Command line: [exonerate -m p2g --showtargetgff -q MrsAaureococcus4.fa -t fastasubseq1_dosprimershits.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query: MsrA.Aureococcus_anophagefferens.3 located on scaffold_4 strand + positions 1209101,1209514
        Target: gi|288565187|gb|GG744010.1|:subseq(4000,2000) Saprolegnia parasitica CBS 223.65 genomic scaffold supercont1.128, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 232
   Query range: 2 -> 138
  Target range: 132 -> 1934

    3 : SerArgArgValAlaThrPheAlaLeuGlyUnkPheTrpThrProGlnGlnLysPheAspLe :   23
        |||  !!.!:!!||||||||||||  !|||   ||||||!:!  !:!!!  !!.|||.!.! 
        SerAspAsnIleAlaThrPheAlaAlaGlyCysPheTrpSerValGluLeuAsnPheGlnAr
  133 : AGCGACAACATTGCGACCTTCGCCGCCGGCTGCTTCTGGAGCGTCGAGCTCAACTTCCAGCG :  193

   24 : uArgAspGlyValIleTrpSerThrValGlyTyrThrSerGlyThrThrProAlaProAsnT :   44
        !! !  !||||||:!!  !!!!  !||||||||||||!:!||| !!! ! !!  !|||!..|
        gIleProGlyValLeuGluThrHisValGlyTyrThrAsnGlyProLysAlaAsnProThrT
  194 : CATCCCCGGCGTCCTCGAGACGCACGTCGGCTACACGAATGGGCCCAAGGCCAACCCGACGT :  256

   45 : yrAspAspLeu<-><-><-><->GlyAspHisThrGluAlaLeuArgLeuGluPheAspGlu :   60
        ||  !!!::!!              !! !|||.!!||||||:!!|||:!!:!!||||||  !
        yrThrGluValCysThrGlyLysThrGlyHisAlaGluAlaValArgIleLysPheAspPro
  257 : ACACCGAGGTGTGCACGGGCAAGACGGGCCACGCTGAGGCTGTCCGCATCAAGTTTGACCCG :  316

   61 : AspValValSerTyrGluAlaLeuValGluGlnPheTrpAspLeuHisAlaProAsnLysGl :   81
        ! !||||||||||||!!:||||||:!!!!::!!||||||..!:!!|||! !|||!..! !  
        AlaValValSerTyrAspAlaLeuLeuAspLysPheTrpSerIleHisAspProThrThrLe
  317 : GCTGTCGTGAGCTACGACGCGCTGCTCGACAAGTTCTGGTCCATCCACGACCCCACAACGCT :  379

   82 : ySerArgGln  >>>> Target Intron 1 >>>>  TyrArgSerAlaIlePheTyrHi :   92
        !!:!!:!|||           1382 bp           |||||||||!.!|||||||||||
        uAsnGlnGln--                         ++TyrArgSerGlyIlePheTyrHi
  380 : CAACCAGCAAaa.........................agTACCGGTCGGGTATCTTTTACCA : 1794

   93 : sAspGluAlaGlnArgGluCysAlaGluArgValGlnAlaGlnLeuPheProSerLysArgT :  113
        |:!!|||! !||||||   ...||||||..!!.!:!!||||||  !  !  !:!!!  !:! 
        sAsnGluGluGlnArgLeuAlaAlaGluGluAlaLysAlaGlnLysAlaGluAlaIleLysA
 1795 : CAACGAAGAGCAGCGCCTCGCGGCCGAGGAGGCCAAGGCGCAGAAGGCCGAAGCTATCAAGG : 1857

  114 : yrValArgAspThrAlaIleGluProAlaAlaGluPhePheProAlaGluAlaTyrHisGln :  133
         !! !  !! !|||! !|||! !||||||!.!   |||!:!! !||||||! !|||||||||
        laGluValValThrGluIleValProAlaGlyIlePheTyrHisAlaGluAspTyrHisGln
 1858 : CCGAAGTCGTCACTGAGATTGTGCCCGCTGGCATTTTCTACCACGCCGAGGACTACCACCAA : 1917

  134 : LysTyrArgGluLys :  138
        ||||||! !||||||
        LysTyrLeuGluLys
 1918 : AAGTACCTCGAAAAG : 1934

vulgar: MsrA.Aureococcus_anophagefferens.3 2 138 . gi|288565187|gb|GG744010.1|:subseq(4000,2000) 132 1934 + 232 M 45 135 G 0 12 M 37 111 5 0 2 I 0 1378 3 0 2 M 54 162
# --- 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|288565187|gb|GG744010.1|:subseq(4000,2000)	exonerate:protein2genome:local	gene	133	1934	232	+	.	gene_id 1 ; sequence MsrA.Aureococcus_anophagefferens.3 ; gene_orientation +
gi|288565187|gb|GG744010.1|:subseq(4000,2000)	exonerate:protein2genome:local	cds	133	390	.	+	.	
gi|288565187|gb|GG744010.1|:subseq(4000,2000)	exonerate:protein2genome:local	exon	133	390	.	+	.	insertions 12 ; deletions 0
gi|288565187|gb|GG744010.1|:subseq(4000,2000)	exonerate:protein2genome:local	splice5	391	392	.	+	.	intron_id 1 ; splice_site "AA"
gi|288565187|gb|GG744010.1|:subseq(4000,2000)	exonerate:protein2genome:local	intron	391	1772	.	+	.	intron_id 1
gi|288565187|gb|GG744010.1|:subseq(4000,2000)	exonerate:protein2genome:local	splice3	1771	1772	.	+	.	intron_id 0 ; splice_site "AG"
gi|288565187|gb|GG744010.1|:subseq(4000,2000)	exonerate:protein2genome:local	cds	1773	1934	.	+	.	
gi|288565187|gb|GG744010.1|:subseq(4000,2000)	exonerate:protein2genome:local	exon	1773	1934	.	+	.	insertions 0 ; deletions 0
gi|288565187|gb|GG744010.1|:subseq(4000,2000)	exonerate:protein2genome:local	similarity	133	1934	232	+	.	alignment_id 1 ; Query MsrA.Aureococcus_anophagefferens.3 ; Align 133 3 135 ; Align 280 48 111 ; Align 1773 85 162
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: MsrA.Aureococcus_anophagefferens.3 located on scaffold_4 strand + positions 1209101,1209514
        Target: gi|288565187|gb|GG744010.1|:subseq(4000,2000) Saprolegnia parasitica CBS 223.65 genomic scaffold supercont1.128, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 110
   Query range: 78 -> 138
  Target range: 393 -> 573

  79 : AsnLysGlySerArgGlnTyrArgSerAlaIlePheTyrHisAspGluAlaGlnArgGluCysA : 100
       ||| ! ! !.!!! !||||||||||||!.!|||!:!||||||..!!!:||||||!:!..!  !|
       AsnAspValGlyThrGlnTyrArgSerGlyIleTyrTyrHisSerAspAlaGlnLysSerLeuA
 394 : AACGACGTTGGCACGCAGTACCGGTCGGGCATTTACTACCACAGCGACGCGCAAAAGTCGCTCG : 457

 101 : laGluArgValGlnAlaGlnLeuPheProSerLysArgTyrValArgAspThrAlaIleGluPr : 121
       ||  !  !  !:!!|||..!  !   ||| !!   |||     !! !! !|||! !:!!!   !
       laLeuAlaSerLysAlaSerAlaGlnProArgPheArgArgProIleValThrGluValValAl
 458 : CGTTGGCCTCCAAGGCGTCGGCGCAGCCGCGCTTTCGCCGACCGATTGTCACGGAGGTCGTCGC : 520

 122 : oAlaAlaGluPhePheProAlaGluAlaTyrHisGlnLysTyrArgGluLys : 138
       !|||! !  !|||!:!  !||||||! !|||||||||::!|||  !||||||
       aAlaGluThrPheTyrValAlaGluAspTyrHisGlnArgTyrLeuGluLys
 521 : GGCCGAGACGTTTTACGTTGCCGAGGACTACCACCAGCGGTACTTGGAAAAG : 573

vulgar: MsrA.Aureococcus_anophagefferens.3 78 138 . gi|288565187|gb|GG744010.1|:subseq(4000,2000) 393 573 + 110 M 60 180
# --- 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|288565187|gb|GG744010.1|:subseq(4000,2000)	exonerate:protein2genome:local	gene	394	573	110	+	.	gene_id 2 ; sequence MsrA.Aureococcus_anophagefferens.3 ; gene_orientation .
gi|288565187|gb|GG744010.1|:subseq(4000,2000)	exonerate:protein2genome:local	cds	394	573	.	+	.	
gi|288565187|gb|GG744010.1|:subseq(4000,2000)	exonerate:protein2genome:local	exon	394	573	.	+	.	insertions 0 ; deletions 0
gi|288565187|gb|GG744010.1|:subseq(4000,2000)	exonerate:protein2genome:local	similarity	394	573	110	+	.	alignment_id 2 ; Query MsrA.Aureococcus_anophagefferens.3 ; Align 394 79 180
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis