<?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="2008-02-20 11:27:52"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C09HBa0036O20-VSZgt/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/cxgn-bacpublish-resources-y6fsIW/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-y6fsIW/sgn_marker_seqs" ref_id="SGN-M872" ref_strand="+" ref_description="SGN-M872 SSR199 [est_by_read_no_qc_info]">
      <seq>cagcaccctgcgcgtcttcttcttcttcttcttccttctccggcgaacgcgaacccagaccagtccatctcgccatcgccgtcgccgtcgccgtgagataatcgtgagacatattattaccaaatataaagcttgaaggagagaggggagcacaacaatggcgaatgaaacaatggctgaacaacaaaagaaacgaacgatggaggcattagagcgaagatttgctcaagcaaaagctgaaattcatcaacagcagcacaagaacaagagagtcgctgttactacaacaaaaactctagctgaaaacaacattggagtcaccacccagagtatcaattcttcgccttcgccactcaaatcaacgactacttcctcagctccgtcatccaaaaaaggccatatatctttttctggccatacatctgctcaagatgttgaactaaataatccagcataccttcagatatcccattcagtagacgataatcttctgaaaattaccactgagatttctggtaaaaacacgactgctaacgatattttgcacgatcttctccaacat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09HBa0036O20-VSZgt/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C09HBa0036O20.1" temp_strand="+" temp_description="C09HBa0036O20.1  AC216445.1 htgs_phase:2 submitted_to_sgn_as:gnl|gbrgsp|C09HBa0036O20 upload_account_name:spain (1 - 118462)">
        <position start="9490" stop="12363"/>
      </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="9790" g_stop="9903" g_length="114"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="114" r_length="114" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="9904" i_stop="10564" i_length="661">
            <donor d_prob="0.987" d_score="1.00"/>
            <acceptor a_prob="0.957" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="10565" g_stop="10845" g_length="281"/>
          <reference_exon_boundary r_type="cDNA" r_start="115" r_stop="395" r_length="281" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="10846" i_stop="11708" i_length="863">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.925" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="11709" g_stop="11744" g_length="36"/>
          <reference_exon_boundary r_type="cDNA" r_start="396" r_stop="431" r_length="36" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="11745" i_stop="11839" i_length="95">
            <donor d_prob="0.998" d_score="0.00"/>
            <acceptor a_prob="0.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="11840" g_stop="11916" g_length="77"/>
          <reference_exon_boundary r_type="cDNA" r_start="432" r_stop="508" r_length="77" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="11917" i_stop="12009" i_length="93">
            <donor d_prob="0.961" d_score="1.00"/>
            <acceptor a_prob="0.880" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="12010" g_stop="12063" g_length="54"/>
          <reference_exon_boundary r_type="cDNA" r_start="509" r_stop="562" r_length="54" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09HBa0036O20.1" gen_strand="+" ref_id="SGN-M872" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>562</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09HBa0036O20.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M872" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="9790" e_stop="9903"/>
          <exon e_start="10565" e_stop="10845"/>
          <exon e_start="11709" e_stop="11744"/>
          <exon e_start="11840" e_stop="11916"/>
          <exon e_start="12010" e_stop="12063"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CAGCACCCTGCGCGTCTTCTTCTTCTTCTTCTTCCTTCTCCGGCGAACGCGAACCCAGACCAGTCCATCTCGCCATCGCCGTCGCCGTCGCCGTGAGATAATCGTGAGACATATGTATTTATTTGAATTTGACAACTTGTATTTTAAATAATATTTGTGGATTTGTTGATATTTGCTTTCTTTCTAATCGGTCTGCTGAAACAAACAGAAGTACTGCTATATATATATATACATATTAATCACTGAATACAAGTTACAATGTAGAATACGCACAACAAAGTAAGGAGAGATTAACCGTAACCAGAAAGGGATGAGATACAAGACTACAGAAAGGAGATGAGAGGATTAGAAAGCCTAAGCTTCCACATAATAGTTTGCGTTACCGTTTGTTCCAACTCCTAGTCTTTTTGAGCGAATGGTGAATAATATTGTAGATTGTTGATATTTGGTTTCTTAAAGAGTTTTTCATCTAACTGTTATGCATAACTTACTTATAGGATAGGTGATATTGCCGAGCATTCATATTTGTATTTTCCACTTTTCAGTTTTCATAATGCTCAATAACTGTAATCAAAATCCCACACCATCTGTTTACAGAAGTGAATGCTTAGCTCCATTCATTTGTTTGCGATAATTAGGATATTTATAGTCATTGTTAAATCATATAAGATTTGTCTGGATTGTATCTTGGCCATTTAAGTGAATTGACCCAAACATTCTCATATCTATCAATTTAACACAATTTTGCTTAATTTTCAATTGTTATTATTATTAGTATTACCAAATATAAAGCTTGAAGGAGAGAGGGGAGCACAACAATGGCGAATGAAACAATGGCTGAACAACAAAAGAAACGAACGATGGAGGCATTAGAGCGAAGATTTGCTCAAGCAAAAGCTGAAATTCATCAACAGCAGCACAAGAACAAGAGAGTCGCTGTTACTACAACAAAAACTCTAGCTGAAAACAACATTGGAGTCACCACCCAGAGTATCAATTCTTCGCCTTCGCCACTCAAATCAACGACTACTTCCTCAGCTCCGTCATCCAAAAAAGGTTTCCTCTTTTATTTTTTTTCTCTGTTTCACTAGTTTTTAATATTTATCAGTCAACTATTGTGGCAGAGCCAAAATATTCATTAAAGGGTTCAAAATGAAGAATTAGGCCAAGGGGATAAAAAAATGTTTTTAGCCTTGTTTGTATATACAGGGTAATTTCTGTTGAATAAACCCCTTGCTTCTACCTGGCTCCACTCCTGAATTCAAGGAATCCTCTATATTCATGTTGTCTATGTTAATAATAGAATTCAACGTATTTTGTATTTTATGCCTGGATATCATAACCAGTATCTCGTTCATGTCTGTGCTTGCATTTGTTCACTCTCTTAGATGACAAAGTAGTTCTGCAAGTTTGAATTAGGTTCAAATATTCACCAAATTCAAATTTCTGTGCGAGATGCCCCGAATGCTCAATTGCTATACTTGAAGCCAATTCATATCCTTCTGTGATTCAAATAGGGTGAATATTATTATTGTAACAATCCTTGCTTGTTCTAGAATTGACTTAGCCATGAAAACAACTTCAATAATTCCATCACCAATTCTTGACTTTGCGCCAACTCAACCATCAAATTTGCAATCTGATTTCAATATATGGTTGCATCATCATTTCTGACATTGACATCCCTGTTAGGGTTCTGAAATCGGTGCTAAACTGTGAATTTTTCTTCTGATATTCTCTTTGATTTATCTGTAAACTTTTGGCATCCAAAAGCAGTGTAACAGTTGGCGTTTTCCAGGAATGTTAGTTAGACATTTTAATGTGATCCCTCTTAATTTCATCCTCCAAAAATAAAAATAAAAATAAAATGAACCCTTATTGATTTATCTCATCCAAACATTTTCCTGGTTTATTTGTAGGCCATATATCTTTTTCTGGCCATACATCTGCTCAAGGTACAACATTTCTCCGTATGCTTCTCTTGCATTTTATCTATAGAAAGGTATACATGAGACTAATCCAGGATGCTAAATTTTGTCCTACCACGTAGATGTTGAACTAAATAATCCAGCATACCTTCAGATATCCCATTCAGTAGACGATAATCTTCTGAAAATTACCACTGAGGTAAGAATAAACGTGATCAGTATGATGTTTCAAGGATGCACACAGCACACTATTAGTAAGTCGTTCATTGCTCATCCTGTTTGTTCGTTGCAGATTTCTGGTAAAAACACGACTGCTAACGATATTTTGCACGATCTTCTCCAACAT</genome_strand>
        <mrna_strand>CAGCACCCTGCGCGTCTTCTTCTTCTTCTTCTTCCTTCTCCGGCGAACGCGAACCCAGACCAGTCCATCTCGCCATCGCCGTCGCCGTCGCCGTGAGATAATCGTGAGACATAT.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TATTACCAAATATAAAGCTTGAAGGAGAGAGGGGAGCACAACAATGGCGAATGAAACAATGGCTGAACAACAAAAGAAACGAACGATGGAGGCATTAGAGCGAAGATTTGCTCAAGCAAAAGCTGAAATTCATCAACAGCAGCACAAGAACAAGAGAGTCGCTGTTACTACAACAAAAACTCTAGCTGAAAACAACATTGGAGTCACCACCCAGAGTATCAATTCTTCGCCTTCGCCACTCAAATCAACGACTACTTCCTCAGCTCCGTCATCCAAAAAAG...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCCATATATCTTTTTCTGGCCATACATCTGCTCAAG...............................................................................................ATGTTGAACTAAATAATCCAGCATACCTTCAGATATCCCATTCAGTAGACGATAATCTTCTGAAAATTACCACTGAG.............................................................................................ATTTCTGGTAAAAACACGACTGCTAACGATATTTTGCACGATCTTCTCCAACAT</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-y6fsIW/sgn_marker_seqs" ref_id="SGN-M872-2" ref_strand="+" ref_description="SGN-M872-2 SSR199-2 [est_by_read]">
      <seq>agcaccctgcgcgtcttcttcttcttcttcttccttctccggcgaacgcgaacccagaccagtccatctcgccatcgccgtcgccgtcgccgtgagataatcgtgagacatattattaccaaatataaagcttgaaggagagaggggagcacaacaatggcgaatgaaacaatggctgaacaacaaaagaaacgaacgatggaggcattagagcgaagatttgctcaagcaaaagctgaaattcatcaacagcagcacaagaacaagagagtcgctgttactacaacaaaaactctagctgaaaacaacattggagtcaccacccagagtatcaattcttcgccttcgccactcaaatcaacgactacttcctcagctccgtcatccaaaaaaggccatatatctttttctggccatacatctgctcaagatgttgaactaaataatccagcataccttcagatatcccattcagtagacgataatcttctgaaaattaccactgagatttctggtaaaaacacgactgctaacgatattttgcacgatcttctccaacatggtgattcagctcagaaatatatgcaggg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09HBa0036O20-VSZgt/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C09HBa0036O20.1" temp_strand="+" temp_description="C09HBa0036O20.1  AC216445.1 htgs_phase:2 submitted_to_sgn_as:gnl|gbrgsp|C09HBa0036O20 upload_account_name:spain (1 - 118462)">
        <position start="9491" stop="12392"/>
      </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="9791" g_stop="9903" g_length="113"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="113" r_length="113" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="9904" i_stop="10564" i_length="661">
            <donor d_prob="0.987" d_score="1.00"/>
            <acceptor a_prob="0.957" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="10565" g_stop="10845" g_length="281"/>
          <reference_exon_boundary r_type="cDNA" r_start="114" r_stop="394" r_length="281" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="10846" i_stop="11708" i_length="863">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.925" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="11709" g_stop="11744" g_length="36"/>
          <reference_exon_boundary r_type="cDNA" r_start="395" r_stop="430" r_length="36" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="11745" i_stop="11839" i_length="95">
            <donor d_prob="0.998" d_score="0.00"/>
            <acceptor a_prob="0.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="11840" g_stop="11916" g_length="77"/>
          <reference_exon_boundary r_type="cDNA" r_start="431" r_stop="507" r_length="77" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="11917" i_stop="12009" i_length="93">
            <donor d_prob="0.961" d_score="1.00"/>
            <acceptor a_prob="0.880" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="12010" g_stop="12092" g_length="83"/>
          <reference_exon_boundary r_type="cDNA" r_start="508" r_stop="590" r_length="83" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09HBa0036O20.1" gen_strand="+" ref_id="SGN-M872-2" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>590</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09HBa0036O20.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M872-2" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="9791" e_stop="9903"/>
          <exon e_start="10565" e_stop="10845"/>
          <exon e_start="11709" e_stop="11744"/>
          <exon e_start="11840" e_stop="11916"/>
          <exon e_start="12010" e_stop="12092"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGCACCCTGCGCGTCTTCTTCTTCTTCTTCTTCCTTCTCCGGCGAACGCGAACCCAGACCAGTCCATCTCGCCATCGCCGTCGCCGTCGCCGTGAGATAATCGTGAGACATATGTATTTATTTGAATTTGACAACTTGTATTTTAAATAATATTTGTGGATTTGTTGATATTTGCTTTCTTTCTAATCGGTCTGCTGAAACAAACAGAAGTACTGCTATATATATATATACATATTAATCACTGAATACAAGTTACAATGTAGAATACGCACAACAAAGTAAGGAGAGATTAACCGTAACCAGAAAGGGATGAGATACAAGACTACAGAAAGGAGATGAGAGGATTAGAAAGCCTAAGCTTCCACATAATAGTTTGCGTTACCGTTTGTTCCAACTCCTAGTCTTTTTGAGCGAATGGTGAATAATATTGTAGATTGTTGATATTTGGTTTCTTAAAGAGTTTTTCATCTAACTGTTATGCATAACTTACTTATAGGATAGGTGATATTGCCGAGCATTCATATTTGTATTTTCCACTTTTCAGTTTTCATAATGCTCAATAACTGTAATCAAAATCCCACACCATCTGTTTACAGAAGTGAATGCTTAGCTCCATTCATTTGTTTGCGATAATTAGGATATTTATAGTCATTGTTAAATCATATAAGATTTGTCTGGATTGTATCTTGGCCATTTAAGTGAATTGACCCAAACATTCTCATATCTATCAATTTAACACAATTTTGCTTAATTTTCAATTGTTATTATTATTAGTATTACCAAATATAAAGCTTGAAGGAGAGAGGGGAGCACAACAATGGCGAATGAAACAATGGCTGAACAACAAAAGAAACGAACGATGGAGGCATTAGAGCGAAGATTTGCTCAAGCAAAAGCTGAAATTCATCAACAGCAGCACAAGAACAAGAGAGTCGCTGTTACTACAACAAAAACTCTAGCTGAAAACAACATTGGAGTCACCACCCAGAGTATCAATTCTTCGCCTTCGCCACTCAAATCAACGACTACTTCCTCAGCTCCGTCATCCAAAAAAGGTTTCCTCTTTTATTTTTTTTCTCTGTTTCACTAGTTTTTAATATTTATCAGTCAACTATTGTGGCAGAGCCAAAATATTCATTAAAGGGTTCAAAATGAAGAATTAGGCCAAGGGGATAAAAAAATGTTTTTAGCCTTGTTTGTATATACAGGGTAATTTCTGTTGAATAAACCCCTTGCTTCTACCTGGCTCCACTCCTGAATTCAAGGAATCCTCTATATTCATGTTGTCTATGTTAATAATAGAATTCAACGTATTTTGTATTTTATGCCTGGATATCATAACCAGTATCTCGTTCATGTCTGTGCTTGCATTTGTTCACTCTCTTAGATGACAAAGTAGTTCTGCAAGTTTGAATTAGGTTCAAATATTCACCAAATTCAAATTTCTGTGCGAGATGCCCCGAATGCTCAATTGCTATACTTGAAGCCAATTCATATCCTTCTGTGATTCAAATAGGGTGAATATTATTATTGTAACAATCCTTGCTTGTTCTAGAATTGACTTAGCCATGAAAACAACTTCAATAATTCCATCACCAATTCTTGACTTTGCGCCAACTCAACCATCAAATTTGCAATCTGATTTCAATATATGGTTGCATCATCATTTCTGACATTGACATCCCTGTTAGGGTTCTGAAATCGGTGCTAAACTGTGAATTTTTCTTCTGATATTCTCTTTGATTTATCTGTAAACTTTTGGCATCCAAAAGCAGTGTAACAGTTGGCGTTTTCCAGGAATGTTAGTTAGACATTTTAATGTGATCCCTCTTAATTTCATCCTCCAAAAATAAAAATAAAAATAAAATGAACCCTTATTGATTTATCTCATCCAAACATTTTCCTGGTTTATTTGTAGGCCATATATCTTTTTCTGGCCATACATCTGCTCAAGGTACAACATTTCTCCGTATGCTTCTCTTGCATTTTATCTATAGAAAGGTATACATGAGACTAATCCAGGATGCTAAATTTTGTCCTACCACGTAGATGTTGAACTAAATAATCCAGCATACCTTCAGATATCCCATTCAGTAGACGATAATCTTCTGAAAATTACCACTGAGGTAAGAATAAACGTGATCAGTATGATGTTTCAAGGATGCACACAGCACACTATTAGTAAGTCGTTCATTGCTCATCCTGTTTGTTCGTTGCAGATTTCTGGTAAAAACACGACTGCTAACGATATTTTGCACGATCTTCTCCAACATGGTGATTCAGCTCAGAAATATATGCAGGG</genome_strand>
        <mrna_strand>AGCACCCTGCGCGTCTTCTTCTTCTTCTTCTTCCTTCTCCGGCGAACGCGAACCCAGACCAGTCCATCTCGCCATCGCCGTCGCCGTCGCCGTGAGATAATCGTGAGACATAT.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TATTACCAAATATAAAGCTTGAAGGAGAGAGGGGAGCACAACAATGGCGAATGAAACAATGGCTGAACAACAAAAGAAACGAACGATGGAGGCATTAGAGCGAAGATTTGCTCAAGCAAAAGCTGAAATTCATCAACAGCAGCACAAGAACAAGAGAGTCGCTGTTACTACAACAAAAACTCTAGCTGAAAACAACATTGGAGTCACCACCCAGAGTATCAATTCTTCGCCTTCGCCACTCAAATCAACGACTACTTCCTCAGCTCCGTCATCCAAAAAAG...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCCATATATCTTTTTCTGGCCATACATCTGCTCAAG...............................................................................................ATGTTGAACTAAATAATCCAGCATACCTTCAGATATCCCATTCAGTAGACGATAATCTTCTGAAAATTACCACTGAG.............................................................................................ATTTCTGGTAAAAACACGACTGCTAACGATATTTTGCACGATCTTCTCCAACATGGTGATTCAGCTCAGAAATATATGCAGGG</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="9790" PGL_stop="12092"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="9790" e_stop="9903"/>
            <exon e_start="10565" e_stop="10845"/>
            <exon e_start="11709" e_stop="11744"/>
            <exon e_start="11840" e_stop="11916"/>
            <exon e_start="12010" e_stop="12092"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.987" acc_prob="0.957" e_score="1.000"/>
          <exon-intron don_prob="0.999" acc_prob="0.925" e_score="1.000"/>
          <exon-intron don_prob="0.998" acc_prob="0.000" e_score="1.000"/>
          <exon-intron don_prob="0.961" acc_prob="0.880" 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="9790" e_stop="9903" e_length="114"/>
          </exon>
          <intron i_serial="1" don_prob="0.987" acc_prob="0.957">
            <gDNA_intron_boundary i_start="9904" i_stop="10564" i_length="661"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="10565" e_stop="10845" e_length="281"/>
          </exon>
          <intron i_serial="2" don_prob="0.999" acc_prob="0.925">
            <gDNA_intron_boundary i_start="10846" i_stop="11708" i_length="863"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="11709" e_stop="11744" e_length="36"/>
          </exon>
          <intron i_serial="3" don_prob="0.998" acc_prob="0.000">
            <gDNA_intron_boundary i_start="11745" i_stop="11839" i_length="95"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="11840" e_stop="11916" e_length="77"/>
          </exon>
          <intron i_serial="4" don_prob="0.961" acc_prob="0.880">
            <gDNA_intron_boundary i_start="11917" i_stop="12009" i_length="93"/>
          </intron>
          <exon e_serial="5" e_score="1.000">
            <gDNA_exon_boundary e_start="12010" e_stop="12092" e_length="83"/>
          </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="9790" stop="9903"/>
              <exon start="10565" stop="10845"/>
              <exon start="11709" stop="11744"/>
              <exon start="11840" stop="11916"/>
              <exon start="12010" stop="12063"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M872" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="9791" stop="9903"/>
              <exon start="10565" stop="10845"/>
              <exon start="11709" stop="11744"/>
              <exon start="11840" stop="11916"/>
              <exon start="12010" stop="12092"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M872-2" 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>CAGCACCCTGCGCGTCTTCTTCTTCTTCTTCTTCCTTCTCCGGCGAACGCGAACCCAGACCAGTCCATCTCGCCATCGCCGTCGCCGTCGCCGTGAGATAATCGTGAGACATAT : TATTACCAAATATAAAGCTTGAAGGAGAGAGGGGAGCACAACAATGGCGAATGAAACAATGGCTGAACAACAAAAGAAACGAACGATGGAGGCATTAGAGCGAAGATTTGCTCAAGCAAAAGCTGAAATTCATCAACAGCAGCACAAGAACAAGAGAGTCGCTGTTACTACAACAAAAACTCTAGCTGAAAACAACATTGGAGTCACCACCCAGAGTATCAATTCTTCGCCTTCGCCACTCAAATCAACGACTACTTCCTCAGCTCCGTCATCCAAAAAAG : GCCATATATCTTTTTCTGGCCATACATCTGCTCAAG : ATGTTGAACTAAATAATCCAGCATACCTTCAGATATCCCATTCAGTAGACGATAATCTTCTGAAAATTACCACTGAG : ATTTCTGGTAAAAACACGACTGCTAACGATATTTTGCACGATCTTCTCCAACATGGTGATTCAGCTCAGAAATATATGCAGGG</gDNA_template>
            <first_frame> Q  H  P  A  R  L  L  L  L  L  L  P  S  P  A  N  A  N  P  D  Q  S  I  S  P  S  P  S  P  S  P  *  D  N  R  E  T  Y  :  Y  Y  Q  I  *  S  L  K  E  R  G  E  H  N  N  G  E  *  N  N  G  *  T  T  K  E  T  N  D  G  G  I  R  A  K  I  C  S  S  K  S  *  N  S  S  T  A  A  Q  E  Q  E  S  R  C  Y  Y  N  K  N  S  S  *  K  Q  H  W  S  H  H  P  E  Y  Q  F  F  A  F  A  T  Q  I  N  D  Y  F  L  S  S  V  I  Q  K  R :   P  Y  I  F  F  W  P  Y  I  C  S  R :   C  *  T  K  *  S  S  I  P  S  D  I  P  F  S  R  R  *  S  S  E  N  Y  H  *   : D  F  W  *  K  H  D  C  *  R  Y  F  A  R  S  S  P  T  W  *  F  S  S  E  I  Y  A  G </first_frame>
            <second_frame>  S  T  L  R  V  F  F  F  F  F  F  L  L  R  R  T  R  T  Q  T  S  P  S  R  H  R  R  R  R  R  R  E  I  I  V  R  H  I :   I  T  K  Y  K  A  *  R  R  E  G  S  T  T  M  A  N  E  T  M  A  E  Q  Q  K  K  R  T  M  E  A  L  E  R  R  F  A  Q  A  K  A  E  I  H  Q  Q  Q  H  K  N  K  R  V  A  V  T  T  T  K  T  L  A  E  N  N  I  G  V  T  T  Q  S  I  N  S  S  P  S  P  L  K  S  T  T  T  S  S  A  P  S  S  K  K   : G  H  I  S  F  S  G  H  T  S  A  Q   : D  V  E  L  N  N  P  A  Y  L  Q  I  S  H  S  V  D  D  N  L  L  K  I  T  T  E  :  I  S  G  K  N  T  T  A  N  D  I  L  H  D  L  L  Q  H  G  D  S  A  Q  K  Y  M  Q   </second_frame>
            <third_frame>   A  P  C  A  S  S  S  S  S  S  S  F  S  G  E  R  E  P  R  P  V  H  L  A  I  A  V  A  V  A  V  R  *  S  *  D  I   : L  L  P  N  I  K  L  E  G  E  R  G  A  Q  Q  W  R  M  K  Q  W  L  N  N  K  R  N  E  R  W  R  H  *  S  E  D  L  L  K  Q  K  L  K  F  I  N  S  S  T  R  T  R  E  S  L  L  L  Q  Q  K  L  *  L  K  T  T  L  E  S  P  P  R  V  S  I  L  R  L  R  H  S  N  Q  R  L  L  P  Q  L  R  H  P  K  K  :  A  I  Y  L  F  L  A  I  H  L  L  K  :  M  L  N  *  I  I  Q  H  T  F  R  Y  P  I  Q  *  T  I  I  F  *  K  L  P  L  R :   F  L  V  K  T  R  L  L  T  I  F  C  T  I  F  S  N  M  V  I  Q  L  R  N  I  C  R  </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C09HBa0036O20.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="10587" stop="10845"/>
                    <exon start="11709" stop="11744"/>
                    <exon start="11840" stop="11916"/>
                    <exon start="12010" stop="12090"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>453</number_coding_nucleotides>
                  <number_encoded_amino_acids>151</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>RREGSTTMANETMAEQQKKRTMEALERRFAQAKAEIHQQQHKNKRVAVTTTKTLAENNIGVTTQSINSSPSPLKSTTTSSAPSSKKGHISFSGHTSAQDVELNNPAYLQISHSVDDNLLKITTEISGKNTTANDILHDLLQHGDSAQKYMQ</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:
$ 4560 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 2280 bytes was the average size of a spliced alignment
$ 5656 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5656 bytes was the average size of a predicted gene location
$ 2 megabytes was the average size of the backtrace matrix
$ 16 backtrace matrices have been allocated
$ 
$ date finished: 2008-02-20 11:28:05
-->
