACTTTATCCATCTGGAAAATGATATACCTTTTCATTTTCTTGCCATTAAGTTGCTGAATCCTTCTTATTCACTTACCATTTCCTCATATTTCCTTCTGTTCTTAATGTCACCAGCAAAAGCTCATCGCAGAGCTGGTAAAGATCCAAGGGGATGGAACAGTAGAGGTTGACCTTACTAAGAGTACGCCTGAAACTTCTGAATTGTTGGAGCTGCGATCTGTTGAAGAACCCACTCTTACTGTAGACAGGATTATCACAGATTTTAATAAGTCAGTTCCAAAGTTGAAAATCGTGGTGCTTATTGTTGGAACCAGGGGAGATGTTCAACCATTTTTGGCTATGGCCAAGAGACTTCAGGCATGTTGGGAGTTCTAAATCACCATGTTTATAGCTGTACTGGTCATACATGTTCTATATCGTTTTCTTCTTAACCATCTGTGCTTGCCTTTATTATTATATCATTGCATTCTATGTTTTTCAGCATCCTTTACAGAATAACCCAAATTTCGGCTTTGAATGACAATTCGTTGGAGAGGTCTGTTAGATGGACTTCTAAGTTCTATTTTACTAGACTTAGTTTCTCCACTTTTCAAGTCTTCTTAGTCACCAACTTTTAAAATTGATTGTTGAGATGCTGTAAGGTAAAAGGATTAGATTGTGTCCCTTGGACCTGGGTAAACCAATTGAGATTTCATTTGAGAATATATTGACGGAGAGAATTTTTAGAGGTGAATTTGGACCTATATGGTTGAAGCAAGTATCAAAAACAAAGGTCACTTGGACCTTGCAATTACTTTGCGCAAGGAAAATTTTGTCTGCTTCAGAGCTGAGGTCTTTTGCTGCTTGACTGGCAAAACATTCTTAATATGCTCTTTACAGTGTGGGTACCATTGGATTTAATTTCTTTTCCTGTCTAAGGTTGGTTTAGCTTTATTTCTTGCTGTTGCCTCTTCTGGAGCACGATTATTTATTTGCCTATTATTTAATTTTCTCATCATTTTTGTGGCCAATATTGGACATTCATGTGAAATAATTGATTATATTTCAACTATAGATTTTGTGTTTCCATATTTCGTGTAGTAGAATTTTGTTGATGTTTGTGCACCTTAATATCTTTGTATTTTGGTTGAGAAAATTGTTCATTTGTAGAGTAAATCGTTCGTTCCTTTTCTAATCAGTTTTATGCATTGACAGGCGTTTGGTCATCATGTCAGGCTGGCAACTCATTCTAACTTCCGTGATTTTGTCAAATCAGGAGGCATAGACTACTACCCATTGGGTGGTGATCCTCGGGTATTGGCAGGATGTAAGAGGTCTTTGGCATGCTTCTTCGTTTTTCTCGTTCTTGTTTTTGTCTATGTTATGAGTACTCTGCTATGGGTATGTATTAGCCCTTTCTTTCTGGGTGGGTAAGTATCTGGTATGAGTAAACATAGTTTTCTGCAATTTTGGGGTGTGCTTCAAAGAATCCACATAAAGTTCTCACATGTGTTCCACACACGCCCTCCCCCCACATCCCTTGCACGCCCAAGACTAGACGAAGCATGGATATCATAACATAGTGCCCTACATTAGGTAACACAATAATGATGATGGGAGTGGCTCTAATTAGTGTTATCAAAAGCAAAAAGCGCAAAAAATCTCTAAGATCTGTTGGGCATTTAAGCGCAACTAACGTGTGGGCTTTAATGAAAAAAAGAGCAAAGGGAGAAAAAATGCAAAGCTATGTTTAGTCCAAGATTAATAATTATAAGCACGAAGGAATGACAAATATATGAAGAAAGAAACTGAAAAAAATAATATGATAAAGTAAAATATCAATTTTTTAGTGCCGCCTCTTCTAAAGAGGCTCATTGGCAAGAAAATGTATGTCATATAACCTTGACGAGGAAACAAAATCGCACCTTAAATAAGTCGAAACACTTTTTGAGCCTCGCATCAGGGCGCCTTTGACAACTCTGGCGCTAATACCAAGCTAAGAAGATGGGTTTAGGCCTAAGTCAATCTCAAAAGTTGGTTCATGCGGTAAGGGTTGCCCAAATCACTAGGAGACTATAGCCACACTTTCAACCAATGGTGAACACTAACATAATCCTATGAGCAATCGTGGTAATATCAAGCTTCTACTTTTTTCCTTTTAGTTAACTTACGCACAGTTTGAAAATTTTTCTTAAATTTTTGGGAAGTTTTCAACATACTTAACAGTCAAATTTGTACTGGAATCTAGTATGAAATAAGTGGCTCATCACATACCTGTTCAAGTAGTAATATGGAATTCCTGTTTGCTGATATCATTTAATATGGATTAAGTTCGTATGTTCTGTGGAATTGCAGATATGGCCAGGAACAAAGGTCTCATTCCTTCTGGACCAGGAGAGATATCTGTACAACGAAAGCAGCTAAAGGCTATAATTGAATCTCTTCTTCCGGCTTGCACTGAGCCAGATATTGAAACTGGTGAACCTTTCAGAGCACAAGCGATTATTGCAAATCCTCCTGCTTATGGTGAGTTCGAAAATAATCTCTATACTCACCACTCATTTCACCTTTTTGATATCTGGACATCTAATTCATGTTTGGTCCATGATTTATAATATCACATGGAGTTGTACATCACTGCTAGTTCTCCAAAAGATACATTTCTGTCTTCTCTTGTTTTTCTTTTTGGGGTGGGGGTGGCGGGTGGTGGTGGTCATATTTTGCCATCATAGAGAACATATGTTTGACTAAATTAGAAAGATATATGTGAGATACTATAAGTAGAGGAGCTACTATATTCTGAGATGGTCTCTTAGTCGCATTGTGGAATTTATCTTAGAAAGGATTAACATGAAGTCAACAAATATGAATTAAATGAACATATTAGTGTGTATGAAGTGAGGATGGGTCACTATGACCTCCGGACACAAGAATCTCAAAGATAACCTTGAAATCATACTCAGGTTAGAATCGTTTGAAATGTCTTTGGCCAAATAACTCTGTTTATTTACTATGAGTTTAATCTCATTTGACTCTTCTAATGTGGAGACCAGAAGCTATCTAGTTTTGACCTTGGGAGGAGTTAAGTCTGAAAAGTTACTCCACCGCCTTAGCTGGGTTTGACTGTTCATATGTTACATATTTAATCTCACACTATCTTCACAGTGCTCCTCTGCTTCTTTTCAATTAGAGTAGACCTATGTCAAGAAGTTGAGTTATTAGCCTATAAAGAAATCCACCTGATTGTATTTTCTGTATCAAATTCACGAGCAGTGTTAATCTGCTTCGAATAAGTACAAGCCCTTCCAAACTGAAAAACTTATTTTGGGAGGTCATTAGCTGAATCTATGGAGGTGTGTATTCTGCACAGCTTTGGCAAGTTGCAAACCGGTTTGGGTTTACTAAACAAAGAGCTTAGAAGGAAGAAGACTTAATCTTGAGCTTGTGCTCTGTAAATAAATGTCGAATAAAATATAAACTGCTTTATATGGTTTTCCTCAATGGTCCCCAAAACAATATTCATTTTTATGCTTTCCGGGACTTTATAGACTCCTTGTATCATAGATAATTCTAGTCCATCAATTGTACAGATATCAGCAACCTCTTGCTGCTATTTTTGTTAACAACATTTATCAGGATTAGTCAACACAACAGGATGCGATTTAGTCCAAGTCAACTTATAAGCATTGTTTTATTTTTTTGGACAGGACATGCACACGTTGCTGAAGCTCTTGGGGTACCCCTCCACATCTTCTTCACAATGCCCTGGACGTAAGCTCTGATTGACACTTTAACTTTATTTTATTGGATATTTCGTATTAACAATATGACAAGTGGATGCACCTGCAATTGCTGTCTTTGTCAATATGCGACCTTGTAAAGTCCATTCCTCTTATAAAACATTGATGAAACAAAATACTGCTATCTGATTTCTATTTTCTTTTCTACAAAAGTTTCCTCTTTGAGAAAAGCCAATTTGTAATAGGTGGTTGTTCTTCACTATGTGAATGTTTTTTAGATTTGATATTGACTAGACCATTATAAGGTGGCATTTGATACCTTACTCGGCCTTGTGGTTAAGATCAAGTGTAGTTTCTGTTCTCACCAGCTTTAACATCTGATACATGGACACTGGCCCACATTATATCAACCATTGGCGTTTCATTTAAAAAATTGAGAAACAGTTTTTGCAAAATTCTTCTAGTTACAACAACCATACGAAAGAAACGTATGAGTTTTGCTACTTTATTTAGATGGAGTTTTGGTTGAAACACAATTTTTGAAATTCCTCAAACTTTTCTTAGGTGGAGCTGCATCGGACACAATTTTTGCTGAAACTTGAAAAACTTTTTGCAGAAACTGCTATTTAATATTTCAATTGAACGCCTTAGTCTGTGACATACAAAGATTAGATGCAAGTGCCCAATTTCTGGAGTAGTTGGTTCTTCTGAATTAGGAAGTTTTATAGATCAATTGGAAGAACTATTATGCACATAGGATATTATGCGAGTCAGTTGCTGAGTTCAGTGTCATTCTTCATTAAATTCTCCCATTTAATATTTTCAACAAGGTACCTTCTCATAGACTTTGTTAATAGACAGGCCAACTTCTGAATTTCCTCACCCGATGGCTCGTGTACCTCAACCTGCTGCGTATTGGGTATGTTATCAGTTTCTTCTTTTGAAAAATATTTTTCCAGTAATTCTTCTGATTCCTGTTAAAACTCTATTTGTCTTCTGCACATTTCAGCTTTCCTACATACTCGTGGATTTACTTGTCTGGTGGGGCATAAGAGGCTACATCAACGATTTTAGGAAAAAGAAGTTAAACCTTCCTCCTATCGCCTACTTCAGTACATACCACGGATCAATTTCTCACTTCCCAACTGGCTACATGTGGAGTCCACATGTTGTGCCAAAGCCTAAAGGTATATGTCAGCTCCTCAATGGTATCTGGATGCTTGTTTTCGTCGTATTGGTCATTCCACTTCTTTTGTTGAAGCAAAACTAATGATTTGTAAATCTCAAAATGAACGGATCAGTTTCTTGTGGAGTATTTCTGTGCTAGTCTCTCTTTCTTCATTCCCATTAATCCCCTTCCCCATCCCTGAATTCATGTAAAGATCTTTTCTTCTTTTTCTAGCTCTACTTCACCCATTGGCTTAGTAATGATGTGTGCTCATACAATCAGTCCACTTGATCTATCATAAAAATATTGAAGCATTCGTTTTTTGCAGATTGGGGCTCTTTGGTTGATATTGTTGGCTATTGTTTCT</genome_strand>
        <mrna_strand>CCTTTTTAAGTCTTGGATTGAGCAGAAAAGAAGACTTTTTTCATCAGTTTTTCAAGAATATTTAGTGTGAAGTGATTAGCATTCTCTTTGATAATCTTAATGA..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTTTGATGCACAGGATTGTTTATGAATTCTTTGGTTGCTGAATTTGCAAGTTTTTTATGTTAGTTGCTGAATCTGGAGTTTAGTTGAATTTGAGTTCTCTTACAGTTGTTTGCGAAGCTTGAAATTTTAGAAGAGTAGGTGTTCAGTTTGGTGAATTTAAGTGGTTTTGGAGTTCATCATTTGAAATGGATAGTAGTGGGCTTAATGGAAATCAGAGTACAAGGGATTCAGAAGTACCGAACAATGCTGATGAACGGTGTGATGCTACCTTTTCCGATGAATTAGATGGCTGGAGAACAAGTTCTTCATCACTTAAGGACATTAGGTCTTCAGATGAGCATACTGATGAGTGTTTGACTCCAGAAATGAAATACGAGAGCACACATCGGAGTTCTAGTCCTCCGCCTCAAGCTCGGAGAG.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTTGGAGCACTGCATTACTGCACCTGTGACTATTGGCGGAGGTCTTTTCCCTGAAGGCCAGGATATGGCATTTTCAAGATCTTTGACTGAGAGGAGGGTTAGTCCAAGACATAATGTAATATTGGATAGACTTTCTGAACGTGGAAAG..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CAAAAGCTCATCGCAGAGCTGGTAAAGATCCAAGGGGATGGAACAGTAGAGGTTGACCTTACTAAGAGTACGCCTGAAACTTCTGAATTGTTGGAGCTGCGATCTGTTGAAGAACCCACTCTTACTGTAGACAGGATTATCACAGATTTTAATAAGTCAGTTCCAAAGTTGAAAATCGTGGTGCTTATTGTTGGAACCAGGGGAGATGTTCAACCATTTTTGGCTATGGCCAAGAGACTTCAG.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCGTTTGGTCATCATGTCAGGCTGGCAACTCATTCTAACTTCCGTGATTTTGTCAAATCAGGAGGCATAGACTACTACCCATTGGGTGGTGATCCTCGGGTATTGGCAGGAT....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATATGGCCAGGAACAAAGGTCTCATTCCTTCTGGACCAGGAGAGATATCTGTACAACGAAAGCAGCTAAAGGCTATAATTGAATCTCTTCTTCCGGCTTGCACTGAGCCAGATATTGAAACTGGTGAACCTTTCAGAGCACAAGCGATTATTGCAAATCCTCCTGCTTATG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GACATGCACACGTTGCTGAAGCTCTTGGGGTACCCCTCCACATCTTCTTCACAATGCCCTGGAC..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCCAACTTCTGAATTTCCTCACCCGATGGCTCGTGTACCTCAACCTGCTGCGTATTGG..........................................................................................CTTTCCTACATACTCGTGGATTTACTTGTCTGGTGGGGCATAAGAGGCTACATCAACGATTTTAGGAAAAAGAAGTTAAACCTTCCTCCTATCGCCTACTTCAGTACATACCACGGATCAATTTCTCACTTCCCAACTGGCTACATGTGGAGTCCACATGTTGTGCCAAAGCCTAAAG.....................................................................................................................................................................................................................................................................................................................ATTGGGGCTCTTTGGTTGATATTGTTGGCTATTGTTTCT</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-m4uMJa/sgn_marker_seqs" ref_id="SGN-M6802-3" ref_strand="+" ref_description="SGN-M6802-3 C2_At1g43620-3 [cosii_markers]">
      <seq>tttcccatttcttagcagattttgatgcacaggatggtttatgagttctggagttgctgaattttgcaagttgtcagcagatttttatgtttgttgctgaatctggagttgagttgaatttgagttctcttacagttgtttgcgaagcttgaaattttggaacactaggtgtgtcagtttggtgaagttaagtggttttggagttcatcagatgaaatggatagtaatgggcttaatggtaatcagagcacaagggattcagaagtaccaaacaatgctgatgaacggtgtgatgctactttttccgatgaattagatggcgggagaacaagttcttcatcacttaaggacattaggtcttcagatgagcatgttgatgagtgtttgactccagaaatgaaatatgagagaacacatcggagttctagtcctccacctctagctcggagaggtttggagcactgcattactgcacctgtgactattggcggagatcttttccctgaangccaggatatggcattttcaagatctttgactgagaggagggttagtccaaggcataatctaatattggatagactttctgaacgtggaaagcaaaagctcattgtggatctggtaaagattcaaggggatggaacagtagaggttgaccttactaagagtacgcctgaaacttctgaattgttggagctgcgatctgttgaagaacccactcttactgtagacaggattatcacaggttttaataagtcagttccaaagttgaaaatcgtggtgcttattgttggaaccaggggagatgttcaaccatttttggctatggccaagagacttcaggcgtttggtcatcatgtcaggctggcaactcattctaacttccacgattttgtcaaatcaggaggcatagacttctacccattgggtggtgatcctcgggtattggcaggatatatggccaggaacaaaggtctcattccttctggaccaggagagatatctgtacaacgaaagcagctaaaggcaataattgaatctcttcttccggcttgcactgaaccagatattgaaactggtgaacctttcagagcacaagcaattattgcaaatcctcctgcttatggacatgcacacgttgctgaagctcttggggtacccctccacatcttcttcaca</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0094K06-flbfK/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0094K06.1" temp_strand="+" temp_description="C04HBa0094K06.1  CU468249.6 htgs_phase:3 submitted_to_sgn_as:C04HBa0094K06 sequenced_by:sanger upload_account_name:uk">
        <position start="40278" stop="47841"/>
      </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="40647" g_stop="41016" g_length="370"/>
          <reference_exon_boundary r_type="cDNA" r_start="81" r_stop="451" r_length="371" r_score="0.938"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="41017" i_stop="42829" i_length="1813">
            <donor d_prob="1.000" d_score="0.92"/>
            <acceptor a_prob="1.000" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="42830" g_stop="42978" g_length="149"/>
          <reference_exon_boundary r_type="cDNA" r_start="452" r_stop="600" r_length="149" r_score="0.973"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="42979" i_stop="43916" i_length="938">
            <donor d_prob="0.657" d_score="0.96"/>
            <acceptor a_prob="0.984" a_score="0.90"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="43917" g_stop="44159" g_length="243"/>
          <reference_exon_boundary r_type="cDNA" r_start="601" r_stop="843" r_length="243" r_score="0.975"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="44160" i_stop="44996" i_length="837">
            <donor d_prob="0.995" d_score="1.00"/>
            <acceptor a_prob="0.985" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="44997" g_stop="45108" g_length="112"/>
          <reference_exon_boundary r_type="cDNA" r_start="844" r_stop="955" r_length="112" r_score="0.973"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="45109" i_stop="46136" i_length="1028">
            <donor d_prob="0.821" d_score="0.98"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="46137" g_stop="46307" g_length="171"/>
          <reference_exon_boundary r_type="cDNA" r_start="956" r_stop="1126" r_length="171" r_score="0.982"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="46308" i_stop="47488" i_length="1181">
            <donor d_prob="0.990" d_score="0.98"/>
            <acceptor a_prob="0.995" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="47489" g_stop="47541" g_length="53"/>
          <reference_exon_boundary r_type="cDNA" r_start="1127" r_stop="1179" r_length="53" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0094K06.1" gen_strand="+" ref_id="SGN-M6802-3" ref_strand="+">
        <total_alignment_score>0.964</total_alignment_score>
        <cumulative_length_of_scored_exons>1098</cumulative_length_of_scored_exons>
        <coverage percentage="0.931" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0094K06.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M6802-3" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="40647" e_stop="41016"/>
          <exon e_start="42830" e_stop="42978"/>
          <exon e_start="43917" e_stop="44159"/>
          <exon e_start="44997" e_stop="45108"/>
          <exon e_start="46137" e_stop="46307"/>
          <exon e_start="47489" e_stop="47541"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTTTTTATGTTAGTTGCTGAATCTGGAGTTTAGTTGAATTTGAGTTCTCTTACAGTTGTTTGCGAAGCTTGAAATTTTAGAAGAGTAGGTGT-TCAGTTTGGTGAATTTAAGTGGTTTTGGAGTTCATCATTTGAAATGGATAGTAGTGGGCTTAATGGAAATCAGAGTACAAGGGATTCAGAAGTACCGAACAATGCTGATGAACGGTGTGATGCTACCTTTTCCGATGAATTAGATGGCTGGAGAACAAGTTCTTCATCACTTAAGGACATTAGGTCTTCAGATGAGCATACTGATGAGTGTTTGACTCCAGAAATGAAATACGAGAGCACACATCGGAGTTCTAGTCCTCCGCCTCAAGCTCGGAGAGGTTAGTGCTTCATCTTCCTAAGCTTTTCTCTGTTGATAAATAATGAATTTGAGAAAACCTGCTACAGATTCTTCCTTGTGCATTTAGTTTAGTCTTCTCTCAATAAATTTAGAATAAGAGTCATGATCTTGGCAAAATGTTATATTGACAAGGATGTAAATGATAGTTAGAGGGGAGAAGTATGAGCGAGTGCCAAGTTACTGGGATAGTAGGACTTCAGAATGATCCTGTGGTTTTTTCTAAAAAAAAACTTTTTTGCTTTTTGTTTCATAATGCTGTTCACTAGGGTGTAATTTGTCTTTGTGGGACGAGTATACTAATAAGTATAATTCTTCTTTGATTGATAGTAAAACTATTTCTTGTGTTGTATCTTTATTCTATTTAATATAAAGTGAATCATGTATGTGTTTTTGTTCTATGTTGGATGACAAAATGGTCTAGGAAACTATCTTATTTATGATGTTAAGCATCATTGTTGTCCTCTGGCTAACAGTTTGATGAATGGAACTATTATTTTCTGTCCCACCAAACGGGCTGGTTCCTTTTCCTTTATTATTCTCTCTCATTACTACTTGTCATCTATGAAATCAATCTAGAAGGAGTTCAAATAATCCTATCTAGATCGACATGTAAGCTTAGTTGTGAATTTCAGACTATTAAGGCTTGTCCTATATTACTCAGCAAGCATTATAGAAAAGATGAGAGTAACTTTTCCTGTCATAGACCTGTATAAATAAATAAAAGTGTTCTGGCTCTAAGTTTTAAGTATATAACTGTGCCTCATCTTACAACTCTGTTCTAAAAGGAGGGTTCATTGACATTTTTCATCTCAAGGTCAAATTATGCCCTTGTCATCCTTTTCTGTCTCTGGAATTCCTTGAGCTAATACACCTCTGTACAGCTATCTGTCGAAAGTCTTGCTTCCTTATAATTGACCATCTGGTTGTTGATTTTGGTTCAAGTTACTTTAAGGGTCACATATTCTATGAAGAGACTGAACTTTTTTTGGGGCTGCAGTGTCTTGCTCGAGTTTCATGAGCTAAATTATATTCACCTGCTTGTTTGGTCCAAATGTGAAGAATTCTTTCCAGTGCTCTATATTCCAAGTTTCACCGCTACCCCTACAAAGGAAAACCAATGCATCAACGAAATTAATGACAAGCAAAACTAACATCATTTGTGGAGGACAGGGTTTGACAGACAACGATGTCAAACCAAGTTACTAAAAGATGGAACCTTGATTTAAAACCAAACATGAAAAATATCAAATACCCAAAAGTCTCCAGAGAACTAACTTTAACTGCTCCGTCTCCTTACAAGAGAAAAATGCTTTTGCTCACGGTTTCTTCTATGCTTCCCTCAAAGCTAAGGTACATTATAGACTTCCTCCTTTGTCACTTCTCACATCAGCTCCACTTTCCTCCCTCCAAAGCAAAAGCTATCTCCTGTATCACATTTAGGATATTCTGCCAGTATGCCGTATTGCTGACAATGATTTCATGTATAGAGTGGCAAAATACTCATGAATTAAACTTGGGAACCTCTTAGCATTGTCTTTCTGAAAATTTAGTAGTAAGAAAATATTGATTTGGTCTTCTATAAGCAATTGAAGCAAATCGTTGCTGCATATGATTCTTTGTTTTTTCTTTTCTTTGCTTTTTCTCTTCTCTTTTGCGTACTTGCTTCAGAAGGGCTTAGACATTTATATCTATGTTGATTGGATAAAGCTGACTATTGTGGTTTACTGGATTAGATGTATTTCTTTCTCATACAGGACTTTTGCATTTTTTTTTTTTTTTTGTTTAACTTGTAGGTTTGGAGCACTGCATTACTGCACCTGTGACTATTGGCGGAGGTCTTTTCCCTGAAGGCCAGGATATGGCATTTTCAAGATCTTTGACTGAGAGGAGGGTTAGTCCAAGACATAATGTAATATTGGATAGACTTTCTGAACGTGGAAAGGTAATTTTGTTATTGACGTCTCCAGCTTTGAGATGCCTATTATCCGACAACCAATTGTGTAGTGCTTTGCTGTGAGATTCTATAATAGTCAACATGGCGTAGGAGTTGAATAGATTTACTAGTCTTGGTTACGATATGCATGTAAATGTGTCAAAAGTTGTTGCAATTTGTTAGAGTTTAATATTTTGTCCTTGACACTAGTTTTGGCTTGAATTTGTTTGATTTGATTGTAAACTTGAAGCATGGAAAGATCCTTTAATGTTGGAGAGTGATAAGGAGTAGAAAAGCTGATATGGGAAGTGCTAAGTGCATGAATAACGAGACTGCTTGTTATCTGAATAAATATGATTTACCTGAACCAATAAAACTTAAAAGAATCCTAGAATGCTGAGCATTATTTTTTCAAATGATGCTTAGACCATGTGAAGCTGGCAATTTGTATTGACCAAGTACTTATTTAGACTTACTGATACAAAATTTACTTTGACCATTTGGTTTTTGAGCTATTTTTTTGCTTTTAACTGATGGAGTTGATATGTATGTTGTAGGGCTCCGCTGAGTCAAGTTGCTATTTAATAAGTGGCTGAAACAAAACCACCCTCTTTAACAAAGTCAATTTTTTCTGCACATAATCACATGTATCCGGCCTGAATCACCGCTTCATACATTAGGTTGTCCATGCCTGTATATGTAAAAATAGCAGCTAATCAAACAGGTTAAGAATTCTTGCTATTTGCCTATGTAAGTATGGATTATGGAGACCCAGGACTGCCCCTCTGCAGCGTCTGAAAGAACCACCACAAATTACTTACATGTGTTTTTTTACTTTATCCATCTGGAAAATGATATACCTTTTCATTTTCTTGCCATTAAGTTGCTGAATCCTTCTTATTCACTTACCATTTCCTCATATTTCCTTCTGTTCTTAATGTCACCAGCAAAAGCTCATCGCAGAGCTGGTAAAGATCCAAGGGGATGGAACAGTAGAGGTTGACCTTACTAAGAGTACGCCTGAAACTTCTGAATTGTTGGAGCTGCGATCTGTTGAAGAACCCACTCTTACTGTAGACAGGATTATCACAGATTTTAATAAGTCAGTTCCAAAGTTGAAAATCGTGGTGCTTATTGTTGGAACCAGGGGAGATGTTCAACCATTTTTGGCTATGGCCAAGAGACTTCAGGCATGTTGGGAGTTCTAAATCACCATGTTTATAGCTGTACTGGTCATACATGTTCTATATCGTTTTCTTCTTAACCATCTGTGCTTGCCTTTATTATTATATCATTGCATTCTATGTTTTTCAGCATCCTTTACAGAATAACCCAAATTTCGGCTTTGAATGACAATTCGTTGGAGAGGTCTGTTAGATGGACTTCTAAGTTCTATTTTACTAGACTTAGTTTCTCCACTTTTCAAGTCTTCTTAGTCACCAACTTTTAAAATTGATTGTTGAGATGCTGTAAGGTAAAAGGATTAGATTGTGTCCCTTGGACCTGGGTAAACCAATTGAGATTTCATTTGAGAATATATTGACGGAGAGAATTTTTAGAGGTGAATTTGGACCTATATGGTTGAAGCAAGTATCAAAAACAAAGGTCACTTGGACCTTGCAATTACTTTGCGCAAGGAAAATTTTGTCTGCTTCAGAGCTGAGGTCTTTTGCTGCTTGACTGGCAAAACATTCTTAATATGCTCTTTACAGTGTGGGTACCATTGGATTTAATTTCTTTTCCTGTCTAAGGTTGGTTTAGCTTTATTTCTTGCTGTTGCCTCTTCTGGAGCACGATTATTTATTTGCCTATTATTTAATTTTCTCATCATTTTTGTGGCCAATATTGGACATTCATGTGAAATAATTGATTATATTTCAACTATAGATTTTGTGTTTCCATATTTCGTGTAGTAGAATTTTGTTGATGTTTGTGCACCTTAATATCTTTGTATTTTGGTTGAGAAAATTGTTCATTTGTAGAGTAAATCGTTCGTTCCTTTTCTAATCAGTTTTATGCATTGACAGGCGTTTGGTCATCATGTCAGGCTGGCAACTCATTCTAACTTCCGTGATTTTGTCAAATCAGGAGGCATAGACTACTACCCATTGGGTGGTGATCCTCGGGTATTGGCAGGATGTAAGAGGTCTTTGGCATGCTTCTTCGTTTTTCTCGTTCTTGTTTTTGTCTATGTTATGAGTACTCTGCTATGGGTATGTATTAGCCCTTTCTTTCTGGGTGGGTAAGTATCTGGTATGAGTAAACATAGTTTTCTGCAATTTTGGGGTGTGCTTCAAAGAATCCACATAAAGTTCTCACATGTGTTCCACACACGCCCTCCCCCCACATCCCTTGCACGCCCAAGACTAGACGAAGCATGGATATCATAACATAGTGCCCTACATTAGGTAACACAATAATGATGATGGGAGTGGCTCTAATTAGTGTTATCAAAAGCAAAAAGCGCAAAAAATCTCTAAGATCTGTTGGGCATTTAAGCGCAACTAACGTGTGGGCTTTAATGAAAAAAAGAGCAAAGGGAGAAAAAATGCAAAGCTATGTTTAGTCCAAGATTAATAATTATAAGCACGAAGGAATGACAAATATATGAAGAAAGAAACTGAAAAAAATAATATGATAAAGTAAAATATCAATTTTTTAGTGCCGCCTCTTCTAAAGAGGCTCATTGGCAAGAAAATGTATGTCATATAACCTTGACGAGGAAACAAAATCGCACCTTAAATAAGTCGAAACACTTTTTGAGCCTCGCATCAGGGCGCCTTTGACAACTCTGGCGCTAATACCAAGCTAAGAAGATGGGTTTAGGCCTAAGTCAATCTCAAAAGTTGGTTCATGCGGTAAGGGTTGCCCAAATCACTAGGAGACTATAGCCACACTTTCAACCAATGGTGAACACTAACATAATCCTATGAGCAATCGTGGTAATATCAAGCTTCTACTTTTTTCCTTTTAGTTAACTTACGCACAGTTTGAAAATTTTTCTTAAATTTTTGGGAAGTTTTCAACATACTTAACAGTCAAATTTGTACTGGAATCTAGTATGAAATAAGTGGCTCATCACATACCTGTTCAAGTAGTAATATGGAATTCCTGTTTGCTGATATCATTTAATATGGATTAAGTTCGTATGTTCTGTGGAATTGCAGATATGGCCAGGAACAAAGGTCTCATTCCTTCTGGACCAGGAGAGATATCTGTACAACGAAAGCAGCTAAAGGCTATAATTGAATCTCTTCTTCCGGCTTGCACTGAGCCAGATATTGAAACTGGTGAACCTTTCAGAGCACAAGCGATTATTGCAAATCCTCCTGCTTATGGTGAGTTCGAAAATAATCTCTATACTCACCACTCATTTCACCTTTTTGATATCTGGACATCTAATTCATGTTTGGTCCATGATTTATAATATCACATGGAGTTGTACATCACTGCTAGTTCTCCAAAAGATACATTTCTGTCTTCTCTTGTTTTTCTTTTTGGGGTGGGGGTGGCGGGTGGTGGTGGTCATATTTTGCCATCATAGAGAACATATGTTTGACTAAATTAGAAAGATATATGTGAGATACTATAAGTAGAGGAGCTACTATATTCTGAGATGGTCTCTTAGTCGCATTGTGGAATTTATCTTAGAAAGGATTAACATGAAGTCAACAAATATGAATTAAATGAACATATTAGTGTGTATGAAGTGAGGATGGGTCACTATGACCTCCGGACACAAGAATCTCAAAGATAACCTTGAAATCATACTCAGGTTAGAATCGTTTGAAATGTCTTTGGCCAAATAACTCTGTTTATTTACTATGAGTTTAATCTCATTTGACTCTTCTAATGTGGAGACCAGAAGCTATCTAGTTTTGACCTTGGGAGGAGTTAAGTCTGAAAAGTTACTCCACCGCCTTAGCTGGGTTTGACTGTTCATATGTTACATATTTAATCTCACACTATCTTCACAGTGCTCCTCTGCTTCTTTTCAATTAGAGTAGACCTATGTCAAGAAGTTGAGTTATTAGCCTATAAAGAAATCCACCTGATTGTATTTTCTGTATCAAATTCACGAGCAGTGTTAATCTGCTTCGAATAAGTACAAGCCCTTCCAAACTGAAAAACTTATTTTGGGAGGTCATTAGCTGAATCTATGGAGGTGTGTATTCTGCACAGCTTTGGCAAGTTGCAAACCGGTTTGGGTTTACTAAACAAAGAGCTTAGAAGGAAGAAGACTTAATCTTGAGCTTGTGCTCTGTAAATAAATGTCGAATAAAATATAAACTGCTTTATATGGTTTTCCTCAATGGTCCCCAAAACAATATTCATTTTTATGCTTTCCGGGACTTTATAGACTCCTTGTATCATAGATAATTCTAGTCCATCAATTGTACAGATATCAGCAACCTCTTGCTGCTATTTTTGTTAACAACATTTATCAGGATTAGTCAACACAACAGGATGCGATTTAGTCCAAGTCAACTTATAAGCATTGTTTTATTTTTTTGGACAGGACATGCACACGTTGCTGAAGCTCTTGGGGTACCCCTCCACATCTTCTTCACA</genome_strand>
        <mrna_strand>ATTTTTATGTTTGTTGCTGAATCTGGAGTTGAGTTGAATTTGAGTTCTCTTACAGTTGTTTGCGAAGCTTGAAATTTTGGAACACTAGGTGTGTCAGTTTGGTGAAGTTAAGTGGTTTTGGAGTTCATCAGATGAAATGGATAGTAATGGGCTTAATGGTAATCAGAGCACAAGGGATTCAGAAGTACCAAACAATGCTGATGAACGGTGTGATGCTACTTTTTCCGATGAATTAGATGGCGGGAGAACAAGTTCTTCATCACTTAAGGACATTAGGTCTTCAGATGAGCATGTTGATGAGTGTTTGACTCCAGAAATGAAATATGAGAGAACACATCGGAGTTCTAGTCCTCCACCTCTAGCTCGGAGAG.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTTGGAGCACTGCATTACTGCACCTGTGACTATTGGCGGAGATCTTTTCCCTGAANGCCAGGATATGGCATTTTCAAGATCTTTGACTGAGAGGAGGGTTAGTCCAAGGCATAATCTAATATTGGATAGACTTTCTGAACGTGGAAAG..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CAAAAGCTCATTGTGGATCTGGTAAAGATTCAAGGGGATGGAACAGTAGAGGTTGACCTTACTAAGAGTACGCCTGAAACTTCTGAATTGTTGGAGCTGCGATCTGTTGAAGAACCCACTCTTACTGTAGACAGGATTATCACAGGTTTTAATAAGTCAGTTCCAAAGTTGAAAATCGTGGTGCTTATTGTTGGAACCAGGGGAGATGTTCAACCATTTTTGGCTATGGCCAAGAGACTTCAG.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCGTTTGGTCATCATGTCAGGCTGGCAACTCATTCTAACTTCCACGATTTTGTCAAATCAGGAGGCATAGACTTCTACCCATTGGGTGGTGATCCTCGGGTATTGGCAGGAT....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATATGGCCAGGAACAAAGGTCTCATTCCTTCTGGACCAGGAGAGATATCTGTACAACGAAAGCAGCTAAAGGCAATAATTGAATCTCTTCTTCCGGCTTGCACTGAACCAGATATTGAAACTGGTGAACCTTTCAGAGCACAAGCAATTATTGCAAATCCTCCTGCTTATG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GACATGCACACGTTGCTGAAGCTCTTGGGGTACCCCTCCACATCTTCTTCACA</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-m4uMJa/sgn_marker_seqs" ref_id="SGN-M6802" ref_strand="+" ref_description="SGN-M6802 C2_At1g43620 [cosii_markers]">
      <seq>gaaagaatttcctcacccattggctcgtgtacctcaaactgctgcatattggctttcctacatagttgcggatttacttatctggtggggcataagaagttacatcaacgagtttaggaaaaagaagctaaaccttcctcctatcgcctacttcagcacgtaccacggatcaatttctcacttcccaactggctacatctggagtccacatgttgttccaaagcctaaagattggggccctttggttgatgttgttggctattgtttcttaaacgatgggagtaactaccaacctcctgaagaatttatcaagtggatccaaaatgggt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0094K06-flbfK/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0094K06.1" temp_strand="+" temp_description="C04HBa0094K06.1  CU468249.6 htgs_phase:3 submitted_to_sgn_as:C04HBa0094K06 sequenced_by:sanger upload_account_name:uk">
        <position start="48093" stop="49415"/>
      </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="48389" g_stop="48440" g_length="52"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="52" r_length="52" r_score="0.846"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="48441" i_stop="48530" i_length="90">
            <donor d_prob="1.000" d_score="0.88"/>
            <acceptor a_prob="0.945" a_score="0.88"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="48531" g_stop="48708" g_length="178"/>
          <reference_exon_boundary r_type="cDNA" r_start="53" r_stop="230" r_length="178" r_score="0.933"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="48709" i_stop="49017" i_length="309">
            <donor d_prob="0.985" d_score="0.96"/>
            <acceptor a_prob="0.872" a_score="0.92"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="49018" g_stop="49116" g_length="99"/>
          <reference_exon_boundary r_type="cDNA" r_start="231" r_stop="329" r_length="99" r_score="0.939"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0094K06.1" gen_strand="+" ref_id="SGN-M6802" ref_strand="+">
        <total_alignment_score>0.921</total_alignment_score>
        <cumulative_length_of_scored_exons>329</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0094K06.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M6802" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="48389" e_stop="48440"/>
          <exon e_start="48531" e_stop="48708"/>
          <exon e_start="49018" e_stop="49116"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTCTGAATTTCCTCACCCGATGGCTCGTGTACCTCAACCTGCTGCGTATTGGGTATGTTATCAGTTTCTTCTTTTGAAAAATATTTTTCCAGTAATTCTTCTGATTCCTGTTAAAACTCTATTTGTCTTCTGCACATTTCAGCTTTCCTACATACTCGTGGATTTACTTGTCTGGTGGGGCATAAGAGGCTACATCAACGATTTTAGGAAAAAGAAGTTAAACCTTCCTCCTATCGCCTACTTCAGTACATACCACGGATCAATTTCTCACTTCCCAACTGGCTACATGTGGAGTCCACATGTTGTGCCAAAGCCTAAAGGTATATGTCAGCTCCTCAATGGTATCTGGATGCTTGTTTTCGTCGTATTGGTCATTCCACTTCTTTTGTTGAAGCAAAACTAATGATTTGTAAATCTCAAAATGAACGGATCAGTTTCTTGTGGAGTATTTCTGTGCTAGTCTCTCTTTCTTCATTCCCATTAATCCCCTTCCCCATCCCTGAATTCATGTAAAGATCTTTTCTTCTTTTTCTAGCTCTACTTCACCCATTGGCTTAGTAATGATGTGTGCTCATACAATCAGTCCACTTGATCTATCATAAAAATATTGAAGCATTCGTTTTTTGCAGATTGGGGCTCTTTGGTTGATATTGTTGGCTATTGTTTCTTAAACCTTGGGAGAAACTACCAACCTCCTGAAGAATTTATCAAGTGGATCCAAAATGGGC</genome_strand>
        <mrna_strand>GAAAGAATTTCCTCACCCATTGGCTCGTGTACCTCAAACTGCTGCATATTGG..........................................................................................CTTTCCTACATAGTTGCGGATTTACTTATCTGGTGGGGCATAAGAAGTTACATCAACGAGTTTAGGAAAAAGAAGCTAAACCTTCCTCCTATCGCCTACTTCAGCACGTACCACGGATCAATTTCTCACTTCCCAACTGGCTACATCTGGAGTCCACATGTTGTTCCAAAGCCTAAAG.....................................................................................................................................................................................................................................................................................................................ATTGGGGCCCTTTGGTTGATGTTGTTGGCTATTGTTTCTTAAACGATGGGAGTAACTACCAACCTCCTGAAGAATTTATCAAGTGGATCCAAAATGGGT</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-m4uMJa/sgn_marker_seqs" ref_id="SGN-M6801" ref_strand="+" ref_description="SGN-M6801 C2_At1g43580 [cosii_markers]">
      <seq>gtggtttgggatttgctgcaattgcatacctcggagtagactctctccggtttctttctccggcatggcatgaaccggttacagccggcaccatggaccataattggcgaatcgctgctattattcgggttccaattttacaaacacctggtcatcggagctccgttcagctataccctttattttcgcaatgatttttttgctctctgctcttctttttgaagccatttctgtccgctctgtcactgccgttcttggtcttgaatggaacagtgatgcatcacctcttcctgatgttggtcagtggttggtgctgtcgttgaatgagaaactacctcaaacagtggttaatatattgagagctcgtataattggattacatcattttctgatgctgtttatcatgcttgctttctctgtactctttgaatcggttgaagctcctggtcttgggcttggtgcaagattcatgttcacaatgggaatcggaaggttacttcgggccataacttttatctccacaattctaccatctgctcgaccatggtgtgcatctgctagattccttgttcctcagcaccctcatccttgggctcagaaatattatgtaccatatgccacagattcaaatgccatacggaacgtcataaactgggacacagcatatgctgatcctggggaatacgatccggagtttcgaccagattggggttcaatgagctttctgattgatttccttcggcctacagctcctgagggatcatctgcttggtatcatctgctaaagaaagcgtcagggggttgcaatgaccttatatatagtggccacatgct</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0094K06-flbfK/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0094K06.1" temp_strand="+" temp_description="C04HBa0094K06.1  CU468249.6 htgs_phase:3 submitted_to_sgn_as:C04HBa0094K06 sequenced_by:sanger upload_account_name:uk">
        <position start="53740" stop="57445"/>
      </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="54040" g_stop="54307" g_length="268"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="273" r_length="273" r_score="0.922"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="54308" i_stop="56349" i_length="2042">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.981" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="56350" g_stop="56744" g_length="395"/>
          <reference_exon_boundary r_type="cDNA" r_start="274" r_stop="668" r_length="395" r_score="0.995"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="56745" i_stop="56979" i_length="235">
            <donor d_prob="0.992" d_score="1.00"/>
            <acceptor a_prob="0.978" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="56980" g_stop="57145" g_length="166"/>
          <reference_exon_boundary r_type="cDNA" r_start="669" r_stop="834" r_length="166" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0094K06.1" gen_strand="+" ref_id="SGN-M6801" ref_strand="+">
        <total_alignment_score>0.972</total_alignment_score>
        <cumulative_length_of_scored_exons>829</cumulative_length_of_scored_exons>
        <coverage percentage="0.994" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0094K06.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M6801" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="54040" e_stop="54307"/>
          <exon e_start="56350" e_stop="56744"/>
          <exon e_start="56980" e_stop="57145"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GTGGTTTGGGATTTGCTGCAATTGCTTACATCGGAGTAGACTATCTCCGGTTTATTTCTCCGGCATGGCATG-ACCGGTTACAGCCGACGCTATGGACCAT-ATTGGCG-ATCGCTGCTATTATTCGGGTTCCA-TTTTACAAACA-CTGGTCATCAGAGCTCCGTTCAGCTATACCATTTATTTTCGCTATGCTTTTTTTGCTCTCTGCTCTTCTTTTTGAAGCCATTTCTGTCCGCTCTGTCACTGCCGTTCTTGGTCTTGAATGGAACAGGTATGTATATGCTTTAAAGTAGTGCTCTTTTTTAATTCATAATTTTATTGATTTGTTTCAATTTTTTGAAGTTTTGGCAAATTTGTGTATATTGGGAAATATGGGTTTCAGATTTGGATGGGAAAACTGACTTGGGGTTGAGTGCATTTTTGAGCTTGTTAATGATAAGTTTGAGTTTGTATTGTGAAGAATGGAAATGATAATTTCTTGTTTGCATCCCAAATCTGATCTAATTTGTGGTTTTCTCAATTGCTCTATAGATTTTGTTACATTGTAAAATCTAAGCAGAGTTAGATGCAGAAATTGGATGAACTATTAGAGAGAATTTGGAGCTACATCATTTTTACTCTGAATGATCAGAAATTGTTATTGAGTTACCTTCAAAATCACACATACATACTTTTGAATTTTTTCATTGAAGATTGCATATATCCATTTATGGGAAAAACACAAGGTTTGGATTTCTATACTGGGATTAATTAAAGCTGATAGATCAGACCAAAAAAATTGGTATAGGTCAATCTCACTTATCCTGGAGACAGAATTAAGAGGGATGCATTTTTCTATATGCTTCGGTTTGCTTAAGTTATGTTGCTCCGACTCTCCAAAATGCTGCCGCACCCATGACTGATCTTCCATAAATGCACTACGTTTGGAGGATCCAACATGCATCTCGACAACAATTTTGTGCAGTACATTGGTATGGGTAATCCTTTGTTAGATTTCAAAAGTAATGAAAATCTTAAGTGGATTAGTTTGTGCTCTTGGTATGTCTTGTGTCTGTGAATAATGGTATTTTGCGTATAATTCTTTCTTGTGATTAATTAAATTCTGTACGTGATGCTCATCATAAATTAAATCCTCACATTCTTCTGCCAAGTGATCCAAATAAGACTGGGATCATGGCACTGTTGCTTTTTAGATACATCTTTTGGAAATGACAAAGCATACGTTGTTTAAGTTTTTACCATGTCACCAGATTGTTAGAATTGGGGAATGGGCGACTTTTTGGATTTTTTAAATTGGGGACTTCTCTGACTGAATTCAAGATGAGTAGACAGAGCTTGGAAACTAATAGAGGAAGTGGAGGAAAACCGGGAAGGTATAAGGCTTAGGAAATCGAGGATGGGAACTTCTTTGAGAATTTTGATAAAGAAGAGGGAGTTTGGAAACCGAGGAGGCAAAGAGACAACTGTGTAAGGATGAAGATGTCAGGTGATAAAAAAAGGGATCTTTTTGAGCTTTTTCCAAAGCTTCTGTACTGAGACACTTTCAAGCAAAATAAAAACAGATAGCTAGTAAAGTCATAACTAAAAGAGAGAACTAATTGTGCTGTATTTGAAATCATATATTAACCTGTGTTGCATGTCTTGGTTAGCTTGGATTGGTTAGGTGTGATCTGTCTTGGGATTCTAGATATGCTAACGTCATCTAGATGTGTAAGGATACATGGTCTAGATTCTAGTGAGATACAATACAACAATGTCTTTTAATAGCAGAATTTCACAAAGATGCTGAATTGATAGTTCTAAAATGCTGTCTAAGGCGAGTAATATAAAGGAAAATCTGGCTTGCATCATCACAATTAACAAACTTTGCCTCCAGTATCACCACTATTAGAAGTTAAACAGTTTGACATTGATTTCCTTTCCTGTTCTTGTTTTTGAGAAATATGTCTATCGTTGAAGCACAATGTGAAGTGGTGAAAGGCTTCTTGAAGCATGGATAAATTTCATTTTTTTTAAAAAAAAAGTCTTACGGATATCTGTAGACACGATCAGAATGCCCTAAAGTGGTTATGTTATCAATCATGGCACGCAACCTTGTTTTGCCTCCTAGAAGATTGAAAGTTTAGACGCATACTTGGTCCCAATTTACAATGTTTGGCTTGTGTCCAGAAAAATAAATTAACAATTGAGTCTTTTTCCTTTTGTAAGCAAAAATAGCAATTATAACTTTGCTTCATTATGTTTGATCTCTCTTCTTTCTTAAATGACCATCTATAGTCTTTACAAGTTCTTCTCTTTGCAATTTATTGACAGTGATGCATCACCTCTTCCTGATGTTGGTCAGTGGTTGGTGCTGTCATTGAATGAGAAACTACCTCAAACAGTGGTTAATATATTGAGAGCTCGTATAATTGGATTACATCATTTTCTGATGCTGTTTATCATGCTTGCTTTCTCTGTACTCTTTGAATCGGTTGAAGCTCCTGGTCTTGGGCTTGGTGCAAGATTCATGTTCACAATGGGAATCGGAAGGCTACTTCGGGCCATAACTTTTATCTCCACAATTCTACCATCTGCTCGACCATGGTGTGCATCTGCTAGATTCCTTGTTCCTCAGCACCCTCATCCTTGGGCTCAGAAATATTATGTACCATATGCCACAGATTCAAATGCCATACGGAACGTCATAAACTGGGACACAGCATATGGTATTTCTCCCTTCTGATCTTCTCTTCTGTCCTGAAATTCTTACTTGGTTCTTCTTTATGAACTGCCAGTCAGAATGATCCAAAATTGAAAAAGCTCTATACATTTGTTCAATAAGAAATGCTGCCTGCGATCAGGAAATCTCATAAAGCCAGTTTCTTTTAGGTCTTTGATGCTGTTGGTTGAATTCTGTACATAGTATTGATCTTTCATTTCTGTCTCTACTTTCGCTTTCAGCTGATCCTGGGGAATACGATCCGGAGTTTCGACCAGATTGGGGTTCAATGAGCTTTCTGATTGATTTCCTTCGGCCTACAGCTCCTGAGGGATCATCTGCTTGGTATCATCTGCTAAAGAAAGCGTCAGGGGGTTGCAATGACCTTATATATAGTGGCCACATGCT</genome_strand>
        <mrna_strand>GTGGTTTGGGATTTGCTGCAATTGCATACCTCGGAGTAGACTCTCTCCGGTTTCTTTCTCCGGCATGGCATGAACCGGTTACAGCCGGCACCATGGACCATAATTGGCGAATCGCTGCTATTATTCGGGTTCCAATTTTACAAACACCTGGTCATCGGAGCTCCGTTCAGCTATACCCTTTATTTTCGCAATGATTTTTTTGCTCTCTGCTCTTCTTTTTGAAGCCATTTCTGTCCGCTCTGTCACTGCCGTTCTTGGTCTTGAATGGAACAG..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGATGCATCACCTCTTCCTGATGTTGGTCAGTGGTTGGTGCTGTCGTTGAATGAGAAACTACCTCAAACAGTGGTTAATATATTGAGAGCTCGTATAATTGGATTACATCATTTTCTGATGCTGTTTATCATGCTTGCTTTCTCTGTACTCTTTGAATCGGTTGAAGCTCCTGGTCTTGGGCTTGGTGCAAGATTCATGTTCACAATGGGAATCGGAAGGTTACTTCGGGCCATAACTTTTATCTCCACAATTCTACCATCTGCTCGACCATGGTGTGCATCTGCTAGATTCCTTGTTCCTCAGCACCCTCATCCTTGGGCTCAGAAATATTATGTACCATATGCCACAGATTCAAATGCCATACGGAACGTCATAAACTGGGACACAGCATATG...........................................................................................................................................................................................................................................CTGATCCTGGGGAATACGATCCGGAGTTTCGACCAGATTGGGGTTCAATGAGCTTTCTGATTGATTTCCTTCGGCCTACAGCTCCTGAGGGATCATCTGCTTGGTATCATCTGCTAAAGAAAGCGTCAGGGGGTTGCAATGACCTTATATATAGTGGCCACATGCT</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-m4uMJa/sgn_marker_seqs" ref_id="SGN-M608-F" ref_strand="+" ref_description="SGN-M608-F CT178-F [rflp_markers_forward]">
      <seq>tcttgtcataacatatagtatttgttgtgtgctgatcaatctatcctttaattaatacgtactcagcatgcacctaaataatttgtatgtgtgttacactactcttgtctttgatgttgtgcacctactttaatttgcatgagtgtgaataatattacgtatattgtttttcttaaaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0094K06-flbfK/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0094K06.1" temp_strand="+" temp_description="C04HBa0094K06.1  CU468249.6 htgs_phase:3 submitted_to_sgn_as:C04HBa0094K06 sequenced_by:sanger upload_account_name:uk">
        <position start="104499" stop="105275"/>
      </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="104799" g_stop="104975" g_length="177"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="177" r_length="177" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="178" polyA_stop="194"/>
      <MATCH_line gen_id="C04HBa0094K06.1" gen_strand="+" ref_id="SGN-M608-F" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>177</cumulative_length_of_scored_exons>
        <coverage percentage="0.912" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0094K06.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M608-F" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="104799" e_stop="104975"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCTTGTCATAACATATAGTATTTGTTGTGTGCTGATCAATCTATCCTTTAATTAATACGTACTCAGCATGCACCTAAATAATTTGTATGTGTGTTACACTACTCTTGTCTTTGATGTTGTGCACCTACTTTAATTTGCATGAGTGTGAATAATATTACGTATATTGTTTTTCTTAAA</genome_strand>
        <mrna_strand>TCTTGTCATAACATATAGTATTTGTTGTGTGCTGATCAATCTATCCTTTAATTAATACGTACTCAGCATGCACCTAAATAATTTGTATGTGTGTTACACTACTCTTGTCTTTGATGTTGTGCACCTACTTTAATTTGCATGAGTGTGAATAATATTACGTATATTGTTTTTCTTAAA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>5</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="39843" PGL_stop="49116"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="39843" e_stop="39945"/>
            <exon e_start="40596" e_stop="41016"/>
            <exon e_start="42830" e_stop="42978"/>
            <exon e_start="43917" e_stop="44159"/>
            <exon e_start="44997" e_stop="45108"/>
            <exon e_start="46137" e_stop="46307"/>
            <exon e_start="47489" e_stop="47552"/>
            <exon e_start="48383" e_stop="48440"/>
            <exon e_start="48531" e_stop="48708"/>
            <exon e_start="49018" e_stop="49116"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.928" acc_prob="0.083" e_score="1.000"/>
          <exon-intron don_prob="1.000" acc_prob="1.000" e_score="1.000"/>
          <exon-intron don_prob="0.657" acc_prob="0.984" e_score="1.000"/>
          <exon-intron don_prob="0.995" acc_prob="0.985" e_score="1.000"/>
          <exon-intron don_prob="0.821" acc_prob="0.999" e_score="1.000"/>
          <exon-intron don_prob="0.990" acc_prob="0.995" e_score="1.000"/>
          <exon-intron don_prob="1.000" acc_prob="0.839" e_score="1.000"/>
          <exon-intron don_prob="1.000" acc_prob="0.945" e_score="1.000"/>
          <exon-intron don_prob="0.985" acc_prob="0.872" e_score="1.000"/>
          <exon-only e_score="0.939"/>
        </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="39843" e_stop="39945" e_length="103"/>
          </exon>
          <intron i_serial="1" don_prob="0.928" acc_prob="0.083">
            <gDNA_intron_boundary i_start="39946" i_stop="40595" i_length="650"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="40596" e_stop="41016" e_length="421"/>
          </exon>
          <intron i_serial="2" don_prob="1.000" acc_prob="1.000">
            <gDNA_intron_boundary i_start="41017" i_stop="42829" i_length="1813"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="42830" e_stop="42978" e_length="149"/>
          </exon>
          <intron i_serial="3" don_prob="0.657" acc_prob="0.984">
            <gDNA_intron_boundary i_start="42979" i_stop="43916" i_length="938"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="43917" e_stop="44159" e_length="243"/>
          </exon>
          <intron i_serial="4" don_prob="0.995" acc_prob="0.985">
            <gDNA_intron_boundary i_start="44160" i_stop="44996" i_length="837"/>
          </intron>
          <exon e_serial="5" e_score="1.000">
            <gDNA_exon_boundary e_start="44997" e_stop="45108" e_length="112"/>
          </exon>
          <intron i_serial="5" don_prob="0.821" acc_prob="0.999">
            <gDNA_intron_boundary i_start="45109" i_stop="46136" i_length="1028"/>
          </intron>
          <exon e_serial="6" e_score="1.000">
            <gDNA_exon_boundary e_start="46137" e_stop="46307" e_length="171"/>
          </exon>
          <intron i_serial="6" don_prob="0.990" acc_prob="0.995">
            <gDNA_intron_boundary i_start="46308" i_stop="47488" i_length="1181"/>
          </intron>
          <exon e_serial="7" e_score="1.000">
            <gDNA_exon_boundary e_start="47489" e_stop="47552" e_length="64"/>
          </exon>
          <intron i_serial="7" don_prob="1.000" acc_prob="0.839">
            <gDNA_intron_boundary i_start="47553" i_stop="48382" i_length="830"/>
          </intron>
          <exon e_serial="8" e_score="1.000">
            <gDNA_exon_boundary e_start="48383" e_stop="48440" e_length="58"/>
          </exon>
          <intron i_serial="8" don_prob="1.000" acc_prob="0.945">
            <gDNA_intron_boundary i_start="48441" i_stop="48530" i_length="90"/>
          </intron>
          <exon e_serial="9" e_score="1.000">
            <gDNA_exon_boundary e_start="48531" e_stop="48708" e_length="178"/>
          </exon>
          <intron i_serial="9" don_prob="0.985" acc_prob="0.872">
            <gDNA_intron_boundary i_start="48709" i_stop="49017" i_length="309"/>
          </intron>
          <exon e_serial="10" e_score="0.939">
            <gDNA_exon_boundary e_start="49018" e_stop="49116" e_length="99"/>
          </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="39843" stop="39945"/>
              <exon start="40596" stop="41016"/>
              <exon start="42830" stop="42978"/>
              <exon start="43917" stop="44159"/>
              <exon start="44997" stop="45108"/>
              <exon start="46137" stop="46307"/>
              <exon start="47489" stop="47552"/>
              <exon start="48383" stop="48440"/>
              <exon start="48531" stop="48708"/>
              <exon start="49018" stop="49056"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M6802-2" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="40647" stop="41016"/>
              <exon start="42830" stop="42978"/>
              <exon start="43917" stop="44159"/>
              <exon start="44997" stop="45108"/>
              <exon start="46137" stop="46307"/>
              <exon start="47489" stop="47541"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M6802-3" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="48389" stop="48440"/>
              <exon start="48531" stop="48708"/>
              <exon start="49018" stop="49116"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M6802" 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>CCTTTTTAAGTCTTGGATTGAGCAGAAAAGAAGACTTTTTTCATCAGTTTTTCAAGAATATTTAGTGTGAAGTGATTAGCATTCTCTTTGATAATCTTAATGA : GTTTTGATGCACAGGATTGTTTATGAATTCTTTGGTTGCTGAATTTGCAAGTTTTTTATGTTAGTTGCTGAATCTGGAGTTTAGTTGAATTTGAGTTCTCTTACAGTTGTTTGCGAAGCTTGAAATTTTAGAAGAGTAGGTGTTCAGTTTGGTGAATTTAAGTGGTTTTGGAGTTCATCATTTGAAATGGATAGTAGTGGGCTTAATGGAAATCAGAGTACAAGGGATTCAGAAGTACCGAACAATGCTGATGAACGGTGTGATGCTACCTTTTCCGATGAATTAGATGGCTGGAGAACAAGTTCTTCATCACTTAAGGACATTAGGTCTTCAGATGAGCATACTGATGAGTGTTTGACTCCAGAAATGAAATACGAGAGCACACATCGGAGTTCTAGTCCTCCGCCTCAAGCTCGGAGAG : GTTTGGAGCACTGCATTACTGCACCTGTGACTATTGGCGGAGGTCTTTTCCCTGAAGGCCAGGATATGGCATTTTCAAGATCTTTGACTGAGAGGAGGGTTAGTCCAAGACATAATGTAATATTGGATAGACTTTCTGAACGTGGAAAG : CAAAAGCTCATCGCAGAGCTGGTAAAGATCCAAGGGGATGGAACAGTAGAGGTTGACCTTACTAAGAGTACGCCTGAAACTTCTGAATTGTTGGAGCTGCGATCTGTTGAAGAACCCACTCTTACTGTAGACAGGATTATCACAGATTTTAATAAGTCAGTTCCAAAGTTGAAAATCGTGGTGCTTATTGTTGGAACCAGGGGAGATGTTCAACCATTTTTGGCTATGGCCAAGAGACTTCAG : GCGTTTGGTCATCATGTCAGGCTGGCAACTCATTCTAACTTCCGTGATTTTGTCAAATCAGGAGGCATAGACTACTACCCATTGGGTGGTGATCCTCGGGTATTGGCAGGAT : ATATGGCCAGGAACAAAGGTCTCATTCCTTCTGGACCAGGAGAGATATCTGTACAACGAAAGCAGCTAAAGGCTATAATTGAATCTCTTCTTCCGGCTTGCACTGAGCCAGATATTGAAACTGGTGAACCTTTCAGAGCACAAGCGATTATTGCAAATCCTCCTGCTTATG : GACATGCACACGTTGCTGAAGCTCTTGGGGTACCCCTCCACATCTTCTTCACAATGCCCTGGAC : GCCAACTTCTGAATTTCCTCACCCGATGGCTCGTGTACCTCAACCTGCTGCGTATTGG : CTTTCCTACATACTCGTGGATTTACTTGTCTGGTGGGGCATAAGAGGCTACATCAACGATTTTAGGAAAAAGAAGTTAAACCTTCCTCCTATCGCCTACTTCAGTACATACCACGGATCAATTTCTCACTTCCCAACTGGCTACATGTGGAGTCCACATGTTGTGCCAAAGCCTAAAG : ATTGGGGCTCTTTGGTTGATATTGTTGGCTATTGTTTCTTAAACCTTGGGAGAAACTACCAACCTCCTGAAGAATTTATCAAGTGGATCCAAAATGGGC</gDNA_template>
            <first_frame> P  F  *  V  L  D  *  A  E  K  K  T  F  F  I  S  F  S  R  I  F  S  V  K  *  L  A  F  S  L  I  I  L  M   : S  F  D  A  Q  D  C  L  *  I  L  W  L  L  N  L  Q  V  F  Y  V  S  C  *  I  W  S  L  V  E  F  E  F  S  Y  S  C  L  R  S  L  K  F  *  K  S  R  C  S  V  W  *  I  *  V  V  L  E  F  I  I  *  N  G  *  *  W  A  *  W  K  S  E  Y  K  G  F  R  S  T  E  Q  C  *  *  T  V  *  C  Y  L  F  R  *  I  R  W  L  E  N  K  F  F  I  T  *  G  H  *  V  F  R  *  A  Y  *  *  V  F  D  S  R  N  E  I  R  E  H  T  S  E  F  *  S  S  A  S  S  S  E  R :   F  G  A  L  H  Y  C  T  C  D  Y  W  R  R  S  F  P  *  R  P  G  Y  G  I  F  K  I  F  D  *  E  E  G  *  S  K  T  *  C  N  I  G  *  T  F  *  T  W  K   : A  K  A  H  R  R  A  G  K  D  P  R  G  W  N  S  R  G  *  P  Y  *  E  Y  A  *  N  F  *  I  V  G  A  A  I  C  *  R  T  H  S  Y  C  R  Q  D  Y  H  R  F  *  *  V  S  S  K  V  E  N  R  G  A  Y  C  W  N  Q  G  R  C  S  T  I  F  G  Y  G  Q  E  T  S   : G  V  W  S  S  C  Q  A  G  N  S  F  *  L  P  *  F  C  Q  I  R  R  H  R  L  L  P  I  G  W  *  S  S  G  I  G  R  I :   Y  G  Q  E  Q  R  S  H  S  F  W  T  R  R  D  I  C  T  T  K  A  A  K  G  Y  N  *  I  S  S  S  G  L  H  *  A  R  Y  *  N  W  *  T  F  Q  S  T  S  D  Y  C  K  S  S  C  L  W :   T  C  T  R  C  *  S  S  W  G  T  P  P  H  L  L  H  N  A  L  D  :  A  N  F  *  I  S  S  P  D  G  S  C  T  S  T  C  C  V  L   : A  F  L  H  T  R  G  F  T  C  L  V  G  H  K  R  L  H  Q  R  F  *  E  K  E  V  K  P  S  S  Y  R  L  L  Q  Y  I  P  R  I  N  F  S  L  P  N  W  L  H  V  E  S  T  C  C  A  K  A  *  R :   L  G  L  F  G  *  Y  C  W  L  L  F  L  K  P  W  E  K  L  P  T  S  *  R  I  Y  Q  V  D  P  K  W   </first_frame>
            <second_frame>  L  F  K  S  W  I  E  Q  K  R  R  L  F  S  S  V  F  Q  E  Y  L  V  *  S  D  *  H  S  L  *  *  S  *  *  :  V  L  M  H  R  I  V  Y  E  F  F  G  C  *  I  C  K  F  F  M  L  V  A  E  S  G  V  *  L  N  L  S  S  L  T  V  V  C  E  A  *  N  F  R  R  V  G  V  Q  F  G  E  F  K  W  F  W  S  S  S  F  E  M  D  S  S  G  L  N  G  N  Q  S  T  R  D  S  E  V  P  N  N  A  D  E  R  C  D  A  T  F  S  D  E  L  D  G  W  R  T  S  S  S  S  L  K  D  I  R  S  S  D  E  H  T  D  E  C  L  T  P  E  M  K  Y  E  S  T  H  R  S  S  S  P  P  P  Q  A  R  R   : G  L  E  H  C  I  T  A  P  V  T  I  G  G  G  L  F  P  E  G  Q  D  M  A  F  S  R  S  L  T  E  R  R  V  S  P  R  H  N  V  I  L  D  R  L  S  E  R  G  K  :  Q  K  L  I  A  E  L  V  K  I  Q  G  D  G  T  V  E  V  D  L  T  K  S  T  P  E  T  S  E  L  L  E  L  R  S  V  E  E  P  T  L  T  V  D  R  I  I  T  D  F  N  K  S  V  P  K  L  K  I  V  V  L  I  V  G  T  R  G  D  V  Q  P  F  L  A  M  A  K  R  L  Q  :  A  F  G  H  H  V  R  L  A  T  H  S  N  F  R  D  F  V  K  S  G  G  I  D  Y  Y  P  L  G  G  D  P  R  V  L  A  G   : Y  M  A  R  N  K  G  L  I  P  S  G  P  G  E  I  S  V  Q  R  K  Q  L  K  A  I  I  E  S  L  L  P  A  C  T  E  P  D  I  E  T  G  E  P  F  R  A  Q  A  I  I  A  N  P  P  A  Y   : G  H  A  H  V  A  E  A  L  G  V  P  L  H  I  F  F  T  M  P  W  T :   P  T  S  E  F  P  H  P  M  A  R  V  P  Q  P  A  A  Y  W  :  L  S  Y  I  L  V  D  L  L  V  W  W  G  I  R  G  Y  I  N  D  F  R  K  K  K  L  N  L  P  P  I  A  Y  F  S  T  Y  H  G  S  I  S  H  F  P  T  G  Y  M  W  S  P  H  V  V  P  K  P  K   : D  W  G  S  L  V  D  I  V  G  Y  C  F  L  N  L  G  R  N  Y  Q  P  P  E  E  F  I  K  W  I  Q  N  G  </second_frame>
            <third_frame>   F  L  S  L  G  L  S  R  K  E  D  F  F  H  Q  F  F  K  N  I  *  C  E  V  I  S  I  L  F  D  N  L  N  E :   F  *  C  T  G  L  F  M  N  S  L  V  A  E  F  A  S  F  L  C  *  L  L  N  L  E  F  S  *  I  *  V  L  L  Q  L  F  A  K  L  E  I  L  E  E  *  V  F  S  L  V  N  L  S  G  F  G  V  H  H  L  K  W  I  V  V  G  L  M  E  I  R  V  Q  G  I  Q  K  Y  R  T  M  L  M  N  G  V  M  L  P  F  P  M  N  *  M  A  G  E  Q  V  L  H  H  L  R  T  L  G  L  Q  M  S  I  L  M  S  V  *  L  Q  K  *  N  T  R  A  H  I  G  V  L  V  L  R  L  K  L  G  E  :  V  W  S  T  A  L  L  H  L  *  L  L  A  E  V  F  S  L  K  A  R  I  W  H  F  Q  D  L  *  L  R  G  G  L  V  Q  D  I  M  *  Y  W  I  D  F  L  N  V  E  S :   K  S  S  S  Q  S  W  *  R  S  K  G  M  E  Q  *  R  L  T  L  L  R  V  R  L  K  L  L  N  C  W  S  C  D  L  L  K  N  P  L  L  L  *  T  G  L  S  Q  I  L  I  S  Q  F  Q  S  *  K  S  W  C  L  L  L  E  P  G  E  M  F  N  H  F  W  L  W  P  R  D  F  R :   R  L  V  I  M  S  G  W  Q  L  I  L  T  S  V  I  L  S  N  Q  E  A  *  T  T  T  H  W  V  V  I  L  G  Y  W  Q  D  :  I  W  P  G  T  K  V  S  F  L  L  D  Q  E  R  Y  L  Y  N  E  S  S  *  R  L  *  L  N  L  F  F  R  L  A  L  S  Q  I  L  K  L  V  N  L  S  E  H  K  R  L  L  Q  I  L  L  L  M  :  D  M  H  T  L  L  K  L  L  G  Y  P  S  T  S  S  S  Q  C  P  G   : R  Q  L  L  N  F  L  T  R  W  L  V  Y  L  N  L  L  R  I  G :   F  P  T  Y  S  W  I  Y  L  S  G  G  A  *  E  A  T  S  T  I  L  G  K  R  S  *  T  F  L  L  S  P  T  S  V  H  T  T  D  Q  F  L  T  S  Q  L  A  T  C  G  V  H  M  L  C  Q  S  L  K  :  I  G  A  L  W  L  I  L  L  A  I  V  S  *  T  L  G  E  T  T  N  L  L  K  N  L  S  S  G  S  K  M  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="C04HBa0094K06.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="40719" stop="41016"/>
                    <exon start="42830" stop="42978"/>
                    <exon start="43917" stop="44159"/>
                    <exon start="44997" stop="45108"/>
                    <exon start="46137" stop="46307"/>
                    <exon start="47489" stop="47552"/>
                    <exon start="48383" stop="48440"/>
                    <exon start="48531" stop="48708"/>
                    <exon start="49018" stop="49115"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>1371</number_coding_nucleotides>
                  <number_encoded_amino_acids>457</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>NFRRVGVQFGEFKWFWSSSFEMDSSGLNGNQSTRDSEVPNNADERCDATFSDELDGWRTSSSSLKDIRSSDEHTDECLTPEMKYESTHRSSSPPPQARRGLEHCITAPVTIGGGLFPEGQDMAFSRSLTERRVSPRHNVILDRLSERGKQKLIAELVKIQGDGTVEVDLTKSTPETSELLELRSVEEPTLTVDRIITDFNKSVPKLKIVVLIVGTRGDVQPFLAMAKRLQAFGHHVRLATHSNFRDFVKSGGIDYYPLGGDPRVLAGYMARNKGLIPSGPGEISVQRKQLKAIIESLLPACTEPDIETGEPFRAQAIIANPPAYGHAHVAEALGVPLHIFFTMPWTPTSEFPHPMARVPQPAAYWLSYILVDLLVWWGIRGYINDFRKKKLNLPPIAYFSTYHGSISHFPTGYMWSPHVVPKPKDWGSLVDIVGYCFLNLGRNYQPPEEFIKWIQNG</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="54040" PGL_stop="57145"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="54040" e_stop="54307"/>
            <exon e_start="56350" e_stop="56744"/>
            <exon e_start="56980" e_stop="57145"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="1.000" acc_prob="0.981" e_score="0.922"/>
          <exon-intron don_prob="0.992" acc_prob="0.978" e_score="0.995"/>
          <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="0.922">
            <gDNA_exon_boundary e_start="54040" e_stop="54307" e_length="268"/>
          </exon>
          <intron i_serial="1" don_prob="1.000" acc_prob="0.981">
            <gDNA_intron_boundary i_start="54308" i_stop="56349" i_length="2042"/>
          </intron>
          <exon e_serial="2" e_score="0.995">
            <gDNA_exon_boundary e_start="56350" e_stop="56744" e_length="395"/>
          </exon>
          <intron i_serial="2" don_prob="0.992" acc_prob="0.978">
            <gDNA_intron_boundary i_start="56745" i_stop="56979" i_length="235"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="56980" e_stop="57145" e_length="166"/>
          </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="54040" stop="54307"/>
              <exon start="56350" stop="56744"/>
              <exon start="56980" stop="57145"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M6801" 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>GTGGTTTGGGATTTGCTGCAATTGCTTACATCGGAGTAGACTATCTCCGGTTTATTTCTCCGGCATGGCATGACCGGTTACAGCCGACGCTATGGACCATATTGGCGATCGCTGCTATTATTCGGGTTCCATTTTACAAACACTGGTCATCAGAGCTCCGTTCAGCTATACCATTTATTTTCGCTATGCTTTTTTTGCTCTCTGCTCTTCTTTTTGAAGCCATTTCTGTCCGCTCTGTCACTGCCGTTCTTGGTCTTGAATGGAACAG : TGATGCATCACCTCTTCCTGATGTTGGTCAGTGGTTGGTGCTGTCATTGAATGAGAAACTACCTCAAACAGTGGTTAATATATTGAGAGCTCGTATAATTGGATTACATCATTTTCTGATGCTGTTTATCATGCTTGCTTTCTCTGTACTCTTTGAATCGGTTGAAGCTCCTGGTCTTGGGCTTGGTGCAAGATTCATGTTCACAATGGGAATCGGAAGGCTACTTCGGGCCATAACTTTTATCTCCACAATTCTACCATCTGCTCGACCATGGTGTGCATCTGCTAGATTCCTTGTTCCTCAGCACCCTCATCCTTGGGCTCAGAAATATTATGTACCATATGCCACAGATTCAAATGCCATACGGAACGTCATAAACTGGGACACAGCATATG : CTGATCCTGGGGAATACGATCCGGAGTTTCGACCAGATTGGGGTTCAATGAGCTTTCTGATTGATTTCCTTCGGCCTACAGCTCCTGAGGGATCATCTGCTTGGTATCATCTGCTAAAGAAAGCGTCAGGGGGTTGCAATGACCTTATATATAGTGGCCACATGCT</gDNA_template>
            <first_frame> V  V  W  D  L  L  Q  L  L  T  S  E  *  T  I  S  G  L  F  L  R  H  G  M  T  G  Y  S  R  R  Y  G  P  Y  W  R  S  L  L  L  F  G  F  H  F  T  N  T  G  H  Q  S  S  V  Q  L  Y  H  L  F  S  L  C  F  F  C  S  L  L  F  F  L  K  P  F  L  S  A  L  S  L  P  F  L  V  L  N  G  T   : V  M  H  H  L  F  L  M  L  V  S  G  W  C  C  H  *  M  R  N  Y  L  K  Q  W  L  I  Y  *  E  L  V  *  L  D  Y  I  I  F  *  C  C  L  S  C  L  L  S  L  Y  S  L  N  R  L  K  L  L  V  L  G  L  V  Q  D  S  C  S  Q  W  E  S  E  G  Y  F  G  P  *  L  L  S  P  Q  F  Y  H  L  L  D  H  G  V  H  L  L  D  S  L  F  L  S  T  L  I  L  G  L  R  N  I  M  Y  H  M  P  Q  I  Q  M  P  Y  G  T  S  *  T  G  T  Q  H  M  :  L  I  L  G  N  T  I  R  S  F  D  Q  I  G  V  Q  *  A  F  *  L  I  S  F  G  L  Q  L  L  R  D  H  L  L  G  I  I  C  *  R  K  R  Q  G  V  A  M  T  L  Y  I  V  A  T  C  </first_frame>
            <second_frame>  W  F  G  I  C  C  N  C  L  H  R  S  R  L  S  P  V  Y  F  S  G  M  A  *  P  V  T  A  D  A  M  D  H  I  G  D  R  C  Y  Y  S  G  S  I  L  Q  T  L  V  I  R  A  P  F  S  Y  T  I  Y  F  R  Y  A  F  F  A  L  C  S  S  F  *  S  H  F  C  P  L  C  H  C  R  S  W  S  *  M  E  Q  :  *  C  I  T  S  S  *  C  W  S  V  V  G  A  V  I  E  *  E  T  T  S  N  S  G  *  Y  I  E  S  S  Y  N  W  I  T  S  F  S  D  A  V  Y  H  A  C  F  L  C  T  L  *  I  G  *  S  S  W  S  W  A  W  C  K  I  H  V  H  N  G  N  R  K  A  T  S  G  H  N  F  Y  L  H  N  S  T  I  C  S  T  M  V  C  I  C  *  I  P  C  S  S  A  P  S  S  L  G  S  E  I  L  C  T  I  C  H  R  F  K  C  H  T  E  R  H  K  L  G  H  S  I  C :   *  S  W  G  I  R  S  G  V  S  T  R  L  G  F  N  E  L  S  D  *  F  P  S  A  Y  S  S  *  G  I  I  C  L  V  S  S  A  K  E  S  V  R  G  L  Q  *  P  Y  I  *  W  P  H  A </second_frame>
            <third_frame>   G  L  G  F  A  A  I  A  Y  I  G  V  D  Y  L  R  F  I  S  P  A  W  H  D  R  L  Q  P  T  L  W  T  I  L  A  I  A  A  I  I  R  V  P  F  Y  K  H  W  S  S  E  L  R  S  A  I  P  F  I  F  A  M  L  F  L  L  S  A  L  L  F  E  A  I  S  V  R  S  V  T  A  V  L  G  L  E  W  N  S :   D  A  S  P  L  P  D  V  G  Q  W  L  V  L  S  L  N  E  K  L  P  Q  T  V  V  N  I  L  R  A  R  I  I  G  L  H  H  F  L  M  L  F  I  M  L  A  F  S  V  L  F  E  S  V  E  A  P  G  L  G  L  G  A  R  F  M  F  T  M  G  I  G  R  L  L  R  A  I  T  F  I  S  T  I  L  P  S  A  R  P  W  C  A  S  A  R  F  L  V  P  Q  H  P  H  P  W  A  Q  K  Y  Y  V  P  Y  A  T  D  S  N  A  I  R  N  V  I  N  W  D  T  A  Y   : A  D  P  G  E  Y  D  P  E  F  R  P  D  W  G  S  M  S  F  L  I  D  F  L  R  P  T  A  P  E  G  S  S  A  W  Y  H  L  L  K  K  A  S  G  G  C  N  D  L  I  Y  S  G  H  M   </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="C04HBa0094K06.1" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="54042" stop="54307"/>
                    <exon start="56350" stop="56744"/>
                    <exon start="56980" stop="57143"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>825</number_coding_nucleotides>
                  <number_encoded_amino_acids>275</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>GLGFAAIAYIGVDYLRFISPAWHDRLQPTLWTILAIAAIIRVPFYKHWSSELRSAIPFIFAMLFLLSALLFEAISVRSVTAVLGLEWNSDASPLPDVGQWLVLSLNEKLPQTVVNILRARIIGLHHFLMLFIMLAFSVLFESVEAPGLGLGARFMFTMGIGRLLRAITFISTILPSARPWCASARFLVPQHPHPWAQKYYVPYATDSNAIRNVINWDTAYADPGEYDPEFRPDWGSMSFLIDFLRPTAPEGSSAWYHLLKKASGGCNDLIYSGHM</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="104799" PGL_stop="104975"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="104799" e_stop="104975"/>
          </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="104799" e_stop="104975" e_length="177"/>
          </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="104799" stop="104975"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M608-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="3" AGS_serial="1" gDNA_strand="+"/>
          <translation>
            <gDNA_template>TCTTGTCATAACATATAGTATTTGTTGTGTGCTGATCAATCTATCCTTTAATTAATACGTACTCAGCATGCACCTAAATAATTTGTATGTGTGTTACACTACTCTTGTCTTTGATGTTGTGCACCTACTTTAATTTGCATGAGTGTGAATAATATTACGTATATTGTTTTTCTTAAA</gDNA_template>
            <first_frame> S  C  H  N  I  *  Y  L  L  C  A  D  Q  S  I  L  *  L  I  R  T  Q  H  A  P  K  *  F  V  C  V  L  H  Y  S  C  L  *  C  C  A  P  T  L  I  C  M  S  V  N  N  I  T  Y  I  V  F  L  K </first_frame>
            <second_frame>  L  V  I  T  Y  S  I  C  C  V  L  I  N  L  S  F  N  *  Y  V  L  S  M  H  L  N  N  L  Y  V  C  Y  T  T  L  V  F  D  V  V  H  L  L  *  F  A  *  V  *  I  I  L  R  I  L  F  F  L   </second_frame>
            <third_frame>   L  S  *  H  I  V  F  V  V  C  *  S  I  Y  P  L  I  N  T  Y  S  A  C  T  *  I  I  C  M  C  V  T  L  L  L  S  L  M  L  C  T  Y  F  N  L  H  E  C  E  *  Y  Y  V  Y  C  F  S  *  </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <none gDNA_id="C04HBa0094K06.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 17 chains have been computed
$ 
$ memory statistics:
$ 10904 bytes spliced alignments in total
$ 5 spliced alignments have been stored
$ 2180 bytes was the average size of a spliced alignment
$ 8232 bytes predicted gene locations in total
$ 3 predicted gene locations have been stored
$ 2744 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 17 backtrace matrices have been allocated
$ 
$ date finished: 2008-04-10 05:52:23
-->
