<?xml version="1.0" encoding="ISO-8859-1"?>
<GTH_output xmlns="http://www.genomethreader.org/GTH_output/" GTH_XML_version="1.1">
  <header xmlns="http://www.genomethreader.org/GTH_output/header/">
    <source program="GenomeThreader" version="0.9.54" build_date="2006-07-28 11:55:15" run_date="2009-02-20 08:31:08"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C00SLf0097P22-lNaBf/GenomeThreader_SGN_E_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C00SLf0097P22-lNaBf/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" 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-C00SLf0097P22-lNaBf/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E237342" ref_strand="+" ref_description="SGN-E237342 [cLEL-7-A8](-)">
      <seq>agtgtccgggctaagggagaaaaaatagctttgtggaccaagaatgctgcaaatgaaacagctcaggttagcattggtaagcaatggaagcagtttctagattacagtgattcggttggcttcatatttcncgacgatgcaaagaggctcgacagaaatgccaagaatcgttacaccgtatagttcttgatgcagtgtgggattgcaagaaacacaattcgtactggaaaggttggtaggtactagtttagtttctcatttgataagcttctggagtgagtaactcgtgtgttggtgattaccctttctaatcgtggaaaattgtttgatttgaatccatgcctctatgtttcgtg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0097P22-lNaBf/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C00SLf0097P22.1" temp_strand="-" temp_description="C00SLf0097P22.1  CU856538.2 htgs_phase:3 submitted_to_sgn_as:C04SLf0097P22 sequenced_by:sanger upload_account_name:uk">
        <position start="10326" stop="8694"/>
      </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="10026" g_stop="9961" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="66" r_length="66" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="9960" i_stop="9367" i_length="594">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.991" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="9366" g_stop="9301" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="67" r_stop="132" r_length="66" r_score="0.985"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="9300" i_stop="9218" i_length="83">
            <donor d_prob="0.886" d_score="0.98"/>
            <acceptor a_prob="0.960" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="9217" g_stop="8994" g_length="224"/>
          <reference_exon_boundary r_type="cDNA" r_start="133" r_stop="356" r_length="224" r_score="0.982"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0097P22.1" gen_strand="-" ref_id="SGN-E237342" ref_strand="+">
        <total_alignment_score>0.986</total_alignment_score>
        <cumulative_length_of_scored_exons>356</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0097P22.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E237342" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="10026" e_stop="9961"/>
          <exon e_start="9366" e_stop="9301"/>
          <exon e_start="9217" e_stop="8994"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAGGTAATTTGCTTTATATTTTTGGTGTCAACGGCCACGTTTGTCATTTTCTTGGATCAAGCGGACAGACATTTTTTGTTGTGTACATACTGTAGTGCTGATGTTTATTCAAAATATACTATGAAATACATTGTACCGTTGAGTATATTGGAAGTTAAGAGGGGAAGTCATCAGATATATAGGAAGTGCTCCTTGTGAGAAATTTCTCTAGTAGGGCTCAAACCCGAGAACCATGGTTAAGGACGGAGGGATCCCTTTGGTGGTATCAAGGGTTAATTATATTATTTCATGTTTCATATGATTGAAACATTTGGATATCCTTGCAAAGTGTGATATTGTTTTGTCTCGTCATTTGTTTTATGCTTCATAAGAATTATCTTTTCTTTCGTCCCCTTCTCTTTGTTTCTTTTTCTCCAGTGTACTTCATTCTTCTAGAATTATATAGTGGTCGGCGTTCCCTTTTGTGCTTCATTGATAATATTGAATCCTTTCAGCTGTTTACCGGTTGATTATTTTTATGTTGGTGCTTATTGCTAGTTTTTTGTTTTTATATCTTTGCAACTATACCTACCATCTTCCTGAAACTTCTCTTTACAGGTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCACGTATGAAATCTTGGTTATCATACGCCTTTAATTCAGTTTCTCTTCAATTAGCAAGACTCATAAAGAATCATCTTCTTTTGCAGGACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAGTTCTTGATGCAGTGTGGGATTGCAAGAAACACAATTCGTACTGGAAAGGTTGGTAGGTACTAGTTTAGTTTCTCATTTGATAAGCTTCTGGTTTGAGTAACTCGTGTGTTGGTGTTTACACTTTCTAATCGTGGAAAATTGTTTGATTTGAATCCATGCCTCTATGTTTCGTG</genome_strand>
        <mrna_strand>AGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAG..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCNC...................................................................................GACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAGTTCTTGATGCAGTGTGGGATTGCAAGAAACACAATTCGTACTGGAAAGGTTGGTAGGTACTAGTTTAGTTTCTCATTTGATAAGCTTCTGGAGTGAGTAACTCGTGTGTTGGTGATTACCCTTTCTAATCGTGGAAAATTGTTTGATTTGAATCCATGCCTCTATGTTTCGTG</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-C00SLf0097P22-lNaBf/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E236869" ref_strand="+" ref_description="SGN-E236869 [cLEL-7-A20](-)">
      <seq>aaaatagctttgtggaccaagaatgctgcaaatgaaacagctcaggttagcattggtaagcaatggaagcagtttctagattacagtgattcggttggcttcatatttcacgacgatgcaaagaggctcgacagaaatgccaagaatcgttacaccgtatagttcttgatgcagtgtgggattgcaagaaacacaattcgtactggaaaggttggtaggtactagtttagtttctcatttgataagcttctggtttgagtaactcgtgtgttggtgtttacactttctaatcgtggaaaattgtttgatttgaatccatgcctctatgtttcgtaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0097P22-lNaBf/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C00SLf0097P22.1" temp_strand="-" temp_description="C00SLf0097P22.1  CU856538.2 htgs_phase:3 submitted_to_sgn_as:C04SLf0097P22 sequenced_by:sanger upload_account_name:uk">
        <position start="10305" stop="8695"/>
      </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="10005" g_stop="9961" g_length="45"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="45" r_length="45" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="9960" i_stop="9367" i_length="594">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.991" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="9366" g_stop="9301" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="46" r_stop="111" r_length="66" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="9300" i_stop="9218" i_length="83">
            <donor d_prob="0.886" d_score="1.00"/>
            <acceptor a_prob="0.960" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="9217" g_stop="8995" g_length="223"/>
          <reference_exon_boundary r_type="cDNA" r_start="112" r_stop="334" r_length="223" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="335" polyA_stop="352"/>
      <MATCH_line gen_id="C00SLf0097P22.1" gen_strand="-" ref_id="SGN-E236869" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>334</cumulative_length_of_scored_exons>
        <coverage percentage="0.949" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0097P22.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E236869" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="10005" e_stop="9961"/>
          <exon e_start="9366" e_stop="9301"/>
          <exon e_start="9217" e_stop="8995"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAGGTAATTTGCTTTATATTTTTGGTGTCAACGGCCACGTTTGTCATTTTCTTGGATCAAGCGGACAGACATTTTTTGTTGTGTACATACTGTAGTGCTGATGTTTATTCAAAATATACTATGAAATACATTGTACCGTTGAGTATATTGGAAGTTAAGAGGGGAAGTCATCAGATATATAGGAAGTGCTCCTTGTGAGAAATTTCTCTAGTAGGGCTCAAACCCGAGAACCATGGTTAAGGACGGAGGGATCCCTTTGGTGGTATCAAGGGTTAATTATATTATTTCATGTTTCATATGATTGAAACATTTGGATATCCTTGCAAAGTGTGATATTGTTTTGTCTCGTCATTTGTTTTATGCTTCATAAGAATTATCTTTTCTTTCGTCCCCTTCTCTTTGTTTCTTTTTCTCCAGTGTACTTCATTCTTCTAGAATTATATAGTGGTCGGCGTTCCCTTTTGTGCTTCATTGATAATATTGAATCCTTTCAGCTGTTTACCGGTTGATTATTTTTATGTTGGTGCTTATTGCTAGTTTTTTGTTTTTATATCTTTGCAACTATACCTACCATCTTCCTGAAACTTCTCTTTACAGGTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCACGTATGAAATCTTGGTTATCATACGCCTTTAATTCAGTTTCTCTTCAATTAGCAAGACTCATAAAGAATCATCTTCTTTTGCAGGACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAGTTCTTGATGCAGTGTGGGATTGCAAGAAACACAATTCGTACTGGAAAGGTTGGTAGGTACTAGTTTAGTTTCTCATTTGATAAGCTTCTGGTTTGAGTAACTCGTGTGTTGGTGTTTACACTTTCTAATCGTGGAAAATTGTTTGATTTGAATCCATGCCTCTATGTTTCGT</genome_strand>
        <mrna_strand>AAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAG..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCAC...................................................................................GACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAGTTCTTGATGCAGTGTGGGATTGCAAGAAACACAATTCGTACTGGAAAGGTTGGTAGGTACTAGTTTAGTTTCTCATTTGATAAGCTTCTGGTTTGAGTAACTCGTGTGTTGGTGTTTACACTTTCTAATCGTGGAAAATTGTTTGATTTGAATCCATGCCTCTATGTTTCGT</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-C00SLf0097P22-lNaBf/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E394175" ref_strand="-" ref_description="SGN-E394175 [TUS-42-M15](-)">
      <seq>actagttctcgggaagctcacttcgaaatgtctacactttctccactgttgaagatttttggggtgcttacaataatatccatcacccaagcaagttaattatgggagcagactttcattgttttaagcacaaaattgagccaaagtgggaagatcctgtatgtgccaatggagggacgtggaaaatgagtttttcgaagggtaaatctgataccagctggctgtatacgctgctggcaatgattggacatcaattcgatcatggagatgaaatttgtggagcagttgttagtgtccgggctaagggagaaaaaatagctttgtggaccaagaatgctgcaaatgaaacagctcaggttagcattggtaagcaatggaagcagtttctagattacagtgattcggttggcttcatatttcacgacgatgcaaagaggctcgacagaaatgccaagaatcgttacaccgtatagttcttgatgcagtgtgggattgcaagaaacacaattcgtactggaaaggttggtaggtactagtttagtttctcatttgataagcttctggtttgagtaactcgtgtgttggtgtttacactttctaatcctggaaaattgtttgatttgaatccatgcctctatgtttcctgaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0097P22-lNaBf/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C00SLf0097P22.1" temp_strand="-" temp_description="C00SLf0097P22.1  CU856538.2 htgs_phase:3 submitted_to_sgn_as:C04SLf0097P22 sequenced_by:sanger upload_account_name:uk">
        <position start="12393" stop="8694"/>
      </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="12097" g_stop="12032" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="64" r_length="64" r_score="0.909"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="12031" i_stop="10363" i_length="1669">
            <donor d_prob="0.993" d_score="1.00"/>
            <acceptor a_prob="0.628" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="10362" g_stop="10197" g_length="166"/>
          <reference_exon_boundary r_type="cDNA" r_start="65" r_stop="230" r_length="166" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="10196" i_stop="10087" i_length="110">
            <donor d_prob="0.000" d_score="1.00"/>
            <acceptor a_prob="0.988" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="10086" g_stop="9961" g_length="126"/>
          <reference_exon_boundary r_type="cDNA" r_start="231" r_stop="356" r_length="126" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="9960" i_stop="9367" i_length="594">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.991" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="9366" g_stop="9301" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="357" r_stop="422" r_length="66" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="9300" i_stop="9218" i_length="83">
            <donor d_prob="0.886" d_score="1.00"/>
            <acceptor a_prob="0.960" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="9217" g_stop="8997" g_length="221"/>
          <reference_exon_boundary r_type="cDNA" r_start="423" r_stop="643" r_length="221" r_score="0.995"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="647" polyA_stop="660"/>
      <MATCH_line gen_id="C00SLf0097P22.1" gen_strand="-" ref_id="SGN-E394175" ref_strand="-">
        <total_alignment_score>0.989</total_alignment_score>
        <cumulative_length_of_scored_exons>645</cumulative_length_of_scored_exons>
        <coverage percentage="0.977" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0097P22.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E394175" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="12097" e_stop="12032"/>
          <exon e_start="10362" e_stop="10197"/>
          <exon e_start="10086" e_stop="9961"/>
          <exon e_start="9366" e_stop="9301"/>
          <exon e_start="9217" e_stop="8997"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAGATTTTTGGGGGTAAGTTTTTTTTTTTCCTCTTTCAAATTGGTGATAGTGTAGTGTAAGGGAAAACAGGGAGTGGATTGCAAGGTGGGGAATCGAATCCTCGAGAAAGTTTAGATAGTCAATTAATTGAGCTACTGAGATTCCTCGGATTTTTTAAAAAAAATAAATTGGGGATAGAGGAAGAGGAAATGGGGGAGACTTTTATAAGGTTATACCGTTGTTAACAAGGTGAAATTTTAGGTAGTTAATCAATTGAGCTACTAAGATTCTTTAGATACGATTTTCGTAAGCTCAAATTGGAAAATAAAAAATTAGATTATTACTAAGGAGCTGAAGAAATTCAGAAATGAGTTACCTTTTGAGCCAGCAGAACCAGTTAAGTTGAGATTTCATTGATTTTAGCTTGTTTTTAATGTTGGTTGTGAATTATGGGGTTTTATTATAATGTTCCAACAATTTTGTTGGTGTTGTAGGACTTTTTTGATTTAGCGTTTTGAATGTGTTCTGATTATCTGCCTTCACATAGGTGATATTGAGGTAAAAATGGCATCTTGATTGATTTTGCTCTCATAATTGTTAGATTTTCTTCTTGTACATTTTGCAGTTTTTAGTTAACTTGCCAAGGTGTTTAGTGGATGCACAATATGCGGTATTACTACGGAATGTCTGAATTGGTTTGAGCTTTAGTTTACCCAAGCTGTATTAGTAATTGCACATTGCTTTGTCCTTTTTTAGTTAGTACTTTCCTTAAAACTGGAATTTTGATCTCTTGGTTACTTGCCAATTTAAATTTTAGTTCATGGATCGGATTCAATGAATAGATATATGCTCTTTGGTGGTGGGAGGACAAGGATAGATAAATTAAACTCGGTAAGGAGAGAAAGTGCAGAATGAATGGAAGTTGAGACATTTTGGAGTATGGGGTGAAGAATGACCTGTGAAGTTTTAGGAAAGAAAAAGTTAACCTTGTTGAATAGTCATATTTCTCTTCCTTGCACAATCTTGTGTAGGAATGCCTTTAATTGGGTTTATATCGTCGGATAGTTTATATTGCTTCAAATCTAAGAAACTCTTTCATATTTGTCAAATGCTCCTATTTTCAACAAAGGATATTTTGAGCTGAAAAGGTAGTTGAATAATGCATTGGTCGTAGTTTTCTCTCCTAAGCAAGATAATATAGTTACTATTTTCAAGTACAACTACTTCTTTTTCTTTAGTTTACGTATAAGAGCAGGTCCTGTATCTACATAGCTGTGATATCTCTATGTGCATTTGTCTTAATATACTATTCACTTGTCTTAATATATTATTCACTTTCAAAAATAAAGACAGATGTGTTTCTATTTCTTAATTAGGCTAAAGTATGCTCATCTCCTCTGTAGATTGATGAGACTTAGCTGCAGGCCAGTTTTTTCAATCTCACGCATAGACTTTTTTATTAAGTCCTATGATTTGAGTAATGTAGGTGGTAATGGTGTGAATTTGATGTCTGCCATGGATGCATGCACCTTGTTTGGTGAGTTCTTTATTGGTCTAATTACTCAAGGCACTTGAGTTATTGTACAACTTGAACGATGACATACCTGTTTGATATTCCACATCATGGATTAGGTCTTTGAAATGCTATTATCCTTTTGGCTCATGATGAAATCTTGAACCATGTTGCTTATTCTACAAACAGTGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACGGTATTCCGAAGTTATTTCCATCCAGCCCTTAATGATAGGTCATTCTAGTAATGTTATTTTCCCCTTTGATATAATTTCCACTCTTGTTTTCTTATATGGAATTATTGTAGCTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAGGTAATTTGCTTTATATTTTTGGTGTCAACGGCCACGTTTGTCATTTTCTTGGATCAAGCGGACAGACATTTTTTGTTGTGTACATACTGTAGTGCTGATGTTTATTCAAAATATACTATGAAATACATTGTACCGTTGAGTATATTGGAAGTTAAGAGGGGAAGTCATCAGATATATAGGAAGTGCTCCTTGTGAGAAATTTCTCTAGTAGGGCTCAAACCCGAGAACCATGGTTAAGGACGGAGGGATCCCTTTGGTGGTATCAAGGGTTAATTATATTATTTCATGTTTCATATGATTGAAACATTTGGATATCCTTGCAAAGTGTGATATTGTTTTGTCTCGTCATTTGTTTTATGCTTCATAAGAATTATCTTTTCTTTCGTCCCCTTCTCTTTGTTTCTTTTTCTCCAGTGTACTTCATTCTTCTAGAATTATATAGTGGTCGGCGTTCCCTTTTGTGCTTCATTGATAATATTGAATCCTTTCAGCTGTTTACCGGTTGATTATTTTTATGTTGGTGCTTATTGCTAGTTTTTTGTTTTTATATCTTTGCAACTATACCTACCATCTTCCTGAAACTTCTCTTTACAGGTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCACGTATGAAATCTTGGTTATCATACGCCTTTAATTCAGTTTCTCTTCAATTAGCAAGACTCATAAAGAATCATCTTCTTTTGCAGGACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAGTTCTTGATGCAGTGTGGGATTGCAAGAAACACAATTCGTACTGGAAAGGTTGGTAGGTACTAGTTTAGTTTCTCATTTGATAAGCTTCTGGTTTGAGTAACTCGTGTGTTGGTGTTTACACTTTCTAATCGTGGAAAATTGTTTGATTTGAATCCATGCCTCTATGTTTC</genome_strand>
        <mrna_strand>ACTAGTT-C-TCGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAGATTTTTGGGG.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACG..............................................................................................................CTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAG..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCAC...................................................................................GACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAGTTCTTGATGCAGTGTGGGATTGCAAGAAACACAATTCGTACTGGAAAGGTTGGTAGGTACTAGTTTAGTTTCTCATTTGATAAGCTTCTGGTTTGAGTAACTCGTGTGTTGGTGTTTACACTTTCTAATCCTGGAAAATTGTTTGATTTGAATCCATGCCTCTATGTTTC</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-C00SLf0097P22-lNaBf/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E352080" ref_strand="+" ref_description="SGN-E352080 [cTOS-13-D4]">
      <seq>tttaccactaaatctcgacaaactgcttggggaagctcacttcgaaatgtctacactttctccactgttgaagatttttggggtgcttacaataatatccatcacccaagcaagttaattatgggagcagactttcattgttttaagcacaaaattgagccaaagtgggaagatcctgtatgtgccaatggagggacgtggaaaatgagtttttcgaagggtaaatctgataccagctggctgtatacgctgctggcaatgattggacatcaattcgatcatggagatgaaatttgtggagcagttgttagtgtccgggctaagggagaaaaaatagctttgtggaccaagaatgctgcaaatgaaacagctcaggttagcattggtaagcaatggaagcagtttctagattacagtgattcggttggcttcatatttcacgacgatgcaaagaggctcgacagaaatgccaagaatcgttacaccgtatagttcttgatgcagtgtgggattgcaagaaacacaattcgtactggaaaggttggtaggtactagtttagtttctcatttgataagcttctggtttgagtaactcgtgtgttggtggttacactttctaatcgtggaaaattgtttgatttgaatccatgcctct</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0097P22-lNaBf/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C00SLf0097P22.1" temp_strand="-" temp_description="C00SLf0097P22.1  CU856538.2 htgs_phase:3 submitted_to_sgn_as:C04SLf0097P22 sequenced_by:sanger upload_account_name:uk">
        <position start="12412" stop="8704"/>
      </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="12114" g_stop="12032" g_length="83"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="83" r_length="83" r_score="0.976"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="12031" i_stop="10363" i_length="1669">
            <donor d_prob="0.993" d_score="1.00"/>
            <acceptor a_prob="0.628" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="10362" g_stop="10197" g_length="166"/>
          <reference_exon_boundary r_type="cDNA" r_start="84" r_stop="249" r_length="166" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="10196" i_stop="10087" i_length="110">
            <donor d_prob="0.000" d_score="1.00"/>
            <acceptor a_prob="0.988" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="10086" g_stop="9961" g_length="126"/>
          <reference_exon_boundary r_type="cDNA" r_start="250" r_stop="375" r_length="126" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="9960" i_stop="9367" i_length="594">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.991" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="9366" g_stop="9301" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="376" r_stop="441" r_length="66" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="9300" i_stop="9218" i_length="83">
            <donor d_prob="0.886" d_score="1.00"/>
            <acceptor a_prob="0.960" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="9217" g_stop="9004" g_length="214"/>
          <reference_exon_boundary r_type="cDNA" r_start="442" r_stop="655" r_length="214" r_score="0.995"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0097P22.1" gen_strand="-" ref_id="SGN-E352080" ref_strand="+">
        <total_alignment_score>0.995</total_alignment_score>
        <cumulative_length_of_scored_exons>655</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0097P22.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E352080" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="12114" e_stop="12032"/>
          <exon e_start="10362" e_stop="10197"/>
          <exon e_start="10086" e_stop="9961"/>
          <exon e_start="9366" e_stop="9301"/>
          <exon e_start="9217" e_stop="9004"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CCTACCACTAAATCTCGACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAGATTTTTGGGGGTAAGTTTTTTTTTTTCCTCTTTCAAATTGGTGATAGTGTAGTGTAAGGGAAAACAGGGAGTGGATTGCAAGGTGGGGAATCGAATCCTCGAGAAAGTTTAGATAGTCAATTAATTGAGCTACTGAGATTCCTCGGATTTTTTAAAAAAAATAAATTGGGGATAGAGGAAGAGGAAATGGGGGAGACTTTTATAAGGTTATACCGTTGTTAACAAGGTGAAATTTTAGGTAGTTAATCAATTGAGCTACTAAGATTCTTTAGATACGATTTTCGTAAGCTCAAATTGGAAAATAAAAAATTAGATTATTACTAAGGAGCTGAAGAAATTCAGAAATGAGTTACCTTTTGAGCCAGCAGAACCAGTTAAGTTGAGATTTCATTGATTTTAGCTTGTTTTTAATGTTGGTTGTGAATTATGGGGTTTTATTATAATGTTCCAACAATTTTGTTGGTGTTGTAGGACTTTTTTGATTTAGCGTTTTGAATGTGTTCTGATTATCTGCCTTCACATAGGTGATATTGAGGTAAAAATGGCATCTTGATTGATTTTGCTCTCATAATTGTTAGATTTTCTTCTTGTACATTTTGCAGTTTTTAGTTAACTTGCCAAGGTGTTTAGTGGATGCACAATATGCGGTATTACTACGGAATGTCTGAATTGGTTTGAGCTTTAGTTTACCCAAGCTGTATTAGTAATTGCACATTGCTTTGTCCTTTTTTAGTTAGTACTTTCCTTAAAACTGGAATTTTGATCTCTTGGTTACTTGCCAATTTAAATTTTAGTTCATGGATCGGATTCAATGAATAGATATATGCTCTTTGGTGGTGGGAGGACAAGGATAGATAAATTAAACTCGGTAAGGAGAGAAAGTGCAGAATGAATGGAAGTTGAGACATTTTGGAGTATGGGGTGAAGAATGACCTGTGAAGTTTTAGGAAAGAAAAAGTTAACCTTGTTGAATAGTCATATTTCTCTTCCTTGCACAATCTTGTGTAGGAATGCCTTTAATTGGGTTTATATCGTCGGATAGTTTATATTGCTTCAAATCTAAGAAACTCTTTCATATTTGTCAAATGCTCCTATTTTCAACAAAGGATATTTTGAGCTGAAAAGGTAGTTGAATAATGCATTGGTCGTAGTTTTCTCTCCTAAGCAAGATAATATAGTTACTATTTTCAAGTACAACTACTTCTTTTTCTTTAGTTTACGTATAAGAGCAGGTCCTGTATCTACATAGCTGTGATATCTCTATGTGCATTTGTCTTAATATACTATTCACTTGTCTTAATATATTATTCACTTTCAAAAATAAAGACAGATGTGTTTCTATTTCTTAATTAGGCTAAAGTATGCTCATCTCCTCTGTAGATTGATGAGACTTAGCTGCAGGCCAGTTTTTTCAATCTCACGCATAGACTTTTTTATTAAGTCCTATGATTTGAGTAATGTAGGTGGTAATGGTGTGAATTTGATGTCTGCCATGGATGCATGCACCTTGTTTGGTGAGTTCTTTATTGGTCTAATTACTCAAGGCACTTGAGTTATTGTACAACTTGAACGATGACATACCTGTTTGATATTCCACATCATGGATTAGGTCTTTGAAATGCTATTATCCTTTTGGCTCATGATGAAATCTTGAACCATGTTGCTTATTCTACAAACAGTGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACGGTATTCCGAAGTTATTTCCATCCAGCCCTTAATGATAGGTCATTCTAGTAATGTTATTTTCCCCTTTGATATAATTTCCACTCTTGTTTTCTTATATGGAATTATTGTAGCTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAGGTAATTTGCTTTATATTTTTGGTGTCAACGGCCACGTTTGTCATTTTCTTGGATCAAGCGGACAGACATTTTTTGTTGTGTACATACTGTAGTGCTGATGTTTATTCAAAATATACTATGAAATACATTGTACCGTTGAGTATATTGGAAGTTAAGAGGGGAAGTCATCAGATATATAGGAAGTGCTCCTTGTGAGAAATTTCTCTAGTAGGGCTCAAACCCGAGAACCATGGTTAAGGACGGAGGGATCCCTTTGGTGGTATCAAGGGTTAATTATATTATTTCATGTTTCATATGATTGAAACATTTGGATATCCTTGCAAAGTGTGATATTGTTTTGTCTCGTCATTTGTTTTATGCTTCATAAGAATTATCTTTTCTTTCGTCCCCTTCTCTTTGTTTCTTTTTCTCCAGTGTACTTCATTCTTCTAGAATTATATAGTGGTCGGCGTTCCCTTTTGTGCTTCATTGATAATATTGAATCCTTTCAGCTGTTTACCGGTTGATTATTTTTATGTTGGTGCTTATTGCTAGTTTTTTGTTTTTATATCTTTGCAACTATACCTACCATCTTCCTGAAACTTCTCTTTACAGGTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCACGTATGAAATCTTGGTTATCATACGCCTTTAATTCAGTTTCTCTTCAATTAGCAAGACTCATAAAGAATCATCTTCTTTTGCAGGACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAGTTCTTGATGCAGTGTGGGATTGCAAGAAACACAATTCGTACTGGAAAGGTTGGTAGGTACTAGTTTAGTTTCTCATTTGATAAGCTTCTGGTTTGAGTAACTCGTGTGTTGGTGTTTACACTTTCTAATCGTGGAAAATTGTTTGATTTGAATCCATGCCTCT</genome_strand>
        <mrna_strand>TTTACCACTAAATCTCGACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAGATTTTTGGGG.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACG..............................................................................................................CTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAG..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCAC...................................................................................GACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAGTTCTTGATGCAGTGTGGGATTGCAAGAAACACAATTCGTACTGGAAAGGTTGGTAGGTACTAGTTTAGTTTCTCATTTGATAAGCTTCTGGTTTGAGTAACTCGTGTGTTGGTGGTTACACTTTCTAATCGTGGAAAATTGTTTGATTTGAATCCATGCCTCT</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-C00SLf0097P22-lNaBf/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E342832" ref_strand="+" ref_description="SGN-E342832 [cTOF-7-B24]">
      <seq>tcacagtgaagcatccagtggagcattcatggactttttggtttgataaccctaccactaaatctcgacaaactgcttggggaagctcacttcgaaatgtctacactttctccactgttgaagatttttggggtgcttacaataatatccatcacccaagcaagttaattatgggagcagactttcattgttttaagcacaaaattgagccaaagtgggaagatcctgtatgtgccaatggagggacgtggaaaatgagtttttcgaagggtaaatctgataccagctggctgtatacgctgctggcaatgattggacatcaattcgatcatggagatgaaatttgtggagcagttgttagtgtccgggctaagggagaaaaaatagctttgtggaccaagaatgctgcaaatgaaacagctcaggttagcattggtaagcaatggaagcagtttctagattacagtgattcggttggcttcatatttcacgacgatgcaaagaggctcgacagaaatgccaagaatcgttacaccgtatagttcttgatgcagtgtgggattgcaagaaacacaattcgtactgnaaaggttggtaggtacctagtttagtttctcatttgataagcttctggtttgagtaactcgtgtgtttggtgtttacactntctaatcgtggaaaattgtttgatttgaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0097P22-lNaBf/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C00SLf0097P22.1" temp_strand="-" temp_description="C00SLf0097P22.1  CU856538.2 htgs_phase:3 submitted_to_sgn_as:C04SLf0097P22 sequenced_by:sanger upload_account_name:uk">
        <position start="12464" stop="8715"/>
      </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="12164" g_stop="12032" g_length="133"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="133" r_length="133" r_score="0.992"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="12031" i_stop="10363" i_length="1669">
            <donor d_prob="0.993" d_score="1.00"/>
            <acceptor a_prob="0.628" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="10362" g_stop="10197" g_length="166"/>
          <reference_exon_boundary r_type="cDNA" r_start="134" r_stop="299" r_length="166" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="10196" i_stop="10087" i_length="110">
            <donor d_prob="0.000" d_score="1.00"/>
            <acceptor a_prob="0.988" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="10086" g_stop="9961" g_length="126"/>
          <reference_exon_boundary r_type="cDNA" r_start="300" r_stop="425" r_length="126" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="9960" i_stop="9367" i_length="594">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.991" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="9366" g_stop="9301" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="426" r_stop="491" r_length="66" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="9300" i_stop="9218" i_length="83">
            <donor d_prob="0.886" d_score="1.00"/>
            <acceptor a_prob="0.960" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="9217" g_stop="9014" g_length="204"/>
          <reference_exon_boundary r_type="cDNA" r_start="492" r_stop="697" r_length="206" r_score="0.966"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0097P22.1" gen_strand="-" ref_id="SGN-E342832" ref_strand="+">
        <total_alignment_score>0.988</total_alignment_score>
        <cumulative_length_of_scored_exons>695</cumulative_length_of_scored_exons>
        <coverage percentage="0.997" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0097P22.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E342832" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="12164" e_stop="12032"/>
          <exon e_start="10362" e_stop="10197"/>
          <exon e_start="10086" e_stop="9961"/>
          <exon e_start="9366" e_stop="9301"/>
          <exon e_start="9217" e_stop="9014"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCACAGTGAAGCATCCATTGGAGCATTCATGGACTTTTTGGTTTGATAACCCTACCACTAAATCTCGACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAGATTTTTGGGGGTAAGTTTTTTTTTTTCCTCTTTCAAATTGGTGATAGTGTAGTGTAAGGGAAAACAGGGAGTGGATTGCAAGGTGGGGAATCGAATCCTCGAGAAAGTTTAGATAGTCAATTAATTGAGCTACTGAGATTCCTCGGATTTTTTAAAAAAAATAAATTGGGGATAGAGGAAGAGGAAATGGGGGAGACTTTTATAAGGTTATACCGTTGTTAACAAGGTGAAATTTTAGGTAGTTAATCAATTGAGCTACTAAGATTCTTTAGATACGATTTTCGTAAGCTCAAATTGGAAAATAAAAAATTAGATTATTACTAAGGAGCTGAAGAAATTCAGAAATGAGTTACCTTTTGAGCCAGCAGAACCAGTTAAGTTGAGATTTCATTGATTTTAGCTTGTTTTTAATGTTGGTTGTGAATTATGGGGTTTTATTATAATGTTCCAACAATTTTGTTGGTGTTGTAGGACTTTTTTGATTTAGCGTTTTGAATGTGTTCTGATTATCTGCCTTCACATAGGTGATATTGAGGTAAAAATGGCATCTTGATTGATTTTGCTCTCATAATTGTTAGATTTTCTTCTTGTACATTTTGCAGTTTTTAGTTAACTTGCCAAGGTGTTTAGTGGATGCACAATATGCGGTATTACTACGGAATGTCTGAATTGGTTTGAGCTTTAGTTTACCCAAGCTGTATTAGTAATTGCACATTGCTTTGTCCTTTTTTAGTTAGTACTTTCCTTAAAACTGGAATTTTGATCTCTTGGTTACTTGCCAATTTAAATTTTAGTTCATGGATCGGATTCAATGAATAGATATATGCTCTTTGGTGGTGGGAGGACAAGGATAGATAAATTAAACTCGGTAAGGAGAGAAAGTGCAGAATGAATGGAAGTTGAGACATTTTGGAGTATGGGGTGAAGAATGACCTGTGAAGTTTTAGGAAAGAAAAAGTTAACCTTGTTGAATAGTCATATTTCTCTTCCTTGCACAATCTTGTGTAGGAATGCCTTTAATTGGGTTTATATCGTCGGATAGTTTATATTGCTTCAAATCTAAGAAACTCTTTCATATTTGTCAAATGCTCCTATTTTCAACAAAGGATATTTTGAGCTGAAAAGGTAGTTGAATAATGCATTGGTCGTAGTTTTCTCTCCTAAGCAAGATAATATAGTTACTATTTTCAAGTACAACTACTTCTTTTTCTTTAGTTTACGTATAAGAGCAGGTCCTGTATCTACATAGCTGTGATATCTCTATGTGCATTTGTCTTAATATACTATTCACTTGTCTTAATATATTATTCACTTTCAAAAATAAAGACAGATGTGTTTCTATTTCTTAATTAGGCTAAAGTATGCTCATCTCCTCTGTAGATTGATGAGACTTAGCTGCAGGCCAGTTTTTTCAATCTCACGCATAGACTTTTTTATTAAGTCCTATGATTTGAGTAATGTAGGTGGTAATGGTGTGAATTTGATGTCTGCCATGGATGCATGCACCTTGTTTGGTGAGTTCTTTATTGGTCTAATTACTCAAGGCACTTGAGTTATTGTACAACTTGAACGATGACATACCTGTTTGATATTCCACATCATGGATTAGGTCTTTGAAATGCTATTATCCTTTTGGCTCATGATGAAATCTTGAACCATGTTGCTTATTCTACAAACAGTGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACGGTATTCCGAAGTTATTTCCATCCAGCCCTTAATGATAGGTCATTCTAGTAATGTTATTTTCCCCTTTGATATAATTTCCACTCTTGTTTTCTTATATGGAATTATTGTAGCTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAGGTAATTTGCTTTATATTTTTGGTGTCAACGGCCACGTTTGTCATTTTCTTGGATCAAGCGGACAGACATTTTTTGTTGTGTACATACTGTAGTGCTGATGTTTATTCAAAATATACTATGAAATACATTGTACCGTTGAGTATATTGGAAGTTAAGAGGGGAAGTCATCAGATATATAGGAAGTGCTCCTTGTGAGAAATTTCTCTAGTAGGGCTCAAACCCGAGAACCATGGTTAAGGACGGAGGGATCCCTTTGGTGGTATCAAGGGTTAATTATATTATTTCATGTTTCATATGATTGAAACATTTGGATATCCTTGCAAAGTGTGATATTGTTTTGTCTCGTCATTTGTTTTATGCTTCATAAGAATTATCTTTTCTTTCGTCCCCTTCTCTTTGTTTCTTTTTCTCCAGTGTACTTCATTCTTCTAGAATTATATAGTGGTCGGCGTTCCCTTTTGTGCTTCATTGATAATATTGAATCCTTTCAGCTGTTTACCGGTTGATTATTTTTATGTTGGTGCTTATTGCTAGTTTTTTGTTTTTATATCTTTGCAACTATACCTACCATCTTCCTGAAACTTCTCTTTACAGGTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCACGTATGAAATCTTGGTTATCATACGCCTTTAATTCAGTTTCTCTTCAATTAGCAAGACTCATAAAGAATCATCTTCTTTTGCAGGACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAGTTCTTGATGCAGTGTGGGATTGCAAGAAACACAATTCGTACTGGAAAGGTTGGTAGGTA-CTAGTTTAGTTTCTCATTTGATAAGCTTCTGGTTTGAGTAACTCGTGTG-TTGGTGTTTACACTTTCTAATCGTGGAAAATTGTTTGATTTGAAT</genome_strand>
        <mrna_strand>TCACAGTGAAGCATCCAGTGGAGCATTCATGGACTTTTTGGTTTGATAACCCTACCACTAAATCTCGACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAGATTTTTGGGG.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACG..............................................................................................................CTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAG..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCAC...................................................................................GACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAGTTCTTGATGCAGTGTGGGATTGCAAGAAACACAATTCGTACTGNAAAGGTTGGTAGGTACCTAGTTTAGTTTCTCATTTGATAAGCTTCTGGTTTGAGTAACTCGTGTGTTTGGTGTTTACACTNTCTAATCGTGGAAAATTGTTTGATTTGAAA</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-C00SLf0097P22-lNaBf/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E265573" ref_strand="-" ref_description="SGN-E265573 [cLEI-14-F16]">
      <seq>aaagagactttcattgtttttagcacaaaattgagccaaagtgggaagctcctgtatgtgccaatggagggacgtggaatctgagtttttcgaagggtacatctgataccagctggctgtatacgctgctggctatgattggacatcaattcgatcatggatatgaaatttgtggagcagttgttagtgtccgggctaagggagaaaaaatagctttgtggcccaagaatgctgcaaatgaaacagctcaggttagcactggtaagcaatgaaagcagtttctagatcacagtgattcggttggcttcatatttcccgacgatgcaaagaggctcgacagaaatgccaagtatcgttactccgtatagttcttgatacagtgtgggattgcaagatacacaattcgtactggaaaggttggtaggtactagtttagtttctcatttgataagcttctggtttgagtaactcgtgtgttggtgtttacactttctaatcgtggaaaactgtttgatttgaaaaaaaaaaaaaaaaaactcga</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0097P22-lNaBf/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C00SLf0097P22.1" temp_strand="-" temp_description="C00SLf0097P22.1  CU856538.2 htgs_phase:3 submitted_to_sgn_as:C04SLf0097P22 sequenced_by:sanger upload_account_name:uk">
        <position start="10620" stop="8715"/>
      </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="10321" g_stop="10197" g_length="125"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="125" r_length="125" r_score="0.936"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="10196" i_stop="10087" i_length="110">
            <donor d_prob="0.000" d_score="0.94"/>
            <acceptor a_prob="0.988" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="10086" g_stop="9961" g_length="126"/>
          <reference_exon_boundary r_type="cDNA" r_start="126" r_stop="251" r_length="126" r_score="0.976"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="9960" i_stop="9367" i_length="594">
            <donor d_prob="0.997" d_score="0.98"/>
            <acceptor a_prob="0.991" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="9366" g_stop="9301" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="252" r_stop="317" r_length="66" r_score="0.939"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="9300" i_stop="9218" i_length="83">
            <donor d_prob="0.886" d_score="0.94"/>
            <acceptor a_prob="0.960" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="9217" g_stop="9016" g_length="202"/>
          <reference_exon_boundary r_type="cDNA" r_start="318" r_stop="519" r_length="202" r_score="0.975"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="520" polyA_stop="537"/>
      <MATCH_line gen_id="C00SLf0097P22.1" gen_strand="-" ref_id="SGN-E265573" ref_strand="-">
        <total_alignment_score>0.961</total_alignment_score>
        <cumulative_length_of_scored_exons>519</cumulative_length_of_scored_exons>
        <coverage percentage="0.959" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0097P22.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E265573" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="10321" e_stop="10197"/>
          <exon e_start="10086" e_stop="9961"/>
          <exon e_start="9366" e_stop="9301"/>
          <exon e_start="9217" e_stop="9016"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACGGTATTCCGAAGTTATTTCCATCCAGCCCTTAATGATAGGTCATTCTAGTAATGTTATTTTCCCCTTTGATATAATTTCCACTCTTGTTTTCTTATATGGAATTATTGTAGCTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAGGTAATTTGCTTTATATTTTTGGTGTCAACGGCCACGTTTGTCATTTTCTTGGATCAAGCGGACAGACATTTTTTGTTGTGTACATACTGTAGTGCTGATGTTTATTCAAAATATACTATGAAATACATTGTACCGTTGAGTATATTGGAAGTTAAGAGGGGAAGTCATCAGATATATAGGAAGTGCTCCTTGTGAGAAATTTCTCTAGTAGGGCTCAAACCCGAGAACCATGGTTAAGGACGGAGGGATCCCTTTGGTGGTATCAAGGGTTAATTATATTATTTCATGTTTCATATGATTGAAACATTTGGATATCCTTGCAAAGTGTGATATTGTTTTGTCTCGTCATTTGTTTTATGCTTCATAAGAATTATCTTTTCTTTCGTCCCCTTCTCTTTGTTTCTTTTTCTCCAGTGTACTTCATTCTTCTAGAATTATATAGTGGTCGGCGTTCCCTTTTGTGCTTCATTGATAATATTGAATCCTTTCAGCTGTTTACCGGTTGATTATTTTTATGTTGGTGCTTATTGCTAGTTTTTTGTTTTTATATCTTTGCAACTATACCTACCATCTTCCTGAAACTTCTCTTTACAGGTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCACGTATGAAATCTTGGTTATCATACGCCTTTAATTCAGTTTCTCTTCAATTAGCAAGACTCATAAAGAATCATCTTCTTTTGCAGGACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAGTTCTTGATGCAGTGTGGGATTGCAAGAAACACAATTCGTACTGGAAAGGTTGGTAGGTACTAGTTTAGTTTCTCATTTGATAAGCTTCTGGTTTGAGTAACTCGTGTGTTGGTGTTTACACTTTCTAATCGTGGAAAATTGTTTGATTTGA</genome_strand>
        <mrna_strand>AAAGAGACTTTCATTGTTTTTAGCACAAAATTGAGCCAAAGTGGGAAGCTCCTGTATGTGCCAATGGAGGGACGTGGAATCTGAGTTTTTCGAAGGGTACATCTGATACCAGCTGGCTGTATACG..............................................................................................................CTGCTGGCTATGATTGGACATCAATTCGATCATGGATATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGCCCAAGAATGCTGCAAATGAAACAGCTCAG..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTAGCACTGGTAAGCAATGAAAGCAGTTTCTAGATCACAGTGATTCGGTTGGCTTCATATTTCCC...................................................................................GACGATGCAAAGAGGCTCGACAGAAATGCCAAGTATCGTTACTCCGTATAGTTCTTGATACAGTGTGGGATTGCAAGATACACAATTCGTACTGGAAAGGTTGGTAGGTACTAGTTTAGTTTCTCATTTGATAAGCTTCTGGTTTGAGTAACTCGTGTGTTGGTGTTTACACTTTCTAATCGTGGAAAACTGTTTGATTTGA</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-C00SLf0097P22-lNaBf/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E234225" ref_strand="+" ref_description="SGN-E234225 [cLEL-8-M11](-)">
      <seq>ttgttttcctatatggaataattgtaactgctggcaatgattggacatcaattcgatcatggaaataaaatttgtggagcaagttgttagtgtccgggctaagggaaaaaaaatagctttgtggaccaagaatgctgcaaatgaaacagctcaggttagcattggtaagcaatggaagcagtttctagattacagtgattcggttggcttcatatttcccgacgatgcaaaaaggctcgacagaaatgccaaaaatcgttacaccgtatagttcttgatgcagtgtgggattgcaaaaaacacaattcgtactggaaaggttggtaggtactagtttagtttctcatttgataagcttctggtttgagtaactcgtgtgttggtgtttaccctttctaatcgtggaaaactgtttgatttgaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0097P22-lNaBf/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C00SLf0097P22.1" temp_strand="-" temp_description="C00SLf0097P22.1  CU856538.2 htgs_phase:3 submitted_to_sgn_as:C04SLf0097P22 sequenced_by:sanger upload_account_name:uk">
        <position start="10413" stop="8715"/>
      </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="10113" g_stop="9961" g_length="153"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="154" r_length="154" r_score="0.948"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="9960" i_stop="9367" i_length="594">
            <donor d_prob="0.997" d_score="0.98"/>
            <acceptor a_prob="0.991" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="9366" g_stop="9301" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="155" r_stop="220" r_length="66" r_score="0.985"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="9300" i_stop="9218" i_length="83">
            <donor d_prob="0.886" d_score="0.98"/>
            <acceptor a_prob="0.960" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="9217" g_stop="9016" g_length="202"/>
          <reference_exon_boundary r_type="cDNA" r_start="221" r_stop="422" r_length="202" r_score="0.975"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="423" polyA_stop="451"/>
      <MATCH_line gen_id="C00SLf0097P22.1" gen_strand="-" ref_id="SGN-E234225" ref_strand="+">
        <total_alignment_score>0.967</total_alignment_score>
        <cumulative_length_of_scored_exons>421</cumulative_length_of_scored_exons>
        <coverage percentage="0.933" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0097P22.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E234225" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="10113" e_stop="9961"/>
          <exon e_start="9366" e_stop="9301"/>
          <exon e_start="9217" e_stop="9016"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTGTTTTCTTATATGGAATTATTGTAGCTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCA-GTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAGGTAATTTGCTTTATATTTTTGGTGTCAACGGCCACGTTTGTCATTTTCTTGGATCAAGCGGACAGACATTTTTTGTTGTGTACATACTGTAGTGCTGATGTTTATTCAAAATATACTATGAAATACATTGTACCGTTGAGTATATTGGAAGTTAAGAGGGGAAGTCATCAGATATATAGGAAGTGCTCCTTGTGAGAAATTTCTCTAGTAGGGCTCAAACCCGAGAACCATGGTTAAGGACGGAGGGATCCCTTTGGTGGTATCAAGGGTTAATTATATTATTTCATGTTTCATATGATTGAAACATTTGGATATCCTTGCAAAGTGTGATATTGTTTTGTCTCGTCATTTGTTTTATGCTTCATAAGAATTATCTTTTCTTTCGTCCCCTTCTCTTTGTTTCTTTTTCTCCAGTGTACTTCATTCTTCTAGAATTATATAGTGGTCGGCGTTCCCTTTTGTGCTTCATTGATAATATTGAATCCTTTCAGCTGTTTACCGGTTGATTATTTTTATGTTGGTGCTTATTGCTAGTTTTTTGTTTTTATATCTTTGCAACTATACCTACCATCTTCCTGAAACTTCTCTTTACAGGTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCACGTATGAAATCTTGGTTATCATACGCCTTTAATTCAGTTTCTCTTCAATTAGCAAGACTCATAAAGAATCATCTTCTTTTGCAGGACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAGTTCTTGATGCAGTGTGGGATTGCAAGAAACACAATTCGTACTGGAAAGGTTGGTAGGTACTAGTTTAGTTTCTCATTTGATAAGCTTCTGGTTTGAGTAACTCGTGTGTTGGTGTTTACACTTTCTAATCGTGGAAAATTGTTTGATTTGA</genome_strand>
        <mrna_strand>TTGTTTTCCTATATGGAATAATTGTAACTGCTGGCAATGATTGGACATCAATTCGATCATGGAAATAAAATTTGTGGAGCAAGTTGTTAGTGTCCGGGCTAAGGGAAAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAG..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCCC...................................................................................GACGATGCAAAAAGGCTCGACAGAAATGCCAAAAATCGTTACACCGTATAGTTCTTGATGCAGTGTGGGATTGCAAAAAACACAATTCGTACTGGAAAGGTTGGTAGGTACTAGTTTAGTTTCTCATTTGATAAGCTTCTGGTTTGAGTAACTCGTGTGTTGGTGTTTACCCTTTCTAATCGTGGAAAACTGTTTGATTTGA</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-C00SLf0097P22-lNaBf/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E746690" ref_strand="+" ref_description="SGN-E746690 [GI|56412233]">
      <seq>atggcagcagctgaaatggagagaacgatgtcgtttgatgcagctgagaagttgaaggccgccgatggaggaggaggagaggtagacgatgaacttgaagaaggtgaaattgttgaagaatcaaatgatacggcatcgtatttagggaaagaaatcacagtgaagcatccattggagcattcatggactttttggtttgataaccctaccactaaatctcgacaaactgcttggggaagctcacttcgaaatgtctacactttctccactgttgaagatttttggggtgcttacaataatatccatcacccaagcaagttaattatgggagcaaactttcattgttttaagcacaaaattgagccaaagtgggaagatcctgtatgtgccaatggagggacgtggaaaatgagtttttcgaagggtaaatctgataccagctggctgtatacgctgctggcaatgattggacatcaattcgatcatggagatgaaatttgtggagcagttgttagtgtccgggctaagggagaaaaaatagctttgtggaccaagaatgctgcaaatgaaacagctcaggttagcattggtaagcaatggaagcagtttctagattacagtgattcggttggcttcatatttcacgacgatgcaaagaggctcgacagaaatgccaagaatcgttacaccgtatag</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0097P22-lNaBf/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C00SLf0097P22.1" temp_strand="-" temp_description="C00SLf0097P22.1  CU856538.2 htgs_phase:3 submitted_to_sgn_as:C04SLf0097P22 sequenced_by:sanger upload_account_name:uk">
        <position start="12618" stop="8867"/>
      </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="12318" g_stop="12032" g_length="287"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="287" r_length="287" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="12031" i_stop="10363" i_length="1669">
            <donor d_prob="0.993" d_score="1.00"/>
            <acceptor a_prob="0.628" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="10362" g_stop="10197" g_length="166"/>
          <reference_exon_boundary r_type="cDNA" r_start="288" r_stop="453" r_length="166" r_score="0.994"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="10196" i_stop="10087" i_length="110">
            <donor d_prob="0.000" d_score="1.00"/>
            <acceptor a_prob="0.988" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="10086" g_stop="9961" g_length="126"/>
          <reference_exon_boundary r_type="cDNA" r_start="454" r_stop="579" r_length="126" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="9960" i_stop="9367" i_length="594">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.991" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="9366" g_stop="9301" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="580" r_stop="645" r_length="66" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="9300" i_stop="9218" i_length="83">
            <donor d_prob="0.886" d_score="1.00"/>
            <acceptor a_prob="0.960" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="9217" g_stop="9167" g_length="51"/>
          <reference_exon_boundary r_type="cDNA" r_start="646" r_stop="696" r_length="51" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0097P22.1" gen_strand="-" ref_id="SGN-E746690" ref_strand="+">
        <total_alignment_score>0.999</total_alignment_score>
        <cumulative_length_of_scored_exons>696</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0097P22.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E746690" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="12318" e_stop="12032"/>
          <exon e_start="10362" e_stop="10197"/>
          <exon e_start="10086" e_stop="9961"/>
          <exon e_start="9366" e_stop="9301"/>
          <exon e_start="9217" e_stop="9167"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATGGCAGCAGCTGAAATGGAGAGAACGATGTCGTTTGATGCAGCTGAGAAGTTGAAGGCCGCCGATGGAGGAGGAGGAGAGGTAGACGATGAACTTGAAGAAGGTGAAATTGTTGAAGAATCAAATGATACGGCATCGTATTTAGGGAAAGAAATCACAGTGAAGCATCCATTGGAGCATTCATGGACTTTTTGGTTTGATAACCCTACCACTAAATCTCGACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAGATTTTTGGGGGTAAGTTTTTTTTTTTCCTCTTTCAAATTGGTGATAGTGTAGTGTAAGGGAAAACAGGGAGTGGATTGCAAGGTGGGGAATCGAATCCTCGAGAAAGTTTAGATAGTCAATTAATTGAGCTACTGAGATTCCTCGGATTTTTTAAAAAAAATAAATTGGGGATAGAGGAAGAGGAAATGGGGGAGACTTTTATAAGGTTATACCGTTGTTAACAAGGTGAAATTTTAGGTAGTTAATCAATTGAGCTACTAAGATTCTTTAGATACGATTTTCGTAAGCTCAAATTGGAAAATAAAAAATTAGATTATTACTAAGGAGCTGAAGAAATTCAGAAATGAGTTACCTTTTGAGCCAGCAGAACCAGTTAAGTTGAGATTTCATTGATTTTAGCTTGTTTTTAATGTTGGTTGTGAATTATGGGGTTTTATTATAATGTTCCAACAATTTTGTTGGTGTTGTAGGACTTTTTTGATTTAGCGTTTTGAATGTGTTCTGATTATCTGCCTTCACATAGGTGATATTGAGGTAAAAATGGCATCTTGATTGATTTTGCTCTCATAATTGTTAGATTTTCTTCTTGTACATTTTGCAGTTTTTAGTTAACTTGCCAAGGTGTTTAGTGGATGCACAATATGCGGTATTACTACGGAATGTCTGAATTGGTTTGAGCTTTAGTTTACCCAAGCTGTATTAGTAATTGCACATTGCTTTGTCCTTTTTTAGTTAGTACTTTCCTTAAAACTGGAATTTTGATCTCTTGGTTACTTGCCAATTTAAATTTTAGTTCATGGATCGGATTCAATGAATAGATATATGCTCTTTGGTGGTGGGAGGACAAGGATAGATAAATTAAACTCGGTAAGGAGAGAAAGTGCAGAATGAATGGAAGTTGAGACATTTTGGAGTATGGGGTGAAGAATGACCTGTGAAGTTTTAGGAAAGAAAAAGTTAACCTTGTTGAATAGTCATATTTCTCTTCCTTGCACAATCTTGTGTAGGAATGCCTTTAATTGGGTTTATATCGTCGGATAGTTTATATTGCTTCAAATCTAAGAAACTCTTTCATATTTGTCAAATGCTCCTATTTTCAACAAAGGATATTTTGAGCTGAAAAGGTAGTTGAATAATGCATTGGTCGTAGTTTTCTCTCCTAAGCAAGATAATATAGTTACTATTTTCAAGTACAACTACTTCTTTTTCTTTAGTTTACGTATAAGAGCAGGTCCTGTATCTACATAGCTGTGATATCTCTATGTGCATTTGTCTTAATATACTATTCACTTGTCTTAATATATTATTCACTTTCAAAAATAAAGACAGATGTGTTTCTATTTCTTAATTAGGCTAAAGTATGCTCATCTCCTCTGTAGATTGATGAGACTTAGCTGCAGGCCAGTTTTTTCAATCTCACGCATAGACTTTTTTATTAAGTCCTATGATTTGAGTAATGTAGGTGGTAATGGTGTGAATTTGATGTCTGCCATGGATGCATGCACCTTGTTTGGTGAGTTCTTTATTGGTCTAATTACTCAAGGCACTTGAGTTATTGTACAACTTGAACGATGACATACCTGTTTGATATTCCACATCATGGATTAGGTCTTTGAAATGCTATTATCCTTTTGGCTCATGATGAAATCTTGAACCATGTTGCTTATTCTACAAACAGTGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACGGTATTCCGAAGTTATTTCCATCCAGCCCTTAATGATAGGTCATTCTAGTAATGTTATTTTCCCCTTTGATATAATTTCCACTCTTGTTTTCTTATATGGAATTATTGTAGCTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAGGTAATTTGCTTTATATTTTTGGTGTCAACGGCCACGTTTGTCATTTTCTTGGATCAAGCGGACAGACATTTTTTGTTGTGTACATACTGTAGTGCTGATGTTTATTCAAAATATACTATGAAATACATTGTACCGTTGAGTATATTGGAAGTTAAGAGGGGAAGTCATCAGATATATAGGAAGTGCTCCTTGTGAGAAATTTCTCTAGTAGGGCTCAAACCCGAGAACCATGGTTAAGGACGGAGGGATCCCTTTGGTGGTATCAAGGGTTAATTATATTATTTCATGTTTCATATGATTGAAACATTTGGATATCCTTGCAAAGTGTGATATTGTTTTGTCTCGTCATTTGTTTTATGCTTCATAAGAATTATCTTTTCTTTCGTCCCCTTCTCTTTGTTTCTTTTTCTCCAGTGTACTTCATTCTTCTAGAATTATATAGTGGTCGGCGTTCCCTTTTGTGCTTCATTGATAATATTGAATCCTTTCAGCTGTTTACCGGTTGATTATTTTTATGTTGGTGCTTATTGCTAGTTTTTTGTTTTTATATCTTTGCAACTATACCTACCATCTTCCTGAAACTTCTCTTTACAGGTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCACGTATGAAATCTTGGTTATCATACGCCTTTAATTCAGTTTCTCTTCAATTAGCAAGACTCATAAAGAATCATCTTCTTTTGCAGGACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAG</genome_strand>
        <mrna_strand>ATGGCAGCAGCTGAAATGGAGAGAACGATGTCGTTTGATGCAGCTGAGAAGTTGAAGGCCGCCGATGGAGGAGGAGGAGAGGTAGACGATGAACTTGAAGAAGGTGAAATTGTTGAAGAATCAAATGATACGGCATCGTATTTAGGGAAAGAAATCACAGTGAAGCATCCATTGGAGCATTCATGGACTTTTTGGTTTGATAACCCTACCACTAAATCTCGACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAGATTTTTGGGG.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAAACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACG..............................................................................................................CTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAG..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCAC...................................................................................GACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAG</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-C00SLf0097P22-lNaBf/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E747178" ref_strand="+" ref_description="SGN-E747178 [GI|7862168]">
      <seq>atggcagcagctgaaatggagagaacgatgtcgtttgatgcagctgagaagttgaaggccgccgatggaggaggaggagaggtagacgatgaacttgaagaaggtgaaattgttgaagaatcaaatgatacggcatcgtatttagggaaagaaatcacagtgaagcatccattggagcattcatggactttttggtttgataaccctaccactaaatctcgacaaactgcttggggaagctcacttcgaaatgtctacactttctccactgttgaaaatttttggggtgcttacaataatatccatcacccaagcaagttaattatgggagcagactttcattgttttaagcacaaaattgagccaaagtgggaagatcctgtatgtgccaatggagggacgtggaaaatgagtttttcgaagggtaaatctgataccagctggctgtatacgctgctggcaatgattggacatcaattcgatcatggagatgaaatttgtggagcagttgttagtgtccgggctaagggagaaaaaatagctttgtggaccaagaatgctgcaaatgaaacagctcaggttagcattggtaagcaatggaagcagtttctagattacagtgattcggttggcttcatatttcacgacgatgcaaagaggctcgacagaaatgccaagaatcgttacaccgtatag</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0097P22-lNaBf/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C00SLf0097P22.1" temp_strand="-" temp_description="C00SLf0097P22.1  CU856538.2 htgs_phase:3 submitted_to_sgn_as:C04SLf0097P22 sequenced_by:sanger upload_account_name:uk">
        <position start="12618" stop="8867"/>
      </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="12318" g_stop="12032" g_length="287"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="287" r_length="287" r_score="0.997"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="12031" i_stop="10363" i_length="1669">
            <donor d_prob="0.993" d_score="0.98"/>
            <acceptor a_prob="0.628" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="10362" g_stop="10197" g_length="166"/>
          <reference_exon_boundary r_type="cDNA" r_start="288" r_stop="453" r_length="166" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="10196" i_stop="10087" i_length="110">
            <donor d_prob="0.000" d_score="1.00"/>
            <acceptor a_prob="0.988" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="10086" g_stop="9961" g_length="126"/>
          <reference_exon_boundary r_type="cDNA" r_start="454" r_stop="579" r_length="126" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="9960" i_stop="9367" i_length="594">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.991" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="9366" g_stop="9301" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="580" r_stop="645" r_length="66" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="9300" i_stop="9218" i_length="83">
            <donor d_prob="0.886" d_score="1.00"/>
            <acceptor a_prob="0.960" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="9217" g_stop="9167" g_length="51"/>
          <reference_exon_boundary r_type="cDNA" r_start="646" r_stop="696" r_length="51" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0097P22.1" gen_strand="-" ref_id="SGN-E747178" ref_strand="+">
        <total_alignment_score>0.999</total_alignment_score>
        <cumulative_length_of_scored_exons>696</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0097P22.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E747178" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="12318" e_stop="12032"/>
          <exon e_start="10362" e_stop="10197"/>
          <exon e_start="10086" e_stop="9961"/>
          <exon e_start="9366" e_stop="9301"/>
          <exon e_start="9217" e_stop="9167"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATGGCAGCAGCTGAAATGGAGAGAACGATGTCGTTTGATGCAGCTGAGAAGTTGAAGGCCGCCGATGGAGGAGGAGGAGAGGTAGACGATGAACTTGAAGAAGGTGAAATTGTTGAAGAATCAAATGATACGGCATCGTATTTAGGGAAAGAAATCACAGTGAAGCATCCATTGGAGCATTCATGGACTTTTTGGTTTGATAACCCTACCACTAAATCTCGACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAGATTTTTGGGGGTAAGTTTTTTTTTTTCCTCTTTCAAATTGGTGATAGTGTAGTGTAAGGGAAAACAGGGAGTGGATTGCAAGGTGGGGAATCGAATCCTCGAGAAAGTTTAGATAGTCAATTAATTGAGCTACTGAGATTCCTCGGATTTTTTAAAAAAAATAAATTGGGGATAGAGGAAGAGGAAATGGGGGAGACTTTTATAAGGTTATACCGTTGTTAACAAGGTGAAATTTTAGGTAGTTAATCAATTGAGCTACTAAGATTCTTTAGATACGATTTTCGTAAGCTCAAATTGGAAAATAAAAAATTAGATTATTACTAAGGAGCTGAAGAAATTCAGAAATGAGTTACCTTTTGAGCCAGCAGAACCAGTTAAGTTGAGATTTCATTGATTTTAGCTTGTTTTTAATGTTGGTTGTGAATTATGGGGTTTTATTATAATGTTCCAACAATTTTGTTGGTGTTGTAGGACTTTTTTGATTTAGCGTTTTGAATGTGTTCTGATTATCTGCCTTCACATAGGTGATATTGAGGTAAAAATGGCATCTTGATTGATTTTGCTCTCATAATTGTTAGATTTTCTTCTTGTACATTTTGCAGTTTTTAGTTAACTTGCCAAGGTGTTTAGTGGATGCACAATATGCGGTATTACTACGGAATGTCTGAATTGGTTTGAGCTTTAGTTTACCCAAGCTGTATTAGTAATTGCACATTGCTTTGTCCTTTTTTAGTTAGTACTTTCCTTAAAACTGGAATTTTGATCTCTTGGTTACTTGCCAATTTAAATTTTAGTTCATGGATCGGATTCAATGAATAGATATATGCTCTTTGGTGGTGGGAGGACAAGGATAGATAAATTAAACTCGGTAAGGAGAGAAAGTGCAGAATGAATGGAAGTTGAGACATTTTGGAGTATGGGGTGAAGAATGACCTGTGAAGTTTTAGGAAAGAAAAAGTTAACCTTGTTGAATAGTCATATTTCTCTTCCTTGCACAATCTTGTGTAGGAATGCCTTTAATTGGGTTTATATCGTCGGATAGTTTATATTGCTTCAAATCTAAGAAACTCTTTCATATTTGTCAAATGCTCCTATTTTCAACAAAGGATATTTTGAGCTGAAAAGGTAGTTGAATAATGCATTGGTCGTAGTTTTCTCTCCTAAGCAAGATAATATAGTTACTATTTTCAAGTACAACTACTTCTTTTTCTTTAGTTTACGTATAAGAGCAGGTCCTGTATCTACATAGCTGTGATATCTCTATGTGCATTTGTCTTAATATACTATTCACTTGTCTTAATATATTATTCACTTTCAAAAATAAAGACAGATGTGTTTCTATTTCTTAATTAGGCTAAAGTATGCTCATCTCCTCTGTAGATTGATGAGACTTAGCTGCAGGCCAGTTTTTTCAATCTCACGCATAGACTTTTTTATTAAGTCCTATGATTTGAGTAATGTAGGTGGTAATGGTGTGAATTTGATGTCTGCCATGGATGCATGCACCTTGTTTGGTGAGTTCTTTATTGGTCTAATTACTCAAGGCACTTGAGTTATTGTACAACTTGAACGATGACATACCTGTTTGATATTCCACATCATGGATTAGGTCTTTGAAATGCTATTATCCTTTTGGCTCATGATGAAATCTTGAACCATGTTGCTTATTCTACAAACAGTGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACGGTATTCCGAAGTTATTTCCATCCAGCCCTTAATGATAGGTCATTCTAGTAATGTTATTTTCCCCTTTGATATAATTTCCACTCTTGTTTTCTTATATGGAATTATTGTAGCTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAGGTAATTTGCTTTATATTTTTGGTGTCAACGGCCACGTTTGTCATTTTCTTGGATCAAGCGGACAGACATTTTTTGTTGTGTACATACTGTAGTGCTGATGTTTATTCAAAATATACTATGAAATACATTGTACCGTTGAGTATATTGGAAGTTAAGAGGGGAAGTCATCAGATATATAGGAAGTGCTCCTTGTGAGAAATTTCTCTAGTAGGGCTCAAACCCGAGAACCATGGTTAAGGACGGAGGGATCCCTTTGGTGGTATCAAGGGTTAATTATATTATTTCATGTTTCATATGATTGAAACATTTGGATATCCTTGCAAAGTGTGATATTGTTTTGTCTCGTCATTTGTTTTATGCTTCATAAGAATTATCTTTTCTTTCGTCCCCTTCTCTTTGTTTCTTTTTCTCCAGTGTACTTCATTCTTCTAGAATTATATAGTGGTCGGCGTTCCCTTTTGTGCTTCATTGATAATATTGAATCCTTTCAGCTGTTTACCGGTTGATTATTTTTATGTTGGTGCTTATTGCTAGTTTTTTGTTTTTATATCTTTGCAACTATACCTACCATCTTCCTGAAACTTCTCTTTACAGGTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCACGTATGAAATCTTGGTTATCATACGCCTTTAATTCAGTTTCTCTTCAATTAGCAAGACTCATAAAGAATCATCTTCTTTTGCAGGACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAG</genome_strand>
        <mrna_strand>ATGGCAGCAGCTGAAATGGAGAGAACGATGTCGTTTGATGCAGCTGAGAAGTTGAAGGCCGCCGATGGAGGAGGAGGAGAGGTAGACGATGAACTTGAAGAAGGTGAAATTGTTGAAGAATCAAATGATACGGCATCGTATTTAGGGAAAGAAATCACAGTGAAGCATCCATTGGAGCATTCATGGACTTTTTGGTTTGATAACCCTACCACTAAATCTCGACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAAATTTTTGGGG.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACG..............................................................................................................CTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAG..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCAC...................................................................................GACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAG</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-C00SLf0097P22-lNaBf/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E746691" ref_strand="+" ref_description="SGN-E746691 [GI|56412231]">
      <seq>atggcagcagctgaaatggagagaacgatgtcgtttgatgcagctgagaagttgaaggccgccgatggaggaggaggagaggtagacgatgaacttgaagaaggtgaaattgttgaagaatcaaatgatacggcatcgtatttagggaaagaaatcacagtgaagcatccattggagcattcatggactttttggtttgataaccctaccactaaatctcgacaaactgcttggggaagctcacttcgaaatgtctacactttctccactgttgaagatttttggggtgcttacaataatatccatcacccaagcaagttaattatgggagcagactttcattgttttaagcacaaaattgagccaaagtgggaagatcctgtatgtgccaatggagggacgtggaaaatgagtttttcgaagggtaaatctgataccagctggctgtatacgctgctggcaatgattggacatcaattcgatcatggagatgaaatttgtggagcagttgttagtgtccgggctaagggagaaaaaatagctttgtggaccaagaatgctgcaaatgaaacagctcaggttagcattggtaagcaatggaagcagtttctagattacagtgattcggttggcttcatatttcacgacgatgcaaagaggctcgacagaaatgccaagaatcgttacaccgtatag</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0097P22-lNaBf/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C00SLf0097P22.1" temp_strand="-" temp_description="C00SLf0097P22.1  CU856538.2 htgs_phase:3 submitted_to_sgn_as:C04SLf0097P22 sequenced_by:sanger upload_account_name:uk">
        <position start="12618" stop="8867"/>
      </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="12318" g_stop="12032" g_length="287"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="287" r_length="287" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="12031" i_stop="10363" i_length="1669">
            <donor d_prob="0.993" d_score="1.00"/>
            <acceptor a_prob="0.628" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="10362" g_stop="10197" g_length="166"/>
          <reference_exon_boundary r_type="cDNA" r_start="288" r_stop="453" r_length="166" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="10196" i_stop="10087" i_length="110">
            <donor d_prob="0.000" d_score="1.00"/>
            <acceptor a_prob="0.988" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="10086" g_stop="9961" g_length="126"/>
          <reference_exon_boundary r_type="cDNA" r_start="454" r_stop="579" r_length="126" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="9960" i_stop="9367" i_length="594">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.991" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="9366" g_stop="9301" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="580" r_stop="645" r_length="66" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="9300" i_stop="9218" i_length="83">
            <donor d_prob="0.886" d_score="1.00"/>
            <acceptor a_prob="0.960" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="9217" g_stop="9167" g_length="51"/>
          <reference_exon_boundary r_type="cDNA" r_start="646" r_stop="696" r_length="51" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0097P22.1" gen_strand="-" ref_id="SGN-E746691" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>696</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0097P22.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E746691" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="12318" e_stop="12032"/>
          <exon e_start="10362" e_stop="10197"/>
          <exon e_start="10086" e_stop="9961"/>
          <exon e_start="9366" e_stop="9301"/>
          <exon e_start="9217" e_stop="9167"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATGGCAGCAGCTGAAATGGAGAGAACGATGTCGTTTGATGCAGCTGAGAAGTTGAAGGCCGCCGATGGAGGAGGAGGAGAGGTAGACGATGAACTTGAAGAAGGTGAAATTGTTGAAGAATCAAATGATACGGCATCGTATTTAGGGAAAGAAATCACAGTGAAGCATCCATTGGAGCATTCATGGACTTTTTGGTTTGATAACCCTACCACTAAATCTCGACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAGATTTTTGGGGGTAAGTTTTTTTTTTTCCTCTTTCAAATTGGTGATAGTGTAGTGTAAGGGAAAACAGGGAGTGGATTGCAAGGTGGGGAATCGAATCCTCGAGAAAGTTTAGATAGTCAATTAATTGAGCTACTGAGATTCCTCGGATTTTTTAAAAAAAATAAATTGGGGATAGAGGAAGAGGAAATGGGGGAGACTTTTATAAGGTTATACCGTTGTTAACAAGGTGAAATTTTAGGTAGTTAATCAATTGAGCTACTAAGATTCTTTAGATACGATTTTCGTAAGCTCAAATTGGAAAATAAAAAATTAGATTATTACTAAGGAGCTGAAGAAATTCAGAAATGAGTTACCTTTTGAGCCAGCAGAACCAGTTAAGTTGAGATTTCATTGATTTTAGCTTGTTTTTAATGTTGGTTGTGAATTATGGGGTTTTATTATAATGTTCCAACAATTTTGTTGGTGTTGTAGGACTTTTTTGATTTAGCGTTTTGAATGTGTTCTGATTATCTGCCTTCACATAGGTGATATTGAGGTAAAAATGGCATCTTGATTGATTTTGCTCTCATAATTGTTAGATTTTCTTCTTGTACATTTTGCAGTTTTTAGTTAACTTGCCAAGGTGTTTAGTGGATGCACAATATGCGGTATTACTACGGAATGTCTGAATTGGTTTGAGCTTTAGTTTACCCAAGCTGTATTAGTAATTGCACATTGCTTTGTCCTTTTTTAGTTAGTACTTTCCTTAAAACTGGAATTTTGATCTCTTGGTTACTTGCCAATTTAAATTTTAGTTCATGGATCGGATTCAATGAATAGATATATGCTCTTTGGTGGTGGGAGGACAAGGATAGATAAATTAAACTCGGTAAGGAGAGAAAGTGCAGAATGAATGGAAGTTGAGACATTTTGGAGTATGGGGTGAAGAATGACCTGTGAAGTTTTAGGAAAGAAAAAGTTAACCTTGTTGAATAGTCATATTTCTCTTCCTTGCACAATCTTGTGTAGGAATGCCTTTAATTGGGTTTATATCGTCGGATAGTTTATATTGCTTCAAATCTAAGAAACTCTTTCATATTTGTCAAATGCTCCTATTTTCAACAAAGGATATTTTGAGCTGAAAAGGTAGTTGAATAATGCATTGGTCGTAGTTTTCTCTCCTAAGCAAGATAATATAGTTACTATTTTCAAGTACAACTACTTCTTTTTCTTTAGTTTACGTATAAGAGCAGGTCCTGTATCTACATAGCTGTGATATCTCTATGTGCATTTGTCTTAATATACTATTCACTTGTCTTAATATATTATTCACTTTCAAAAATAAAGACAGATGTGTTTCTATTTCTTAATTAGGCTAAAGTATGCTCATCTCCTCTGTAGATTGATGAGACTTAGCTGCAGGCCAGTTTTTTCAATCTCACGCATAGACTTTTTTATTAAGTCCTATGATTTGAGTAATGTAGGTGGTAATGGTGTGAATTTGATGTCTGCCATGGATGCATGCACCTTGTTTGGTGAGTTCTTTATTGGTCTAATTACTCAAGGCACTTGAGTTATTGTACAACTTGAACGATGACATACCTGTTTGATATTCCACATCATGGATTAGGTCTTTGAAATGCTATTATCCTTTTGGCTCATGATGAAATCTTGAACCATGTTGCTTATTCTACAAACAGTGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACGGTATTCCGAAGTTATTTCCATCCAGCCCTTAATGATAGGTCATTCTAGTAATGTTATTTTCCCCTTTGATATAATTTCCACTCTTGTTTTCTTATATGGAATTATTGTAGCTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAGGTAATTTGCTTTATATTTTTGGTGTCAACGGCCACGTTTGTCATTTTCTTGGATCAAGCGGACAGACATTTTTTGTTGTGTACATACTGTAGTGCTGATGTTTATTCAAAATATACTATGAAATACATTGTACCGTTGAGTATATTGGAAGTTAAGAGGGGAAGTCATCAGATATATAGGAAGTGCTCCTTGTGAGAAATTTCTCTAGTAGGGCTCAAACCCGAGAACCATGGTTAAGGACGGAGGGATCCCTTTGGTGGTATCAAGGGTTAATTATATTATTTCATGTTTCATATGATTGAAACATTTGGATATCCTTGCAAAGTGTGATATTGTTTTGTCTCGTCATTTGTTTTATGCTTCATAAGAATTATCTTTTCTTTCGTCCCCTTCTCTTTGTTTCTTTTTCTCCAGTGTACTTCATTCTTCTAGAATTATATAGTGGTCGGCGTTCCCTTTTGTGCTTCATTGATAATATTGAATCCTTTCAGCTGTTTACCGGTTGATTATTTTTATGTTGGTGCTTATTGCTAGTTTTTTGTTTTTATATCTTTGCAACTATACCTACCATCTTCCTGAAACTTCTCTTTACAGGTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCACGTATGAAATCTTGGTTATCATACGCCTTTAATTCAGTTTCTCTTCAATTAGCAAGACTCATAAAGAATCATCTTCTTTTGCAGGACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAG</genome_strand>
        <mrna_strand>ATGGCAGCAGCTGAAATGGAGAGAACGATGTCGTTTGATGCAGCTGAGAAGTTGAAGGCCGCCGATGGAGGAGGAGGAGAGGTAGACGATGAACTTGAAGAAGGTGAAATTGTTGAAGAATCAAATGATACGGCATCGTATTTAGGGAAAGAAATCACAGTGAAGCATCCATTGGAGCATTCATGGACTTTTTGGTTTGATAACCCTACCACTAAATCTCGACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAGATTTTTGGGG.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACG..............................................................................................................CTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAG..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCAC...................................................................................GACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAG</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-C00SLf0097P22-lNaBf/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E398060" ref_strand="-" ref_description="SGN-E398060 [TUS-38-M16](-)">
      <seq>atgggagcagactttcattgttttaagcacaaaattgagccacagtgggaagatcctgtatgtgccaatggagggacgtggaaaatgagtttttcgaagggtaaatctgataccacctggctgtatacgctgctggcaatgattggacatcaattccatcatggagatgaaatttgtggagcagttgttagtgtccgggctaagggagaaaaaatagctttgtggaccaagaatgctgcaaatgaaacagctcaggttagcattggaaagcaatggaagcagtttctagattacagtgattcggttggcttcatatttcacga</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0097P22-lNaBf/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C00SLf0097P22.1" temp_strand="-" temp_description="C00SLf0097P22.1  CU856538.2 htgs_phase:3 submitted_to_sgn_as:C04SLf0097P22 sequenced_by:sanger upload_account_name:uk">
        <position start="10625" stop="9000"/>
      </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="10325" g_stop="10197" g_length="129"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="129" r_length="129" r_score="0.984"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="10196" i_stop="10087" i_length="110">
            <donor d_prob="0.000" d_score="0.98"/>
            <acceptor a_prob="0.988" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="10086" g_stop="9961" g_length="126"/>
          <reference_exon_boundary r_type="cDNA" r_start="130" r_stop="255" r_length="126" r_score="0.992"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="9960" i_stop="9367" i_length="594">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.991" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="9366" g_stop="9301" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="256" r_stop="321" r_length="66" r_score="0.985"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0097P22.1" gen_strand="-" ref_id="SGN-E398060" ref_strand="-">
        <total_alignment_score>0.988</total_alignment_score>
        <cumulative_length_of_scored_exons>321</cumulative_length_of_scored_exons>
        <coverage percentage="0.994" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0097P22.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E398060" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="10325" e_stop="10197"/>
          <exon e_start="10086" e_stop="9961"/>
          <exon e_start="9366" e_stop="9301"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACGGTATTCCGAAGTTATTTCCATCCAGCCCTTAATGATAGGTCATTCTAGTAATGTTATTTTCCCCTTTGATATAATTTCCACTCTTGTTTTCTTATATGGAATTATTGTAGCTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAGGTAATTTGCTTTATATTTTTGGTGTCAACGGCCACGTTTGTCATTTTCTTGGATCAAGCGGACAGACATTTTTTGTTGTGTACATACTGTAGTGCTGATGTTTATTCAAAATATACTATGAAATACATTGTACCGTTGAGTATATTGGAAGTTAAGAGGGGAAGTCATCAGATATATAGGAAGTGCTCCTTGTGAGAAATTTCTCTAGTAGGGCTCAAACCCGAGAACCATGGTTAAGGACGGAGGGATCCCTTTGGTGGTATCAAGGGTTAATTATATTATTTCATGTTTCATATGATTGAAACATTTGGATATCCTTGCAAAGTGTGATATTGTTTTGTCTCGTCATTTGTTTTATGCTTCATAAGAATTATCTTTTCTTTCGTCCCCTTCTCTTTGTTTCTTTTTCTCCAGTGTACTTCATTCTTCTAGAATTATATAGTGGTCGGCGTTCCCTTTTGTGCTTCATTGATAATATTGAATCCTTTCAGCTGTTTACCGGTTGATTATTTTTATGTTGGTGCTTATTGCTAGTTTTTTGTTTTTATATCTTTGCAACTATACCTACCATCTTCCTGAAACTTCTCTTTACAGGTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCAC</genome_strand>
        <mrna_strand>ATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCACAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCACCTGGCTGTATACG..............................................................................................................CTGCTGGCAATGATTGGACATCAATTCCATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAG..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTAGCATTGGAAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCAC</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-C00SLf0097P22-lNaBf/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E341772" ref_strand="+" ref_description="SGN-E341772 [cTOF-9-M5]">
      <seq>ttgaaggccgccgatggaggaggaggagaggtagacgatgaacttgaagaaagtgaaattgttgaagaatcaaatgatacggcatcgtatttagggaaagaaatcacagtgaagcatccagtggagcattcatggactttttggtttgataaccctaccactaaatctcgacaaactgcttggggaagctcacttcgaaatgtctacactttctccactgttgaagatttttggggtgcttacaataatatccatcacccaagcaagttaattatgggagcagactttcattgttttaagcacaaaattgagccaaagtgggaagatcctgtatgtgccaatggagggacgtggaaaatgagtttttcgaagggtaaatctgataccagctggctgtatacgctgctggcaatgattggacatcaattcgatcatggagatgaaatttg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0097P22-lNaBf/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C00SLf0097P22.1" temp_strand="-" temp_description="C00SLf0097P22.1  CU856538.2 htgs_phase:3 submitted_to_sgn_as:C04SLf0097P22 sequenced_by:sanger upload_account_name:uk">
        <position start="12567" stop="9740"/>
      </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="12267" g_stop="12032" g_length="236"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="236" r_length="236" r_score="0.992"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="12031" i_stop="10363" i_length="1669">
            <donor d_prob="0.993" d_score="1.00"/>
            <acceptor a_prob="0.628" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="10362" g_stop="10197" g_length="166"/>
          <reference_exon_boundary r_type="cDNA" r_start="237" r_stop="402" r_length="166" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="10196" i_stop="10087" i_length="110">
            <donor d_prob="0.000" d_score="1.00"/>
            <acceptor a_prob="0.988" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="10086" g_stop="10040" g_length="47"/>
          <reference_exon_boundary r_type="cDNA" r_start="403" r_stop="449" r_length="47" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0097P22.1" gen_strand="-" ref_id="SGN-E341772" ref_strand="+">
        <total_alignment_score>0.995</total_alignment_score>
        <cumulative_length_of_scored_exons>449</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0097P22.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E341772" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="12267" e_stop="12032"/>
          <exon e_start="10362" e_stop="10197"/>
          <exon e_start="10086" e_stop="10040"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTGAAGGCCGCCGATGGAGGAGGAGGAGAGGTAGACGATGAACTTGAAGAAGGTGAAATTGTTGAAGAATCAAATGATACGGCATCGTATTTAGGGAAAGAAATCACAGTGAAGCATCCATTGGAGCATTCATGGACTTTTTGGTTTGATAACCCTACCACTAAATCTCGACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAGATTTTTGGGGGTAAGTTTTTTTTTTTCCTCTTTCAAATTGGTGATAGTGTAGTGTAAGGGAAAACAGGGAGTGGATTGCAAGGTGGGGAATCGAATCCTCGAGAAAGTTTAGATAGTCAATTAATTGAGCTACTGAGATTCCTCGGATTTTTTAAAAAAAATAAATTGGGGATAGAGGAAGAGGAAATGGGGGAGACTTTTATAAGGTTATACCGTTGTTAACAAGGTGAAATTTTAGGTAGTTAATCAATTGAGCTACTAAGATTCTTTAGATACGATTTTCGTAAGCTCAAATTGGAAAATAAAAAATTAGATTATTACTAAGGAGCTGAAGAAATTCAGAAATGAGTTACCTTTTGAGCCAGCAGAACCAGTTAAGTTGAGATTTCATTGATTTTAGCTTGTTTTTAATGTTGGTTGTGAATTATGGGGTTTTATTATAATGTTCCAACAATTTTGTTGGTGTTGTAGGACTTTTTTGATTTAGCGTTTTGAATGTGTTCTGATTATCTGCCTTCACATAGGTGATATTGAGGTAAAAATGGCATCTTGATTGATTTTGCTCTCATAATTGTTAGATTTTCTTCTTGTACATTTTGCAGTTTTTAGTTAACTTGCCAAGGTGTTTAGTGGATGCACAATATGCGGTATTACTACGGAATGTCTGAATTGGTTTGAGCTTTAGTTTACCCAAGCTGTATTAGTAATTGCACATTGCTTTGTCCTTTTTTAGTTAGTACTTTCCTTAAAACTGGAATTTTGATCTCTTGGTTACTTGCCAATTTAAATTTTAGTTCATGGATCGGATTCAATGAATAGATATATGCTCTTTGGTGGTGGGAGGACAAGGATAGATAAATTAAACTCGGTAAGGAGAGAAAGTGCAGAATGAATGGAAGTTGAGACATTTTGGAGTATGGGGTGAAGAATGACCTGTGAAGTTTTAGGAAAGAAAAAGTTAACCTTGTTGAATAGTCATATTTCTCTTCCTTGCACAATCTTGTGTAGGAATGCCTTTAATTGGGTTTATATCGTCGGATAGTTTATATTGCTTCAAATCTAAGAAACTCTTTCATATTTGTCAAATGCTCCTATTTTCAACAAAGGATATTTTGAGCTGAAAAGGTAGTTGAATAATGCATTGGTCGTAGTTTTCTCTCCTAAGCAAGATAATATAGTTACTATTTTCAAGTACAACTACTTCTTTTTCTTTAGTTTACGTATAAGAGCAGGTCCTGTATCTACATAGCTGTGATATCTCTATGTGCATTTGTCTTAATATACTATTCACTTGTCTTAATATATTATTCACTTTCAAAAATAAAGACAGATGTGTTTCTATTTCTTAATTAGGCTAAAGTATGCTCATCTCCTCTGTAGATTGATGAGACTTAGCTGCAGGCCAGTTTTTTCAATCTCACGCATAGACTTTTTTATTAAGTCCTATGATTTGAGTAATGTAGGTGGTAATGGTGTGAATTTGATGTCTGCCATGGATGCATGCACCTTGTTTGGTGAGTTCTTTATTGGTCTAATTACTCAAGGCACTTGAGTTATTGTACAACTTGAACGATGACATACCTGTTTGATATTCCACATCATGGATTAGGTCTTTGAAATGCTATTATCCTTTTGGCTCATGATGAAATCTTGAACCATGTTGCTTATTCTACAAACAGTGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACGGTATTCCGAAGTTATTTCCATCCAGCCCTTAATGATAGGTCATTCTAGTAATGTTATTTTCCCCTTTGATATAATTTCCACTCTTGTTTTCTTATATGGAATTATTGTAGCTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTG</genome_strand>
        <mrna_strand>TTGAAGGCCGCCGATGGAGGAGGAGGAGAGGTAGACGATGAACTTGAAGAAAGTGAAATTGTTGAAGAATCAAATGATACGGCATCGTATTTAGGGAAAGAAATCACAGTGAAGCATCCAGTGGAGCATTCATGGACTTTTTGGTTTGATAACCCTACCACTAAATCTCGACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAGATTTTTGGGG.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACG..............................................................................................................CTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTG</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-C00SLf0097P22-lNaBf/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E302041" ref_strand="+" ref_description="SGN-E302041 [cLEX-3-L16]">
      <seq>agcagcaaaaatggcagcagctgaaatggagagaacgatgtcgtttgatgcagctgagaagttgaaggccgccgatggaggaggaggagaggtagaccatgaacttgaagaaggtgaaattgttgaagaatcaaatgatacggcatcgtatttagggaaagaaatcacagtgaagcatccagtggagcattcatggactttttggtttgataaccctaccactaaatctcgacaaactgcttggggaagctcacttcgaaatgtctacactttctccactgttgaagatttttggggtgcttacaataatatccatcacccaagcaagttaattatgggagcagactttcattgttttaagcacaaaattgagccaaagtgggaagatcctgtatgtgccaatggagggacgtggaaaatgagtttttcgaagggtaaatctgataccagctggctgtatacgctgctggcaatgattggacatcaattcgatcatggagatgaaattt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0097P22-lNaBf/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C00SLf0097P22.1" temp_strand="-" temp_description="C00SLf0097P22.1  CU856538.2 htgs_phase:3 submitted_to_sgn_as:C04SLf0097P22 sequenced_by:sanger upload_account_name:uk">
        <position start="12628" stop="9741"/>
      </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="12328" g_stop="12032" g_length="297"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="297" r_length="297" r_score="0.993"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="12031" i_stop="10363" i_length="1669">
            <donor d_prob="0.993" d_score="1.00"/>
            <acceptor a_prob="0.628" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="10362" g_stop="10197" g_length="166"/>
          <reference_exon_boundary r_type="cDNA" r_start="298" r_stop="463" r_length="166" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="10196" i_stop="10087" i_length="110">
            <donor d_prob="0.000" d_score="1.00"/>
            <acceptor a_prob="0.988" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="10086" g_stop="10041" g_length="46"/>
          <reference_exon_boundary r_type="cDNA" r_start="464" r_stop="509" r_length="46" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0097P22.1" gen_strand="-" ref_id="SGN-E302041" ref_strand="+">
        <total_alignment_score>0.996</total_alignment_score>
        <cumulative_length_of_scored_exons>509</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0097P22.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E302041" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="12328" e_stop="12032"/>
          <exon e_start="10362" e_stop="10197"/>
          <exon e_start="10086" e_stop="10041"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGCAGCAAAAATGGCAGCAGCTGAAATGGAGAGAACGATGTCGTTTGATGCAGCTGAGAAGTTGAAGGCCGCCGATGGAGGAGGAGGAGAGGTAGACGATGAACTTGAAGAAGGTGAAATTGTTGAAGAATCAAATGATACGGCATCGTATTTAGGGAAAGAAATCACAGTGAAGCATCCATTGGAGCATTCATGGACTTTTTGGTTTGATAACCCTACCACTAAATCTCGACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAGATTTTTGGGGGTAAGTTTTTTTTTTTCCTCTTTCAAATTGGTGATAGTGTAGTGTAAGGGAAAACAGGGAGTGGATTGCAAGGTGGGGAATCGAATCCTCGAGAAAGTTTAGATAGTCAATTAATTGAGCTACTGAGATTCCTCGGATTTTTTAAAAAAAATAAATTGGGGATAGAGGAAGAGGAAATGGGGGAGACTTTTATAAGGTTATACCGTTGTTAACAAGGTGAAATTTTAGGTAGTTAATCAATTGAGCTACTAAGATTCTTTAGATACGATTTTCGTAAGCTCAAATTGGAAAATAAAAAATTAGATTATTACTAAGGAGCTGAAGAAATTCAGAAATGAGTTACCTTTTGAGCCAGCAGAACCAGTTAAGTTGAGATTTCATTGATTTTAGCTTGTTTTTAATGTTGGTTGTGAATTATGGGGTTTTATTATAATGTTCCAACAATTTTGTTGGTGTTGTAGGACTTTTTTGATTTAGCGTTTTGAATGTGTTCTGATTATCTGCCTTCACATAGGTGATATTGAGGTAAAAATGGCATCTTGATTGATTTTGCTCTCATAATTGTTAGATTTTCTTCTTGTACATTTTGCAGTTTTTAGTTAACTTGCCAAGGTGTTTAGTGGATGCACAATATGCGGTATTACTACGGAATGTCTGAATTGGTTTGAGCTTTAGTTTACCCAAGCTGTATTAGTAATTGCACATTGCTTTGTCCTTTTTTAGTTAGTACTTTCCTTAAAACTGGAATTTTGATCTCTTGGTTACTTGCCAATTTAAATTTTAGTTCATGGATCGGATTCAATGAATAGATATATGCTCTTTGGTGGTGGGAGGACAAGGATAGATAAATTAAACTCGGTAAGGAGAGAAAGTGCAGAATGAATGGAAGTTGAGACATTTTGGAGTATGGGGTGAAGAATGACCTGTGAAGTTTTAGGAAAGAAAAAGTTAACCTTGTTGAATAGTCATATTTCTCTTCCTTGCACAATCTTGTGTAGGAATGCCTTTAATTGGGTTTATATCGTCGGATAGTTTATATTGCTTCAAATCTAAGAAACTCTTTCATATTTGTCAAATGCTCCTATTTTCAACAAAGGATATTTTGAGCTGAAAAGGTAGTTGAATAATGCATTGGTCGTAGTTTTCTCTCCTAAGCAAGATAATATAGTTACTATTTTCAAGTACAACTACTTCTTTTTCTTTAGTTTACGTATAAGAGCAGGTCCTGTATCTACATAGCTGTGATATCTCTATGTGCATTTGTCTTAATATACTATTCACTTGTCTTAATATATTATTCACTTTCAAAAATAAAGACAGATGTGTTTCTATTTCTTAATTAGGCTAAAGTATGCTCATCTCCTCTGTAGATTGATGAGACTTAGCTGCAGGCCAGTTTTTTCAATCTCACGCATAGACTTTTTTATTAAGTCCTATGATTTGAGTAATGTAGGTGGTAATGGTGTGAATTTGATGTCTGCCATGGATGCATGCACCTTGTTTGGTGAGTTCTTTATTGGTCTAATTACTCAAGGCACTTGAGTTATTGTACAACTTGAACGATGACATACCTGTTTGATATTCCACATCATGGATTAGGTCTTTGAAATGCTATTATCCTTTTGGCTCATGATGAAATCTTGAACCATGTTGCTTATTCTACAAACAGTGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACGGTATTCCGAAGTTATTTCCATCCAGCCCTTAATGATAGGTCATTCTAGTAATGTTATTTTCCCCTTTGATATAATTTCCACTCTTGTTTTCTTATATGGAATTATTGTAGCTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTT</genome_strand>
        <mrna_strand>AGCAGCAAAAATGGCAGCAGCTGAAATGGAGAGAACGATGTCGTTTGATGCAGCTGAGAAGTTGAAGGCCGCCGATGGAGGAGGAGGAGAGGTAGACCATGAACTTGAAGAAGGTGAAATTGTTGAAGAATCAAATGATACGGCATCGTATTTAGGGAAAGAAATCACAGTGAAGCATCCAGTGGAGCATTCATGGACTTTTTGGTTTGATAACCCTACCACTAAATCTCGACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAGATTTTTGGGG.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACG..............................................................................................................CTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTT</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>13</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="12328" PGL_stop="8994"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="12328" e_stop="12032"/>
            <exon e_start="10362" e_stop="10197"/>
            <exon e_start="10086" e_stop="9961"/>
            <exon e_start="9366" e_stop="9301"/>
            <exon e_start="9217" e_stop="8994"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.993" acc_prob="0.628" e_score="1.000"/>
          <exon-intron don_prob="0.000" acc_prob="0.988" e_score="1.000"/>
          <exon-intron don_prob="0.997" acc_prob="0.991" e_score="1.000"/>
          <exon-intron don_prob="0.886" acc_prob="0.960" 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="1.000">
            <gDNA_exon_boundary e_start="12328" e_stop="12032" e_length="297"/>
          </exon>
          <intron i_serial="1" don_prob="0.993" acc_prob="0.628">
            <gDNA_intron_boundary i_start="12031" i_stop="10363" i_length="1669"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="10362" e_stop="10197" e_length="166"/>
          </exon>
          <intron i_serial="2" don_prob="0.000" acc_prob="0.988">
            <gDNA_intron_boundary i_start="10196" i_stop="10087" i_length="110"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="10086" e_stop="9961" e_length="126"/>
          </exon>
          <intron i_serial="3" don_prob="0.997" acc_prob="0.991">
            <gDNA_intron_boundary i_start="9960" i_stop="9367" i_length="594"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="9366" e_stop="9301" e_length="66"/>
          </exon>
          <intron i_serial="4" don_prob="0.886" acc_prob="0.960">
            <gDNA_intron_boundary i_start="9300" i_stop="9218" i_length="83"/>
          </intron>
          <exon e_serial="5" e_score="1.000">
            <gDNA_exon_boundary e_start="9217" e_stop="8994" e_length="224"/>
          </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="12328" stop="12032"/>
              <exon start="10362" stop="10197"/>
              <exon start="10086" stop="10041"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E302041" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="12318" stop="12032"/>
              <exon start="10362" stop="10197"/>
              <exon start="10086" stop="9961"/>
              <exon start="9366" stop="9301"/>
              <exon start="9217" stop="9167"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E746690" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="12318" stop="12032"/>
              <exon start="10362" stop="10197"/>
              <exon start="10086" stop="9961"/>
              <exon start="9366" stop="9301"/>
              <exon start="9217" stop="9167"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E747178" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="12318" stop="12032"/>
              <exon start="10362" stop="10197"/>
              <exon start="10086" stop="9961"/>
              <exon start="9366" stop="9301"/>
              <exon start="9217" stop="9167"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E746691" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="12267" stop="12032"/>
              <exon start="10362" stop="10197"/>
              <exon start="10086" stop="10040"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E341772" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="12164" stop="12032"/>
              <exon start="10362" stop="10197"/>
              <exon start="10086" stop="9961"/>
              <exon start="9366" stop="9301"/>
              <exon start="9217" stop="9014"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E342832" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="12114" stop="12032"/>
              <exon start="10362" stop="10197"/>
              <exon start="10086" stop="9961"/>
              <exon start="9366" stop="9301"/>
              <exon start="9217" stop="9004"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E352080" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="12097" stop="12032"/>
              <exon start="10362" stop="10197"/>
              <exon start="10086" stop="9961"/>
              <exon start="9366" stop="9301"/>
              <exon start="9217" stop="8997"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E394175" strand="-"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="10325" stop="10197"/>
              <exon start="10086" stop="9961"/>
              <exon start="9366" stop="9301"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E398060" strand="-"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="10321" stop="10197"/>
              <exon start="10086" stop="9961"/>
              <exon start="9366" stop="9301"/>
              <exon start="9217" stop="9016"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E265573" strand="-"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="10026" stop="9961"/>
              <exon start="9366" stop="9301"/>
              <exon start="9217" stop="8994"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E237342" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="10005" stop="9961"/>
              <exon start="9366" stop="9301"/>
              <exon start="9217" stop="8995"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E236869" 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>AGCAGCAAAAATGGCAGCAGCTGAAATGGAGAGAACGATGTCGTTTGATGCAGCTGAGAAGTTGAAGGCCGCCGATGGAGGAGGAGGAGAGGTAGACGATGAACTTGAAGAAGGTGAAATTGTTGAAGAATCAAATGATACGGCATCGTATTTAGGGAAAGAAATCACAGTGAAGCATCCATTGGAGCATTCATGGACTTTTTGGTTTGATAACCCTACCACTAAATCTCGACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAGATTTTTGGGG : TGCTTACAATAATATCCATCACCCAAGCAAGTTAATTATGGGAGCAGACTTTCATTGTTTTAAGCACAAAATTGAGCCAAAGTGGGAAGATCCTGTATGTGCCAATGGAGGGACGTGGAAAATGAGTTTTTCGAAGGGTAAATCTGATACCAGCTGGCTGTATACG : CTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAG : GTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCAC : GACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAGTTCTTGATGCAGTGTGGGATTGCAAGAAACACAATTCGTACTGGAAAGGTTGGTAGGTACTAGTTTAGTTTCTCATTTGATAAGCTTCTGGTTTGAGTAACTCGTGTGTTGGTGTTTACACTTTCTAATCGTGGAAAATTGTTTGATTTGAATCCATGCCTCTATGTTTCGTG</gDNA_template>
            <first_frame> S  S  K  N  G  S  S  *  N  G  E  N  D  V  V  *  C  S  *  E  V  E  G  R  R  W  R  R  R  R  G  R  R  *  T  *  R  R  *  N  C  *  R  I  K  *  Y  G  I  V  F  R  E  R  N  H  S  E  A  S  I  G  A  F  M  D  F  L  V  *  *  P  Y  H  *  I  S  T  N  C  L  G  K  L  T  S  K  C  L  H  F  L  H  C  *  R  F  L  G  :  C  L  Q  *  Y  P  S  P  K  Q  V  N  Y  G  S  R  L  S  L  F  *  A  Q  N  *  A  K  V  G  R  S  C  M  C  Q  W  R  D  V  E  N  E  F  F  E  G  *  I  *  Y  Q  L  A  V  Y   : A  A  G  N  D  W  T  S  I  R  S  W  R  *  N  L  W  S  S  C  *  C  P  G  *  G  R  K  N  S  F  V  D  Q  E  C  C  K  *  N  S  S   : G  *  H  W  *  A  M  E  A  V  S  R  L  Q  *  F  G  W  L  H  I  S   : R  R  C  K  E  A  R  Q  K  C  Q  E  S  L  H  R  I  V  L  D  A  V  W  D  C  K  K  H  N  S  Y  W  K  G  W  *  V  L  V  *  F  L  I  *  *  A  S  G  L  S  N  S  C  V  G  V  Y  T  F  *  S  W  K  I  V  *  F  E  S  M  P  L  C  F  V </first_frame>
            <second_frame>  A  A  K  M  A  A  A  E  M  E  R  T  M  S  F  D  A  A  E  K  L  K  A  A  D  G  G  G  G  E  V  D  D  E  L  E  E  G  E  I  V  E  E  S  N  D  T  A  S  Y  L  G  K  E  I  T  V  K  H  P  L  E  H  S  W  T  F  W  F  D  N  P  T  T  K  S  R  Q  T  A  W  G  S  S  L  R  N  V  Y  T  F  S  T  V  E  D  F  W  G :   A  Y  N  N  I  H  H  P  S  K  L  I  M  G  A  D  F  H  C  F  K  H  K  I  E  P  K  W  E  D  P  V  C  A  N  G  G  T  W  K  M  S  F  S  K  G  K  S  D  T  S  W  L  Y  T  :  L  L  A  M  I  G  H  Q  F  D  H  G  D  E  I  C  G  A  V  V  S  V  R  A  K  G  E  K  I  A  L  W  T  K  N  A  A  N  E  T  A  Q  :  V  S  I  G  K  Q  W  K  Q  F  L  D  Y  S  D  S  V  G  F  I  F  H  :  D  D  A  K  R  L  D  R  N  A  K  N  R  Y  T  V  *  F  L  M  Q  C  G  I  A  R  N  T  I  R  T  G  K  V  G  R  Y  *  F  S  F  S  F  D  K  L  L  V  *  V  T  R  V  L  V  F  T  L  S  N  R  G  K  L  F  D  L  N  P  C  L  Y  V  S   </second_frame>
            <third_frame>   Q  Q  K  W  Q  Q  L  K  W  R  E  R  C  R  L  M  Q  L  R  S  *  R  P  P  M  E  E  E  E  R  *  T  M  N  L  K  K  V  K  L  L  K  N  Q  M  I  R  H  R  I  *  G  K  K  S  Q  *  S  I  H  W  S  I  H  G  L  F  G  L  I  T  L  P  L  N  L  D  K  L  L  G  E  A  H  F  E  M  S  T  L  S  P  L  L  K  I  F  G   : V  L  T  I  I  S  I  T  Q  A  S  *  L  W  E  Q  T  F  I  V  L  S  T  K  L  S  Q  S  G  K  I  L  Y  V  P  M  E  G  R  G  K  *  V  F  R  R  V  N  L  I  P  A  G  C  I  R :   C  W  Q  *  L  D  I  N  S  I  M  E  M  K  F  V  E  Q  L  L  V  S  G  L  R  E  K  K  *  L  C  G  P  R  M  L  Q  M  K  Q  L  R :   L  A  L  V  S  N  G  S  S  F  *  I  T  V  I  R  L  A  S  Y  F  T :   T  M  Q  R  G  S  T  E  M  P  R  I  V  T  P  Y  S  S  *  C  S  V  G  L  Q  E  T  Q  F  V  L  E  R  L  V  G  T  S  L  V  S  H  L  I  S  F  W  F  E  *  L  V  C  W  C  L  H  F  L  I  V  E  N  C  L  I  *  I  H  A  S  M  F  R  </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="C00SLf0097P22.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="12327" stop="12032"/>
                    <exon start="10362" stop="10197"/>
                    <exon start="10086" stop="9961"/>
                    <exon start="9366" stop="9301"/>
                    <exon start="9217" stop="9167"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>702</number_coding_nucleotides>
                  <number_encoded_amino_acids>234</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>AAKMAAAEMERTMSFDAAEKLKAADGGGGEVDDELEEGEIVEESNDTASYLGKEITVKHPLEHSWTFWFDNPTTKSRQTAWGSSLRNVYTFSTVEDFWGAYNNIHHPSKLIMGADFHCFKHKIEPKWEDPVCANGGTWKMSFSKGKSDTSWLYTLLAMIGHQFDHGDEICGAVVSVRAKGEKIALWTKNAANETAQVSIGKQWKQFLDYSDSVGFIFHDDAKRLDRNAKNRYTV*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
      <AGS_information>
        <AGS_line AGS_serial="2">
          <exon_coordinates>
            <exon e_start="10113" e_stop="9961"/>
            <exon e_start="9366" e_stop="9301"/>
            <exon e_start="9217" e_stop="8994"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.997" acc_prob="0.991" e_score="0.948"/>
          <exon-intron don_prob="0.886" acc_prob="0.960" 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="0.948">
            <gDNA_exon_boundary e_start="10113" e_stop="9961" e_length="153"/>
          </exon>
          <intron i_serial="1" don_prob="0.997" acc_prob="0.991">
            <gDNA_intron_boundary i_start="9960" i_stop="9367" i_length="594"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="9366" e_stop="9301" e_length="66"/>
          </exon>
          <intron i_serial="2" don_prob="0.886" acc_prob="0.960">
            <gDNA_intron_boundary i_start="9300" i_stop="9218" i_length="83"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="9217" e_stop="8994" e_length="224"/>
          </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="10113" stop="9961"/>
              <exon start="9366" stop="9301"/>
              <exon start="9217" stop="9016"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E234225" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="10026" stop="9961"/>
              <exon start="9366" stop="9301"/>
              <exon start="9217" stop="8994"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E237342" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="10005" stop="9961"/>
              <exon start="9366" stop="9301"/>
              <exon start="9217" stop="8995"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E236869" 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="2" gDNA_strand="-"/>
          <translation>
            <gDNA_template>TTGTTTTCTTATATGGAATTATTGTAGCTGCTGGCAATGATTGGACATCAATTCGATCATGGAGATGAAATTTGTGGAGCAGTTGTTAGTGTCCGGGCTAAGGGAGAAAAAATAGCTTTGTGGACCAAGAATGCTGCAAATGAAACAGCTCAG : GTTAGCATTGGTAAGCAATGGAAGCAGTTTCTAGATTACAGTGATTCGGTTGGCTTCATATTTCAC : GACGATGCAAAGAGGCTCGACAGAAATGCCAAGAATCGTTACACCGTATAGTTCTTGATGCAGTGTGGGATTGCAAGAAACACAATTCGTACTGGAAAGGTTGGTAGGTACTAGTTTAGTTTCTCATTTGATAAGCTTCTGGTTTGAGTAACTCGTGTGTTGGTGTTTACACTTTCTAATCGTGGAAAATTGTTTGATTTGAATCCATGCCTCTATGTTTCGTG</gDNA_template>
            <first_frame> L  F  S  Y  M  E  L  L  *  L  L  A  M  I  G  H  Q  F  D  H  G  D  E  I  C  G  A  V  V  S  V  R  A  K  G  E  K  I  A  L  W  T  K  N  A  A  N  E  T  A  Q  :  V  S  I  G  K  Q  W  K  Q  F  L  D  Y  S  D  S  V  G  F  I  F  H  :  D  D  A  K  R  L  D  R  N  A  K  N  R  Y  T  V  *  F  L  M  Q  C  G  I  A  R  N  T  I  R  T  G  K  V  G  R  Y  *  F  S  F  S  F  D  K  L  L  V  *  V  T  R  V  L  V  F  T  L  S  N  R  G  K  L  F  D  L  N  P  C  L  Y  V  S   </first_frame>
            <second_frame>  C  F  L  I  W  N  Y  C  S  C  W  Q  *  L  D  I  N  S  I  M  E  M  K  F  V  E  Q  L  L  V  S  G  L  R  E  K  K  *  L  C  G  P  R  M  L  Q  M  K  Q  L  R :   L  A  L  V  S  N  G  S  S  F  *  I  T  V  I  R  L  A  S  Y  F  T :   T  M  Q  R  G  S  T  E  M  P  R  I  V  T  P  Y  S  S  *  C  S  V  G  L  Q  E  T  Q  F  V  L  E  R  L  V  G  T  S  L  V  S  H  L  I  S  F  W  F  E  *  L  V  C  W  C  L  H  F  L  I  V  E  N  C  L  I  *  I  H  A  S  M  F  R  </second_frame>
            <third_frame>   V  F  L  Y  G  I  I  V  A  A  G  N  D  W  T  S  I  R  S  W  R  *  N  L  W  S  S  C  *  C  P  G  *  G  R  K  N  S  F  V  D  Q  E  C  C  K  *  N  S  S   : G  *  H  W  *  A  M  E  A  V  S  R  L  Q  *  F  G  W  L  H  I  S   : R  R  C  K  E  A  R  Q  K  C  Q  E  S  L  H  R  I  V  L  D  A  V  W  D  C  K  K  H  N  S  Y  W  K  G  W  *  V  L  V  *  F  L  I  *  *  A  S  G  L  S  N  S  C  V  G  V  Y  T  F  *  S  W  K  I  V  *  F  E  S  M  P  L  C  F  V </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="C00SLf0097P22.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="2" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="10086" stop="9961"/>
                    <exon start="9366" stop="9301"/>
                    <exon start="9217" stop="9167"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>240</number_coding_nucleotides>
                  <number_encoded_amino_acids>80</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LLAMIGHQFDHGDEICGAVVSVRAKGEKIALWTKNAANETAQVSIGKQWKQFLDYSDSVGFIFHDDAKRLDRNAKNRYTV*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 20 chains have been computed
$ 
$ memory statistics:
$ 27592 bytes spliced alignments in total
$ 13 spliced alignments have been stored
$ 2122 bytes was the average size of a spliced alignment
$ 5872 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5872 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 25 backtrace matrices have been allocated
$ 
$ date finished: 2009-02-20 08:32:16
-->
