### Scipio v1.4 (20100622-unreleased) output
# query file    /tmp/DLdl2OChY6nh.fasta
# target file   /genomes/genomes_jgi/Phytophthora_sojae_P6497_v2_supercontigs.fasta
# BLAT output   /tmp/4raCZKacnLBd.psl
# Timestamp     Sat Jun 26 15:32:47 2010

--- 
PhrP62__fl: 
- matchings: 
  - overlap: 
    mismatchlist: 
    - 2
    - 7
    - 10
    - 30
    - 81
    - 84
    - 93
    - 94
    - 107
    - 110
    - 111
    - 118
    - 137
    - 152
    - 153
    - 154
    - 156
    - 158
    - 159
    - 160
    - 161
    - 162
    - 168
    - 215
    - 219
    - 222
    - 234
    - 235
    - 238
    - 241
    - 242
    - 247
    - 250
    - 251
    - 258
    - 260
    - 261
    - 263
    - 265
    - 266
    - 270
    - 285
    - 286
    - 287
    - 290
    - 361
    - 362
    - 363
    - 370
    - 386
    - 388
    - 389
    - 390
    - 391
    - 392
    - 394
    - 396
    - 400
    prot_start: 0
    nucl_end: 1200
    prot_end: 400
    translation: MSSCEGDAVDGVCVRYACKCGHLAPVSSLFFSETCEKLVCRLPGCSVEEFESYYCGNLLVNLPSKEASMYQNRSSRCFSCPACETALSTAFHESKQRFFFLCAHCRWDSLELGLADDDLDALVMTAITRERQAAHEDVFQALHSHYSTLSSSSSSGNAFASTPGAAFGRSSSLQLLADSMKELQREHQMKKFRLQRMAEMGGWKYDQALAKVQEKEQWLLEQRREHQWPELQKQLTALQTQGTSWGEDTPEKTRETLEKLAQTSDMGQVSTLHQRLLNPLDQSSDADRLFPSRPLLRVKRTWRCVESIERGTAGILVKPQISPMSGDSSLPVSASWFKKANLAAQYVPVVTFQRLPYRAEGGGGVECVLLVENPLDDAIRITFRSASASGEESTENGQ
    dna_start: 3068364
    type: exon
    seqshifts: 
    - prot_start: 3
      nucl_end: 9
      prot_end: 3
      dna_start: 3068373
      nucl_start: 9
      dna_end: 3068376
    - prot_start: 162
      nucl_end: 495
      prot_end: 165
      dna_start: 3068853
      nucl_start: 486
      dna_end: 3068853
    undeterminedlist: []

    nucl_start: 0
    seq: atgtcttcctgcgagggtgatgcggtcgacggcgtgtgcgtccgctacgcgtgcaagtgcgggcacctggcgcccgtgagctctctgttcttcagcgagacgtgcgagaagctggtgtgccgcctgccgggctgcagcgtggaggagttcgagtcgtactactgcgggaacctgctggtgaacctgccgtccaaggaggccagcatgtaccagaaccgctcgagccgctgcttcagctgccccgcgtgcgagacggcgctgtccacggccttccacgagagcaagcagcgtttcttcttcctgtgcgcgcactgccgctgggactcgctggagctggggctggcggacgacgacctggacgcgctggtcatgacggccatcacgcgggagcgccaggcggcgcacgaggacgtcttccaggcgctgcactcgcactactcgacgctgtcgagctcttcttcttccggcaacgccttcgcgtcgacgccaggggcggcttttggccgcagcagctcgctccagctgctggccgactcgatgaaggagctgcagcgcgagcaccagatgaagaagttcaggctgcagaggatggcggagatgggcggctggaagtacgaccaggccctggcgaaggtgcaggagaaggagcagtggctgctggagcagcggcgtgagcaccagtggccggagctgcagaagcagctcaccgccctgcagacccaagggacgtcgtggggggaagacacgcctgagaagacccgagagacactggagaaactcgcgcagacaagtgacatggggcaggtgtcgacacttcaccaacgactgttgaatccgctggatcaatcgagtgatgcggatcgacttttcccctcgcgcccgctgcttcgggtgaagcgcacgtggcggtgcgtggaatcaattgagcgtggcacggccggtatccttgtaaagccgcagatcagcccgatgagtggagatagctcactgcccgtatccgcgtcgtggttcaagaaggcgaatctggcggcgcagtacgtgcccgtcgtaacgtttcagagactgccgtacagggctgaaggtggcggtggtgttgaatgtgttttgctcgtggaaaaccctctggatgatgctattcgcatcacattccgctctgcctctgcaagtggagaagagtcaactgaaaatggacag
    inframe_stopcodons: []

    dna_end: 3069558
  - dna_start: 3069558
    type: intron
    nucl_start: 1200
    seq: gtgcgttggaaaagggtgtattaattttgcagggactttggacgctgatgtgtatatcgtatag
    dna_end: 3069622
  - overlap: 
    mismatchlist: 
    - 401
    - 402
    - 403
    - 406
    - 436
    - 439
    - 454
    prot_start: 400
    nucl_end: 1362
    prot_end: 454
    translation: IVLQDSTPIIVGPYEDPNLADAFIDDEPPFGANGDQHNAMLLQATRNLIKIKLT
    dna_start: 3069622
    type: exon
    seqshifts: []

    undeterminedlist: []

    nucl_start: 1200
    seq: attgtgttacaagattcgactccgatcattgtggggccgtacgaagatccgaacctcgcagacgctttcatcgatgatgagccgcccttcggtgctaatggcgaccagcacaacgcaatgctgctccaagctactagaaaccttatcaagattaagctcacc
    inframe_stopcodons: []

    dna_end: 3069784
  - dna_start: 3069784
    type: intron
    nucl_start: 1362
    seq: gtaagcttgtgtagccatcgcttgttcaacgtcatcagcattaacaaggtttttgtggcgcccatgttgttacag
    dna_end: 3069859
  - overlap: 
    mismatchlist: 
    - 455
    - 456
    - 459
    - 460
    - 461
    - 462
    - 463
    - 465
    - 468
    - 492
    - 506
    - 507
    prot_start: 454
    nucl_end: 1521
    prot_end: 507
    translation: IAVNSTAEHPSSTISARFIMDTEKFDEDANEVIENSLQSVPVVITAPIPE
    dna_start: 3069859
    type: exon
    seqshifts: 
    - prot_start: 502
      nucl_end: 1515
      prot_end: 505
      dna_start: 3070003
      nucl_start: 1506
      dna_end: 3070003
    undeterminedlist: []

    nucl_start: 1362
    seq: atcgctgtcaattctactgctgaacacccgagctcaaccatctcggcccgatttatcatggatacagaaaagtttgatgaagatgcgaacgaagttatcgagaattcgctgcagagtgtcccggtagtgatcacggcgccaatcccggaa
    inframe_stopcodons: []

    dna_end: 3070009
  unmatched: 6
  prot_start: 0
  stopcodon: taa
  downstream: taatgcgctttacaagctgcgttcccctcttaaagtgtaatcgccatcggaatctgtttgcgataccatggaagtcagaacaccagcagtccaaatgtgaaccttacattatgaagtcgtctgtgtccacgctatccagaatagtcgcgcctgttcatttggaggaaatggagttgccggcggacttggatgggttccatgctgttttgaagcgccggatccgtgatcaaagcgagattgaggagtgccgcgaggactactccgccgagaaaaaggttgccgcacaaagggctgtggcagcacgcgtaagagaccttgtttggatcggaagacttgcgccacttgaatcagcactaacaacactatcccttaggagatccgtcatgttgttggccagacgggttgcttttgtctggattgcctactccaccggaagcaagaatggcgaattggagatgtcaacacagccatcgtaggaccaagggaccaatggcaacagtacacatgggggaacgcagaacgacagtgtctgtactcggaagattcaactaccacgaccaagccagtcttgacgccttccatttcggagaaaattcgagttcacgactcgaaggatcgaatttggacagtcgagcgggctgcaaaattcgttgctgtgcgtgaatcgagccgatatgtctggtcgaaagtgataactgcaaaattaatcctagcgttgttctttttgcgctaccataggtcgcgtccggcaaataccacacgcttatgcttaccggtaggggaaaaaatattatgtgaggtagagaatgctcagctaatgatattcatgtatgagcagagtctgcagtcgtttttgcgagtggggacaatacctacggcgcccttggggttgccggtggggtcagtgcaagcaggtctgcaccaggcaaagtggaaacaggattggatgatgttggcggctgcgtaaagatgattgccgccagtggattcgcgtcgttcgctcttgttggttcgttttgctgtgttctgcatacactattttacatgtagatctcacccgcgttcattcagtgttgccaatccctgacccagtccagcggccaacatccaaaggagccaagcaaaatcgagggcggctgacctcgctggaaaggatggctcgaggtcgagctcattctcttcagcgaatgtcaacacaagctaaactagacattgcaatgaatgctgcagccgtcaataatcgtacgtctgtcagttcacctactgcctccaggaggagttactcatgactgcgtttaacttcgtccaccgctgtataagttgtttcgtggggccgaggcgattacggggtactgggacatggggacacagaatcgtcagcaactcctcgtgtgataaagattttcaactcgatgcgagtaacatgcgtgagcgctggtttgcatcacgttctggtgctcacagaactagatggtgtctatgcgtttggagacggaagcaatggaaagttagggttgggtacgttgaaaaatacttcttttttcttattttcgaaatagggattctaatgccattgtaggggatacgaatcctcgtttgtccccggccagaattacgagtctcgatgggctgaatgtggtccatgtttctgctggtgatgaacactcagttgtcatgactggagagactttctttaatcggcaggtgtactcgtggggcctcgggaagaacgggtatggatctgctgtacgtactcgttgaatgagctaccagttttatcgacgcgtgtcttgataggcgtctgggccacaatgatgagttaacaaggttgaagccaactcgcgtaaactgtttccgtggacgggtacgattgctagaatgttgtgcactgacagatcgagggaattgatagtacttgtttgcagaaagttatcactcttgttgctgggggagctcataatcttgcaacgtcgggtgcgtgcagaacacctaaaaacaat
  additional: 1
  prot_end: 507
  ID: 1
  dna_start: 3068364
  reason: sequence shift/mismatches
  downstream_gap: 
  upstream_gap: 
  target_len: 9680717
  strand: +
  target: scaffold_1
  upstream: aaatcgctttggagcttttcgcactgcttctccagtcgacgccgttgaatatccacagtgctcttttgttcgaagaggatctcgaaagcgttctggcgtgccttgtacagttcaattaccgctgccgctggtctggtctttagatcttccagcgatactccatctatgagttacatactgggattagactttgcttggtcaagaacaaaaaatacatacaaacttactcttggcttctttcacaatcggctcgaagtagtcgtagaattgcttgtgagcctcctccacaagcatagcactctcctgcagcaacgtcatccgttagataacgccggtacagccatgactcaatcaactttttacgacggacgtacaatgcgcttgagggactgggcattgcgctcttcactctgccgcagcttttgggttgtctggtacagtttttcctgcaggatggatgacgatctggatgcctcgatcaaatcaaccaactgcagcatacacgtcgtgaattagcggtttattcagttgcgaagtgcgcagggtgtccacttacctcggccttaagcttgcgttcagttgactgaagctgcatgatttgttcgttcagctcgcgaacttcacgggcaccgtcgagtgtttcctgcgcgccaagcaaactggaagctgcatgttcagcctccatactcttctgcttgagctgggattctagcaaacgaatctttgattcaaggatattgtcctcgctctgaggaacatcaacacgaataaatacacagcatgcatgaaactaagccggcttgtactaacctgcgatgaagtcgatgacgagtcttgggctgcttccagctcatccttcaggagctgaatctgtcgccatgcacaataacagaagcttgttagctacactcgttctcttgaccttttgcaactctatcgcaccttcaatgcagattgccgagactgtgtgcgcagctggctggtcgcttcgagcgccttctccttccactcgttcagcttgccctcgactagttccagctgagcttccaactcaaccactttcttctctagctgcaacttctctgctgagtgttcgttcgtgacattcttcagttccttcagcgtctcttcctcctcagtcacagcgaacttcagctggcggcgtagttggtccaactgcacatctctctccttgagttcgatctggtgtcgctgtgagttagtcccaagctggatccggagcgtctccacctcgcgcttcagttgatcactctgccacatccaccacacaagcgcaatcagcctcgacagcactaaacagcagtcaataacctaaaaggaccccaccttggagactgcgaggctctcgatctcgagtcgctggcgcttattcgtcctcgcgctttcactctcctccacctgcttcgctgtggaattgcaacagcccaattgctcgtcagtgttcagccctccacgccttctcaatgcattgcatcatcgtcgtccgcaccttccctccgctccttttccagctctcgcacgcgctcctggagctgccacacgtactctgacgagaagcttctgctactgcttttcagcggcgtgtccatgccgtccaggaagctgtcgctggatccggctttggactggggacgaaagagacaaaaaggtggcaagaggttggcgttgtacagcgttagttaaattgtggctgcaaggagggcaaggacgtccagagtgggggtcgcgcgcaccttcacggagctgctgtcgtccacgtagaagacttgcgacgggtccttggggatcggagagcacaggaacgacgaagacagcgccttctgcttgccctcggccatcgccccgttggatcaattgaactgagcgcgccaaatggtgtgcaatttatgtggtagattcgtgatcgaaacataacgcctctcatggacagtatgtaacgcctggatccggtgcttatattctgtcactatccatagagg
  score: 0.684
  prot_seq: MTSEGDVVDDVCVRYACKCGHLAPVSSLFYSETCEKLVCRLPGCSVEEFESYYCGNLLVNLPSKEASMYQNRSSRCFSCPTCENALSTAFHENEQRFFFLCAHCRWESLSVGLADDDPDALVMTAITRERQAAHEDIFQALHSHYSTLSSSPANGGAAGVLSASSGAPFGRSSSLQLLADSMKELQREHQMKKFRLQRMAEMGGWKYDQALAKVEEKERWLMEQRREHQWPELSMQLAALSKQGTSYGEESPEKTREVLRNLSQKCDMGEVSTLHQRLLNPLDQAREADQLFPSRPLLRVKRTWRCVESIERGTAGILVKPQISPMSGDSSLPVSASWFKKANLAAQYVPVVTFQRLPYRVGEGGGVECILLVENPLDDAIRITFHSTPTASEDSNENGYVDFQDLTPIIVGPYEDPNLADAFIDDEPPFGANGDEHNTMLLQATRNLIKIKLPLSVNAATTIPISTLSARFIMDTEKFDEDANEVIENSLLSVPVVITAPIIKIGD
  prot_len: 507
  status: incomplete
  undetermined: 0
  mismatches: 77
  matches: 424
  dna_end: 3070009