Command line: [exonerate -m p2g --showtargetgff -q pstk.query.U_to_X -t gi|511782584|gb|CM001949.1|.fastasubseq]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000052_2.0 # Protein # Phosphoseryl-tRNA kinase  (PSTK) # Human (Homo sapiens) 
        Target: gi|511782584|gb|CM001949.1|:subseq(115605213,106764) Chlorocebus sabaeus isolate 1994-021 chromosome 9, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 1583
   Query range: 0 -> 334
  Target range: 49999 -> 56764

     1 : MetLysThrAlaGluAsnIleArgGlyThrGlySerAspGlyProArgLysArgGlyLeu :    20
         |||||||||||||||!.!! !|||||||||||||||||||||||||||||||||! !|||
         MetLysThrAlaGluThrThrArgGlyThrGlySerAspGlyProArgLysArgValLeu
 50000 : ATGAAGACCGCCGAGACCACCAGAGGAACAGGCAGCGACGGCCCGCGAAAACGAGTCCTC : 50057

    21 : CysValLeuCysGlyLeuProAlaAlaGlyLysSerThrPheAlaArgAlaLeuAlaHis :    40
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         CysValLeuCysGlyLeuProAlaAlaGlyLysSerThrPheAlaArgAlaLeuAlaHis
 50058 : TGCGTCCTCTGCGGCCTCCCCGCGGCAGGAAAATCGACTTTCGCGCGCGCCCTCGCCCAC : 50117

    41 : ArgLeuGlnGlnGluGlnGlyTrpAlaIleGlyValValAlaTyrAspAspValMetPro :    60
         ||||||!:!||||||||||||||||||:!!||||||||||||||||||||||||||||||
         ArgLeuArgGlnGluGlnGlyTrpAlaValGlyValValAlaTyrAspAspValMetPro
 50118 : CGCCTGCGGCAGGAGCAGGGTTGGGCCGTTGGTGTTGTCGCGTATGATGATGTCATGCCC : 50177

    61 : AspAlaPheLeuAlaGlyAlaArgAlaArgProAla  >>>> Target Intron 1 > :    73
         ||||||||||||||||||! !|||||||||||||||           2073 bp      
         AspAlaPheLeuAlaGlyGluArgAlaArgProAla++                      
 50178 : GACGCGTTTCTCGCCGGGGAAAGAGCGCGACCGGCGgt...................... : 50218

    74 : >>>  ProSerGlnTrpLysLeuLeuArgGlnGluLeuLeuLysTyrLeuGluTyrPheL :    91
              |||||||||||||||||||||||||||||||||||||||||||||||||||||||
            ++ProSerGlnTrpLysLeuLeuArgGlnGluLeuLeuLysTyrLeuGluTyrPheL
 50219 : ...agCCATCCCAGTGGAAATTGCTTCGACAGGAACTGTTGAAGTACCTGGAATACTTCT : 52343

    92 : euMetAlaValIleAsnGlyCysGlnMetSerValProProAsnArgThrGluAlaMetT :   111
         |||||||||||||||||||||||||||||||||||||||||!:!||||||||||||||||
         euMetAlaValIleAsnGlyCysGlnMetSerValProProSerArgThrGluAlaMetT
 52344 : TGATGGCCGTCATTAATGGGTGTCAGATGTCTGTCCCACCCAGCAGGACTGAAGCCATGT : 52403

   112 : rpGluAspPheIleThrCysLeuLysAspGlnAspLeuIlePheSerAlaAlaPheGluA :   131
         |||||||||||||||||||||||||||||||||||||||||||||||||||||!:!||||
         rpGluAspPheIleThrCysLeuLysAspGlnAspLeuIlePheSerAlaAlaTyrGluA
 52404 : GGGAAGATTTTATAACCTGCCTAAAGGATCAAGATCTGATATTTTCTGCAGCATATGAGG : 52463

   132 : laGlnSerCysTyrLeuLeuThrLysThrAlaValSerArgProLeuPheLeuValLeuA :   151
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         laGlnSerCysTyrLeuLeuThrLysThrAlaValSerArgProLeuPheLeuValLeuA
 52464 : CCCAGTCTTGCTACCTCTTAACAAAAACTGCTGTTTCTAGACCTTTGTTTCTGGTTTTGG : 52523

   152 : spAspAsnPheTyrTyrGlnSerMetArgTyrGluValTyrGlnLeuAlaArgLys{T}  :   170
         |||||||||||||||||||||||||||||||||||||| !!|||||||||||||||{|} 
         spAspAsnPheTyrTyrGlnSerMetArgTyrGluValAsnGlnLeuAlaArgLys{T}+
 52524 : ATGACAATTTTTATTATCAGAGTATGAGATATGAAGTCAACCAGCTGGCTCGGAAA{T}g : 52581

   171 :  >>>> Target Intron 2 >>>>  {yr}SerLeuGlyPheCysGlnLeuPheLeuA :   180
                    244 bp           {||}||||||||||||||||||||||||||||
         +                         ++{yr}SerLeuGlyPheCysGlnLeuPheLeuA
 52582 : t.........................ag{AT}TCATTGGGCTTTTGCCAGCTCTTTTTAG : 52854

   181 : spCysProLeuGluThrCysLeuGlnArgAsnGlyGlnArgProGlnAlaLeuProProG :   200
         ||||||||||||||||||||||||||||||||.!!|||||||||||||||||||||||||
         spCysProLeuGluThrCysLeuGlnArgAsnSerGlnArgProGlnAlaLeuProProG
 52855 : ATTGTCCTCTTGAGACCTGTTTACAGAGGAATAGCCAGAGGCCACAGGCACTGCCTCCTG : 52914

   201 : luThrIleHisLeuMetGlyArgLysLeuGluLysProAsnProGluLysAsnAlaTrpG :   220
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         luThrIleHisLeuMetGlyArgLysLeuGluLysProAsnProGluLysAsnAlaTrpG
 52915 : AGACCATCCACCTGATGGGAAGAAAGCTAGAAAAGCCCAACCCTGAGAAAAATGCTTGGG : 52974

   221 : luHisAsnSerLeuThrIleProSerProAlaCysAlaSerGluAla{Se}  >>>> Ta :   236
         |||||||||||||||||||||||||||||||||||!.!|||||||||{||}         
         luHisAsnSerLeuThrIleProSerProAlaCysGlySerGluAla{Se}++       
 52975 : AACACAACAGCCTCACAATTCCGAGTCCAGCATGTGGTTCGGAGGCC{AG}gt....... : 53026

   237 : rget Intron 3 >>>>  {r}LeuGluValThrAspLeuLeuLeuThrAlaLeuGluA :   249
           2593 bp           {|}|||||||||||||||||||||||||||||||||||||
                           ++{r}LeuGluValThrAspLeuLeuLeuThrAlaLeuGluA
 53027 : ..................ag{C}CTGGAGGTGACTGATTTATTGCTCACTGCTTTGGAAA : 55654

   250 : snProValLysTyrAlaGluAspAsnMetGluGlnLys  >>>> Target Intron 4 :   262
         ||||||||||||||||||||||||||||||||||||||            487 bp    
         snProValLysTyrAlaGluAspAsnMetGluGlnLys++                    
 55655 : ATCCGGTAAAATATGCTGAGGACAATATGGAACAAAAGgt.................... : 55695

   263 :  >>>>  AspThrAspArgIleIleCysSerThrAsnIleLeuHisLysThrAspGlnTh :   279
                !!:|||||||||||||||||||||||||||||||||||||||.!!||||||||
              ++GluThrAspArgIleIleCysSerThrAsnIleLeuHisLysAlaAspGlnTh
 55696 : .....agGAGACAGATAGAATTATTTGTTCAACTAACATTCTTCATAAAGCTGATCAGAC : 56231

   280 : rLeuArgArgIleValSerGlnThrMetLysGluAlaLys{G}  >>>> Target Int :   293
         |||||||||||||||||||||||||||||||! !||||||{|}            366 b
         rLeuArgArgIleValSerGlnThrMetLysGlyAlaLys{G}++               
 56232 : ACTCCGAAGGATTGTATCTCAGACAATGAAGGGAGCAAAA{G}gt............... : 56276

   294 : ron 5 >>>>  {ly}AsnGlnGluAlaPheSerGluMetThrPheLysGlnArgTrpVa :   308
         p           {||}|||||||||!.!||||||||||||||||||||||||||||||! 
                   -+{ly}AsnGlnGluGlyPheSerGluMetThrPheLysGlnArgTrpGl
 56277 : ..........gg{GT}AATCAGGAAGGCTTCTCAGAGATGACATTTAAGCAAAGATGGGA : 56684

   309 : lArgAlaAsnHisAlaAlaIleTrpArgIleIleLeuGlyAsnGluHisIleLysCysAr :   328
         !|||||||||||||||! !|||||||||||||||||||||||||||||||||||||||||
         uArgAlaAsnHisAlaAspIleTrpArgIleIleLeuGlyAsnGluHisIleLysCysAr
 56685 : AAGAGCGAACCATGCAGATATCTGGAGGATCATTCTAGGCAATGAACACATCAAGTGCAG : 56744

   329 : gSerAlaLysValGlyTrp :   334
         |||| !!:!!|||||||||
         gSerProGluValGlyTrp
 56745 : AAGCCCAGAGGTTGGCTGG : 56764

vulgar: SPP00000052_2.0 0 334 . gi|511782584|gb|CM001949.1|:subseq(115605213,106764) 49999 56764 + 1583 M 72 216 5 0 2 I 0 2069 3 0 2 M 97 291 S 0 1 5 0 2 I 0 240 3 0 2 S 1 2 M 65 195 S 0 2 5 0 2 I 0 2589 3 0 2 S 1 1 M 25 75 5 0 2 I 0 483 3 0 2 M 31 93 S 0 1 5 0 2 I 0 362 3 0 2 S 1 2 M 41 123
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-05
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	gene	50000	56764	1583	+	.	gene_id 1 ; sequence SPP00000052_2.0 ; gene_orientation +
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	cds	50000	50215	.	+	.	
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	exon	50000	50215	.	+	.	insertions 0 ; deletions 0
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	splice5	50216	50217	.	+	.	intron_id 1 ; splice_site "GT"
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	intron	50216	52288	.	+	.	intron_id 1
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	splice3	52287	52288	.	+	.	intron_id 0 ; splice_site "AG"
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	cds	52289	52580	.	+	.	
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	exon	52289	52580	.	+	.	insertions 0 ; deletions 0
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	splice5	52581	52582	.	+	.	intron_id 2 ; splice_site "GT"
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	intron	52581	52824	.	+	.	intron_id 2
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	splice3	52823	52824	.	+	.	intron_id 1 ; splice_site "AG"
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	cds	52825	53023	.	+	.	
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	exon	52825	53023	.	+	.	insertions 0 ; deletions 0
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	splice5	53024	53025	.	+	.	intron_id 3 ; splice_site "GT"
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	intron	53024	55616	.	+	.	intron_id 3
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	splice3	55615	55616	.	+	.	intron_id 2 ; splice_site "AG"
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	cds	55617	55692	.	+	.	
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	exon	55617	55692	.	+	.	insertions 0 ; deletions 0
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	splice5	55693	55694	.	+	.	intron_id 4 ; splice_site "GT"
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	intron	55693	56179	.	+	.	intron_id 4
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	splice3	56178	56179	.	+	.	intron_id 3 ; splice_site "AG"
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	cds	56180	56273	.	+	.	
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	exon	56180	56273	.	+	.	insertions 0 ; deletions 0
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	splice5	56274	56275	.	+	.	intron_id 5 ; splice_site "GT"
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	intron	56274	56639	.	+	.	intron_id 5
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	splice3	56638	56639	.	+	.	intron_id 4 ; splice_site "GG"
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	cds	56640	56764	.	+	.	
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	exon	56640	56764	.	+	.	insertions 0 ; deletions 0
gi|511782584|gb|CM001949.1|:subseq(115605213,106764)	exonerate:protein2genome:local	similarity	50000	56764	1583	+	.	alignment_id 1 ; Query SPP00000052_2.0 ; Align 50000 1 216 ; Align 52289 73 291 ; Align 52827 171 195 ; Align 55618 237 75 ; Align 56180 262 93 ; Align 56642 294 123
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis