Command line: [exonerate -m p2g --showtargetgff -q MrsAaureococcus4.fa --exhaustive -t 2fastasubseq.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query: MsrA.Aureococcus_anophagefferens.3 located on scaffold_4 strand + positions 1209101,1209514
        Target: gi|299737313|gb|GL376576.1|:subseq(30000,1000) Pythium ultimum DAOM BR144 unplaced genomic scaffold scf_1117875581461, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 139
   Query range: 5 -> 138
  Target range: 175 -> 610

   6 : ValAlaThrPheAlaLeuGlyUnkPheTrpThrProGlnGlnLysPheAspLeuArgAspGlyV :  27
       |||||||||||||||  !|||   ||||||  !  !|||!    !|||.!.! !! ! !!||||
       ValAlaThrPheAlaAlaGlyCysPheTrpGlyValGlnLeuAlaPheGlnArgLeuHisGlyV
 176 : GTGGCGACTTTCGCGGCAGGCTGCTTCTGGGGCGTGCAGCTTGCGTTCCAGCGTCTCCATGGCG : 239

  28 : alIleTrpSerThrValGlyTyrThrSerGlyThrThrProAlaProAsnTyrAspAspLeu<- :  48
       |||||   !!!||||||||||||.!!..!||||||..!  !  !|||:::||| ! .!.:!!  
       alIleAspThrThrValGlyTyrAlaGlnGlyThrValGluAsnProSerTyrLysGlnValAr
 240 : TCATCGACACGACTGTGGGGTACGCGCAGGGAACGGTGGAAAACCCGTCGTACAAACAGGTTCG : 302

  49 : ><-><-><->GlyAspHisThrGluAlaLeuArgLeuGluPheAspGluAspValValSerTyr :  65
                   !! !|||.!!||||||:!!|||:!!! !!:!:!!! ! !!! !:!!||||||
       gThrGlyLysThrGlyHisAlaGluAlaIleArgIleValTyrAsnValHisGluIleSerTyr
 303 : AACGGGGAAAACGGGCCATGCCGAGGCCATCCGCATCGTGTACAACGTGCATGAGATCTCGTAT : 365

  66 : GluAlaLeuValGluGlnPheTrpAspLeuHisAlaPro<-><-><-><-><-><-><->AsnL :  80
       ...  !|||:!!!!::!!||||||...:!!|||! !|||                     ||| 
       SerGlnLeuLeuAspLysPheTrpSerIleHisAspProThrThrLeuAsnArgGlnLysAsnA
 366 : TCCCAGCTGCTCGACAAATTCTGGTCGATTCACGACCCAACGACGCTCAACCGCCAGAAGAACG : 431

  81 : ysGlySerArgGlnTyrArgSerAlaIlePheTyrHisAspGluAlaGlnArgGluCysAlaGl : 101
       ! ! !.!!! !||||||||||||!.!|||!:!  !|||..!!!:! !||||||:!!   |||  
       spValGlyThrGlnTyrArgSerGlyIleTyrValHisSerAspAspGlnArgLysGluAlaLe
 432 : ACGTGGGCACGCAGTACCGCTCAGGGATCTACGTCCACAGCGACGACCAACGAAAAGAAGCACT : 494

 102 : uArgValGlnAlaGlnLeuPheProSerLysArgTyrValArgAspThrAlaIleGluProAla : 122
          !  !   ||||||! !     !  !  !  ! !   !! !!  |||! !:!:||| !!|||
       uAlaSerPheAlaGlnArgGlnLysHisLeuLeuLysProIleValThrGluValGluAlaAla
 495 : CGCGTCATTTGCGCAACGCCAGAAGCACCTGTTGAAGCCCATTGTAACCGAAGTGGAGGCCGCC : 557

 123 : AlaGlu<->PhePheProAlaGluAlaTyrHisGlnLysTyrArgGluLys : 138
       ||||||   |||!:: !!||||||! !|||||||||:!!|||  !! !|||
       AlaGluSerPheTrpSerAlaGluGluTyrHisGlnGlnTyrLeuAlaLys
 558 : GCAGAGTCGTTCTGGTCCGCAGAGGAGTACCACCAACAGTACTTGGCGAAA : 610

vulgar: MsrA.Aureococcus_anophagefferens.3 5 138 . gi|299737313|gb|GL376576.1|:subseq(30000,1000) 175 610 + 139 M 42 126 G 0 12 M 31 93 G 0 21 M 46 138 G 0 3 M 14 42
# --- 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|299737313|gb|GL376576.1|:subseq(30000,1000)	exonerate:protein2genome:local	gene	176	610	139	+	.	gene_id 1 ; sequence MsrA.Aureococcus_anophagefferens.3 ; gene_orientation .
gi|299737313|gb|GL376576.1|:subseq(30000,1000)	exonerate:protein2genome:local	cds	176	610	.	+	.	
gi|299737313|gb|GL376576.1|:subseq(30000,1000)	exonerate:protein2genome:local	exon	176	610	.	+	.	insertions 36 ; deletions 0
gi|299737313|gb|GL376576.1|:subseq(30000,1000)	exonerate:protein2genome:local	similarity	176	610	139	+	.	alignment_id 1 ; Query MsrA.Aureococcus_anophagefferens.3 ; Align 176 6 126 ; Align 314 48 93 ; Align 428 79 138 ; Align 569 125 42
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis