Command line: [exonerate -m p2g --showtargetgff -q query.selI.P.infestans.fa -t SelI.L.donovani_BPK282A1_2.fastasubseq.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query: SelI_Phytophtora infestans
        Target: contig_03:subseq(329000,6000) [revcomp]
         Model: protein2genome:local
     Raw score: 356
   Query range: 38 -> 232
  Target range: 4210 -> 3549

   39 : LysTyrValSerGlnGluGlySerGluLysLeuArgThrTyrGluTyrHisGlyAlaAspAs :   59
        ...|||:!! !!  !!!:!.!!.!|||||||||  !  !|||!  |||!.!.!!! !|||..
        SerTyrLeuProAlaAspAlaLysGluLysLeuAlaLeuTyrValTyrArgSerGluAspAr
 4210 : TCCTACCTACCCGCAGATGCCAAGGAGAAGCTAGCGCTCTACGTCTACCGCAGCGAGGACCG : 4150

   60 : nSerLeuValTyrLys<->ValLeuThrProMetAsnAsnPheLeuValLysLeuLeuProL :   79
        !|||! !:!!|||!!.   :!!! !  !|||:!!  !...   :!!||| ! ! !||||||:
        gSerTyrLeuTyrAsnHisMetTrpArgProLeuCysArgLysValValAspTyrLeuProV
 4149 : CAGCTATCTCTACAACCACATGTGGCGGCCGCTGTGCCGAAAGGTGGTGGATTACCTGCCGG : 4087

   80 : euTrpLeuAlaProAsnLeuIleThrLeuIleGlyLeuIleLeuValGlyGlySerHisThr :   99
        !!|||||||||||||||:!!||||||:!!  !!.!|||   !!!||||||  !!!!|||  !
        alTrpLeuAlaProAsnIleIleThrValAlaAlaLeuAlaPheValGlyThrThrHisGly
 4086 : TGTGGCTGGCGCCGAACATCATTACCGTCGCCGCCCTCGCGTTCGTGGGCACCACCCATGGC : 4027

  100 : LeuPheValPheLeuCysProPheLeuVal  >>>> Target Intron 1 >>>>  Gly :  110
        |||.!.!.!!:!! !   |||   |||..!            72 bp              !
        LeuLeuAlaTyrTyrMetProLysLeuThr++                         -+Pro
 4026 : CTTCTAGCGTACTACATGCCGAAGTTGACGgt.........................cgCCG : 3922

  111 : AspAlaProTrpTrpAlaMetValValAlaAlaLeuAlaLeuPheThrTyrGlnThrLeuAs :  131
            !!|||  !!::!.!.!.|||:!!||||||:!!|||||||||  !||||||  !|||||
        ProProProAlaPheValPheValLeuAlaAlaValAlaLeuPheLeuTyrGlnLeuLeuAs
 3921 : CCGCCGCCGGCGTTTGTGTTCGTTCTTGCGGCGGTCGCGCTTTTCCTCTACCAGCTCCTCGA : 3859

  132 : pAsnLeuAspGlyLysGlnAlaArgArgThrLysSerSerSerProLeuGlyLeuLeuPheA :  152
        ||||||||||||| ! |||||||||||||||   !!!|||||||||||||||:!!|||.!.|
        pAsnLeuAspGlyHisGlnAlaArgArgThrGlyThrSerSerProLeuGlyMetLeuMetA
 3858 : CAACCTCGACGGGCATCAAGCGCGCCGCACCGGCACCTCGAGTCCGCTGGGGATGCTCATGG : 3796

  153 : spHisGlyCysValAlaLeuAsnValSerValGlyThrMetThrMetAlaSerIleLeuGln :  172
        |||||||||||! !|||:!!|||  !! !:!!|||.!!:!!:!!:!:|||!!!   :!!..!
        spHisGlyCysAspAlaValAsnCysIleIleGlyAlaLeuSerValAlaThrAlaValSer
 3795 : ACCACGGCTGCGACGCCGTTAACTGCATCATCGGCGCTCTGTCTGTTGCAACGGCGGTGTCG : 3736

  173 : MetGlyThrThrTrpArgThrLeuGlyPheValLeuSerGlyHisPheVal-PheIlePheA :  193
           ||| !!:!!|||!:!|||! !  !.!!||||||!:!  !  !.!!..!#|||.!!.!. 
        AlaGlyProSerTrpLysThrTrpLeuIleValLeuAsnThrValIleThr#PhePheLeuA
 3735 : GCCGGGCCGTCCTGGAAGACGTGGCTGATTGTGCTCAACACGGTCATCACGTTTTTTCCTGA : 3672

  194 : laThrTrp<->GluTyrTyrSerGlySerLeuGluLeuProLeuTyrAsnGlyProThrGlu :  212
         !||||||   ||||||||| !!|||  !|||! !||||||:!!  !|||||||||!.!|||
        snThrTrpGluGluTyrTyrArgGlyValLeuValLeuProValIleAsnGlyProAsnGlu
 3671 : ACACCTGGGAGGAGTACTACCGTGGCGTGCTCGTGCTACCCGTCATCAACGGCCCCAACGAA : 3612

  213 : GlyTyrLeuIleGlyIleAlaLeuLysLeuValThrAlaValValGlyValGlyPheTrp :  232
        |||  !||||||!.!|||!.!:!! ! |||  !||||||  !||||||! !  !   |||
        GlyIleLeuIleAlaIleGlyValTyrLeuTrpThrAlaTrpValGlyGlyProGlnTrp
 3611 : GGCATCCTCATTGCGATCGGCGTCTACCTGTGGACAGCGTGGGTAGGGGGGCCGCAGTGG : 3550

vulgar: SelI_Phytophtora 38 232 . contig_03:subseq(329000,6000) 4210 3549 - 356 M 26 78 G 0 3 M 45 135 5 0 2 I 0 68 3 0 2 M 80 240 F 0 1 M 6 18 G 0 3 M 37 111
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-11-28
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
contig_03:subseq(329000,6000)	exonerate:protein2genome:local	gene	3550	4210	356	-	.	gene_id 1 ; sequence SelI_Phytophtora ; gene_orientation +
contig_03:subseq(329000,6000)	exonerate:protein2genome:local	cds	3995	4210	.	-	.	
contig_03:subseq(329000,6000)	exonerate:protein2genome:local	exon	3995	4210	.	-	.	insertions 3 ; deletions 0
contig_03:subseq(329000,6000)	exonerate:protein2genome:local	splice5	3993	3994	.	-	.	intron_id 1 ; splice_site "GT"
contig_03:subseq(329000,6000)	exonerate:protein2genome:local	intron	3923	3994	.	-	.	intron_id 1
contig_03:subseq(329000,6000)	exonerate:protein2genome:local	splice3	3923	3924	.	-	.	intron_id 0 ; splice_site "CG"
contig_03:subseq(329000,6000)	exonerate:protein2genome:local	cds	3550	3922	.	-	.	
contig_03:subseq(329000,6000)	exonerate:protein2genome:local	exon	3550	3922	.	-	.	insertions 3 ; deletions 0 ; frameshifts 1
contig_03:subseq(329000,6000)	exonerate:protein2genome:local	similarity	3550	4210	356	-	.	alignment_id 1 ; Query SelI_Phytophtora ; Align 4211 39 78 ; Align 4130 65 135 ; Align 3923 110 240 ; Align 3682 190 18 ; Align 3661 196 111
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SelI_Phytophtora infestans
        Target: contig_03:subseq(329000,6000) [revcomp]
         Model: protein2genome:local
     Raw score: 214
   Query range: 301 -> 387
  Target range: 3042 -> 2784

  302 : LeuValAlaPheThrArgLeuLeuProPheValValIleAsnThrLeuAlaGlyLeuTrpAl :  322
        |||  !|||.!!:!!||||||:!!|||.!!||||||:!!!..  !  !|||.!!  !|||  
        LeuHisAlaLeuSerArgLeuValProLeuValValValThrPheThrAlaSerAlaTrpLe
 3042 : CTGCACGCCCTCTCACGCCTCGTCCCGCTCGTCGTCGTCACGTTCACGGCGAGCGCGTGGCT : 2982

  323 : aLeuTyrSerProSerAspIlePheSerThrHisProArgMetPheLeuTrpMetLeuGlyL :  343
        !|||  !|||  !..!||||||||| !!  !|||||||||!!:|||! !|||! !:!!||||
        uLeuThrSerAsnAspAspIlePheArgArgHisProArgIlePheCysTrpThrValGlyL
 2981 : TCTCACCTCGAACGATGACATTTTCCGGCGGCACCCGCGCATCTTCTGTTGGACGGTGGGAC : 2919

  344 : euLeuAsnSerLysLeuValLeuHisLeuMetLeuAlaHisLeuCysGlyGluGluTyrHis :  363
        ||||| !!!!!||||||!.!:!!||||||||||||||||||||||||.!!!  |||!:!! !
        euLeuTyrThrLysLeuAlaIleHisLeuMetLeuAlaHisLeuCysSerAlaGluPheLeu
 2918 : TGCTCTATACGAAGCTGGCCATACATCTCATGTTGGCGCACCTCTGCAGCGCCGAGTTCCTC : 2859

  364 : ProPheArgLysThrLeuValProIlePheTyrValAlaGlyHisCysAlaPheCysMetVa :  384
        |||||||||:::||||||!.!|||.!! !   !:!!..!! !|||  !  !.!!  !   ||
        ProPheArgArgThrLeuAlaProPheValLeuLeuCysValHisValTrpLeuThrTyrVa
 2858 : CCCTTCCGCCGCACCCTCGCGCCGTTCGTGCTCCTCTGCGTACACGTCTGGCTCACCTATGT : 2796

  385 : lGluGlyIle :  387
        |.....!:!!
        lArgAsnVal
 2795 : GCGCAACGTC : 2785

vulgar: SelI_Phytophtora 301 387 . contig_03:subseq(329000,6000) 3042 2784 - 214 M 86 258
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-11-28
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
contig_03:subseq(329000,6000)	exonerate:protein2genome:local	gene	2785	3042	214	-	.	gene_id 2 ; sequence SelI_Phytophtora ; gene_orientation .
contig_03:subseq(329000,6000)	exonerate:protein2genome:local	cds	2785	3042	.	-	.	
contig_03:subseq(329000,6000)	exonerate:protein2genome:local	exon	2785	3042	.	-	.	insertions 0 ; deletions 0
contig_03:subseq(329000,6000)	exonerate:protein2genome:local	similarity	2785	3042	214	-	.	alignment_id 2 ; Query SelI_Phytophtora ; Align 3043 302 258
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
