<?xml version="1.0" encoding="ISO-8859-1"?>
<GTH_output xmlns="http://www.genomethreader.org/GTH_output/" GTH_XML_version="1.1">
  <header xmlns="http://www.genomethreader.org/GTH_output/header/">
    <source program="GenomeThreader" version="0.9.54" build_date="2006-07-28 11:55:15" run_date="2009-01-16 00:05:42"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04SLm0127L14-bd3tp/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C04SLm0127L14-bd3tp/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" type="ESTcDNA"/>
    </reference_files>
    <splice_site_parameters parameter_type="Bayesian" species="arabidopsis"/>
    <parameters>
      <parameter name="bssmfile" value="arabidopsis"/>
      <parameter name="scorematrixfile" value="BLOSUM62"/>
      <parameter name="searchmode" value="forward=True,reverse=True)"/>
      <parameter name="translationtable" value="1"/>
      <parameter name="frompos" value="0"/>
      <parameter name="topos" value="0"/>
      <parameter name="width" value="0"/>
      <parameter name="verbose" value="False"/>
      <parameter name="skipalignmentout" value="False"/>
      <parameter name="showintronmaxlen" value="120"/>
      <parameter name="minorflen" value="64"/>
      <parameter name="showseqnums" value="False"/>
      <parameter name="gs2out" value="False"/>
      <parameter name="maskpolyatails" value="False"/>
      <parameter name="noautoindex" value="False"/>
      <parameter name="minmatchlen" value="20"/>
      <parameter name="seedlength" value="16"/>
      <parameter name="exdrop" value="2"/>
      <parameter name="online" value="False"/>
      <parameter name="inverse" value="False"/>
      <parameter name="exact" value="False"/>
      <parameter name="chainwf" value="0.500000"/>
      <parameter name="gcmaxgapwidth" value="1000000"/>
      <parameter name="gcmincoverage" value="50"/>
      <parameter name="introncutout" value="False"/>
      <parameter name="autointroncutout" value="0"/>
      <parameter name="icinitialdelta" value="50"/>
      <parameter name="iciterations" value="2"/>
      <parameter name="icdeltaincrease" value="50"/>
      <parameter name="icminremintronlen" value="10"/>
      <parameter name="nou12intronmodel" value="False"/>
      <parameter name="u12donorprob" value="0.990000"/>
      <parameter name="u12donorprob1mism" value="0.900000"/>
      <parameter name="probies" value="0.500000"/>
      <parameter name="probdelgen" value="0.030000"/>
      <parameter name="identityweight" value="2.000000"/>
      <parameter name="mismatchweight" value="-2.000000"/>
      <parameter name="undetcharweight" value="0.000000"/>
      <parameter name="deletionweight" value="-4.000000"/>
      <parameter name="dpminexonlen" value="5"/>
      <parameter name="dpminintronlen" value="50"/>
      <parameter name="shortexonpenal" value="100"/>
      <parameter name="shortintronpenal" value="100"/>
      <parameter name="wzerotransition" value="80"/>
      <parameter name="wdecreasedoutput" value="80"/>
      <parameter name="leadcutoffsmode" value="RELAXED"/>
      <parameter name="termcutoffsmode" value="STRICT"/>
      <parameter name="cutoffsminexonlen" value="5"/>
      <parameter name="scoreminexonlen" value="50"/>
      <parameter name="minaveragessp" value="0.500000"/>
      <parameter name="minalignmentscore" value="0.900000"/>
      <parameter name="maxalignmentscore" value="1.000000"/>
      <parameter name="mincoverage" value="0.900000"/>
      <parameter name="maxcoverage" value="100.000000"/>
      <parameter name="intermediate" value="False"/>
      <parameter name="sortags" value="False"/>
      <parameter name="sortagswf" value="1.000000"/>
      <parameter name="first" value="0"/>
      <parameter name="exondistri" value="False"/>
      <parameter name="introndistri" value="False"/>
      <parameter name="refseqcovdistri" value="False"/>
    </parameters>
    <overall_reference_type>ESTcDNA</overall_reference_type>
  </header>
  <alignment_module>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C04SLm0127L14-bd3tp/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M3054" ref_strand="+" ref_description="SGN-M3054 cLPT-5-B19 [est_clones]">
      <seq>cttctcataattaaaaataattacctcgccttcatcagatctggtcgttggttgagccgcctttgcttgtgtgcatctcgattgatttatggggttgcttattgtctagctcacaagtacaggtttggagttgaaatttgaaacatagcgtatcatattttcaagcctttgatgactcagactgagacctcattttagtaactttaacgagaggttttgtttgacttattcacgtgaaatggcagagcttttcggatatacagcatgcagacaattattgcaaatgttcatttcaattatattcttccatgtttccgagtacattctggcacttgtctttcatgggaagtcgaatgtatcttttaagtcgcttttgataagcaaacattatgtactagcaatgttttgctccttgatagaataccttattgaaatctatttctttcccggcttaaaggaatattggtggataagtaattttggcctcgcaatggttgttctcggagaaatcataaagaagttggcaattgtgacagc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0127L14-bd3tp/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04SLm0127L14.1" temp_strand="-" temp_description="C04SLm0127L14.1  CU856252.3 htgs_phase:3 submitted_to_sgn_as:C04SLm0127L14 sequenced_by:sanger upload_account_name:uk">
        <position start="12738" stop="10550"/>
      </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="12439" g_stop="12392" g_length="48"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="49" r_length="49" r_score="0.896"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="12391" i_stop="12241" i_length="151">
            <donor d_prob="0.778" d_score="0.90"/>
            <acceptor a_prob="0.993" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="12240" g_stop="12168" g_length="73"/>
          <reference_exon_boundary r_type="cDNA" r_start="50" r_stop="122" r_length="73" r_score="0.945"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="12167" i_stop="11265" i_length="903">
            <donor d_prob="0.000" d_score="0.92"/>
            <acceptor a_prob="0.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="11264" g_stop="10850" g_length="415"/>
          <reference_exon_boundary r_type="cDNA" r_start="123" r_stop="537" r_length="415" r_score="0.990"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04SLm0127L14.1" gen_strand="-" ref_id="SGN-M3054" ref_strand="+">
        <total_alignment_score>0.984</total_alignment_score>
        <cumulative_length_of_scored_exons>536</cumulative_length_of_scored_exons>
        <coverage percentage="0.998" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0127L14.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M3054" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="12439" e_stop="12392"/>
          <exon e_start="12240" e_stop="12168"/>
          <exon e_start="11264" e_stop="10850"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTTCTCTTAATT-AAAATAATTACCTCGCCTTCATCAGATCTGGTTGTTGTATGTAAATCTCCTTAATCTGTTCTTCGTTTAATCTTGCCCTCTTGGTTGAATTCATTTTATTTTGTGCATCTTCGGTATGTTTTCGTATTTGAATGAACTGAATTTGTTGTTTTCTGTTTTTGTTTCTGTTCTTCTTTTGTGGATTTAGGGTTGAGCCGCCTTTGCTTGTGTGCATCTCGATTAATTTATGGGGTAGCTTATCGTCTAGCTCACAGGTACAGGTTCAGTTTAGTGTTGCTGCTGATACTCGAACTGGGGATTTTTCAGTTTTTTTTTCAACTCACTAGGTCATTCCCTTGGGCGGGGTGAATTTTATAGGGCAATTTATGGTGTTCGTGAACCTATGGTATATCTATCAACTTAGATATTTTGGGTAGATACTCCGTTGAATTAATCTAATATTATCTGTTGACATTGATGCTACAAAAAAAGAAGCTTAAATGGTGCACTTGATGCTAAAAAAAAGTTCGTTGTTTTAATGGTGCAGCGATGTTATAAAAATTCTATATCTTCATCTGCCATTGTGGACTCATGATAGAACTCAATTTTCGAGTCATTTACTAAATGATACTGATGATATCTGTGCTGTAGATGTTGATTTCTAGGATAACTTTTTTATTAAGTTGCTTTTATCTCAATTAGTTCGTTAAAGAATGTGATAGTTAAATAGTTAATAACTTGTTATTTTTCATGATTTAGTGATGGGAGTGTTAAATCACAAGTTATCAAGTGTAGTGAAAATGTGCCTGAATCCGGTTAGTTTGGATAGGTGTTATGTTGATTGATTGATTTTTACTTTATTAGAGAGTCCAATATCTAAAAGCTCTGTATTGACCCCAAAATCCCATTGATAATGTTTGAAGAAGAACCGTGAGAGCTAAGGGATCACTATGATATCTAAGCTTACGTAGAGTAAGAGATTGTATAAACTGATATTGGAGACGAACTGAAAATGATCTTGTGTATAATGCACGTATAGAATCTAAGTTCTGTTATGTGATGTCTTTGTTCCTGAATGGTGCTTGCATAAATTTGCAGGGAAATGTCATTCTTAAAGGATAGTTTCATTGATTCTGAAGCCCATTTTGTGGTGCTAATTGTACAGAGCTCATCAACATTTTCAGGTTTGGAGTTGAAATTTGAAACATAGCGTATCATATTTTCAAGCCTTTGATGACTCAGACTGAGACCTCATTTTAGTAACTTTAACGAGAGGTTTTGTTTGACTTATTCGCGTGAAATGGCAGAGCTTTTTGGATATACAGCATGCAGACAATTATTGCAAATGTTCATTTCAATTATATTCTTCCATGTTTCCGAGTACATTCTGGCACTTGTCTTTCATGGGAAGTCGAATGTATCTTTTAAGTCGCTTTTGATAAGCAAACATTATGTACTAGCAATGTTTTGCTCCTTGATAGAATACCTTATTGAAATCTATTTCTTTCCCGGCTTAAAGGAATATTGGTGGATAAGTAATTTTGGCCTCGCAATGGTTGTCCTCGGAGAAATCATAAGGAAGTTGGCAATTGTGACAGC</genome_strand>
        <mrna_strand>CTTCTCATAATTAAAAATAATTACCTCGCCTTCATCAGATCTGGTCGTT.......................................................................................................................................................GGTTGAGCCGCCTTTGCTTGTGTGCATCTCGATTGATTTATGGGGTTGCTTATTGTCTAGCTCACAAGTACAG.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTTGGAGTTGAAATTTGAAACATAGCGTATCATATTTTCAAGCCTTTGATGACTCAGACTGAGACCTCATTTTAGTAACTTTAACGAGAGGTTTTGTTTGACTTATTCACGTGAAATGGCAGAGCTTTTCGGATATACAGCATGCAGACAATTATTGCAAATGTTCATTTCAATTATATTCTTCCATGTTTCCGAGTACATTCTGGCACTTGTCTTTCATGGGAAGTCGAATGTATCTTTTAAGTCGCTTTTGATAAGCAAACATTATGTACTAGCAATGTTTTGCTCCTTGATAGAATACCTTATTGAAATCTATTTCTTTCCCGGCTTAAAGGAATATTGGTGGATAAGTAATTTTGGCCTCGCAATGGTTGTTCTCGGAGAAATCATAAAGAAGTTGGCAATTGTGACAGC</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C04SLm0127L14-bd3tp/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M7768-2" ref_strand="+" ref_description="SGN-M7768-2 C2_At3g17040-2 [cosii_markers]">
      <seq>gagcacgatatttgttcaagcaggcaacaaggtgtaaccgaaaaagttgtgctagttggctggcatgggctcaactagaggctcagttagagaataaccgtactgctaggcaactgtttgagaaagcagttcaagccagtccgaaaaataggttcgcgtggcatgtatggggagtttttgaagctaatctgggaaatattgaccaaggaaggaaacttctgacaatagggcacatgatgaatcctagagatcctgtcctcctccagtcacttggtttgatagaatacaagaactccagtgcaaaccttgcacgagttctattccgaagggcatctcaactggatccaaggcaccaaccagtttggattgcttggggttggatggagtggaaagaaggaaacatttccacagctcgagaactataccagaaagctctatcgatcaactcaactactgaaagtgcagcacgctgtcttcaggcttggggtgttttggagcaaagagctggaaatctatcagctgctcgaagattatttagatcgtctctgaacataaactctcagagctatataacatggatgacatgggcaaatttggaggaagatcaaggtaactctatccgtgcagaggaaattcgtaacctctactttcaacagcgtactgaagttgttgatgatgagtcgtggattatgggcttcttagacgtcattgatccagcgattgatagcataaagaggctcttgaatttagatcaaaattcttattacaaggtaaaagagtctacttctaatactactgctggagacgacgttgaggggagcacagaagaatcagcttccccctcctcggctaacgtcaatgacaataacatagatacaggaagtggctttgatttagatgattttatccgtgtaatgctgtctttggacccttcaaaactggaagttcagcttacaacatctctgaaggaccctc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0127L14-bd3tp/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04SLm0127L14.1" temp_strand="+" temp_description="C04SLm0127L14.1  CU856252.3 htgs_phase:3 submitted_to_sgn_as:C04SLm0127L14 sequenced_by:sanger upload_account_name:uk">
        <position start="20083" stop="22739"/>
      </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="20383" g_stop="20444" g_length="62"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="62" r_length="62" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="20445" i_stop="20548" i_length="104">
            <donor d_prob="0.979" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="20549" g_stop="20608" g_length="60"/>
          <reference_exon_boundary r_type="cDNA" r_start="63" r_stop="122" r_length="60" r_score="0.950"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="20609" i_stop="21047" i_length="439">
            <donor d_prob="0.999" d_score="0.94"/>
            <acceptor a_prob="0.880" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="21048" g_stop="21293" g_length="246"/>
          <reference_exon_boundary r_type="cDNA" r_start="123" r_stop="368" r_length="246" r_score="0.955"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="21294" i_stop="21526" i_length="233">
            <donor d_prob="0.986" d_score="0.92"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="21527" g_stop="21637" g_length="111"/>
          <reference_exon_boundary r_type="cDNA" r_start="369" r_stop="479" r_length="111" r_score="0.955"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="21638" i_stop="21835" i_length="198">
            <donor d_prob="0.998" d_score="0.90"/>
            <acceptor a_prob="0.969" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="21836" g_stop="22012" g_length="177"/>
          <reference_exon_boundary r_type="cDNA" r_start="480" r_stop="656" r_length="177" r_score="0.989"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="22013" i_stop="22120" i_length="108">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.850" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="22121" g_stop="22439" g_length="319"/>
          <reference_exon_boundary r_type="cDNA" r_start="657" r_stop="975" r_length="319" r_score="0.962"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04SLm0127L14.1" gen_strand="+" ref_id="SGN-M7768-2" ref_strand="+">
        <total_alignment_score>0.966</total_alignment_score>
        <cumulative_length_of_scored_exons>975</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0127L14.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M7768-2" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="20383" e_stop="20444"/>
          <exon e_start="20549" e_stop="20608"/>
          <exon e_start="21048" e_stop="21293"/>
          <exon e_start="21527" e_stop="21637"/>
          <exon e_start="21836" e_stop="22012"/>
          <exon e_start="22121" e_stop="22439"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GAGCACGATATTTGTTCAAGCAGGCAACAAGGTGTAACCGAAAAAGTTGTGCTAGTTGGCTGGTAAGAGTCATTCAAAAACTTTAATCTGTCTCAGCTCTTTTCGAGTGGTTTATGCACATGTCATTTCTGGATTCCTTATAGTGGTTCTGTATTATCTTTTGTAGGCATGGGCTCAACTAGAGGCTCAGTTAGAGAATAACCGTTCCGCTAGGCAGCTGTTTGAGGTTTGTATTTTCTGAAGTTGATCCTTTCCTATCATCATTGAACATTTCCTTTTGGCATATTACATGAGCAATCACTCAAAGTTGGAGTGCTTAACTCAAATTTGGCTCGGCTAGGAAGTAAACACTCTACCTTAGAAGAGTGCACATCTGGTCTCAACTGACAACTAAACACTCCAACTCGTCCAATATTCATTTGGCACATAAATTTTGGAGGTGTCTAGATGATCATTTTGTAAGTTCGACTATTCAACTGACACAATGAAGACTAGTTGAGGTGTCTAGATGTGCACTTCCCGATTTTGAGTGTTTACCTGCTAGTTGAGGCCAAGTTTTGAGTGTTTGTTCATGTATTATGAGTTTCCTTTTAATTTGATGCCTCTGTCACTTTATTTTCAATTTTGTTTATAATTCTTGTACTTGATACTCCTAAACAAAGCAGAAAGCAGTTCAAGCCAGTCCGAAAAATAGGTTCGCGTGGCATGTATGGGGAGTTTTTGAAGCTAATCTAGGAAATATTGATCAAGGAAGGAAACTTCTAACAATAGGGCACATGGTGAATCCTAGAGATCCTGTTCTTCTCCAATCACTTGGTTTGATAGAATACAAGAACTCCAGTGCAAACCTTGCACGAGTTCTATTCCGAAGAGCGTCTCAACTAGATCCAAGGCATCAACCAGTTTGGATTGTAAGACCTTTCGTTTCAATAGTAAATGCTATAGAATATCGAATAAACTCATTTACTAAAAGACTCACTCGAATCGTTCAAGCTCTTGACATGGTTAATAGATGATGAAAGACTAAAAGAACTGAATACATTTGATGAACCTCATCACTGCCTTTTCCATATGTTCTCAACAGTCTTAAGATAATAAAACTTGTAACTTTAACAACTGAATACCTAACTTGGTACTGATTTAGGCTTGGGGTTGGATGGAGTGGAAAGAAGGAAACATTTCCACAGCTCGAGAACTATACCAGAAGGCTCTATCGATCAACTCAACAACTGAAAGTGCTGCGCGTTGTCTTCAGGTAATGCTCATTTCTAATAGATAGAGTAAGTTTCTAGTTTGCTTTTCGTAAGACATTTTGATGCAAATTGTGGAGGTTAGTCCAAACTCGTAACTCTGGCTTGCAGCTTAGTCTGTCCTTTGTTCCAACAAGTAGTATATTCTGGTTATATGTAATCTTCTCCACATAGGAAATGTACTAAAGAGTTGTTTACTATAGGCTTGGGGTGTTTTGGAGCAAAGAGCTGGAAATCTATCAGCTGCTCGAAGACTATTTAGATCGTCTCTGAACATAAACTCTCAGAGCTATATAACATGGATGACATGGGCAAATTTAGAGGAAGATCAAGGTAACTCTATCCGTGCAGAGGAAATTCGTAACCTCTACTTTCAACAGGTATATGAGTCATTTCCTTCTATGACCACATTTCAAGCATTGTTATACATCAGTGTTCCATATAGCTGCTCTTCTCCCTAACATCACTAGACGTTTTTGTTGACACAGCGTACTGAAGTTGTTGATGATGAGTCGTGGATTATGGGCTTCTTAGACGTCATTGACCCAGCGATTGACAGCATAAAGAGGCTCTTGAATCTAGATCAGAACTCTTACTACAAGGTAAAAGAGTCTGCTTCTAATACTACTGCTGGAGACGACGTTGAGGGGAGCACAGAAGAATCAGCTTCTCCCTCCTCGGCTAACGTCAATGACAATAACATAGATACAGGAAGTGGCTTTGATTTAGATGATTTTATCAGTGTAATGCTGTCTTTAGACCCTTCAAAGCTGGAAGTTCAGCTTACAACATCTCTTAAGGACCCTC</genome_strand>
        <mrna_strand>GAGCACGATATTTGTTCAAGCAGGCAACAAGGTGTAACCGAAAAAGTTGTGCTAGTTGGCTG........................................................................................................GCATGGGCTCAACTAGAGGCTCAGTTAGAGAATAACCGTACTGCTAGGCAACTGTTTGAG.......................................................................................................................................................................................................................................................................................................................................................................................................................................................AAAGCAGTTCAAGCCAGTCCGAAAAATAGGTTCGCGTGGCATGTATGGGGAGTTTTTGAAGCTAATCTGGGAAATATTGACCAAGGAAGGAAACTTCTGACAATAGGGCACATGATGAATCCTAGAGATCCTGTCCTCCTCCAGTCACTTGGTTTGATAGAATACAAGAACTCCAGTGCAAACCTTGCACGAGTTCTATTCCGAAGGGCATCTCAACTGGATCCAAGGCACCAACCAGTTTGGATT.........................................................................................................................................................................................................................................GCTTGGGGTTGGATGGAGTGGAAAGAAGGAAACATTTCCACAGCTCGAGAACTATACCAGAAAGCTCTATCGATCAACTCAACTACTGAAAGTGCAGCACGCTGTCTTCAG......................................................................................................................................................................................................GCTTGGGGTGTTTTGGAGCAAAGAGCTGGAAATCTATCAGCTGCTCGAAGATTATTTAGATCGTCTCTGAACATAAACTCTCAGAGCTATATAACATGGATGACATGGGCAAATTTGGAGGAAGATCAAGGTAACTCTATCCGTGCAGAGGAAATTCGTAACCTCTACTTTCAACAG............................................................................................................CGTACTGAAGTTGTTGATGATGAGTCGTGGATTATGGGCTTCTTAGACGTCATTGATCCAGCGATTGATAGCATAAAGAGGCTCTTGAATTTAGATCAAAATTCTTATTACAAGGTAAAAGAGTCTACTTCTAATACTACTGCTGGAGACGACGTTGAGGGGAGCACAGAAGAATCAGCTTCCCCCTCCTCGGCTAACGTCAATGACAATAACATAGATACAGGAAGTGGCTTTGATTTAGATGATTTTATCCGTGTAATGCTGTCTTTGGACCCTTCAAAACTGGAAGTTCAGCTTACAACATCTCTGAAGGACCCTC</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C04SLm0127L14-bd3tp/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M7768" ref_strand="+" ref_description="SGN-M7768 C2_At3g17040 [cosii_markers]">
      <seq>ttgtgctagttggctggcatgggctcaactagaggctcagttagagaatgaccgttccgctaggcagctgtttgagaaagcagttcaagccagtccgaaaaataggttcgcgtggcatgtatggggagtttttgaagctaatctaggaaatattgatcaaggaaggaaacttctaacaatagggcacatggtgaatcctagagatcctgttcttctccaatcacttggtttgatagaatacaagaactccagtgcaaaccttgcacgagttctattccgaagagcgtctcaactagatccaaggcatcaaccagtttggattgcttggggttggatggagtggaaagaaggaaacatttccacagctcgagaactataccagaaggctctatcgatcaactcaacaactgaaagtgctgcgcgttgtcttcaggcttggggtgttttggagcaaagagctggaaatctatcagctgctcgaagactatttagatcgtctctgaacataaactctcagagctatataacatggatgacatgggcaaatttagaggaagatcaaggtaactctatccgtgcagaggaaattcgtaacctctactttcaacagcgtactgaagttgttgatgatgagtcgtggattatgggcttcttagacgtcattgacccagcgattgacagcataaagaggctcttgaatctagatcagaactcttactacaaggtaaaagagtctgcttctaatactactgctggagacgacgttgaggggagcacagaagaatcagcttctccctcctcggctaacgtcaatgacaataacatagatacaggaagtggctttgatttagatgattttatcagtgtaatgctgtctttagacccttcaaagctggaagttcagcttacaacatctcttaaggaccctccgaaaatcgccagaactactaatggggtgtggcgaccatcgacaaagactagtagaacatcaacaacactttgattttacaacaacaacgacatacttaatgtaacctcactagtgtggtctgggagggcggagaacgaaaggtgatgtgttgcagccttacctttacctcgtgaaggtagagagactgtttctgactcagctcaatataaagtttattgttctttagtgggaattgcaacattcattaatgttgtcaaatgaagaagtcttggtccacattttgtaaattacttaggaatattgagaagaattgtataaatttgattgtaagaagaaggcaaatctacacatataatcccccccacattgtataaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0127L14-bd3tp/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04SLm0127L14.1" temp_strand="+" temp_description="C04SLm0127L14.1  CU856252.3 htgs_phase:3 submitted_to_sgn_as:C04SLm0127L14 sequenced_by:sanger upload_account_name:uk">
        <position start="20234" stop="23097"/>
      </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="20429" g_stop="20444" g_length="16"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="16" r_length="16" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="20445" i_stop="20548" i_length="104">
            <donor d_prob="0.979" d_score="0.00"/>
            <acceptor a_prob="1.000" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="20549" g_stop="20608" g_length="60"/>
          <reference_exon_boundary r_type="cDNA" r_start="17" r_stop="76" r_length="60" r_score="0.983"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="20609" i_stop="21047" i_length="439">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.880" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="21048" g_stop="21293" g_length="246"/>
          <reference_exon_boundary r_type="cDNA" r_start="77" r_stop="322" r_length="246" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="21294" i_stop="21526" i_length="233">
            <donor d_prob="0.986" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="21527" g_stop="21637" g_length="111"/>
          <reference_exon_boundary r_type="cDNA" r_start="323" r_stop="433" r_length="111" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="21638" i_stop="21835" i_length="198">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="0.969" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="21836" g_stop="22012" g_length="177"/>
          <reference_exon_boundary r_type="cDNA" r_start="434" r_stop="610" r_length="177" r_score="1.000"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="22013" i_stop="22120" i_length="108">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.850" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="22121" g_stop="22813" g_length="693"/>
          <reference_exon_boundary r_type="cDNA" r_start="611" r_stop="1304" r_length="694" r_score="0.974"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04SLm0127L14.1" gen_strand="+" ref_id="SGN-M7768" ref_strand="+">
        <total_alignment_score>0.985</total_alignment_score>
        <cumulative_length_of_scored_exons>1303</cumulative_length_of_scored_exons>
        <coverage percentage="0.993" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0127L14.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M7768" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="20429" e_stop="20444"/>
          <exon e_start="20549" e_stop="20608"/>
          <exon e_start="21048" e_stop="21293"/>
          <exon e_start="21527" e_stop="21637"/>
          <exon e_start="21836" e_stop="22012"/>
          <exon e_start="22121" e_stop="22813"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTGTGCTAGTTGGCTGGTAAGAGTCATTCAAAAACTTTAATCTGTCTCAGCTCTTTTCGAGTGGTTTATGCACATGTCATTTCTGGATTCCTTATAGTGGTTCTGTATTATCTTTTGTAGGCATGGGCTCAACTAGAGGCTCAGTTAGAGAATAACCGTTCCGCTAGGCAGCTGTTTGAGGTTTGTATTTTCTGAAGTTGATCCTTTCCTATCATCATTGAACATTTCCTTTTGGCATATTACATGAGCAATCACTCAAAGTTGGAGTGCTTAACTCAAATTTGGCTCGGCTAGGAAGTAAACACTCTACCTTAGAAGAGTGCACATCTGGTCTCAACTGACAACTAAACACTCCAACTCGTCCAATATTCATTTGGCACATAAATTTTGGAGGTGTCTAGATGATCATTTTGTAAGTTCGACTATTCAACTGACACAATGAAGACTAGTTGAGGTGTCTAGATGTGCACTTCCCGATTTTGAGTGTTTACCTGCTAGTTGAGGCCAAGTTTTGAGTGTTTGTTCATGTATTATGAGTTTCCTTTTAATTTGATGCCTCTGTCACTTTATTTTCAATTTTGTTTATAATTCTTGTACTTGATACTCCTAAACAAAGCAGAAAGCAGTTCAAGCCAGTCCGAAAAATAGGTTCGCGTGGCATGTATGGGGAGTTTTTGAAGCTAATCTAGGAAATATTGATCAAGGAAGGAAACTTCTAACAATAGGGCACATGGTGAATCCTAGAGATCCTGTTCTTCTCCAATCACTTGGTTTGATAGAATACAAGAACTCCAGTGCAAACCTTGCACGAGTTCTATTCCGAAGAGCGTCTCAACTAGATCCAAGGCATCAACCAGTTTGGATTGTAAGACCTTTCGTTTCAATAGTAAATGCTATAGAATATCGAATAAACTCATTTACTAAAAGACTCACTCGAATCGTTCAAGCTCTTGACATGGTTAATAGATGATGAAAGACTAAAAGAACTGAATACATTTGATGAACCTCATCACTGCCTTTTCCATATGTTCTCAACAGTCTTAAGATAATAAAACTTGTAACTTTAACAACTGAATACCTAACTTGGTACTGATTTAGGCTTGGGGTTGGATGGAGTGGAAAGAAGGAAACATTTCCACAGCTCGAGAACTATACCAGAAGGCTCTATCGATCAACTCAACAACTGAAAGTGCTGCGCGTTGTCTTCAGGTAATGCTCATTTCTAATAGATAGAGTAAGTTTCTAGTTTGCTTTTCGTAAGACATTTTGATGCAAATTGTGGAGGTTAGTCCAAACTCGTAACTCTGGCTTGCAGCTTAGTCTGTCCTTTGTTCCAACAAGTAGTATATTCTGGTTATATGTAATCTTCTCCACATAGGAAATGTACTAAAGAGTTGTTTACTATAGGCTTGGGGTGTTTTGGAGCAAAGAGCTGGAAATCTATCAGCTGCTCGAAGACTATTTAGATCGTCTCTGAACATAAACTCTCAGAGCTATATAACATGGATGACATGGGCAAATTTAGAGGAAGATCAAGGTAACTCTATCCGTGCAGAGGAAATTCGTAACCTCTACTTTCAACAGGTATATGAGTCATTTCCTTCTATGACCACATTTCAAGCATTGTTATACATCAGTGTTCCATATAGCTGCTCTTCTCCCTAACATCACTAGACGTTTTTGTTGACACAGCGTACTGAAGTTGTTGATGATGAGTCGTGGATTATGGGCTTCTTAGACGTCATTGACCCAGCGATTGACAGCATAAAGAGGCTCTTGAATCTAGATCAGAACTCTTACTACAAGGTAAAAGAGTCTGCTTCTAATACTACTGCTGGAGACGACGTTGAGGGGAGCACAGAAGAATCAGCTTCTCCCTCCTCGGCTAACGTCAATGACAATAACATAGATACAGGAAGTGGCTTTGATTTAGATGATTTTATCAGTGTAATGCTGTCTTTAGACCCTTCAAAGCTGGAAGTTCAGCTTACAACATCTCTTAAGGACCCTCCGAAAATCGCCAGAACTACTAATGGGGTGTGGCGACCATCGACAAAGACTAGTAGAACATCAACAACACTTTGATTTTACAACAACAACGACATACTTAATGTAACCTCACTAGTGTGGTCTGGGAGGGCGGAGGACGAAAGGTGATGTGTTGCAGCCTTACCTTTACCTCGTGAAGGTAGAGAGACTGTTTCTGACTCAGCTCAATATGAAGTTTATTGTTCTTTAGTGGGAATTGCAACATTCATTAATGTTGTCAAATGAAGAAGTCTTGGTCCACATTTTGTAAATTACTTAGGAATATTGAGAAGAATTGTATAAATTTGATTGTGAAAGAGATACAAATCTACACATATTAT-GAGTAAACATTGTATA</genome_strand>
        <mrna_strand>TTGTGCTAGTTGGCTG........................................................................................................GCATGGGCTCAACTAGAGGCTCAGTTAGAGAATGACCGTTCCGCTAGGCAGCTGTTTGAG.......................................................................................................................................................................................................................................................................................................................................................................................................................................................AAAGCAGTTCAAGCCAGTCCGAAAAATAGGTTCGCGTGGCATGTATGGGGAGTTTTTGAAGCTAATCTAGGAAATATTGATCAAGGAAGGAAACTTCTAACAATAGGGCACATGGTGAATCCTAGAGATCCTGTTCTTCTCCAATCACTTGGTTTGATAGAATACAAGAACTCCAGTGCAAACCTTGCACGAGTTCTATTCCGAAGAGCGTCTCAACTAGATCCAAGGCATCAACCAGTTTGGATT.........................................................................................................................................................................................................................................GCTTGGGGTTGGATGGAGTGGAAAGAAGGAAACATTTCCACAGCTCGAGAACTATACCAGAAGGCTCTATCGATCAACTCAACAACTGAAAGTGCTGCGCGTTGTCTTCAG......................................................................................................................................................................................................GCTTGGGGTGTTTTGGAGCAAAGAGCTGGAAATCTATCAGCTGCTCGAAGACTATTTAGATCGTCTCTGAACATAAACTCTCAGAGCTATATAACATGGATGACATGGGCAAATTTAGAGGAAGATCAAGGTAACTCTATCCGTGCAGAGGAAATTCGTAACCTCTACTTTCAACAG............................................................................................................CGTACTGAAGTTGTTGATGATGAGTCGTGGATTATGGGCTTCTTAGACGTCATTGACCCAGCGATTGACAGCATAAAGAGGCTCTTGAATCTAGATCAGAACTCTTACTACAAGGTAAAAGAGTCTGCTTCTAATACTACTGCTGGAGACGACGTTGAGGGGAGCACAGAAGAATCAGCTTCTCCCTCCTCGGCTAACGTCAATGACAATAACATAGATACAGGAAGTGGCTTTGATTTAGATGATTTTATCAGTGTAATGCTGTCTTTAGACCCTTCAAAGCTGGAAGTTCAGCTTACAACATCTCTTAAGGACCCTCCGAAAATCGCCAGAACTACTAATGGGGTGTGGCGACCATCGACAAAGACTAGTAGAACATCAACAACACTTTGATTTTACAACAACAACGACATACTTAATGTAACCTCACTAGTGTGGTCTGGGAGGGCGGAGAACGAAAGGTGATGTGTTGCAGCCTTACCTTTACCTCGTGAAGGTAGAGAGACTGTTTCTGACTCAGCTCAATATAAAGTTTATTGTTCTTTAGTGGGAATTGCAACATTCATTAATGTTGTCAAATGAAGAAGTCTTGGTCCACATTTTGTAAATTACTTAGGAATATTGAGAAGAATTGTATAAATTTGATTGTAAGAAGAAGGCAAATCTACACATATAATCCCCCCCACATTGTATA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C04SLm0127L14-bd3tp/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M1554" ref_strand="+" ref_description="SGN-M1554 T0707 [cos_markers]">
      <seq>gaagttgttgatgatgagtcgtggattatgggcttcttagacgtcattgacccagcgattgacagcataaagaggctcttgaatctagatcagaactcttactacaaggtaaaagagtctgcttctaatactactgctggagacgacgttgaggggagcacagaagaatcagcttctccctcctcggctaacgtcaatgacaataacatagatacaggaagtggctttgatttagatgattttatcagtgtaatgctgtctttagacccttcaaagctggaagttcagcttacaacatctcttaaggaccctccgaaaatcgccagaactactaatggggtgtggcgaccatcgacaaagactagtagaacatcaacaacactttgattttacaacaacaacgacatacttaatgtaacctcactagtgtggtctgggagggcggaggacgaaaggtgatgtgttgcagccttacctttacctcgtgaaagtagagagactgtttctgactcagctcaatatg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0127L14-bd3tp/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04SLm0127L14.1" temp_strand="+" temp_description="C04SLm0127L14.1  CU856252.3 htgs_phase:3 submitted_to_sgn_as:C04SLm0127L14 sequenced_by:sanger upload_account_name:uk">
        <position start="21827" stop="22949"/>
      </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="22127" g_stop="22649" g_length="523"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="523" r_length="523" r_score="0.998"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04SLm0127L14.1" gen_strand="+" ref_id="SGN-M1554" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>523</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0127L14.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M1554" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="22127" e_stop="22649"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GAAGTTGTTGATGATGAGTCGTGGATTATGGGCTTCTTAGACGTCATTGACCCAGCGATTGACAGCATAAAGAGGCTCTTGAATCTAGATCAGAACTCTTACTACAAGGTAAAAGAGTCTGCTTCTAATACTACTGCTGGAGACGACGTTGAGGGGAGCACAGAAGAATCAGCTTCTCCCTCCTCGGCTAACGTCAATGACAATAACATAGATACAGGAAGTGGCTTTGATTTAGATGATTTTATCAGTGTAATGCTGTCTTTAGACCCTTCAAAGCTGGAAGTTCAGCTTACAACATCTCTTAAGGACCCTCCGAAAATCGCCAGAACTACTAATGGGGTGTGGCGACCATCGACAAAGACTAGTAGAACATCAACAACACTTTGATTTTACAACAACAACGACATACTTAATGTAACCTCACTAGTGTGGTCTGGGAGGGCGGAGGACGAAAGGTGATGTGTTGCAGCCTTACCTTTACCTCGTGAAGGTAGAGAGACTGTTTCTGACTCAGCTCAATATG</genome_strand>
        <mrna_strand>GAAGTTGTTGATGATGAGTCGTGGATTATGGGCTTCTTAGACGTCATTGACCCAGCGATTGACAGCATAAAGAGGCTCTTGAATCTAGATCAGAACTCTTACTACAAGGTAAAAGAGTCTGCTTCTAATACTACTGCTGGAGACGACGTTGAGGGGAGCACAGAAGAATCAGCTTCTCCCTCCTCGGCTAACGTCAATGACAATAACATAGATACAGGAAGTGGCTTTGATTTAGATGATTTTATCAGTGTAATGCTGTCTTTAGACCCTTCAAAGCTGGAAGTTCAGCTTACAACATCTCTTAAGGACCCTCCGAAAATCGCCAGAACTACTAATGGGGTGTGGCGACCATCGACAAAGACTAGTAGAACATCAACAACACTTTGATTTTACAACAACAACGACATACTTAATGTAACCTCACTAGTGTGGTCTGGGAGGGCGGAGGACGAAAGGTGATGTGTTGCAGCCTTACCTTTACCTCGTGAAAGTAGAGAGACTGTTTCTGACTCAGCTCAATATG</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C04SLm0127L14-bd3tp/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M3892" ref_strand="+" ref_description="SGN-M3892 cLER-16-J6 [est_clones]">
      <seq>caacacataaactgtactgctgttgctgtaattctcttaaagaacaatggctgctctctcagtagccaacacttctcttaaggttaacaacaaaggattctctgaattctctggtttgagaacctcatcagctgttccatttgggaggaaaactaatgatgatttgttctctgttgctggcttacaaacctctgctattggaggaaggaagaacaagaggatagtaactgaggcaaagttgaaagtggctatcaatggatttggaagaattggaaggaacttcttgaggtgctggcatggtagaaaagactcacctcttgatgtcattgccatcaatgacactggtggtgtcaagcaagcctctcaccttctcaaatatgactccacccttggcatctttgatgctgacgtcaagccggttggcactgatggcatctctgtcgatggaaaagtcatccaagtcgtctccaaccgtgaccctgtgaacctcccatggggagaacttggagttgacttagtcatagaaggtaccggagtttttgtagacagagaaggtgccggtaaacacatccaggccggagccaaaaaggtgctcatcaccgcccccggaaaaggtgacatccctacttatgttgttggtgtcaatgc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0127L14-bd3tp/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04SLm0127L14.1" temp_strand="+" temp_description="C04SLm0127L14.1  CU856252.3 htgs_phase:3 submitted_to_sgn_as:C04SLm0127L14 sequenced_by:sanger upload_account_name:uk">
        <position start="25331" stop="28175"/>
      </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="25631" g_stop="25712" g_length="82"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="82" r_length="82" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="25713" i_stop="25828" i_length="116">
            <donor d_prob="0.994" d_score="1.00"/>
            <acceptor a_prob="0.974" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="25829" g_stop="25942" g_length="114"/>
          <reference_exon_boundary r_type="cDNA" r_start="83" r_stop="196" r_length="114" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="25943" i_stop="26840" i_length="898">
            <donor d_prob="0.989" d_score="1.00"/>
            <acceptor a_prob="0.996" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="26841" g_stop="27142" g_length="302"/>
          <reference_exon_boundary r_type="cDNA" r_start="197" r_stop="498" r_length="302" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="27143" i_stop="27725" i_length="583">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.988" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="27726" g_stop="27875" g_length="150"/>
          <reference_exon_boundary r_type="cDNA" r_start="499" r_stop="648" r_length="150" r_score="0.993"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04SLm0127L14.1" gen_strand="+" ref_id="SGN-M3892" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>648</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0127L14.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M3892" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="25631" e_stop="25712"/>
          <exon e_start="25829" e_stop="25942"/>
          <exon e_start="26841" e_stop="27142"/>
          <exon e_start="27726" e_stop="27875"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CAACACATAAACTGTACTGCTGTTGCTGTAATTCTCTTAAAGAACAATGGCTGCTCTCTCAGTAGCCAACACTTCTCTTAAGGTACCTCATTCACTCGTCCTGCATTCCATCTTATTATTAATTGATCCTGACTTGTTCGGGACTGAGACGTACGTAGTTATGAATATGTTTGTTGTTTTCTTAAAACTGATGGACAGGTTAACAACAAAGGATTCTCTGAATTCTCTGGTTTGAGAACCTCATCAGCTGTTCCATTTGGGAGGAAAACTAATGATGATTTGTTCTCTGTTGCTGGCTTACAAACCTCTGCTGTGAGTATTATTATACAACTACTACTATTATTGCATCATAAGATAGTTTAAGTTCTGTGCACCGACGATGTAAAACATTTATACGCTATCAGGTCATAGCCTTTAATTAGTATTGATAGTGTAAAAAATCTAACATTGTCGGTGTATACAACTTGAATCCTTACAAAGTTTAAGGAAAAAAGAATATGTATCCTTCATGTCTTGTTGTGATCAAGATGTGCTCTAAATTTTTTTTCGGGGGAAAAAAGACAGATATACCCCCGAATAATCGTAAATGGTATGCAGATACACTCCGTCATACTTTTGAGACATTAGTGCCCCTACTATCCAAAAACTAGAGCATATATGACCTTCACTCTAACGGAAGACTAAATAGGGACACGTGGCGCAATCTTATATGTTGATAAATGTCGGATCGATGGATAAGATTGTGACATGTGTATGTCTGTTAATATAAAGGGTATATATGCTCTAGTTTTTGAACAGTAGGGGCAACAATGTTCCAAAAGTATGACGGAGGGTACTTGCATACCACTTACGATAGTTCAAGGGTATATTTGTCCTTTTTCCTTTTCTTTCCCTTGTATGTTCTACCTTTTCTATGTTGAAAGCAGCCTCCATACAAAGATCTTTATGCAAATTCATCAATTTGATAAGTTTTAAGGAAGATCAAACACTATAAAATGAATGATAACATTGTATAAACATCTAAATTGTATTTCCTTCCTATGTTATGTTGCTCGGACTGTCCAAAATTGTTGTTGCACCCATGTCGGGTTCTCCCAAAATGTACTACTTTTGGAGTATCCGACATGCACTTGTCAGCATTTTTTGACGAGTCTGAGTAACATAGCTTCCAACGATGTTTCTTGTGGTAATTGGATTTAATGAAATGTAGATTGGAGGAAGGAAGAACAAGAGGATAGTAACTGAGGCAAAGTTGAAAGTGGCTATCAATGGATTTGGAAGAATTGGAAGGAACTTCTTGAGGTGCTGGCATGGTAGAAAAGACTCACCTCTTGATGTCATTGCCATCAATGACACTGGTGGTGTCAAGCAAGCCTCTCACCTTCTCAAATATGACTCCACCCTTGGCATCTTTGATGCTGACGTCAAGCCGGTTGGCACTGATGGCATCTCTGTCGATGGAAAAGTCATCCAAGTCGTCTCCAACCGTGACCCTGTGAACCTCCCATGGGGGTATGTTCTTTCATACTAACATATAACAAAACAGATTTAAGTTGTATATGTTTACACGTAGTGTAACTAATTTACATTATACGTTTGCAGATTCAGGAAACTCATATTATTAGTTGTCTAAACAGAAACAGTCGTTCTAAGTTTTAATAGCCATGAATTATAGACTTAAGGGTAACAACCAAACCTAAACTATCACATTTTTGCGAGTTTCATACGTCAGCTATCCATTGTTCTACTTAGTACTTACATACCTAAACTGACACATTTTTGCGAGCTTCATACCTCAACTATTACTTGCTTCATATTAAAAAATACCTTGATGTTGAGTTGGCCTACATGCCTGTTGTTGATTGAGAACAAATATATGGCCAACTTGAGAGATAGTTTAGGTACAAAAAGAGAACAATGGATAGTTGAGATATGAAACTCGCGAGGAAGTGATAGTTTAAGTGTTTAATTATCATTAACTCTGAATTAAAACATGATTAATTTAGCTCATGTAGTGTCTAACATATAGTACTAGCTTGAGATACCTAGTAAACATCTAAACTATTGTTCAAAATGTGTTCTGTAATTTGTTCAGAGAACTTGGAGTTGACTTAGTCATAGAAGGTACCGGAGTTTTTGTAGACAGAGAAGGTGCCGGTAAACACATCCAGGCCGGAGCCAAGAAGGTGCTCATCACCGCCCCCGGAAAAGGTGACATCCCTACTTATGTTGTTGGTGTCAATGC</genome_strand>
        <mrna_strand>CAACACATAAACTGTACTGCTGTTGCTGTAATTCTCTTAAAGAACAATGGCTGCTCTCTCAGTAGCCAACACTTCTCTTAAG....................................................................................................................GTTAACAACAAAGGATTCTCTGAATTCTCTGGTTTGAGAACCTCATCAGCTGTTCCATTTGGGAGGAAAACTAATGATGATTTGTTCTCTGTTGCTGGCTTACAAACCTCTGCT..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATTGGAGGAAGGAAGAACAAGAGGATAGTAACTGAGGCAAAGTTGAAAGTGGCTATCAATGGATTTGGAAGAATTGGAAGGAACTTCTTGAGGTGCTGGCATGGTAGAAAAGACTCACCTCTTGATGTCATTGCCATCAATGACACTGGTGGTGTCAAGCAAGCCTCTCACCTTCTCAAATATGACTCCACCCTTGGCATCTTTGATGCTGACGTCAAGCCGGTTGGCACTGATGGCATCTCTGTCGATGGAAAAGTCATCCAAGTCGTCTCCAACCGTGACCCTGTGAACCTCCCATGGGG.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGAACTTGGAGTTGACTTAGTCATAGAAGGTACCGGAGTTTTTGTAGACAGAGAAGGTGCCGGTAAACACATCCAGGCCGGAGCCAAAAAGGTGCTCATCACCGCCCCCGGAAAAGGTGACATCCCTACTTATGTTGTTGGTGTCAATGC</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="12439" PGL_stop="10850"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="12439" e_stop="12392"/>
            <exon e_start="12240" e_stop="12168"/>
            <exon e_start="11264" e_stop="10850"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.778" acc_prob="0.993" e_score="0.896"/>
          <exon-intron don_prob="0.000" acc_prob="0.000" e_score="0.945"/>
          <exon-only e_score="0.990"/>
        </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="0.896">
            <gDNA_exon_boundary e_start="12439" e_stop="12392" e_length="48"/>
          </exon>
          <intron i_serial="1" don_prob="0.778" acc_prob="0.993">
            <gDNA_intron_boundary i_start="12391" i_stop="12241" i_length="151"/>
          </intron>
          <exon e_serial="2" e_score="0.945">
            <gDNA_exon_boundary e_start="12240" e_stop="12168" e_length="73"/>
          </exon>
          <intron i_serial="2" don_prob="0.000" acc_prob="0.000">
            <gDNA_intron_boundary i_start="12167" i_stop="11265" i_length="903"/>
          </intron>
          <exon e_serial="3" e_score="0.990">
            <gDNA_exon_boundary e_start="11264" e_stop="10850" e_length="415"/>
          </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="12439" stop="12392"/>
              <exon start="12240" stop="12168"/>
              <exon start="11264" stop="10850"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M3054" 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>TTTCTCTTAATTAAAATAATTACCTCGCCTTCATCAGATCTGGTTGTT : GGTTGAGCCGCCTTTGCTTGTGTGCATCTCGATTAATTTATGGGGTAGCTTATCGTCTAGCTCACAGGTACAG : GTTTGGAGTTGAAATTTGAAACATAGCGTATCATATTTTCAAGCCTTTGATGACTCAGACTGAGACCTCATTTTAGTAACTTTAACGAGAGGTTTTGTTTGACTTATTCGCGTGAAATGGCAGAGCTTTTTGGATATACAGCATGCAGACAATTATTGCAAATGTTCATTTCAATTATATTCTTCCATGTTTCCGAGTACATTCTGGCACTTGTCTTTCATGGGAAGTCGAATGTATCTTTTAAGTCGCTTTTGATAAGCAAACATTATGTACTAGCAATGTTTTGCTCCTTGATAGAATACCTTATTGAAATCTATTTCTTTCCCGGCTTAAAGGAATATTGGTGGATAAGTAATTTTGGCCTCGCAATGGTTGTCCTCGGAGAAATCATAAGGAAGTTGGCAATTGTGACAGC</gDNA_template>
            <first_frame> F  L  L  I  K  I  I  T  S  P  S  S  D  L  V  V  :  G  *  A  A  F  A  C  V  H  L  D  *  F  M  G  *  L  I  V  *  L  T  G  T   : G  L  E  L  K  F  E  T  *  R  I  I  F  S  S  L  *  *  L  R  L  R  P  H  F  S  N  F  N  E  R  F  C  L  T  Y  S  R  E  M  A  E  L  F  G  Y  T  A  C  R  Q  L  L  Q  M  F  I  S  I  I  F  F  H  V  S  E  Y  I  L  A  L  V  F  H  G  K  S  N  V  S  F  K  S  L  L  I  S  K  H  Y  V  L  A  M  F  C  S  L  I  E  Y  L  I  E  I  Y  F  F  P  G  L  K  E  Y  W  W  I  S  N  F  G  L  A  M  V  V  L  G  E  I  I  R  K  L  A  I  V  T   </first_frame>
            <second_frame>  F  S  *  L  K  *  L  P  R  L  H  Q  I  W  L  L :   V  E  P  P  L  L  V  C  I  S  I  N  L  W  G  S  L  S  S  S  S  Q  V  Q  :  V  W  S  *  N  L  K  H  S  V  S  Y  F  Q  A  F  D  D  S  D  *  D  L  I  L  V  T  L  T  R  G  F  V  *  L  I  R  V  K  W  Q  S  F  L  D  I  Q  H  A  D  N  Y  C  K  C  S  F  Q  L  Y  S  S  M  F  P  S  T  F  W  H  L  S  F  M  G  S  R  M  Y  L  L  S  R  F  *  *  A  N  I  M  Y  *  Q  C  F  A  P  *  *  N  T  L  L  K  S  I  S  F  P  A  *  R  N  I  G  G  *  V  I  L  A  S  Q  W  L  S  S  E  K  S  *  G  S  W  Q  L  *  Q  </second_frame>
            <third_frame>   S  L  N  *  N  N  Y  L  A  F  I  R  S  G  C   : W  L  S  R  L  C  L  C  A  S  R  L  I  Y  G  V  A  Y  R  L  A  H  R  Y  R :   F  G  V  E  I  *  N  I  A  Y  H  I  F  K  P  L  M  T  Q  T  E  T  S  F  *  *  L  *  R  E  V  L  F  D  L  F  A  *  N  G  R  A  F  W  I  Y  S  M  Q  T  I  I  A  N  V  H  F  N  Y  I  L  P  C  F  R  V  H  S  G  T  C  L  S  W  E  V  E  C  I  F  *  V  A  F  D  K  Q  T  L  C  T  S  N  V  L  L  L  D  R  I  P  Y  *  N  L  F  L  S  R  L  K  G  I  L  V  D  K  *  F  W  P  R  N  G  C  P  R  R  N  H  K  E  V  G  N  C  D  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/">
            <orf_entry>
              <id_line>
                <gDNA id="C04SLm0127L14.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="11211" stop="10852"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>360</number_coding_nucleotides>
                  <number_encoded_amino_acids>120</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LRLRPHFSNFNERFCLTYSREMAELFGYTACRQLLQMFISIIFFHVSEYILALVFHGKSNVSFKSLLISKHYVLAMFCSLIEYLIEIYFFPGLKEYWWISNFGLAMVVLGEIIRKLAIVT</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="20383" PGL_stop="22813"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="20383" e_stop="20444"/>
            <exon e_start="20549" e_stop="20608"/>
            <exon e_start="21048" e_stop="21293"/>
            <exon e_start="21527" e_stop="21637"/>
            <exon e_start="21836" e_stop="22012"/>
            <exon e_start="22121" e_stop="22813"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.979" acc_prob="1.000" e_score="1.000"/>
          <exon-intron don_prob="0.999" acc_prob="0.880" e_score="0.983"/>
          <exon-intron don_prob="0.986" acc_prob="0.999" e_score="1.000"/>
          <exon-intron don_prob="0.998" acc_prob="0.969" e_score="1.000"/>
          <exon-intron don_prob="0.999" acc_prob="0.850" e_score="1.000"/>
          <exon-only e_score="0.974"/>
        </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="20383" e_stop="20444" e_length="62"/>
          </exon>
          <intron i_serial="1" don_prob="0.979" acc_prob="1.000">
            <gDNA_intron_boundary i_start="20445" i_stop="20548" i_length="104"/>
          </intron>
          <exon e_serial="2" e_score="0.983">
            <gDNA_exon_boundary e_start="20549" e_stop="20608" e_length="60"/>
          </exon>
          <intron i_serial="2" don_prob="0.999" acc_prob="0.880">
            <gDNA_intron_boundary i_start="20609" i_stop="21047" i_length="439"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="21048" e_stop="21293" e_length="246"/>
          </exon>
          <intron i_serial="3" don_prob="0.986" acc_prob="0.999">
            <gDNA_intron_boundary i_start="21294" i_stop="21526" i_length="233"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="21527" e_stop="21637" e_length="111"/>
          </exon>
          <intron i_serial="4" don_prob="0.998" acc_prob="0.969">
            <gDNA_intron_boundary i_start="21638" i_stop="21835" i_length="198"/>
          </intron>
          <exon e_serial="5" e_score="1.000">
            <gDNA_exon_boundary e_start="21836" e_stop="22012" e_length="177"/>
          </exon>
          <intron i_serial="5" don_prob="0.999" acc_prob="0.850">
            <gDNA_intron_boundary i_start="22013" i_stop="22120" i_length="108"/>
          </intron>
          <exon e_serial="6" e_score="0.974">
            <gDNA_exon_boundary e_start="22121" e_stop="22813" e_length="693"/>
          </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="20383" stop="20444"/>
              <exon start="20549" stop="20608"/>
              <exon start="21048" stop="21293"/>
              <exon start="21527" stop="21637"/>
              <exon start="21836" stop="22012"/>
              <exon start="22121" stop="22439"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M7768-2" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="20429" stop="20444"/>
              <exon start="20549" stop="20608"/>
              <exon start="21048" stop="21293"/>
              <exon start="21527" stop="21637"/>
              <exon start="21836" stop="22012"/>
              <exon start="22121" stop="22813"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M7768" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="22127" stop="22649"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1554" 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>GAGCACGATATTTGTTCAAGCAGGCAACAAGGTGTAACCGAAAAAGTTGTGCTAGTTGGCTG : GCATGGGCTCAACTAGAGGCTCAGTTAGAGAATAACCGTTCCGCTAGGCAGCTGTTTGAG : AAAGCAGTTCAAGCCAGTCCGAAAAATAGGTTCGCGTGGCATGTATGGGGAGTTTTTGAAGCTAATCTAGGAAATATTGATCAAGGAAGGAAACTTCTAACAATAGGGCACATGGTGAATCCTAGAGATCCTGTTCTTCTCCAATCACTTGGTTTGATAGAATACAAGAACTCCAGTGCAAACCTTGCACGAGTTCTATTCCGAAGAGCGTCTCAACTAGATCCAAGGCATCAACCAGTTTGGATT : GCTTGGGGTTGGATGGAGTGGAAAGAAGGAAACATTTCCACAGCTCGAGAACTATACCAGAAGGCTCTATCGATCAACTCAACAACTGAAAGTGCTGCGCGTTGTCTTCAG : GCTTGGGGTGTTTTGGAGCAAAGAGCTGGAAATCTATCAGCTGCTCGAAGACTATTTAGATCGTCTCTGAACATAAACTCTCAGAGCTATATAACATGGATGACATGGGCAAATTTAGAGGAAGATCAAGGTAACTCTATCCGTGCAGAGGAAATTCGTAACCTCTACTTTCAACAG : CGTACTGAAGTTGTTGATGATGAGTCGTGGATTATGGGCTTCTTAGACGTCATTGACCCAGCGATTGACAGCATAAAGAGGCTCTTGAATCTAGATCAGAACTCTTACTACAAGGTAAAAGAGTCTGCTTCTAATACTACTGCTGGAGACGACGTTGAGGGGAGCACAGAAGAATCAGCTTCTCCCTCCTCGGCTAACGTCAATGACAATAACATAGATACAGGAAGTGGCTTTGATTTAGATGATTTTATCAGTGTAATGCTGTCTTTAGACCCTTCAAAGCTGGAAGTTCAGCTTACAACATCTCTTAAGGACCCTCCGAAAATCGCCAGAACTACTAATGGGGTGTGGCGACCATCGACAAAGACTAGTAGAACATCAACAACACTTTGATTTTACAACAACAACGACATACTTAATGTAACCTCACTAGTGTGGTCTGGGAGGGCGGAGGACGAAAGGTGATGTGTTGCAGCCTTACCTTTACCTCGTGAAGGTAGAGAGACTGTTTCTGACTCAGCTCAATATGAAGTTTATTGTTCTTTAGTGGGAATTGCAACATTCATTAATGTTGTCAAATGAAGAAGTCTTGGTCCACATTTTGTAAATTACTTAGGAATATTGAGAAGAATTGTATAAATTTGATTGTGAAAGAGATACAAATCTACACATATTATGAGTAAACATTGTATA</gDNA_template>
            <first_frame> E  H  D  I  C  S  S  R  Q  Q  G  V  T  E  K  V  V  L  V  G  W :   H  G  L  N  *  R  L  S  *  R  I  T  V  P  L  G  S  C  L  R :   K  Q  F  K  P  V  R  K  I  G  S  R  G  M  Y  G  E  F  L  K  L  I  *  E  I  L  I  K  E  G  N  F  *  Q  *  G  T  W  *  I  L  E  I  L  F  F  S  N  H  L  V  *  *  N  T  R  T  P  V  Q  T  L  H  E  F  Y  S  E  E  R  L  N  *  I  Q  G  I  N  Q  F  G  L :   L  G  V  G  W  S  G  K  K  E  T  F  P  Q  L  E  N  Y  T  R  R  L  Y  R  S  T  Q  Q  L  K  V  L  R  V  V  F  R :   L  G  V  F  W  S  K  E  L  E  I  Y  Q  L  L  E  D  Y  L  D  R  L  *  T  *  T  L  R  A  I  *  H  G  *  H  G  Q  I  *  R  K  I  K  V  T  L  S  V  Q  R  K  F  V  T  S  T  F  N  S :   V  L  K  L  L  M  M  S  R  G  L  W  A  S  *  T  S  L  T  Q  R  L  T  A  *  R  G  S  *  I  *  I  R  T  L  T  T  R  *  K  S  L  L  L  I  L  L  L  E  T  T  L  R  G  A  Q  K  N  Q  L  L  P  P  R  L  T  S  M  T  I  T  *  I  Q  E  V  A  L  I  *  M  I  L  S  V  *  C  C  L  *  T  L  Q  S  W  K  F  S  L  Q  H  L  L  R  T  L  R  K  S  P  E  L  L  M  G  C  G  D  H  R  Q  R  L  V  E  H  Q  Q  H  F  D  F  T  T  T  T  T  Y  L  M  *  P  H  *  C  G  L  G  G  R  R  T  K  G  D  V  L  Q  P  Y  L  Y  L  V  K  V  E  R  L  F  L  T  Q  L  N  M  K  F  I  V  L  *  W  E  L  Q  H  S  L  M  L  S  N  E  E  V  L  V  H  I  L  *  I  T  *  E  Y  *  E  E  L  Y  K  F  D  C  E  R  D  T  N  L  H  I  L  *  V  N  I  V   </first_frame>
            <second_frame>  S  T  I  F  V  Q  A  G  N  K  V  *  P  K  K  L  C  *  L  A   : G  M  G  S  T  R  G  S  V  R  E  *  P  F  R  *  A  A  V  *   : E  S  S  S  S  Q  S  E  K  *  V  R  V  A  C  M  G  S  F  *  S  *  S  R  K  Y  *  S  R  K  E  T  S  N  N  R  A  H  G  E  S  *  R  S  C  S  S  P  I  T  W  F  D  R  I  Q  E  L  Q  C  K  P  C  T  S  S  I  P  K  S  V  S  T  R  S  K  A  S  T  S  L  D   : C  L  G  L  D  G  V  E  R  R  K  H  F  H  S  S  R  T  I  P  E  G  S  I  D  Q  L  N  N  *  K  C  C  A  L  S  S   : G  L  G  C  F  G  A  K  S  W  K  S  I  S  C  S  K  T  I  *  I  V  S  E  H  K  L  S  E  L  Y  N  M  D  D  M  G  K  F  R  G  R  S  R  *  L  Y  P  C  R  G  N  S  *  P  L  L  S  T   : A  Y  *  S  C  *  *  *  V  V  D  Y  G  L  L  R  R  H  *  P  S  D  *  Q  H  K  E  A  L  E  S  R  S  E  L  L  L  Q  G  K  R  V  C  F  *  Y  Y  C  W  R  R  R  *  G  E  H  R  R  I  S  F  S  L  L  G  *  R  Q  *  Q  *  H  R  Y  R  K  W  L  *  F  R  *  F  Y  Q  C  N  A  V  F  R  P  F  K  A  G  S  S  A  Y  N  I  S  *  G  P  S  E  N  R  Q  N  Y  *  W  G  V  A  T  I  D  K  D  *  *  N  I  N  N  T  L  I  L  Q  Q  Q  R  H  T  *  C  N  L  T  S  V  V  W  E  G  G  G  R  K  V  M  C  C  S  L  T  F  T  S  *  R  *  R  D  C  F  *  L  S  S  I  *  S  L  L  F  F  S  G  N  C  N  I  H  *  C  C  Q  M  K  K  S  W  S  T  F  C  K  L  L  R  N  I  E  K  N  C  I  N  L  I  V  K  E  I  Q  I  Y  T  Y  Y  E  *  T  L  Y  </second_frame>
            <third_frame>   A  R  Y  L  F  K  Q  A  T  R  C  N  R  K  S  C  A  S  W  L  :  A  W  A  Q  L  E  A  Q  L  E  N  N  R  S  A  R  Q  L  F  E  :  K  A  V  Q  A  S  P  K  N  R  F  A  W  H  V  W  G  V  F  E  A  N  L  G  N  I  D  Q  G  R  K  L  L  T  I  G  H  M  V  N  P  R  D  P  V  L  L  Q  S  L  G  L  I  E  Y  K  N  S  S  A  N  L  A  R  V  L  F  R  R  A  S  Q  L  D  P  R  H  Q  P  V  W  I  :  A  W  G  W  M  E  W  K  E  G  N  I  S  T  A  R  E  L  Y  Q  K  A  L  S  I  N  S  T  T  E  S  A  A  R  C  L  Q  :  A  W  G  V  L  E  Q  R  A  G  N  L  S  A  A  R  R  L  F  R  S  S  L  N  I  N  S  Q  S  Y  I  T  W  M  T  W  A  N  L  E  E  D  Q  G  N  S  I  R  A  E  E  I  R  N  L  Y  F  Q  Q  :  R  T  E  V  V  D  D  E  S  W  I  M  G  F  L  D  V  I  D  P  A  I  D  S  I  K  R  L  L  N  L  D  Q  N  S  Y  Y  K  V  K  E  S  A  S  N  T  T  A  G  D  D  V  E  G  S  T  E  E  S  A  S  P  S  S  A  N  V  N  D  N  N  I  D  T  G  S  G  F  D  L  D  D  F  I  S  V  M  L  S  L  D  P  S  K  L  E  V  Q  L  T  T  S  L  K  D  P  P  K  I  A  R  T  T  N  G  V  W  R  P  S  T  K  T  S  R  T  S  T  T  L  *  F  Y  N  N  N  D  I  L  N  V  T  S  L  V  W  S  G  R  A  E  D  E  R  *  C  V  A  A  L  P  L  P  R  E  G  R  E  T  V  S  D  S  A  Q  Y  E  V  Y  C  S  L  V  G  I  A  T  F  I  N  V  V  K  *  R  S  L  G  P  H  F  V  N  Y  L  G  I  L  R  R  I  V  *  I  *  L  *  K  R  Y  K  S  T  H  I  M  S  K  H  C  I </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C04SLm0127L14.1" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="20385" stop="20444"/>
                    <exon start="20549" stop="20608"/>
                    <exon start="21048" stop="21293"/>
                    <exon start="21527" stop="21637"/>
                    <exon start="21836" stop="22012"/>
                    <exon start="22121" stop="22513"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>1044</number_coding_nucleotides>
                  <number_encoded_amino_acids>348</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>ARYLFKQATRCNRKSCASWLAWAQLEAQLENNRSARQLFEKAVQASPKNRFAWHVWGVFEANLGNIDQGRKLLTIGHMVNPRDPVLLQSLGLIEYKNSSANLARVLFRRASQLDPRHQPVWIAWGWMEWKEGNISTARELYQKALSINSTTESAARCLQAWGVLEQRAGNLSAARRLFRSSLNINSQSYITWMTWANLEEDQGNSIRAEEIRNLYFQQRTEVVDDESWIMGFLDVIDPAIDSIKRLLNLDQNSYYKVKESASNTTAGDDVEGSTEESASPSSANVNDNNIDTGSGFDLDDFISVMLSLDPSKLEVQLTTSLKDPPKIARTTNGVWRPSTKTSRTSTTL*</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="25631" PGL_stop="27875"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="25631" e_stop="25712"/>
            <exon e_start="25829" e_stop="25942"/>
            <exon e_start="26841" e_stop="27142"/>
            <exon e_start="27726" e_stop="27875"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.994" acc_prob="0.974" e_score="1.000"/>
          <exon-intron don_prob="0.989" acc_prob="0.996" e_score="1.000"/>
          <exon-intron don_prob="1.000" acc_prob="0.988" e_score="1.000"/>
          <exon-only e_score="0.993"/>
        </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="25631" e_stop="25712" e_length="82"/>
          </exon>
          <intron i_serial="1" don_prob="0.994" acc_prob="0.974">
            <gDNA_intron_boundary i_start="25713" i_stop="25828" i_length="116"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="25829" e_stop="25942" e_length="114"/>
          </exon>
          <intron i_serial="2" don_prob="0.989" acc_prob="0.996">
            <gDNA_intron_boundary i_start="25943" i_stop="26840" i_length="898"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="26841" e_stop="27142" e_length="302"/>
          </exon>
          <intron i_serial="3" don_prob="1.000" acc_prob="0.988">
            <gDNA_intron_boundary i_start="27143" i_stop="27725" i_length="583"/>
          </intron>
          <exon e_serial="4" e_score="0.993">
            <gDNA_exon_boundary e_start="27726" e_stop="27875" e_length="150"/>
          </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="25631" stop="25712"/>
              <exon start="25829" stop="25942"/>
              <exon start="26841" stop="27142"/>
              <exon start="27726" stop="27875"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M3892" 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>CAACACATAAACTGTACTGCTGTTGCTGTAATTCTCTTAAAGAACAATGGCTGCTCTCTCAGTAGCCAACACTTCTCTTAAG : GTTAACAACAAAGGATTCTCTGAATTCTCTGGTTTGAGAACCTCATCAGCTGTTCCATTTGGGAGGAAAACTAATGATGATTTGTTCTCTGTTGCTGGCTTACAAACCTCTGCT : ATTGGAGGAAGGAAGAACAAGAGGATAGTAACTGAGGCAAAGTTGAAAGTGGCTATCAATGGATTTGGAAGAATTGGAAGGAACTTCTTGAGGTGCTGGCATGGTAGAAAAGACTCACCTCTTGATGTCATTGCCATCAATGACACTGGTGGTGTCAAGCAAGCCTCTCACCTTCTCAAATATGACTCCACCCTTGGCATCTTTGATGCTGACGTCAAGCCGGTTGGCACTGATGGCATCTCTGTCGATGGAAAAGTCATCCAAGTCGTCTCCAACCGTGACCCTGTGAACCTCCCATGGGG : AGAACTTGGAGTTGACTTAGTCATAGAAGGTACCGGAGTTTTTGTAGACAGAGAAGGTGCCGGTAAACACATCCAGGCCGGAGCCAAGAAGGTGCTCATCACCGCCCCCGGAAAAGGTGACATCCCTACTTATGTTGTTGGTGTCAATGC</gDNA_template>
            <first_frame> Q  H  I  N  C  T  A  V  A  V  I  L  L  K  N  N  G  C  S  L  S  S  Q  H  F  S  *   : G  *  Q  Q  R  I  L  *  I  L  W  F  E  N  L  I  S  C  S  I  W  E  E  N  *  *  *  F  V  L  C  C  W  L  T  N  L  C   : Y  W  R  K  E  E  Q  E  D  S  N  *  G  K  V  E  S  G  Y  Q  W  I  W  K  N  W  K  E  L  L  E  V  L  A  W  *  K  R  L  T  S  *  C  H  C  H  Q  *  H  W  W  C  Q  A  S  L  S  P  S  Q  I  *  L  H  P  W  H  L  *  C  *  R  Q  A  G  W  H  *  W  H  L  C  R  W  K  S  H  P  S  R  L  Q  P  *  P  C  E  P  P  M  G  :  R  T  W  S  *  L  S  H  R  R  Y  R  S  F  C  R  Q  R  R  C  R  *  T  H  P  G  R  S  Q  E  G  A  H  H  R  P  R  K  R  *  H  P  Y  L  C  C  W  C  Q  C </first_frame>
            <second_frame>  N  T  *  T  V  L  L  L  L  *  F  S  *  R  T  M  A  A  L  S  V  A  N  T  S  L  K  :  V  N  N  K  G  F  S  E  F  S  G  L  R  T  S  S  A  V  P  F  G  R  K  T  N  D  D  L  F  S  V  A  G  L  Q  T  S  A  :  I  G  G  R  K  N  K  R  I  V  T  E  A  K  L  K  V  A  I  N  G  F  G  R  I  G  R  N  F  L  R  C  W  H  G  R  K  D  S  P  L  D  V  I  A  I  N  D  T  G  G  V  K  Q  A  S  H  L  L  K  Y  D  S  T  L  G  I  F  D  A  D  V  K  P  V  G  T  D  G  I  S  V  D  G  K  V  I  Q  V  V  S  N  R  D  P  V  N  L  P  W  G :   E  L  G  V  D  L  V  I  E  G  T  G  V  F  V  D  R  E  G  A  G  K  H  I  Q  A  G  A  K  K  V  L  I  T  A  P  G  K  G  D  I  P  T  Y  V  V  G  V  N   </second_frame>
            <third_frame>   T  H  K  L  Y  C  C  C  C  N  S  L  K  E  Q  W  L  L  S  Q  *  P  T  L  L  L  R :   L  T  T  K  D  S  L  N  S  L  V  *  E  P  H  Q  L  F  H  L  G  G  K  L  M  M  I  C  S  L  L  L  A  Y  K  P  L  L :   L  E  E  G  R  T  R  G  *  *  L  R  Q  S  *  K  W  L  S  M  D  L  E  E  L  E  G  T  S  *  G  A  G  M  V  E  K  T  H  L  L  M  S  L  P  S  M  T  L  V  V  S  S  K  P  L  T  F  S  N  M  T  P  P  L  A  S  L  M  L  T  S  S  R  L  A  L  M  A  S  L  S  M  E  K  S  S  K  S  S  P  T  V  T  L  *  T  S  H  G   : E  N  L  E  L  T  *  S  *  K  V  P  E  F  L  *  T  E  K  V  P  V  N  T  S  R  P  E  P  R  R  C  S  S  P  P  P  E  K  V  T  S  L  L  M  L  L  V  S  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="C04SLm0127L14.1" strand="+"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="25671" stop="25712"/>
                    <exon start="25829" stop="25942"/>
                    <exon start="26841" stop="27142"/>
                    <exon start="27726" stop="27873"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>606</number_coding_nucleotides>
                  <number_encoded_amino_acids>202</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>RTMAALSVANTSLKVNNKGFSEFSGLRTSSAVPFGRKTNDDLFSVAGLQTSAIGGRKNKRIVTEAKLKVAINGFGRIGRNFLRCWHGRKDSPLDVIAINDTGGVKQASHLLKYDSTLGIFDADVKPVGTDGISVDGKVIQVVSNRDPVNLPWGELGVDLVIEGTGVFVDREGAGKHIQAGAKKVLITAPGKGDIPTYVVGVN</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 22 chains have been computed
$ 
$ memory statistics:
$ 10648 bytes spliced alignments in total
$ 5 spliced alignments have been stored
$ 2129 bytes was the average size of a spliced alignment
$ 8200 bytes predicted gene locations in total
$ 3 predicted gene locations have been stored
$ 2733 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 23 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-16 00:05:47
-->
