<?xml version="1.0" encoding="ISO-8859-1"?>
<GTH_output xmlns="http://www.genomethreader.org/GTH_output/" GTH_XML_version="1.1">
  <header xmlns="http://www.genomethreader.org/GTH_output/header/">
    <source program="GenomeThreader" version="0.9.54" build_date="2006-07-28 11:55:15" run_date="2008-04-17 21:29:45"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0308B07-75M5e/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/cxgn-bacpublish-resources-BYUjxz/sgn_marker_seqs" type="ESTcDNA"/>
    </reference_files>
    <splice_site_parameters parameter_type="Bayesian" species="arabidopsis"/>
    <parameters>
      <parameter name="bssmfile" value="arabidopsis"/>
      <parameter name="scorematrixfile" value="BLOSUM62"/>
      <parameter name="searchmode" value="forward=True,reverse=True)"/>
      <parameter name="translationtable" value="1"/>
      <parameter name="frompos" value="0"/>
      <parameter name="topos" value="0"/>
      <parameter name="width" value="0"/>
      <parameter name="verbose" value="False"/>
      <parameter name="skipalignmentout" value="False"/>
      <parameter name="showintronmaxlen" value="120"/>
      <parameter name="minorflen" value="64"/>
      <parameter name="showseqnums" value="False"/>
      <parameter name="gs2out" value="False"/>
      <parameter name="maskpolyatails" value="False"/>
      <parameter name="noautoindex" value="False"/>
      <parameter name="minmatchlen" value="20"/>
      <parameter name="seedlength" value="16"/>
      <parameter name="exdrop" value="2"/>
      <parameter name="online" value="False"/>
      <parameter name="inverse" value="False"/>
      <parameter name="exact" value="False"/>
      <parameter name="chainwf" value="0.500000"/>
      <parameter name="gcmaxgapwidth" value="1000000"/>
      <parameter name="gcmincoverage" value="50"/>
      <parameter name="introncutout" value="False"/>
      <parameter name="autointroncutout" value="0"/>
      <parameter name="icinitialdelta" value="50"/>
      <parameter name="iciterations" value="2"/>
      <parameter name="icdeltaincrease" value="50"/>
      <parameter name="icminremintronlen" value="10"/>
      <parameter name="nou12intronmodel" value="False"/>
      <parameter name="u12donorprob" value="0.990000"/>
      <parameter name="u12donorprob1mism" value="0.900000"/>
      <parameter name="probies" value="0.500000"/>
      <parameter name="probdelgen" value="0.030000"/>
      <parameter name="identityweight" value="2.000000"/>
      <parameter name="mismatchweight" value="-2.000000"/>
      <parameter name="undetcharweight" value="0.000000"/>
      <parameter name="deletionweight" value="-4.000000"/>
      <parameter name="dpminexonlen" value="5"/>
      <parameter name="dpminintronlen" value="50"/>
      <parameter name="shortexonpenal" value="100"/>
      <parameter name="shortintronpenal" value="100"/>
      <parameter name="wzerotransition" value="80"/>
      <parameter name="wdecreasedoutput" value="80"/>
      <parameter name="leadcutoffsmode" value="RELAXED"/>
      <parameter name="termcutoffsmode" value="STRICT"/>
      <parameter name="cutoffsminexonlen" value="5"/>
      <parameter name="scoreminexonlen" value="50"/>
      <parameter name="minaveragessp" value="0.500000"/>
      <parameter name="minalignmentscore" value="0.900000"/>
      <parameter name="maxalignmentscore" value="1.000000"/>
      <parameter name="mincoverage" value="0.900000"/>
      <parameter name="maxcoverage" value="100.000000"/>
      <parameter name="intermediate" value="False"/>
      <parameter name="sortags" value="False"/>
      <parameter name="sortagswf" value="1.000000"/>
      <parameter name="first" value="0"/>
      <parameter name="exondistri" value="False"/>
      <parameter name="introndistri" value="False"/>
      <parameter name="refseqcovdistri" value="False"/>
    </parameters>
    <overall_reference_type>ESTcDNA</overall_reference_type>
  </header>
  <alignment_module>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/cxgn-bacpublish-resources-BYUjxz/sgn_marker_seqs" ref_id="SGN-M7481" ref_strand="+" ref_description="SGN-M7481 C2_At2g41380 [cosii_markers]">
      <seq>aacttacaaaaaaaaaaaatggcaaatttgttcattaagcaagcacaacaatattcaaagggtaggccaagttaccctcaagaattattcaatttcattgcttctaaaacaccttctcatgatcttgtttgggatgttggtactggtagtggccaggctgctcaatctttagctaagctttacaagaatgtgatagctacagacacaagtccaaagcagcttgaatttgcagcaaaggttccaaatgttcaatacatatgtacctctcctaagttgtcaaaatccgaaatcgaaacaaaaataggatcagaatcaagtgtagatttagtaacaattgcacaagcaatgcattggtttgatctaccaactttttatgaacatgttaaatggttactcaagaaaccaaatggtgttatagcatcatggtgttacactacacctaaaataaacaactcagtagatgcaatatttgataaattttacacaagtgatgctggaccttattgggaatcaccaagaaaattggtcgatgaaaagtatgaaactattgattttccatttgaggctatagatggatgtgatcataatggaccatttgagttcaagattgagaaagttatggacttggattcttgttttacatacttgaagtcatggtcagcttatcaaactgcaaaagaaaagggtgttgagttgttaagtgaagatgttgttgaaaaatttacaagtgcttggaatgaagatgggaagagtgagaaaaaagtgatttatcctatttacttgaggattggaaaagttggaaatttggattgaaagtgtaaagcaaatacaattagttatgtgcacttgatcatctatttattttgtatgttatttctcttagttgttattgttatgtatcttttaataataataaagtatctaagtactaattaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaactcgaactagttctc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0308B07-75M5e/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0308B07.2" temp_strand="+" temp_description="C04HBa0308B07.2  CT990558.4 htgs_phase:3 submitted_to_sgn_as:C04HBa0308B07 sequenced_by:sanger upload_account_name:uk">
        <position start="7806" stop="10428"/>
      </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="8106" g_stop="8273" g_length="168"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="168" r_length="168" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="8274" i_stop="9356" i_length="1083">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.988" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="9357" g_stop="10123" g_length="767"/>
          <reference_exon_boundary r_type="cDNA" r_start="169" r_stop="935" r_length="767" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="938" polyA_stop="974"/>
      <MATCH_line gen_id="C04HBa0308B07.2" gen_strand="+" ref_id="SGN-M7481" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>935</cumulative_length_of_scored_exons>
        <coverage percentage="0.946" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0308B07.2" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M7481" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="8106" e_stop="8273"/>
          <exon e_start="9357" e_stop="10123"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AACTTACAAAAAAAAAAAATGGCAAATTTGTTCATTAAGCAAGCACAACAATATTCAAAGGGTAGGCCAAGTTACCCTCAAGAATTATTCAATTTCATTGCTTCTAAAACACCTTCTCATGATCTTGTTTGGGATGTTGGTACTGGTAGTGGCCAGGCTGCTCAATCTGTAAGTCTCTATTTCTCCACGGTCAATCAAAAATTTCGTTAAGAATATTTTTTTTTAACTACGGAAAGTAATATCTAACCTATCCTTATTCAAAGTGGGTTAAGATCGGAAAAATTATACCGTATAGATTGATACTATCAATTATACTTGCATGTTTAATCTCATTAGTGAATATTCTGACTCTGTCCTGAATTATATAATTTGAGTGTTCATTGACTGATTTTTCATGCTGTAGAATCATATTTTTTTTCCTTTTATAAATGAATGACTTTGTTTAATTTGGTTGAATGGTTGGTCTAAAGTTATGGTAAATATATAATGTTCATTTTCAGGTCTTAAACACCTTAAATAAAAAATTAAAATTAAAATATTGCTAAAAATGAATTGATCTTTGTGAAACAAATCAAAAAAATTAAATTATTTCTTTTTAAACGAAGTGAATCTTATTATAATTGCATAGGAAACAGTAGTCCTCTGTTTATTTAGATAGTCCATCTGGAAAAACAAGAAATCTAGTATTCCGTTTCACTTTATATAACATGATTTTCATATTAATTTTTTCTAAATAGAATGTCATCCTTCTATATTAGTATAATATATAAATGTGCTCCTTAATTTATCTCATTCCACATTTATGTTTTTTTTTATCTTTAGTTTGTCTTATTTTATATTTATGCTCTTTAATTTTAGGTATGCATAAGCAGATACTTAAATTTATATAAACTTGAACAAGTAGACACATGAGTCTTACGTAGGACAACACATGTAGGAGATCATATAGGACAAAAAATAACAGGTAAGATGTCATGCGGGACATGTGTGTCTACTTGTTCAACTTTATACAAATTTAAGTGTCTATTTATGCACACCCAAAGTTGAAGAACATAAACATAATTTGAAGCCAAGTTAAAGGACATATTTATGTATTATGTCTTCTATATTTAAAACATCTATTCATTTTTGGCCGGCATAACGTAAATTTCATCATATGTCAAACTCCACCGCATAAATTGAAACAGTCCTTAGTGTTCATAAACTTGTTTCTTTTATCCTAACTTCCTCCAAAAATGTTGTGTTCCTCAGTTAGCTAAGCTTTACAAGAATGTGATAGCTACAGACACAAGTCCAAAGCAGCTTGAATTTGCAGCAAAGGTTCCAAATGTTCAATACATATGTACCTCTCCTAAGTTGTCAAAATCCGAAATCGAAACAAAAATAGGATCAGAATCAAGTGTAGATTTAGTAACAATTGCACAAGCAATGCATTGGTTTGATCTACCAACTTTTTATGAACATGTTAAATGGTTACTCAAGAAACCAAATGGTGTTATAGCATCATGGTGTTACACTACACCTAAAATAAACAACTCAGTAGATGCAATATTTGATAAATTTTACACAAGTGATGCTGGACCTTATTGGGAATCACCAAGAAAATTGGTCGATGAAAAGTATGAAACTATTGATTTTCCATTTGAGGCTATAGATGGATGTGATCATAATGGACCATTTGAGTTCAAGATTGAGAAAGTTATGGACTTGGATTCTTGTTTTACATACTTGAAGTCATGGTCAGCTTATCAAACTGCAAAAGAAAAGGGTGTTGAGTTGTTAAGTGAAGATGTTGTTGAAAAATTTACAAGTGCTTGGAATGAAGATGGGAAGAGTGAGAAAAAAGTGATTTATCCTATTTACTTGAGGATTGGAAAAGTTGGAAATTTGGATTGAAAGTGTAAAGCAAATACAATTAGTTATGTGCACTTGATCATCTATTTATTTTGTATGTTATTTCTCTTAGTTGTTATTGTTATGTATCTTTTAATAATAATAAAGTATCTAAGTACTAATTA</genome_strand>
        <mrna_strand>AACTTACAAAAAAAAAAAATGGCAAATTTGTTCATTAAGCAAGCACAACAATATTCAAAGGGTAGGCCAAGTTACCCTCAAGAATTATTCAATTTCATTGCTTCTAAAACACCTTCTCATGATCTTGTTTGGGATGTTGGTACTGGTAGTGGCCAGGCTGCTCAATCT...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTAGCTAAGCTTTACAAGAATGTGATAGCTACAGACACAAGTCCAAAGCAGCTTGAATTTGCAGCAAAGGTTCCAAATGTTCAATACATATGTACCTCTCCTAAGTTGTCAAAATCCGAAATCGAAACAAAAATAGGATCAGAATCAAGTGTAGATTTAGTAACAATTGCACAAGCAATGCATTGGTTTGATCTACCAACTTTTTATGAACATGTTAAATGGTTACTCAAGAAACCAAATGGTGTTATAGCATCATGGTGTTACACTACACCTAAAATAAACAACTCAGTAGATGCAATATTTGATAAATTTTACACAAGTGATGCTGGACCTTATTGGGAATCACCAAGAAAATTGGTCGATGAAAAGTATGAAACTATTGATTTTCCATTTGAGGCTATAGATGGATGTGATCATAATGGACCATTTGAGTTCAAGATTGAGAAAGTTATGGACTTGGATTCTTGTTTTACATACTTGAAGTCATGGTCAGCTTATCAAACTGCAAAAGAAAAGGGTGTTGAGTTGTTAAGTGAAGATGTTGTTGAAAAATTTACAAGTGCTTGGAATGAAGATGGGAAGAGTGAGAAAAAAGTGATTTATCCTATTTACTTGAGGATTGGAAAAGTTGGAAATTTGGATTGAAAGTGTAAAGCAAATACAATTAGTTATGTGCACTTGATCATCTATTTATTTTGTATGTTATTTCTCTTAGTTGTTATTGTTATGTATCTTTTAATAATAATAAAGTATCTAAGTACTAATTA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/cxgn-bacpublish-resources-BYUjxz/sgn_marker_seqs" ref_id="SGN-M1679" ref_strand="+" ref_description="SGN-M1679 T0954 [cos_markers]">
      <seq>taaaacaccttctcatgatcttgtttgggatgttggtactggtagtggccaggctgctcaatctttagctaagctttacaagaatgtgatagctacagacacaagtccaaagcagcttgaatttgcagcaaaggttccaaatgttcaatacatatgtacctctcctaagttgtcaaaatccgaaatcgaaacaaaaataggatcagaatcaagtgtagatttagtaacaattgcacaagcaatgcattggtttgatctaccaactttttatgaacatgttaaatggttactcaagaaaccaaatggtgttatagcatcatggtgttacactacacctaaaataaacaactcagtagatgcaatatttgataaattttacacaagtgatgctggaccttattgggaatcaccaagaaaattggtcgatgaaaagtatgaaactat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0308B07-75M5e/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0308B07.2" temp_strand="+" temp_description="C04HBa0308B07.2  CT990558.4 htgs_phase:3 submitted_to_sgn_as:C04HBa0308B07 sequenced_by:sanger upload_account_name:uk">
        <position start="7910" stop="10036"/>
      </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="8210" g_stop="8273" g_length="64"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="64" r_length="64" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="8274" i_stop="9356" i_length="1083">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.988" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="9357" g_stop="9736" g_length="380"/>
          <reference_exon_boundary r_type="cDNA" r_start="65" r_stop="444" r_length="380" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0308B07.2" gen_strand="+" ref_id="SGN-M1679" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>444</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0308B07.2" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M1679" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="8210" e_stop="8273"/>
          <exon e_start="9357" e_stop="9736"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TAAAACACCTTCTCATGATCTTGTTTGGGATGTTGGTACTGGTAGTGGCCAGGCTGCTCAATCTGTAAGTCTCTATTTCTCCACGGTCAATCAAAAATTTCGTTAAGAATATTTTTTTTTAACTACGGAAAGTAATATCTAACCTATCCTTATTCAAAGTGGGTTAAGATCGGAAAAATTATACCGTATAGATTGATACTATCAATTATACTTGCATGTTTAATCTCATTAGTGAATATTCTGACTCTGTCCTGAATTATATAATTTGAGTGTTCATTGACTGATTTTTCATGCTGTAGAATCATATTTTTTTTCCTTTTATAAATGAATGACTTTGTTTAATTTGGTTGAATGGTTGGTCTAAAGTTATGGTAAATATATAATGTTCATTTTCAGGTCTTAAACACCTTAAATAAAAAATTAAAATTAAAATATTGCTAAAAATGAATTGATCTTTGTGAAACAAATCAAAAAAATTAAATTATTTCTTTTTAAACGAAGTGAATCTTATTATAATTGCATAGGAAACAGTAGTCCTCTGTTTATTTAGATAGTCCATCTGGAAAAACAAGAAATCTAGTATTCCGTTTCACTTTATATAACATGATTTTCATATTAATTTTTTCTAAATAGAATGTCATCCTTCTATATTAGTATAATATATAAATGTGCTCCTTAATTTATCTCATTCCACATTTATGTTTTTTTTTATCTTTAGTTTGTCTTATTTTATATTTATGCTCTTTAATTTTAGGTATGCATAAGCAGATACTTAAATTTATATAAACTTGAACAAGTAGACACATGAGTCTTACGTAGGACAACACATGTAGGAGATCATATAGGACAAAAAATAACAGGTAAGATGTCATGCGGGACATGTGTGTCTACTTGTTCAACTTTATACAAATTTAAGTGTCTATTTATGCACACCCAAAGTTGAAGAACATAAACATAATTTGAAGCCAAGTTAAAGGACATATTTATGTATTATGTCTTCTATATTTAAAACATCTATTCATTTTTGGCCGGCATAACGTAAATTTCATCATATGTCAAACTCCACCGCATAAATTGAAACAGTCCTTAGTGTTCATAAACTTGTTTCTTTTATCCTAACTTCCTCCAAAAATGTTGTGTTCCTCAGTTAGCTAAGCTTTACAAGAATGTGATAGCTACAGACACAAGTCCAAAGCAGCTTGAATTTGCAGCAAAGGTTCCAAATGTTCAATACATATGTACCTCTCCTAAGTTGTCAAAATCCGAAATCGAAACAAAAATAGGATCAGAATCAAGTGTAGATTTAGTAACAATTGCACAAGCAATGCATTGGTTTGATCTACCAACTTTTTATGAACATGTTAAATGGTTACTCAAGAAACCAAATGGTGTTATAGCATCATGGTGTTACACTACACCTAAAATAAACAACTCAGTAGATGCAATATTTGATAAATTTTACACAAGTGATGCTGGACCTTATTGGGAATCACCAAGAAAATTGGTCGATGAAAAGTATGAAACTAT</genome_strand>
        <mrna_strand>TAAAACACCTTCTCATGATCTTGTTTGGGATGTTGGTACTGGTAGTGGCCAGGCTGCTCAATCT...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTAGCTAAGCTTTACAAGAATGTGATAGCTACAGACACAAGTCCAAAGCAGCTTGAATTTGCAGCAAAGGTTCCAAATGTTCAATACATATGTACCTCTCCTAAGTTGTCAAAATCCGAAATCGAAACAAAAATAGGATCAGAATCAAGTGTAGATTTAGTAACAATTGCACAAGCAATGCATTGGTTTGATCTACCAACTTTTTATGAACATGTTAAATGGTTACTCAAGAAACCAAATGGTGTTATAGCATCATGGTGTTACACTACACCTAAAATAAACAACTCAGTAGATGCAATATTTGATAAATTTTACACAAGTGATGCTGGACCTTATTGGGAATCACCAAGAAAATTGGTCGATGAAAAGTATGAAACTAT</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/cxgn-bacpublish-resources-BYUjxz/sgn_marker_seqs" ref_id="SGN-M1730" ref_strand="+" ref_description="SGN-M1730 T1054 [cos_markers]">
      <seq>gaactagtctcgattttttatttttattttttaaaagaagatttgaacttttattaacaaatttaagattcagccatgcaagctgtcaaagcttcttccttttcaccatttcacctcaacttgaactcaaccagttcatttcccaaaactaccaacttgtatattcaacaaaattatgaaaaccccatttcttgttttccctcaattcagacacaaaatgcaaaattcaaggtttttactgctacttccccaagtgtttcaacagaatcagaaaccccatttgatgaaaagactgaaaatgaaaatcaagaagagaaatttgagtggtatgctgagtggtacccaataatgccaatttgtgatcttgataagaggaggccacatggaaagaaagtgatggggattgatgtggttgtgtggtgggataggaatgagaaagaatggaaagtaatggatgattcttgtcctcatagatatgctccactttctgaaggaagaattgatcaatggggaagattgcagtgtgtgtatcat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0308B07-75M5e/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0308B07.2" temp_strand="+" temp_description="C04HBa0308B07.2  CT990558.4 htgs_phase:3 submitted_to_sgn_as:C04HBa0308B07 sequenced_by:sanger upload_account_name:uk">
        <position start="22226" stop="23348"/>
      </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="22515" g_stop="23048" g_length="534"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="534" r_length="534" r_score="0.987"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0308B07.2" gen_strand="+" ref_id="SGN-M1730" ref_strand="+">
        <total_alignment_score>0.987</total_alignment_score>
        <cumulative_length_of_scored_exons>534</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0308B07.2" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M1730" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="22515" e_stop="23048"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GGAGTTCTGAAGATTTTTTATTTTTATTTTTTAAAAGAAGATTTGAACTTTTATTAACAAATTTAAGATTCAGCCATGCAAGCTGTCAAAGCTTCTTCCTTTTCACCATTTCACCTCAACTTGAACTCAACCAGTTCATTTCCCAAAACTACCAACTTGTATATTCAACAAAATTATGAAAACCCCATTTCTTGTTTTCCCTCAATTCAGACACAAAATGCAAAATTCAAGGTTTTTACTGCTACTTCCCCAAGTGTTTCAACAGAATCAGAAACCCCATTTGATGAAAAGACTGAAAATGAAAATCAAGAAGAGAAATTTGAGTGGTATGCTGAGTGGTACCCAATAATGCCAATTTGTGATCTTGATAAGAGGAGGCCACATGGAAAGAAAGTGATGGGGATTGATGTGGTTGTGTGGTGGGATAGGAATGAGAAAGAATGGAAAGTAATGGATGATTCTTGTCCTCATAGATATGCTCCACTTTCTGAAGGAAGAATTGATCAATGGGGAAGATTGCAGTGTGTGTATCAT</genome_strand>
        <mrna_strand>GAACTAGTCTCGATTTTTTATTTTTATTTTTTAAAAGAAGATTTGAACTTTTATTAACAAATTTAAGATTCAGCCATGCAAGCTGTCAAAGCTTCTTCCTTTTCACCATTTCACCTCAACTTGAACTCAACCAGTTCATTTCCCAAAACTACCAACTTGTATATTCAACAAAATTATGAAAACCCCATTTCTTGTTTTCCCTCAATTCAGACACAAAATGCAAAATTCAAGGTTTTTACTGCTACTTCCCCAAGTGTTTCAACAGAATCAGAAACCCCATTTGATGAAAAGACTGAAAATGAAAATCAAGAAGAGAAATTTGAGTGGTATGCTGAGTGGTACCCAATAATGCCAATTTGTGATCTTGATAAGAGGAGGCCACATGGAAAGAAAGTGATGGGGATTGATGTGGTTGTGTGGTGGGATAGGAATGAGAAAGAATGGAAAGTAATGGATGATTCTTGTCCTCATAGATATGCTCCACTTTCTGAAGGAAGAATTGATCAATGGGGAAGATTGCAGTGTGTGTATCAT</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/cxgn-bacpublish-resources-BYUjxz/sgn_marker_seqs" ref_id="SGN-M8365" ref_strand="-" ref_description="SGN-M8365 C2_At4g25650 [cosii_markers]">
      <seq>ggaagaccacttgacataactatcacgaagttggatgtaaatgtcattactgcaaaccagggacctggacggaacacatttgttccgccttgtgtgtattatagttattttgctttcggaggatctcagggaaaaacaactgctgtatcatctggaactgtacaggaaaaaccttcagctgagaagcagaaaaaagcacttttagttttcatctgtattccggttagtccaggtcatagcagaattatatttgcatctccaagaaactttgccacttgggcagatcgaataattccacgttggatatttcacctgggacaaaatctaattctggattctgatttgtatcttcttcatgtggaggagcgcaagctaaaggaaattggctcttacaattggcataaagcttgctatgtgccaacaaaggcagatgccattgttgttgcttttagaaggtggctaaacaaatatgcaggtggtcaagttgattggcgtggaaagtacaatggagacctcccgccaactcctccaagggagcagctgctggacaggtattggactcatacagtgagttgcacaagttgcaatctcgcatataaaagtctcaatgctcttgaagtcgtactgcagatcgtctccattggtgccattggaattgttgctgctttaaagcagggcacattgtctgcggtgacaaggtattccttggtcaccgttgcattactatgcttcgtggcctcgagatggttatctcatttcatatacaaaaatttccatttccacgattacgaccatgcctttcgttaacacttgagtactttcatatgactgaacattcactgtataaacatattccttgtagttgaaatttgcagaaaagtttgttaaaaaaaaaaaaaaaaaaaactcgactcgtgc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0308B07-75M5e/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0308B07.2" temp_strand="+" temp_description="C04HBa0308B07.2  CT990558.4 htgs_phase:3 submitted_to_sgn_as:C04HBa0308B07 sequenced_by:sanger upload_account_name:uk">
        <position start="24941" stop="27671"/>
      </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="25241" g_stop="25405" g_length="165"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="165" r_length="165" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="25406" i_stop="25492" i_length="87">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.963" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="25493" g_stop="25690" g_length="198"/>
          <reference_exon_boundary r_type="cDNA" r_start="166" r_stop="363" r_length="198" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="25691" i_stop="26692" i_length="1002">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="0.954" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="26693" g_stop="26880" g_length="188"/>
          <reference_exon_boundary r_type="cDNA" r_start="364" r_stop="551" r_length="188" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="26881" i_stop="27033" i_length="153">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.980" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="27034" g_stop="27370" g_length="337"/>
          <reference_exon_boundary r_type="cDNA" r_start="552" r_stop="888" r_length="337" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="889" polyA_stop="907"/>
      <MATCH_line gen_id="C04HBa0308B07.2" gen_strand="+" ref_id="SGN-M8365" ref_strand="-">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>888</cumulative_length_of_scored_exons>
        <coverage percentage="0.967" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0308B07.2" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M8365" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="25241" e_stop="25405"/>
          <exon e_start="25493" e_stop="25690"/>
          <exon e_start="26693" e_stop="26880"/>
          <exon e_start="27034" e_stop="27370"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GGAAGACCACTTGACATAACTATCACGAAGTTGGATGTAAATGTCATTACTGCAAACCAGGGACCTGGACGGAACACATTTGTTCCGCCTTGTGTGTATTATAGTTATTTTGCTTTCGGAGGATCTCAGGGAAAAACAACTGCTGTATCATCTGGAACTGTACAGGTAATTCTTGTGCCTTCCATATTATTAGTCTTTTTTCAACATTTATTTGGTACTCTTTGCAGCAGTTTAAATAAATATTTCGTGCAGGAAAAACCTTCAGCTGAGAAGCAGAAAAAAGCACTTTTAGTTTTCATCTGTATTCCGGTTAGTCCAGGTCATAGCAGAATTATATTTGCATCTCCAAGAAACTTTGCCACTTGGGCAGATCGAATAATTCCACGTTGGATATTTCACCTGGGACAAAATCTAATTCTGGATTCTGATTTGTATCTTCTTCATGTGGAGGTAAATCCATTCTTTATTGCATCTTTTCCATTTCTATTGTGTACTTGTTAAATTTAGCTGTCCCTCAGAAGGTTGTTAGCTTAAAAAAAAGAGAAGACTTGTGATTTACACATCCCTGAAGCTTTAGAGATGTTTACTATGCAAGGACCCTTTTCGCGTCCCATGAAAAGGAAACAAGCATATATGTTGAGCTAAATTTGTTGAAACCCCTTCAAGTTACCAGACGGAAAGTTTTAGATTTATGGTCAAACTCAAGAGTGGAGATCCCATAGCTTTTTTCTGCTTCTCAGCTGAAGGTTTTTCCTTCTCCAGAATCTAAACTGGCATAGCTTCTGGAGCTGGAACTATCAATAGGAACTTCTCTATACTGTTACTTTTAGGCAATATCATGATTCGATGCTATTTTCACTACTCTTGTATACTACTCAACAAAGTAACTCTAGACATGTGAACCGCTTTTTTCCGACTCTAATCTTCTAACTTGTCTCAAGTTGTGTTAAAAGCTACTGGAATACTTTTCGATGGAAAGCTGAGGATGTGTGGGATTTATTTCATCAAAAACTTTTAGTTTCTACCAGTCCATTCCCCTTTCTTCACTTTCTCCTTTTCTTCTTGTCTGCGGCTTTACTCTCCCCATCTGTTAATATTTATGTTGTGGTTGTCTTTTTACTCTGTGCTTTACTTTTGACAATCAAATGAAATGAACAACAAAAACAACCATACAGATAGCCAAATAAACACCTTTAGTTGCACGGGATTGTTCCAGCTCTCCAACTTCACGAGGCTTCATCCACCTGTTCAAAATTAGCCTAGGAGTTCAATGCTCATGTTACCACCTTTTACTTCAAACAATAAATCTTGAGCATAGTCTCGCTATTGGAACATATTGCATGACTGTTTGTAAGTTAGATTCCGGTGAAGCGTTGGTGCTTTTAGGTGAAAATTTCCATTTACAATATGACGAGTTGTCCTTTCTCATTCAATTTGTTTTCCATTATGAAGGAGCGCAAGCTAAAGGAAATTGGCTCTTACAATTGGCATAAAGCTTGCTATGTGCCAACAAAGGCAGATGCCATTGTTGTTGCTTTTAGAAGGTGGCTAAACAAATATGCAGGTGGTCAAGTTGATTGGCGTGGAAAGTACAATGGAGACCTCCCGCCAACTCCTCCAAGGGAGCAGCTGCTGGACAGGTTCGTACATTGATTCCCACACTTCTAATATAGATTCTTCATTAATTCTAGTGTAAACAAGTTTTGGACCTGTAAGGATAGACTTTCGAGAACCTTTTAGAGACGAAGACGTTGGGTTAAAAGTGTAAATGATATGTTTATACTTCCTTTCAGGTATTGGACTCATACAGTGAGTTGCACAAGTTGCAATCTCGCATATAAAAGTCTCAATGCTCTTGAAGTCGTACTGCAGATCGTCTCCATTGGTGCCATTGGAATTGTTGCTGCTTTAAAGCAGGGCACATTGTCTGCGGTGACAAGGTATTCCTTGGTCACCGTTGCATTACTATGCTTCGTGGCCTCGAGATGGTTATCTCATTTCATATACAAAAATTTCCATTTCCACGATTACGACCATGCCTTTCGTTAACACTTGAGTACTTTCATATGACTGAACATTCACTGTATAAACATATTCCTTGTAGTTGAAATTTGCAGAAAAGTTTGTTAA</genome_strand>
        <mrna_strand>GGAAGACCACTTGACATAACTATCACGAAGTTGGATGTAAATGTCATTACTGCAAACCAGGGACCTGGACGGAACACATTTGTTCCGCCTTGTGTGTATTATAGTTATTTTGCTTTCGGAGGATCTCAGGGAAAAACAACTGCTGTATCATCTGGAACTGTACAG.......................................................................................GAAAAACCTTCAGCTGAGAAGCAGAAAAAAGCACTTTTAGTTTTCATCTGTATTCCGGTTAGTCCAGGTCATAGCAGAATTATATTTGCATCTCCAAGAAACTTTGCCACTTGGGCAGATCGAATAATTCCACGTTGGATATTTCACCTGGGACAAAATCTAATTCTGGATTCTGATTTGTATCTTCTTCATGTGGAG..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GAGCGCAAGCTAAAGGAAATTGGCTCTTACAATTGGCATAAAGCTTGCTATGTGCCAACAAAGGCAGATGCCATTGTTGTTGCTTTTAGAAGGTGGCTAAACAAATATGCAGGTGGTCAAGTTGATTGGCGTGGAAAGTACAATGGAGACCTCCCGCCAACTCCTCCAAGGGAGCAGCTGCTGGACAG.........................................................................................................................................................GTATTGGACTCATACAGTGAGTTGCACAAGTTGCAATCTCGCATATAAAAGTCTCAATGCTCTTGAAGTCGTACTGCAGATCGTCTCCATTGGTGCCATTGGAATTGTTGCTGCTTTAAAGCAGGGCACATTGTCTGCGGTGACAAGGTATTCCTTGGTCACCGTTGCATTACTATGCTTCGTGGCCTCGAGATGGTTATCTCATTTCATATACAAAAATTTCCATTTCCACGATTACGACCATGCCTTTCGTTAACACTTGAGTACTTTCATATGACTGAACATTCACTGTATAAACATATTCCTTGTAGTTGAAATTTGCAGAAAAGTTTGTTAA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>4</total_number_ESTs_reported>
    </alignment_module>
  <PGL_module xmlns="http://www.genomethreader.org/GTH_output/PGL_module/">
    <predicted_gene_location>
      <PGL_line PGL_serial="1" PGL_strand="+" PGL_start="8106" PGL_stop="10123"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="8106" e_stop="8273"/>
            <exon e_start="9357" e_stop="10123"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.999" acc_prob="0.988" 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="8106" e_stop="8273" e_length="168"/>
          </exon>
          <intron i_serial="1" don_prob="0.999" acc_prob="0.988">
            <gDNA_intron_boundary i_start="8274" i_stop="9356" i_length="1083"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="9357" e_stop="10123" e_length="767"/>
          </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="8106" stop="8273"/>
              <exon start="9357" stop="10123"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M7481" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="8210" stop="8273"/>
              <exon start="9357" stop="9736"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1679" 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>AACTTACAAAAAAAAAAAATGGCAAATTTGTTCATTAAGCAAGCACAACAATATTCAAAGGGTAGGCCAAGTTACCCTCAAGAATTATTCAATTTCATTGCTTCTAAAACACCTTCTCATGATCTTGTTTGGGATGTTGGTACTGGTAGTGGCCAGGCTGCTCAATCT : TTAGCTAAGCTTTACAAGAATGTGATAGCTACAGACACAAGTCCAAAGCAGCTTGAATTTGCAGCAAAGGTTCCAAATGTTCAATACATATGTACCTCTCCTAAGTTGTCAAAATCCGAAATCGAAACAAAAATAGGATCAGAATCAAGTGTAGATTTAGTAACAATTGCACAAGCAATGCATTGGTTTGATCTACCAACTTTTTATGAACATGTTAAATGGTTACTCAAGAAACCAAATGGTGTTATAGCATCATGGTGTTACACTACACCTAAAATAAACAACTCAGTAGATGCAATATTTGATAAATTTTACACAAGTGATGCTGGACCTTATTGGGAATCACCAAGAAAATTGGTCGATGAAAAGTATGAAACTATTGATTTTCCATTTGAGGCTATAGATGGATGTGATCATAATGGACCATTTGAGTTCAAGATTGAGAAAGTTATGGACTTGGATTCTTGTTTTACATACTTGAAGTCATGGTCAGCTTATCAAACTGCAAAAGAAAAGGGTGTTGAGTTGTTAAGTGAAGATGTTGTTGAAAAATTTACAAGTGCTTGGAATGAAGATGGGAAGAGTGAGAAAAAAGTGATTTATCCTATTTACTTGAGGATTGGAAAAGTTGGAAATTTGGATTGAAAGTGTAAAGCAAATACAATTAGTTATGTGCACTTGATCATCTATTTATTTTGTATGTTATTTCTCTTAGTTGTTATTGTTATGTATCTTTTAATAATAATAAAGTATCTAAGTACTAATTA</gDNA_template>
            <first_frame> N  L  Q  K  K  K  M  A  N  L  F  I  K  Q  A  Q  Q  Y  S  K  G  R  P  S  Y  P  Q  E  L  F  N  F  I  A  S  K  T  P  S  H  D  L  V  W  D  V  G  T  G  S  G  Q  A  A  Q  S  :  L  A  K  L  Y  K  N  V  I  A  T  D  T  S  P  K  Q  L  E  F  A  A  K  V  P  N  V  Q  Y  I  C  T  S  P  K  L  S  K  S  E  I  E  T  K  I  G  S  E  S  S  V  D  L  V  T  I  A  Q  A  M  H  W  F  D  L  P  T  F  Y  E  H  V  K  W  L  L  K  K  P  N  G  V  I  A  S  W  C  Y  T  T  P  K  I  N  N  S  V  D  A  I  F  D  K  F  Y  T  S  D  A  G  P  Y  W  E  S  P  R  K  L  V  D  E  K  Y  E  T  I  D  F  P  F  E  A  I  D  G  C  D  H  N  G  P  F  E  F  K  I  E  K  V  M  D  L  D  S  C  F  T  Y  L  K  S  W  S  A  Y  Q  T  A  K  E  K  G  V  E  L  L  S  E  D  V  V  E  K  F  T  S  A  W  N  E  D  G  K  S  E  K  K  V  I  Y  P  I  Y  L  R  I  G  K  V  G  N  L  D  *  K  C  K  A  N  T  I  S  Y  V  H  L  I  I  Y  L  F  C  M  L  F  L  L  V  V  I  V  M  Y  L  L  I  I  I  K  Y  L  S  T  N   </first_frame>
            <second_frame>  T  Y  K  K  K  K  W  Q  I  C  S  L  S  K  H  N  N  I  Q  R  V  G  Q  V  T  L  K  N  Y  S  I  S  L  L  L  K  H  L  L  M  I  L  F  G  M  L  V  L  V  V  A  R  L  L  N  L :   *  L  S  F  T  R  M  *  *  L  Q  T  Q  V  Q  S  S  L  N  L  Q  Q  R  F  Q  M  F  N  T  Y  V  P  L  L  S  C  Q  N  P  K  S  K  Q  K  *  D  Q  N  Q  V  *  I  *  *  Q  L  H  K  Q  C  I  G  L  I  Y  Q  L  F  M  N  M  L  N  G  Y  S  R  N  Q  M  V  L  *  H  H  G  V  T  L  H  L  K  *  T  T  Q  *  M  Q  Y  L  I  N  F  T  Q  V  M  L  D  L  I  G  N  H  Q  E  N  W  S  M  K  S  M  K  L  L  I  F  H  L  R  L  *  M  D  V  I  I  M  D  H  L  S  S  R  L  R  K  L  W  T  W  I  L  V  L  H  T  *  S  H  G  Q  L  I  K  L  Q  K  K  R  V  L  S  C  *  V  K  M  L  L  K  N  L  Q  V  L  G  M  K  M  G  R  V  R  K  K  *  F  I  L  F  T  *  G  L  E  K  L  E  I  W  I  E  S  V  K  Q  I  Q  L  V  M  C  T  *  S  S  I  Y  F  V  C  Y  F  S  *  L  L  L  L  C  I  F  *  *  *  *  S  I  *  V  L  I  </second_frame>
            <third_frame>   L  T  K  K  K  N  G  K  F  V  H  *  A  S  T  T  I  F  K  G  *  A  K  L  P  S  R  I  I  Q  F  H  C  F  *  N  T  F  S  *  S  C  L  G  C  W  Y  W  *  W  P  G  C  S  I   : F  S  *  A  L  Q  E  C  D  S  Y  R  H  K  S  K  A  A  *  I  C  S  K  G  S  K  C  S  I  H  M  Y  L  S  *  V  V  K  I  R  N  R  N  K  N  R  I  R  I  K  C  R  F  S  N  N  C  T  S  N  A  L  V  *  S  T  N  F  L  *  T  C  *  M  V  T  Q  E  T  K  W  C  Y  S  I  M  V  L  H  Y  T  *  N  K  Q  L  S  R  C  N  I  *  *  I  L  H  K  *  C  W  T  L  L  G  I  T  K  K  I  G  R  *  K  V  *  N  Y  *  F  S  I  *  G  Y  R  W  M  *  S  *  W  T  I  *  V  Q  D  *  E  S  Y  G  L  G  F  L  F  Y  I  L  E  V  M  V  S  L  S  N  C  K  R  K  G  C  *  V  V  K  *  R  C  C  *  K  I  Y  K  C  L  E  *  R  W  E  E  *  E  K  S  D  L  S  Y  L  L  E  D  W  K  S  W  K  F  G  L  K  V  *  S  K  Y  N  *  L  C  A  L  D  H  L  F  I  L  Y  V  I  S  L  S  C  Y  C  Y  V  S  F  N  N  N  K  V  S  K  Y  *  L </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0308B07.2" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="8106" stop="8273"/>
                    <exon start="9357" stop="10001"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>810</number_coding_nucleotides>
                  <number_encoded_amino_acids>270</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>NLQKKKMANLFIKQAQQYSKGRPSYPQELFNFIASKTPSHDLVWDVGTGSGQAAQSLAKLYKNVIATDTSPKQLEFAAKVPNVQYICTSPKLSKSEIETKIGSESSVDLVTIAQAMHWFDLPTFYEHVKWLLKKPNGVIASWCYTTPKINNSVDAIFDKFYTSDAGPYWESPRKLVDEKYETIDFPFEAIDGCDHNGPFEFKIEKVMDLDSCFTYLKSWSAYQTAKEKGVELLSEDVVEKFTSAWNEDGKSEKKVIYPIYLRIGKVGNLD*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="2" PGL_strand="+" PGL_start="22515" PGL_stop="23048"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="22515" e_stop="23048"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.987"/>
        </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="0.987">
            <gDNA_exon_boundary e_start="22515" e_stop="23048" e_length="534"/>
          </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="22515" stop="23048"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1730" strand="+"/>
          </PGS_line>
        </supporting_evidence>
        <three_phase_translation xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/">
          <description PGL_serial="2" AGS_serial="1" gDNA_strand="+"/>
          <translation>
            <gDNA_template>GGAGTTCTGAAGATTTTTTATTTTTATTTTTTAAAAGAAGATTTGAACTTTTATTAACAAATTTAAGATTCAGCCATGCAAGCTGTCAAAGCTTCTTCCTTTTCACCATTTCACCTCAACTTGAACTCAACCAGTTCATTTCCCAAAACTACCAACTTGTATATTCAACAAAATTATGAAAACCCCATTTCTTGTTTTCCCTCAATTCAGACACAAAATGCAAAATTCAAGGTTTTTACTGCTACTTCCCCAAGTGTTTCAACAGAATCAGAAACCCCATTTGATGAAAAGACTGAAAATGAAAATCAAGAAGAGAAATTTGAGTGGTATGCTGAGTGGTACCCAATAATGCCAATTTGTGATCTTGATAAGAGGAGGCCACATGGAAAGAAAGTGATGGGGATTGATGTGGTTGTGTGGTGGGATAGGAATGAGAAAGAATGGAAAGTAATGGATGATTCTTGTCCTCATAGATATGCTCCACTTTCTGAAGGAAGAATTGATCAATGGGGAAGATTGCAGTGTGTGTATCAT</gDNA_template>
            <first_frame> G  V  L  K  I  F  Y  F  Y  F  L  K  E  D  L  N  F  Y  *  Q  I  *  D  S  A  M  Q  A  V  K  A  S  S  F  S  P  F  H  L  N  L  N  S  T  S  S  F  P  K  T  T  N  L  Y  I  Q  Q  N  Y  E  N  P  I  S  C  F  P  S  I  Q  T  Q  N  A  K  F  K  V  F  T  A  T  S  P  S  V  S  T  E  S  E  T  P  F  D  E  K  T  E  N  E  N  Q  E  E  K  F  E  W  Y  A  E  W  Y  P  I  M  P  I  C  D  L  D  K  R  R  P  H  G  K  K  V  M  G  I  D  V  V  V  W  W  D  R  N  E  K  E  W  K  V  M  D  D  S  C  P  H  R  Y  A  P  L  S  E  G  R  I  D  Q  W  G  R  L  Q  C  V  Y  H </first_frame>
            <second_frame>  E  F  *  R  F  F  I  F  I  F  *  K  K  I  *  T  F  I  N  K  F  K  I  Q  P  C  K  L  S  K  L  L  P  F  H  H  F  T  S  T  *  T  Q  P  V  H  F  P  K  L  P  T  C  I  F  N  K  I  M  K  T  P  F  L  V  F  P  Q  F  R  H  K  M  Q  N  S  R  F  L  L  L  L  P  Q  V  F  Q  Q  N  Q  K  P  H  L  M  K  R  L  K  M  K  I  K  K  R  N  L  S  G  M  L  S  G  T  Q  *  C  Q  F  V  I  L  I  R  G  G  H  M  E  R  K  *  W  G  L  M  W  L  C  G  G  I  G  M  R  K  N  G  K  *  W  M  I  L  V  L  I  D  M  L  H  F  L  K  E  E  L  I  N  G  E  D  C  S  V  C  I   </second_frame>
            <third_frame>   S  S  E  D  F  L  F  L  F  F  K  R  R  F  E  L  L  L  T  N  L  R  F  S  H  A  S  C  Q  S  F  F  L  F  T  I  S  P  Q  L  E  L  N  Q  F  I  S  Q  N  Y  Q  L  V  Y  S  T  K  L  *  K  P  H  F  L  F  S  L  N  S  D  T  K  C  K  I  Q  G  F  Y  C  Y  F  P  K  C  F  N  R  I  R  N  P  I  *  *  K  D  *  K  *  K  S  R  R  E  I  *  V  V  C  *  V  V  P  N  N  A  N  L  *  S  *  *  E  E  A  T  W  K  E  S  D  G  D  *  C  G  C  V  V  G  *  E  *  E  R  M  E  S  N  G  *  F  L  S  S  *  I  C  S  T  F  *  R  K  N  *  S  M  G  K  I  A  V  C  V  S  </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0308B07.2" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="22581" stop="23048"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>468</number_coding_nucleotides>
                  <number_encoded_amino_acids>156</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>DSAMQAVKASSFSPFHLNLNSTSSFPKTTNLYIQQNYENPISCFPSIQTQNAKFKVFTATSPSVSTESETPFDEKTENENQEEKFEWYAEWYPIMPICDLDKRRPHGKKVMGIDVVVWWDRNEKEWKVMDDSCPHRYAPLSEGRIDQWGRLQCVYH</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="3" PGL_strand="+" PGL_start="25241" PGL_stop="27370"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="25241" e_stop="25405"/>
            <exon e_start="25493" e_stop="25690"/>
            <exon e_start="26693" e_stop="26880"/>
            <exon e_start="27034" e_stop="27370"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="1.000" acc_prob="0.963" e_score="1.000"/>
          <exon-intron don_prob="0.998" acc_prob="0.954" e_score="1.000"/>
          <exon-intron don_prob="1.000" acc_prob="0.980" 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="25241" e_stop="25405" e_length="165"/>
          </exon>
          <intron i_serial="1" don_prob="1.000" acc_prob="0.963">
            <gDNA_intron_boundary i_start="25406" i_stop="25492" i_length="87"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="25493" e_stop="25690" e_length="198"/>
          </exon>
          <intron i_serial="2" don_prob="0.998" acc_prob="0.954">
            <gDNA_intron_boundary i_start="25691" i_stop="26692" i_length="1002"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="26693" e_stop="26880" e_length="188"/>
          </exon>
          <intron i_serial="3" don_prob="1.000" acc_prob="0.980">
            <gDNA_intron_boundary i_start="26881" i_stop="27033" i_length="153"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="27034" e_stop="27370" e_length="337"/>
          </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="25241" stop="25405"/>
              <exon start="25493" stop="25690"/>
              <exon start="26693" stop="26880"/>
              <exon start="27034" stop="27370"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M8365" strand="-"/>
          </PGS_line>
        </supporting_evidence>
        <three_phase_translation xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/">
          <description PGL_serial="3" AGS_serial="1" gDNA_strand="+"/>
          <translation>
            <gDNA_template>GGAAGACCACTTGACATAACTATCACGAAGTTGGATGTAAATGTCATTACTGCAAACCAGGGACCTGGACGGAACACATTTGTTCCGCCTTGTGTGTATTATAGTTATTTTGCTTTCGGAGGATCTCAGGGAAAAACAACTGCTGTATCATCTGGAACTGTACAG : GAAAAACCTTCAGCTGAGAAGCAGAAAAAAGCACTTTTAGTTTTCATCTGTATTCCGGTTAGTCCAGGTCATAGCAGAATTATATTTGCATCTCCAAGAAACTTTGCCACTTGGGCAGATCGAATAATTCCACGTTGGATATTTCACCTGGGACAAAATCTAATTCTGGATTCTGATTTGTATCTTCTTCATGTGGAG : GAGCGCAAGCTAAAGGAAATTGGCTCTTACAATTGGCATAAAGCTTGCTATGTGCCAACAAAGGCAGATGCCATTGTTGTTGCTTTTAGAAGGTGGCTAAACAAATATGCAGGTGGTCAAGTTGATTGGCGTGGAAAGTACAATGGAGACCTCCCGCCAACTCCTCCAAGGGAGCAGCTGCTGGACAG : GTATTGGACTCATACAGTGAGTTGCACAAGTTGCAATCTCGCATATAAAAGTCTCAATGCTCTTGAAGTCGTACTGCAGATCGTCTCCATTGGTGCCATTGGAATTGTTGCTGCTTTAAAGCAGGGCACATTGTCTGCGGTGACAAGGTATTCCTTGGTCACCGTTGCATTACTATGCTTCGTGGCCTCGAGATGGTTATCTCATTTCATATACAAAAATTTCCATTTCCACGATTACGACCATGCCTTTCGTTAACACTTGAGTACTTTCATATGACTGAACATTCACTGTATAAACATATTCCTTGTAGTTGAAATTTGCAGAAAAGTTTGTTAA</gDNA_template>
            <first_frame> G  R  P  L  D  I  T  I  T  K  L  D  V  N  V  I  T  A  N  Q  G  P  G  R  N  T  F  V  P  P  C  V  Y  Y  S  Y  F  A  F  G  G  S  Q  G  K  T  T  A  V  S  S  G  T  V  Q  :  E  K  P  S  A  E  K  Q  K  K  A  L  L  V  F  I  C  I  P  V  S  P  G  H  S  R  I  I  F  A  S  P  R  N  F  A  T  W  A  D  R  I  I  P  R  W  I  F  H  L  G  Q  N  L  I  L  D  S  D  L  Y  L  L  H  V  E  :  E  R  K  L  K  E  I  G  S  Y  N  W  H  K  A  C  Y  V  P  T  K  A  D  A  I  V  V  A  F  R  R  W  L  N  K  Y  A  G  G  Q  V  D  W  R  G  K  Y  N  G  D  L  P  P  T  P  P  R  E  Q  L  L  D  R :   Y  W  T  H  T  V  S  C  T  S  C  N  L  A  Y  K  S  L  N  A  L  E  V  V  L  Q  I  V  S  I  G  A  I  G  I  V  A  A  L  K  Q  G  T  L  S  A  V  T  R  Y  S  L  V  T  V  A  L  L  C  F  V  A  S  R  W  L  S  H  F  I  Y  K  N  F  H  F  H  D  Y  D  H  A  F  R  *  H  L  S  T  F  I  *  L  N  I  H  C  I  N  I  F  L  V  V  E  I  C  R  K  V  C  * </first_frame>
            <second_frame>  E  D  H  L  T  *  L  S  R  S  W  M  *  M  S  L  L  Q  T  R  D  L  D  G  T  H  L  F  R  L  V  C  I  I  V  I  L  L  S  E  D  L  R  E  K  Q  L  L  Y  H  L  E  L  Y  R :   K  N  L  Q  L  R  S  R  K  K  H  F  *  F  S  S  V  F  R  L  V  Q  V  I  A  E  L  Y  L  H  L  Q  E  T  L  P  L  G  Q  I  E  *  F  H  V  G  Y  F  T  W  D  K  I  *  F  W  I  L  I  C  I  F  F  M  W  R :   S  A  S  *  R  K  L  A  L  T  I  G  I  K  L  A  M  C  Q  Q  R  Q  M  P  L  L  L  L  L  E  G  G  *  T  N  M  Q  V  V  K  L  I  G  V  E  S  T  M  E  T  S  R  Q  L  L  Q  G  S  S  C  W  T   : G  I  G  L  I  Q  *  V  A  Q  V  A  I  S  H  I  K  V  S  M  L  L  K  S  Y  C  R  S  S  P  L  V  P  L  E  L  L  L  L  *  S  R  A  H  C  L  R  *  Q  G  I  P  W  S  P  L  H  Y  Y  A  S  W  P  R  D  G  Y  L  I  S  Y  T  K  I  S  I  S  T  I  T  T  M  P  F  V  N  T  *  V  L  S  Y  D  *  T  F  T  V  *  T  Y  S  L  *  L  K  F  A  E  K  F  V   </second_frame>
            <third_frame>   K  T  T  *  H  N  Y  H  E  V  G  C  K  C  H  Y  C  K  P  G  T  W  T  E  H  I  C  S  A  L  C  V  L  *  L  F  C  F  R  R  I  S  G  K  N  N  C  C  I  I  W  N  C  T   : G  K  T  F  S  *  E  A  E  K  S  T  F  S  F  H  L  Y  S  G  *  S  R  S  *  Q  N  Y  I  C  I  S  K  K  L  C  H  L  G  R  S  N  N  S  T  L  D  I  S  P  G  T  K  S  N  S  G  F  *  F  V  S  S  S  C  G   : G  A  Q  A  K  G  N  W  L  L  Q  L  A  *  S  L  L  C  A  N  K  G  R  C  H  C  C  C  F  *  K  V  A  K  Q  I  C  R  W  S  S  *  L  A  W  K  V  Q  W  R  P  P  A  N  S  S  K  G  A  A  A  G  Q  :  V  L  D  S  Y  S  E  L  H  K  L  Q  S  R  I  *  K  S  Q  C  S  *  S  R  T  A  D  R  L  H  W  C  H  W  N  C  C  C  F  K  A  G  H  I  V  C  G  D  K  V  F  L  G  H  R  C  I  T  M  L  R  G  L  E  M  V  I  S  F  H  I  Q  K  F  P  F  P  R  L  R  P  C  L  S  L  T  L  E  Y  F  H  M  T  E  H  S  L  Y  K  H  I  P  C  S  *  N  L  Q  K  S  L  L  </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0308B07.2" strand="+"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="25241" stop="25405"/>
                    <exon start="25493" stop="25690"/>
                    <exon start="26693" stop="26880"/>
                    <exon start="27034" stop="27289"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>804</number_coding_nucleotides>
                  <number_encoded_amino_acids>268</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>GRPLDITITKLDVNVITANQGPGRNTFVPPCVYYSYFAFGGSQGKTTAVSSGTVQEKPSAEKQKKALLVFICIPVSPGHSRIIFASPRNFATWADRIIPRWIFHLGQNLILDSDLYLLHVEERKLKEIGSYNWHKACYVPTKADAIVVAFRRWLNKYAGGQVDWRGKYNGDLPPTPPREQLLDRYWTHTVSCTSCNLAYKSLNALEVVLQIVSIGAIGIVAALKQGTLSAVTRYSLVTVALLCFVASRWLSHFIYKNFHFHDYDHAFR*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 16 chains have been computed
$ 
$ memory statistics:
$ 7856 bytes spliced alignments in total
$ 4 spliced alignments have been stored
$ 1964 bytes was the average size of a spliced alignment
$ 8008 bytes predicted gene locations in total
$ 3 predicted gene locations have been stored
$ 2669 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 18 backtrace matrices have been allocated
$ 
$ date finished: 2008-04-17 21:29:52
-->
