<?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="2007-12-13 18:56:51"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-heLKW/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/cxgn-bacpublish-resources-2kL80w/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-2kL80w/sgn_marker_seqs" ref_id="T1046" ref_strand="+" ref_description="T1046">
      <seq>tgttgaagctgtcttcaaggattctgaagaacatcatgtaacagagaaaaaggaagagcagccaactcccatgaatgcattcgagttgatttcaatgtcaaaaggactcaaccttgggaatctcttcgatgaacaggaatttaagagagaaacaaggttcacatctaaatgctcggccaatgaaattatcagtaagattgaagaagctgcaaagcccctcggttttgatgttcacaaaaagaactacaagatgagacttgaaaatgtcaaagctggaagaaaagggaaccttaatgttgccactgaggtatttcaagttgccccttctcttcatatggttgaagtccgaaaggcaaaaggagatactttggaattccacaagttctacaagaatctttcgactagtctagaggatgtagtgtggaaaactgaagaggacatgcaagctaggtagtattactaccatgaactgcaattgcataagcttttgctggtcccacaatctgtgtaaaaaactttgcaacttggttctttctttccc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-heLKW/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C11HBa0029C01.1" temp_strand="-" temp_description="C11HBa0029C01.1  AC212430.1 htgs_phase:2 submitted_to_sgn_as:C11HBa0029C01 sequenced_by:ivf-caas">
        <position start="68729" stop="65736"/>
      </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="68429" g_stop="68402" g_length="28"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="28" r_length="28" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="68401" i_stop="68295" i_length="107">
            <donor d_prob="0.944" d_score="0.00"/>
            <acceptor a_prob="0.987" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="68294" g_stop="68187" g_length="108"/>
          <reference_exon_boundary r_type="cDNA" r_start="29" r_stop="136" r_length="108" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="68186" i_stop="67372" i_length="815">
            <donor d_prob="0.990" d_score="1.00"/>
            <acceptor a_prob="0.981" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="67371" g_stop="67258" g_length="114"/>
          <reference_exon_boundary r_type="cDNA" r_start="137" r_stop="250" r_length="114" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="67257" i_stop="67170" i_length="88">
            <donor d_prob="0.978" d_score="1.00"/>
            <acceptor a_prob="0.988" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="67169" g_stop="67113" g_length="57"/>
          <reference_exon_boundary r_type="cDNA" r_start="251" r_stop="307" r_length="57" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="67112" i_stop="66968" i_length="145">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="66967" g_stop="66893" g_length="75"/>
          <reference_exon_boundary r_type="cDNA" r_start="308" r_stop="382" r_length="75" r_score="1.000"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="66892" i_stop="66195" i_length="698">
            <donor d_prob="0.934" d_score="1.00"/>
            <acceptor a_prob="0.986" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="66194" g_stop="66036" g_length="159"/>
          <reference_exon_boundary r_type="cDNA" r_start="383" r_stop="541" r_length="159" r_score="0.994"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C11HBa0029C01.1" gen_strand="-" ref_id="T1046" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>541</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C11HBa0029C01.1" gen_strand="-"/>
        <rDNA rDNA_id="T1046" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="68429" e_stop="68402"/>
          <exon e_start="68294" e_stop="68187"/>
          <exon e_start="67371" e_stop="67258"/>
          <exon e_start="67169" e_stop="67113"/>
          <exon e_start="66967" e_stop="66893"/>
          <exon e_start="66194" e_stop="66036"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TGTTGAAGCTGTCTTCAAGGATTCTGAAGTGAGCACACTGAAATGTTGAACAAGTTTTTCATTGAATTCAGAGGAAAGAATTGATTGTTGTATAGTCATCCTCATGTGGTTCTCTTTTCCTTGACACAACAACAGGAACATCATGTAACAGAGAAAAAGGAAGAGCAGCCAACTCCCATGAATGCATTCGAGTTGATTTCAATGTCAAAAGGACTCAACCTTGGGAATCTCTTCGATGAACAGGTTACCGACTATGAACTTCGATTTTTATTTGTTACTTATGTTGCATGTTTTGGAACTTTTGTTTGATTTTGCATGGTTTTTGTGCCATGAATTACATCAGTGTATAGTTGTACTTCTCAGTAGGATATGCTATAATGAAGTTTCATGTGAATGTCAAAGACTTAATGCTTACTTGGTAACCATTGAATAATTCTTTGTTCATTCCCAAACACTCTAAATAACAATGGGAAAGAAGTAAAGATTCTATGATGTGTAGTAAAACTAGTACCTTCGCATTTACATAAAATAATAGACGTCTTCTAACAGACATGAGCCTAAATGCCCTGAGTTGAGCTAACCTGCTAAATTCATCAAGTTTAGCTGTTAAATAAGCGCTAGATGCTTCAAAATGCTGCGGCAATATTGCATGCATACACAAACTAACTTCCATCTCTTTCTCCTGTGTGTTGAATTCCGTTATCCATTTTACAGAAGGCTTTTAGATTATTATTCAGAATTCTCAGTTTTTGATTTGCAGCTAAGTAATCTCATATGAGTGAGGATGCAAATCCACTAATTAAAAAATGAAAAAACTGTTAAAGGACTAATTACAGAAAAATGAATTCCTAAGTTCATTTTACTCCCTGTCTGAATAAAACTGACCTTTCTTTATTACTCTACTCAAAAAACTTGGTCTCTTTTCCCGAATGGCCATTTTTCCCACCAACAATTCAAATCAATATAAATTGGTATTCCACCTTGTCGGAGAAATTGATGATTTGTGTATTGCTATAATATTACTTCATTCACAGATGTTTTGATTCCGACATTCACAGGAATTTAAGAGAGAAACAAGGTTCACATCTAAATGCTCGGCCAATGAAATTATCAGTAAGATTGAAGAAGCTGCAAAGCCCCTCGGTTTTGATGTTCACAAAAAGAACTACAAGGTGGTGATGTATTTCAAGTATGCATTTCAATTGGCATGTAGATTCCTAATAAAGTTAAATTAATTCGCATTCTACTCTTTTACTTCAGATGAGACTTGAAAATGTCAAAGCTGGAAGAAAAGGGAACCTTAATGTTGCCACTGAGGTATGCTCAATGTGCATAGCTAGTCATCTACAATTATCTTATTTTACTTTAACCTTTTGCAGTTTGTGTTGAGGATAGCCATAAGTTCTTTGGAATTTGAATCTTTAATCATCATAGCCTGAACACTGTTTGGTCTTGAATGTAGGTATTTCAAGTTGCCCCTTCTCTTCATATGGTTGAAGTCCGAAAGGCAAAAGGAGATACTTTGGAATTCCACAAGGTACCATATTCCGCTAACTGCCGAAAAAGTTATCTAAATGACGATGCTGAAATGTGTAGATCACCATTAGTAGGTTTTCGTAGGCCAATACAAGCTAATTGCTCGTGAATGAGCAACATAGTCTTGAAGTTACTGTTCGACACAAGATAGCAACAAAAAAGTAAGAGGTTGTAGGCATGTTTTTAGATTAGGTGAGAGAAGTTATAGCGTCTCTTTGAAATGACCATAACATTGTTATTCATTGTCCCTCAAAACATGGATGGTTTGATCTTAGTTACAGGGTCCACTTTAGAGCCTTAGAACGGTGATATCATCTTGTAACCTCTTATGTCACAATGGACAACATGATTTTTGTATTGCTGTAATAGGAATTAAAACCCGTGTGCCTCGTATTAGAGAGACGACTCACCATGAGTCTTGGACAACTCCAGATAAAAGAAGAGTACAGAAAATATAAAGAAGCCAAGAACCATGGGAAAGTGAGAGAGGATGGAAGAAACTAATGGATGTTTAGCCTAATAAAGATCACACTAGTGTCTGTATACCTGTTTTCTACTTTATAGTTTCCAATAAGGCATAGGTTTTTGCTTTGTTTTGTCTATCGGAAATGCAAGCACCTCGTTGATTTTTAGATCCTACTAGTTCGAGCTAATTGTTCGATCTCATGCTAATCATTTTGTTGCTCATTCTTGATGCAGTTCTACAAGAATCTTTCGACTAGTCTAGAGGATGTAGTGTGGAAAACTGAAGAGGACATGCAAGCTAGGTAGTATTACTACCATGAACTGCAATTGCATAAGCTTTTGCTGGTCCCACAATCTGTGTAAAAAACTTTGCAACTTGTTTCTTTCTTTCCC</genome_strand>
        <mrna_strand>TGTTGAAGCTGTCTTCAAGGATTCTGAA...........................................................................................................GAACATCATGTAACAGAGAAAAAGGAAGAGCAGCCAACTCCCATGAATGCATTCGAGTTGATTTCAATGTCAAAAGGACTCAACCTTGGGAATCTCTTCGATGAACAG...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GAATTTAAGAGAGAAACAAGGTTCACATCTAAATGCTCGGCCAATGAAATTATCAGTAAGATTGAAGAAGCTGCAAAGCCCCTCGGTTTTGATGTTCACAAAAAGAACTACAAG........................................................................................ATGAGACTTGAAAATGTCAAAGCTGGAAGAAAAGGGAACCTTAATGTTGCCACTGAG.................................................................................................................................................GTATTTCAAGTTGCCCCTTCTCTTCATATGGTTGAAGTCCGAAAGGCAAAAGGAGATACTTTGGAATTCCACAAG..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTCTACAAGAATCTTTCGACTAGTCTAGAGGATGTAGTGTGGAAAACTGAAGAGGACATGCAAGCTAGGTAGTATTACTACCATGAACTGCAATTGCATAAGCTTTTGCTGGTCCCACAATCTGTGTAAAAAACTTTGCAACTTGGTTCTTTCTTTCCC</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-2kL80w/sgn_marker_seqs" ref_id="T1029" ref_strand="+" ref_description="T1029">
      <seq>tctcttcacttcattcacagctcaaaaatctcctccattaatcttcgttttcgagtcttctctaatcagccatgggctctgatgcagatatggaggactatggattcgagtattcagaggaggaacctgaagagcaggatgttgatattgagaaccaatactacaactccaaaggcttggctgaaacagacccagaggcagcacttgagggttttgctgaagtacttcgtatggaacctgagaaggctgattggggatttaaagcctgaaagcaaactgttaagctttactataagctagggaagtacaagggaatgatggacgcttacagagaaatgctaacctacatcaagtcagctgtgacacgaaattatagtgaaaagtgtataaacaatatcatggatttcgtctcaggatcagctagtcagaactttgatctcctacaagagttctaccaaacaacattgaaagccc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-heLKW/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C11HBa0029C01.1" temp_strand="-" temp_description="C11HBa0029C01.1  AC212430.1 htgs_phase:2 submitted_to_sgn_as:C11HBa0029C01 sequenced_by:ivf-caas">
        <position start="109673" stop="105472"/>
      </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="109373" g_stop="109293" g_length="81"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="81" r_length="81" r_score="0.988"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="109292" i_stop="109200" i_length="93">
            <donor d_prob="0.999" 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="109199" g_stop="109107" g_length="93"/>
          <reference_exon_boundary r_type="cDNA" r_start="82" r_stop="174" r_length="93" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="109106" i_stop="106971" i_length="2136">
            <donor d_prob="0.980" 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="106970" g_stop="106892" g_length="79"/>
          <reference_exon_boundary r_type="cDNA" r_start="175" r_stop="253" r_length="79" r_score="0.987"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="106891" i_stop="105993" i_length="899">
            <donor d_prob="0.993" d_score="0.98"/>
            <acceptor a_prob="0.895" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="105992" g_stop="105772" g_length="221"/>
          <reference_exon_boundary r_type="cDNA" r_start="254" r_stop="474" r_length="221" r_score="0.991"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C11HBa0029C01.1" gen_strand="-" ref_id="T1029" ref_strand="+">
        <total_alignment_score>0.992</total_alignment_score>
        <cumulative_length_of_scored_exons>474</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C11HBa0029C01.1" gen_strand="-"/>
        <rDNA rDNA_id="T1029" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="109373" e_stop="109293"/>
          <exon e_start="109199" e_stop="109107"/>
          <exon e_start="106970" e_stop="106892"/>
          <exon e_start="105992" e_stop="105772"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCTCTTCACTTCATCCACAGCTCAAAAATCTCCTCCATTAATCTTCGTTTTCGAGTCTTCTCTAATCAGCCATGGGCTCTGGTAATTTACTCTTTCTAACTAGCTATTTTTTTTGTGTTAATCTGATTTTGTGAATGTTAATGTAAGTGTATTTTCAAATTTTTTTGTTTGAAGATGCAGATATGGAGGACTATGGATTCGAGTATTCAGAGGAGGAACCTGAAGAGCAGGATGTTGATATTGAGAACCAATACTACAACTCCAAAGGTTTTCAAATTTTGAATGTTGTAATTATGCTGATAAATTTTATGCTTTTGTTTTGATTTTACTTCCTCTACTTGGATTACAAAAAAATCAGCTGCGTTAGTTACTTCTCTTCGGAAAAAACTTTTGCGAACAAACTAAATTTGCATTAAAATTTTCACACATTAACCTGAGGAAAACAATTAAGGTATTGAATATGCATCATGTATGTGAATGTTTATAGTTTAGTATGTGTTAATTTAAGTTTGATTACTATGTTAGATGTTATTTTGATTGTTTCAGTTGGGAAACAGTAAAGAGGTCTTTGTTTGTTAACTTGGCTAATTTGTTAGATTATAGAGGAAAGTACTTTAAGGAAGATCTGTTAAGAAAGAGCAGTTGTTGCTTGAGAAAATTGGGAGGACTTGAAATTGGAAATTACTAAGAAAGGTGATTAAGTCAATATTTTCTTTTGATTTGAATTAGGGAAAAACTTAATACTAAATTGTTAAAGAGAATAATATAATTTGGATTGTTAAATTTAGAGTTTTGTATTTCGAACATAATGCTCCAACTTCCTTCTTTTTGTTTTTGGGATAACCGTTGGCTCATGGTTCTCAACACACTTCATTGATCACTTTGGGTCTTGGCCACACTTTTGGGAGAGCACCAAATTGCTTATTATCATTTCCAAGGTGACAGAACAAAATATTGTGGTCTGCTACAAGACGAGCAATCGCGGTGACTCTGCATTGTTGAGTTTACCTGTAAACTGTATTAACAGAGGTGAATATTGGGTTGAAATTTAAGGAACGCATTGATCCCTTCTTTTTCGTGAAAGCGTAACACCCTTAAAGGGGCATTTGATTTGGTCAATCTATTATGTCTGGATTCTGAAATAAGGTAGTTATCGGCTGCATGATATGGCTTCAAATTCAATGTTTTTTCTGCACTTTTAGGAGTGAAACCTGGACATATAGAGGAGAAATCTAGGCCGCTAATTATGTTCATTTGTAAAAGGAACTTCAAGGAGTAGGAAAGAAGGCATATTAGCTCAGTATATTTTAGACATTGCAGGGTCCTTATAGTTAATTTTCTTCTTTTAACTTTCTTTTGATGGTTTGTTTTAATCACCTGTATCATTGAGTTACGTATGGGAGTAGTGCTTTAATTTATAGGACATAAGTTTGGGAAGTTAATTATCAAAGAGAAAAGGCAAGTCTGCTCTTTGTCCTCTGGAATTTTATCCCTCGTGATTTTGTTCTCAGGGAAAGGCTTCCATAGATTTATTTAGTGTTGGAAGGTTGGAAAAGGAGAATCCATCCCTTATCCTATATAAGTTCTAGGATTGTAATGGTTGAATTTTGTCACAGCAAGGTTAGGGAAAGCCATAATTTTATCTATTAGAGTCAAGTCGGTCATAAGGTTGTCTATTAGAGCCAAGTCGGTCATAAGGTTGTCTATTAGAGCCAAGTTGGTTTACAGTTGCCATGATTTTCTATTTTCTTTGGTTCTAAACAATGTTAGAGAAAGTGAAGATTGTAGCAGTGATGTTTCTCTCACTTGACTCCCCTGTCTTTTTCTGTGGAGACGCCTATGAAGTGTGATGCTCTATGTGAAACAGATCTTTTGTATAATACAATTATTTCCCAATGATTTTGTATGAATGTGATGACAGTTGCGAGGGAAGAACTTGCAAACGTAGAAGTTACCCAGATATTAAATAATCTGAAAAAGCAAACTGTACCAGTAGCAGCAACAGATACTCCTGTAAAGAAATCCTTGGTTGTAAGGGAGTAACAGATTATGCTATGTGCTATGTAATGGTGTTGATTTTATCTACCGAGTTCCAAACCGTGCAACAGCTGATCCTTGGGAATTTCTCAGTTGTCAAAACAATAGTACTCCCTGGATATAAGATAGTTATAAGTCATGTGATATCCTATGTAATGGCATTGACTTTATCTACTGAGCTTCGAATTGCAGCTGCTTCTCGGGAATTTCTTTGTTATAAAAAAAAGGGTGTTGACTTTAACACAACTATGTGGATAATCTATATATGCATCTTAAACTACTTATCTTGGACTAATATCTCTTATCTTTTTTTCCTCTCTTTGGACATGTTTTCCTACTAATATTCCGTGATTATGTCATTCATAGGCTTGGCTGAAACAGACCCAGAGGCAGCACTTGAGGGTTTTGCTGAAGTAGTTCGTATGGAACCTGAGAAGGCTGATTGGTAAGAAATTGAAAGTAATAAAAATTTGTGCAGTATGGTAGTTGTTAAACTGATCAGCTAACTCCCTTTGTGTTTGTTTTATAAAGAGAATAGATGGCTGTGTATTTGTGAGATTTGTGAGGCCAGAGACTGATGTGATGGATATGTCCATACGAAGTTCAGGGTCATTAAGAACTGCATGTTCTCATTGCAGTTAATTTTATGTCTCAAGTAAACTACTACAACCTTGTATTAATTGACATGCAATTACAGCCTAAGAAACAAGCTGATGATGAATTATGAGAAACTGCAAGTTGAGATAGATTGTATTTTCTTCATTATGTAAATGCTTGTATGGGCATGTGGGAGAAGATCCTGATAGTTTATTTAACTTTTATCATTCTTACAAGCCTGTGGAGAAAAATGTTGACCTTCCAAGTGCAGATAATTGTTTGACAAGAACTGGAAATATTTTTCAGATTTCTCCCTTTGGGTCTCTTGCTCCTATTTGGTTTACATGTGTGAAATTTAAAAAATTTCAGAAACTTTTGCTCTGAGCACTTAGGTTGAGACCTCTAGTTCATTGTCAGATCTGATATGTTTGGTTTTTTTTTTTTCGCTTTTTATGTTGTTTCGTGAATTTGGTAACTTGATATTAATCACTGAGAATACTTGTGCACACGTTATAATTGTAATCCAAAAGGCGTCTTACTATTTCCCAAATTTGCTTCTTGTTCATGTGATTTGATGCTTCTTAGAAAACTTCGTAATTGTATTGCTAAAAGTTGTGGTGCTATTTTACACCTTTGCTTCTTCTTTTATGTAATTTGATGCTTTGTAAGTAAAGGTCTCTTGCAAGTTTTAAAATTCTCTGAAATACGCTGTCTGTGGCACTTACCAACTGTTCTTATTGTTTTTAGGGGATTTAAAGCCTTAAAGCAAACTGTTAAGCTTTACTATAAGCTAGGGAAGTACAAGGGAATGATGGACGCTTACAGAGAAATGCTAACCTACATCAAGTCAGCTGTGACAAGAAATTATAGTGAAAAGTGTATAAACAATATCATGGATTTCGTCTCAGGATCAGCTAGTCAGAACTTTGATCTCCTACAAGAGTTCTACCAAACAACATTGAAAGCCC</genome_strand>
        <mrna_strand>TCTCTTCACTTCATTCACAGCTCAAAAATCTCCTCCATTAATCTTCGTTTTCGAGTCTTCTCTAATCAGCCATGGGCTCTG.............................................................................................ATGCAGATATGGAGGACTATGGATTCGAGTATTCAGAGGAGGAACCTGAAGAGCAGGATGTTGATATTGAGAACCAATACTACAACTCCAAAG........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCTTGGCTGAAACAGACCCAGAGGCAGCACTTGAGGGTTTTGCTGAAGTACTTCGTATGGAACCTGAGAAGGCTGATTG...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GGGATTTAAAGCCTGAAAGCAAACTGTTAAGCTTTACTATAAGCTAGGGAAGTACAAGGGAATGATGGACGCTTACAGAGAAATGCTAACCTACATCAAGTCAGCTGTGACACGAAATTATAGTGAAAAGTGTATAAACAATATCATGGATTTCGTCTCAGGATCAGCTAGTCAGAACTTTGATCTCCTACAAGAGTTCTACCAAACAACATTGAAAGCCC</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>2</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="68429" PGL_stop="66036"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="68429" e_stop="68402"/>
            <exon e_start="68294" e_stop="68187"/>
            <exon e_start="67371" e_stop="67258"/>
            <exon e_start="67169" e_stop="67113"/>
            <exon e_start="66967" e_stop="66893"/>
            <exon e_start="66194" e_stop="66036"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.944" acc_prob="0.987" e_score="1.000"/>
          <exon-intron don_prob="0.990" acc_prob="0.981" e_score="1.000"/>
          <exon-intron don_prob="0.978" acc_prob="0.988" e_score="1.000"/>
          <exon-intron don_prob="1.000" acc_prob="0.998" e_score="1.000"/>
          <exon-intron don_prob="0.934" acc_prob="0.986" e_score="1.000"/>
          <exon-only e_score="0.994"/>
        </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="68429" e_stop="68402" e_length="28"/>
          </exon>
          <intron i_serial="1" don_prob="0.944" acc_prob="0.987">
            <gDNA_intron_boundary i_start="68401" i_stop="68295" i_length="107"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="68294" e_stop="68187" e_length="108"/>
          </exon>
          <intron i_serial="2" don_prob="0.990" acc_prob="0.981">
            <gDNA_intron_boundary i_start="68186" i_stop="67372" i_length="815"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="67371" e_stop="67258" e_length="114"/>
          </exon>
          <intron i_serial="3" don_prob="0.978" acc_prob="0.988">
            <gDNA_intron_boundary i_start="67257" i_stop="67170" i_length="88"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="67169" e_stop="67113" e_length="57"/>
          </exon>
          <intron i_serial="4" don_prob="1.000" acc_prob="0.998">
            <gDNA_intron_boundary i_start="67112" i_stop="66968" i_length="145"/>
          </intron>
          <exon e_serial="5" e_score="1.000">
            <gDNA_exon_boundary e_start="66967" e_stop="66893" e_length="75"/>
          </exon>
          <intron i_serial="5" don_prob="0.934" acc_prob="0.986">
            <gDNA_intron_boundary i_start="66892" i_stop="66195" i_length="698"/>
          </intron>
          <exon e_serial="6" e_score="0.994">
            <gDNA_exon_boundary e_start="66194" e_stop="66036" e_length="159"/>
          </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="68429" stop="68402"/>
              <exon start="68294" stop="68187"/>
              <exon start="67371" stop="67258"/>
              <exon start="67169" stop="67113"/>
              <exon start="66967" stop="66893"/>
              <exon start="66194" stop="66036"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="T1046" 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>TGTTGAAGCTGTCTTCAAGGATTCTGAA : GAACATCATGTAACAGAGAAAAAGGAAGAGCAGCCAACTCCCATGAATGCATTCGAGTTGATTTCAATGTCAAAAGGACTCAACCTTGGGAATCTCTTCGATGAACAG : GAATTTAAGAGAGAAACAAGGTTCACATCTAAATGCTCGGCCAATGAAATTATCAGTAAGATTGAAGAAGCTGCAAAGCCCCTCGGTTTTGATGTTCACAAAAAGAACTACAAG : ATGAGACTTGAAAATGTCAAAGCTGGAAGAAAAGGGAACCTTAATGTTGCCACTGAG : GTATTTCAAGTTGCCCCTTCTCTTCATATGGTTGAAGTCCGAAAGGCAAAAGGAGATACTTTGGAATTCCACAAG : TTCTACAAGAATCTTTCGACTAGTCTAGAGGATGTAGTGTGGAAAACTGAAGAGGACATGCAAGCTAGGTAGTATTACTACCATGAACTGCAATTGCATAAGCTTTTGCTGGTCCCACAATCTGTGTAAAAAACTTTGCAACTTGTTTCTTTCTTTCCC</gDNA_template>
            <first_frame> C  *  S  C  L  Q  G  F  *   : R  T  S  C  N  R  E  K  G  R  A  A  N  S  H  E  C  I  R  V  D  F  N  V  K  R  T  Q  P  W  E  S  L  R  *  T   : G  I  *  E  R  N  K  V  H  I  *  M  L  G  Q  *  N  Y  Q  *  D  *  R  S  C  K  A  P  R  F  *  C  S  Q  K  E  L  Q   : D  E  T  *  K  C  Q  S  W  K  K  R  E  P  *  C  C  H  *   : G  I  S  S  C  P  F  S  S  Y  G  *  S  P  K  G  K  R  R  Y  F  G  I  P  Q   : V  L  Q  E  S  F  D  *  S  R  G  C  S  V  E  N  *  R  G  H  A  S  *  V  V  L  L  P  *  T  A  I  A  *  A  F  A  G  P  T  I  C  V  K  N  F  A  T  C  F  F  L  S  </first_frame>
            <second_frame>  V  E  A  V  F  K  D  S  E  :  E  H  H  V  T  E  K  K  E  E  Q  P  T  P  M  N  A  F  E  L  I  S  M  S  K  G  L  N  L  G  N  L  F  D  E  Q  :  E  F  K  R  E  T  R  F  T  S  K  C  S  A  N  E  I  I  S  K  I  E  E  A  A  K  P  L  G  F  D  V  H  K  K  N  Y  K  :  M  R  L  E  N  V  K  A  G  R  K  G  N  L  N  V  A  T  E  :  V  F  Q  V  A  P  S  L  H  M  V  E  V  R  K  A  K  G  D  T  L  E  F  H  K  :  F  Y  K  N  L  S  T  S  L  E  D  V  V  W  K  T  E  E  D  M  Q  A  R  *  Y  Y  Y  H  E  L  Q  L  H  K  L  L  L  V  P  Q  S  V  *  K  T  L  Q  L  V  S  F  F  P </second_frame>
            <third_frame>   L  K  L  S  S  R  I  L  K :   N  I  M  *  Q  R  K  R  K  S  S  Q  L  P  *  M  H  S  S  *  F  Q  C  Q  K  D  S  T  L  G  I  S  S  M  N  R :   N  L  R  E  K  Q  G  S  H  L  N  A  R  P  M  K  L  S  V  R  L  K  K  L  Q  S  P  S  V  L  M  F  T  K  R  T  T  R :   *  D  L  K  M  S  K  L  E  E  K  G  T  L  M  L  P  L  R :   Y  F  K  L  P  L  L  F  I  W  L  K  S  E  R  Q  K  E  I  L  W  N  S  T  S :   S  T  R  I  F  R  L  V  *  R  M  *  C  G  K  L  K  R  T  C  K  L  G  S  I  T  T  M  N  C  N  C  I  S  F  C  W  S  H  N  L  C  K  K  L  C  N  L  F  L  S  F   </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="C11HBa0029C01.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="68428" stop="68402"/>
                    <exon start="68294" stop="68187"/>
                    <exon start="67371" stop="67258"/>
                    <exon start="67169" stop="67113"/>
                    <exon start="66967" stop="66893"/>
                    <exon start="66194" stop="66123"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>450</number_coding_nucleotides>
                  <number_encoded_amino_acids>150</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>VEAVFKDSEEHHVTEKKEEQPTPMNAFELISMSKGLNLGNLFDEQEFKRETRFTSKCSANEIISKIEEAAKPLGFDVHKKNYKMRLENVKAGRKGNLNVATEVFQVAPSLHMVEVRKAKGDTLEFHKFYKNLSTSLEDVVWKTEEDMQAR*</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="109373" PGL_stop="105772"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="109373" e_stop="109293"/>
            <exon e_start="109199" e_stop="109107"/>
            <exon e_start="106970" e_stop="106892"/>
            <exon e_start="105992" e_stop="105772"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.999" acc_prob="1.000" e_score="0.988"/>
          <exon-intron don_prob="0.980" acc_prob="0.999" e_score="1.000"/>
          <exon-intron don_prob="0.993" acc_prob="0.895" e_score="0.987"/>
          <exon-only e_score="0.991"/>
        </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="0.988">
            <gDNA_exon_boundary e_start="109373" e_stop="109293" e_length="81"/>
          </exon>
          <intron i_serial="1" don_prob="0.999" acc_prob="1.000">
            <gDNA_intron_boundary i_start="109292" i_stop="109200" i_length="93"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="109199" e_stop="109107" e_length="93"/>
          </exon>
          <intron i_serial="2" don_prob="0.980" acc_prob="0.999">
            <gDNA_intron_boundary i_start="109106" i_stop="106971" i_length="2136"/>
          </intron>
          <exon e_serial="3" e_score="0.987">
            <gDNA_exon_boundary e_start="106970" e_stop="106892" e_length="79"/>
          </exon>
          <intron i_serial="3" don_prob="0.993" acc_prob="0.895">
            <gDNA_intron_boundary i_start="106891" i_stop="105993" i_length="899"/>
          </intron>
          <exon e_serial="4" e_score="0.991">
            <gDNA_exon_boundary e_start="105992" e_stop="105772" e_length="221"/>
          </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="109373" stop="109293"/>
              <exon start="109199" stop="109107"/>
              <exon start="106970" stop="106892"/>
              <exon start="105992" stop="105772"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="T1029" 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>TCTCTTCACTTCATCCACAGCTCAAAAATCTCCTCCATTAATCTTCGTTTTCGAGTCTTCTCTAATCAGCCATGGGCTCTG : ATGCAGATATGGAGGACTATGGATTCGAGTATTCAGAGGAGGAACCTGAAGAGCAGGATGTTGATATTGAGAACCAATACTACAACTCCAAAG : GCTTGGCTGAAACAGACCCAGAGGCAGCACTTGAGGGTTTTGCTGAAGTAGTTCGTATGGAACCTGAGAAGGCTGATTG : GGGATTTAAAGCCTTAAAGCAAACTGTTAAGCTTTACTATAAGCTAGGGAAGTACAAGGGAATGATGGACGCTTACAGAGAAATGCTAACCTACATCAAGTCAGCTGTGACAAGAAATTATAGTGAAAAGTGTATAAACAATATCATGGATTTCGTCTCAGGATCAGCTAGTCAGAACTTTGATCTCCTACAAGAGTTCTACCAAACAACATTGAAAGCCC</gDNA_template>
            <first_frame> S  L  H  F  I  H  S  S  K  I  S  S  I  N  L  R  F  R  V  F  S  N  Q  P  W  A  L  :  M  Q  I  W  R  T  M  D  S  S  I  Q  R  R  N  L  K  S  R  M  L  I  L  R  T  N  T  T  T  P  K  :  A  W  L  K  Q  T  Q  R  Q  H  L  R  V  L  L  K  *  F  V  W  N  L  R  R  L  I   : G  D  L  K  P  *  S  K  L  L  S  F  T  I  S  *  G  S  T  R  E  *  W  T  L  T  E  K  C  *  P  T  S  S  Q  L  *  Q  E  I  I  V  K  S  V  *  T  I  S  W  I  S  S  Q  D  Q  L  V  R  T  L  I  S  Y  K  S  S  T  K  Q  H  *  K  P </first_frame>
            <second_frame>  L  F  T  S  S  T  A  Q  K  S  P  P  L  I  F  V  F  E  S  S  L  I  S  H  G  L  * :   C  R  Y  G  G  L  W  I  R  V  F  R  G  G  T  *  R  A  G  C  *  Y  *  E  P  I  L  Q  L  Q  R :   L  G  *  N  R  P  R  G  S  T  *  G  F  C  *  S  S  S  Y  G  T  *  E  G  *  L  :  G  I  *  S  L  K  A  N  C  *  A  L  L  *  A  R  E  V  Q  G  N  D  G  R  L  Q  R  N  A  N  L  H  Q  V  S  C  D  K  K  L  *  *  K  V  Y  K  Q  Y  H  G  F  R  L  R  I  S  *  S  E  L  *  S  P  T  R  V  L  P  N  N  I  E  S   </second_frame>
            <third_frame>   S  S  L  H  P  Q  L  K  N  L  L  H  *  S  S  F  S  S  L  L  *  S  A  M  G  S   : D  A  D  M  E  D  Y  G  F  E  Y  S  E  E  E  P  E  E  Q  D  V  D  I  E  N  Q  Y  Y  N  S  K   : G  L  A  E  T  D  P  E  A  A  L  E  G  F  A  E  V  V  R  M  E  P  E  K  A  D  W :   G  F  K  A  L  K  Q  T  V  K  L  Y  Y  K  L  G  K  Y  K  G  M  M  D  A  Y  R  E  M  L  T  Y  I  K  S  A  V  T  R  N  Y  S  E  K  C  I  N  N  I  M  D  F  V  S  G  S  A  S  Q  N  F  D  L  L  Q  E  F  Y  Q  T  T  L  K  A  </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="C11HBa0029C01.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="109308" stop="109293"/>
                    <exon start="109199" stop="109107"/>
                    <exon start="106970" stop="106892"/>
                    <exon start="105992" stop="105773"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>408</number_coding_nucleotides>
                  <number_encoded_amino_acids>136</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>SAMGSDADMEDYGFEYSEEEPEEQDVDIENQYYNSKGLAETDPEAALEGFAEVVRMEPEKADWGFKALKQTVKLYYKLGKYKGMMDAYREMLTYIKSAVTRNYSEKCINNIMDFVSGSASQNFDLLQEFYQTTLKA</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 4 chains have been computed
$ 
$ memory statistics:
$ 4560 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 2280 bytes was the average size of a spliced alignment
$ 6960 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3480 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 4 backtrace matrices have been allocated
$ 
$ date finished: 2007-12-13 18:56:55
-->
