Command line: [exonerate -q dselM_U_prot.fasta -t D_pse01.fasta -m protein2genome -W 3 --showtargetgff yes]
C4 Alignment display:
  Model: protein2genome
  Raw score: 320
  Aligned positions 0->124 of query
  Aligned positions 10509->10940 of target

Query: dSelM
Target: gi|40360379|gb|AADE01002080.1| Drosophila pseudoobscura strain MV2-25 chromosome XL Cont4735, whole genome shotgun sequence

     1 : MetProProLysArgAsnLysLysAlaGlu  >>>> Target Intron 1 >>>>  A :    10
         |||||||||||||||..!||||||!.!               68 bp            |
         MetProProLysArgArgLysLysValIle                             A
 10510 : ATGCCGCCGAAGCGACGTAAGAAAGTGATTgt.........................agG : 10607

    11 : laProIleAlaGluArgAspAlaGlyGluGluLeuAspProAsnAlaProValLeuTyrV :    30
         || !!.!!!.!     !  !!.!!.!! !!  |||||||||:::  !||||||||||||:
         laThrPheValProAspProGlyAlaAlaAlaLeuAspProSerGlnProValLeuTyrI
 10608 : CCACATTTGTGCCTGATCCTGGGGCAGCAGCCCTGGATCCTTCGCAGCCAGTCCTCTACA : 10667

    31 : alGluHisCysArgSerUnkArgValPheArgArgArgAlaGluGluLeuHisSerAlaL :    50
         !!|||||||||||||||   |||||||||||||||||||||||||||||||||:!!||||
         leGluHisCysArgSer***ArgValPheArgArgArgAlaGluGluLeuHisAlaAlaL
 10668 : TCGAACACTGCCGCTCCTGACGCGTTTTCCGTCGTCGGGCCGAAGAGCTACACGCGGCTC : 10727

    51 : euArgGluArgGlyLeuGlnGlnLeuGlnLeuGlnLeuAsnAlaLeuGlyAlaProArgA :    70
         ||!:!||||||||||||||||||||||||||||||||||||!.!  !|||.!!|||||||
         euGlnGluArgGlyLeuGlnGlnLeuGlnLeuGlnLeuAsnValGluGlyThrProArgA
 10728 : TGCAAGAGCGCGGTCTCCAGCAGCTGCAGCTTCAGCTGAATGTCGAAGGGACGCCTCGTC : 10787

    71 : rgGlyAlaPheGluLeuSerLeuSerAlaGlyGlyMetGlyLysGlnGluGlnValAlaL :    90
         |||||||||||||||||  !|||:!!  !      ..!  !! !  !||||||  !  !|
         rgGlyAlaPheGluLeuHisLeuAlaLys------GlnProThrThrGluGlnHisPheL
 10788 : GTGGAGCGTTCGAGCTGCACTTGGCCAAG------CAGCCGACAACGGAGCAGCATTTTC : 10841

    91 : euTrpSerGlyLeuLysArgGlyProProArgAlaArgLysPheProThrValGluGluV :   110
         ||||||||||||||||||||    !!|||||||||!:!||||||||| !!|||!!:!!:|
         euTrpSerGlyLeuLysArg---ThrProArgAlaGlnLysPheProProValAspAspV
 10842 : TTTGGTCTGGCCTAAAACGT---ACTCCACGTGCCCAAAAGTTTCCCCCTGTCGACGATG : 10898

   111 : alTyrAspArgIleValGlyIleLeuGlyAspGlnGlnGlu :   124
         ||!:!    !!||||||! !!!:||||||.!.  !..!|||
         alPheArgTrpIleValGluMetLeuGlyGlnValMetGlu
 10899 : TATTTCGGTGGATTGTCGAGATGCTTGGACAGGTAATGGAA : 10940

vulgar: dSelM 0 124 . gi|40360379|gb|AADE01002080.1| 10509 10940 - 320 M 10 30 5 0 2 I 0 64 3 0 2 M 70 210 G 2 0 M 15 45 G 1 0 M 26 78