<?xml version="1.0" encoding="ISO-8859-1"?>
<GTH_output xmlns="http://www.genomethreader.org/GTH_output/" GTH_XML_version="1.1">
  <header xmlns="http://www.genomethreader.org/GTH_output/header/">
    <source program="GenomeThreader" version="0.9.54" build_date="2006-07-28 11:55:15" run_date="2009-01-18 08:28:28"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C12HBa0062P09-3YKp6/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C12HBa0062P09-3YKp6/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" type="ESTcDNA"/>
    </reference_files>
    <splice_site_parameters parameter_type="Bayesian" species="arabidopsis"/>
    <parameters>
      <parameter name="bssmfile" value="arabidopsis"/>
      <parameter name="scorematrixfile" value="BLOSUM62"/>
      <parameter name="searchmode" value="forward=True,reverse=True)"/>
      <parameter name="translationtable" value="1"/>
      <parameter name="frompos" value="0"/>
      <parameter name="topos" value="0"/>
      <parameter name="width" value="0"/>
      <parameter name="verbose" value="False"/>
      <parameter name="skipalignmentout" value="False"/>
      <parameter name="showintronmaxlen" value="120"/>
      <parameter name="minorflen" value="64"/>
      <parameter name="showseqnums" value="False"/>
      <parameter name="gs2out" value="False"/>
      <parameter name="maskpolyatails" value="False"/>
      <parameter name="noautoindex" value="False"/>
      <parameter name="minmatchlen" value="20"/>
      <parameter name="seedlength" value="16"/>
      <parameter name="exdrop" value="2"/>
      <parameter name="online" value="False"/>
      <parameter name="inverse" value="False"/>
      <parameter name="exact" value="False"/>
      <parameter name="chainwf" value="0.500000"/>
      <parameter name="gcmaxgapwidth" value="1000000"/>
      <parameter name="gcmincoverage" value="50"/>
      <parameter name="introncutout" value="False"/>
      <parameter name="autointroncutout" value="0"/>
      <parameter name="icinitialdelta" value="50"/>
      <parameter name="iciterations" value="2"/>
      <parameter name="icdeltaincrease" value="50"/>
      <parameter name="icminremintronlen" value="10"/>
      <parameter name="nou12intronmodel" value="False"/>
      <parameter name="u12donorprob" value="0.990000"/>
      <parameter name="u12donorprob1mism" value="0.900000"/>
      <parameter name="probies" value="0.500000"/>
      <parameter name="probdelgen" value="0.030000"/>
      <parameter name="identityweight" value="2.000000"/>
      <parameter name="mismatchweight" value="-2.000000"/>
      <parameter name="undetcharweight" value="0.000000"/>
      <parameter name="deletionweight" value="-4.000000"/>
      <parameter name="dpminexonlen" value="5"/>
      <parameter name="dpminintronlen" value="50"/>
      <parameter name="shortexonpenal" value="100"/>
      <parameter name="shortintronpenal" value="100"/>
      <parameter name="wzerotransition" value="80"/>
      <parameter name="wdecreasedoutput" value="80"/>
      <parameter name="leadcutoffsmode" value="RELAXED"/>
      <parameter name="termcutoffsmode" value="STRICT"/>
      <parameter name="cutoffsminexonlen" value="5"/>
      <parameter name="scoreminexonlen" value="50"/>
      <parameter name="minaveragessp" value="0.500000"/>
      <parameter name="minalignmentscore" value="0.900000"/>
      <parameter name="maxalignmentscore" value="1.000000"/>
      <parameter name="mincoverage" value="0.900000"/>
      <parameter name="maxcoverage" value="100.000000"/>
      <parameter name="intermediate" value="False"/>
      <parameter name="sortags" value="False"/>
      <parameter name="sortagswf" value="1.000000"/>
      <parameter name="first" value="0"/>
      <parameter name="exondistri" value="False"/>
      <parameter name="introndistri" value="False"/>
      <parameter name="refseqcovdistri" value="False"/>
    </parameters>
    <overall_reference_type>ESTcDNA</overall_reference_type>
  </header>
  <alignment_module>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C12HBa0062P09-3YKp6/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M2983" ref_strand="+" ref_description="SGN-M2983 cLET-8-E15 [est_clones]">
      <seq>gctggagagtggagaaagatctgcagcgaagatggaggcagcaagaagtgtgaaagatgtttccccccatgattttgtcaaggcttatgccgctcatctcaagcgctccggaaagatggagcttcctgaatggactgatatagttaagactggtaagctaaaggagcttgccccatatgatgctgattggtactacatcagagctgcttccatggcaaggaagatctatttgagaggaggtattggtgttggtggtttccgaagaatctatggtggaaaccagaggaatggaagccgtccacgtcacttttgcaagagcagtggttcagttgcacgccacattcttcaacagttgcagaacatgaacatcattgactttgagcctaagggcggaaggaggatcacatccagtggtcagcgggatcttgaccaagttgccggaagaattgctgttgcttgttaagagagagatgagttcattccattttatgaatacatgagttagctcaaacttattggttctgtttggacctaaatag</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12HBa0062P09-3YKp6/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C12HBa0062P09.1" temp_strand="+" temp_description="C12HBa0062P09.1  AC217335.1 htgs_phase:2 submitted_to_sgn_as:C12HBa0062P09*** upload_account_name:italy SEQUENCING IN PROGRESS ***">
        <position start="67468" stop="69664"/>
      </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="67768" g_stop="67882" g_length="115"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="115" r_length="115" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="67883" i_stop="68261" i_length="379">
            <donor d_prob="0.992" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="68262" g_stop="68352" g_length="91"/>
          <reference_exon_boundary r_type="cDNA" r_start="116" r_stop="206" r_length="91" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="68353" i_stop="68431" i_length="79">
            <donor d_prob="0.995" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="68432" g_stop="68615" g_length="184"/>
          <reference_exon_boundary r_type="cDNA" r_start="207" r_stop="390" r_length="184" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="68616" i_stop="69215" i_length="600">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.992" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="69216" g_stop="69364" g_length="149"/>
          <reference_exon_boundary r_type="cDNA" r_start="391" r_stop="539" r_length="149" r_score="0.987"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12HBa0062P09.1" gen_strand="+" ref_id="SGN-M2983" ref_strand="+">
        <total_alignment_score>0.996</total_alignment_score>
        <cumulative_length_of_scored_exons>539</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12HBa0062P09.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M2983" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="67768" e_stop="67882"/>
          <exon e_start="68262" e_stop="68352"/>
          <exon e_start="68432" e_stop="68615"/>
          <exon e_start="69216" e_stop="69364"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GCTGGAGAGTGGAGAAAGATCTGCAGCGAAGATGGAGGCAGCAAGAAGTGTGAAAGATGTTTCCCCCCATGATTTTGTCAAGGCTTATGCCGCTCATCTCAAGCGCTCCGGAAAGGTCTATACGAATTGAATTTCGTTTTACATTCATATTTGCTTCGATTTTCTCAACTGATTTACCTCTTACATCATTGAATATAGCAATAGAAACAACGCAGAATTTGTAGCTATTTGCTGGATTGAAAGATTTTCAAATTTCAATTTTGTATACACGCTTCCTGCTAAAATATAGAAATGATATTTGTTCTTCTTCTTGTTGGATTCAATGGACCTTTGCCCCCTTTTACCCTGTTAATTTCCCTACTGGAAGTTATTTGCTCAGATCTGCCTTATTATCTACCATAAAGTACTTTGTTTTCTTGTTAATTCCAGCCACTGCAATTTAATGCATGTTTGGGCTTGTCTATTCATGCTTATTGTACCTTTGATTTTTGCAGATGGAGCTTCCTGAATGGACTGATATAGTTAAGACTGGTAAGCTAAAGGAGCTTGCCCCATATGATGCTGATTGGTACTACATCAGAGCTGGTATGTCTCATCTCCATTATCAGATGAAGGAACTTATCCATTGTTTCTAACTTTTTTTTTTTTTTTTGATGTATGGCAGCTTCCATGGCAAGGAAGATCTATTTGAGAGGAGGTATTGGTGTTGGTGGTTTCCGAAGAATCTATGGTGGAAACCAGAGGAATGGAAGCCGTCCACGTCACTTTTGCAAGAGCAGTGGTTCAGTTGCACGCCACATTCTTCAACAGTTGCAGAACATGAACATCATTGACTTTGAGCCTAAGGGGTAAGTAGTAACCTTTTGCTCTCTAATTAATGCTGAATTTGATGTGTCTCCTTATTCTGTAGTGGTTGTATGAATGAAATCCATTGATCAGTCAGAAACCTGTTTGTTTACATAACTGATGGGGTTTTCTCCTGCTTTTTCTGAGGTTGTTTGTCATGTGATATGAATATATGCGGATGCGTTAATCATTGTATGGAGCCAGCAAAATTTAAGAAAATCACGAGGAGTCTGGCTAGTCTTGCTTAGAAAAAGAGTGATTTCAGTGATAATAATTGTGCTTAAATCAATTAATAAAACTCTCTTTATTTAGGAAAGAGGTCAAAGACAATTGCAAAAAGAGTGACTGCTCCCTTTATAGTAAGACTTTGATATTTGTGAGTGATTGATTAAACAGGGAAACGATAAGAGGTTGCTGACTTTTCAATTGAAAATAACATGGCTTAAATGAATCTAGATGAAGTATTTCACCTTGTTCTGAATGGAGAGACATCCTTATTGCTAGCGAATGCTCACAACTCAACTTTATTAGCTGCATTAAGAATGAAATCGATGAATATCTAGTTATTTGTCTGTCTAATTTAAAATTCTCTCTTTATCTAGCGGAAGGAGGATCACATCCAGTGGTCAGCGGGATCTTGACCAAGTTGCCGGAAGAATTGCTGTTGCTTGTTAAGAGAGAGATGAGTTCATTCAATTTTATGAATACATGAGTTAGCTCAAACTTATTGTTTCTGTTTGGACCTAAATAG</genome_strand>
        <mrna_strand>GCTGGAGAGTGGAGAAAGATCTGCAGCGAAGATGGAGGCAGCAAGAAGTGTGAAAGATGTTTCCCCCCATGATTTTGTCAAGGCTTATGCCGCTCATCTCAAGCGCTCCGGAAAG...........................................................................................................................................................................................................................................................................................................................................................................................ATGGAGCTTCCTGAATGGACTGATATAGTTAAGACTGGTAAGCTAAAGGAGCTTGCCCCATATGATGCTGATTGGTACTACATCAGAGCTG...............................................................................CTTCCATGGCAAGGAAGATCTATTTGAGAGGAGGTATTGGTGTTGGTGGTTTCCGAAGAATCTATGGTGGAAACCAGAGGAATGGAAGCCGTCCACGTCACTTTTGCAAGAGCAGTGGTTCAGTTGCACGCCACATTCTTCAACAGTTGCAGAACATGAACATCATTGACTTTGAGCCTAAGGG........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CGGAAGGAGGATCACATCCAGTGGTCAGCGGGATCTTGACCAAGTTGCCGGAAGAATTGCTGTTGCTTGTTAAGAGAGAGATGAGTTCATTCCATTTTATGAATACATGAGTTAGCTCAAACTTATTGGTTCTGTTTGGACCTAAATAG</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-C12HBa0062P09-3YKp6/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M236-F" ref_strand="+" ref_description="SGN-M236-F CT189-F [rflp_markers_forward]">
      <seq>caagatctgcagcgaagatggaggcagcaagaagtgtgaaagatgtttccccccatgattttgtcaaggcttatgccgctcatctcaagcgctccggaaagatggagcttcctgaatggactgatatagttaagactggtaagctaaaggagcttgccccatatgatgctgattggtactacatcagagctgcttccatggcaaggaagatctatttgagaggaggtattggtgttggtggtttccgaagaatctatggtggaaaccagaggaatggaagccgtccacgtcacttttgcaagagcagtggttcagttgcacgccacattcttcaacagttgcagaacatgaacatcattgactttgagcctaagggcggaaggaggatcacatccagtggtcagcgggatcttgaccaaggtgccggacagattgctgttgcttgttaagagagagatgagctcattcaattttatgaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12HBa0062P09-3YKp6/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C12HBa0062P09.1" temp_strand="+" temp_description="C12HBa0062P09.1  AC217335.1 htgs_phase:2 submitted_to_sgn_as:C12HBa0062P09*** upload_account_name:italy SEQUENCING IN PROGRESS ***">
        <position start="67483" stop="69618"/>
      </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="67782" g_stop="67882" g_length="101"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="101" r_length="101" r_score="0.990"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="67883" i_stop="68261" i_length="379">
            <donor d_prob="0.992" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="68262" g_stop="68352" g_length="91"/>
          <reference_exon_boundary r_type="cDNA" r_start="102" r_stop="192" r_length="91" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="68353" i_stop="68431" i_length="79">
            <donor d_prob="0.995" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="68432" g_stop="68615" g_length="184"/>
          <reference_exon_boundary r_type="cDNA" r_start="193" r_stop="376" r_length="184" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="68616" i_stop="69215" i_length="600">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.992" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="69216" g_stop="69318" g_length="103"/>
          <reference_exon_boundary r_type="cDNA" r_start="377" r_stop="479" r_length="103" r_score="0.951"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12HBa0062P09.1" gen_strand="+" ref_id="SGN-M236-F" ref_strand="+">
        <total_alignment_score>0.987</total_alignment_score>
        <cumulative_length_of_scored_exons>479</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12HBa0062P09.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M236-F" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="67782" e_stop="67882"/>
          <exon e_start="68262" e_stop="68352"/>
          <exon e_start="68432" e_stop="68615"/>
          <exon e_start="69216" e_stop="69318"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAAGATCTGCAGCGAAGATGGAGGCAGCAAGAAGTGTGAAAGATGTTTCCCCCCATGATTTTGTCAAGGCTTATGCCGCTCATCTCAAGCGCTCCGGAAAGGTCTATACGAATTGAATTTCGTTTTACATTCATATTTGCTTCGATTTTCTCAACTGATTTACCTCTTACATCATTGAATATAGCAATAGAAACAACGCAGAATTTGTAGCTATTTGCTGGATTGAAAGATTTTCAAATTTCAATTTTGTATACACGCTTCCTGCTAAAATATAGAAATGATATTTGTTCTTCTTCTTGTTGGATTCAATGGACCTTTGCCCCCTTTTACCCTGTTAATTTCCCTACTGGAAGTTATTTGCTCAGATCTGCCTTATTATCTACCATAAAGTACTTTGTTTTCTTGTTAATTCCAGCCACTGCAATTTAATGCATGTTTGGGCTTGTCTATTCATGCTTATTGTACCTTTGATTTTTGCAGATGGAGCTTCCTGAATGGACTGATATAGTTAAGACTGGTAAGCTAAAGGAGCTTGCCCCATATGATGCTGATTGGTACTACATCAGAGCTGGTATGTCTCATCTCCATTATCAGATGAAGGAACTTATCCATTGTTTCTAACTTTTTTTTTTTTTTTTGATGTATGGCAGCTTCCATGGCAAGGAAGATCTATTTGAGAGGAGGTATTGGTGTTGGTGGTTTCCGAAGAATCTATGGTGGAAACCAGAGGAATGGAAGCCGTCCACGTCACTTTTGCAAGAGCAGTGGTTCAGTTGCACGCCACATTCTTCAACAGTTGCAGAACATGAACATCATTGACTTTGAGCCTAAGGGGTAAGTAGTAACCTTTTGCTCTCTAATTAATGCTGAATTTGATGTGTCTCCTTATTCTGTAGTGGTTGTATGAATGAAATCCATTGATCAGTCAGAAACCTGTTTGTTTACATAACTGATGGGGTTTTCTCCTGCTTTTTCTGAGGTTGTTTGTCATGTGATATGAATATATGCGGATGCGTTAATCATTGTATGGAGCCAGCAAAATTTAAGAAAATCACGAGGAGTCTGGCTAGTCTTGCTTAGAAAAAGAGTGATTTCAGTGATAATAATTGTGCTTAAATCAATTAATAAAACTCTCTTTATTTAGGAAAGAGGTCAAAGACAATTGCAAAAAGAGTGACTGCTCCCTTTATAGTAAGACTTTGATATTTGTGAGTGATTGATTAAACAGGGAAACGATAAGAGGTTGCTGACTTTTCAATTGAAAATAACATGGCTTAAATGAATCTAGATGAAGTATTTCACCTTGTTCTGAATGGAGAGACATCCTTATTGCTAGCGAATGCTCACAACTCAACTTTATTAGCTGCATTAAGAATGAAATCGATGAATATCTAGTTATTTGTCTGTCTAATTTAAAATTCTCTCTTTATCTAGCGGAAGGAGGATCACATCCAGTGGTCAGCGGGATCTTGACCAAGTTGCCGGAAGAATTGCTGTTGCTTGTTAAGAGAGAGATGAGTTCATTCAATTTTATGAA</genome_strand>
        <mrna_strand>CAAGATCTGCAGCGAAGATGGAGGCAGCAAGAAGTGTGAAAGATGTTTCCCCCCATGATTTTGTCAAGGCTTATGCCGCTCATCTCAAGCGCTCCGGAAAG...........................................................................................................................................................................................................................................................................................................................................................................................ATGGAGCTTCCTGAATGGACTGATATAGTTAAGACTGGTAAGCTAAAGGAGCTTGCCCCATATGATGCTGATTGGTACTACATCAGAGCTG...............................................................................CTTCCATGGCAAGGAAGATCTATTTGAGAGGAGGTATTGGTGTTGGTGGTTTCCGAAGAATCTATGGTGGAAACCAGAGGAATGGAAGCCGTCCACGTCACTTTTGCAAGAGCAGTGGTTCAGTTGCACGCCACATTCTTCAACAGTTGCAGAACATGAACATCATTGACTTTGAGCCTAAGGG........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CGGAAGGAGGATCACATCCAGTGGTCAGCGGGATCTTGACCAAGGTGCCGGACAGATTGCTGTTGCTTGTTAAGAGAGAGATGAGCTCATTCAATTTTATGAA</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-C12HBa0062P09-3YKp6/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M236-R" ref_strand="-" ref_description="SGN-M236-R CT189-R [rflp_markers_reverse]">
      <seq>cagagctgcttccatggcaaggaagatctatttgagaggaggtattggtgttggtggtttccgaagaatctatggtggaaaccagaggaatggaagccgtccacgtcacttttgcaagagcagtggttcagttgcacgccacattcttcaacagttgcagaacatgaacatcattgactttgagcctaagggcggaaggaggatcacatccagtggtcagcgggatcttgaccaagttgccggaagaattgctgttgcttgttaagagagagatgagttcattcaattttatgaatacatgagttagctcaaacttattgtttctgtttggacctaaatagatttagggtattgttgaattaaattgtggatgttttgccttttcagaattgtctttctcagtatgtcaagttttgcccttttagtaccctgaagtgtgtattgtggcatatgttgcattcaatgcatcattacttcataattatacataaatccctgagattcaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12HBa0062P09-3YKp6/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C12HBa0062P09.1" temp_strand="+" temp_description="C12HBa0062P09.1  AC217335.1 htgs_phase:2 submitted_to_sgn_as:C12HBa0062P09*** upload_account_name:italy SEQUENCING IN PROGRESS ***">
        <position start="68128" stop="69828"/>
      </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="68345" g_stop="68352" g_length="8"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="8" r_length="8" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="68353" i_stop="68431" i_length="79">
            <donor d_prob="0.995" d_score="0.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="68432" g_stop="68615" g_length="184"/>
          <reference_exon_boundary r_type="cDNA" r_start="9" r_stop="192" r_length="184" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="68616" i_stop="69215" i_length="600">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.992" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="69216" g_stop="69528" g_length="313"/>
          <reference_exon_boundary r_type="cDNA" r_start="193" r_stop="505" r_length="313" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="506" polyA_stop="518"/>
      <MATCH_line gen_id="C12HBa0062P09.1" gen_strand="+" ref_id="SGN-M236-R" ref_strand="-">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>505</cumulative_length_of_scored_exons>
        <coverage percentage="0.975" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12HBa0062P09.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M236-R" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="68345" e_stop="68352"/>
          <exon e_start="68432" e_stop="68615"/>
          <exon e_start="69216" e_stop="69528"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CAGAGCTGGTATGTCTCATCTCCATTATCAGATGAAGGAACTTATCCATTGTTTCTAACTTTTTTTTTTTTTTTTGATGTATGGCAGCTTCCATGGCAAGGAAGATCTATTTGAGAGGAGGTATTGGTGTTGGTGGTTTCCGAAGAATCTATGGTGGAAACCAGAGGAATGGAAGCCGTCCACGTCACTTTTGCAAGAGCAGTGGTTCAGTTGCACGCCACATTCTTCAACAGTTGCAGAACATGAACATCATTGACTTTGAGCCTAAGGGGTAAGTAGTAACCTTTTGCTCTCTAATTAATGCTGAATTTGATGTGTCTCCTTATTCTGTAGTGGTTGTATGAATGAAATCCATTGATCAGTCAGAAACCTGTTTGTTTACATAACTGATGGGGTTTTCTCCTGCTTTTTCTGAGGTTGTTTGTCATGTGATATGAATATATGCGGATGCGTTAATCATTGTATGGAGCCAGCAAAATTTAAGAAAATCACGAGGAGTCTGGCTAGTCTTGCTTAGAAAAAGAGTGATTTCAGTGATAATAATTGTGCTTAAATCAATTAATAAAACTCTCTTTATTTAGGAAAGAGGTCAAAGACAATTGCAAAAAGAGTGACTGCTCCCTTTATAGTAAGACTTTGATATTTGTGAGTGATTGATTAAACAGGGAAACGATAAGAGGTTGCTGACTTTTCAATTGAAAATAACATGGCTTAAATGAATCTAGATGAAGTATTTCACCTTGTTCTGAATGGAGAGACATCCTTATTGCTAGCGAATGCTCACAACTCAACTTTATTAGCTGCATTAAGAATGAAATCGATGAATATCTAGTTATTTGTCTGTCTAATTTAAAATTCTCTCTTTATCTAGCGGAAGGAGGATCACATCCAGTGGTCAGCGGGATCTTGACCAAGTTGCCGGAAGAATTGCTGTTGCTTGTTAAGAGAGAGATGAGTTCATTCAATTTTATGAATACATGAGTTAGCTCAAACTTATTGTTTCTGTTTGGACCTAAATAGATTTAGGGTATTGTTGAATTAAATTGTGGATGTTTTGCCTTTTCAGAATTGTCTTTCTCAGTATGTCAAGTTTTGCCCTTTTAGTACCCTGAAGTGTGTATTGTGGCATATGTTGCATTCAATGCATCATTACTTCATAATTATACATAAATCCCTGAGATTCA</genome_strand>
        <mrna_strand>CAGAGCTG...............................................................................CTTCCATGGCAAGGAAGATCTATTTGAGAGGAGGTATTGGTGTTGGTGGTTTCCGAAGAATCTATGGTGGAAACCAGAGGAATGGAAGCCGTCCACGTCACTTTTGCAAGAGCAGTGGTTCAGTTGCACGCCACATTCTTCAACAGTTGCAGAACATGAACATCATTGACTTTGAGCCTAAGGG........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CGGAAGGAGGATCACATCCAGTGGTCAGCGGGATCTTGACCAAGTTGCCGGAAGAATTGCTGTTGCTTGTTAAGAGAGAGATGAGTTCATTCAATTTTATGAATACATGAGTTAGCTCAAACTTATTGTTTCTGTTTGGACCTAAATAGATTTAGGGTATTGTTGAATTAAATTGTGGATGTTTTGCCTTTTCAGAATTGTCTTTCTCAGTATGTCAAGTTTTGCCCTTTTAGTACCCTGAAGTGTGTATTGTGGCATATGTTGCATTCAATGCATCATTACTTCATAATTATACATAAATCCCTGAGATTCA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>3</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="67768" PGL_stop="69528"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="67768" e_stop="67882"/>
            <exon e_start="68262" e_stop="68352"/>
            <exon e_start="68432" e_stop="68615"/>
            <exon e_start="69216" e_stop="69528"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.992" acc_prob="1.000" e_score="1.000"/>
          <exon-intron don_prob="0.995" acc_prob="0.999" e_score="1.000"/>
          <exon-intron don_prob="0.999" acc_prob="0.992" 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="67768" e_stop="67882" e_length="115"/>
          </exon>
          <intron i_serial="1" don_prob="0.992" acc_prob="1.000">
            <gDNA_intron_boundary i_start="67883" i_stop="68261" i_length="379"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="68262" e_stop="68352" e_length="91"/>
          </exon>
          <intron i_serial="2" don_prob="0.995" acc_prob="0.999">
            <gDNA_intron_boundary i_start="68353" i_stop="68431" i_length="79"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="68432" e_stop="68615" e_length="184"/>
          </exon>
          <intron i_serial="3" don_prob="0.999" acc_prob="0.992">
            <gDNA_intron_boundary i_start="68616" i_stop="69215" i_length="600"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="69216" e_stop="69528" e_length="313"/>
          </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="67768" stop="67882"/>
              <exon start="68262" stop="68352"/>
              <exon start="68432" stop="68615"/>
              <exon start="69216" stop="69364"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M2983" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="67782" stop="67882"/>
              <exon start="68262" stop="68352"/>
              <exon start="68432" stop="68615"/>
              <exon start="69216" stop="69318"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M236-F" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="68345" stop="68352"/>
              <exon start="68432" stop="68615"/>
              <exon start="69216" stop="69528"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M236-R" 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>GCTGGAGAGTGGAGAAAGATCTGCAGCGAAGATGGAGGCAGCAAGAAGTGTGAAAGATGTTTCCCCCCATGATTTTGTCAAGGCTTATGCCGCTCATCTCAAGCGCTCCGGAAAG : ATGGAGCTTCCTGAATGGACTGATATAGTTAAGACTGGTAAGCTAAAGGAGCTTGCCCCATATGATGCTGATTGGTACTACATCAGAGCTG : CTTCCATGGCAAGGAAGATCTATTTGAGAGGAGGTATTGGTGTTGGTGGTTTCCGAAGAATCTATGGTGGAAACCAGAGGAATGGAAGCCGTCCACGTCACTTTTGCAAGAGCAGTGGTTCAGTTGCACGCCACATTCTTCAACAGTTGCAGAACATGAACATCATTGACTTTGAGCCTAAGGG : CGGAAGGAGGATCACATCCAGTGGTCAGCGGGATCTTGACCAAGTTGCCGGAAGAATTGCTGTTGCTTGTTAAGAGAGAGATGAGTTCATTCAATTTTATGAATACATGAGTTAGCTCAAACTTATTGTTTCTGTTTGGACCTAAATAGATTTAGGGTATTGTTGAATTAAATTGTGGATGTTTTGCCTTTTCAGAATTGTCTTTCTCAGTATGTCAAGTTTTGCCCTTTTAGTACCCTGAAGTGTGTATTGTGGCATATGTTGCATTCAATGCATCATTACTTCATAATTATACATAAATCCCTGAGATTCA</gDNA_template>
            <first_frame> A  G  E  W  R  K  I  C  S  E  D  G  G  S  K  K  C  E  R  C  F  P  P  *  F  C  Q  G  L  C  R  S  S  Q  A  L  R  K   : D  G  A  S  *  M  D  *  Y  S  *  D  W  *  A  K  G  A  C  P  I  *  C  *  L  V  L  H  Q  S  C :   F  H  G  K  E  D  L  F  E  R  R  Y  W  C  W  W  F  P  K  N  L  W  W  K  P  E  E  W  K  P  S  T  S  L  L  Q  E  Q  W  F  S  C  T  P  H  S  S  T  V  A  E  H  E  H  H  *  L  *  A  *  G  :  R  K  E  D  H  I  Q  W  S  A  G  S  *  P  S  C  R  K  N  C  C  C  L  L  R  E  R  *  V  H  S  I  L  *  I  H  E  L  A  Q  T  Y  C  F  C  L  D  L  N  R  F  R  V  L  L  N  *  I  V  D  V  L  P  F  Q  N  C  L  S  Q  Y  V  K  F  C  P  F  S  T  L  K  C  V  L  W  H  M  L  H  S  M  H  H  Y  F  I  I  I  H  K  S  L  R  F  </first_frame>
            <second_frame>  L  E  S  G  E  R  S  A  A  K  M  E  A  A  R  S  V  K  D  V  S  P  H  D  F  V  K  A  Y  A  A  H  L  K  R  S  G  K  :  M  E  L  P  E  W  T  D  I  V  K  T  G  K  L  K  E  L  A  P  Y  D  A  D  W  Y  Y  I  R  A   : A  S  M  A  R  K  I  Y  L  R  G  G  I  G  V  G  G  F  R  R  I  Y  G  G  N  Q  R  N  G  S  R  P  R  H  F  C  K  S  S  G  S  V  A  R  H  I  L  Q  Q  L  Q  N  M  N  I  I  D  F  E  P  K  G :   G  R  R  I  T  S  S  G  Q  R  D  L  D  Q  V  A  G  R  I  A  V  A  C  *  E  R  D  E  F  I  Q  F  Y  E  Y  M  S  *  L  K  L  I  V  S  V  W  T  *  I  D  L  G  Y  C  *  I  K  L  W  M  F  C  L  F  R  I  V  F  L  S  M  S  S  F  A  L  L  V  P  *  S  V  Y  C  G  I  C  C  I  Q  C  I  I  T  S  *  L  Y  I  N  P  *  D  S </second_frame>
            <third_frame>   W  R  V  E  K  D  L  Q  R  R  W  R  Q  Q  E  V  *  K  M  F  P  P  M  I  L  S  R  L  M  P  L  I  S  S  A  P  E  R :   W  S  F  L  N  G  L  I  *  L  R  L  V  S  *  R  S  L  P  H  M  M  L  I  G  T  T  S  E  L  :  L  P  W  Q  G  R  S  I  *  E  E  V  L  V  L  V  V  S  E  E  S  M  V  E  T  R  G  M  E  A  V  H  V  T  F  A  R  A  V  V  Q  L  H  A  T  F  F  N  S  C  R  T  *  T  S  L  T  L  S  L  R   : A  E  G  G  S  H  P  V  V  S  G  I  L  T  K  L  P  E  E  L  L  L  L  V  K  R  E  M  S  S  F  N  F  M  N  T  *  V  S  S  N  L  L  F  L  F  G  P  K  *  I  *  G  I  V  E  L  N  C  G  C  F  A  F  S  E  L  S  F  S  V  C  Q  V  L  P  F  *  Y  P  E  V  C  I  V  A  Y  V  A  F  N  A  S  L  L  H  N  Y  T  *  I  P  E  I   </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C12HBa0062P09.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="67769" stop="67882"/>
                    <exon start="68262" stop="68352"/>
                    <exon start="68432" stop="68615"/>
                    <exon start="69216" stop="69288"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>459</number_coding_nucleotides>
                  <number_encoded_amino_acids>153</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LESGERSAAKMEAARSVKDVSPHDFVKAYAAHLKRSGKMELPEWTDIVKTGKLKELAPYDADWYYIRAASMARKIYLRGGIGVGGFRRIYGGNQRNGSRPRHFCKSSGSVARHILQQLQNMNIIDFEPKGGRRITSSGQRDLDQVAGRIAVAC*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 14 chains have been computed
$ 
$ memory statistics:
$ 6072 bytes spliced alignments in total
$ 3 spliced alignments have been stored
$ 2024 bytes was the average size of a spliced alignment
$ 5624 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5624 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 16 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-18 08:28:35
-->
