Command line: [exonerate -m p2g --showtargetgff -q 1B.query.dir/M.PSTK.1.fa.x.fa -t 3B.fastasub.dir/1.M.PSTK.1.fa.x.fa]
Hostname: [ws101043]

C4 Alignment:
------------
         Query: SPP00000052_2.0 # Protein # Phosphoseryl-tRNA kinase  (PSTK) # Human (Homo sapiens)
        Target: gi|398921680|gb|JH767798.1|:subseq(10174851,107557) Ceratotherium simum simum unplaced genomic scaffold scaffold00076, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 1327
   Query range: 0 -> 346
  Target range: 57557 -> 49956

     1 : MetLysThrAlaGluAsnIleArgGlyThrGlySerAspGlyProArgLysArgGlyLeu :    20
         |||||||||!.!|||:!!  !||||||  !||||||!  ||||||||||||! !||||||
         MetLysThrGlyGluAspAlaArgGlyGluGlySerAlaGlyProArgLysLeuGlyLeu
 57557 : ATGAAGACCGGCGAGGACGCCAGAGGAGAGGGCAGCGCGGGACCGCGGAAGCTAGGACTC : 57500

    21 : CysValLeuCysGlyLeuProAlaAlaGlyLysSerThrPheAlaArgAlaLeuAlaHis :    40
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||::!|||
         CysValLeuCysGlyLeuProAlaAlaGlyLysSerThrPheAlaArgAlaLeuSerHis
 57499 : TGCGTCCTCTGCGGCCTGCCAGCAGCAGGAAAATCGACCTTCGCGCGGGCTCTCAGCCAC : 57440

    41 : ArgLeuGlnGlnGluGlnGlyTrpAlaIleGlyValValAlaTyrAspAspValMetPro :    60
         !:!|||!:!||||||!:!|||||||||:!: !!|||||||||||||||||||||||||||
         GlnLeuArgGlnGluArgGlyTrpAlaValCysValValAlaTyrAspAspValMetPro
 57439 : CAGCTACGGCAAGAGCGGGGCTGGGCCGTGTGCGTCGTCGCCTATGATGACGTCATGCCG : 57380

    61 : AspAlaPheLeuAlaGlyAlaArgAlaArgProAla  >>>> Target Intron 1 > :    73
         ||||||||||||! !! !|||!!!|||||||||  !           2105 bp      
         AspAlaPheLeuGluGluAlaSerAlaArgProLeu++                      
 57379 : GACGCGTTCCTCGAGGAGGCGAGCGCACGGCCATTGgt...................... : 57339

    74 : >>>  ProSerGlnTrpLysLeuLeuArgGlnGluLeuLeuLysTyrLeuGluTyrPheL :    91
              |||||||||||||||||||||||||||||||||||||||||||||||||||||||
            ++ProSerGlnTrpLysLeuLeuArgGlnGluLeuLeuLysTyrLeuGluTyrPheL
 57338 : ...agCCATCCCAATGGAAATTGCTTCGACAGGAACTCTTGAAGTACCTAGAATACTTCC : 55182

    92 : euMetAlaValIleAsnGlyCysGlnMetSerValProProAsnArgThrGluAlaMetT :   111
         ||||||||||||||||||||||||||||||||!.!|||||||||||||||||||||||||
         euMetAlaValIleAsnGlyCysGlnMetSerAlaProProAsnArgThrGluAlaMetT
 55181 : TGATGGCTGTCATTAACGGGTGTCAGATGTCTGCGCCACCCAACAGGACTGAAGCCATGT : 55122

   112 : rpGluAspPheIleThrCysLeuLysAspGlnAspLeuIlePheSerAlaAlaPheGluA :   131
         ||:!!|||||||||||||||||||||:!!||||||||||||! !|||||||||.!!||||
         rpLysAspPheIleThrCysLeuLysAsnGlnAspLeuIleSerSerAlaAlaLeuGluA
 55121 : GGAAAGATTTTATAACCTGCTTAAAGAATCAAGATCTGATATCTTCTGCAGCGCTTGAGG : 55062

   132 : laGlnSerCysTyrLeuLeuThrLysThrAlaValSerArgProLeuPheLeuValLeuA :   151
         |||||||||||||||||||||||||||||||||||||||||||||||||||||:!!||||
         laGlnSerCysTyrLeuLeuThrLysThrAlaValSerArgProLeuPheLeuIleLeuA
 55061 : CCCAGTCTTGCTACCTCTTAACAAAGACTGCTGTTTCTAGACCTTTGTTTTTGATTTTAG : 55002

   152 : spAspAsnPheTyrTyrGlnSerMetArgTyrGluValTyrGlnLeuAlaArgLys{T}  :   170
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||{|} 
         spAspAsnPheTyrTyrGlnSerMetArgTyrGluValTyrGlnLeuAlaArgLys{T}+
 55001 : ATGACAACTTTTATTATCAAAGTATGAGATATGAAGTCTACCAACTGGCTCGGAAA{T}g : 54944

   171 :  >>>> Target Intron 2 >>>>  {yr}SerLeuGlyPheCysGlnLeuPheLeuA :   180
                    242 bp           {||}||||||||||||||||||||||||||||
         +                         ++{yr}SerLeuGlyPheCysGlnLeuPheLeuA
 54943 : t.........................ag{AT}TCATTAGGCTTTTGCCAGCTCTTTTTAG : 54673

   181 : spCysProLeuGluThrCysLeuGlnArgAsnGlyGlnArgProGlnAlaLeuProProG :   200
         ||||| !!||||||||||||||||||||||||! !|||||||||!:!.!!|||||| !!|
         spCysSerLeuGluThrCysLeuGlnArgAsnAspGlnArgProArgThrLeuProAlaG
 54672 : ATTGTTCTCTCGAGACCTGTTTACAGAGGAATGACCAGAGACCACGGACACTGCCTGCCG : 54613

   201 : luThrIleHisLeuMetGlyArgLysLeuGluLysProAsnProGluLysAsnAlaTrpG :   220
         ||||||||||||||||||||||||||:!!|||||||||||||||||||||||||||||||
         luThrIleHisLeuMetGlyArgLysIleGluLysProAsnProGluLysAsnAlaTrpG
 54612 : AGACCATCCACCTGATGGGAAGAAAGATAGAAAAGCCCAACCCTGAGAAAAATGCTTGGG : 54553

   221 : luHisAsnSerLeuThrIleProSerProAlaCysAlaSerGluAla{Se}  >>>> Ta :   236
         ||||||||||||||||||||! !||||||:!!|||:!!:!!||||||{||}         
         luHisAsnSerLeuThrIleGlnSerProSerCysSerAlaGluAla{Se}++       
 54552 : AACACAACAGCCTCACAATTCAGAGTCCATCATGTTCTGCTGAGGCC{AG}gt....... : 54501

   237 : rget Intron 3 >>>>  {r}LeuGluValThrAspLeuLeuLeuThrAlaLeuGluA :   249
           3280 bp           {|}|||:!!:!!||||||||||||||||||||||||||||
                           ++{r}LeuGlnLeuThrAspLeuLeuLeuThrAlaLeuGluA
 54500 : ..................ag{C}CTGCAGTTGACTGATTTATTGCTTACTGCTTTGGAAA : 51186

   250 : snProValLysTyrAlaGluAspAsnMetGluGlnLys  >>>> Target Intron 4 :   262
         ||||||||||||||!.!|||||||||:!!|||||||||            548 bp    
         snProValLysTyrValGluAspAsnValGluGlnLys++                    
 51185 : ATCCAGTGAAATATGTTGAGGACAATGTGGAACAAAAGgt.................... : 51145

   263 :  >>>>  AspThrAspArgIleIleCysSerThrAsnIleLeuHisLysThrAspGlnTh :   279
                !!:||||||||||||||||||||||||||||||||||||:!!.!!||||||||
              ++GluThrAspArgIleIleCysSerThrAsnIleLeuHisGlnAlaAspGlnTh
 51144 : .....agGAAACAGACAGAATTATTTGTTCAACTAACATTCTCCATCAAGCTGATCAGAC : 50548

   280 : rLeuArgArgIleValSerGlnThrMetLysGluAlaLys{G}  >>>> Target Int :   293
         ||||||||||||||||||||||||||||||||||||||||{|}            372 b
         rLeuArgArgIleValSerGlnThrMetLysGluAlaLys{G}++               
 50547 : ACTCCGACGAATTGTCTCTCAGACGATGAAGGAAGCAAAA{G}gt............... : 50503

   294 : ron 5 >>>>  {ly}AsnGlnGluAlaPheSer<->GluMetThrPheLysGlnArgTr :   307
         p           {||}|||||||||!.!||||||   |||||||||||||||||||||!!
                   -+{ly}AsnGlnGluGlyPheSerGluGluMetThrPheLysGlnArgCy
 50502 : ..........gg{GT}AATCAGGAAGGCTTCTCAGAGGAGATGACATTTAAGCAGAGATG : 50089

   308 : p<-><-><->ValArgAlaAsnHisAlaAlaIleTrpArg<->IleIleLeuGlyAsnGl :   323
                   ! ! !!|||!:!! !|||! !! !||||||   ||||||! ! !!..!! 
         sGlu***LysGluGlyAlaSerProAlaAspThrTrpArgLysIleIleProArgArgGl
 50088 : TGAATGAAAGGAAGGAGCAAGCCCTGCAGATACCTGGAGGAAAATCATTCCACGCCGTGG : 50029

   324 : uHisIleLysCysArgSerAlaLysVal-GlyTrpLeuGlnCysCysArgIleGluLysA :   343
         !|||||||||||||||||| !!:!!|||#.!!!! |||  !|||! !|||! !||||||!
         yHisIleLysCysArgSerProGluVal#SerCysLeuValCysSerArgThrGluLysS
 50028 : ACACATCAAGTGCAGAAGCCCAGAGGTCAAGTTGTTTGGTATGTTCTAGAACAGAAAAGA : 49968

   344 : rgProLeuSer :   346
         !!|||||||||
         erProLeuSer
 49967 : GTCCATTGAGT : 49957

vulgar: SPP00000052_2.0 0 346 . gi|398921680|gb|JH767798.1|:subseq(10174851,107557) 57557 49956 - 1327 M 72 216 5 0 2 I 0 2101 3 0 2 M 97 291 S 0 1 5 0 2 I 0 238 3 0 2 S 1 2 M 65 195 S 0 2 5 0 2 I 0 3276 3 0 2 S 1 1 M 25 75 5 0 2 I 0 544 3 0 2 M 31 93 S 0 1 5 0 2 I 0 368 3 0 2 S 1 2 M 6 18 G 0 3 M 8 24 G 0 9 M 10 30 G 0 3 M 15 45 F 0 1 M 14 42
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2014-11-25
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	gene	49957	57557	1327	-	.	gene_id 1 ; sequence SPP00000052_2.0 ; gene_orientation +
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	cds	57342	57557	.	-	.	
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	exon	57342	57557	.	-	.	insertions 0 ; deletions 0
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	splice5	57340	57341	.	-	.	intron_id 1 ; splice_site "GT"
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	intron	55237	57341	.	-	.	intron_id 1
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	splice3	55237	55238	.	-	.	intron_id 0 ; splice_site "AG"
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	cds	54945	55236	.	-	.	
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	exon	54945	55236	.	-	.	insertions 0 ; deletions 0
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	splice5	54943	54944	.	-	.	intron_id 2 ; splice_site "GT"
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	intron	54703	54944	.	-	.	intron_id 2
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	splice3	54703	54704	.	-	.	intron_id 1 ; splice_site "AG"
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	cds	54504	54702	.	-	.	
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	exon	54504	54702	.	-	.	insertions 0 ; deletions 0
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	splice5	54502	54503	.	-	.	intron_id 3 ; splice_site "GT"
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	intron	51224	54503	.	-	.	intron_id 3
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	splice3	51224	51225	.	-	.	intron_id 2 ; splice_site "AG"
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	cds	51148	51223	.	-	.	
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	exon	51148	51223	.	-	.	insertions 0 ; deletions 0
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	splice5	51146	51147	.	-	.	intron_id 4 ; splice_site "GT"
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	intron	50600	51147	.	-	.	intron_id 4
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	splice3	50600	50601	.	-	.	intron_id 3 ; splice_site "AG"
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	cds	50506	50599	.	-	.	
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	exon	50506	50599	.	-	.	insertions 0 ; deletions 0
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	splice5	50504	50505	.	-	.	intron_id 5 ; splice_site "GT"
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	intron	50134	50505	.	-	.	intron_id 5
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	splice3	50134	50135	.	-	.	intron_id 4 ; splice_site "GG"
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	cds	49957	50133	.	-	.	
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	exon	49957	50133	.	-	.	insertions 15 ; deletions 0 ; frameshifts 1
gi|398921680|gb|JH767798.1|:subseq(10174851,107557)	exonerate:protein2genome:local	similarity	49957	57557	1327	-	.	alignment_id 1 ; Query SPP00000052_2.0 ; Align 57558 1 216 ; Align 55237 73 291 ; Align 54701 171 195 ; Align 51223 237 75 ; Align 50600 262 93 ; Align 50132 294 18 ; Align 50111 300 24 ; Align 50078 308 30 ; Align 50045 318 45 ; Align 49999 333 42
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
