<?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="2009-01-07 14:26:18"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C12HBa0144B17-J6Rk0/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C12HBa0144B17-J6Rk0/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-C12HBa0144B17-J6Rk0/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U346814" ref_strand="+" ref_description="SGN-U346814        Tomato 200607 #1 [1 ESTs aligned] arabidopsis/peptide: AT5G07920.1 | Symbol: None | diacylglycerol kinase 1 (DGK1), identical to diacylglycerol kinase 1 (Diglyceride kinase 1, DGK 1, DAG kinase 1) (Arabidopsis thaliana) SWISS-PROT:Q39017 | chr5:2524779-2529331 REVERSE | Aliases: F13G24.120, F13G24_120 (evalue: 1e-67, score=253) genbank/nr: gi|15241456|ref|NP_196409.1| diacylglycerol kinase (ATDGK1) [Arabidopsis thaliana] gi|20141593|sp|Q39017|KDG1_ARATH Diacylglycerol kinase 1 (Diglyceride kinase 1) (DGK 1) (DAG kinase 1) gi|6562306|emb|CAB62604.1| diacylglycerol kinase (ATDGK1) [Arabidopsis thaliana] gi|10176726|dbj|BAB09956.1| diacylglycerol kinase ATDGK1 homolog [Arabidopsis thaliana] gi|28393496|gb|AAO42169.1| putative diacylglycerol kinase (ATDGK1) [Arabidopsis thaliana](evalue: 8e-66, score=253)">
      <seq>ctatgtctccatctcaaactcttggaccaatggtggcatcagagagttcttttaattgctgcaacacttgtggtgcagcagctcatcttagttgctcattgaatgctcttaaggattgcaaatgtgtatcaatgtttggatataagcacgtggtacaccaatgggcagttcggtggacagaggtggcagatcaaccagatgaatcctgtttctgcagctactgtgaagagccgtgcagcagttcatttcttgggggttcccctgtatggtgctgcttgtggtgtcagcgcctggttcacgtttattgccatgctaatatgttcaatgaaacaggtgatatttgtgacttgggcccttttaaaaggcttattttatcgcctcttcatattaaagagttaactaggacatcctctggtggactgcttagttccatcacacaaggagccaatgagattgcatcttcagtacgtgctagtattagaagtcacagcacgaaatacaaacacaaacacaataacaaaaaaaatggtaaatgtggtttc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12HBa0144B17-J6Rk0/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C12HBa0144B17.1" temp_strand="-" temp_description="C12HBa0144B17.1  AC213008.2 htgs_phase:3 submitted_to_sgn_as:C12HBa0144B17 upload_account_name:italy">
        <position start="1398" stop="258"/>
      </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="1098" g_stop="558" g_length="541"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="542" r_length="542" r_score="0.993"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12HBa0144B17.1" gen_strand="-" ref_id="SGN-U346814" ref_strand="+">
        <total_alignment_score>0.993</total_alignment_score>
        <cumulative_length_of_scored_exons>541</cumulative_length_of_scored_exons>
        <coverage percentage="0.998" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12HBa0144B17.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U346814" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1098" e_stop="558"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTATGTCTCCATCTCAAACTCTTGGACCAATGGTGGCATCAGAGAGTTCTTTTAATTGCTGCAACACTTGTGGTGCAGCAGCTCATCTTAGTTGCTCATTGAATGCTCTTAAGGATTGCAAATGTGTATCAATGTTTGGATATAAGCACGTGGTACACCAATGGGCAGTTCGGTGGACAGAGGTGGCAGATCAACCAGATGAATCCTGTTTCTGCAGCTACTGTGAAGAGCCGTGCAGCAGTTCATTTCTTGGGGGTTCCCCTGTATGGTGCTGCTTGTGGTGTCAGCGCCTGGTTCACGTTTATTGCCATGCTAATATGTTCAATGAAACAGGTGATATTTGTGACTTGGGCCCTTTTAAAAGGCTTATTTTATCGCCTCTTCATATTAAAGAGTTAACTAGGACATCCTCTGGTGGACTGCTTAGTTCCATCACACAAGGAGCCAATGAGATTGCATCTTCAGTACGTGCTAGTATTAGAAGTCAAAGCAAGAAATACAAACACAAACACAATAACAAAAAAAATGG-AAATGTGGTTTC</genome_strand>
        <mrna_strand>CTATGTCTCCATCTCAAACTCTTGGACCAATGGTGGCATCAGAGAGTTCTTTTAATTGCTGCAACACTTGTGGTGCAGCAGCTCATCTTAGTTGCTCATTGAATGCTCTTAAGGATTGCAAATGTGTATCAATGTTTGGATATAAGCACGTGGTACACCAATGGGCAGTTCGGTGGACAGAGGTGGCAGATCAACCAGATGAATCCTGTTTCTGCAGCTACTGTGAAGAGCCGTGCAGCAGTTCATTTCTTGGGGGTTCCCCTGTATGGTGCTGCTTGTGGTGTCAGCGCCTGGTTCACGTTTATTGCCATGCTAATATGTTCAATGAAACAGGTGATATTTGTGACTTGGGCCCTTTTAAAAGGCTTATTTTATCGCCTCTTCATATTAAAGAGTTAACTAGGACATCCTCTGGTGGACTGCTTAGTTCCATCACACAAGGAGCCAATGAGATTGCATCTTCAGTACGTGCTAGTATTAGAAGTCACAGCACGAAATACAAACACAAACACAATAACAAAAAAAATGGTAAATGTGGTTTC</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-C12HBa0144B17-J6Rk0/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U330593" ref_strand="+" ref_description="SGN-U330593        Tomato 200607 #1 [2 ESTs aligned]">
      <seq>ctcgaaaagcgctgcaaccctctcctctccatcctttctcatttcggttagaagcaggaggtggaggaccactagttaacgcccctttcctctcctctactctctcctgcgagaaagcaatagtcatctaccggtgaaacaacaagcagttctgacgatgcaagccatcagcgagagcgcgaaaccagtatcagttgcgaccggcgaagagctccagcaaagcaacaacactttggcaagtagttgtgagccaccaccaacagcagttgtggccaatcaccaacggaactccatgggaacgatagctttgaccagcgacgcaacaacaacaacgaggttgttcaggcttaaaatcccagtcatgaagcgtatgtcgatggagtttgtttagaatattgagttttgttaaaagacggatcttcaacaaatacatgtagataagttttcgattaattctaaagcctgcattttcaattctttggtgactttcattcaagtgagtatgtttaagttgaatttcatatatcctcttatttttatggcagttttcgtgattaatttatactgattttagttttcttgtgaaagcatgtttaggttgcgattctctattcaagggtttgttcatcacttctatcatgatctggctttaatttgtgaagtttattttagtgtactggttgcaatgagtctgtactctaacatatgggttgcacattcttgttatttatataataaagtccagtttatgatttcctttgataatttcttctttctaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12HBa0144B17-J6Rk0/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C12HBa0144B17.1" temp_strand="-" temp_description="C12HBa0144B17.1  AC213008.2 htgs_phase:3 submitted_to_sgn_as:C12HBa0144B17 upload_account_name:italy">
        <position start="28937" stop="27558"/>
      </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="28637" g_stop="27858" g_length="780"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="780" r_length="780" r_score="0.931"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12HBa0144B17.1" gen_strand="-" ref_id="SGN-U330593" ref_strand="+">
        <total_alignment_score>0.931</total_alignment_score>
        <cumulative_length_of_scored_exons>780</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12HBa0144B17.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U330593" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="28637" e_stop="27858"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTCCAAAAGCGCTGCAACCCTCTCTTCTGCATCCTTTCTCGTTCCGGTTAGAAGCAGGAGGTGGAGGACCACTAGTTAACGCCCCTTCCCTCTCCTCTCCTCTCTCCTGCGAGAAAGCAATAGTCATCTACTGGTGAAACAACAAGCAGTTCTGATGACGCGAGCCATCAGCGAGAGCGCAAAACCAGTTTCAGTTGCGATCGGCGAAGAGCTCCCGCAAAGCAACAACACTTTGGCAAGTAGTCGCGAGCCACCACCAACAGCAGGTGTGGCCAATCACCAGCGAAACTCCATGGGAACGATAGCTTCGACCAGCGACGCAACAATAACAACGAGGTTGTTCAAGCTTATAATCCCAGTCATGAAGTGTATGTCGATGGAGTTTGTTTAGAATATTGAGTTTTGTTAAAAGACAGATGTTCAACAAATACATCTTGATAAG-TTTCGATTAATTCTAAAGCCTGCATTTTCAATTCTTTGGTGATTTTCATTTAAGTGGGTATGTTTAAGTTGAATTTCACATATCCTCTTATTTTAATGGTATTTTCTGTGATTAATATATAGTGATTTTAGTTTTCTTGTGAAAACATGTTTAGGTTGAGATTCTCTATTCAAGGTTTTTTTCATCACTTCTATCATGATCTGGCTGTAATTTGTGATGTTTCTTATAGTGTACTGGTTGTAATGAGTCTGTACTCTAACATATGGGTTGCACATTCTTGTTATTTATATAATAAAGTCTAGTGTATGATTTCCTTTGATTAATTTCTTCTTTCTAAA</genome_strand>
        <mrna_strand>CTCGAAAAGCGCTGCAACCCTCTCCTCTCCATCCTTTCTCATTTCGGTTAGAAGCAGGAGGTGGAGGACCACTAGTTAACGCCCCTTTCCTCTCCTCTACTCTCTCCTGCGAGAAAGCAATAGTCATCTACCGGTGAAACAACAAGCAGTTCTGACGATGCAAGCCATCAGCGAGAGCGCGAAACCAGTATCAGTTGCGACCGGCGAAGAGCTCCAGCAAAGCAACAACACTTTGGCAAGTAGTTGTGAGCCACCACCAACAGCAGTTGTGGCCAATCACCAACGGAACTCCATGGGAACGATAGCTTTGACCAGCGACGCAACAACAACAACGAGGTTGTTCAGGCTTAAAATCCCAGTCATGAAGCGTATGTCGATGGAGTTTGTTTAGAATATTGAGTTTTGTTAAAAGACGGATCTTCAACAAATACATGTAGATAAGTTTTCGATTAATTCTAAAGCCTGCATTTTCAATTCTTTGGTGACTTTCATTCAAGTGAGTATGTTTAAGTTGAATTTCATATATCCTCTTATTTTTATGGCAGTTTTCGTGATTAATTTATACTGATTTTAGTTTTCTTGTGAAAGCATGTTTAGGTTGCGATTCTCTATTCAAGGGTTTGTTCATCACTTCTATCATGATCTGGCTTTAATTTGTGAAGTTTATTTTAGTGTACTGGTTGCAATGAGTCTGTACTCTAACATATGGGTTGCACATTCTTGTTATTTATATAATAAAGTCCAGTTTATGATTTCCTTTGA-TAATTTCTTCTTTCTAAA</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-C12HBa0144B17-J6Rk0/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U341777" ref_strand="+" ref_description="SGN-U341777        Tomato 200607 #1 [1 ESTs aligned] genbank/nr: gi|53689767|gb|AAU89777.1| gag-pol polyprotein-like [Solanum tuberosum] (evalue: 3e-08, score=62)">
      <seq>tgagcagctcgaccaatttttccttttctattgctgtcaaatggatactgactcgggtttctctaaccgactcgtcatctcctaagttgactatctatctctcatccaggttgggatttttattatctgcaaggttcctcaagtcgtcagtaaggtgttcaggcatcatagtttcctcatcatattcatcacattcatcttcattgactttacttagttcatcgtgttcgtgacatgtcatgatattggcaagtttagattcatttttactgaaaataaactaaagcaatcatgttagatagaaagaatttaaatgtatatattagaaagtaatttgcaaaggcaagataaaaaataaacgaggcttttcattggaaaaaaggcgtacaactttgatcatgactcatgtcaatgtgagtcatttcctttttaagcattacgatgaaaataacgtgacataaaaggttgtttcgggcctcgttcgaactacaccaattttcaaaagtaaaacttcaaatcttgtctttgtctaccaagcaattcgatgaatcataagtggagtggccacccaattctttagcatctcttcaggtttggcatctcgtatggtgggtgtcgcagtgcattcttccaagatcacaacacaatctccttcatcaaacaatcgtcccatcccttacacttcaccattaccctcggactctaaagctttagccacaaataactggtacaattctggaataggctttggtatatcaaggccatgtttcttccttgcttctacttcgaataattcc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12HBa0144B17-J6Rk0/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C12HBa0144B17.1" temp_strand="+" temp_description="C12HBa0144B17.1  AC213008.2 htgs_phase:3 submitted_to_sgn_as:C12HBa0144B17 upload_account_name:italy">
        <position start="45429" stop="46827"/>
      </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="45729" g_stop="46527" g_length="799"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="797" r_length="797" r_score="0.950"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12HBa0144B17.1" gen_strand="+" ref_id="SGN-U341777" ref_strand="+">
        <total_alignment_score>0.950</total_alignment_score>
        <cumulative_length_of_scored_exons>799</cumulative_length_of_scored_exons>
        <coverage percentage="1.003" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12HBa0144B17.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U341777" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="45729" e_stop="46527"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TAAGTAGCTCAACCAATTTTTCCTTTTCTATTGCTGTCAAATGTATACTGACTCGGGTTTCTCTAACCGACTCGTCATCTCCAAAGTTGACTATCTCTGTCTCATCCAGGTTGGGATTTTTATTATCTGCAAGGTTCCTCAAGTCGTTAGTAAGGTGTTCAGGCATCATAGTTTCCTCATCATATTCTTCACATTCATCTTCATTGACTTTACTTAGTTCATCGTGTTCGTGACATGTCATGACATTGGCAAGTTTAGATTCATTTTTATTGAAAAGAAAATAAAGCAATCATGTTAGATAGAAAGAATTTAAATGTATATATCAGAAAGTAATTTGCAGAGGTAAGATAAAAAATAAACGAGGTTTTTCATTGGAAAAAAGGTGTACAAACTTTGATCATGACTCATGTCAATGTGAGTCCTTTCTTTTTTAAACATTACGATGAAAATAAAGTGACATAAAAGTTTATTTCGGGCCTCGTCCGAACTACACCGATTTTCAAAAGTAAAACTTCAAATTCTTGTCTTTGTCTACCAAGCAATTCGATGAATCATAAGTGGAGTGGCCACCCAATTCTGTAGCATCTCTTCAGGTTTGGCATCTCGGATGGTGGGTGTCGCAGTGCATTCTTCCAAGATCACAGCACAATCTCCTTCATCAAAAAATCATCCCATCCCTTCCACTAGACCATCACTCTCGGACTCTAAAGCTTTAGCAACAAATAACTGGTACAATTCTGGAATAGGCTTTGGTATATCAAGGCCATGTTTCTTCCTTGCTTCTGCTTCGAATAATTCC</genome_strand>
        <mrna_strand>TGAGCAGCTCGACCAATTTTTCCTTTTCTATTGCTGTCAAATGGATACTGACTCGGGTTTCTCTAACCGACTCGTCATCTCCTAAGTTGACTATCTATCTCTCATCCAGGTTGGGATTTTTATTATCTGCAAGGTTCCTCAAGTCGTCAGTAAGGTGTTCAGGCATCATAGTTTCCTCATCATATTCATCACATTCATCTTCATTGACTTTACTTAGTTCATCGTGTTCGTGACATGTCATGATATTGGCAAGTTTAGATTCATTTTTACTGAAAATAAACTAAAGCAATCATGTTAGATAGAAAGAATTTAAATGTATATATTAGAAAGTAATTTGCAAAGGCAAGATAAAAAATAAACGAGGCTTTTCATTGGAAAAAAGGCGTAC-AACTTTGATCATGACTCATGTCAATGTGAGTCATTTCCTTTTTAAGCATTACGATGAAAATAACGTGACATAAAAGGTTGTTTCGGGCCTCGTTCGAACTACACCAATTTTCAAAAGTAAAACTTCAAA-TCTTGTCTTTGTCTACCAAGCAATTCGATGAATCATAAGTGGAGTGGCCACCCAATTCTTTAGCATCTCTTCAGGTTTGGCATCTCGTATGGTGGGTGTCGCAGTGCATTCTTCCAAGATCACAACACAATCTCCTTCATCAAACAATCGTCCCATCCCTTACACTTCACCATTACCCTCGGACTCTAAAGCTTTAGCCACAAATAACTGGTACAATTCTGGAATAGGCTTTGGTATATCAAGGCCATGTTTCTTCCTTGCTTCTACTTCGAATAATTCC</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-C12HBa0144B17-J6Rk0/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U334937" ref_strand="+" ref_description="SGN-U334937        Tomato 200607 #1 [1 ESTs aligned] arabidopsis/peptide: AT5G61170.1 | Symbol: None | 40S ribosomal protein S19 (RPS19C), 40S ribsomal protein S19, Oryza sativa, SWISSPROT:RS19_ORYSA | chr5:24628325-24629582 FORWARD | Aliases: MAF19.23, MAF19_23 (evalue: 1e-54, score=211) genbank/nr: 40S(evalue: 1e-57, score=226)">
      <seq>aaagatctgcagcgaagatggaggcagcaagaactgtgaaagatgtttccccccatgattttgtcaaggcttatgccgctcatctcaagcgctccggaaagatggagcttcctgaatggactgatatagttaagactggtaagctaaaggagcttgccccatatgatgctgattggtactacatcaaagctgcttccatggcaaggaagatctatttgagaggaggtattggtgttggtggtttccgaagaatctatggtggaaaccagaggaatggaagccgtccacgtcacttttgcaagagcagtggttcagttgcacgccacattcttcaacagttgcagaacatgaacatcattgactttgagcctaagggcggaaggaggatcacatccagtggtcagcgggatcttgaccaagttgccggaagaattgctgttgcttgttaagagagagatgagttcattcaattttatgaatacatgagttagctcaaacttattgtttctgtttggacctaaatagatttagggtattgttgaattaaattgtggatgttttgccttttcagaattgtctttctcagtatgtcaagttttgcccttttagtaccctgaagtgtgtattgtggcatatgttgcattcaatgcatcattacttcataattatacataaatccctgagattcagtgcttgtttnnnaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12HBa0144B17-J6Rk0/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C12HBa0144B17.1" temp_strand="+" temp_description="C12HBa0144B17.1  AC213008.2 htgs_phase:3 submitted_to_sgn_as:C12HBa0144B17 upload_account_name:italy">
        <position start="102652" stop="105008"/>
      </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="102952" g_stop="103052" g_length="101"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="101" r_length="101" r_score="0.990"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="103053" i_stop="103431" i_length="379">
            <donor d_prob="0.992" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="103432" g_stop="103522" g_length="91"/>
          <reference_exon_boundary r_type="cDNA" r_start="102" r_stop="192" r_length="91" r_score="0.989"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="103523" i_stop="103601" i_length="79">
            <donor d_prob="0.995" d_score="0.98"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="103602" g_stop="103785" g_length="184"/>
          <reference_exon_boundary r_type="cDNA" r_start="193" r_stop="376" r_length="184" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="103786" i_stop="104385" i_length="600">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.992" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="104386" g_stop="104704" g_length="319"/>
          <reference_exon_boundary r_type="cDNA" r_start="377" r_stop="695" r_length="319" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="713" polyA_stop="763"/>
      <MATCH_line gen_id="C12HBa0144B17.1" gen_strand="+" ref_id="SGN-U334937" ref_strand="+">
        <total_alignment_score>0.997</total_alignment_score>
        <cumulative_length_of_scored_exons>695</cumulative_length_of_scored_exons>
        <coverage percentage="0.911" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12HBa0144B17.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U334937" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="102952" e_stop="103052"/>
          <exon e_start="103432" e_stop="103522"/>
          <exon e_start="103602" e_stop="103785"/>
          <exon e_start="104386" e_stop="104704"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAAGATCTGCAGCGAAGATGGAGGCAGCAAGAAGTGTGAAAGATGTTTCCCCCCATGATTTTGTCAAGGCTTATGCCGCTCATCTCAAGCGCTCCGGAAAGGTCTATACGAATTGAATTTCGTTTTACATTCATATTTGCTTCGATTTTCTCAACTGATTTACCTCTTACATCATTGAATATAGCAATAGAAACAACGCAGAATTTGTAGCTATTTGCTGGATTGAAAGATTTTCAAATTTCAATTTTGTATACACGCTTCCTGCTAAAATATAGAAATGATATTTGTTCTTCTTCTTGTTGGATTCAATGGACCTTTGCCCCCTTTTACCCTGTTAATTTCCCTACTGGAAGTTATTTGCTCAGATCTGCCTTATTATCTACCATAAAGTACTTTGTTTTCTTGTTAATTCCAGCCACTGCAATTTAATGCATGTTTGGGCTTGTCTATTCATGCTTATTGTACCTTTGATTTTTGCAGATGGAGCTTCCTGAATGGACTGATATAGTTAAGACTGGTAAGCTAAAGGAGCTTGCCCCATATGATGCTGATTGGTACTACATCAGAGCTGGTATGTCTCATCTCCATTATCAGATGAAGGAACTTATCCATTGTTTCTAACTTTTTTTTTTTTTTTTGATGTATGGCAGCTTCCATGGCAAGGAAGATCTATTTGAGAGGAGGTATTGGTGTTGGTGGTTTCCGAAGAATCTATGGTGGAAACCAGAGGAATGGAAGCCGTCCACGTCACTTTTGCAAGAGCAGTGGTTCAGTTGCACGCCACATTCTTCAACAGTTGCAGAACATGAACATCATTGACTTTGAGCCTAAGGGGTAAGTAGTAACCTTTTGCTCTCTAATTAATGCTGAATTTGATGTGTCTCCTTATTCTGTAGTGGTTGTATGAATGAAATCCATTGATCAGTCAGAAACCTGTTTGTTTACATAACTGATGGGGTTTTCTCCTGCTTTTTCTGAGGTTGTTTGTCATGTGATATGAATATATGCGGATGCGTTAATCATTGTATGGAGCCAGCAAAATTTAAGAAAATCACGAGGAGTCTGGCTAGTCTTGCTTAGAAAAAGAGTGATTTCAGTGATAATAATTGTGCTTAAATCAATTAATAAAACTCTCTTTATTTAGGAAAGAGGTCAAAGACAATTGCAAAAAGAGTGACTGCTCCCTTTATAGTAAGACTTTGATATTTGTGAGTGATTGATTAAACAGGGAAACGATAAGAGGTTGCTGACTTTTCAATTGAAAATAACATGGCTTAAATGAATCTAGATGAAGTATTTCACCTTGTTCTGAATGGAGAGACATCCTTATTGCTAGCGAATGCTCACAACTCAACTTTATTAGCTGCATTAAGAATGAAATCGATGAATATCTAGTTATTTGTCTGTCTAATTTAAAATTCTCTCTTTATCTAGCGGAAGGAGGATCACATCCAGTGGTCAGCGGGATCTTGACCAAGTTGCCGGAAGAATTGCTGTTGCTTGTTAAGAGAGAGATGAGTTCATTCAATTTTATGAATACATGAGTTAGCTCAAACTTATTGTTTCTGTTTGGACCTAAATAGATTTAGGGTATTGTTGAATTAAATTGTGGATGTTTTGCCTTTTCAGAATTGTCTTTCTCAGTATGTCAAGTTTTGCCCTTTTAGTACCCTGAAGTGTGTATTGTGGCATATGTTGCATTCAATGCATCATTACTTCATAATTATACATAAATCCCTGAGATTCAGTGCTT</genome_strand>
        <mrna_strand>AAAGATCTGCAGCGAAGATGGAGGCAGCAAGAACTGTGAAAGATGTTTCCCCCCATGATTTTGTCAAGGCTTATGCCGCTCATCTCAAGCGCTCCGGAAAG...........................................................................................................................................................................................................................................................................................................................................................................................ATGGAGCTTCCTGAATGGACTGATATAGTTAAGACTGGTAAGCTAAAGGAGCTTGCCCCATATGATGCTGATTGGTACTACATCAAAGCTG...............................................................................CTTCCATGGCAAGGAAGATCTATTTGAGAGGAGGTATTGGTGTTGGTGGTTTCCGAAGAATCTATGGTGGAAACCAGAGGAATGGAAGCCGTCCACGTCACTTTTGCAAGAGCAGTGGTTCAGTTGCACGCCACATTCTTCAACAGTTGCAGAACATGAACATCATTGACTTTGAGCCTAAGGG........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CGGAAGGAGGATCACATCCAGTGGTCAGCGGGATCTTGACCAAGTTGCCGGAAGAATTGCTGTTGCTTGTTAAGAGAGAGATGAGTTCATTCAATTTTATGAATACATGAGTTAGCTCAAACTTATTGTTTCTGTTTGGACCTAAATAGATTTAGGGTATTGTTGAATTAAATTGTGGATGTTTTGCCTTTTCAGAATTGTCTTTCTCAGTATGTCAAGTTTTGCCCTTTTAGTACCCTGAAGTGTGTATTGTGGCATATGTTGCATTCAATGCATCATTACTTCATAATTATACATAAATCCCTGAGATTCAGTGCTT</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>4</total_number_ESTs_reported>
    </alignment_module>
  <PGL_module xmlns="http://www.genomethreader.org/GTH_output/PGL_module/">
    <predicted_gene_location>
      <PGL_line PGL_serial="1" PGL_strand="-" PGL_start="1098" PGL_stop="558"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="1098" e_stop="558"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.993"/>
        </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="0.993">
            <gDNA_exon_boundary e_start="1098" e_stop="558" e_length="541"/>
          </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="1098" stop="558"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U346814" 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>CTATGTCTCCATCTCAAACTCTTGGACCAATGGTGGCATCAGAGAGTTCTTTTAATTGCTGCAACACTTGTGGTGCAGCAGCTCATCTTAGTTGCTCATTGAATGCTCTTAAGGATTGCAAATGTGTATCAATGTTTGGATATAAGCACGTGGTACACCAATGGGCAGTTCGGTGGACAGAGGTGGCAGATCAACCAGATGAATCCTGTTTCTGCAGCTACTGTGAAGAGCCGTGCAGCAGTTCATTTCTTGGGGGTTCCCCTGTATGGTGCTGCTTGTGGTGTCAGCGCCTGGTTCACGTTTATTGCCATGCTAATATGTTCAATGAAACAGGTGATATTTGTGACTTGGGCCCTTTTAAAAGGCTTATTTTATCGCCTCTTCATATTAAAGAGTTAACTAGGACATCCTCTGGTGGACTGCTTAGTTCCATCACACAAGGAGCCAATGAGATTGCATCTTCAGTACGTGCTAGTATTAGAAGTCAAAGCAAGAAATACAAACACAAACACAATAACAAAAAAAATGGAAATGTGGTTTC</gDNA_template>
            <first_frame> L  C  L  H  L  K  L  L  D  Q  W  W  H  Q  R  V  L  L  I  A  A  T  L  V  V  Q  Q  L  I  L  V  A  H  *  M  L  L  R  I  A  N  V  Y  Q  C  L  D  I  S  T  W  Y  T  N  G  Q  F  G  G  Q  R  W  Q  I  N  Q  M  N  P  V  S  A  A  T  V  K  S  R  A  A  V  H  F  L  G  V  P  L  Y  G  A  A  C  G  V  S  A  W  F  T  F  I  A  M  L  I  C  S  M  K  Q  V  I  F  V  T  W  A  L  L  K  G  L  F  Y  R  L  F  I  L  K  S  *  L  G  H  P  L  V  D  C  L  V  P  S  H  K  E  P  M  R  L  H  L  Q  Y  V  L  V  L  E  V  K  A  R  N  T  N  T  N  T  I  T  K  K  M  E  M  W  F  </first_frame>
            <second_frame>  Y  V  S  I  S  N  S  W  T  N  G  G  I  R  E  F  F  *  L  L  Q  H  L  W  C  S  S  S  S  *  L  L  I  E  C  S  *  G  L  Q  M  C  I  N  V  W  I  *  A  R  G  T  P  M  G  S  S  V  D  R  G  G  R  S  T  R  *  I  L  F  L  Q  L  L  *  R  A  V  Q  Q  F  I  S  W  G  F  P  C  M  V  L  L  V  V  S  A  P  G  S  R  L  L  P  C  *  Y  V  Q  *  N  R  *  Y  L  *  L  G  P  F  *  K  A  Y  F  I  A  S  S  Y  *  R  V  N  *  D  I  L  W  W  T  A  *  F  H  H  T  R  S  Q  *  D  C  I  F  S  T  C  *  Y  *  K  S  K  Q  E  I  Q  T  Q  T  Q  *  Q  K  K  W  K  C  G  F </second_frame>
            <third_frame>   M  S  P  S  Q  T  L  G  P  M  V  A  S  E  S  S  F  N  C  C  N  T  C  G  A  A  A  H  L  S  C  S  L  N  A  L  K  D  C  K  C  V  S  M  F  G  Y  K  H  V  V  H  Q  W  A  V  R  W  T  E  V  A  D  Q  P  D  E  S  C  F  C  S  Y  C  E  E  P  C  S  S  S  F  L  G  G  S  P  V  W  C  C  L  W  C  Q  R  L  V  H  V  Y  C  H  A  N  M  F  N  E  T  G  D  I  C  D  L  G  P  F  K  R  L  I  L  S  P  L  H  I  K  E  L  T  R  T  S  S  G  G  L  L  S  S  I  T  Q  G  A  N  E  I  A  S  S  V  R  A  S  I  R  S  Q  S  K  K  Y  K  H  K  H  N  N  K  K  N  G  N  V  V   </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="C12HBa0144B17.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="1096" stop="560"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>537</number_coding_nucleotides>
                  <number_encoded_amino_acids>179</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>MSPSQTLGPMVASESSFNCCNTCGAAAHLSCSLNALKDCKCVSMFGYKHVVHQWAVRWTEVADQPDESCFCSYCEEPCSSSFLGGSPVWCCLWCQRLVHVYCHANMFNETGDICDLGPFKRLILSPLHIKELTRTSSGGLLSSITQGANEIASSVRASIRSQSKKYKHKHNNKKNGNVV</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="28637" PGL_stop="27858"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="28637" e_stop="27858"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.931"/>
        </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="0.931">
            <gDNA_exon_boundary e_start="28637" e_stop="27858" e_length="780"/>
          </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="28637" stop="27858"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U330593" 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>CTCCAAAAGCGCTGCAACCCTCTCTTCTGCATCCTTTCTCGTTCCGGTTAGAAGCAGGAGGTGGAGGACCACTAGTTAACGCCCCTTCCCTCTCCTCTCCTCTCTCCTGCGAGAAAGCAATAGTCATCTACTGGTGAAACAACAAGCAGTTCTGATGACGCGAGCCATCAGCGAGAGCGCAAAACCAGTTTCAGTTGCGATCGGCGAAGAGCTCCCGCAAAGCAACAACACTTTGGCAAGTAGTCGCGAGCCACCACCAACAGCAGGTGTGGCCAATCACCAGCGAAACTCCATGGGAACGATAGCTTCGACCAGCGACGCAACAATAACAACGAGGTTGTTCAAGCTTATAATCCCAGTCATGAAGTGTATGTCGATGGAGTTTGTTTAGAATATTGAGTTTTGTTAAAAGACAGATGTTCAACAAATACATCTTGATAAGTTTCGATTAATTCTAAAGCCTGCATTTTCAATTCTTTGGTGATTTTCATTTAAGTGGGTATGTTTAAGTTGAATTTCACATATCCTCTTATTTTAATGGTATTTTCTGTGATTAATATATAGTGATTTTAGTTTTCTTGTGAAAACATGTTTAGGTTGAGATTCTCTATTCAAGGTTTTTTTCATCACTTCTATCATGATCTGGCTGTAATTTGTGATGTTTCTTATAGTGTACTGGTTGTAATGAGTCTGTACTCTAACATATGGGTTGCACATTCTTGTTATTTATATAATAAAGTCTAGTGTATGATTTCCTTTGATTAATTTCTTCTTTCTAAA</gDNA_template>
            <first_frame> L  Q  K  R  C  N  P  L  F  C  I  L  S  R  S  G  *  K  Q  E  V  E  D  H  *  L  T  P  L  P  S  P  L  L  S  P  A  R  K  Q  *  S  S  T  G  E  T  T  S  S  S  D  D  A  S  H  Q  R  E  R  K  T  S  F  S  C  D  R  R  R  A  P  A  K  Q  Q  H  F  G  K  *  S  R  A  T  T  N  S  R  C  G  Q  S  P  A  K  L  H  G  N  D  S  F  D  Q  R  R  N  N  N  N  E  V  V  Q  A  Y  N  P  S  H  E  V  Y  V  D  G  V  C  L  E  Y  *  V  L  L  K  D  R  C  S  T  N  T  S  *  *  V  S  I  N  S  K  A  C  I  F  N  S  L  V  I  F  I  *  V  G  M  F  K  L  N  F  T  Y  P  L  I  L  M  V  F  S  V  I  N  I  *  *  F  *  F  S  C  E  N  M  F  R  L  R  F  S  I  Q  G  F  F  H  H  F  Y  H  D  L  A  V  I  C  D  V  S  Y  S  V  L  V  V  M  S  L  Y  S  N  I  W  V  A  H  S  C  Y  L  Y  N  K  V  *  C  M  I  S  F  D  *  F  L  L  S  K </first_frame>
            <second_frame>  S  K  S  A  A  T  L  S  S  A  S  F  L  V  P  V  R  S  R  R  W  R  T  T  S  *  R  P  F  P  L  L  S  S  L  L  R  E  S  N  S  H  L  L  V  K  Q  Q  A  V  L  M  T  R  A  I  S  E  S  A  K  P  V  S  V  A  I  G  E  E  L  P  Q  S  N  N  T  L  A  S  S  R  E  P  P  P  T  A  G  V  A  N  H  Q  R  N  S  M  G  T  I  A  S  T  S  D  A  T  I  T  T  R  L  F  K  L  I  I  P  V  M  K  C  M  S  M  E  F  V  *  N  I  E  F  C  *  K  T  D  V  Q  Q  I  H  L  D  K  F  R  L  I  L  K  P  A  F  S  I  L  W  *  F  S  F  K  W  V  C  L  S  *  I  S  H  I  L  L  F  *  W  Y  F  L  *  L  I  Y  S  D  F  S  F  L  V  K  T  C  L  G  *  D  S  L  F  K  V  F  F  I  T  S  I  M  I  W  L  *  F  V  M  F  L  I  V  Y  W  L  *  *  V  C  T  L  T  Y  G  L  H  I  L  V  I  Y  I  I  K  S  S  V  *  F  P  L  I  N  F  F  F  L   </second_frame>
            <third_frame>   P  K  A  L  Q  P  S  L  L  H  P  F  S  F  R  L  E  A  G  G  G  G  P  L  V  N  A  P  S  L  S  S  P  L  S  C  E  K  A  I  V  I  Y  W  *  N  N  K  Q  F  *  *  R  E  P  S  A  R  A  Q  N  Q  F  Q  L  R  S  A  K  S  S  R  K  A  T  T  L  W  Q  V  V  A  S  H  H  Q  Q  Q  V  W  P  I  T  S  E  T  P  W  E  R  *  L  R  P  A  T  Q  Q  *  Q  R  G  C  S  S  L  *  S  Q  S  *  S  V  C  R  W  S  L  F  R  I  L  S  F  V  K  R  Q  M  F  N  K  Y  I  L  I  S  F  D  *  F  *  S  L  H  F  Q  F  F  G  D  F  H  L  S  G  Y  V  *  V  E  F  H  I  S  S  Y  F  N  G  I  F  C  D  *  Y  I  V  I  L  V  F  L  *  K  H  V  *  V  E  I  L  Y  S  R  F  F  S  S  L  L  S  *  S  G  C  N  L  *  C  F  L  *  C  T  G  C  N  E  S  V  L  *  H  M  G  C  T  F  L  L  F  I  *  *  S  L  V  Y  D  F  L  *  L  I  S  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="C12HBa0144B17.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="28558" stop="28247"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>309</number_coding_nucleotides>
                  <number_encoded_amino_acids>103</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>RPFPLLSSLLRESNSHLLVKQQAVLMTRAISESAKPVSVAIGEELPQSNNTLASSREPPPTAGVANHQRNSMGTIASTSDATITTRLFKLIIPVMKCMSMEFV*</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="45729" PGL_stop="46527"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="45729" e_stop="46527"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.950"/>
        </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="0.950">
            <gDNA_exon_boundary e_start="45729" e_stop="46527" e_length="799"/>
          </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="45729" stop="46527"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U341777" 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>TAAGTAGCTCAACCAATTTTTCCTTTTCTATTGCTGTCAAATGTATACTGACTCGGGTTTCTCTAACCGACTCGTCATCTCCAAAGTTGACTATCTCTGTCTCATCCAGGTTGGGATTTTTATTATCTGCAAGGTTCCTCAAGTCGTTAGTAAGGTGTTCAGGCATCATAGTTTCCTCATCATATTCTTCACATTCATCTTCATTGACTTTACTTAGTTCATCGTGTTCGTGACATGTCATGACATTGGCAAGTTTAGATTCATTTTTATTGAAAAGAAAATAAAGCAATCATGTTAGATAGAAAGAATTTAAATGTATATATCAGAAAGTAATTTGCAGAGGTAAGATAAAAAATAAACGAGGTTTTTCATTGGAAAAAAGGTGTACAAACTTTGATCATGACTCATGTCAATGTGAGTCCTTTCTTTTTTAAACATTACGATGAAAATAAAGTGACATAAAAGTTTATTTCGGGCCTCGTCCGAACTACACCGATTTTCAAAAGTAAAACTTCAAATTCTTGTCTTTGTCTACCAAGCAATTCGATGAATCATAAGTGGAGTGGCCACCCAATTCTGTAGCATCTCTTCAGGTTTGGCATCTCGGATGGTGGGTGTCGCAGTGCATTCTTCCAAGATCACAGCACAATCTCCTTCATCAAAAAATCATCCCATCCCTTCCACTAGACCATCACTCTCGGACTCTAAAGCTTTAGCAACAAATAACTGGTACAATTCTGGAATAGGCTTTGGTATATCAAGGCCATGTTTCTTCCTTGCTTCTGCTTCGAATAATTCC</gDNA_template>
            <first_frame> *  V  A  Q  P  I  F  P  F  L  L  L  S  N  V  Y  *  L  G  F  L  *  P  T  R  H  L  Q  S  *  L  S  L  S  H  P  G  W  D  F  Y  Y  L  Q  G  S  S  S  R  *  *  G  V  Q  A  S  *  F  P  H  H  I  L  H  I  H  L  H  *  L  Y  L  V  H  R  V  R  D  M  S  *  H  W  Q  V  *  I  H  F  Y  *  K  E  N  K  A  I  M  L  D  R  K  N  L  N  V  Y  I  R  K  *  F  A  E  V  R  *  K  I  N  E  V  F  H  W  K  K  G  V  Q  T  L  I  M  T  H  V  N  V  S  P  F  F  F  K  H  Y  D  E  N  K  V  T  *  K  F  I  S  G  L  V  R  T  T  P  I  F  K  S  K  T  S  N  S  C  L  C  L  P  S  N  S  M  N  H  K  W  S  G  H  P  I  L  *  H  L  F  R  F  G  I  S  D  G  G  C  R  S  A  F  F  Q  D  H  S  T  I  S  F  I  K  K  S  S  H  P  F  H  *  T  I  T  L  G  L  *  S  F  S  N  K  *  L  V  Q  F  W  N  R  L  W  Y  I  K  A  M  F  L  P  C  F  C  F  E  *  F  </first_frame>
            <second_frame>  K  *  L  N  Q  F  F  L  F  Y  C  C  Q  M  Y  T  D  S  G  F  S  N  R  L  V  I  S  K  V  D  Y  L  C  L  I  Q  V  G  I  F  I  I  C  K  V  P  Q  V  V  S  K  V  F  R  H  H  S  F  L  I  I  F  F  T  F  I  F  I  D  F  T  *  F  I  V  F  V  T  C  H  D  I  G  K  F  R  F  I  F  I  E  K  K  I  K  Q  S  C  *  I  E  R  I  *  M  Y  I  S  E  S  N  L  Q  R  *  D  K  K  *  T  R  F  F  I  G  K  K  V  Y  K  L  *  S  *  L  M  S  M  *  V  L  S  F  L  N  I  T  M  K  I  K  *  H  K  S  L  F  R  A  S  S  E  L  H  R  F  S  K  V  K  L  Q  I  L  V  F  V  Y  Q  A  I  R  *  I  I  S  G  V  A  T  Q  F  C  S  I  S  S  G  L  A  S  R  M  V  G  V  A  V  H  S  S  K  I  T  A  Q  S  P  S  S  K  N  H  P  I  P  S  T  R  P  S  L  S  D  S  K  A  L  A  T  N  N  W  Y  N  S  G  I  G  F  G  I  S  R  P  C  F  F  L  A  S  A  S  N  N  S </second_frame>
            <third_frame>   S  S  S  T  N  F  S  F  S  I  A  V  K  C  I  L  T  R  V  S  L  T  D  S  S  S  P  K  L  T  I  S  V  S  S  R  L  G  F  L  L  S  A  R  F  L  K  S  L  V  R  C  S  G  I  I  V  S  S  S  Y  S  S  H  S  S  S  L  T  L  L  S  S  S  C  S  *  H  V  M  T  L  A  S  L  D  S  F  L  L  K  R  K  *  S  N  H  V  R  *  K  E  F  K  C  I  Y  Q  K  V  I  C  R  G  K  I  K  N  K  R  G  F  S  L  E  K  R  C  T  N  F  D  H  D  S  C  Q  C  E  S  F  L  F  *  T  L  R  *  K  *  S  D  I  K  V  Y  F  G  P  R  P  N  Y  T  D  F  Q  K  *  N  F  K  F  L  S  L  S  T  K  Q  F  D  E  S  *  V  E  W  P  P  N  S  V  A  S  L  Q  V  W  H  L  G  W  W  V  S  Q  C  I  L  P  R  S  Q  H  N  L  L  H  Q  K  I  I  P  S  L  P  L  D  H  H  S  R  T  L  K  L  *  Q  Q  I  T  G  T  I  L  E  *  A  L  V  Y  Q  G  H  V  S  S  L  L  L  L  R  I  I   </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C12HBa0144B17.1" strand="+"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="46279" stop="46527"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>249</number_coding_nucleotides>
                  <number_encoded_amino_acids>83</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>IISGVATQFCSISSGLASRMVGVAVHSSKITAQSPSSKNHPIPSTRPSLSDSKALATNNWYNSGIGFGISRPCFFLASASNNS</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C12HBa0144B17.1" strand="+"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="45731" stop="45961"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>228</number_coding_nucleotides>
                  <number_encoded_amino_acids>76</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>SSSTNFSFSIAVKCILTRVSLTDSSSPKLTISVSSRLGFLLSARFLKSLVRCSGIIVSSSYSSHSSSLTLLSSSCS*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C12HBa0144B17.1" strand="+"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="3"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="45736" stop="45945"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>207</number_coding_nucleotides>
                  <number_encoded_amino_acids>69</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LNQFFLFYCCQMYTDSGFSNRLVISKVDYLCLIQVGIFIICKVPQVVSKVFRHHSFLIIFFTFIFIDFT*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="4" PGL_strand="+" PGL_start="102952" PGL_stop="104704"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="102952" e_stop="103052"/>
            <exon e_start="103432" e_stop="103522"/>
            <exon e_start="103602" e_stop="103785"/>
            <exon e_start="104386" e_stop="104704"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.992" acc_prob="1.000" e_score="0.990"/>
          <exon-intron don_prob="0.995" acc_prob="0.999" e_score="0.989"/>
          <exon-intron don_prob="0.999" acc_prob="0.992" e_score="1.000"/>
          <exon-only e_score="1.000"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="0.990">
            <gDNA_exon_boundary e_start="102952" e_stop="103052" e_length="101"/>
          </exon>
          <intron i_serial="1" don_prob="0.992" acc_prob="1.000">
            <gDNA_intron_boundary i_start="103053" i_stop="103431" i_length="379"/>
          </intron>
          <exon e_serial="2" e_score="0.989">
            <gDNA_exon_boundary e_start="103432" e_stop="103522" e_length="91"/>
          </exon>
          <intron i_serial="2" don_prob="0.995" acc_prob="0.999">
            <gDNA_intron_boundary i_start="103523" i_stop="103601" i_length="79"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="103602" e_stop="103785" e_length="184"/>
          </exon>
          <intron i_serial="3" don_prob="0.999" acc_prob="0.992">
            <gDNA_intron_boundary i_start="103786" i_stop="104385" i_length="600"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="104386" e_stop="104704" e_length="319"/>
          </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="102952" stop="103052"/>
              <exon start="103432" stop="103522"/>
              <exon start="103602" stop="103785"/>
              <exon start="104386" stop="104704"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U334937" 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="4" AGS_serial="1" gDNA_strand="+"/>
          <translation>
            <gDNA_template>AAAGATCTGCAGCGAAGATGGAGGCAGCAAGAAGTGTGAAAGATGTTTCCCCCCATGATTTTGTCAAGGCTTATGCCGCTCATCTCAAGCGCTCCGGAAAG : ATGGAGCTTCCTGAATGGACTGATATAGTTAAGACTGGTAAGCTAAAGGAGCTTGCCCCATATGATGCTGATTGGTACTACATCAGAGCTG : CTTCCATGGCAAGGAAGATCTATTTGAGAGGAGGTATTGGTGTTGGTGGTTTCCGAAGAATCTATGGTGGAAACCAGAGGAATGGAAGCCGTCCACGTCACTTTTGCAAGAGCAGTGGTTCAGTTGCACGCCACATTCTTCAACAGTTGCAGAACATGAACATCATTGACTTTGAGCCTAAGGG : CGGAAGGAGGATCACATCCAGTGGTCAGCGGGATCTTGACCAAGTTGCCGGAAGAATTGCTGTTGCTTGTTAAGAGAGAGATGAGTTCATTCAATTTTATGAATACATGAGTTAGCTCAAACTTATTGTTTCTGTTTGGACCTAAATAGATTTAGGGTATTGTTGAATTAAATTGTGGATGTTTTGCCTTTTCAGAATTGTCTTTCTCAGTATGTCAAGTTTTGCCCTTTTAGTACCCTGAAGTGTGTATTGTGGCATATGTTGCATTCAATGCATCATTACTTCATAATTATACATAAATCCCTGAGATTCAGTGCTT</gDNA_template>
            <first_frame> K  D  L  Q  R  R  W  R  Q  Q  E  V  *  K  M  F  P  P  M  I  L  S  R  L  M  P  L  I  S  S  A  P  E  R :   W  S  F  L  N  G  L  I  *  L  R  L  V  S  *  R  S  L  P  H  M  M  L  I  G  T  T  S  E  L  :  L  P  W  Q  G  R  S  I  *  E  E  V  L  V  L  V  V  S  E  E  S  M  V  E  T  R  G  M  E  A  V  H  V  T  F  A  R  A  V  V  Q  L  H  A  T  F  F  N  S  C  R  T  *  T  S  L  T  L  S  L  R   : A  E  G  G  S  H  P  V  V  S  G  I  L  T  K  L  P  E  E  L  L  L  L  V  K  R  E  M  S  S  F  N  F  M  N  T  *  V  S  S  N  L  L  F  L  F  G  P  K  *  I  *  G  I  V  E  L  N  C  G  C  F  A  F  S  E  L  S  F  S  V  C  Q  V  L  P  F  *  Y  P  E  V  C  I  V  A  Y  V  A  F  N  A  S  L  L  H  N  Y  T  *  I  P  E  I  Q  C   </first_frame>
            <second_frame>  K  I  C  S  E  D  G  G  S  K  K  C  E  R  C  F  P  P  *  F  C  Q  G  L  C  R  S  S  Q  A  L  R  K   : D  G  A  S  *  M  D  *  Y  S  *  D  W  *  A  K  G  A  C  P  I  *  C  *  L  V  L  H  Q  S  C :   F  H  G  K  E  D  L  F  E  R  R  Y  W  C  W  W  F  P  K  N  L  W  W  K  P  E  E  W  K  P  S  T  S  L  L  Q  E  Q  W  F  S  C  T  P  H  S  S  T  V  A  E  H  E  H  H  *  L  *  A  *  G  :  R  K  E  D  H  I  Q  W  S  A  G  S  *  P  S  C  R  K  N  C  C  C  L  L  R  E  R  *  V  H  S  I  L  *  I  H  E  L  A  Q  T  Y  C  F  C  L  D  L  N  R  F  R  V  L  L  N  *  I  V  D  V  L  P  F  Q  N  C  L  S  Q  Y  V  K  F  C  P  F  S  T  L  K  C  V  L  W  H  M  L  H  S  M  H  H  Y  F  I  I  I  H  K  S  L  R  F  S  A  </second_frame>
            <third_frame>   R  S  A  A  K  M  E  A  A  R  S  V  K  D  V  S  P  H  D  F  V  K  A  Y  A  A  H  L  K  R  S  G  K  :  M  E  L  P  E  W  T  D  I  V  K  T  G  K  L  K  E  L  A  P  Y  D  A  D  W  Y  Y  I  R  A   : A  S  M  A  R  K  I  Y  L  R  G  G  I  G  V  G  G  F  R  R  I  Y  G  G  N  Q  R  N  G  S  R  P  R  H  F  C  K  S  S  G  S  V  A  R  H  I  L  Q  Q  L  Q  N  M  N  I  I  D  F  E  P  K  G :   G  R  R  I  T  S  S  G  Q  R  D  L  D  Q  V  A  G  R  I  A  V  A  C  *  E  R  D  E  F  I  Q  F  Y  E  Y  M  S  *  L  K  L  I  V  S  V  W  T  *  I  D  L  G  Y  C  *  I  K  L  W  M  F  C  L  F  R  I  V  F  L  S  M  S  S  F  A  L  L  V  P  *  S  V  Y  C  G  I  C  C  I  Q  C  I  I  T  S  *  L  Y  I  N  P  *  D  S  V  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="C12HBa0144B17.1" strand="+"/>
                <serials PGL_serial="4" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="102954" stop="103052"/>
                    <exon start="103432" stop="103522"/>
                    <exon start="103602" stop="103785"/>
                    <exon start="104386" stop="104458"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>444</number_coding_nucleotides>
                  <number_encoded_amino_acids>148</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>RSAAKMEAARSVKDVSPHDFVKAYAAHLKRSGKMELPEWTDIVKTGKLKELAPYDADWYYIRAASMARKIYLRGGIGVGGFRRIYGGNQRNGSRPRHFCKSSGSVARHILQQLQNMNIIDFEPKGGRRITSSGQRDLDQVAGRIAVAC*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 35 chains have been computed
$ 
$ memory statistics:
$ 8400 bytes spliced alignments in total
$ 4 spliced alignments have been stored
$ 2100 bytes was the average size of a spliced alignment
$ 9152 bytes predicted gene locations in total
$ 4 predicted gene locations have been stored
$ 2288 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 41 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-07 14:26:40
-->
