<?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="2009-01-15 15:08:13"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0024G05-dipBD/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C04HBa0024G05-dipBD/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-C04HBa0024G05-dipBD/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U342535" ref_strand="+" ref_description="SGN-U342535        Tomato 200607 #1 [1 ESTs aligned] arabidopsis/peptide: | Symbol: R1 | ribonucleoside-diphosphate reductase small chain, putative / ribonucleotide reductase, putative, similar to ribonucleotide reductase GI:4151068 from (Nicotiana tabacum) | chr2:9300435-9304922 FORWARD | Aliases: R1, F7D8.11, F7D8_11(evalue: 9e-88, score=320) genbank/nr: gi|55741418|ref|XP_550374.1| putative ribonucleotide reductase [Oryza sativa (japonica cultivar-group)] >gi|55296229|dbj|BAD67970.1| putative ribonucleotide reductase [Oryza sativa (japonica cultivar-group)] >gi|55296056|dbj|BAD67618.1| putative ribonucleotide reductase [Oryza sativa (japonica cultivar-group)] (evalue: 6e-88, score=327)">
      <seq>ctgcttcctgatatgcatgatatatgataccattgagggcatatatgatactcttacggaatgtgctgttattagcaaatcagctgggggaattggcgtatctgtgcacaacatacgtgctactgggagttatattcgcggaacaaacggaacatcaaatgggattgttcctatgctgcgtgtgtttaatgatactgccagatatgttgatcaagggggtggcaaaagaaagggcgcttttgctgtctaccttgagccttggcatgctgatgtatttgaatttctggatttaaaaaaaaaccatgggaaggaagagaatcgggcacgagaacttttctatgctctttgggtgccagatctattta</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0024G05-dipBD/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0024G05.1" temp_strand="+" temp_description="C04HBa0024G05.1  CU019619.10 htgs_phase:3 submitted_to_sgn_as:C04HBa0024G05 sequenced_by:sanger upload_account_name:uk">
        <position start="81670" stop="82884"/>
      </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="81970" g_stop="82202" g_length="233"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="233" r_length="233" r_score="0.983"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="82203" i_stop="82296" i_length="94">
            <donor d_prob="0.901" d_score="1.00"/>
            <acceptor a_prob="0.913" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="82297" g_stop="82373" g_length="77"/>
          <reference_exon_boundary r_type="cDNA" r_start="234" r_stop="310" r_length="77" r_score="0.987"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="82374" i_stop="82529" i_length="156">
            <donor d_prob="0.998" d_score="0.98"/>
            <acceptor a_prob="0.964" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="82530" g_stop="82584" g_length="55"/>
          <reference_exon_boundary r_type="cDNA" r_start="311" r_stop="365" r_length="55" r_score="0.982"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0024G05.1" gen_strand="+" ref_id="SGN-U342535" ref_strand="+">
        <total_alignment_score>0.984</total_alignment_score>
        <cumulative_length_of_scored_exons>365</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0024G05.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U342535" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="81970" e_stop="82202"/>
          <exon e_start="82297" e_stop="82373"/>
          <exon e_start="82530" e_stop="82584"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTGCTTCCTGATATGCATGAAAGATGATAGCATTGAGGGCATATATGATACTCTTACGGAATGTGCTGTTATTAGCAAATCAGCTGGGGGAATTGGCGTATCTGTGCACAACATACGTGCTACTGGGAGTTATATTCGTGGAACAAACGGAACATCAAATGGGATTGTTCCTATGCTGCGTGTGTTTAATGATACTGCCAGATATGTTGATCAAGGGGGTGGCAAAAGAAAGGGTGTGTCCTCATTTTTGTGCTTGTTTAGATAATTCTAGAAGTTTAGGGTGTAGAGACTACCTTCACTTTTCTCACTCTGTAATGCTGTGTTTAGGCGCTTTTGCTGTCTACCTTGAGCCTTGGCATGCTGATGTATTTGAATTTCTGGATTTAAGAAAAAACCATGGGAAGGTATGGTACTCTTTTTTATCATCAATTGTTTAATATATTGTCTATTGGGCCTGCACCTGCTCTCTGTCACTGCACTAGATTGCTGTACTCCTTTCATATGGCAAAGCTTGTCTGTACTCAGCAATTTGACAAGACATGATGTTTCCTTTTCTTCAGGAAGAGAATCGGGCACGAGATCTTTTCTATGCTCTTTGGGTGCCAGATCTATTTA</genome_strand>
        <mrna_strand>CTGCTTCCTGATATGCATGATATATGATACCATTGAGGGCATATATGATACTCTTACGGAATGTGCTGTTATTAGCAAATCAGCTGGGGGAATTGGCGTATCTGTGCACAACATACGTGCTACTGGGAGTTATATTCGCGGAACAAACGGAACATCAAATGGGATTGTTCCTATGCTGCGTGTGTTTAATGATACTGCCAGATATGTTGATCAAGGGGGTGGCAAAAGAAAGG..............................................................................................GCGCTTTTGCTGTCTACCTTGAGCCTTGGCATGCTGATGTATTTGAATTTCTGGATTTAAAAAAAAACCATGGGAAG............................................................................................................................................................GAAGAGAATCGGGCACGAGAACTTTTCTATGCTCTTTGGGTGCCAGATCTATTTA</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-C04HBa0024G05-dipBD/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U344035" ref_strand="+" ref_description="SGN-U344035        Tomato 200607 #1 [1 ESTs aligned] arabidopsis/peptide: | Symbol: R1 | ribonucleoside-diphosphate reductase small chain, putative / ribonucleotide reductase, putative, similar to ribonucleotide reductase GI:4151068 from (Nicotiana tabacum) | chr2:9300435-9304922 FORWARD | Aliases: R1, F7D8.11, F7D8_11(evalue: 2e-35, score=144) genbank/nr: gi|4151068|emb|CAA71816.1| ribonucleotide reductase [Nicotiana tabacum](evalue: 3e-41, score=169)">
      <seq>acatgatgatggttctgtgcagaaaatccctgaaattccagatgatcttaaagttatttataagactgtctgggagatcaagcaacggaccctggttgacatggctgtagaccgtggttgctacatagatcagagtcaaagcctcaacatccatatggatcaacccaactttggaaagctcacttcccttcattttcatgcttggtccaggggtttgaaaactggaatgtactatctacgatca</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0024G05-dipBD/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0024G05.1" temp_strand="+" temp_description="C04HBa0024G05.1  CU019619.10 htgs_phase:3 submitted_to_sgn_as:C04HBa0024G05 sequenced_by:sanger upload_account_name:uk">
        <position start="84148" stop="85242"/>
      </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="84448" g_stop="84510" g_length="63"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="63" r_length="63" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="84511" i_stop="84593" i_length="83">
            <donor d_prob="0.985" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="84594" g_stop="84741" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="64" r_stop="211" r_length="148" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="84742" i_stop="84975" i_length="234">
            <donor d_prob="0.996" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="84976" g_stop="85008" g_length="33"/>
          <reference_exon_boundary r_type="cDNA" r_start="212" r_stop="244" r_length="33" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0024G05.1" gen_strand="+" ref_id="SGN-U344035" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>244</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0024G05.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U344035" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="84448" e_stop="84510"/>
          <exon e_start="84594" e_stop="84741"/>
          <exon e_start="84976" e_stop="85008"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ACATGATGATGGTTCTGTGCAGAAAATCCCTGAAATTCCAGATGATCTTAAAGTTATTTATAAGTATGAACTTTCACTAATTACTTGTTCAGTTTTTATATACACTTCATTTCCACTTACATTCTAATACTGTTCACTGACTTCAGGACTGTCTGGGAGATCAAGCAACGGACCCTGGTTGACATGGCTGTAGACCGTGGTTGCTACATAGATCAGAGTCAAAGCCTCAACATCCATATGGATCAACCCAACTTTGGAAAGCTCACTTCCCTTCATTTTCATGCTTGGTCCAGGGTACACTTCAATTTTCACATTATAAGTTTTGTTGATCTTTTGAAGAGTGCATAAGCACTAAGAAATGGTCTGGTATATTGTTACTCAATAGTTTAGTACAAACATCCATTTAAAGAGATCTTTTAGCGACTAGTGAATGTAGTTGTCAGACTACAACAGCATGAACAGATCTTTGTAGGTTCCATCTTCACAGGTCAATTTTGAGTCTGAGTTTCATCTTTCTTGTTATTGTAGGGTTTGAAAACTGGAATGTACTATCTACGATCA</genome_strand>
        <mrna_strand>ACATGATGATGGTTCTGTGCAGAAAATCCCTGAAATTCCAGATGATCTTAAAGTTATTTATAA...................................................................................GACTGTCTGGGAGATCAAGCAACGGACCCTGGTTGACATGGCTGTAGACCGTGGTTGCTACATAGATCAGAGTCAAAGCCTCAACATCCATATGGATCAACCCAACTTTGGAAAGCTCACTTCCCTTCATTTTCATGCTTGGTCCAGG..........................................................................................................................................................................................................................................GGTTTGAAAACTGGAATGTACTATCTACGATCA</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="81970" PGL_stop="82584"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="81970" e_stop="82202"/>
            <exon e_start="82297" e_stop="82373"/>
            <exon e_start="82530" e_stop="82584"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.901" acc_prob="0.913" e_score="0.983"/>
          <exon-intron don_prob="0.998" acc_prob="0.964" e_score="0.987"/>
          <exon-only e_score="0.982"/>
        </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="0.983">
            <gDNA_exon_boundary e_start="81970" e_stop="82202" e_length="233"/>
          </exon>
          <intron i_serial="1" don_prob="0.901" acc_prob="0.913">
            <gDNA_intron_boundary i_start="82203" i_stop="82296" i_length="94"/>
          </intron>
          <exon e_serial="2" e_score="0.987">
            <gDNA_exon_boundary e_start="82297" e_stop="82373" e_length="77"/>
          </exon>
          <intron i_serial="2" don_prob="0.998" acc_prob="0.964">
            <gDNA_intron_boundary i_start="82374" i_stop="82529" i_length="156"/>
          </intron>
          <exon e_serial="3" e_score="0.982">
            <gDNA_exon_boundary e_start="82530" e_stop="82584" e_length="55"/>
          </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="81970" stop="82202"/>
              <exon start="82297" stop="82373"/>
              <exon start="82530" stop="82584"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U342535" 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>CTGCTTCCTGATATGCATGAAAGATGATAGCATTGAGGGCATATATGATACTCTTACGGAATGTGCTGTTATTAGCAAATCAGCTGGGGGAATTGGCGTATCTGTGCACAACATACGTGCTACTGGGAGTTATATTCGTGGAACAAACGGAACATCAAATGGGATTGTTCCTATGCTGCGTGTGTTTAATGATACTGCCAGATATGTTGATCAAGGGGGTGGCAAAAGAAAGG : GCGCTTTTGCTGTCTACCTTGAGCCTTGGCATGCTGATGTATTTGAATTTCTGGATTTAAGAAAAAACCATGGGAAG : GAAGAGAATCGGGCACGAGATCTTTTCTATGCTCTTTGGGTGCCAGATCTATTTA</gDNA_template>
            <first_frame> L  L  P  D  M  H  E  R  *  *  H  *  G  H  I  *  Y  S  Y  G  M  C  C  Y  *  Q  I  S  W  G  N  W  R  I  C  A  Q  H  T  C  Y  W  E  L  Y  S  W  N  K  R  N  I  K  W  D  C  S  Y  A  A  C  V  *  *  Y  C  Q  I  C  *  S  R  G  W  Q  K  K  G :   R  F  C  C  L  P  *  A  L  A  C  *  C  I  *  I  S  G  F  K  K  K  P  W  E   : G  R  E  S  G  T  R  S  F  L  C  S  L  G  A  R  S  I   </first_frame>
            <second_frame>  C  F  L  I  C  M  K  D  D  S  I  E  G  I  Y  D  T  L  T  E  C  A  V  I  S  K  S  A  G  G  I  G  V  S  V  H  N  I  R  A  T  G  S  Y  I  R  G  T  N  G  T  S  N  G  I  V  P  M  L  R  V  F  N  D  T  A  R  Y  V  D  Q  G  G  G  K  R  K   : G  A  F  A  V  Y  L  E  P  W  H  A  D  V  F  E  F  L  D  L  R  K  N  H  G  K  :  E  E  N  R  A  R  D  L  F  Y  A  L  W  V  P  D  L  F  </second_frame>
            <third_frame>   A  S  *  Y  A  *  K  M  I  A  L  R  A  Y  M  I  L  L  R  N  V  L  L  L  A  N  Q  L  G  E  L  A  Y  L  C  T  T  Y  V  L  L  G  V  I  F  V  E  Q  T  E  H  Q  M  G  L  F  L  C  C  V  C  L  M  I  L  P  D  M  L  I  K  G  V  A  K  E  R  :  A  L  L  L  S  T  L  S  L  G  M  L  M  Y  L  N  F  W  I  *  E  K  T  M  G  R :   K  R  I  G  H  E  I  F  S  M  L  F  G  C  Q  I  Y  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="C04HBa0024G05.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="81971" stop="82202"/>
                    <exon start="82297" stop="82373"/>
                    <exon start="82530" stop="82583"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>363</number_coding_nucleotides>
                  <number_encoded_amino_acids>121</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>CFLICMKDDSIEGIYDTLTECAVISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADVFEFLDLRKNHGKEENRARDLFYALWVPDLF</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="84448" PGL_stop="85008"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="84448" e_stop="84510"/>
            <exon e_start="84594" e_stop="84741"/>
            <exon e_start="84976" e_stop="85008"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.985" acc_prob="0.998" e_score="1.000"/>
          <exon-intron don_prob="0.996" 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="84448" e_stop="84510" e_length="63"/>
          </exon>
          <intron i_serial="1" don_prob="0.985" acc_prob="0.998">
            <gDNA_intron_boundary i_start="84511" i_stop="84593" i_length="83"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="84594" e_stop="84741" e_length="148"/>
          </exon>
          <intron i_serial="2" don_prob="0.996" acc_prob="0.999">
            <gDNA_intron_boundary i_start="84742" i_stop="84975" i_length="234"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="84976" e_stop="85008" e_length="33"/>
          </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="84448" stop="84510"/>
              <exon start="84594" stop="84741"/>
              <exon start="84976" stop="85008"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U344035" 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>ACATGATGATGGTTCTGTGCAGAAAATCCCTGAAATTCCAGATGATCTTAAAGTTATTTATAA : GACTGTCTGGGAGATCAAGCAACGGACCCTGGTTGACATGGCTGTAGACCGTGGTTGCTACATAGATCAGAGTCAAAGCCTCAACATCCATATGGATCAACCCAACTTTGGAAAGCTCACTTCCCTTCATTTTCATGCTTGGTCCAGG : GGTTTGAAAACTGGAATGTACTATCTACGATCA</gDNA_template>
            <first_frame> T  *  *  W  F  C  A  E  N  P  *  N  S  R  *  S  *  S  Y  L  *  :  D  C  L  G  D  Q  A  T  D  P  G  *  H  G  C  R  P  W  L  L  H  R  S  E  S  K  P  Q  H  P  Y  G  S  T  Q  L  W  K  A  H  F  P  S  F  S  C  L  V  Q   : G  F  E  N  W  N  V  L  S  T  I  </first_frame>
            <second_frame>  H  D  D  G  S  V  Q  K  I  P  E  I  P  D  D  L  K  V  I  Y  K :   T  V  W  E  I  K  Q  R  T  L  V  D  M  A  V  D  R  G  C  Y  I  D  Q  S  Q  S  L  N  I  H  M  D  Q  P  N  F  G  K  L  T  S  L  H  F  H  A  W  S  R  :  G  L  K  T  G  M  Y  Y  L  R  S </second_frame>
            <third_frame>   M  M  M  V  L  C  R  K  S  L  K  F  Q  M  I  L  K  L  F  I   : R  L  S  G  R  S  S  N  G  P  W  L  T  W  L  *  T  V  V  A  T  *  I  R  V  K  A  S  T  S  I  W  I  N  P  T  L  E  S  S  L  P  F  I  F  M  L  G  P  G :   V  *  K  L  E  C  T  I  Y  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="C04HBa0024G05.1" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="84449" stop="84510"/>
                    <exon start="84594" stop="84741"/>
                    <exon start="84976" stop="85008"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>243</number_coding_nucleotides>
                  <number_encoded_amino_acids>81</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>HDDGSVQKIPEIPDDLKVIYKTVWEIKQRTLVDMAVDRGCYIDQSQSLNIHMDQPNFGKLTSLHFHAWSRGLKTGMYYLRS</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 29 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
$ 6832 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3416 bytes was the average size of a predicted gene location
$ 2 megabytes was the average size of the backtrace matrix
$ 40 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-15 15:08:51
-->
