### Scipio v1.3 output
# query file    /tmp/MXgT6JrMvK8q.fasta
# target file   /genomes/genomes_ncbi/Fusarium_oxysporum_f__sp__lycopersici_4286_v1_supercontigs.fasta
# BLAT output   /tmp/Ytz84u1jgjo3.psl
# Timestamp     Tue Jun  8 14:32:02 2010

--- 
Protein: 
- matchings: 
  - overlap: 
    mismatchlist: 
    - 17
    prot_start: 0
    nucl_end: 284
    prot_end: 95
    translation: MALVIPYTYIQCPCSDNSPPDLPQARQSQSSDERTFDPRDPRSNYSLYPLEYLLYCEDCQQIRCPRCVNEEVVTYYCPNCLFEVPSSNLRSDGNR
    dna_start: 3169997
    type: exon
    seqshifts: []

    undeterminedlist: []

    nucl_start: 0
    seq: atggcgctcgtgataccttacacgtacatccaatgtccgtgttccgacaactctcccccagatctcccccaagcgcgtcaatcacaatcctccgacgaacgaacctttgacccccgcgatcctcgctcaaactacagcctctaccctctcgagtacctcctctactgcgaagactgccagcaaatacgatgtccgcgatgtgtgaatgaggaggttgttacatattactgcccaaactgcctgtttgaggttcccagtagtaacttgcgcagcgacgggaatag
    inframe_stopcodons: []

    dna_end: 3170281
  - dna_start: 3170281
    type: intron
    nucl_start: 284
    seq: gtaaataacacaaagacgtggtccagactaagcctgacatgcgcctcatag
    dna_end: 3170332
  - overlap: 
    mismatchlist: []

    prot_start: 95
    nucl_end: 1653
    prot_end: 551
    translation: CTRSCYQCPVCIGPLQVMETPIEKDQSHLGADIPGPQYALYCQYCNWTSTEIGIKFDKPNGIHSQLSKINNGGDLKLTAKELKERRKENPDEPPLADSDVDTDLQYANLKSFYQSQLADTNAASSGISPLNDTTGYGSPAASLSRIMAMYTGHGHARKRNGPSEXVMREALSAEEGLKLADLDESAQIKKLHQEGWDATATIQQNLEQAEVQRFQDGLRPIPHLLRTKRSKRCSVCRHIISKPENKVTSTRFKIRLVAKSYIPTITIKPLNPTAGTVPTTQRPQILEERPLKPLTPHHYIITFKNPLFDGIKVTLATPNSTPGRFSSKVTILCPQFDIDANTDMWDDALKDDDRDKKRKGEESSGQPEAGKIWERGRNWVSIILEVVPASLRLDGQKDKSPLKEDEDILEIPMFVRMEWEPDSQQDVGAASAKEKDAQERRELAYWCVLGVGRISHD
    dna_start: 3170332
    type: exon
    seqshifts: 
    - prot_start: 259
      nucl_end: 777
      prot_end: 259
      dna_start: 3170825
      nucl_start: 777
      dna_end: 3170826
    undeterminedlist: 
    - 259
    nucl_start: 284
    seq: atgtacccgaagctgttaccaatgtcccgtgtgtattggtcctctccaggttatggaaacacctatagagaaagaccagtcacaccttggcgccgacatcccagggcctcaatacgcactgtattgccagtactgcaactggacctccaccgagataggcatcaagtttgacaagcctaacggtattcactcgcagctctccaagatcaacaatggaggagatctcaagctcaccgcgaaagaactcaaggagcgtcgcaaggagaacccagatgagccacctcttgccgatagcgatgtcgatacagatcttcagtatgccaatttgaagtcattctaccagtcgcagctcgcagatacaaatgctgcctcgagcggcatatctccactgaatgacactaccggctatggatcgcctgcagcgtcgttgtctcgtatcatggctatgtacactggtcacggacatgcccgcaagcgcaatggtccttcagaatgttatgcgtgaggctctttcggcagaggaaggtctgaaattggcggatctggatgaatcagctcagatcaagaaactgcaccaggaggggtgggatgctacggctactatacagcagaaccttgaacaagcagaggttcagagattccaggatggtttacggcctataccacatctcctcagaacgaagcgctctaagcgttgctctgtgtgtcggcatattatctccaagccagaaaataaggtcacgtcgacacggttcaagatcagacttgtcgcaaagtcgtatatccctacgatcaccatcaagcctctcaaccccacagctggaacagtccctaccacgcagcgtcctcaaattctagaagagcgaccgctcaagcccctcacccctcatcactacatcataaccttcaagaaccctttgttcgatggtatcaaggtcacacttgctacgccaaacagtacacctggcaggttctccagcaaagtgactattctctgtcctcaattcgatattgatgccaacacggatatgtgggatgatgctctgaaggacgatgacagagacaaaaagcgaaaaggtgaagagagcagtggtcagcctgaggccggtaagatttgggagcgagggcgcaactgggtcagcatcatcttggaagtggttccggcttcactccgacttgacggtcaaaaggacaagagtccattgaaggaggatgaggatattctggagatacccatgtttgtgaggatggaatgggagcctgactctcagcaagacgtcggtgcagcatctgcaaaggaaaaggatgctcaggaaaggagggagctggcttattggtgtgtgcttggagttggccgcatcagtcacgat
    inframe_stopcodons: []

    dna_end: 3171702
  unmatched: 0
  prot_start: 0
  stopcodon: taa
  downstream: taaagatagaaaaggcatgcacatgagacatagatctagatacccaataattggacgaagtcatggacgggaagaagtgtttaagttgtcttgtcaaatcatacgcagcttgcttgtaacatttatcaagctactttctttaagacgccaagcccctttttttgaccaaccaaccatttgtgaaaaacactcccagcccgaatcagggaaaaatagtcatttcttctatttcatctcgaaaaaggtaacgcacagacttagtagtcggcgggaccgctctgagggaactcgaagttgacgttgcggcctgtcaaacgtcggtagacctcagagtaggtgtcgaggcggtagtcaacaccaccacgctccttctcgtcgaggatgaccttgaggagcttggagccgtcctccttggtgcggacgcgcttgccgacgatctcgacggggtaggtgagatcctcgaggatggcgtcgtggacagcagtgagagttcgcgaacgggggcgcttctgcttctgggtgttgcgagagcgggcggatcgcttggggcggggcaagatgcggcgagaagcgaggatcaggacatggcggtcagagaacttcttctcgagctcacgggtgagactggggagtattagtattgagtctgagattagaagaatgaggagatatcttaccgctgctggacgcggtggaagccctgcagggaagggacggggacaaagatgacaatagccttcttgccgtggccaacctcgatctagtcaagatcccaagtcagcatgcgagctccaggacgaaaccttggaccgcttcccgtcctgttccacagaagtcaatgatactccggctggcactcctccgccccgacgacatgtgtaagcgcatcaagtcaagtatctctcgaatatcgaggtcattttcgacggaaaagtgcgcggtcgggaggcggagaggccattgcgagaacagtgcagttttcttatgtgggaacaggatttctcgaaacgagacctaagttcggaattctttgtttcatggtattctcacctcacgggcagagacgatctgcagaggtcgcagggcaaccttgaggtcggaggtgttggactcgaggtcgaagagagcctgagcgatgctggtctcaagctcggaggggttctgcctcgaagggctgttgggagcgatcttgttaagggcctgggcgctcattttgacggctggttcgactacgtgggattgacgacgacgaagttgatggtgttgcgcgggccgcttggaatttttgatagtaggcaatttcaaaaagtcgctaaattggggttttaccctttacttttctgtgggcggtccgtgcgtcggtgaggatgttgaggttgatgcctgaggcttgagtctagcacaccgaatcttcaccttgttgtcagtggatccagtcaccaatcgtccagaaggggaaatcgactacacttacacagcgtcccgtgtttcgtggacttgatgcaatgaaaggaaagcaatcaagtcaaaggttgcacagcatttcagaagtattcacttatgaatatgcatgatttcaaatcaactctgcttgaatctaagacacgaagccgtgtaactcctgcagctcaaccacactcacaaccacttcaaatggtagaaagcatctccgagacgtccgatgatgaaacaatgcatcgtttacaacattcgtatcaaacatcctgatcctctatccagtttttactgttacacattctaaccctcaccgccctcggggtcctcctcatcctcatcaccgagctgcttatcaacatcctgctggaccttttcacctgtcgtgtcccttgcgatctcggcagccttcataccgccagccgtgagccacaggaagtgatttgtcttgaactggtcaatctggttgaagaacatgtgaaacctgtcgtgtcttgttagccctgtccgacttgtgcatacgtcagtacttacgagttgtcctt
  additional: 1
  prot_end: 551
  ID: 1
  dna_start: 3169997
  reason: sequence shift/mismatches
  downstream_gap: 
  upstream_gap: 
  target_len: 4034155
  strand: +
  target: gi|145202742|gb|DS231697.1| Fusarium oxysporum f. sp. lycopersici 4286 supercont2.2 genomic scaffold, whole genome shotgun sequence
  upstream: agtatgtattgtacaccgtttatcagcccatgggactctccgatccgatctatcggagcatctcgaacaccatccaccgaagctagtaggagcattaccttaggctttggtcacagcttgcgcaatacaagtcaagttacagcaaagagaagttggtgtgtgtctctgcatgatgcatcgacagtcacacaacaccacgaacagaatcaatgatgatgatgatcatcgttcttttaaccggtcgccccgggcaaacttgacagcctaagcaagcaatcttgaagagagagtggcgtaatttctttcatggtcaacgaaattgtgttaatctgtgacgtcccgaaatttcgggaattaaaacagggcctctactactccacgggtcttgtctttgttaggcagatttcttcagctccactgggatatgccagattatctcaacagcaaggatcatctacagctacaatccctgactcttgatacatatttacgacaattgtttctgtaaccgccatttatcactctctcagctccggtctgacaacgaattgtcaacttgtgaatggcaacccaaaaccctcagccgcaccgatggggactcgaaggcgtcgggagaccttcaatactcgaacccttttggggaattcagccaagcctagttttctgcttggaccaaggggcaggtccaaagactccagacaggccagagctagagtcagcccagaccaggggcgggacctgaccatcactcgttctggctctagctcaacatgcagagtaagccaagcatgaagtcttcttctgtcatcatgaaataatagcctttgaacgatcgtgaactaaacacctcttctctgcccgtaactcaaagaaccccgcaattgccatgtcgtgcaggcgtcatatgataactagagccaacagggcaatattgactgaatacagaatcaatggagaccggagtccgagtcctcgggttcggaactgaagtcatacaacttcagaagggattctcgttgagtgaaagcgttgagcgaaagccctcgcaagacaaggcgagacggaaaagctcgttaacaaggttgagcttgtctgttgcatgtcagacttgtacggtctagacgcatctggtgccagatcccgtctttcgcttcccgccttatagctgaactcgccactaacaaatagtctcaaacgcggtggacagctttacagtatgctgcacgggatgggatggcattcagggttcaagcttggagcattagccaccctcagttgtgtgtttcaccaagcgaagcttcgaccactaccaaaggtcttttttcctgacaacgccacagtctcggaatgcatgaaatgtgctgaatagagggcttattcatgcttctgcagacgagagtcagggcattaggggattgctcattgaaggctgctggaagccattctgcgttatggtttaaagggtaccaaccaagactcatataaatagacttcaggatgagacaagaccacagtaatatacctagaggcaagaaaagggcctccgtcctaggcaacaaaatctaggtcggtcagtgtaagtttagggggagcatacgcatgataccgagttgaaacaactggtattcatgaccgttgagaggaatgttgaaccgactcagctctccaatactcccagtgaggctgtgagctgagtgtgagaggagtgttgaggacagccaacgtttttcacttttgctttttgtaattttagtaaatgatacaatttgttaagttcaaatggaaagacatgattagtttattcttactataagttcactgatattagtgctactcgggaggtgcatttagttgaatgaatctatgtagaccctgattggcccctcaccgagtgaccatagctctactcacctcacaccgagaacaaagaccccagtttcaagacagctcccttcccaacttcaacccgagtctgccaaactccacgacctcccactgcc
  score: 0.995
  prot_seq: MALVIPYTYIQCPCSDQSPPDLPQARQSQSSDERTFDPRDPRSNYSLYPLEYLLYCEDCQQIRCPRCVNEEVVTYYCPNCLFEVPSSNLRSDGNRCTRSCYQCPVCIGPLQVMETPIEKDQSHLGADIPGPQYALYCQYCNWTSTEIGIKFDKPNGIHSQLSKINNGGDLKLTAKELKERRKENPDEPPLADSDVDTDLQYANLKSFYQSQLADTNAASSGISPLNDTTGYGSPAASLSRIMAMYTGHGHARKRNGPSXVMREALSAEEGLKLADLDESAQIKKLHQEGWDATATIQQNLEQAEVQRFQDGLRPIPHLLRTKRSKRCSVCRHIISKPENKVTSTRFKIRLVAKSYIPTITIKPLNPTAGTVPTTQRPQILEERPLKPLTPHHYIITFKNPLFDGIKVTLATPNSTPGRFSSKVTILCPQFDIDANTDMWDDALKDDDRDKKRKGEESSGQPEAGKIWERGRNWVSIILEVVPASLRLDGQKDKSPLKEDEDILEIPMFVRMEWEPDSQQDVGAASAKEKDAQERRELAYWCVLGVGRISHD
  prot_len: 551
  status: incomplete
  undetermined: 1
  mismatches: 1
  matches: 549
  dna_end: 3171702