Command line: [exonerate -m p2g --showtargetgff -q query.selI.P.infestans.fa -t SelI.C.fasciculata_2.fastasubseq.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query: SelI_Phytophtora infestans
        Target: Cf_Contig603:subseq(0,5000)  |  | 1 to 51230
         Model: protein2genome:local
     Raw score: 388
   Query range: 38 -> 232
  Target range: 111 -> 771

  39 : LysTyrValSerGlnGluGlySerGluLysLeuArgThrTyrGluTyrHisGlyAlaAspAsnS :  60
       ...|||:!! !!.!.!!:!.!!.!! !||||||  !  !|||!  |||!.!|||! !|||..!|
       SerTyrLeuProAspAspAlaLysAlaLysLeuAlaHisTyrValTyrArgGlyGluAspArgS
 112 : TCCTATCTGCCTGATGATGCCAAGGCGAAGCTGGCCCACTACGTCTACCGCGGCGAGGACCGCA : 175

  61 : erLeuValTyrLys<->ValLeuThrProMetAsnAsnPheLeuValLysLeuLeuProLeuTr :  80
       ||! !:!!|||!!.   :!!! !  !|||:!:  !..!   :!!|||!  ! !||||||:!!||
       erTyrLeuTyrAsnHisMetTrpArgProLeuCysArgLysValValThrTyrLeuProValTr
 176 : GCTACCTCTACAACCACATGTGGCGCCCCCTCTGTCGCAAGGTCGTCACCTACCTCCCGGTGTG : 238

  81 : pLeuAlaProAsnLeuIleThrLeuIleGlyLeuIleLeuValGlyGlySerHisThrLeuPhe : 101
       |||||||||||||:!!||||||:!!  !!.!|||:!!!!!|||.!!  !!!!|||.!!|||.!!
       pLeuAlaProAsnValIleThrValAlaAlaLeuValPheValSerLeuThrHisAlaLeuLeu
 239 : GCTCGCCCCGAACGTGATCACCGTCGCCGCGCTTGTCTTCGTCAGTCTCACCCACGCGCTACTT : 301

 102 : ValPheLeuCysProPheLeuValGlyAsp  >>>> Target Intron 1 >>>>  AlaPr : 113
       !.!|||! !   |||   !!!..!! ! !             72 bp             !!||
       AlaPheTyrMetProLysPheThrValLys+-                         -+ProPr
 302 : GCCTTCTATATGCCCAAGTTCACCGTGAAGga.........................cgCCGCC : 409

 114 : oTrpTrpAlaMetValValAlaAlaLeuAlaLeuPheThrTyrGlnThrLeuAspAsnLeuAsp : 134
       |   !::!.!:!!|||:!!||||||:!!|||||||||  !||||||  !|||||||||||||||
       oAlaTyrValLeuValLeuAlaAlaValAlaLeuPheLeuTyrGlnLeuLeuAspAsnLeuAsp
 410 : CGCCTACGTCCTGGTGCTGGCTGCTGTCGCTCTCTTCCTCTACCAGCTGCTGGACAACCTCGAC : 472

 135 : GlyLysGlnAlaArgArgThrLysSerSerSerProLeuGlyLeuLeuPheAspHisGlyCysV : 156
       ||| ! |||||||||||||||   !!!|||||||||||||||||||||.!.||||||||||||!
       GlyHisGlnAlaArgArgThrGlyThrSerSerProLeuGlyLeuLeuMetAspHisGlyCysA
 473 : GGGCACCAAGCACGCCGCACCGGCACCTCCAGCCCGCTGGGCCTTCTCATGGATCACGGCTGCG : 538

 157 : alAlaLeuAsnValSerValGlyThrMetThrMetAlaSerIleLeuGlnMetGlyThrThrTr : 177
        !|||:!!|||  !  !:!!|||  !:!::!!:!:|||:!!:!!:!!..!   ||| !!  !||
       spAlaIleAsnCysValIleGlyGlyLeuSerValAlaAlaValValSerAlaGlyProCysTr
 539 : ATGCCATCAACTGCGTGATCGGTGGCCTCTCTGTTGCCGCGGTCGTGTCAGCAGGGCCGTGCTG : 601

 178 : pArgThrLeuGlyPheValLeuSerGlyHisPheValPheIlePheAlaThrTrp<->GluTyr : 197
       |!:!|||! !  !.!!!.!|||!:!  !! !.!!||||||.!!.!!  !||||||   ||||||
       pLysThrTrpThrIleAlaLeuAsnThrLeuIleValPhePheLeuAsnThrTrpGluGluTyr
 602 : GAAGACGTGGACGATTGCCCTCAACACCCTTATCGTCTTCTTTCTCAATACCTGGGAGGAGTAC : 664

 198 : TyrSerGlySerLeuGluLeuProLeuTyrAsnGlyProThrGluGlyTyrLeuIleGlyIleA : 219
       ||| !!|||  !|||! !||||||:!!  !|||||||||!.!||||||  !||||||!.!|||!
       TyrArgGlyValLeuValLeuProValIleAsnGlyProAsnGluGlyIleLeuIleAlaIleG
 665 : TACCGCGGCGTGTTGGTGCTGCCGGTGATCAACGGCCCGAACGAGGGCATCCTCATCGCGATCG : 730

 220 : laLeuLysLeuValThrAlaValValGlyValGlyPheTrp : 232
       .!:!! ! |||  !||||||  !!.!|||! !  !   |||
       lyIleTyrLeuTrpThrAlaTrpAlaGlyGlyProGlnTrp
 731 : GCATTTACTTGTGGACGGCGTGGGCGGGTGGGCCGCAGTGG : 771

vulgar: SelI_Phytophtora 38 232 . Cf_Contig603:subseq(0,5000) 111 771 + 388 M 26 78 G 0 3 M 47 141 5 0 2 I 0 68 3 0 2 M 84 252 G 0 3 M 37 111
# --- 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
#
Cf_Contig603:subseq(0,5000)	exonerate:protein2genome:local	gene	112	771	388	+	.	gene_id 1 ; sequence SelI_Phytophtora ; gene_orientation +
Cf_Contig603:subseq(0,5000)	exonerate:protein2genome:local	cds	112	333	.	+	.	
Cf_Contig603:subseq(0,5000)	exonerate:protein2genome:local	exon	112	333	.	+	.	insertions 3 ; deletions 0
Cf_Contig603:subseq(0,5000)	exonerate:protein2genome:local	splice5	334	335	.	+	.	intron_id 1 ; splice_site "GA"
Cf_Contig603:subseq(0,5000)	exonerate:protein2genome:local	intron	334	405	.	+	.	intron_id 1
Cf_Contig603:subseq(0,5000)	exonerate:protein2genome:local	splice3	404	405	.	+	.	intron_id 0 ; splice_site "CG"
Cf_Contig603:subseq(0,5000)	exonerate:protein2genome:local	cds	406	771	.	+	.	
Cf_Contig603:subseq(0,5000)	exonerate:protein2genome:local	exon	406	771	.	+	.	insertions 3 ; deletions 0
Cf_Contig603:subseq(0,5000)	exonerate:protein2genome:local	similarity	112	771	388	+	.	alignment_id 1 ; Query SelI_Phytophtora ; Align 112 39 78 ; Align 193 65 141 ; Align 406 112 252 ; Align 661 196 111
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SelI_Phytophtora infestans
        Target: Cf_Contig603:subseq(0,5000)  |  | 1 to 51230
         Model: protein2genome:local
     Raw score: 227
   Query range: 301 -> 387
  Target range: 1281 -> 1539

  302 : LeuValAlaPheThrArgLeuLeuProPheValValIleAsnThrLeuAlaGlyLeuTrpAl :  322
        |||  !|||.!!:!!||||||:!!|||.!.|||||||||!..  !:!!!.!..!:!!|||  
        LeuHisAlaLeuSerArgLeuIleProLeuValValIleThrLeuMetGlyAsnValTrpPh
 1282 : CTCCACGCCCTCTCTCGCCTCATCCCGCTGGTGGTGATTACGCTAATGGGCAACGTGTGGTT : 1342

  323 : aLeuTyrSerProSerAspIlePheSerThrHisProArgMetPheLeuTrpMetLeuGlyL :  343
        !|||   |||! !..!|||:!!||| !!  !|||||||||:!:|||! !|||!  :!!||||
        eLeuThrSerGlnGluAspValPheArgArgHisProArgLeuPheCysTrpThrValGlyL
 1343 : TCTGACGTCGCAGGAGGATGTCTTTCGCCGCCACCCCCGCCTCTTCTGCTGGACCGTTGGGC : 1405

  344 : euLeuAsnSerLysLeuValLeuHisLeuMetLeuAlaHisLeuCysGlyGluGluTyrHis :  363
        ||||| !!!!!||||||!.!:!!|||||||||:!!:!!||||||||||||!  |||!:!|||
        euLeuTyrThrLysLeuAlaValHisLeuMetValSerHisLeuCysGlyAlaGluPheHis
 1406 : TGCTGTACACGAAACTGGCTGTCCATCTGATGGTGTCGCACCTGTGCGGGGCCGAGTTTCAC : 1465

  364 : ProPheArgLysThrLeuValProIlePheTyrValAlaGlyHisCysAlaPheCysMetVa :  384
        |||||||||:::|||!!!:!!|||.!!.!!  ! !!!.!!.!|||  !..!.!!  !   :!
        ProPheArgArgThrPheLeuProPheLeuLeuPheGlyAlaHisIleCysLeuThrTyrLe
 1466 : CCCTTCCGCCGCACCTTCTTGCCCTTTCTCCTCTTCGGCGCGCACATCTGCCTCACCTATCT : 1528

  385 : lGluGlyIle :  387
        !.!...!:!!
        uHisAsnVal
 1529 : GCACAACGTC : 1539

vulgar: SelI_Phytophtora 301 387 . Cf_Contig603:subseq(0,5000) 1281 1539 + 227 M 86 258
# --- 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
#
Cf_Contig603:subseq(0,5000)	exonerate:protein2genome:local	gene	1282	1539	227	+	.	gene_id 2 ; sequence SelI_Phytophtora ; gene_orientation .
Cf_Contig603:subseq(0,5000)	exonerate:protein2genome:local	cds	1282	1539	.	+	.	
Cf_Contig603:subseq(0,5000)	exonerate:protein2genome:local	exon	1282	1539	.	+	.	insertions 0 ; deletions 0
Cf_Contig603:subseq(0,5000)	exonerate:protein2genome:local	similarity	1282	1539	227	+	.	alignment_id 2 ; Query SelI_Phytophtora ; Align 1282 302 258
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
