### Scipio v1.4 (20100627-unreleased) output
# query file    /tmp/ezww2EYuo5qd.fasta
# target file   /genomes/genomes_jgi/Thielavia_heterothallica_ATCC_42464_v1_supercontigs.fasta
# BLAT output   /tmp/7eQTzfuN5wYy.psl
# Timestamp     Thu Jul  1 10:17:16 2010

--- 
Th_CAP1: 
- matchings: 
  - overlap: 
    mismatchlist: []

    prot_start: 0
    nucl_end: 57
    prot_end: 19
    translation: MSSHKAIVSSFVEGAPPGE
    dna_start: 2683209
    type: exon
    seqshifts: []

    undeterminedlist: []

    nucl_start: 0
    seq: atgtcttctcacaaggccatcgtttcctcctttgtggagggagctccaccgggagag
    inframe_stopcodons: []

    dna_end: 2683266
  - dna_start: 2683266
    type: intron
    nucl_start: 57
    seq: gtgagcttgccgcccaatctcttgacctcggcggaggctgcagtcaagaatacttactaactcgcatcgactcag
    dna_end: 2683341
  - overlap: 
    mismatchlist: []

    prot_start: 19
    nucl_end: 76
    prot_end: 25
    translation: LSDVVA
    dna_start: 2683341
    type: exon
    seqshifts: []

    undeterminedlist: []

    nucl_start: 57
    seq: ctctcggacgttgtcgcag
    inframe_stopcodons: []

    dna_end: 2683360
  - dna_start: 2683360
    type: intron
    nucl_start: 76
    seq: gcacgtagttcgcgcacactcggttctaaccgcttcatctgaccgaccccgccgcag
    dna_end: 2683417
  - overlap: 
    mismatchlist: []

    prot_start: 25
    nucl_end: 335
    prot_end: 112
    translation: DIKALTISSPGLVNELGPAFQKYNEEQFTTVKLPGGSQPVIISSHSALGNGRYYDLESSCSFAFDHITQKASAVESYVPEGDGVDLA
    dna_start: 2683417
    type: exon
    seqshifts: []

    undeterminedlist: []

    nucl_start: 76
    seq: acatcaaagccctgaccatctccagcccgggcttggtcaacgagttgggcccggccttccaaaagtataacgaggagcagtttacgacagtcaagcttccggggggtagccagccggttatcatcagctcgcacagtgccctgggcaacggtcggtactacgacctcgagagctcgtgcagcttcgctttcgaccacatcacacaaaaggccagcgcggtggagagctacgtgcccgagggcgacggtgtggatctggc
    inframe_stopcodons: []

    dna_end: 2683676
  - dna_start: 2683676
    type: intron
    nucl_start: 335
    seq: gtatggcctcccgagttaggaggacctcatgatggatacacggctaatgctgcgggttgccag
    dna_end: 2683739
  - overlap: 
    mismatchlist: []

    prot_start: 112
    nucl_end: 473
    prot_end: 158
    translation: KSILKGLSTYVNEHFTNAAYGAYPIENGSKIAIIIVANKYSPNNFW
    dna_start: 2683739
    type: exon
    seqshifts: []

    undeterminedlist: []

    nucl_start: 335
    seq: aaaatcgatcctcaaggggctatcgacctacgttaacgagcacttcacgaacgcggcctacggcgcctaccccatagaaaacggctccaagattgccatcatcatcgttgcgaacaagtacagcccgaacaacttttg
    inframe_stopcodons: []

    dna_end: 2683877
  - dna_start: 2683877
    type: intron
    nucl_start: 473
    seq: gtacggagagcccgaggaacaagaacactcccgccccccacgacttctaccatgctaaccacacctcccag
    dna_end: 2683948
  - overlap: 
    mismatchlist: []

    prot_start: 158
    nucl_end: 819
    prot_end: 273
    translation: NGRWRSLYIFNPASSALEGSIKVDVHYYEDGNVRLLTNKSATATVPSGTGAAIAKEISAGERKYQEELNRSFTSLSEGAFKALRRQLPVTRQKIEWDKVASYRLGQDIGGGSSRR
    dna_start: 2683948
    type: exon
    seqshifts: []

    undeterminedlist: []

    nucl_start: 473
    seq: gaacgggcggtggcgctcgctctacatcttcaacccggcctcgagcgctctggagggatccatcaaggtcgacgtgcactactacgaggacggcaacgtccggctgctgaccaacaagtcggcgacggcgaccgtgccgtccggcaccggggcggctatcgccaaggagatttcggcaggcgagcgcaagtaccaggaagagctgaaccggagcttcactagcctgagcgagggcgctttcaaagcgctgcggagacagctccccgtcacgaggcagaagatcgagtgggacaaggttgcgagctacaggttgggacaggatatcggtggtgggtcgtcgaggagg
    inframe_stopcodons: []

    dna_end: 2684294
  unmatched: 0
  prot_start: 0
  stopcodon: tag
  downstream: tagacgagtacgtccgtagttcgctcgagggccggttattatagtatgtcgaaacacggacaaatgccatctagcacagggtgcagttcataaagaagaggaaagtacaaagagaaaagggaaaaaggctagggaaaagaaaaagaaaaagaaaaaaagaagcgggcaaatgcgcacaaagcaagtgcagtgcggagaaggtgagatctgcgtaatctttcatgtcggccacctcgcgattccgcttaacgcgaagttccagagaggttaccacagtacacagattaccgagagacgcttccgaaggcgagcttaatcggtgcgacggtctggggctggtaagcaactccaaagattgaggtgtgggcggtgggtacactgtcggaggtctgtgggcgtgaaaactagcgggaacaacccgatcccggaaaacggtcaccgcaacccccggagaacacagttcccctccgtcggtacgcatccctggcatgtcttcttgctagctggtctgagcacggccggccagtgcacgcagattcagcaaaatgctgtgtcaacccggatcgcagagtccgaatcgtaccatagtgaatttggacgaatcacagtccggatggcatgattctaaagcgtcctcattggtcacaggggggccaagcggcattcggagtgggactcccgcccaggggctcagcggaattcgagtcgtccacttgcctgcctgtccctccggggttccttctccaaaagccggtcggaacctgttgatctttttcgtgactgttccctctcctctgaccaccgcctttcatcagcccgccgccgcgccgacaccatcgtctctcgtcgttgtcccagtttccgagcttttggtacgcctctcgacctcaattgcctcggatcgcaccgcctatcgagagcgctcgcgtgtaccgtgctaacgaaccacttgtccagagaaaagtccccgacatttcggagtcccgacaacgattcaaggcagtcaagatggcctctaccaaggagctcacctaccaggatgttgccgagcacaacaccaagaaggatctctacgtcgtgatccacgacgagatctacgactgctccaagtttgtggacgagcacccgtaagtgtcatgaattttttttctccctttccagttcgaacctccggccgcttatcatctcccgtgccggtttccgacggattccccgcatccgcccgcccagagataaccgttcatgctaacgagttgaaaacaaacagtggtggtgaggaggtcctactcgacgtcgctggccaggacgccactgaggcgtttgaggatgtcggccacagcgacgaggcccgcgaaacgctcaagcagctcaaagtcggcactttgaagcgcggcgtaagcaacccggaatgcgcagatcgctccaagaggagaagttggaacggataagctgacggcaggacgtttccgtttagcccggcgaccccaagcccaagactcccgcccccggtgccgttgccccagctgccaacaacaccactgccggttttggtgtgggtctctacgccatcatcctcatcggcggtctgatcggttacgctgcctacacctatctccagcaacagcaggctgcggcccaggcctgaatttgtggggtctcaccacttggtgactcgggtagcggaggcagataggagctttatcttatttaatggcgatgctttctttttgggtcactctgcgctacgacattgaattctaggaatcatgatggggaaggctaccagcgtctggtcgagagtgtctcgggttctggcctgggatgtgcttggatggcggcttgtggtgggcgccatgcatagactgctgtctggtaccgacctaggattggcgtcttgcgttttgtcgttgttcaacaaacgggtcatgttaatggctggatgatatctgtattccagatgttcatgtactgggcattgaggcgagcagcaagccaagctc
  additional: 0
  prot_end: 273
  ID: 9
  dna_start: 2683209
  reason: 
  downstream_gap: 
  upstream_gap: 
  target_len: 4696796
  strand: +
  target: scaffold_5
  upstream: gggagggacctcccaaagccgtcgcaagccgacgccgccgtcatccacctcccaatcttcgcatttccacccgcatctcacgcctacttgctcctaaccatgcacggcgaccctccgtgaaagagactggcagaaggagacctcgactcccccatcggcaatgaagcattcgtcattccgcaccctctcgagggcattggcgcgtggttcgcctctctccccgtccgcccctgcgctcgtctgctcccaacgccggcggcagtactcgactcacccgcccaatgcgaggctgaacctacctatcgactactcgacaaccccgttgctgtctcacacatcacaatccgccctgagcaaccccgagctgccgccagaggtgcgcaatggaacgacgaagcgcctgaacctcttccaggccatcaacgacgcgctctcgatcgccctcgccgaggacgagtcggtcatgatcttcggcgaggacgtggcctttggcggcgtcttccgctgcaccggcaagctggccgagacgtacggggccgaccgcgtcttcaacacgccgctgaccgagcagggcatcgtgggcttcgccatcggggtcgccgccgagggcatgcggcccgtcgccgagatccagttcgccgactacgtctaccccgccttcgaccagctggtcaatgaggcggccaagttccgctaccgcgacggcgcctgcggccggagcgtgggcgggctaacggtgcgcatgccctgcggcggcgtcggccacggcgctctctaccattcgcagtcgcccgagagcctgttcacacacatccccggtctgcgggtcatcatgccccggtcgccgctccaggccaaagggctgctgctgtcggccatccgcagcaacgacccctgcgtgttcatggagcccaagatcctgtaccgggccgccgtcgagcaggtccccaccgccgcctacacgctgccactgtccaaggccgaggtgctcaaggaaggatccgacgtcaccattgtctcctatggtcagccgctgtacaagtgcgaggccgccctcaagcaggccgagagggacctgggcatctcggtggaactgatcgacttgcggaccatctacccgtgggacaaggagactgtcttcaagagcgtcaggaagaccgggcggtgtcttgtcgtccacgaggccatgatcaatgctggcgtcggggctgaggtggctgcagcaatccaggaagacccggataccttcatcaggctagaggccccggttgctcgcgtggccgggttcagcatacatacgcccttgatgtatgaggccttcaatgcaccagacgttgcgagtaagtttttcttttcttttcttttcttttctttttttttttttttgcttctttcttcctttctttctctttctctcttcgcagctggattcacgagccgtgctaaccttgttaaggaatatatgacaacatcaagaaagtcctagagtattaaacctattccgaagatagggtatatgacgaagccagttcgctgcgtaaaagcgatcgatcgcgttgagagagaggcgtggcgttggcggggcggagtggcgcattttcggcagaaattggcattaggcttatagttaagacaccgtgtgcaatgcaaatggtcgtcactgaatataaagcaatcgcttatatcgtctgaagcttggcgattttaggttgagttcagggcttcctttgagcgggacacagctgctcgatatcagatgaaactcgggcggtttctctctcccctgcccgctgttcttggcactcctggctgcggcccgcattgtgccccgcatcctcccctactccgtacacgctccgtaattccatcagctgcgcgcccgtcggacaccaccgacaaacgcccggtctgacaccatcaggtaccgcgcaacttacgccgttggaagtgtctgagaacttctttatttcataccggcctgagcgtattcctgagaagca
  score: 1.0
  prot_seq: MSSHKAIVSSFVEGAPPGELSDVVADIKALTISSPGLVNELGPAFQKYNEEQFTTVKLPGGSQPVIISSHSALGNGRYYDLESSCSFAFDHITQKASAVESYVPEGDGVDLAKSILKGLSTYVNEHFTNAAYGAYPIENGSKIAIIIVANKYSPNNFWNGRWRSLYIFNPASSALEGSIKVDVHYYEDGNVRLLTNKSATATVPSGTGAAIAKEISAGERKYQEELNRSFTSLSEGAFKALRRQLPVTRQKIEWDKVASYRLGQDIGGGSSRR
  prot_len: 273
  status: auto
  undetermined: 0
  mismatches: 0
  matches: 273
  dna_end: 2684294