Command line: [exonerate -m p2g --showtargetgff -q query.selI.P.infestans.fa -t SelI.P.capsici.fastasubseq.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query: SelI_Phytophtora infestans
        Target: PHYCAscaffold_26:subseq(674000,12000) [revcomp]
         Model: protein2genome:local
     Raw score: 396
   Query range: 121 -> 370
  Target range: 6888 -> 6006

  122 : LeuAlaLeuPheThrTyrGlnThrLeuAspAsnLeuAspGlyLysGlnAlaArgArgThrLy :  142
        |||  !:!!  !..!||||||! !||||||     !||||||||||||||||||!:!|||  
        LeuLeuIleThrValTyrGlnIleLeuAspValAlaAspGlyLysGlnAlaArgLysThrGl
 6888 : CTTCTCATTACTGTCTACCAGATTTTGGACGTGGCGGACGGCAAACAGGCGCGTAAAACTGG : 6828

  143 : sSerSerSerProLeuGlyLeuLeuPheAspHisGlyCysValAlaLeuAsnValSerValG :  163
         !:!||||||||||||||||||||||||||||||||||||! !||||||||||||  !|||.
        yAsnSerSerProLeuGlyLeuLeuPheAspHisGlyCysAspAlaLeuAsnValValValS
 6827 : TAATTCGTCGCCATTGGGTCTGTTGTTTGACCACGGGTGCGATGCACTCAATGTGGTTGTCA : 6765

  164 : lyThrMetThrMetAlaSerIleLeuGlnMetGlyThrThrTrpArg  >>>> Target I :  179
        !!.!!   |||.!.||||||!  :!!..!:!:||| !!|||!:: !!            61 
        erAlaCysThrPheAlaSerThrIleMetLeuGlyProThrTyrTrp++             
 6764 : GTGCGTGCACATTTGCGTCCACGATCATGCTTGGACCGACGTATTGGgt............. : 6715

  180 : ntron 1 >>>>  ThrLeuGlyPheValLeuSerGlyHisPheValPheIlePheAlaThr :  194
        bp            :!!|||  !.!! !!|||:!!  !   .!.||||||.!!.!.||||||
                    ++SerLeuLeuIlePheLeuAlaProAlaMetValPhePheMetAlaThr
 6714 : ............agTCGCTGCTGATTTTCCTTGCACCTGCGATGGTGTTCTTCATGGCGACT : 6611

  195 : Trp<->GluTyrTyrSerGlySerLeuGluLeuProLeuTyrAsnGlyProThrGluGlyTy :  214
        |||   |||||||||!!!|||!!!|||! !||||||:!!  !|||||||||!.!||||||  
        TrpGluGluTyrTyrThrGlyThrLeuAlaLeuProIleIleAsnGlyProAsnGluGlyLe
 6610 : TGGGAGGAATACTACACGGGAACACTGGCGCTTCCTATCATCAACGGGCCCAATGAAGGCCT : 6548

  215 : rLeuIleGlyIleAlaLeuLysLeuValThrAlaValValGlyValGlyPheTrpAsnGlnG :  235
         ||||||  !  !:!!:!! ! :!!! !||||||:!!||||||  !  ! ! |||!..||| 
        uLeuIleMetTyrSerIleTyrIleGlyThrAlaIleValGlyProThrValTrpThrGlnP
 6547 : GCTGATTATGTACTCGATCTACATCGGCACTGCTATCGTTGGACCGACGGTGTGGACGCAGC : 6485

  236 : luMetIleGluGlyValGlnAsnAsnSerLeuPheValIleValThrMetIleSerSerCys :  255
         !!  |||  !  !  !.!.   |||!:!  !  !|||.!!|||   :!!|||!!!! !  !
        roAsnIleLeuPheProAspLeuAsnAsnAsnHisValPheVal---LeuIleThrIleThr
 6484 : CGAACATCCTGTTCCCGGATTTAAACAACAATCATGTCTTCGTT---TTGATTACGATCACT : 6428

  256 : PheThrLeuLeuValLysTyrValGlyGlyLeuIlePheCysIleProAlaValArgPheAl :  276
          !.!!:!!  !  !   !   !!.!!|||  !:!!!:!   .!!  !  ! !!  !     
        SerAlaIleGlyGlnCysLeuPheSerGlyGluLeuTyrValPheIleTyrPhePheAlaLy
 6427 : AGCGCAATTGGACAGTGCTTATTCAGCGGTGAGTTATACGTGTTTATTTATTTTTTTGCAAA : 6365

  277 : aAsnLeuSerMetPheCysPheIleThrSerValArgAsnAlaLeuHisAlaValArgLeuA :  297
        !||||||!!!:!:! !..! ! .!!  !  !!.!! !  !|||:!!!.!:!!:!!..!  !!
        sAsnLeuThrValCysAlaValPheArgValAlaIleValAlaIleArgSerMetGluArgL
 6364 : GAATCTTACAGTTTGTGCTGTGTTTCGTGTAGCTATTGTTGCCATTCGTTCGATGGAGAGGA : 6302

  298 : snGlnAspSerValLeuValAlaPheThrArgLeuLeuProPheValValIleAsnThrLeu :  317
        !.    ! ..!! !  !!.!|||.!.  ! !!:!!  !||||||:!!!.!:!!     !|||
        ysAlaLysAspGlyAlaAlaAlaLeuPheGlyIleThrProPheIleAlaLeuValPheLeu
 6301 : AAGCTAAGGATGGTGCGGCGGCACTGTTTGGCATTACTCCTTTCATCGCTCTCGTGTTCTTG : 6242

  318 : AlaGlyLeuTrpAlaLeuTyrSerProSerAspIlePheSerThrHisProArgMetPheLe :  338
        :!!!.!||||||!.!|||!::||||||||||||:!:|||!!!  !|||||||||:!:.!!:!
        SerAlaLeuTrpValLeuTrpSerProSerAspValPheThrAspHisProArgLeuLeuIl
 6241 : TCTGCACTTTGGGTGCTTTGGTCCCCGTCTGATGTGTTTACGGACCACCCACGTCTCCTCAT : 6179

  339 : uTrpMetLeuGlyLeuLeuAsnSerLys  >>>> Target Intron 2 >>>>  LeuVa :  349
        !|||!  :!!|||!!!:!!  !:!!|||            74 bp            :!!||
        eTrpThrValGlyPheValPheAlaLys++                         ++MetVa
 6178 : CTGGACTGTGGGGTTCGTATTCGCAAAGgt.........................agATGGT : 6072

  350 : lLeuHisLeuMetLeuAlaHisLeuCysGlyGluGluTyrHisProPheArgLysThrLeuV :  370
        |:!!|||:!!||||||:!!|||:!!|||! !|||  !|||     !.!.|||||||||!!!:
        lMetHisMetMetLeuSerHisMetCysGluGluProTyrTrpLeuLeuArgLysThrPheL
 6071 : GATGCACATGATGCTCTCGCACATGTGTGAAGAGCCGTACTGGTTGCTGCGCAAGACGTTCC : 6009

  371 : al :  370
        !!
        eu
 6008 : TG : 6007

vulgar: SelI_Phytophtora 121 370 . PHYCAscaffold_26:subseq(674000,12000) 6888 6006 - 396 M 57 171 5 0 2 I 0 57 3 0 2 M 17 51 G 0 3 M 54 162 G 1 0 M 97 291 5 0 2 I 0 70 3 0 2 M 23 69
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-11-24
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
PHYCAscaffold_26:subseq(674000,12000)	exonerate:protein2genome:local	gene	6007	6888	396	-	.	gene_id 1 ; sequence SelI_Phytophtora ; gene_orientation +
PHYCAscaffold_26:subseq(674000,12000)	exonerate:protein2genome:local	cds	6718	6888	.	-	.	
PHYCAscaffold_26:subseq(674000,12000)	exonerate:protein2genome:local	exon	6718	6888	.	-	.	insertions 0 ; deletions 0
PHYCAscaffold_26:subseq(674000,12000)	exonerate:protein2genome:local	splice5	6716	6717	.	-	.	intron_id 1 ; splice_site "GT"
PHYCAscaffold_26:subseq(674000,12000)	exonerate:protein2genome:local	intron	6657	6717	.	-	.	intron_id 1
PHYCAscaffold_26:subseq(674000,12000)	exonerate:protein2genome:local	splice3	6657	6658	.	-	.	intron_id 0 ; splice_site "AG"
PHYCAscaffold_26:subseq(674000,12000)	exonerate:protein2genome:local	cds	6150	6656	.	-	.	
PHYCAscaffold_26:subseq(674000,12000)	exonerate:protein2genome:local	exon	6150	6656	.	-	.	insertions 3 ; deletions 1
PHYCAscaffold_26:subseq(674000,12000)	exonerate:protein2genome:local	splice5	6148	6149	.	-	.	intron_id 2 ; splice_site "GT"
PHYCAscaffold_26:subseq(674000,12000)	exonerate:protein2genome:local	intron	6076	6149	.	-	.	intron_id 2
PHYCAscaffold_26:subseq(674000,12000)	exonerate:protein2genome:local	splice3	6076	6077	.	-	.	intron_id 1 ; splice_site "AG"
PHYCAscaffold_26:subseq(674000,12000)	exonerate:protein2genome:local	cds	6007	6075	.	-	.	
PHYCAscaffold_26:subseq(674000,12000)	exonerate:protein2genome:local	exon	6007	6075	.	-	.	insertions 0 ; deletions 0
PHYCAscaffold_26:subseq(674000,12000)	exonerate:protein2genome:local	similarity	6007	6888	396	-	.	alignment_id 1 ; Query SelI_Phytophtora ; Align 6889 122 171 ; Align 6657 179 51 ; Align 6603 196 162 ; Align 6441 251 291 ; Align 6076 348 69
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
