<?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="2009-01-16 20:42:21"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C06HBa0066P09-je666/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C06HBa0066P09-je666/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" type="ESTcDNA"/>
    </reference_files>
    <splice_site_parameters parameter_type="Bayesian" species="arabidopsis"/>
    <parameters>
      <parameter name="bssmfile" value="arabidopsis"/>
      <parameter name="scorematrixfile" value="BLOSUM62"/>
      <parameter name="searchmode" value="forward=True,reverse=True)"/>
      <parameter name="translationtable" value="1"/>
      <parameter name="frompos" value="0"/>
      <parameter name="topos" value="0"/>
      <parameter name="width" value="0"/>
      <parameter name="verbose" value="False"/>
      <parameter name="skipalignmentout" value="False"/>
      <parameter name="showintronmaxlen" value="120"/>
      <parameter name="minorflen" value="64"/>
      <parameter name="showseqnums" value="False"/>
      <parameter name="gs2out" value="False"/>
      <parameter name="maskpolyatails" value="False"/>
      <parameter name="noautoindex" value="False"/>
      <parameter name="minmatchlen" value="20"/>
      <parameter name="seedlength" value="16"/>
      <parameter name="exdrop" value="2"/>
      <parameter name="online" value="False"/>
      <parameter name="inverse" value="False"/>
      <parameter name="exact" value="False"/>
      <parameter name="chainwf" value="0.500000"/>
      <parameter name="gcmaxgapwidth" value="1000000"/>
      <parameter name="gcmincoverage" value="50"/>
      <parameter name="introncutout" value="False"/>
      <parameter name="autointroncutout" value="0"/>
      <parameter name="icinitialdelta" value="50"/>
      <parameter name="iciterations" value="2"/>
      <parameter name="icdeltaincrease" value="50"/>
      <parameter name="icminremintronlen" value="10"/>
      <parameter name="nou12intronmodel" value="False"/>
      <parameter name="u12donorprob" value="0.990000"/>
      <parameter name="u12donorprob1mism" value="0.900000"/>
      <parameter name="probies" value="0.500000"/>
      <parameter name="probdelgen" value="0.030000"/>
      <parameter name="identityweight" value="2.000000"/>
      <parameter name="mismatchweight" value="-2.000000"/>
      <parameter name="undetcharweight" value="0.000000"/>
      <parameter name="deletionweight" value="-4.000000"/>
      <parameter name="dpminexonlen" value="5"/>
      <parameter name="dpminintronlen" value="50"/>
      <parameter name="shortexonpenal" value="100"/>
      <parameter name="shortintronpenal" value="100"/>
      <parameter name="wzerotransition" value="80"/>
      <parameter name="wdecreasedoutput" value="80"/>
      <parameter name="leadcutoffsmode" value="RELAXED"/>
      <parameter name="termcutoffsmode" value="STRICT"/>
      <parameter name="cutoffsminexonlen" value="5"/>
      <parameter name="scoreminexonlen" value="50"/>
      <parameter name="minaveragessp" value="0.500000"/>
      <parameter name="minalignmentscore" value="0.900000"/>
      <parameter name="maxalignmentscore" value="1.000000"/>
      <parameter name="mincoverage" value="0.900000"/>
      <parameter name="maxcoverage" value="100.000000"/>
      <parameter name="intermediate" value="False"/>
      <parameter name="sortags" value="False"/>
      <parameter name="sortagswf" value="1.000000"/>
      <parameter name="first" value="0"/>
      <parameter name="exondistri" value="False"/>
      <parameter name="introndistri" value="False"/>
      <parameter name="refseqcovdistri" value="False"/>
    </parameters>
    <overall_reference_type>ESTcDNA</overall_reference_type>
  </header>
  <alignment_module>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C06HBa0066P09-je666/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U324842" ref_strand="+" ref_description="SGN-U324842        Tomato 200607 #1 [5 ESTs aligned] arabidopsis/peptide: | Symbol: None | zinc knuckle (CCHC-type) family protein, contains Pfam domain, PF00098: Zinc knuckle | chr2:3820372-3820734 REVERSE | Aliases: F7B19.19, F7B19_19(evalue: 4e-09, score=58.5) genbank/nr: gi|53689765|gb|AAU89775.1| pol polyprotein-like [Solanum tuberosum] (evalue: 2e-102, score=374)">
      <seq>taaggttgagaatcgaagaggataataaggctgcagaaaagaggtcacgtggtaattcagcaatatctggagtaaattttgttgaagaagattccacaaaattcaagaaaagaaagaaagcatctggtccaaaacgcaatcctcctaagaagaaattcaatggaaactgctttaattgtggtaaacatggtcatagggctaatgaatgccggggtcctaagaaggacaagaaaaagaaggatcaagcaaacttggctgaatccaaaggagaaatggacgatctctgtgcaatgctttcagaatgtaacttggttggaaatccaagagaatggtggatagattctggtgcctcatgccatgtttgtgccaacaaagaattattttcatcatatactctagcacttacagatgaaaaattatttatggcaaactccgctgttgcaaaggtggaaggaactggcaaagtcctattaaagatgacatcaggcaaggtagtgactttgaatatggtctcatatgttccagaattgagaaataatttagtttcaattccaattctgaccaagaatggatttaaatgtgtatttgtttttgataaagtagtagtaagcaaaaatgatatgtatgtaggaaaagactaccttagtgatggccttttcaaactcaatgtaattgcagttgatatgaataaagattttgcttctttttaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C06HBa0066P09-je666/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C06HBa0066P09.1" temp_strand="+" temp_description="C06HBa0066P09.1  AC211037.1 htgs_phase:1 submitted_to_sgn_as:C06HBa0066P09 sequenced_by:cbsg upload_account_name:netherlands [organism=Solanum lycopersicum]">
        <position start="30643" stop="31941"/>
      </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="30943" g_stop="31641" g_length="699"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="709" r_length="709" r_score="0.926"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="710" polyA_stop="744"/>
      <MATCH_line gen_id="C06HBa0066P09.1" gen_strand="+" ref_id="SGN-U324842" ref_strand="+">
        <total_alignment_score>0.926</total_alignment_score>
        <cumulative_length_of_scored_exons>699</cumulative_length_of_scored_exons>
        <coverage percentage="0.940" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C06HBa0066P09.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U324842" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="30943" e_stop="31641"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TAAGGTTGAAAAATCGAAGAGGATAATAAGGCTGCAGAAAAGAGGTCACGTGGTAATTCAGCAATATCTGGAGTAAATTTTGTTGAAGAAGATTCCACAAAATTAAAGAAAAGAAAGAAAGCATCTGGTCCAAAAAACAATCCTCCTAAGAAGAAATTCAATGGAAACTACTTTAATTGTGGTAAACATGATCATAGGTCTAATGAATGCCGGGGTCCTAAGAAGGACAAGAAAAAGAAGGATCAAGCAAACTTGGCTGAATCCAAATGAGAAATGGACGATCTCTGTGCAATGCTTTCAGAATGTAACTTTGTTTGAAATCCAAGAGAATGGTGGATAGATTCTGGTGCCTCATTCCATGTGTGTGCCAACAAAGAATTATTTTCATCATATACTCCAGCACTTGCAGATGAAAAATTGTTTATGGCAAACTCCGTTGTTGCAAAGGTAGAAGTAACTGGCAAAGTCCTATTGAAGATGCTATCAGGCAAGGTGGTGACTTTGAATAGGGTCTCATATGTTCC-------AG----AATTTAGTTTCAATTCCATTTCTGACCAAGAATGGATTTAAATGTGTATTTGTTTCTAATAAAGTAGTAGTAAGCAAAAATGATATGTATGTAGGACAAGTCTACCTTAGTGATGGCCTTTTCAAACTCAATGTAATTGCAGTTGATATGAATAAAGATTTTGCTTCTTCTTA</genome_strand>
        <mrna_strand>TAAGGTTG-AGAATCGAAGAGGATAATAAGGCTGCAGAAAAGAGGTCACGTGGTAATTCAGCAATATCTGGAGTAAATTTTGTTGAAGAAGATTCCACAAAATTCAAGAAAAGAAAGAAAGCATCTGGTCCAAAACGCAATCCTCCTAAGAAGAAATTCAATGGAAACTGCTTTAATTGTGGTAAACATGGTCATAGGGCTAATGAATGCCGGGGTCCTAAGAAGGACAAGAAAAAGAAGGATCAAGCAAACTTGGCTGAATCCAAAGGAGAAATGGACGATCTCTGTGCAATGCTTTCAGAATGTAACTTGGTTGGAAATCCAAGAGAATGGTGGATAGATTCTGGTGCCTCATGCCATGTTTGTGCCAACAAAGAATTATTTTCATCATATACTCTAGCACTTACAGATGAAAAATTATTTATGGCAAACTCCGCTGTTGCAAAGGTGGAAGGAACTGGCAAAGTCCTATTAAAGATGACATCAGGCAAGGTAGTGACTTTGAATATGGTCTCATATGTTCCAGAATTGAGAAATAATTTAGTTTCAATTCCAATTCTGACCAAGAATGGATTTAAATGTGTATTTGTTTTTGATAAAGTAGTAGTAAGCAAAAATGATATGTATGTAGGAAAAGACTACCTTAGTGATGGCCTTTTCAAACTCAATGTAATTGCAGTTGATATGAATAAAGATTTTGCTTCTTTTTA</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-C06HBa0066P09-je666/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U336908" ref_strand="+" ref_description="SGN-U336908        Tomato 200607 #1 [1 ESTs aligned] arabidopsis/peptide: | Symbol: None | pentatricopeptide (PPR) repeat-containing protein, low similarity to fertility restorer (Petunia x hybrida) GI:22128587, post-transcriptional control of chloroplast gene expression CRP1 (Zea mays) GI:3289002; contains Pfam profile PF01535: PPR repeat | chr2:13394081-13397783 REVERSE | Aliases: T28P16.11, T28P16_11(evalue: 5e-36, score=147) genbank/nr: gi|15224671|ref|NP_180698.1| pentatricopeptide (PPR) repeat-containing protein [Arabidopsis thaliana] gi|25408152|pir||C84720 hypothetical protein At2g31400 [imported] - Arabidopsis thaliana gi|4589961|gb|AAD26479.1| unknown protein [Arabidopsis thaliana](evalue: 3e-34, score=147)">
      <seq>actgactcatgtttggtgtcttatctaacttttttccagaaacaaggtgctcaattggttgtacttgaaggaaaacgttcggaagtgctcaattggttgttaactgactaatatcacctttgcattgccataaattaccactgactcatatttggtgtcttatctaacttttttccagaaacaaggtgctcaattggttgtacttgaaggaaaacgttcggaagtgctcaattggttgttaactgactaatatcacctttgcattgccataaattactactgactcatatttggtgtcttatctaacttttttccagaaacaaggtgctcaattggttgtacttgaaggaaaacgttcagaagtgtgggaaaatacatggtccacttcttgtttggatctgcatttgatgtcttcaggggctgcatgtgcaatggtccacgcatggttgcttagtatacggtctatagtgtttgaaggccacgagttaccaaagatgctgagcattttgactggctggggcaagcacagcaagataacaggtgat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C06HBa0066P09-je666/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C06HBa0066P09.1" temp_strand="+" temp_description="C06HBa0066P09.1  AC211037.1 htgs_phase:1 submitted_to_sgn_as:C06HBa0066P09 sequenced_by:cbsg upload_account_name:netherlands [organism=Solanum lycopersicum]">
        <position start="40171" stop="41407"/>
      </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="40471" g_stop="40972" g_length="502"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="502" r_length="502" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="40973" i_stop="41064" i_length="92">
            <donor d_prob="0.993" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="41065" g_stop="41107" g_length="43"/>
          <reference_exon_boundary r_type="cDNA" r_start="503" r_stop="545" r_length="43" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C06HBa0066P09.1" gen_strand="+" ref_id="SGN-U336908" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>545</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C06HBa0066P09.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U336908" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="40471" e_stop="40972"/>
          <exon e_start="41065" e_stop="41107"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ACTGACTCATGTTTGGTGTCTTATCTAACTTTTTTCCAGAAACAAGGTGCTCAATTGGTTGTACTTGAAGGAAAACGTTCGGAAGTGCTCAATTGGTTGTTAACTGACTAATATCACCTTTGCATTGCCATAAATTACCACTGACTCATATTTGGTGTCTTATCTAACTTTTTTCCAGAAACAAGGTGCTCAATTGGTTGTACTTGAAGGAAAACGTTCGGAAGTGCTCAATTGGTTGTTAACTGACTAATATCACCTTTGCATTGCCATAAATTACTACTGACTCATATTTGGTGTCTTATCTAACTTTTTTCCAGAAACAAGGTGCTCAATTGGTTGTACTTGAAGGAAAACGTTCAGAAGTGTGGGAAAATACATGGTCCACTTCTTGTTTGGATCTGCATTTGATGTCTTCAGGGGCTGCATGTGCAATGGTCCACGCATGGTTGCTTAGTATACGGTCTATAGTGTTTGAAGGCCACGAGTTACCAAAGATGCTGAGGTATTTCCTCTAATTCTCTTATATTTTTTTCAAAGTCGGACAAACTACAAGAGTGATATATAATGAATGAAATGTTCAACTGTCCTCTGCAGCATTTTGACTGGCTGGGGCAAGCACAGCAAGATAACAGGTGAT</genome_strand>
        <mrna_strand>ACTGACTCATGTTTGGTGTCTTATCTAACTTTTTTCCAGAAACAAGGTGCTCAATTGGTTGTACTTGAAGGAAAACGTTCGGAAGTGCTCAATTGGTTGTTAACTGACTAATATCACCTTTGCATTGCCATAAATTACCACTGACTCATATTTGGTGTCTTATCTAACTTTTTTCCAGAAACAAGGTGCTCAATTGGTTGTACTTGAAGGAAAACGTTCGGAAGTGCTCAATTGGTTGTTAACTGACTAATATCACCTTTGCATTGCCATAAATTACTACTGACTCATATTTGGTGTCTTATCTAACTTTTTTCCAGAAACAAGGTGCTCAATTGGTTGTACTTGAAGGAAAACGTTCAGAAGTGTGGGAAAATACATGGTCCACTTCTTGTTTGGATCTGCATTTGATGTCTTCAGGGGCTGCATGTGCAATGGTCCACGCATGGTTGCTTAGTATACGGTCTATAGTGTTTGAAGGCCACGAGTTACCAAAGATGCTGAG............................................................................................CATTTTGACTGGCTGGGGCAAGCACAGCAAGATAACAGGTGAT</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-C06HBa0066P09-je666/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U328315" ref_strand="+" ref_description="SGN-U328315        Tomato 200607 #1 [3 ESTs aligned] arabidopsis/peptide: | Symbol: None | expressed protein | chr2:19418630-19419221 REVERSE | Aliases: T8I13.11(evalue: 2e-10, score=62.4) genbank/nr: gi|18407313|ref|NP_566098.1| expressed protein [Arabidopsis thaliana] gi|25370835|pir||B84913 hypothetical protein At2g47270 [imported] - Arabidopsis thaliana gi|2275205|gb|AAB63827.1| expressed protein [Arabidopsis thaliana](evalue: 1e-08, score=62.4)">
      <seq>taaagattcaacatatataaacataatttcttatgggtattttttctcatactcctaacaagggaaagtttgatttaagcgattccttccaacgccatataaggagacaaagagtcacgacttataacgtaaggcatgtcaaaagacgcaaaagtgttgtgatgaagagaaggatacgcgtagaacgttctagaaggttcgaggatgagattggaagtaaagtcaagatactcaagaagttgattccaattaactgtgaagatttggggctggaagggattttcagagagacagctgattacattttggctttagaaatgagaattaaggctatgcaagatatggtaaatgtattgtcacattctaatcactaaatcatgtattattttattattatattgtgtcaaaaatgacttatatacagattaattaactgatgttgtttctttgttcattcatcaatgttaatgtgaatgtctacaattgtgaaattgcaaaactatatagttatgtaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C06HBa0066P09-je666/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C06HBa0066P09.1" temp_strand="+" temp_description="C06HBa0066P09.1  AC211037.1 htgs_phase:1 submitted_to_sgn_as:C06HBa0066P09 sequenced_by:cbsg upload_account_name:netherlands [organism=Solanum lycopersicum]">
        <position start="42795" stop="43910"/>
      </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="43095" g_stop="43610" g_length="516"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="516" r_length="516" r_score="0.990"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="517" polyA_stop="565"/>
      <MATCH_line gen_id="C06HBa0066P09.1" gen_strand="+" ref_id="SGN-U328315" ref_strand="+">
        <total_alignment_score>0.990</total_alignment_score>
        <cumulative_length_of_scored_exons>516</cumulative_length_of_scored_exons>
        <coverage percentage="0.913" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C06HBa0066P09.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U328315" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="43095" e_stop="43610"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TAAAGATTCAACATATATAAACATAATTTCTTATGGGTATTTTTTCTCATACTCCTAACAAGGGAAAGTTTGATTTAAGCGATTCCTTCCAATGCGATATAAGCAGACAAAGAGTCACGACTTATAACGTAAGGCATGTCAAAAGGTGCAAAAGTGTTGTGATGAAGAGAAGGATACGCGTAGAACGTTCTAGAAGGTTCGAGGATGAGATTGGAAGTAAAGTCAAGATACTCAAGAAGTTGATTCCAATTAACTGTGAAGATTTGGGGCTGGAAGGGATTTTCAGAGAGACAGCTGATTACATTTTGGCTTTAGAAATGAGAATTAAGGCTATGCAAGATATGGTAAATGTATTGTCACATTCTAATCACTAAATCATGTATTATTTTATTATTATATTGTGTCAAAAATGACTTATATACAGATTAATTAACTGATGTTGTTTCTTTGTTCATTCATCAATGTTAATGTGAATGTCTACAATTGTGAAATTGCAAAACTATATAGTTATGTAAA</genome_strand>
        <mrna_strand>TAAAGATTCAACATATATAAACATAATTTCTTATGGGTATTTTTTCTCATACTCCTAACAAGGGAAAGTTTGATTTAAGCGATTCCTTCCAACGCCATATAAGGAGACAAAGAGTCACGACTTATAACGTAAGGCATGTCAAAAGACGCAAAAGTGTTGTGATGAAGAGAAGGATACGCGTAGAACGTTCTAGAAGGTTCGAGGATGAGATTGGAAGTAAAGTCAAGATACTCAAGAAGTTGATTCCAATTAACTGTGAAGATTTGGGGCTGGAAGGGATTTTCAGAGAGACAGCTGATTACATTTTGGCTTTAGAAATGAGAATTAAGGCTATGCAAGATATGGTAAATGTATTGTCACATTCTAATCACTAAATCATGTATTATTTTATTATTATATTGTGTCAAAAATGACTTATATACAGATTAATTAACTGATGTTGTTTCTTTGTTCATTCATCAATGTTAATGTGAATGTCTACAATTGTGAAATTGCAAAACTATATAGTTATGTAAA</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="30943" PGL_stop="31641"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="30943" e_stop="31641"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.926"/>
        </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="0.926">
            <gDNA_exon_boundary e_start="30943" e_stop="31641" e_length="699"/>
          </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="30943" stop="31641"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U324842" 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>TAAGGTTGAAAAATCGAAGAGGATAATAAGGCTGCAGAAAAGAGGTCACGTGGTAATTCAGCAATATCTGGAGTAAATTTTGTTGAAGAAGATTCCACAAAATTAAAGAAAAGAAAGAAAGCATCTGGTCCAAAAAACAATCCTCCTAAGAAGAAATTCAATGGAAACTACTTTAATTGTGGTAAACATGATCATAGGTCTAATGAATGCCGGGGTCCTAAGAAGGACAAGAAAAAGAAGGATCAAGCAAACTTGGCTGAATCCAAATGAGAAATGGACGATCTCTGTGCAATGCTTTCAGAATGTAACTTTGTTTGAAATCCAAGAGAATGGTGGATAGATTCTGGTGCCTCATTCCATGTGTGTGCCAACAAAGAATTATTTTCATCATATACTCCAGCACTTGCAGATGAAAAATTGTTTATGGCAAACTCCGTTGTTGCAAAGGTAGAAGTAACTGGCAAAGTCCTATTGAAGATGCTATCAGGCAAGGTGGTGACTTTGAATAGGGTCTCATATGTTCCAGAATTTAGTTTCAATTCCATTTCTGACCAAGAATGGATTTAAATGTGTATTTGTTTCTAATAAAGTAGTAGTAAGCAAAAATGATATGTATGTAGGACAAGTCTACCTTAGTGATGGCCTTTTCAAACTCAATGTAATTGCAGTTGATATGAATAAAGATTTTGCTTCTTCTTA</gDNA_template>
            <first_frame> *  G  *  K  I  E  E  D  N  K  A  A  E  K  R  S  R  G  N  S  A  I  S  G  V  N  F  V  E  E  D  S  T  K  L  K  K  R  K  K  A  S  G  P  K  N  N  P  P  K  K  K  F  N  G  N  Y  F  N  C  G  K  H  D  H  R  S  N  E  C  R  G  P  K  K  D  K  K  K  K  D  Q  A  N  L  A  E  S  K  *  E  M  D  D  L  C  A  M  L  S  E  C  N  F  V  *  N  P  R  E  W  W  I  D  S  G  A  S  F  H  V  C  A  N  K  E  L  F  S  S  Y  T  P  A  L  A  D  E  K  L  F  M  A  N  S  V  V  A  K  V  E  V  T  G  K  V  L  L  K  M  L  S  G  K  V  V  T  L  N  R  V  S  Y  V  P  E  F  S  F  N  S  I  S  D  Q  E  W  I  *  M  C  I  C  F  *  *  S  S  S  K  Q  K  *  Y  V  C  R  T  S  L  P  *  *  W  P  F  Q  T  Q  C  N  C  S  *  Y  E  *  R  F  C  F  F  L </first_frame>
            <second_frame>  K  V  E  K  S  K  R  I  I  R  L  Q  K  R  G  H  V  V  I  Q  Q  Y  L  E  *  I  L  L  K  K  I  P  Q  N  *  R  K  E  R  K  H  L  V  Q  K  T  I  L  L  R  R  N  S  M  E  T  T  L  I  V  V  N  M  I  I  G  L  M  N  A  G  V  L  R  R  T  R  K  R  R  I  K  Q  T  W  L  N  P  N  E  K  W  T  I  S  V  Q  C  F  Q  N  V  T  L  F  E  I  Q  E  N  G  G  *  I  L  V  P  H  S  M  C  V  P  T  K  N  Y  F  H  H  I  L  Q  H  L  Q  M  K  N  C  L  W  Q  T  P  L  L  Q  R  *  K  *  L  A  K  S  Y  *  R  C  Y  Q  A  R  W  *  L  *  I  G  S  H  M  F  Q  N  L  V  S  I  P  F  L  T  K  N  G  F  K  C  V  F  V  S  N  K  V  V  V  S  K  N  D  M  Y  V  G  Q  V  Y  L  S  D  G  L  F  K  L  N  V  I  A  V  D  M  N  K  D  F  A  S  S   </second_frame>
            <third_frame>   R  L  K  N  R  R  G  *  *  G  C  R  K  E  V  T  W  *  F  S  N  I  W  S  K  F  C  *  R  R  F  H  K  I  K  E  K  K  E  S  I  W  S  K  K  Q  S  S  *  E  E  I  Q  W  K  L  L  *  L  W  *  T  *  S  *  V  *  *  M  P  G  S  *  E  G  Q  E  K  E  G  S  S  K  L  G  *  I  Q  M  R  N  G  R  S  L  C  N  A  F  R  M  *  L  C  L  K  S  K  R  M  V  D  R  F  W  C  L  I  P  C  V  C  Q  Q  R  I  I  F  I  I  Y  S  S  T  C  R  *  K  I  V  Y  G  K  L  R  C  C  K  G  R  S  N  W  Q  S  P  I  E  D  A  I  R  Q  G  G  D  F  E  *  G  L  I  C  S  R  I  *  F  Q  F  H  F  *  P  R  M  D  L  N  V  Y  L  F  L  I  K  *  *  *  A  K  M  I  C  M  *  D  K  S  T  L  V  M  A  F  S  N  S  M  *  L  Q  L  I  *  I  K  I  L  L  L  L  </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C06HBa0066P09.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="30952" stop="31212"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>258</number_coding_nucleotides>
                  <number_encoded_amino_acids>86</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>KIEEDNKAAEKRSRGNSAISGVNFVEEDSTKLKKRKKASGPKNNPPKKKFNGNYFNCGKHDHRSNECRGPKKDKKKKDQANLAESK*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C06HBa0066P09.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="31261" stop="31509"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>246</number_coding_nucleotides>
                  <number_encoded_amino_acids>82</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>NPREWWIDSGASFHVCANKELFSSYTPALADEKLFMANSVVAKVEVTGKVLLKMLSGKVVTLNRVSYVPEFSFNSISDQEWI*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C06HBa0066P09.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="3"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="31049" stop="31282"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>231</number_coding_nucleotides>
                  <number_encoded_amino_acids>77</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>RKERKHLVQKTILLRRNSMETTLIVVNMIIGLMNAGVLRRTRKRRIKQTWLNPNEKWTISVQCFQNVTLFEIQENGG*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C06HBa0066P09.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="4"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="31448" stop="31639"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>192</number_coding_nucleotides>
                  <number_encoded_amino_acids>64</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>IGSHMFQNLVSIPFLTKNGFKCVFVSNKVVVSKNDMYVGQVYLSDGLFKLNVIAVDMNKDFASS</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="40471" PGL_stop="41107"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="40471" e_stop="40972"/>
            <exon e_start="41065" e_stop="41107"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.993" acc_prob="0.999" 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="40471" e_stop="40972" e_length="502"/>
          </exon>
          <intron i_serial="1" don_prob="0.993" acc_prob="0.999">
            <gDNA_intron_boundary i_start="40973" i_stop="41064" i_length="92"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="41065" e_stop="41107" e_length="43"/>
          </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="40471" stop="40972"/>
              <exon start="41065" stop="41107"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U336908" 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>ACTGACTCATGTTTGGTGTCTTATCTAACTTTTTTCCAGAAACAAGGTGCTCAATTGGTTGTACTTGAAGGAAAACGTTCGGAAGTGCTCAATTGGTTGTTAACTGACTAATATCACCTTTGCATTGCCATAAATTACCACTGACTCATATTTGGTGTCTTATCTAACTTTTTTCCAGAAACAAGGTGCTCAATTGGTTGTACTTGAAGGAAAACGTTCGGAAGTGCTCAATTGGTTGTTAACTGACTAATATCACCTTTGCATTGCCATAAATTACTACTGACTCATATTTGGTGTCTTATCTAACTTTTTTCCAGAAACAAGGTGCTCAATTGGTTGTACTTGAAGGAAAACGTTCAGAAGTGTGGGAAAATACATGGTCCACTTCTTGTTTGGATCTGCATTTGATGTCTTCAGGGGCTGCATGTGCAATGGTCCACGCATGGTTGCTTAGTATACGGTCTATAGTGTTTGAAGGCCACGAGTTACCAAAGATGCTGAG : CATTTTGACTGGCTGGGGCAAGCACAGCAAGATAACAGGTGAT</gDNA_template>
            <first_frame> T  D  S  C  L  V  S  Y  L  T  F  F  Q  K  Q  G  A  Q  L  V  V  L  E  G  K  R  S  E  V  L  N  W  L  L  T  D  *  Y  H  L  C  I  A  I  N  Y  H  *  L  I  F  G  V  L  S  N  F  F  P  E  T  R  C  S  I  G  C  T  *  R  K  T  F  G  S  A  Q  L  V  V  N  *  L  I  S  P  L  H  C  H  K  L  L  L  T  H  I  W  C  L  I  *  L  F  S  R  N  K  V  L  N  W  L  Y  L  K  E  N  V  Q  K  C  G  K  I  H  G  P  L  L  V  W  I  C  I  *  C  L  Q  G  L  H  V  Q  W  S  T  H  G  C  L  V  Y  G  L  *  C  L  K  A  T  S  Y  Q  R  C  *   : A  F  *  L  A  G  A  S  T  A  R  *  Q  V   </first_frame>
            <second_frame>  L  T  H  V  W  C  L  I  *  L  F  S  R  N  K  V  L  N  W  L  Y  L  K  E  N  V  R  K  C  S  I  G  C  *  L  T  N  I  T  F  A  L  P  *  I  T  T  D  S  Y  L  V  S  Y  L  T  F  F  Q  K  Q  G  A  Q  L  V  V  L  E  G  K  R  S  E  V  L  N  W  L  L  T  D  *  Y  H  L  C  I  A  I  N  Y  Y  *  L  I  F  G  V  L  S  N  F  F  P  E  T  R  C  S  I  G  C  T  *  R  K  T  F  R  S  V  G  K  Y  M  V  H  F  L  F  G  S  A  F  D  V  F  R  G  C  M  C  N  G  P  R  M  V  A  *  Y  T  V  Y  S  V  *  R  P  R  V  T  K  D  A  E  :  H  F  D  W  L  G  Q  A  Q  Q  D  N  R  *  </second_frame>
            <third_frame>   *  L  M  F  G  V  L  S  N  F  F  P  E  T  R  C  S  I  G  C  T  *  R  K  T  F  G  S  A  Q  L  V  V  N  *  L  I  S  P  L  H  C  H  K  L  P  L  T  H  I  W  C  L  I  *  L  F  S  R  N  K  V  L  N  W  L  Y  L  K  E  N  V  R  K  C  S  I  G  C  *  L  T  N  I  T  F  A  L  P  *  I  T  T  D  S  Y  L  V  S  Y  L  T  F  F  Q  K  Q  G  A  Q  L  V  V  L  E  G  K  R  S  E  V  W  E  N  T  W  S  T  S  C  L  D  L  H  L  M  S  S  G  A  A  C  A  M  V  H  A  W  L  L  S  I  R  S  I  V  F  E  G  H  E  L  P  K  M  L  S :   I  L  T  G  W  G  K  H  S  K  I  T  G  D </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="C06HBa0066P09.1" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="40743" stop="40972"/>
                    <exon start="41065" stop="41107"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>273</number_coding_nucleotides>
                  <number_encoded_amino_acids>91</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>ITTDSYLVSYLTFFQKQGAQLVVLEGKRSEVWENTWSTSCLDLHLMSSGAACAMVHAWLLSIRSIVFEGHELPKMLSILTGWGKHSKITGD</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="3" PGL_strand="+" PGL_start="43095" PGL_stop="43610"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="43095" e_stop="43610"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.990"/>
        </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="0.990">
            <gDNA_exon_boundary e_start="43095" e_stop="43610" e_length="516"/>
          </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="43095" stop="43610"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U328315" strand="+"/>
          </PGS_line>
        </supporting_evidence>
        <three_phase_translation xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/">
          <description PGL_serial="3" AGS_serial="1" gDNA_strand="+"/>
          <translation>
            <gDNA_template>TAAAGATTCAACATATATAAACATAATTTCTTATGGGTATTTTTTCTCATACTCCTAACAAGGGAAAGTTTGATTTAAGCGATTCCTTCCAATGCGATATAAGCAGACAAAGAGTCACGACTTATAACGTAAGGCATGTCAAAAGGTGCAAAAGTGTTGTGATGAAGAGAAGGATACGCGTAGAACGTTCTAGAAGGTTCGAGGATGAGATTGGAAGTAAAGTCAAGATACTCAAGAAGTTGATTCCAATTAACTGTGAAGATTTGGGGCTGGAAGGGATTTTCAGAGAGACAGCTGATTACATTTTGGCTTTAGAAATGAGAATTAAGGCTATGCAAGATATGGTAAATGTATTGTCACATTCTAATCACTAAATCATGTATTATTTTATTATTATATTGTGTCAAAAATGACTTATATACAGATTAATTAACTGATGTTGTTTCTTTGTTCATTCATCAATGTTAATGTGAATGTCTACAATTGTGAAATTGCAAAACTATATAGTTATGTAAA</gDNA_template>
            <first_frame> *  R  F  N  I  Y  K  H  N  F  L  W  V  F  F  L  I  L  L  T  R  E  S  L  I  *  A  I  P  S  N  A  I  *  A  D  K  E  S  R  L  I  T  *  G  M  S  K  G  A  K  V  L  *  *  R  E  G  Y  A  *  N  V  L  E  G  S  R  M  R  L  E  V  K  S  R  Y  S  R  S  *  F  Q  L  T  V  K  I  W  G  W  K  G  F  S  E  R  Q  L  I  T  F  W  L  *  K  *  E  L  R  L  C  K  I  W  *  M  Y  C  H  I  L  I  T  K  S  C  I  I  L  L  L  Y  C  V  K  N  D  L  Y  T  D  *  L  T  D  V  V  S  L  F  I  H  Q  C  *  C  E  C  L  Q  L  *  N  C  K  T  I  *  L  C  K </first_frame>
            <second_frame>  K  D  S  T  Y  I  N  I  I  S  Y  G  Y  F  F  S  Y  S  *  Q  G  K  V  *  F  K  R  F  L  P  M  R  Y  K  Q  T  K  S  H  D  L  *  R  K  A  C  Q  K  V  Q  K  C  C  D  E  E  K  D  T  R  R  T  F  *  K  V  R  G  *  D  W  K  *  S  Q  D  T  Q  E  V  D  S  N  *  L  *  R  F  G  A  G  R  D  F  Q  R  D  S  *  L  H  F  G  F  R  N  E  N  *  G  Y  A  R  Y  G  K  C  I  V  T  F  *  S  L  N  H  V  L  F  Y  Y  Y  I  V  S  K  M  T  Y  I  Q  I  N  *  L  M  L  F  L  C  S  F  I  N  V  N  V  N  V  Y  N  C  E  I  A  K  L  Y  S  Y  V   </second_frame>
            <third_frame>   K  I  Q  H  I  *  T  *  F  L  M  G  I  F  S  H  T  P  N  K  G  K  F  D  L  S  D  S  F  Q  C  D  I  S  R  Q  R  V  T  T  Y  N  V  R  H  V  K  R  C  K  S  V  V  M  K  R  R  I  R  V  E  R  S  R  R  F  E  D  E  I  G  S  K  V  K  I  L  K  K  L  I  P  I  N  C  E  D  L  G  L  E  G  I  F  R  E  T  A  D  Y  I  L  A  L  E  M  R  I  K  A  M  Q  D  M  V  N  V  L  S  H  S  N  H  *  I  M  Y  Y  F  I  I  I  L  C  Q  K  *  L  I  Y  R  L  I  N  *  C  C  F  F  V  H  S  S  M  L  M  *  M  S  T  I  V  K  L  Q  N  Y  I  V  M  *  </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="C06HBa0066P09.1" strand="+"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="43121" stop="43468"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>345</number_coding_nucleotides>
                  <number_encoded_amino_acids>115</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>FLMGIFSHTPNKGKFDLSDSFQCDISRQRVTTYNVRHVKRCKSVVMKRRIRVERSRRFEDEIGSKVKILKKLIPINCEDLGLEGIFRETADYILALEMRIKAMQDMVNVLSHSNH*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 18 chains have been computed
$ 
$ memory statistics:
$ 5592 bytes spliced alignments in total
$ 3 spliced alignments have been stored
$ 1864 bytes was the average size of a spliced alignment
$ 7912 bytes predicted gene locations in total
$ 3 predicted gene locations have been stored
$ 2637 bytes was the average size of a predicted gene location
$ 1 megabytes was the average size of the backtrace matrix
$ 23 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-16 20:42:47
-->
