<?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="2009-07-24 21:01:14"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C07HBa0056M08-ne0Au/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C07HBa0056M08-ne0Au/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" 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-C07HBa0056M08-ne0Au/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M2031" ref_strand="+" ref_description="SGN-M2031 T1479 [cos_markers]">
      <seq>atcactcaaaaaggaagaagaagaagaagacaagaggatattggaatgtagaacaataatatttggtgttatacttggaataccgaataattactttcggaaggcgggaaaaagaatccctccccatattgtcaaagccttaaacttctctgacacacaacaatgggggatcttcattctgcagaagaacatggaataactcaaatttcagctgtcatttttgatttggatggtacccttttgagtacagagcacttgacaaaggaaattctgaaggaatttctggctggatacgggaaggtgccagataaggagaaggaaaagaaaagattggggatggcccacaaagagtacgctattggcattgtcagtgattacgacctccctatcacgcccgatcagtatgtccaagctgtcatgcccttttatcatgacttgtggttgcaagcaaaagcgcttcctggtgctaatcgccttataagacatttccataagcatggagttccctttgcccttgcttcaaattccaaaaggaaaaacatagataagaaagtctc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0056M08-ne0Au/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07HBa0056M08.2" temp_strand="+" temp_description="C07HBa0056M08.2  AC212620.2 htgs_phase:2 submitted_to_sgn_as:gi|239582803|gb|AC212620.2| upload_account_name:france Solanum lycopersicum chromosome 7 clone C07HBa0056M08, *** SEQUENCING IN PROGRESS ***, 2 ordered pieces">
        <position start="12388" stop="15237"/>
      </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="12721" g_stop="12789" g_length="69"/>
          <reference_exon_boundary r_type="cDNA" r_start="55" r_stop="123" r_length="69" r_score="0.957"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="12790" i_stop="12891" i_length="102">
            <donor d_prob="0.898" d_score="0.96"/>
            <acceptor a_prob="0.990" a_score="0.82"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="12892" g_stop="13018" g_length="127"/>
          <reference_exon_boundary r_type="cDNA" r_start="124" r_stop="250" r_length="127" r_score="0.921"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="13019" i_stop="13635" i_length="617">
            <donor d_prob="0.951" d_score="1.00"/>
            <acceptor a_prob="0.978" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="13636" g_stop="13822" g_length="187"/>
          <reference_exon_boundary r_type="cDNA" r_start="251" r_stop="437" r_length="187" r_score="0.989"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="13823" i_stop="14817" i_length="995">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="14818" g_stop="14937" g_length="120"/>
          <reference_exon_boundary r_type="cDNA" r_start="438" r_stop="557" r_length="120" r_score="0.992"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07HBa0056M08.2" gen_strand="+" ref_id="SGN-M2031" ref_strand="+">
        <total_alignment_score>0.968</total_alignment_score>
        <cumulative_length_of_scored_exons>503</cumulative_length_of_scored_exons>
        <coverage percentage="0.903" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0056M08.2" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M2031" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="12721" e_stop="12789"/>
          <exon e_start="12892" e_stop="13018"/>
          <exon e_start="13636" e_stop="13822"/>
          <exon e_start="14818" e_stop="14937"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AATAATATTTGGCGTTATACTTGGAATACCGAATAATTACTTTCGGAAGGCGGGAAAAAGAATCCCTGTGTAAGCACCTTTGCCCAATTGCAAATTGGAATTTGATCCTTTCGTTAAAATATCTCTTTAAAATCCTAAACATTCTATGTTATTTTTCTGCTCATTCATCAGATTTCACAGCAAAGACTTAAACTTCTCTGACACACAACAATGGGGGATCTTCATTCTGCAGAAGAACATGGAAAAACTCAAATTTCAGCTGTCATTTTTGATTTGGATGGTACCCTTTTGAGTACAGGTCCTCTTTTTCCACTCCCTTTTTAGTTTTATATTTTTCTGGATTTGTAGCATTTGTGTTTTGGGATCTAGTTTTTTTTTTTGTTACTATAAGTTCAACTGAATCGTGTTTTTGACTCTTGCAATGTATGAATATAGTCCCTGTTTTTAAGGTGTTTGAGTCAGCTTGCGCGTAGTACTTATATCTCTGATGTCATTGTCACCTCCCACCAGCAACCTGTATTAGGTATGAGGTAACTCTGTCCACCAAGTTTATGACATATGAGAAGAAATTAGCTAGTGTTTTTGTCTTTGCTTGGATTTGAATATGAGACCATATGATTTTCAGTCTACTTTATTGACGACCACTAGATCACACCTTTGGGTGCCTCTATAAGTACCATTTTGTGGGATGCAATTTAAGTGGGATGAAGTTTAAGAAAGAAGGATTGAGTTATAAAACTCATAATCTAATTAGGCCCATAGAAACAATTTTAAAAGTGAAGTGCATATGATATGTTAAGGATGCGTATGCACCACGTTACCCGGACTCCACTTGTGGGATTAAACTTGGGTATGTTGTTGTATGCATCTCACTCTGAGCCCGGTGATACTAAATCTTGGATATGTTTGTTTTAGAGCACTTGACAAAGGAAATTCTGAAGGAATTTCTGGCTGGATATGGGAAGGTGCCAGATAAGGAGAAGGAAAAGAAAAGATTGGGGATGGCCCAGAAAGAGTACGCTATTGGCATTGTCAGTGATTACGACCTCCCTATCACGCCCGATCAGTATGTCCAAGCTGTCATGCCCTTTTATCATGACTTGTAAGTGTTTTTTGAACCATGTCTCTCAATATATTAGTTGTTTCTTTTTATTTTGGATATTCACTTGTAAACTACTATAAAGCATAATTGGTTGACACTTGACAGCGGCAGATCTAGTGCATTAGTTATGGATTTGTCCAAATAGAGACGGACCTACAACATAACTTATGGGTTCACGAAAACTCAGTGATTTTTGCTCAAACCCGGTATATGTATCAATCCACTAAATATTGGACTGTGAACCCAATTATTATTGTATATTAACTTGAGGTCACTGTAGGAATCCATAAACTTCAAATCTTGGATCTGTCTTGGAGTCCAAACTAATACCTTTGGTTCAAACTCAATATATGTGTAAAAAGTCCATGAAATAGTATAAAACATAGTATCCGAACACAATAAATTAATAGGTTGAGGTAGAATTCAGAGCTCAAAGCCATTAAGTCCAAATCCTAGATCCACCTATGTTGTTTGATGTCATCTTCTTACAAAATCATCATATTTGTGGATTTCATTGTACTTCATATTGGATAGTAACATGGTTATTGATCCTTACATTCTCCTATTGCTCTTACATGTTGGATATAAGTCTTCTTCATGTTGCTTCAAGCCTTCAAGAGCACATGCATCTTCGCGTTTTCGTACACTGTTACAAAGTTGTATTCTTAATGTCTTCGAGTGAAATGTTCTGTGATAATGTCTCCGATTCAAGTTGATGACATGATGAGAATGAAATACTTGTTGCCATGACATCTTTAATAATTTGATTAGCCACACAATATTCATTCTCTGCTCTGCATAACTAACAGAATCTAGTAAAACACTATGCGCTAGTTGCCTCCACTTGTCTATAATTTTGCACATCATCTCACATTGTATTAACGGTGTGATTAATGAGCTAGGATCAGCTTCCCTGCACTGATTTATGACATTCAATGATTAAGCAATTGGCAACAGAGTATTCATGTATAGTTTTTTTTCCTGTTTTGTTGCAGGTGGTTGCAAGCAAAAGCACTTCCTGGTGCTAATCGCCTTATAAGACATTTCCATAAGCATGGAGTTCCCTTTGCCCTTGCTTCAAATTCCAAAAGGAAAAACATAGATAAGAAAGTCTC</genome_strand>
        <mrna_strand>AATAATATTTGGTGTTATACTTGGAATACCGAATAATTACTTTCGGAAGGCGGGAAAAAGAATCCCTCC......................................................................................................CCATATTGTCAAAGCCTTAAACTTCTCTGACACACAACAATGGGGGATCTTCATTCTGCAGAAGAACATGGAATAACTCAAATTTCAGCTGTCATTTTTGATTTGGATGGTACCCTTTTGAGTACAG.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGCACTTGACAAAGGAAATTCTGAAGGAATTTCTGGCTGGATACGGGAAGGTGCCAGATAAGGAGAAGGAAAAGAAAAGATTGGGGATGGCCCACAAAGAGTACGCTATTGGCATTGTCAGTGATTACGACCTCCCTATCACGCCCGATCAGTATGTCCAAGCTGTCATGCCCTTTTATCATGACTT...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGGTTGCAAGCAAAAGCGCTTCCTGGTGCTAATCGCCTTATAAGACATTTCCATAAGCATGGAGTTCCCTTTGCCCTTGCTTCAAATTCCAAAAGGAAAAACATAGATAAGAAAGTCTC</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>1</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="12721" PGL_stop="14937"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="12721" e_stop="12789"/>
            <exon e_start="12892" e_stop="13018"/>
            <exon e_start="13636" e_stop="13822"/>
            <exon e_start="14818" e_stop="14937"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.898" acc_prob="0.990" e_score="0.957"/>
          <exon-intron don_prob="0.951" acc_prob="0.978" e_score="0.921"/>
          <exon-intron don_prob="0.998" acc_prob="1.000" e_score="0.989"/>
          <exon-only e_score="0.992"/>
        </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="0.957">
            <gDNA_exon_boundary e_start="12721" e_stop="12789" e_length="69"/>
          </exon>
          <intron i_serial="1" don_prob="0.898" acc_prob="0.990">
            <gDNA_intron_boundary i_start="12790" i_stop="12891" i_length="102"/>
          </intron>
          <exon e_serial="2" e_score="0.921">
            <gDNA_exon_boundary e_start="12892" e_stop="13018" e_length="127"/>
          </exon>
          <intron i_serial="2" don_prob="0.951" acc_prob="0.978">
            <gDNA_intron_boundary i_start="13019" i_stop="13635" i_length="617"/>
          </intron>
          <exon e_serial="3" e_score="0.989">
            <gDNA_exon_boundary e_start="13636" e_stop="13822" e_length="187"/>
          </exon>
          <intron i_serial="3" don_prob="0.998" acc_prob="1.000">
            <gDNA_intron_boundary i_start="13823" i_stop="14817" i_length="995"/>
          </intron>
          <exon e_serial="4" e_score="0.992">
            <gDNA_exon_boundary e_start="14818" e_stop="14937" e_length="120"/>
          </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="12721" stop="12789"/>
              <exon start="12892" stop="13018"/>
              <exon start="13636" stop="13822"/>
              <exon start="14818" stop="14937"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M2031" 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>AATAATATTTGGCGTTATACTTGGAATACCGAATAATTACTTTCGGAAGGCGGGAAAAAGAATCCCTGT : ATTTCACAGCAAAGACTTAAACTTCTCTGACACACAACAATGGGGGATCTTCATTCTGCAGAAGAACATGGAAAAACTCAAATTTCAGCTGTCATTTTTGATTTGGATGGTACCCTTTTGAGTACAG : AGCACTTGACAAAGGAAATTCTGAAGGAATTTCTGGCTGGATATGGGAAGGTGCCAGATAAGGAGAAGGAAAAGAAAAGATTGGGGATGGCCCAGAAAGAGTACGCTATTGGCATTGTCAGTGATTACGACCTCCCTATCACGCCCGATCAGTATGTCCAAGCTGTCATGCCCTTTTATCATGACTT : GTGGTTGCAAGCAAAAGCACTTCCTGGTGCTAATCGCCTTATAAGACATTTCCATAAGCATGGAGTTCCCTTTGCCCTTGCTTCAAATTCCAAAAGGAAAAACATAGATAAGAAAGTCTC</gDNA_template>
            <first_frame> N  N  I  W  R  Y  T  W  N  T  E  *  L  L  S  E  G  G  K  K  N  P  C  :  I  S  Q  Q  R  L  K  L  L  *  H  T  T  M  G  D  L  H  S  A  E  E  H  G  K  T  Q  I  S  A  V  I  F  D  L  D  G  T  L  L  S  T   : E  H  L  T  K  E  I  L  K  E  F  L  A  G  Y  G  K  V  P  D  K  E  K  E  K  K  R  L  G  M  A  Q  K  E  Y  A  I  G  I  V  S  D  Y  D  L  P  I  T  P  D  Q  Y  V  Q  A  V  M  P  F  Y  H  D  L :   W  L  Q  A  K  A  L  P  G  A  N  R  L  I  R  H  F  H  K  H  G  V  P  F  A  L  A  S  N  S  K  R  K  N  I  D  K  K  V   </first_frame>
            <second_frame>  I  I  F  G  V  I  L  G  I  P  N  N  Y  F  R  K  A  G  K  R  I  P  V :   F  H  S  K  D  L  N  F  S  D  T  Q  Q  W  G  I  F  I  L  Q  K  N  M  E  K  L  K  F  Q  L  S  F  L  I  W  M  V  P  F  *  V  Q  :  S  T  *  Q  R  K  F  *  R  N  F  W  L  D  M  G  R  C  Q  I  R  R  R  K  R  K  D  W  G  W  P  R  K  S  T  L  L  A  L  S  V  I  T  T  S  L  S  R  P  I  S  M  S  K  L  S  C  P  F  I  M  T   : C  G  C  K  Q  K  H  F  L  V  L  I  A  L  *  D  I  S  I  S  M  E  F  P  L  P  L  L  Q  I  P  K  G  K  T  *  I  R  K  S  </second_frame>
            <third_frame>   *  Y  L  A  L  Y  L  E  Y  R  I  I  T  F  G  R  R  E  K  E  S  L   : Y  F  T  A  K  T  *  T  S  L  T  H  N  N  G  G  S  S  F  C  R  R  T  W  K  N  S  N  F  S  C  H  F  *  F  G  W  Y  P  F  E  Y  R :   A  L  D  K  G  N  S  E  G  I  S  G  W  I  W  E  G  A  R  *  G  E  G  K  E  K  I  G  D  G  P  E  R  V  R  Y  W  H  C  Q  *  L  R  P  P  Y  H  A  R  S  V  C  P  S  C  H  A  L  L  S  *  L  :  V  V  A  S  K  S  T  S  W  C  *  S  P  Y  K  T  F  P  *  A  W  S  S  L  C  P  C  F  K  F  Q  K  E  K  H  R  *  E  S  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="C07HBa0056M08.2" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="12922" stop="13018"/>
                    <exon start="13636" stop="13822"/>
                    <exon start="14818" stop="14935"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>402</number_coding_nucleotides>
                  <number_encoded_amino_acids>134</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>HTTMGDLHSAEEHGKTQISAVIFDLDGTLLSTEHLTKEILKEFLAGYGKVPDKEKEKKRLGMAQKEYAIGIVSDYDLPITPDQYVQAVMPFYHDLWLQAKALPGANRLIRHFHKHGVPFALASNSKRKNIDKKV</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 6 chains have been computed
$ 
$ memory statistics:
$ 2024 bytes spliced alignments in total
$ 1 spliced alignments have been stored
$ 2024 bytes was the average size of a spliced alignment
$ 5624 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5624 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 6 backtrace matrices have been allocated
$ 
$ date finished: 2009-07-24 21:01:18
-->
