<?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="2009-01-19 11:20:30"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C09SLf0040K20-Bhtyp/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C09SLf0040K20-Bhtyp/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-C09SLf0040K20-Bhtyp/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U346757" ref_strand="+" ref_description="SGN-U346757        Tomato 200607 #1 [1 ESTs aligned] arabidopsis/peptide: AT2G30310.1 | Symbol: None | GDSL-motif lipase/hydrolase family protein, similar to family II lipases EXL3 GI:15054386, EXL1 GI:15054382 from (Arabidopsis thaliana); contains Pfam profile PF00657: GDSL-like Lipase/Acylhydrolase | chr2:12930132-12931448 FORWARD | Aliases: T9D9.12, T9D9_12 (evalue: 9e-91, score=330) genbank/nr: gi|15227734|ref|NP_180590.1| GDSL-motif lipase/hydrolase protein [Arabidopsis thaliana] gi|25336269|pir||H84706 probable GDSL-motif lipase/hydrolase [imported] - Arabidopsis thaliana gi|2347208|gb|AAC16947.1| putative GDSL-motif lipase/hydrolase [Arabidopsis thaliana](evalue: 7e-89, score=330)">
      <seq>gggtattgctattacctgttttgctttcattctattggtccaacattgcatcatcatcaatgcgaaatcggtgcccaagttccctgccattctcatctttggagattcaacagttgatactggaaataacaattacatatctacaatatttcaaggtaatcatcgtccgtatggggaaaactttcctgggcggattcccacaggaagattttcggatgggaaactggtaccggactttttggcatctatgttagggatcaaagaatacattcctcctttcctacaaccagatctatcaaacaatgatcttctaactggtgtcagctttgcatctgctggctccggatatgatgacctaacaacaacagcatctaaagtaatccctatgtctgatcaaataaaatattttgagcaatacatacagaacctccaacttattattggagaagagaaagctcagaaactcgttagtcgtgcattgattgttataagtgcagggactaacgacttcatattcaatttctatgatatcccaacaagaagacatcaatataatataacaggatatcaagattttttgcagagtctactccaaaactttgttgaggatctatataatcttggttgtcggaacatgcttgttgctgggcttcctcctgttggttgtcttccaatacaaataactgcaaagtccccatttctgagaaagtgcattaaagaggagaattttgatgcccaatcctataatgtcaaacttgcaacattgctaaaacaaatacaagacgcccttttaggaagcaacatcgtgtattcagattcatatcatccctttatgcatatgat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09SLf0040K20-Bhtyp/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C09SLf0040K20.1" temp_strand="+" temp_description="C09SLf0040K20.1  AC234215.1 htgs_phase:3 submitted_to_sgn_as:gnl|gbrgsp|C09SLf0040K20 upload_account_name:spain (1 - 36062)">
        <position start="14653" stop="16174"/>
      </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="14953" g_stop="15559" g_length="607"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="607" r_length="607" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="15560" i_stop="15638" i_length="79">
            <donor d_prob="0.996" d_score="1.00"/>
            <acceptor a_prob="0.987" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="15639" g_stop="15874" g_length="236"/>
          <reference_exon_boundary r_type="cDNA" r_start="608" r_stop="843" r_length="236" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09SLf0040K20.1" gen_strand="+" ref_id="SGN-U346757" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>843</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09SLf0040K20.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U346757" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="14953" e_stop="15559"/>
          <exon e_start="15639" e_stop="15874"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GGGTATTGCTATTACCTGTTTTGCTTTCATTCTATTGGTCCAACATTGCATCATCATCAATGCGAAATCGGTGCCCAAGTTCCCTGCCATTCTCATCTTTGGAGATTCAACAGTTGATACTGGAAATAACAATTACATATCTACAATATTTCAAGGTAATCATCGTCCGTATGGGGAAAACTTTCCTGGGCGGATTCCCACAGGAAGATTTTCGGATGGGAAACTGGTACCGGACTTTTTGGCATCTATGTTAGGGATCAAAGAATACATTCCTCCTTTCCTACAACCAGATCTATCAAACAATGATCTTCTAACTGGTGTCAGCTTTGCATCTGCTGGCTCCGGATATGATGACCTAACAACAACAGCATCTAAAGTAATCCCTATGTCTGATCAAATAAAATATTTTGAGCAATACATACAGAACCTCCAACTTATTATTGGAGAAGAGAAAGCTCAGAAACTCGTTAGTCGTGCATTGATTGTTATAAGTGCAGGGACTAACGACTTCATATTCAATTTCTATGATATCCCAACAAGAAGACATCAATATAATATAACAGGATATCAAGATTTTTTGCAGAGTCTACTCCAAAACTTTGTTGAGGTATGTAATTATAATTCTAACACGTAATTATAACTCTACAAGTCAAATCATGAGTCTCATTGTTCCATTACCTTTTCAGGATCTATATAATCTTGGTTGTCGGAACATGCTTGTTGCTGGGCTTCCTCCTGTTGGTTGTCTTCCAATACAAATAACTGCAAAGTCCCCATTTCTGAGAAAGTGCATTAAAGAGGAGAATTTTGATGCCCAATCCTATAATGTCAAACTTGCAACATTGCTAAAACAAATACAAGACGCCCTTTTAGGAAGCAACATCGTGTATTCAGATTCATATCATCCCTTTATGCATATGAT</genome_strand>
        <mrna_strand>GGGTATTGCTATTACCTGTTTTGCTTTCATTCTATTGGTCCAACATTGCATCATCATCAATGCGAAATCGGTGCCCAAGTTCCCTGCCATTCTCATCTTTGGAGATTCAACAGTTGATACTGGAAATAACAATTACATATCTACAATATTTCAAGGTAATCATCGTCCGTATGGGGAAAACTTTCCTGGGCGGATTCCCACAGGAAGATTTTCGGATGGGAAACTGGTACCGGACTTTTTGGCATCTATGTTAGGGATCAAAGAATACATTCCTCCTTTCCTACAACCAGATCTATCAAACAATGATCTTCTAACTGGTGTCAGCTTTGCATCTGCTGGCTCCGGATATGATGACCTAACAACAACAGCATCTAAAGTAATCCCTATGTCTGATCAAATAAAATATTTTGAGCAATACATACAGAACCTCCAACTTATTATTGGAGAAGAGAAAGCTCAGAAACTCGTTAGTCGTGCATTGATTGTTATAAGTGCAGGGACTAACGACTTCATATTCAATTTCTATGATATCCCAACAAGAAGACATCAATATAATATAACAGGATATCAAGATTTTTTGCAGAGTCTACTCCAAAACTTTGTTGAG...............................................................................GATCTATATAATCTTGGTTGTCGGAACATGCTTGTTGCTGGGCTTCCTCCTGTTGGTTGTCTTCCAATACAAATAACTGCAAAGTCCCCATTTCTGAGAAAGTGCATTAAAGAGGAGAATTTTGATGCCCAATCCTATAATGTCAAACTTGCAACATTGCTAAAACAAATACAAGACGCCCTTTTAGGAAGCAACATCGTGTATTCAGATTCATATCATCCCTTTATGCATATGAT</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="14953" PGL_stop="15874"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="14953" e_stop="15559"/>
            <exon e_start="15639" e_stop="15874"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.996" acc_prob="0.987" 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="14953" e_stop="15559" e_length="607"/>
          </exon>
          <intron i_serial="1" don_prob="0.996" acc_prob="0.987">
            <gDNA_intron_boundary i_start="15560" i_stop="15638" i_length="79"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="15639" e_stop="15874" e_length="236"/>
          </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="14953" stop="15559"/>
              <exon start="15639" stop="15874"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U346757" 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>GGGTATTGCTATTACCTGTTTTGCTTTCATTCTATTGGTCCAACATTGCATCATCATCAATGCGAAATCGGTGCCCAAGTTCCCTGCCATTCTCATCTTTGGAGATTCAACAGTTGATACTGGAAATAACAATTACATATCTACAATATTTCAAGGTAATCATCGTCCGTATGGGGAAAACTTTCCTGGGCGGATTCCCACAGGAAGATTTTCGGATGGGAAACTGGTACCGGACTTTTTGGCATCTATGTTAGGGATCAAAGAATACATTCCTCCTTTCCTACAACCAGATCTATCAAACAATGATCTTCTAACTGGTGTCAGCTTTGCATCTGCTGGCTCCGGATATGATGACCTAACAACAACAGCATCTAAAGTAATCCCTATGTCTGATCAAATAAAATATTTTGAGCAATACATACAGAACCTCCAACTTATTATTGGAGAAGAGAAAGCTCAGAAACTCGTTAGTCGTGCATTGATTGTTATAAGTGCAGGGACTAACGACTTCATATTCAATTTCTATGATATCCCAACAAGAAGACATCAATATAATATAACAGGATATCAAGATTTTTTGCAGAGTCTACTCCAAAACTTTGTTGAG : GATCTATATAATCTTGGTTGTCGGAACATGCTTGTTGCTGGGCTTCCTCCTGTTGGTTGTCTTCCAATACAAATAACTGCAAAGTCCCCATTTCTGAGAAAGTGCATTAAAGAGGAGAATTTTGATGCCCAATCCTATAATGTCAAACTTGCAACATTGCTAAAACAAATACAAGACGCCCTTTTAGGAAGCAACATCGTGTATTCAGATTCATATCATCCCTTTATGCATATGAT</gDNA_template>
            <first_frame> G  Y  C  Y  Y  L  F  C  F  H  S  I  G  P  T  L  H  H  H  Q  C  E  I  G  A  Q  V  P  C  H  S  H  L  W  R  F  N  S  *  Y  W  K  *  Q  L  H  I  Y  N  I  S  R  *  S  S  S  V  W  G  K  L  S  W  A  D  S  H  R  K  I  F  G  W  E  T  G  T  G  L  F  G  I  Y  V  R  D  Q  R  I  H  S  S  F  P  T  T  R  S  I  K  Q  *  S  S  N  W  C  Q  L  C  I  C  W  L  R  I  *  *  P  N  N  N  S  I  *  S  N  P  Y  V  *  S  N  K  I  F  *  A  I  H  T  E  P  P  T  Y  Y  W  R  R  E  S  S  E  T  R  *  S  C  I  D  C  Y  K  C  R  D  *  R  L  H  I  Q  F  L  *  Y  P  N  K  K  T  S  I  *  Y  N  R  I  S  R  F  F  A  E  S  T  P  K  L  C  *   : G  S  I  *  S  W  L  S  E  H  A  C  C  W  A  S  S  C  W  L  S  S  N  T  N  N  C  K  V  P  I  S  E  K  V  H  *  R  G  E  F  *  C  P  I  L  *  C  Q  T  C  N  I  A  K  T  N  T  R  R  P  F  R  K  Q  H  R  V  F  R  F  I  S  S  L  Y  A  Y  D </first_frame>
            <second_frame>  G  I  A  I  T  C  F  A  F  I  L  L  V  Q  H  C  I  I  I  N  A  K  S  V  P  K  F  P  A  I  L  I  F  G  D  S  T  V  D  T  G  N  N  N  Y  I  S  T  I  F  Q  G  N  H  R  P  Y  G  E  N  F  P  G  R  I  P  T  G  R  F  S  D  G  K  L  V  P  D  F  L  A  S  M  L  G  I  K  E  Y  I  P  P  F  L  Q  P  D  L  S  N  N  D  L  L  T  G  V  S  F  A  S  A  G  S  G  Y  D  D  L  T  T  T  A  S  K  V  I  P  M  S  D  Q  I  K  Y  F  E  Q  Y  I  Q  N  L  Q  L  I  I  G  E  E  K  A  Q  K  L  V  S  R  A  L  I  V  I  S  A  G  T  N  D  F  I  F  N  F  Y  D  I  P  T  R  R  H  Q  Y  N  I  T  G  Y  Q  D  F  L  Q  S  L  L  Q  N  F  V  E  :  D  L  Y  N  L  G  C  R  N  M  L  V  A  G  L  P  P  V  G  C  L  P  I  Q  I  T  A  K  S  P  F  L  R  K  C  I  K  E  E  N  F  D  A  Q  S  Y  N  V  K  L  A  T  L  L  K  Q  I  Q  D  A  L  L  G  S  N  I  V  Y  S  D  S  Y  H  P  F  M  H  M   </second_frame>
            <third_frame>   V  L  L  L  P  V  L  L  S  F  Y  W  S  N  I  A  S  S  S  M  R  N  R  C  P  S  S  L  P  F  S  S  L  E  I  Q  Q  L  I  L  E  I  T  I  T  Y  L  Q  Y  F  K  V  I  I  V  R  M  G  K  T  F  L  G  G  F  P  Q  E  D  F  R  M  G  N  W  Y  R  T  F  W  H  L  C  *  G  S  K  N  T  F  L  L  S  Y  N  Q  I  Y  Q  T  M  I  F  *  L  V  S  A  L  H  L  L  A  P  D  M  M  T  *  Q  Q  Q  H  L  K  *  S  L  C  L  I  K  *  N  I  L  S  N  T  Y  R  T  S  N  L  L  L  E  K  R  K  L  R  N  S  L  V  V  H  *  L  L  *  V  Q  G  L  T  T  S  Y  S  I  S  M  I  S  Q  Q  E  D  I  N  I  I  *  Q  D  I  K  I  F  C  R  V  Y  S  K  T  L  L  R :   I  Y  I  I  L  V  V  G  T  C  L  L  L  G  F  L  L  L  V  V  F  Q  Y  K  *  L  Q  S  P  H  F  *  E  S  A  L  K  R  R  I  L  M  P  N  P  I  M  S  N  L  Q  H  C  *  N  K  Y  K  T  P  F  *  E  A  T  S  C  I  Q  I  H  I  I  P  L  C  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="C09SLf0040K20.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="14954" stop="15559"/>
                    <exon start="15639" stop="15872"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>840</number_coding_nucleotides>
                  <number_encoded_amino_acids>280</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>GIAITCFAFILLVQHCIIINAKSVPKFPAILIFGDSTVDTGNNNYISTIFQGNHRPYGENFPGRIPTGRFSDGKLVPDFLASMLGIKEYIPPFLQPDLSNNDLLTGVSFASAGSGYDDLTTTASKVIPMSDQIKYFEQYIQNLQLIIGEEKAQKLVSRALIVISAGTNDFIFNFYDIPTRRHQYNITGYQDFLQSLLQNFVEDLYNLGCRNMLVAGLPPVGCLPIQITAKSPFLRKCIKEENFDAQSYNVKLATLLKQIQDALLGSNIVYSDSYHPFMHM</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 11 chains have been computed
$ 
$ memory statistics:
$ 2280 bytes spliced alignments in total
$ 1 spliced alignments have been stored
$ 2280 bytes was the average size of a spliced alignment
$ 5560 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5560 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 12 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-19 11:20:43
-->
