Command line: [exonerate -E -m p2g --showtargetgff -q pstk_mus.fa -t pstk_Mus_Sparasitica_fragment1.fa]
Hostname: [luke]

C4 Alignment:
------------
         Query: PSTK;gi|117167838|gb|AAI15504.2|Mus musculus #QUERY
        Target: gi|288565285|gb|GG743912.1|:subseq(265174,10000) Saprolegnia parasitica CBS 223.65 genomic scaffold supercont1.30, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 104
   Query range: 148 -> 294
  Target range: 5292 -> 4704

  149 : LeuValLeuAspAspAsnPheTyrTyrGlnSerMetArgTyr--GluValTyrGlnLeuAla :  168
        |||:!!||||||||||||.!.||||||!::|||||||||   ##:!!|||!  ||||||..!
        LeuLeuLeuAspAspAsnMetTyrTyrArgSerMetArg---##LysValLeuGlnLeuCys
 5292 : CTGCTCTTGGATGACAACATGTACTACCGCAGCATGCGC---AAAAAGTCTTGCAGCTGTGT : 5236

  169 : ArgLys{T}  >>>> Target Intron 1 >>>>  {yr}SerLeuGlyPheCysGlnLe :  178
        |||:!!{ }            45 bp            {  }!:!  !|||||| !!  !:!
        ArgGln{A}++                         ++{rg}AsnAlaGlyPheGlyValIl
 5235 : CGACAG{C}gt.........................ag{GA}AATGCAGGCTTTGGTGTGAT : 5161

  179 : uPheLeuAspCysProLeuGluThrCysLeuLysArgAsnGlyGluArgSerGlnProLeuP :  199
        !  !:!!|||     !! !!!:  !|||! !   ||||||!.!! !|||..!..!|||:!!|
        eHisValAspThrLysProAspLeuCysArgAlaArgAsnAlaAlaArgGlnSerProValP
 5160 : TCACGTGGACACGAAGCCCGACCTTTGCCGCGCCCGCAATGCCGCACGGCAGTCGCCGGTTC : 5098

  200 : roAspGluThrIleGlnLeuMetGlyArgLysIleGluLysProAsnProGluLysAsnAla :  219
        |||||! !..!.!!!::! !|||  !  !   .!!|||  !|||!:!|||...! !:!! !!
        roAspValValPheArgArgMetHisAlaLeuPheGluProProSerProSerMetHisPro
 5097 : CGGACGTAGTCTTTCGCCGAATGCACGCTCTCTTCGAGCCACCAAGTCCAAGCATGCATCCG : 5038

  220 : TrpGluHisAsnSerLeuIleIleGlnSerSerAlaCysSer{Le}  >>>> Target In :  234
        ||||||  !...|||:!!:!!:!!.!.! !|||:!!..!..!{  }            56 b
        TrpGluAlaArgSerIleValValAspLeuSerSerAlaAsp{Al}+-              
 5037 : TGGGAAGCCCGATCGATCGTCGTCGACTTGAGCTCCGCCGAC{GC}ga.............. : 4989

  235 : tron 2 >>>>  {u}GluAlaSerLeuGluValThrGlyLeuLeuLeuThrAlaLeuGluA :  250
        p            {!}!  |||  !! !!  !.!  !!.!:!!:!!  !  !|||:!!! !!
                   ++{a}AlaAlaLeuHisAlaAlaLeuAlaMetIleAlaGluAlaValAlaT
 4988 : ...........ag{A}GCTGCACTTCACGCTGCGCTCGCGATGATCGCGGAGGCGGTGGCGA : 4889

  251 : snPro<->IleLysCysValGluAspAsnThrGluGlnLys  >>>> Target Intron  :  263
        ..|||   :!! !    ..!:!!!!:! !..!   :!!|||            47 bp    
        hrProGluValAspThrThrGlnGluIleValLeuGluLys++                   
 4888 : CACCTGAAGTCGACACAACCCAAGAAATCGTCCTTGAAAAGgt................... : 4845

  264 : 3 >>>>  GluThrAspArgIleIleCysSerThrAsnIleLeuHisLysAlaAspGluThr :  280
                |||  !..!|||        !  !.!!!:!:!:||||||::!||||||   ..!
              ++GluArgSerArgAlaAlaThrLeuAlaSerValLeuHisArgAlaAspLeuVal
 4844 : ......agGAACGCAGCCGGGCGGCGACCCTCGCCAGCGTGCTTCACCGAGCGGACCTCGTC : 4749

  281 : LeuArgArgThrValSerGlnThrMetArgGluAlaLysAsp :  294
        ||||||!:!  !|||.!!|||! !:!:|||!!:||||||!!:
        LeuArgGlnLeuValGlyGlnIleLeuArgAspAlaLysGlu
 4748 : TTGCGCCAGCTCGTGGGACAGATCCTTCGGGATGCCAAGGAA : 4705

vulgar: PSTK;gi|117167838|gb|AAI15504.2|Mus 148 294 . gi|288565285|gb|GG743912.1|:subseq(265174,10000) 5292 4704 - 104 M 13 39 G 1 0 F 0 2 M 8 24 S 0 1 5 0 2 I 0 41 3 0 2 S 1 2 M 62 186 S 0 2 5 0 2 I 0 52 3 0 2 S 1 1 M 17 51 G 0 3 M 11 33 5 0 2 I 0 43 3 0 2 M 32 96
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-03-15
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	gene	4705	5292	104	-	.	gene_id 1 ; sequence PSTK;gi|117167838|gb|AAI15504.2|Mus ; gene_orientation +
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	cds	5227	5292	.	-	.	
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	exon	5227	5292	.	-	.	insertions 0 ; deletions 1 ; frameshifts 2
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	splice5	5225	5226	.	-	.	intron_id 1 ; splice_site "GT"
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	intron	5182	5226	.	-	.	intron_id 1
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	splice3	5182	5183	.	-	.	intron_id 0 ; splice_site "AG"
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	cds	4992	5181	.	-	.	
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	exon	4992	5181	.	-	.	insertions 0 ; deletions 0
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	splice5	4990	4991	.	-	.	intron_id 2 ; splice_site "GA"
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	intron	4936	4991	.	-	.	intron_id 2
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	splice3	4936	4937	.	-	.	intron_id 1 ; splice_site "AG"
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	cds	4848	4935	.	-	.	
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	exon	4848	4935	.	-	.	insertions 3 ; deletions 0
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	splice5	4846	4847	.	-	.	intron_id 3 ; splice_site "GT"
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	intron	4801	4847	.	-	.	intron_id 3
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	splice3	4801	4802	.	-	.	intron_id 2 ; splice_site "AG"
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	cds	4705	4800	.	-	.	
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	exon	4705	4800	.	-	.	insertions 0 ; deletions 0
gi|288565285|gb|GG743912.1|:subseq(265174,10000)	exonerate:protein2genome:local	similarity	4705	5292	104	-	.	alignment_id 1 ; Query PSTK;gi|117167838|gb|AAI15504.2|Mus ; Align 5293 149 39 ; Align 5252 163 24 ; Align 5180 172 186 ; Align 4935 235 51 ; Align 4881 252 33 ; Align 4801 263 96
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
