<?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="2009-12-01 06:06:24"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" 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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E318754" ref_strand="+" ref_description="SGN-E318754 [cTOB-11-C19]">
      <seq>tccaactcttctctgcctcttacttgtatctgctagcggcggcagtgaatctatctcaaaccctaatctcaacatggcgacgcctcagattagtaaaaagcgaaagtttgttgcggatggagttttttttgcggagttgaacgaagtgcttacaagagagctggcggaggatggttactcgggagttgaagttagggttactcccgtgcgaactgaaatcatcattagagccactcgtactcagaacgttcttggtgagaaaggtaggaggatcagggagctgacttcagttgttcataagcgttttaatttcaaggaaaacactgttgagctctatgctgagaaagtcaacaataggggtctctgtgccattgctcaggcagagtcactgcgatacaagttacttggaggacttgctgtccgaagggcttgctatggtgttctgagatttgtaatggagagtgga</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2207" stop="193"/>
      </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="1907" g_stop="1802" g_length="106"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="106" r_length="106" r_score="0.906"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.986" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="107" r_stop="254" r_length="148" r_score="0.980"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.98"/>
            <acceptor a_prob="1.000" a_score="0.92"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="513" g_length="172"/>
          <reference_exon_boundary r_type="cDNA" r_start="255" r_stop="426" r_length="172" r_score="0.965"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E318754" ref_strand="+">
        <total_alignment_score>0.955</total_alignment_score>
        <cumulative_length_of_scored_exons>426</cumulative_length_of_scored_exons>
        <coverage percentage="0.914" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E318754" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1907" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="513"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCCAACTCTTCACTGCCTCTCATTTGTATCTTCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTGGAGGACTTGCTGTCCGAAG</genome_strand>
        <mrna_strand>TCCAACTCTTCTCTGCCTCTTACTTGTATCTGCTAGCGGCGGCAGTGAATCTATCTCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGTTGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGCTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGAGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAGAAAGGTAGGAGGATCAGGGAGCTGACTTCAGTTGTTCATAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCTGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAGTTACTTGGAGGACTTGCTGTCCGAAG</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E324155" ref_strand="+" ref_description="SGN-E324155 [cTOC-4-C18]">
      <seq>ttgtctgcctcttacttgtatgtgctagcggcggcagtgaatctatctcaaaccctaatctcaacatggcgacgcctcagattagtaaaaagcgaaagtttgttgcggatggagttttttttgcggagttgaacgaagtgcttacaagagagctggcggaggatggttactcgggagttgaagttagggttactcccgtgcgaactgaaatcatcattagagccactcgtactcagaacgttcttggtgagaaaggtaggaggatcagggagctgacttcagttgttcagaagcgttttaatttcaaggaaaacactgttgagctctatgctgagaaagtcaacaataggggtctctgtgccattgctcaagcagagtcactgcgatacaagttacttggaggacttgctgtccgaaaggcttgctatggtgttctgagatttgtaatggagagtggag</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2199" stop="193"/>
      </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="1899" g_stop="1802" g_length="98"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="98" r_length="98" r_score="0.878"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.986" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="99" r_stop="246" r_length="148" r_score="0.980"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.98"/>
            <acceptor a_prob="1.000" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="513" g_length="172"/>
          <reference_exon_boundary r_type="cDNA" r_start="247" r_stop="418" r_length="172" r_score="0.959"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E324155" ref_strand="+">
        <total_alignment_score>0.947</total_alignment_score>
        <cumulative_length_of_scored_exons>418</cumulative_length_of_scored_exons>
        <coverage percentage="0.911" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E324155" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1899" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="513"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTCACTGCCTCTCATTTGTATCTTCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTGGAGGACTTGCTGTCCGAAG</genome_strand>
        <mrna_strand>TTGTCTGCCTCTTACTTGTATGTGCTAGCGGCGGCAGTGAATCTATCTCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGTTGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGCTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGAGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAGAAAGGTAGGAGGATCAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCTGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAAGCAGAGTCACTGCGATACAAGTTACTTGGAGGACTTGCTGTCCGAAA</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E442262" ref_strand="+" ref_description="SGN-E442262 [cSTA-32-D15]">
      <seq>ggcggcagtgaatcaatatcaaaccctaatctcaacatggcgacgcctcagattagtaaaaagcgaaagtttgtagcagatggagttttttttgcggagttgaacgaagtgctgacaagagagctggcggaggatggttactcgggagttgaagttagggttactcccatgcgaactgaaatcatcattagagccactcgtactcagaacgttcttggtgagaaaggtaggaggatcagggagctgacttcagttgttcagaagcgttttaatttcaaggaaaacagtgttgagctctatgcagagaaagtcaacaataggggtctctgtgccattgctcatgcagagtcactgcgatacaagttacttggaggacttgctgtccgaagggcttgctatggtgttctgagatttgtaatggagagtggagc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2170" stop="193"/>
      </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="1870" g_stop="1802" g_length="69"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="69" r_length="69" r_score="0.971"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.986" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="70" r_stop="217" r_length="148" r_score="0.966"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.96"/>
            <acceptor a_prob="1.000" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="513" g_length="172"/>
          <reference_exon_boundary r_type="cDNA" r_start="218" r_stop="389" r_length="172" r_score="0.965"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E442262" ref_strand="+">
        <total_alignment_score>0.967</total_alignment_score>
        <cumulative_length_of_scored_exons>389</cumulative_length_of_scored_exons>
        <coverage percentage="0.903" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E442262" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1870" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="513"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTGGAGGACTTGCTGTCCGAAG</genome_strand>
        <mrna_strand>GGCGGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGTAGCAGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTGACAAGAGAGCTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCATGCGAACTGAAATCATCATTAGAGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAGAAAGGTAGGAGGATCAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACAGTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCATGCAGAGTCACTGCGATACAAGTTACTTGGAGGACTTGCTGTCCGAAG</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E467402" ref_strand="+" ref_description="SGN-E467402 [cSTB-48-N9]">
      <seq>cggcagtgaatcaatatcaaaccctaatctcaacatggcgacgcctcagattagtaaaaagcgaaagtttgtagcagatggagttttttttgcggagttgaacgaagtgctgacaagagagctggcggaggatggttactcgggagttgaagttagggttactcccatgcgaactgaaatcatcattagagccactcgtactcagaacgttcttggtgagaaaggtaggaggatcagggagctgacttcagttgttcagaagcgttttaatttcaaggaaaacagtgttgagctctatgcagagaaagtcaacaataggggtctctgtgccattgctcaggcagagtcactgcgatacaagttacttggaggacttgctgtccgaagggcttgctatggtgttctgagatttgtaatggagagtggagc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2168" stop="193"/>
      </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="1868" g_stop="1802" g_length="67"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="67" r_length="67" r_score="0.970"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.986" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="68" r_stop="215" r_length="148" r_score="0.966"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.96"/>
            <acceptor a_prob="1.000" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="513" g_length="172"/>
          <reference_exon_boundary r_type="cDNA" r_start="216" r_stop="387" r_length="172" r_score="0.971"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E467402" ref_strand="+">
        <total_alignment_score>0.969</total_alignment_score>
        <cumulative_length_of_scored_exons>387</cumulative_length_of_scored_exons>
        <coverage percentage="0.902" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E467402" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1868" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="513"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTGGAGGACTTGCTGTCCGAAG</genome_strand>
        <mrna_strand>CGGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGTAGCAGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTGACAAGAGAGCTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCATGCGAACTGAAATCATCATTAGAGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAGAAAGGTAGGAGGATCAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACAGTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAGTTACTTGGAGGACTTGCTGTCCGAAG</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E281280" ref_strand="-" ref_description="SGN-E281280 [cLEL-1-G16](-)">
      <seq>gcacgagaatctatctcaaaccctaatctcaacatggcgacgcctcagattagtaaaaagcgaaagtttgttgccgctggagttttttttgcggagttgaacgaagtgcttacaagagagctggcggaggatggttactcgggagttgaagttagggttactcccgtgcgaactgaaatcatcattagagccactcgtactcagaacgttcttggtgagaaaggtaggaggatcagggagctgacttcagttgttcagaagcgttttaatttcaaggaaaacactgttgagctctatgctgagaaagtcaacaataggggtctctgtgccattgctcaggcagagtcactgcgatacaagttacttggaggacttgctgtccgaagggcttgctatggtgttctgagatttgtaatggagag</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2166" stop="193"/>
      </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="1866" g_stop="1802" g_length="65"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="66" r_length="66" r_score="0.908"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.986" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="67" r_stop="214" r_length="148" r_score="0.966"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.98"/>
            <acceptor a_prob="1.000" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="513" g_length="172"/>
          <reference_exon_boundary r_type="cDNA" r_start="215" r_stop="386" r_length="172" r_score="0.971"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E281280" ref_strand="-">
        <total_alignment_score>0.958</total_alignment_score>
        <cumulative_length_of_scored_exons>385</cumulative_length_of_scored_exons>
        <coverage percentage="0.912" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E281280" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="1866" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="513"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GCA-GTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTGGAGGACTTGCTGTCCGAAG</genome_strand>
        <mrna_strand>GCACGAGAATCTATCTCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGTTGCCGCTGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGCTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGAGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAGAAAGGTAGGAGGATCAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCTGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAGTTACTTGGAGGACTTGCTGTCCGAAG</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E725452" ref_strand="+" ref_description="SGN-E725452 [LA03BH03]">
      <seq>cagtgaatcaatatcaaaccctaatctcaacatggcgacgcctcatattagtaaaaaacgaaagtttgtagcggatggagttttttttgcggagttgaacgaagtgcttacaagagagttggcggagaatggttactcgggagttgaagttagggttactcccgtgcgaactgaaatcatctttagggccactcgtactcagaacgttcttggtgaaaaaggtaggagaattagggagctgacttcagttgttcagaagcgttttaatttcaaggataacactgttgagctctatgcagagaaagtcaacaataggggtctctgtgccattgctcaggcagagtcactgcgatacaaattacttgnaggacttgctgtccgaagggcttgctatggtgttctgcgatttgtaat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2165" stop="193"/>
      </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="1865" g_stop="1802" g_length="64"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="64" r_length="64" r_score="0.984"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.986" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="65" r_stop="212" r_length="148" r_score="0.986"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.98"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="513" g_length="172"/>
          <reference_exon_boundary r_type="cDNA" r_start="213" r_stop="384" r_length="172" r_score="0.988"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E725452" ref_strand="+">
        <total_alignment_score>0.987</total_alignment_score>
        <cumulative_length_of_scored_exons>384</cumulative_length_of_scored_exons>
        <coverage percentage="0.928" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E725452" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1865" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="513"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTGGAGGACTTGCTGTCCGAAG</genome_strand>
        <mrna_strand>CAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCATATTAGTAAAAAACGAAAG.....................................................................................TTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGAATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCTTTAGGGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGATAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTGNAGGACTTGCTGTCCGAAG</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E584537" ref_strand="+" ref_description="SGN-E584537 [10364]">
      <seq>gcctcagattagtaaaaagcgaaagtttgtagcagatggagttttttttgcggagttgaacgaagtgctgacaagagagctggcggaggatggttactcgggagttgaagttagggttactcccatgcgaactgaaatcatcattagagccactcgtactcagaacgttcttggtgagaaaggtaggaggatcagggagcttatttcagttgttcagaagcgttttaatttcaaggaaaacagtgttgagctctatgcagagaaagtcaacaataggggtctctgtgccattgctcaggcagagtcactgcgatacaagttacttggaggacttgctgtccgaagggcttgctatggtgttctg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2126" stop="193"/>
      </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="1826" g_stop="1802" g_length="25"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="25" r_length="25" r_score="0.960"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.00"/>
            <acceptor a_prob="0.986" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="26" r_stop="173" r_length="148" r_score="0.966"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.96"/>
            <acceptor a_prob="1.000" a_score="0.90"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="513" g_length="172"/>
          <reference_exon_boundary r_type="cDNA" r_start="174" r_stop="345" r_length="172" r_score="0.959"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E584537" ref_strand="+">
        <total_alignment_score>0.962</total_alignment_score>
        <cumulative_length_of_scored_exons>345</cumulative_length_of_scored_exons>
        <coverage percentage="0.948" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E584537" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1826" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="513"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTGGAGGACTTGCTGTCCGAAG</genome_strand>
        <mrna_strand>GCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGTAGCAGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTGACAAGAGAGCTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCATGCGAACTGAAATCATCATTAGAGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAGAAAGGTAGGAGGATCAGGGAGCTTATTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACAGTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAGTTACTTGGAGGACTTGCTGTCCGAAG</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E206585" ref_strand="+" ref_description="SGN-E206585 [cLEC-31-A16]">
      <seq>ctctgcctcttacttgtatctgctagcggcggcagtgaatctatctaaaaccctaatctcaacatggcgacgcctcagattagtaaaaagcgaaagtttgctgcggatggagttttttttgcggagttgaacgaactgcttacaagagagctggcggaggatggttactcgggagttgaagttagggttactcccgtgcgaactgaaatcatcattagagccactcgtactcagaacgttcttggtgagaaaggtacgaggatcatggagctgacttcagttgttcacaagcgttttaatttcaaggaaaacactgttgagctctatgctgagaaagtcaacaataggggtctctgtgccattgctcacgcagagtcactgcgatacaagttacttggaggacttgctg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2197" stop="220"/>
      </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="1897" g_stop="1802" g_length="96"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="96" r_length="96" r_score="0.885"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.96"/>
            <acceptor a_prob="0.986" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="97" r_stop="244" r_length="148" r_score="0.966"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.98"/>
            <acceptor a_prob="1.000" a_score="0.88"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="520" g_length="165"/>
          <reference_exon_boundary r_type="cDNA" r_start="245" r_stop="409" r_length="165" r_score="0.945"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E206585" ref_strand="+">
        <total_alignment_score>0.939</total_alignment_score>
        <cumulative_length_of_scored_exons>409</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E206585" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1897" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="520"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CACTGCCTCTCATTTGTATCTTCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTGGAGGACTTGCTG</genome_strand>
        <mrna_strand>CTCTGCCTCTTACTTGTATCTGCTAGCGGCGGCAGTGAATCTATCTAAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGCTGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAACTGCTTACAAGAGAGCTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGAGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAGAAAGGTACGAGGATCATGGAGCTGACTTCAGTTGTTCACAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCTGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCACGCAGAGTCACTGCGATACAAGTTACTTGGAGGACTTGCTG</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E250347" ref_strand="+" ref_description="SGN-E250347 [cLEG-6-C19]">
      <seq>ggatggagttttttttgcggagttgaacgaagtgcttactatagagctggcggaggatggttactcgggagttgaagttagggttactcccgtgcgaactgaaatcatcattagagccactcgtactcagaacgttcttggtgagaaaggtaggaggatcacggagctgacttcagttgttcagaagcgttttaatttcaaggaaaacactgttgagctctatgctgagaaagtcaacaataggggtctatgtgccattgctcatgcacagtcactgctatacaagttacttggaggacttgctg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2008" stop="220"/>
      </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="1708" g_stop="1569" g_length="140"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="140" r_length="140" r_score="0.971"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.98"/>
            <acceptor a_prob="1.000" a_score="0.92"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="684" g_stop="520" g_length="165"/>
          <reference_exon_boundary r_type="cDNA" r_start="141" r_stop="305" r_length="165" r_score="0.939"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E250347" ref_strand="+">
        <total_alignment_score>0.954</total_alignment_score>
        <cumulative_length_of_scored_exons>305</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E250347" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1708" e_stop="1569"/>
          <exon e_start="684" e_stop="520"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTGGAGGACTTGCTG</genome_strand>
        <mrna_strand>GGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACTATAGAGCTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGAGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAGAAAGGTAGGAGGATCACGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCTGAGAAAGTCAACAATAGGGGTCTATGTGCCATTGCTCATGCACAGTCACTGCTATACAAGTTACTTGGAGGACTTGCTG</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E239876" ref_strand="+" ref_description="SGN-E239876 [cLED-29-J8]">
      <seq>tactcgggagttgaagttagggttactcccgtgcgaactgaaatcatcattagggccactcgtactcagaacgttcttggtgaaaaaggtaggagaattagggagctgacttcagttgttcagaagcgttttaatttcaaggaaaacactgttgagctctatgcagagaaagtcaacaataggggtctctgtgccattgctcaggcagagtcactgcgatacaaattacttggaggac</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="1947" stop="226"/>
      </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="1647" g_stop="1569" g_length="79"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="79" r_length="79" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="684" g_stop="526" g_length="159"/>
          <reference_exon_boundary r_type="cDNA" r_start="80" r_stop="238" r_length="159" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E239876" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>238</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E239876" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1647" e_stop="1569"/>
          <exon e_start="684" e_stop="526"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTGGAGGAC</genome_strand>
        <mrna_strand>TACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTGGAGGAC</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E277167" ref_strand="-" ref_description="SGN-E277167 [cLEL-3-D6](-)">
      <seq>cacgagattgtatcttccatcggccgcagtgaatcaatatcaaaccctaatgtaggatggcgacgcctcagattactaacaaacgaaagtttgtagcggatggagttttttttgcggagttgaacgaagtgcttacaagagagttggcggaggatggttactcgggagttgaagttagggttactcccgtgcgaactgaaatcatcattagggccactcgtactcagaacgttcttggtgaaaaaggtaggagaattagggagctgacttcagttgttcagaagcgttttaatttcaaggaaaacactgttgagctctatgcagagaaagtcaacaataggggtctctgtgccattgctcaggcagagtcactgcgatacaaattacttggagg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2184" stop="228"/>
      </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="1891" g_stop="1802" g_length="90"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="89" r_length="89" r_score="0.878"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.88"/>
            <acceptor a_prob="0.986" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="90" r_stop="237" r_length="148" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" 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="684" g_stop="528" g_length="157"/>
          <reference_exon_boundary r_type="cDNA" r_start="238" r_stop="394" r_length="157" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E277167" ref_strand="-">
        <total_alignment_score>0.972</total_alignment_score>
        <cumulative_length_of_scored_exons>395</cumulative_length_of_scored_exons>
        <coverage percentage="1.003" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E277167" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="1891" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="528"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTCTCATTTGTATCTTCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTGGAGG</genome_strand>
        <mrna_strand>CACGAGATTGTATCTTCCATCGGCCGCAGTGAATCAATATCAAACCCTAATGT-AGGATGGCGACGCCTCAGATTACTAACAAACGAAAG.....................................................................................TTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTGGAGG</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E325034" ref_strand="+" ref_description="SGN-E325034 [cTOC-13-O21]">
      <seq>aactcttctctggctcttacttgtatctgctagcggcggcagtgaatctatctcaaaccctaatctcaacatggcgacgcctcagattagtaaaaagcgaaagtttgttgcggatggagttttttttgcggagttgaacgaagcgcttacaagagagctggcggaggatggttactcgcgagttgaagttagggttactcccgtgcgaactgaaatcatcattagagccactcgtactcagaacgttcttggtgagaaaggtaggaggatcagggagctgacttcagttgttcagaagcgttttaatttcaaggaaaacactgttgagctctatgctgagaaagtcaacaataggggtctctgtgccattgctcangcagagtcactgcgatacaagttacttgg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2204" stop="231"/>
      </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="1904" g_stop="1802" g_length="103"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="103" r_length="103" r_score="0.893"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.986" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="104" r_stop="251" r_length="148" r_score="0.966"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.98"/>
            <acceptor a_prob="1.000" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="531" g_length="154"/>
          <reference_exon_boundary r_type="cDNA" r_start="252" r_stop="405" r_length="154" r_score="0.961"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E325034" ref_strand="+">
        <total_alignment_score>0.946</total_alignment_score>
        <cumulative_length_of_scored_exons>405</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E325034" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1904" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="531"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AACTCTTCACTGCCTCTCATTTGTATCTTCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTGG</genome_strand>
        <mrna_strand>AACTCTTCTCTGGCTCTTACTTGTATCTGCTAGCGGCGGCAGTGAATCTATCTCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGTTGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGCGCTTACAAGAGAGCTGGCGGAGGATGGTTACTCGCGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGAGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAGAAAGGTAGGAGGATCAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCTGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCANGCAGAGTCACTGCGATACAAGTTACTTGG</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E472612" ref_strand="+" ref_description="SGN-E472612 [cSTB-29-I8]">
      <seq>aaagagcccaacttctaacctgccttaaatctttgacaaaccctttctcctctatactcatcgaactcttctttgcctcttacttgtatctgctagcggcggcagtgaatcaatatcaaaccctaatctcaacatggcgacgcctcagattagtaaaaagcgaaagtttgtagcagatggagttttttttgcggagttgaacgaagtgctgacaagagagctggcggaggatggttactcgggagttgaagttagggttactcccatgcgaactgaaatcatcattagagccactcgtactcagaacgttcttggtgagaaaggtaggaggatcagggagctgacttcagttgttcagaagcgttttaatttcaaggaaaacagtgttgagctctatgcagagaaagtcaacaataggggtctctgtgccattgctcaggcagagtcactgcgatacaagttacttg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2268" stop="232"/>
      </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="1967" g_stop="1802" g_length="166"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="166" r_length="166" r_score="0.892"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.986" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="167" r_stop="314" r_length="148" r_score="0.966"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.96"/>
            <acceptor a_prob="1.000" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="532" g_length="153"/>
          <reference_exon_boundary r_type="cDNA" r_start="315" r_stop="467" r_length="153" r_score="0.967"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E472612" ref_strand="+">
        <total_alignment_score>0.940</total_alignment_score>
        <cumulative_length_of_scored_exons>467</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E472612" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1967" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="532"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGAGAGCCCAACTAGTAACCTGCCTTAAATCTTTGACAAACCCTTTCTCCCTTGTCCTAATCCAACTCTTCACTGCCTCTCATTTGTATCTTCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTG</genome_strand>
        <mrna_strand>AAAGAGCCCAACTTCTAACCTGCCTTAAATCTTTGACAAACCCTTTCTCCTCTATACTCATCGAACTCTTCTTTGCCTCTTACTTGTATCTGCTAGCGGCGGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGTAGCAGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTGACAAGAGAGCTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCATGCGAACTGAAATCATCATTAGAGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAGAAAGGTAGGAGGATCAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACAGTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAGTTACTTG</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E445951" ref_strand="+" ref_description="SGN-E445951 [cSTA-19-K24]">
      <seq>cgtttctaccctgtcccaagcgaactcttcactgcctctcattcgtatctgccatcggccgcagtgaatcaatatcaaaccctaatctcaacatggcgacgcctcagattagtaaaaagcgaaagtttgtagcggatggagttttttttgcggagttgaacgaagtgctgacaagagagttggcggaggatggttactcgggagttgaagttagggttactcccatgcgaactgaaatcatcattagggctactcgtactcaaaacgttcttggtgaaaaaggtaggaggattagggagctgacttcagttgttcagaagcgctttaatttcaaggaaaatagtgttgagctctatgcagagaaagtcaacaataggggtctgtgtgccattgctcaagcagagtcactgcgata</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2226" stop="243"/>
      </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="1926" g_stop="1802" g_length="125"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="125" r_length="125" r_score="0.928"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.986" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="126" r_stop="273" r_length="148" r_score="0.973"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.94"/>
            <acceptor a_prob="1.000" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="543" g_length="142"/>
          <reference_exon_boundary r_type="cDNA" r_start="274" r_stop="415" r_length="142" r_score="0.958"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E445951" ref_strand="+">
        <total_alignment_score>0.954</total_alignment_score>
        <cumulative_length_of_scored_exons>415</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E445951" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1926" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="543"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CCTTTCTCCCTTGTCCTAATCCAACTCTTCACTGCCTCTCATTTGTATCTTCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATA</genome_strand>
        <mrna_strand>CGTTTCTACCCTGTCCCAAGCGAACTCTTCACTGCCTCTCATTCGTATCTGCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTGACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCATGCGAACTGAAATCATCATTAGGGCTACTCGTACTCAAAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAAAAAGGTAGGAGGATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGCTTTAATTTCAAGGAAAATAGTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTGTGTGCCATTGCTCAAGCAGAGTCACTGCGATA</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E200163" ref_strand="+" ref_description="SGN-E200163 [cLEB-7-B21]">
      <seq>gcacgagctcaaaccctaatctcaacatggcgacgcctcagattagtaaaaagcgaaagtttgttgcggatggagggttttttgcggagttgaacgaagtgcttacaagagagctggcggaggatggttactcgggagttgaagttagggttactcccgtgcgaactgaaatcatcattagagccactcgtactcagaacgttcttggtgagaaaggtaggaggatcagggagctgacttcagttgttcagaagcgttttaatttcaaggaaaacactgttgagctctatgctgagaaagtcaacaataggggtctctgtgccattgctcaggcagagtcac</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2161" stop="250"/>
      </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="1861" g_stop="1802" g_length="60"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="59" r_length="59" r_score="0.900"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.986" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="60" r_stop="207" r_length="148" r_score="0.966"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.98"/>
            <acceptor a_prob="1.000" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="550" g_length="135"/>
          <reference_exon_boundary r_type="cDNA" r_start="208" r_stop="342" r_length="135" r_score="0.970"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E200163" ref_strand="+">
        <total_alignment_score>0.956</total_alignment_score>
        <cumulative_length_of_scored_exons>343</cumulative_length_of_scored_exons>
        <coverage percentage="1.003" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E200163" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1861" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="550"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCAC</genome_strand>
        <mrna_strand>GCA-CGAGCTCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGTTGCGGATGGAGGGTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGCTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGAGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAGAAAGGTAGGAGGATCAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCTGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCAC</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E300241" ref_strand="+" ref_description="SGN-E300241 [cLEW-17-F15]">
      <seq>cccgtgcgaactgatgccttcataatggccactcgtactcagaacgttcttggtgaaaaaggtaggagaattagggagctgacttcagttgttcagaagcggtttaatttcaaggaaaacactgttgagctctatgcagagaaagtcaacaataggggtctctgtgccattgctc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="1903" stop="262"/>
      </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="1620" g_stop="1569" g_length="52"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="52" r_length="52" r_score="0.885"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.88"/>
            <acceptor a_prob="1.000" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="684" g_stop="562" g_length="123"/>
          <reference_exon_boundary r_type="cDNA" r_start="53" r_stop="175" r_length="123" r_score="0.992"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E300241" ref_strand="+">
        <total_alignment_score>0.960</total_alignment_score>
        <cumulative_length_of_scored_exons>175</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E300241" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1620" e_stop="1569"/>
          <exon e_start="684" e_stop="562"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTC</genome_strand>
        <mrna_strand>CCCGTGCGAACTGATGCCTTCATAATGGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGGTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTC</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E443612" ref_strand="+" ref_description="SGN-E443612 [cSTA-39-I1]">
      <seq>tttgtatctgccatcggccgcagtgaatcaatatcaaaccctaatctcaacatggcgacgcctcagattagtaaaaagcgaaagtttgtagcggatggagttttttttgcggagttgaacgaagtgctgacaagagagttggcggaggatggttactcgggagttgaagttagggttactcccatgcgaactgaaatcatcattagggctactcgtactcaaaacgttcttggtgaaaaaggtaggaggattagggagctgacttcagttgttcagaagcgttttaatttcaaggaaaatagtgttgagctctatgcagagaaagtcaacaataggggtcttgtgtgcca</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2185" stop="271"/>
      </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="1885" g_stop="1802" g_length="84"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="84" r_length="84" r_score="0.976"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.986" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="85" r_stop="232" r_length="148" r_score="0.973"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.94"/>
            <acceptor a_prob="1.000" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="568" g_length="117"/>
          <reference_exon_boundary r_type="cDNA" r_start="233" r_stop="350" r_length="118" r_score="0.949"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E443612" ref_strand="+">
        <total_alignment_score>0.966</total_alignment_score>
        <cumulative_length_of_scored_exons>349</cumulative_length_of_scored_exons>
        <coverage percentage="0.997" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E443612" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1885" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="568"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTTGTATCTTCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTC-TCTGTGCCA</genome_strand>
        <mrna_strand>TTTGTATCTGCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTGACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCATGCGAACTGAAATCATCATTAGGGCTACTCGTACTCAAAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAAAAAGGTAGGAGGATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAATAGTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTTGTGTGCCA</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E238306" ref_strand="+" ref_description="SGN-E238306 [cLED-17-E13]">
      <seq>ttgtatcttccatcggccgcagtgaatcaatatcaaaccctaatctcaacatggcgacgcctcagattagtaaaaaacgaaagtttgtagcggatggagttttttttgcggagttgaacgaagtgcttacaagagagttggcggaggatggttactcgggagttgaagttagggttactcccgtgcgaactgaaatcatcattagggccactcgtactcagaacgttcttggtgaaaaaggtaggagaattagggagctgacttcagttgttcagaagcgttttaatttcaaggaaaacactgttgagctctatgcagagaaagtcaacaataggggtctc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2184" stop="275"/>
      </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="1884" g_stop="1802" g_length="83"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="83" r_length="83" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.986" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="84" r_stop="231" r_length="148" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" 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="684" g_stop="575" g_length="110"/>
          <reference_exon_boundary r_type="cDNA" r_start="232" r_stop="341" r_length="110" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E238306" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>341</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E238306" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1884" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="575"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTGTATCTTCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTC</genome_strand>
        <mrna_strand>TTGTATCTTCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAG.....................................................................................TTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTC</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E298274" ref_strand="+" ref_description="SGN-E298274 [cLEW-18-O8]">
      <seq>ttctctgcctcttacttgtatctgctagcggcggcagtgaagctatctcaaagcctaatctcaacatggcgacgcctcagattagtaaaaagcgaaagtttgttgcggatggagttttttttgcggagttgaacgaagtgcttacaagagagctggcggaggatggttactcgggagttgaagttagggttactcccgtgcgaactgaaatcatcattagagccactcgtactcagaacgttcttggtgagaaaggtaggaggatcagggagctgacttcagttgttcagaagcgttttaatttcaaggaaaacacttgtgagctctatgctgagaaagtcaacaataggg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2199" stop="280"/>
      </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="1899" g_stop="1802" g_length="98"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="98" r_length="98" r_score="0.878"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.96"/>
            <acceptor a_prob="0.986" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="99" r_stop="246" r_length="148" r_score="0.980"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.98"/>
            <acceptor a_prob="1.000" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="580" g_length="105"/>
          <reference_exon_boundary r_type="cDNA" r_start="247" r_stop="351" r_length="105" r_score="0.943"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E298274" ref_strand="+">
        <total_alignment_score>0.940</total_alignment_score>
        <cumulative_length_of_scored_exons>351</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E298274" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1899" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="580"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTCACTGCCTCTCATTTGTATCTTCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGG</genome_strand>
        <mrna_strand>TTCTCTGCCTCTTACTTGTATCTGCTAGCGGCGGCAGTGAAGCTATCTCAAAGCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGTTGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGCTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGAGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAGAAAGGTAGGAGGATCAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTTGTGAGCTCTATGCTGAGAAAGTCAACAATAGGG</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E444275" ref_strand="+" ref_description="SGN-E444275 [cSTA-42-G10]">
      <seq>catttgtatctgccatcggccgcagtgaatcaatatcaaaccctaatctcaacatggcgacgcctcagattagtaaaaagcgaaagtttgtagcggatggagttttttttgcggagttgaacgaagtgctgacaagagagttggcggaggatggttactcgggagttgaagttagggttactcccatgcgaactgaaatcatcattagggctactcgtactcaaaacgttcttggtgaaaaaggtaggaggattagggagctgacttcagttgttcagaagcgttttaatttcaaggaaaatagtgttgagctctatgcagagaaagtcaacaatag</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2187" stop="282"/>
      </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="1887" g_stop="1802" g_length="86"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="86" r_length="86" r_score="0.977"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.986" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="87" r_stop="234" r_length="148" r_score="0.973"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.94"/>
            <acceptor a_prob="1.000" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="582" g_length="103"/>
          <reference_exon_boundary r_type="cDNA" r_start="235" r_stop="337" r_length="103" r_score="0.971"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E444275" ref_strand="+">
        <total_alignment_score>0.973</total_alignment_score>
        <cumulative_length_of_scored_exons>337</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E444275" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1887" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="582"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CATTTGTATCTTCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAG</genome_strand>
        <mrna_strand>CATTTGTATCTGCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTGACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCATGCGAACTGAAATCATCATTAGGGCTACTCGTACTCAAAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAAAAAGGTAGGAGGATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAATAGTGTTGAGCTCTATGCAGAGAAAGTCAACAATAG</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E318926" ref_strand="+" ref_description="SGN-E318926 [cTOB-11-D2]">
      <seq>tctatctcaaaccctaatctcaacatggcgacgcctcagattagtaaaaagcgaaagtttgttgcggatggagttttttttgcggagttgaacgaaatgcttacaagagagctggcggaggatggttactcgggagttgaagttagggttactcccgtgcgaactgaaatcatcattagagccactcgtactcagaacgttcttggtgagaaaggtaggaggatcagggagctgacttcagttgttcagaagcgttttaatttcaaggaaaacactgttgagctctatgctgagaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2158" stop="294"/>
      </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="1858" g_stop="1802" g_length="57"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="57" r_length="57" r_score="0.947"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.986" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="58" r_stop="205" r_length="148" r_score="0.973"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.98"/>
            <acceptor a_prob="1.000" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="594" g_length="91"/>
          <reference_exon_boundary r_type="cDNA" r_start="206" r_stop="296" r_length="91" r_score="0.956"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E318926" ref_strand="+">
        <total_alignment_score>0.963</total_alignment_score>
        <cumulative_length_of_scored_exons>296</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E318926" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1858" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="594"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAA</genome_strand>
        <mrna_strand>TCTATCTCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGTTGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAATGCTTACAAGAGAGCTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGAGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAGAAAGGTAGGAGGATCAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCTGAGAA</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E210130" ref_strand="+" ref_description="SGN-E210130 [cLEC-40-L5]">
      <seq>tcaaaccctaatcttaacatggcgacgcctcagattaataaaaagcgaaagtctgttgcggatggagttttttttgcggagttgaacgaagtgcttacaagagagctggcggaggatggttactcgggagttgaagttagggttactcccgcgcgaactgaaatcatcattagagccactcgttctcagaacgttcttggtgagaaaggtaggaggatcaaggagctgacttgagttgttcataagcgttttaatttcaaggaaaacactgttgagctctatgctgagaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2152" stop="294"/>
      </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="1852" g_stop="1802" g_length="51"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="51" r_length="51" r_score="0.941"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.94"/>
            <acceptor a_prob="0.986" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="52" r_stop="199" r_length="148" r_score="0.959"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.94"/>
            <acceptor a_prob="1.000" a_score="0.88"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="594" g_length="91"/>
          <reference_exon_boundary r_type="cDNA" r_start="200" r_stop="290" r_length="91" r_score="0.923"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E210130" ref_strand="+">
        <total_alignment_score>0.945</total_alignment_score>
        <cumulative_length_of_scored_exons>290</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E210130" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1852" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="594"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAA</genome_strand>
        <mrna_strand>TCAAACCCTAATCTTAACATGGCGACGCCTCAGATTAATAAAAAGCGAAAG.....................................................................................TCTGTTGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGCTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGCGCGAACTGAAATCATCATTAGAGCCACTCGTTCTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAGAAAGGTAGGAGGATCAAGGAGCTGACTTGAGTTGTTCATAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCTGAGAA</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E400102" ref_strand="+" ref_description="SGN-E400102 [cSTC-4-H8]">
      <seq>ccgtattgaatcaatatcaaaccctaatctgaacatggttacgcctcagattattaaaaagcgaaagtttgtagcggatggagttttttttgcggagttgaacgaagtgctgacaagagagttggcggaggatggttactcgggagttgaagttagggttactcccatgcgaactgaaatcatcattagggctactcgtactcaaaacgttcttggtgaaaaaggtaggaggattagggagctgacttcagttgttcataagcgttttaatttcatggaaaatagtgtcgagctctatg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2168" stop="301"/>
      </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="1868" g_stop="1802" g_length="67"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="67" r_length="67" r_score="0.896"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.90"/>
            <acceptor a_prob="0.986" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="68" r_stop="215" r_length="148" r_score="0.973"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.94"/>
            <acceptor a_prob="1.000" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="601" g_length="84"/>
          <reference_exon_boundary r_type="cDNA" r_start="216" r_stop="299" r_length="84" r_score="0.929"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E400102" ref_strand="+">
        <total_alignment_score>0.943</total_alignment_score>
        <cumulative_length_of_scored_exons>299</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E400102" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1868" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="601"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATG</genome_strand>
        <mrna_strand>CCGTATTGAATCAATATCAAACCCTAATCTGAACATGGTTACGCCTCAGATTATTAAAAAGCGAAAG.....................................................................................TTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTGACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCATGCGAACTGAAATCATCATTAGGGCTACTCGTACTCAAAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAAAAAGGTAGGAGGATTAGGGAGCTGACTTCAGTTGTTCATAAGCGTTTTAATTTCATGGAAAATAGTGTCGAGCTCTATG</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E443613" ref_strand="+" ref_description="SGN-E443613 [cSTA-39-I3]">
      <seq>tttgtatctgccatcggccgcagtgaatcaatatcaaaccctaatctcaacatggcgacgcctcagattagttaaaagcgaaagtttgtagcggatggagttttttttgcggagttgaacgaagtgctgacaagagagttggcggaggatggttactccggagttgaagttagggttactcccatgcgaactgaaatcatcattagggctactcgtactcaaaacgttcttggtgaaaaaggtaggaggattagggagctgacttcagttgttcagaagcgttttaatttcaaggaaaat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2185" stop="318"/>
      </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="1885" g_stop="1802" g_length="84"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="84" r_length="84" r_score="0.964"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.96"/>
            <acceptor a_prob="0.986" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="85" r_stop="232" r_length="148" r_score="0.966"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.94"/>
            <acceptor a_prob="1.000" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="617" g_length="68"/>
          <reference_exon_boundary r_type="cDNA" r_start="233" r_stop="300" r_length="68" r_score="0.971"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E443613" ref_strand="+">
        <total_alignment_score>0.967</total_alignment_score>
        <cumulative_length_of_scored_exons>300</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E443613" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1885" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="617"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTTGTATCTTCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAAC</genome_strand>
        <mrna_strand>TTTGTATCTGCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTTAAAAGCGAAAG.....................................................................................TTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTGACAAGAGAGTTGGCGGAGGATGGTTACTCCGGAGTTGAAGTTAGGGTTACTCCCATGCGAACTGAAATCATCATTAGGGCTACTCGTACTCAAAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAAAAAGGTAGGAGGATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAAT</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E447643" ref_strand="+" ref_description="SGN-E447643 [cSTA-28-I1]">
      <seq>ggcggcagtgaatcaatatcaaaccctaatctcaacatggcgacgcctcagattagtaaaaagcgaaagtttgtagcagatggagttttttttgcggagttgaacgaagtgctgacaaaagagctggcggaggatggttactcgggagttgaagttagggttactcccatgcgaactgaaatcatcattagagccactcgtactcaaaacgttcttggtgagaaaagtaggaggatcagggagctgacttcagttgttcaaaagcgttttaatttcaaggaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2170" stop="319"/>
      </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="1870" g_stop="1802" g_length="69"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="69" r_length="69" r_score="0.971"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.986" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="70" r_stop="217" r_length="148" r_score="0.953"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.94"/>
            <acceptor a_prob="1.000" a_score="0.90"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="619" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="218" r_stop="283" r_length="66" r_score="0.924"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E447643" ref_strand="+">
        <total_alignment_score>0.951</total_alignment_score>
        <cumulative_length_of_scored_exons>283</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E447643" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1870" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="619"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAA</genome_strand>
        <mrna_strand>GGCGGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGTAGCAGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTGACAAAAGAGCTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCATGCGAACTGAAATCATCATTAGAGCCACTCGTACTCAAAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAGAAAAGTAGGAGGATCAGGGAGCTGACTTCAGTTGTTCAAAAGCGTTTTAATTTCAAGGAAA</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E557582" ref_strand="+" ref_description="SGN-E557582 [16403]">
      <seq>tgcctctcatttgtatctgccatcggccgcagtgaatcaatatcaaaccctaattctcaacataggcgacgcctcagattagtaaaaagcgaaagtttgtagcggatggagttttttttgcggagttgaacgaagtgctgacaagagagttggcggaggatggttactcgggagttgaagttagggttactcccatgcgaactgaaatcatcattagggctactcgtactcaaaacgttcttggtgaaaaaggtaggaggattagggagctgacttcagttgt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="2194" stop="345"/>
      </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="1894" g_stop="1802" g_length="93"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="95" r_length="95" r_score="0.935"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85">
            <donor d_prob="0.999" d_score="0.90"/>
            <acceptor a_prob="0.986" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="1716" g_stop="1569" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="96" r_stop="243" r_length="148" r_score="0.973"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.94"/>
            <acceptor a_prob="1.000" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="684" g_stop="645" g_length="40"/>
          <reference_exon_boundary r_type="cDNA" r_start="244" r_stop="283" r_length="40" r_score="0.975"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E557582" ref_strand="+">
        <total_alignment_score>0.959</total_alignment_score>
        <cumulative_length_of_scored_exons>281</cumulative_length_of_scored_exons>
        <coverage percentage="0.993" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E557582" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1894" e_stop="1802"/>
          <exon e_start="1716" e_stop="1569"/>
          <exon e_start="684" e_stop="645"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TGCCTCTCATTTGTATCTTCCATCGGCCGCAGTGAATCAATATCAAACCCTAA-TCTCAACAT-GGCGACGCCTCAGATTAGTAAAAAACGAAAGGTACGTCAGTTCAACTTCTCGCTGTGATTTTAGATCCAACTGAATATTTATAGTATGCCATGATTTGATTTTTGTATGTGTCTAGTTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGT</genome_strand>
        <mrna_strand>TGCCTCTCATTTGTATCTGCCATCGGCCGCAGTGAATCAATATCAAACCCTAATTCTCAACATAGGCGACGCCTCAGATTAGTAAAAAGCGAAAG.....................................................................................TTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTGACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCATGCGAACTGAAATCATCATTAGGGCTACTCGTACTCAAAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAAAAAGGTAGGAGGATTAGGGAGCTGACTTCAGTTGT</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E372869" ref_strand="+" ref_description="SGN-E372869 [TUS-32-N20](-)">
      <seq>agaattacaaaagagagaaaagaagagtgagacatcacagaggaaaataatctttaaggaaaaatagagagtgtgagcgatattgtagtgagatggaaaaatcaaaagagtgttatttcttttgaatgtgtagtgatctttagagttttactcaaacatacaagtgtaaaatccttactatagtgatattcgttgcttctcttgggtcgtggtttttctcttatttaggagggtttccacgtaaaaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="13408" stop="12564"/>
      </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="13108" g_stop="12870" g_length="239"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="240" r_length="240" r_score="0.933"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="243" polyA_stop="263"/>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E372869" ref_strand="+">
        <total_alignment_score>0.933</total_alignment_score>
        <cumulative_length_of_scored_exons>239</cumulative_length_of_scored_exons>
        <coverage percentage="0.909" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E372869" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="13108" e_stop="12870"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGAATTACAAAGGAGAGAAAAGAAGACTGAGGCATCACAGAGGAAAATATTCTGTGAGGAAAAATAGAGAGTGTGAGCGATATTGTAGTGAGGTGGAAAAATC-AAAGACTGTTATTTCTTTTGAATGTGTAGTGGTCTTTGGAGTTTTACTCAGACATACAAGTGTAAAATCCTTGCTATAGTGATATTCGTTGCTCCTCTCGGGTCGTGGTTTTTCTCTTATTTAGGAGGGTTTCCAC</genome_strand>
        <mrna_strand>AGAATTACAAAAGAGAGAAAAGAAGAGTGAGACATCACAGAGGAAAATAATCTTTAAGGAAAAATAGAGAGTGTGAGCGATATTGTAGTGAGATGGAAAAATCAAAAGAGTGTTATTTCTTTTGAATGTGTAGTGATCTTTAGAGTTTTACTCAAACATACAAGTGTAAAATCCTTACTATAGTGATATTCGTTGCTTCTCTTGGGTCGTGGTTTTTCTCTTATTTAGGAGGGTTTCCAC</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E298763" ref_strand="+" ref_description="SGN-E298763 [cLET-44-E9]">
      <seq>gaattacaaaagagagaaaagaagagtgagacatcacagaggaaaataatctctaaggaaaaatagagagtgtgagcgatattgtagtgagatggaaaaatcaaaagagtgttatttcttttgaatgtgtagtgatctttagagttttactcaaacatacaagtgtaaaatccttactatagtgatattcgttgcttctcttgggtcgtggtttttctcttatttaggagggtttccacg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="13407" stop="12569"/>
      </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="13107" g_stop="12870" g_length="238"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="239" r_length="239" r_score="0.933"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E298763" ref_strand="+">
        <total_alignment_score>0.933</total_alignment_score>
        <cumulative_length_of_scored_exons>238</cumulative_length_of_scored_exons>
        <coverage percentage="0.992" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E298763" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="13107" e_stop="12870"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GAATTACAAAGGAGAGAAAAGAAGACTGAGGCATCACAGAGGAAAATATTCTGTGAGGAAAAATAGAGAGTGTGAGCGATATTGTAGTGAGGTGGAAAAATC-AAAGACTGTTATTTCTTTTGAATGTGTAGTGGTCTTTGGAGTTTTACTCAGACATACAAGTGTAAAATCCTTGCTATAGTGATATTCGTTGCTCCTCTCGGGTCGTGGTTTTTCTCTTATTTAGGAGGGTTTCCAC</genome_strand>
        <mrna_strand>GAATTACAAAAGAGAGAAAAGAAGAGTGAGACATCACAGAGGAAAATAATCTCTAAGGAAAAATAGAGAGTGTGAGCGATATTGTAGTGAGATGGAAAAATCAAAAGAGTGTTATTTCTTTTGAATGTGTAGTGATCTTTAGAGTTTTACTCAAACATACAAGTGTAAAATCCTTACTATAGTGATATTCGTTGCTTCTCTTGGGTCGTGGTTTTTCTCTTATTTAGGAGGGTTTCCAC</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E372870" ref_strand="+" ref_description="SGN-E372870 [TUS-32-N20]">
      <seq>gaattacaaaagagagaaaagaagagtgagacatcacagaggaaaataatctctaaggaaaaatagagagtgtgagcgatattgtagtgagatggaaaaatcaaaagagtgttatttcttttgaatgtgtagtgatctttagagttttactcaaacatacaagtgtaaaatccttactatagtgatattcgttgcttctcttgggtcgtggtttttctcttatttaggagggtttccacgtaaaaaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="13407" stop="12564"/>
      </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="13107" g_stop="12870" g_length="238"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="239" r_length="239" r_score="0.933"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="242" polyA_stop="263"/>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E372870" ref_strand="+">
        <total_alignment_score>0.933</total_alignment_score>
        <cumulative_length_of_scored_exons>238</cumulative_length_of_scored_exons>
        <coverage percentage="0.905" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E372870" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="13107" e_stop="12870"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GAATTACAAAGGAGAGAAAAGAAGACTGAGGCATCACAGAGGAAAATATTCTGTGAGGAAAAATAGAGAGTGTGAGCGATATTGTAGTGAGGTGGAAAAATC-AAAGACTGTTATTTCTTTTGAATGTGTAGTGGTCTTTGGAGTTTTACTCAGACATACAAGTGTAAAATCCTTGCTATAGTGATATTCGTTGCTCCTCTCGGGTCGTGGTTTTTCTCTTATTTAGGAGGGTTTCCAC</genome_strand>
        <mrna_strand>GAATTACAAAAGAGAGAAAAGAAGAGTGAGACATCACAGAGGAAAATAATCTCTAAGGAAAAATAGAGAGTGTGAGCGATATTGTAGTGAGATGGAAAAATCAAAAGAGTGTTATTTCTTTTGAATGTGTAGTGATCTTTAGAGTTTTACTCAAACATACAAGTGTAAAATCCTTACTATAGTGATATTCGTTGCTTCTCTTGGGTCGTGGTTTTTCTCTTATTTAGGAGGGTTTCCAC</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E378778" ref_strand="+" ref_description="SGN-E378778 [TUS-32-N20]">
      <seq>gaattacaaaagagagaaaagaagagtgagacatcacagaggaaaataatctctaaggaaaaatagagagtgtgagcgatattgtagtgagatggaaaaatcaaaagagtgttatttcttttgaatgtgtagtgatctttagagttttactcaaacatacaagtgtaaaatccttactatagtgatattcgttgcttctcttgggtcgtggtttttctcttatttaggagggtttccacgtaaaaaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="13407" stop="12564"/>
      </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="13107" g_stop="12870" g_length="238"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="239" r_length="239" r_score="0.933"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="242" polyA_stop="263"/>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E378778" ref_strand="+">
        <total_alignment_score>0.933</total_alignment_score>
        <cumulative_length_of_scored_exons>238</cumulative_length_of_scored_exons>
        <coverage percentage="0.905" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E378778" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="13107" e_stop="12870"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GAATTACAAAGGAGAGAAAAGAAGACTGAGGCATCACAGAGGAAAATATTCTGTGAGGAAAAATAGAGAGTGTGAGCGATATTGTAGTGAGGTGGAAAAATC-AAAGACTGTTATTTCTTTTGAATGTGTAGTGGTCTTTGGAGTTTTACTCAGACATACAAGTGTAAAATCCTTGCTATAGTGATATTCGTTGCTCCTCTCGGGTCGTGGTTTTTCTCTTATTTAGGAGGGTTTCCAC</genome_strand>
        <mrna_strand>GAATTACAAAAGAGAGAAAAGAAGAGTGAGACATCACAGAGGAAAATAATCTCTAAGGAAAAATAGAGAGTGTGAGCGATATTGTAGTGAGATGGAAAAATCAAAAGAGTGTTATTTCTTTTGAATGTGTAGTGATCTTTAGAGTTTTACTCAAACATACAAGTGTAAAATCCTTACTATAGTGATATTCGTTGCTTCTCTTGGGTCGTGGTTTTTCTCTTATTTAGGAGGGTTTCCAC</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E705627" ref_strand="+" ref_description="SGN-E705627 [FA27CG08]">
      <seq>ctcgtagtcagtcaatatgagggttcgcttggggaccctcaaatgttgatcacgttgagggtgtagattgggatcgtgataaaaggtaacaactcgatatatcctgaaagttcagtcactgttattgaagcacggaagagttggatgggtctcatgtattccatattagcaaaattatgtgtgctactcaaagttgaaaggataaatttgccaggtgcgcttaagatggtggcttgggaagaatgattttattcttgatcaaggtctttgagtgaaattggatggaatagtggaaccaactcaaaagatacacatttggtattggatacaagcctactcctaaagaagtctcatcgtctaatctcaaaaagaaaagtggcattcccttaccacaacctatcccactcttgaatcagtcatttcaagacattgcacaagaatattcagaggaaagtgttgagataacctcaaaaacttgttcattgaagaagttgaatgcaatatgagtttggaggattgcattgaggcctggaccacatgggatactatgcttggagatactttgaacaattggacttgtaacccgtccacggttcccacaaaatattggtagatgattgtattagaattaacaaaatagcatggtctaaatttgtggggtccattcccatgtaccaaactttgaataactctctgncaatttcaaagtttggcaaatttggtgctgaattatttttcaactttacttaattttcaatagtaggtaagctatgaagaaaaacaattgtttttcttctatagcacatttggagggtagtgcatttgtttttcaataaatggag</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="19261" stop="17820"/>
      </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="18961" g_stop="18120" g_length="842"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="842" r_length="842" r_score="0.993"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E705627" ref_strand="+">
        <total_alignment_score>0.993</total_alignment_score>
        <cumulative_length_of_scored_exons>842</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E705627" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="18961" e_stop="18120"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTCGTAGTCAGTCAATATGAGGGTTCGCTTGGGGACCCTCAAATGTTGATCACGTTGAGGGTGTAGATTGGGATCGTGATAAAAGGTAACAACTCGATATATCCTGAAAGTTCAGTCACTGTTATTGAAGCACGGAAGAGTTGGATGGGTCTCATGTATTCCATATTAGCAAAATTATGTGTGCTACTCAAAGTTGAAAGGATAAATTTGCCAGGTGCGCTTAAGATGGTGGCTTGGGAAGAATGATTTTATTCTTGATCAAGGTCTTTGAGTGAAATTGGATGGAATAGTGGAACCAACTCAAAAGATACACATTTGGTATTGGATACAAGCCTACTCCTAAAGAAGTCTCATCGTCTAATCTCAAAAAGAAAAGTGGCATTCCCTTACCACAACCTATCCCACTCTTGAATCAGTCATTTCAAGACATTGCACAAGAATATTCAGAGGAAAGTGTTGAGATAACCTCAAAAACTTGTTCATTGAAGAAGTTGAATGCAATATGAGTTTGGAGGATTGCATTGAGGCCTGGACCACATGGGATACTATGCTTGGAGATACTTTGAACAATTGGACTTGTAACCCGTCCACGGTTCCCACAAAATATTGGTAGATGATTGTATTAGAATTAACAAAATAGCATGGTCTAAATTTGTGGGGTCCATTCCCATGTACCAAACTTTGAATAACTCTCTGCAAATTTCAAAGTTTGGCAAATTTGGTGCTGAATTATTTTTCAACTTTACTTAATTTTCAATAGTAGGTAAGCTATGAAGAAAAACAATTGTTTTTCTTCTATAGCACATTTGGAGGGTAGTGCATTTGTTTTCAATAAAATGGAG</genome_strand>
        <mrna_strand>CTCGTAGTCAGTCAATATGAGGGTTCGCTTGGGGACCCTCAAATGTTGATCACGTTGAGGGTGTAGATTGGGATCGTGATAAAAGGTAACAACTCGATATATCCTGAAAGTTCAGTCACTGTTATTGAAGCACGGAAGAGTTGGATGGGTCTCATGTATTCCATATTAGCAAAATTATGTGTGCTACTCAAAGTTGAAAGGATAAATTTGCCAGGTGCGCTTAAGATGGTGGCTTGGGAAGAATGATTTTATTCTTGATCAAGGTCTTTGAGTGAAATTGGATGGAATAGTGGAACCAACTCAAAAGATACACATTTGGTATTGGATACAAGCCTACTCCTAAAGAAGTCTCATCGTCTAATCTCAAAAAGAAAAGTGGCATTCCCTTACCACAACCTATCCCACTCTTGAATCAGTCATTTCAAGACATTGCACAAGAATATTCAGAGGAAAGTGTTGAGATAACCTCAAAAACTTGTTCATTGAAGAAGTTGAATGCAATATGAGTTTGGAGGATTGCATTGAGGCCTGGACCACATGGGATACTATGCTTGGAGATACTTTGAACAATTGGACTTGTAACCCGTCCACGGTTCCCACAAAATATTGGTAGATGATTGTATTAGAATTAACAAAATAGCATGGTCTAAATTTGTGGGGTCCATTCCCATGTACCAAACTTTGAATAACTCTCTGNCAATTTCAAAGTTTGGCAAATTTGGTGCTGAATTATTTTTCAACTTTACTTAATTTTCAATAGTAGGTAAGCTATGAAGAAAAACAATTGTTTTTCTTCTATAGCACATTTGGAGGGTAGTGCATTTGTTTTTCAATAAATGGAG</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato_potato" ref_id="SGN-E713600" ref_strand="+" ref_description="SGN-E713600 [FB09AD03]">
      <seq>ggaccctcaaatgttgatcacgttgagggtgtagattgggatcgtgataaaaggtaacaactcgatatatcctgaaagttcagtcactgttattgaagcacggaagagttggatgggtctcatgtattccatattagcaaaattatgtgtgctactcaaagttgaaaggataaatttgccaggtgcgcttaagatggtggcttgggaagaatgattttattcttgatcaaggtctttgagtgaaattggatggaatagtggaaccaactcaaaagatacacatttggtattggatacaagcctactcctaaagaagtctcatcgtctaatctcaaaaagaaaagtggcattcccttaccacaacctatcccactcttgaatcagtcatttcaagacattgcacaagaatattcagaggaaagtgttgagataacctcaaaaacttgttcattgaagaagttgaatgcaatatgagtttggaggattgcattgaggcctggaccacatgggatactatgcttggagatactttgaacaattggacttgtaacccgtccacggttcccacaaaatattggtagatgattgtattagaattaacaaaatagcatggtctaaatttgtggggtccattcccatgtaccaaactttgaataactctctgcaaatttcaaagtttggca</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="19229" stop="17947"/>
      </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="18929" g_stop="18247" g_length="683"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="683" r_length="683" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-E713600" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>683</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E713600" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="18929" e_stop="18247"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GGACCCTCAAATGTTGATCACGTTGAGGGTGTAGATTGGGATCGTGATAAAAGGTAACAACTCGATATATCCTGAAAGTTCAGTCACTGTTATTGAAGCACGGAAGAGTTGGATGGGTCTCATGTATTCCATATTAGCAAAATTATGTGTGCTACTCAAAGTTGAAAGGATAAATTTGCCAGGTGCGCTTAAGATGGTGGCTTGGGAAGAATGATTTTATTCTTGATCAAGGTCTTTGAGTGAAATTGGATGGAATAGTGGAACCAACTCAAAAGATACACATTTGGTATTGGATACAAGCCTACTCCTAAAGAAGTCTCATCGTCTAATCTCAAAAAGAAAAGTGGCATTCCCTTACCACAACCTATCCCACTCTTGAATCAGTCATTTCAAGACATTGCACAAGAATATTCAGAGGAAAGTGTTGAGATAACCTCAAAAACTTGTTCATTGAAGAAGTTGAATGCAATATGAGTTTGGAGGATTGCATTGAGGCCTGGACCACATGGGATACTATGCTTGGAGATACTTTGAACAATTGGACTTGTAACCCGTCCACGGTTCCCACAAAATATTGGTAGATGATTGTATTAGAATTAACAAAATAGCATGGTCTAAATTTGTGGGGTCCATTCCCATGTACCAAACTTTGAATAACTCTCTGCAAATTTCAAAGTTTGGCA</genome_strand>
        <mrna_strand>GGACCCTCAAATGTTGATCACGTTGAGGGTGTAGATTGGGATCGTGATAAAAGGTAACAACTCGATATATCCTGAAAGTTCAGTCACTGTTATTGAAGCACGGAAGAGTTGGATGGGTCTCATGTATTCCATATTAGCAAAATTATGTGTGCTACTCAAAGTTGAAAGGATAAATTTGCCAGGTGCGCTTAAGATGGTGGCTTGGGAAGAATGATTTTATTCTTGATCAAGGTCTTTGAGTGAAATTGGATGGAATAGTGGAACCAACTCAAAAGATACACATTTGGTATTGGATACAAGCCTACTCCTAAAGAAGTCTCATCGTCTAATCTCAAAAAGAAAAGTGGCATTCCCTTACCACAACCTATCCCACTCTTGAATCAGTCATTTCAAGACATTGCACAAGAATATTCAGAGGAAAGTGTTGAGATAACCTCAAAAACTTGTTCATTGAAGAAGTTGAATGCAATATGAGTTTGGAGGATTGCATTGAGGCCTGGACCACATGGGATACTATGCTTGGAGATACTTTGAACAATTGGACTTGTAACCCGTCCACGGTTCCCACAAAATATTGGTAGATGATTGTATTAGAATTAACAAAATAGCATGGTCTAAATTTGTGGGGTCCATTCCCATGTACCAAACTTTGAATAACTCTCTGCAAATTTCAAAGTTTGGCA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>32</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="1967" PGL_stop="513"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="1967" e_stop="1802"/>
            <exon e_start="1716" e_stop="1569"/>
            <exon e_start="684" e_stop="513"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.999" acc_prob="0.986" e_score="0.892"/>
          <exon-intron don_prob="0.997" acc_prob="1.000" e_score="1.000"/>
          <exon-only e_score="1.000"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="0.892">
            <gDNA_exon_boundary e_start="1967" e_stop="1802" e_length="166"/>
          </exon>
          <intron i_serial="1" don_prob="0.999" acc_prob="0.986">
            <gDNA_intron_boundary i_start="1801" i_stop="1717" i_length="85"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="1716" e_stop="1569" e_length="148"/>
          </exon>
          <intron i_serial="2" don_prob="0.997" acc_prob="1.000">
            <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="684" e_stop="513" e_length="172"/>
          </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="1967" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="532"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E472612" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1926" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="543"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E445951" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1907" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="513"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E318754" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1904" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="531"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E325034" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1899" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="513"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E324155" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1899" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="580"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E298274" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1897" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="520"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E206585" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1894" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="645"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E557582" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1891" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="528"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E277167" strand="-"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1887" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="582"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E444275" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1885" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="568"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E443612" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1885" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="617"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E443613" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1884" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="575"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E238306" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1870" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="513"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E442262" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1870" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="619"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E447643" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1868" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="513"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E467402" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1868" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="601"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E400102" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1866" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="513"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E281280" strand="-"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1865" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="513"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E725452" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1861" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="550"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E200163" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1858" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="594"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E318926" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1852" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="594"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E210130" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1826" stop="1802"/>
              <exon start="1716" stop="1569"/>
              <exon start="684" stop="513"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E584537" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1708" stop="1569"/>
              <exon start="684" stop="520"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E250347" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1647" stop="1569"/>
              <exon start="684" stop="526"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E239876" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1620" stop="1569"/>
              <exon start="684" stop="562"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E300241" 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>AGAGAGCCCAACTAGTAACCTGCCTTAAATCTTTGACAAACCCTTTCTCCCTTGTCCTAATCCAACTCTTCACTGCCTCTCATTTGTATCTTCCATCGGCCGCAGTGAATCAATATCAAACCCTAATCTCAACATGGCGACGCCTCAGATTAGTAAAAAACGAAAG : TTTGTAGCGGATGGAGTTTTTTTTGCGGAGTTGAACGAAGTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTG : GTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAATTACTTGGAGGACTTGCTGTCCGAAG</gDNA_template>
            <first_frame> R  E  P  N  *  *  P  A  L  N  L  *  Q  T  L  S  P  L  S  *  S  N  S  S  L  P  L  I  C  I  F  H  R  P  Q  *  I  N  I  K  P  *  S  Q  H  G  D  A  S  D  *  *  K  T  K   : V  C  S  G  W  S  F  F  C  G  V  E  R  S  A  Y  K  R  V  G  G  G  W  L  L  G  S  *  S  *  G  Y  S  R  A  N  *  N  H  H  *  G  H  S  Y  S  E  R  S  W :   *  K  R  *  E  N  *  G  A  D  F  S  C  S  E  A  F  *  F  Q  G  K  H  C  *  A  L  C  R  E  S  Q  Q  *  G  S  L  C  H  C  S  G  R  V  T  A  I  Q  I  T  W  R  T  C  C  P  K </first_frame>
            <second_frame>  E  S  P  T  S  N  L  P  *  I  F  D  K  P  F  L  P  C  P  N  P  T  L  H  C  L  S  F  V  S  S  I  G  R  S  E  S  I  S  N  P  N  L  N  M  A  T  P  Q  I  S  K  K  R  K  :  F  V  A  D  G  V  F  F  A  E  L  N  E  V  L  T  R  E  L  A  E  D  G  Y  S  G  V  E  V  R  V  T  P  V  R  T  E  I  I  I  R  A  T  R  T  Q  N  V  L   : G  E  K  G  R  R  I  R  E  L  T  S  V  V  Q  K  R  F  N  F  K  E  N  T  V  E  L  Y  A  E  K  V  N  N  R  G  L  C  A  I  A  Q  A  E  S  L  R  Y  K  L  L  G  G  L  A  V  R   </second_frame>
            <third_frame>   R  A  Q  L  V  T  C  L  K  S  L  T  N  P  F  S  L  V  L  I  Q  L  F  T  A  S  H  L  Y  L  P  S  A  A  V  N  Q  Y  Q  T  L  I  S  T  W  R  R  L  R  L  V  K  N  E  S :   L  *  R  M  E  F  F  L  R  S  *  T  K  C  L  Q  E  S  W  R  R  M  V  T  R  E  L  K  L  G  L  L  P  C  E  L  K  S  S  L  G  P  L  V  L  R  T  F  L  :  V  K  K  V  G  E  L  G  S  *  L  Q  L  F  R  S  V  L  I  S  R  K  T  L  L  S  S  M  Q  R  K  S  T  I  G  V  S  V  P  L  L  R  Q  S  H  C  D  T  N  Y  L  E  D  L  L  S  E  </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C00SLf0138K20.2" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="1939" stop="1802"/>
                    <exon start="1716" stop="1569"/>
                    <exon start="684" stop="515"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>456</number_coding_nucleotides>
                  <number_encoded_amino_acids>152</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>IFDKPFLPCPNPTLHCLSFVSSIGRSESISNPNLNMATPQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFNFKENTVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVR</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="13108" PGL_stop="12870"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="13108" e_stop="12870"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.933"/>
        </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="0.933">
            <gDNA_exon_boundary e_start="13108" e_stop="12870" e_length="239"/>
          </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="13108" stop="12870"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E372869" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="13107" stop="12870"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E298763" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="13107" stop="12870"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E372870" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="13107" stop="12870"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E378778" 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>AGAATTACAAAGGAGAGAAAAGAAGACTGAGGCATCACAGAGGAAAATATTCTGTGAGGAAAAATAGAGAGTGTGAGCGATATTGTAGTGAGGTGGAAAAATCAAAGACTGTTATTTCTTTTGAATGTGTAGTGGTCTTTGGAGTTTTACTCAGACATACAAGTGTAAAATCCTTGCTATAGTGATATTCGTTGCTCCTCTCGGGTCGTGGTTTTTCTCTTATTTAGGAGGGTTTCCAC</gDNA_template>
            <first_frame> R  I  T  K  E  R  K  E  D  *  G  I  T  E  E  N  I  L  *  G  K  I  E  S  V  S  D  I  V  V  R  W  K  N  Q  R  L  L  F  L  L  N  V  *  W  S  L  E  F  Y  S  D  I  Q  V  *  N  P  C  Y  S  D  I  R  C  S  S  R  V  V  V  F  L  L  F  R  R  V  S   </first_frame>
            <second_frame>  E  L  Q  R  R  E  K  K  T  E  A  S  Q  R  K  I  F  C  E  E  K  *  R  V  *  A  I  L  *  *  G  G  K  I  K  D  C  Y  F  F  *  M  C  S  G  L  W  S  F  T  Q  T  Y  K  C  K  I  L  A  I  V  I  F  V  A  P  L  G  S  W  F  F  S  Y  L  G  G  F  P  </second_frame>
            <third_frame>   N  Y  K  G  E  K  R  R  L  R  H  H  R  G  K  Y  S  V  R  K  N  R  E  C  E  R  Y  C  S  E  V  E  K  S  K  T  V  I  S  F  E  C  V  V  V  F  G  V  L  L  R  H  T  S  V  K  S  L  L  *  *  Y  S  L  L  L  S  G  R  G  F  S  L  I  *  E  G  F  H </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="C00SLf0138K20.2"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="3" PGL_strand="-" PGL_start="18961" PGL_stop="18120"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="18961" e_stop="18120"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <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="0.993">
            <gDNA_exon_boundary e_start="18961" e_stop="18120" e_length="842"/>
          </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="18961" stop="18120"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E705627" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="18929" stop="18247"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E713600" 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>CTCGTAGTCAGTCAATATGAGGGTTCGCTTGGGGACCCTCAAATGTTGATCACGTTGAGGGTGTAGATTGGGATCGTGATAAAAGGTAACAACTCGATATATCCTGAAAGTTCAGTCACTGTTATTGAAGCACGGAAGAGTTGGATGGGTCTCATGTATTCCATATTAGCAAAATTATGTGTGCTACTCAAAGTTGAAAGGATAAATTTGCCAGGTGCGCTTAAGATGGTGGCTTGGGAAGAATGATTTTATTCTTGATCAAGGTCTTTGAGTGAAATTGGATGGAATAGTGGAACCAACTCAAAAGATACACATTTGGTATTGGATACAAGCCTACTCCTAAAGAAGTCTCATCGTCTAATCTCAAAAAGAAAAGTGGCATTCCCTTACCACAACCTATCCCACTCTTGAATCAGTCATTTCAAGACATTGCACAAGAATATTCAGAGGAAAGTGTTGAGATAACCTCAAAAACTTGTTCATTGAAGAAGTTGAATGCAATATGAGTTTGGAGGATTGCATTGAGGCCTGGACCACATGGGATACTATGCTTGGAGATACTTTGAACAATTGGACTTGTAACCCGTCCACGGTTCCCACAAAATATTGGTAGATGATTGTATTAGAATTAACAAAATAGCATGGTCTAAATTTGTGGGGTCCATTCCCATGTACCAAACTTTGAATAACTCTCTGCAAATTTCAAAGTTTGGCAAATTTGGTGCTGAATTATTTTTCAACTTTACTTAATTTTCAATAGTAGGTAAGCTATGAAGAAAAACAATTGTTTTTCTTCTATAGCACATTTGGAGGGTAGTGCATTTGTTTTCAATAAAATGGAG</gDNA_template>
            <first_frame> L  V  V  S  Q  Y  E  G  S  L  G  D  P  Q  M  L  I  T  L  R  V  *  I  G  I  V  I  K  G  N  N  S  I  Y  P  E  S  S  V  T  V  I  E  A  R  K  S  W  M  G  L  M  Y  S  I  L  A  K  L  C  V  L  L  K  V  E  R  I  N  L  P  G  A  L  K  M  V  A  W  E  E  *  F  Y  S  *  S  R  S  L  S  E  I  G  W  N  S  G  T  N  S  K  D  T  H  L  V  L  D  T  S  L  L  L  K  K  S  H  R  L  I  S  K  R  K  V  A  F  P  Y  H  N  L  S  H  S  *  I  S  H  F  K  T  L  H  K  N  I  Q  R  K  V  L  R  *  P  Q  K  L  V  H  *  R  S  *  M  Q  Y  E  F  G  G  L  H  *  G  L  D  H  M  G  Y  Y  A  W  R  Y  F  E  Q  L  D  L  *  P  V  H  G  S  H  K  I  L  V  D  D  C  I  R  I  N  K  I  A  W  S  K  F  V  G  S  I  P  M  Y  Q  T  L  N  N  S  L  Q  I  S  K  F  G  K  F  G  A  E  L  F  F  N  F  T  *  F  S  I  V  G  K  L  *  R  K  T  I  V  F  L  L  *  H  I  W  R  V  V  H  L  F  S  I  K  W   </first_frame>
            <second_frame>  S  *  S  V  N  M  R  V  R  L  G  T  L  K  C  *  S  R  *  G  C  R  L  G  S  *  *  K  V  T  T  R  Y  I  L  K  V  Q  S  L  L  L  K  H  G  R  V  G  W  V  S  C  I  P  Y  *  Q  N  Y  V  C  Y  S  K  L  K  G  *  I  C  Q  V  R  L  R  W  W  L  G  K  N  D  F  I  L  D  Q  G  L  *  V  K  L  D  G  I  V  E  P  T  Q  K  I  H  I  W  Y  W  I  Q  A  Y  S  *  R  S  L  I  V  *  S  Q  K  E  K  W  H  S  L  T  T  T  Y  P  T  L  E  S  V  I  S  R  H  C  T  R  I  F  R  G  K  C  *  D  N  L  K  N  L  F  I  E  E  V  E  C  N  M  S  L  E  D  C  I  E  A  W  T  T  W  D  T  M  L  G  D  T  L  N  N  W  T  C  N  P  S  T  V  P  T  K  Y  W  *  M  I  V  L  E  L  T  K  *  H  G  L  N  L  W  G  P  F  P  C  T  K  L  *  I  T  L  C  K  F  Q  S  L  A  N  L  V  L  N  Y  F  S  T  L  L  N  F  Q  *  *  V  S  Y  E  E  K  Q  L  F  F  F  Y  S  T  F  G  G  *  C  I  C  F  Q  *  N  G  </second_frame>
            <third_frame>   R  S  Q  S  I  *  G  F  A  W  G  P  S  N  V  D  H  V  E  G  V  D  W  D  R  D  K  R  *  Q  L  D  I  S  *  K  F  S  H  C  Y  *  S  T  E  E  L  D  G  S  H  V  F  H  I  S  K  I  M  C  A  T  Q  S  *  K  D  K  F  A  R  C  A  *  D  G  G  L  G  R  M  I  L  F  L  I  K  V  F  E  *  N  W  M  E  *  W  N  Q  L  K  R  Y  T  F  G  I  G  Y  K  P  T  P  K  E  V  S  S  S  N  L  K  K  K  S  G  I  P  L  P  Q  P  I  P  L  L  N  Q  S  F  Q  D  I  A  Q  E  Y  S  E  E  S  V  E  I  T  S  K  T  C  S  L  K  K  L  N  A  I  *  V  W  R  I  A  L  R  P  G  P  H  G  I  L  C  L  E  I  L  *  T  I  G  L  V  T  R  P  R  F  P  Q  N  I  G  R  *  L  Y  *  N  *  Q  N  S  M  V  *  I  C  G  V  H  S  H  V  P  N  F  E  *  L  S  A  N  F  K  V  W  Q  I  W  C  *  I  I  F  Q  L  Y  L  I  F  N  S  R  *  A  M  K  K  N  N  C  F  S  S  I  A  H  L  E  G  S  A  F  V  F  N  K  M  E </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C00SLf0138K20.2" strand="-"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="18671" stop="18456"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>213</number_coding_nucleotides>
                  <number_encoded_amino_acids>71</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>WNQLKRYTFGIGYKPTPKEVSSSNLKKKSGIPLPQPIPLLNQSFQDIAQEYSEESVEITSKTCSLKKLNAI*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 139 chains have been computed
$ 
$ memory statistics:
$ 67424 bytes spliced alignments in total
$ 32 spliced alignments have been stored
$ 2107 bytes was the average size of a spliced alignment
$ 8136 bytes predicted gene locations in total
$ 3 predicted gene locations have been stored
$ 2712 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 141 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 06:07:54
-->
