Command line: [exonerate -m p2g --showtargetgff -q MrsAaureococcus4.fa --exhaustive -t 3fastasubseq.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query: MsrA.Aureococcus_anophagefferens.3 located on scaffold_4 strand + positions 1209101,1209514
        Target: gi|299737269|gb|GL376620.1|:subseq(204000,1000) Pythium ultimum DAOM BR144 unplaced genomic scaffold scf_1117875582023, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 118
   Query range: 5 -> 138
  Target range: 307 -> 739

   6 : ValAlaThrPheAlaLeuGlyUnkPheTrpThrProGlnGlnLysPheAspLeuArgAspGlyV :  27
       ||||||  !||||||  !|||   ||||||  !  !:!!!    !|||.!.! !  !   ||||
       ValAlaTyrPheAlaAlaGlyCysPheTrpGlyValGluLeuAlaPheGlnArgValProGlyV
 308 : GTCGCGTACTTCGCCGCCGGCTGCTTCTGGGGCGTCGAGCTCGCGTTCCAGCGCGTGCCGGGCG : 371

  28 : alIleTrpSerThrValGlyTyrThrSerGlyThrThrProAlaProAsnTyrAspAspLeu<- :  48
       ||:!!   !!!||||||||||||.!!..!|||  !  !  !  ! !!!..||| ! .!.:!!  
       alLeuHisThrThrValGlyTyrAlaGlnGlyHisGlnGluAsnAlaThrTyrLysGlnValCy
 372 : TGCTCCACACAACCGTGGGCTACGCGCAGGGCCACCAGGAGAACGCCACGTACAAGCAGGTGTG : 434

  49 : ><-><-><->GlyAspHisThrGluAlaLeuArgLeuGluPheAspGluAspValValSerTyr :  65
                   !! !|||.!!|||.!!:!!!:!:!!|||||||||! !..!! !|||!!!|||
       sSerGlyLysThrGlyHisAlaGluThrIleLysIleGluPheAspAlaSerGluValThrTyr
 435 : CTCGGGCAAGACGGGCCACGCCGAGACGATCAAAATCGAGTTCGACGCGAGTGAGGTGACGTAT : 497

  66 : GluAlaLeuValGluGlnPheTrpAspLeuHisAlaProAsnLysGlySerArg<-><-><->< :  84
       ! !  !|||:!!!!::!!||||||...:!!|||! !|||!..! !  !!:!|||          
       AlaGlnLeuLeuAspLysPheTrpSerIleHisAspProThrThrLeuAsnArgGlnLysGluA
 498 : GCGCAGCTGCTCGACAAGTTCTGGTCGATCCACGACCCCACGACGCTCAACCGCCAGAAGGAGG : 563

  85 : -><-><-><->GlnTyrArgSerAlaIlePheTyrHisAspGluAlaGlnArgGluCysAlaGl : 101
                  ||||||||||||!.!|||!:!|||   :!!!!:! !|||!:!  !   |||  
       spValGlyThrGlnTyrArgSerGlyIleTyrTyrValAsnAspGluGlnLysThrGlnAlaIl
 564 : ACGTCGGCACGCAGTACCGCTCGGGCATTTACTACGTGAACGACGAGCAGAAGACGCAAGCGAT : 626

 102 : uArgValGlnAlaGlnLeuPheProSerLysArgTyrValArgAspThrAlaIleGluProAla : 122
          !  !:!!! !  !! !   ! !!.!!  ..! ! ..!! !!  |||! !||||||  !  !
       eAlaSerLysGluAlaGlnGlnGlnLysThrGluLysThrIleValThrGluIleGluGluPhe
 627 : CGCTTCGAAGGAAGCGCAGCAGCAGAAGACTGAAAAGACCATCGTGACTGAGATCGAAGAGTTC : 689

 123 : AlaGluPhePheProAlaGluAlaTyrHisGlnLysTyrArgGluLys : 138
         !! !|||!::  !||||||! !|||||||||:!!|||  !||||||
       ArgValPheTrpValAlaGluGluTyrHisGlnGlnTyrLeuGluLys
 690 : CGCGTGTTCTGGGTGGCTGAGGAATACCACCAGCAGTACTTGGAGAAG : 739

vulgar: MsrA.Aureococcus_anophagefferens.3 5 138 . gi|299737269|gb|GL376620.1|:subseq(204000,1000) 307 739 + 118 M 42 126 G 0 12 M 36 108 G 0 21 M 55 165
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-03-04
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|299737269|gb|GL376620.1|:subseq(204000,1000)	exonerate:protein2genome:local	gene	308	739	118	+	.	gene_id 1 ; sequence MsrA.Aureococcus_anophagefferens.3 ; gene_orientation .
gi|299737269|gb|GL376620.1|:subseq(204000,1000)	exonerate:protein2genome:local	cds	308	739	.	+	.	
gi|299737269|gb|GL376620.1|:subseq(204000,1000)	exonerate:protein2genome:local	exon	308	739	.	+	.	insertions 33 ; deletions 0
gi|299737269|gb|GL376620.1|:subseq(204000,1000)	exonerate:protein2genome:local	similarity	308	739	118	+	.	alignment_id 1 ; Query MsrA.Aureococcus_anophagefferens.3 ; Align 308 6 126 ; Align 446 48 108 ; Align 575 84 165
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis