Command line: [exonerate -m p2g --showtargetgff -q seqaahsx/selO.hs.fa -t selo.hs.subseq.fa]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000019_1.0 # Protein # Selenoprotein O (SelO) # Homo sapiens # Complete
        Target: GL192526.1:subseq(1683744,28237) dna:scaffold scaffold:ailMel1:GL192526.1:1:2211372:1 REF
         Model: protein2genome:local
     Raw score: 2347
   Query range: 116 -> 669
  Target range: 6418 -> 18237

   117 : GluAlaGluAlaAlaLeuPhePheSerGlyAsnAlaLeuLeuProGlyAlaGluProAla :   136
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         GluAlaGluAlaAlaLeuPhePheSerGlyAsnAlaLeuLeuProGlyAlaGluProAla
  6419 : GAGGCCGAGGCCGCGCTCTTCTTCAGCGGCAACGCGCTGCTGCCGGGCGCCGAGCCCGCC :  6476

   137 : AlaHisCysTyrCysGlyHisGlnPheGlyGlnPheAlaGlyGlnLeuGlyAspGlyAla :   156
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         AlaHisCysTyrCysGlyHisGlnPheGlyGlnPheAlaGlyGlnLeuGlyAspGlyAla
  6477 : GCGCACTGCTACTGCGGCCACCAGTTTGGCCAGTTCGCAGGGCAGCTGGGCGACGGCGCC :  6536

   157 : AlaMetTyrLeuGlyGluValCysThrAlaThrGlyGluArgTrpGluLeuGlnLeuLys :   176
         ||||||||||||||||||||||||||||||.!!||||||||||||||||||||||||:!!
         AlaMetTyrLeuGlyGluValCysThrAlaAlaGlyGluArgTrpGluLeuGlnLeuGln
  6537 : GCCATGTACCTGGGCGAGGTGTGCACGGCAGCGGGCGAGCGCTGGGAGCTGCAGCTCCAG :  6596

   177 : GlyAlaGlyProThrPro  >>>> Target Intron 1 >>>>  PheSerArgGlnA :   187
         !  ...      ...! !           3380 bp             !||||||||||
         UnkUnkUnkUnkUnkGln++                         --AspSerArgGlnA
  6597 : GNNNNNNNNNNNNNNCAGgt.........................ttGATTCCAGACAGG : 10009

   188 : laAspGlyArgLysValLeuArgSerSerIleArgGluPheLeuCysSerGluAlaMetP :   207
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         laAspGlyArgLysValLeuArgSerSerIleArgGluPheLeuCysSerGluAlaMetP
 10010 : CCGACGGCCGCAAAGTGCTGCGGTCGAGCATCCGCGAGTTCCTGTGCAGTGAGGCCATGT : 10069

   208 : heHisLeuGlyValProThrThrArgAlaGlyAlaCysValThrSerGluSerThrValV :   227
         |||||||||||:!!|||||||||||||||||||||||||||||||||..!||||||||||
         heHisLeuGlyIleProThrThrArgAlaGlyAlaCysValThrSerArgSerThrValV
 10070 : TCCACCTGGGCATCCCCACCACACGGGCCGGGGCCTGCGTCACATCGCGGTCCACGGTCG : 10129

   228 : alArgAspValPheTyrAspGlyAsnProLysTyrGluGlnCysThrValValLeuArgV :   247
         |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||:
         alArgAspValPheTyrAspGlyAsnProLysTyrGluGlnCysThrValValLeuArgI
 10130 : TGCGAGACGTGTTCTATGACGGTAACCCGAAGTACGAGCAGTGCACGGTGGTGCTGCGTA : 10189

   248 : alAlaSerThrPheIle{Ar}  >>>> Target Intron 2 >>>>  {g}PheGlyS :   256
         !!||||||||||||:!!{||}           1175 bp           {|}|||||||
         leAlaSerThrPheLeu{Ar}++                         ++{g}PheGlyS
 10190 : TAGCTTCCACTTTCCTA{AG}gt.........................ag{G}TTCGGGT : 11391

   257 : erPheGluIlePheLysSerAlaAspGluHisThrGlyArgAlaGlyProSerValGlyA :   276
         |||||||||||||||||||||||||||||||||||||||||! !||||||||||||||||
         erPheGluIlePheLysSerAlaAspGluHisThrGlyArgGluGlyProSerValGlyA
 11392 : CCTTTGAGATTTTTAAGTCCGCAGACGAGCACACGGGGCGCGAGGGCCCTAGCGTGGGGA : 11451

   277 : rgAsnAspIleArgValGlnLeuLeuAspTyrValIleSerSerPheTyrProGluIleG :   296
         ||||||||||||||||||||:!!||||||||||||||||||!!!||||||||||||||||
         rgAsnAspIleArgValGlnMetLeuAspTyrValIleSerThrPheTyrProGluIleG
 11452 : GAAATGACATCCGAGTGCAGATGCTGGACTACGTGATCAGCACCTTTTACCCTGAGATCC : 11511

   297 : lnAlaAlaHisAlaSerAspSerValGlnArgAsnAlaAlaPhePheArgGlu  >>>>  :   314
         ||||||||||||||.!!||| !!||||||||||||||||||||||||||||||       
         lnAlaAlaHisAlaGlyAspArgValGlnArgAsnAlaAlaPhePheArgGlu++     
 11512 : AGGCCGCGCACGCCGGTGACCGTGTGCAGAGGAATGCCGCCTTCTTCCGGGAGgt..... : 11567

   315 : Target Intron 3 >>>>  ValThrArgArgThrAlaArgMetValAlaGluTrpGl :   326
              690 bp           |||||||||||||||||||||:!!||||||||||||||
                             ++ValThrArgArgThrAlaArgValValAlaGluTrpGl
 11568 : ....................agGTGACCCGCCGCACGGCCCGGGTGGTGGCTGAGTGGCA : 12291

   327 : nCysValGlyPheCysHisGlyValLeuAsnThrAspAsnMetSerIleLeuGlyLeuTh :   346
         |||||||||||||||||||||||||||||||||||||||||||||||||:!!||||||||
         nCysValGlyPheCysHisGlyValLeuAsnThrAspAsnMetSerIleValGlyLeuTh
 12292 : GTGTGTGGGCTTCTGCCACGGCGTGCTCAACACGGACAACATGAGCATCGTGGGGCTTAC : 12351

   347 : rIleAspTyrGlyProPheGlyPheLeuAsp{Ar}  >>>> Target Intron 4 >> :   357
         |||||||||||||||||||||||||||||||{||}            433 bp       
         rIleAspTyrGlyProPheGlyPheLeuAsp{Ar}++                       
 12352 : CATCGACTACGGGCCCTTCGGCTTCCTGGAC{AG}gt....................... : 12388

   358 : >>  {g}TyrAspProAspHisValCysAsnAlaSerAspAsnThrGlyArgTyrAlaTy :   375
             {|}||||||||||||||||||||||||||||||||||||.!!||||||||||||||
           ++{g}TyrAspProAspHisValCysAsnAlaSerAspAsnAlaGlyArgTyrAlaTy
 12389 : ..ag{G}TACGACCCCGACCACGTGTGCAATGCCTCCGACAACGCCGGGCGCTACGCATA : 12871

   376 : rSerLysGlnProGluValCysArgTrpAsnLeuArgLysLeuAlaGluAlaLeuGlnPr :   395
         ||||||||||||||||||||||!:!|||||||||!:!||||||  !|||||||||:!!||
         rSerLysGlnProGluValCysLysTrpAsnLeuGlnLysLeuLeuGluAlaLeuGluPr
 12872 : CAGCAAGCAGCCCGAGGTGTGCAAGTGGAACCTGCAGAAGCTGCTGGAGGCTCTGGAACC : 12931

   396 : oGluLeuProLeuGluLeuGlyGluAlaIleLeuAlaGluGluPheAspAlaGluPheGl :   415
         ||||||||||! !|||! !||||||||||||||||||! !||||||||||||||||||!:
         oGluLeuProArgGluGlnGlyGluAlaIleLeuAlaValGluPheAspAlaGluPheAr
 12932 : CGAGCTGCCCCGCGAGCAGGGGGAGGCCATCCTGGCCGTGGAGTTCGACGCGGAGTTCCG : 12991

   416 : nArgHisTyrLeuGlnLysMetArgArgLysLeuGlyLeuValGlnValGluLeuGluGl :   435
         :||||||||||||||||||||||||||||||||||||||||||!::!.!||||||!!:! 
         gArgHisTyrLeuGlnLysMetArgArgLysLeuGlyLeuValArgAlaGluLeuAspGl
 12992 : CCGGCACTACCTGCAGAAGATGCGCAGGAAGCTGGGCCTGGTGCGCGCCGAACTGGACGG : 13051

   436 : uAspGlyAlaLeuValSerLysLeuLeuGluThrMetHisLeuThr{G}  >>>> Targ :   451
          |||!.!|||||||||:!!  !|||||||||||||||!.!||||||{|}           
         yAspAlaAlaLeuValAlaGlyLeuLeuGluThrMetArgLeuThr{G}++         
 13052 : CGACGCAGCGCTGGTGGCCGGGCTCCTGGAGACCATGCGCCTGACT{G}gt......... : 13102

   452 : et Intron 5 >>>>  {ly}AlaAspPheThrAsnThrPheTyrLeuLeuSerSerPh :   464
         3427 bp           {||}||||||||||||||||||||||||||||||||||||||
                         ++{ly}AlaAspPheThrAsnThrPheTyrLeuLeuSerSerPh
 13103 : ................ag{GG}GCCGACTTCACAAACACCTTCTACTTGCTGAGCTCCTT : 16565

   465 : eProValGluLeuGluSerProGlyLeuAlaGluPheLeuAlaArgLeuMetGluGlnCy :   484
         |||||||! !! !||||||! !|||||| !!||||||||||||  !|||!  ! !|||||
         eProValGlyProGluSerLeuGlyLeuProGluPheLeuAlaAlaLeuThrAlaGlnCy
 16566 : CCCAGTCGGGCCAGAGTCCCTGGGCCTACCTGAGTTCCTGGCCGCGCTGACCGCACAGTG : 16625

   485 : sAlaSerLeuGluGluLeuArgLeuAlaPheArgProGlnMetAspPro{Ar}  >>>>  :   501
         |||||||||||||||||||!:!|||||||||||||||||||||||||||{||}       
         sAlaSerLeuGluGluLeuLysLeuAlaPheArgProGlnMetAspPro{Ar}++     
 16626 : TGCCTCCCTGGAGGAGCTGAAGCTCGCCTTCCGACCCCAGATGGATCCC{CG}gt..... : 16680

   502 : Target Intron 6 >>>>  {g}GlnLeuSerMetMetLeuMetLeuAlaGlnSerAs :   513
              800 bp           {|}|||||||||||||||||||||||||||||||||||
                             ++{g}GlnLeuSerMetMetLeuMetLeuAlaGlnSerAs
 16681 : ....................ag{G}CAGCTCTCGATGATGCTGATGCTGGCACAGTCCAA : 17512

   514 : nProGlnLeuPheAlaLeuMetGlyThrArgAlaGlyIleAlaArgGluLeuGluArgVa :   533
         |||||||||||||||||||!!:||||||||||||..!|||.!!!:!||||||||||||||
         nProGlnLeuPheAlaLeuIleGlyThrArgAlaAsnIleThrLysGluLeuGluArgVa
 17513 : CCCTCAGCTCTTCGCGCTCATCGGCACACGGGCAAACATCACGAAGGAGCTGGAACGCGT : 17572

   534 : lGluGlnGlnSerArgLeuGluGlnLeuSerAlaAlaGluLeuGlnSerArgAsnGlnGl :   553
         ||||||||||||||||||||||||||||||| !!|||||||||! !|||!:!|||::!||
         lGluGlnGlnSerArgLeuGluGlnLeuSerProAlaGluLeuLeuSerLysAsnArgGl
 17573 : GGAGCAGCAGTCGCGGCTGGAGCAGCTGAGCCCGGCGGAGTTGCTGAGCAAGAACAGGGG : 17632

   554 : yHisTrpAlaAspTrpLeuGlnAlaTyr{Ar}  >>>> Target Intron 7 >>>>  :   563
         ||||||||||!!:|||||||||! !|||{||}            143 bp          
         yHisTrpAlaGluTrpLeuGlnGluTyr{Ar}++                         +
 17633 : CCACTGGGCTGAGTGGCTCCAGGAGTAC{AG}gt.........................a : 17805

   564 :  {g}AlaArgLeuAspLysAspLeuGluGlyAlaGlyAspAlaAlaAlaTrpGlnAlaGl :   582
          {|}|||||||||!!::!!|||  !||||||!.!||||||::!! !||||||||||||||
         +{g}AlaArgLeuGluGluAspArgGluGlyValGlyAspSerAspAlaTrpGlnAlaGl
 17806 : g{G}GCCCGACTGGAGGAGGACAGGGAGGGCGTCGGCGACAGCGATGCCTGGCAGGCTGA : 17862

   583 : uHisValArgValMetHisAlaAsnAsnProLysTyrValLeuArgAsnTyrIleAlaGl :   602
         |!.!..!|||||||||||||||||||||||||||||||||||||||||||||||||||||
         uArgThrArgValMetHisAlaAsnAsnProLysTyrValLeuArgAsnTyrIleAlaGl
 17863 : GCGCACACGTGTCATGCACGCCAACAACCCCAAGTACGTCCTGCGGAACTACATTGCACA : 17922

   603 : nAsnAlaIleGluAlaAlaGluArgGlyAspPheSerGlu  >>>> Target Intron :   616
         ||||||||||||||||||||||!.!|||||||||||||||            103 bp  
         nAsnAlaIleGluAlaAlaGluAsnGlyAspPheSerGlu+-                  
 17923 : AAATGCCATCGAGGCCGCCGAGAACGGAGACTTCTCAGAGgc.................. : 17966

   617 :  8 >>>>  ValArgArgValLeuLysLeuLeuGluThrProTyrHisCysGluAlaGly :   632
                  ||||||||||||||||||||||||||||||||||||||| ! !!:!.!! !
                ++ValArgArgValLeuLysLeuLeuGluThrProTyrHisArgAspGlyGlu
 17967 : .......agGTGAGGCGGGTGCTGAAGCTACTGGAAACCCCTTACCACAGGGACGGGGAG : 18115

   633 : AlaAlaThrAspAlaGluAlaThrGluAlaAspGlyAlaAspGlyArgGlnArg<-><-> :   651
         |||.!!  !! ! !!||||||||||||.!!!!:||||||! !|||  !.!.!!!      
         AlaThrGluValProGluAlaThrGluThrGluGlyAlaGlyGlyAlaAspSerGlyGly
 18116 : GCCACCGAGGTCCCAGAGGCCACCGAGACTGAGGGGGCTGGCGGGGCAGACAGTGGGGGG : 18175

   652 : <->SerTyrSerSerLysProProLeuTrpAlaAlaGluLeuCysValThrUnkSerSer :   669
            ||||||||||||||||||||||||||||||||||||||||||||||||   ||||||
         LeuSerTyrSerSerLysProProLeuTrpAlaAlaGluLeuCysValThr***SerSer
 18176 : CTCTCCTACAGCAGCAAGCCCCCACTGTGGGCGGCTGAACTGTGCGTGACGTGATCCTCG : 18235

vulgar: SPP00000019_1.0 116 669 . GL192526.1:subseq(1683744,28237) 6418 18237 + 2347 M 66 198 5 0 2 I 0 3376 3 0 2 M 70 210 S 0 2 5 0 2 I 0 1171 3 0 2 S 1 1 M 60 180 5 0 2 I 0 686 3 0 2 M 43 129 S 0 2 5 0 2 I 0 429 3 0 2 S 1 1 M 93 279 S 0 1 5 0 2 I 0 3423 3 0 2 S 1 2 M 49 147 S 0 2 5 0 2 I 0 796 3 0 2 S 1 1 M 61 183 S 0 2 5 0 2 I 0 139 3 0 2 S 1 1 M 52 156 5 0 2 I 0 99 3 0 2 M 35 105 G 0 9 M 19 57
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2012-12-04
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	gene	6419	18237	2347	+	.	gene_id 1 ; sequence SPP00000019_1.0 ; gene_orientation +
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	cds	6419	6616	.	+	.	
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	exon	6419	6616	.	+	.	insertions 0 ; deletions 0
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	splice5	6617	6618	.	+	.	intron_id 1 ; splice_site "GT"
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	intron	6617	9996	.	+	.	intron_id 1
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	splice3	9995	9996	.	+	.	intron_id 0 ; splice_site "TT"
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	cds	9997	10208	.	+	.	
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	exon	9997	10208	.	+	.	insertions 0 ; deletions 0
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	splice5	10209	10210	.	+	.	intron_id 2 ; splice_site "GT"
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	intron	10209	11383	.	+	.	intron_id 2
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	splice3	11382	11383	.	+	.	intron_id 1 ; splice_site "AG"
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	cds	11384	11564	.	+	.	
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	exon	11384	11564	.	+	.	insertions 0 ; deletions 0
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	splice5	11565	11566	.	+	.	intron_id 3 ; splice_site "GT"
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	intron	11565	12254	.	+	.	intron_id 3
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	splice3	12253	12254	.	+	.	intron_id 2 ; splice_site "AG"
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	cds	12255	12385	.	+	.	
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	exon	12255	12385	.	+	.	insertions 0 ; deletions 0
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	splice5	12386	12387	.	+	.	intron_id 4 ; splice_site "GT"
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	intron	12386	12818	.	+	.	intron_id 4
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	splice3	12817	12818	.	+	.	intron_id 3 ; splice_site "AG"
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	cds	12819	13099	.	+	.	
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	exon	12819	13099	.	+	.	insertions 0 ; deletions 0
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	splice5	13100	13101	.	+	.	intron_id 5 ; splice_site "GT"
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	intron	13100	16526	.	+	.	intron_id 5
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	splice3	16525	16526	.	+	.	intron_id 4 ; splice_site "AG"
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	cds	16527	16677	.	+	.	
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	exon	16527	16677	.	+	.	insertions 0 ; deletions 0
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	splice5	16678	16679	.	+	.	intron_id 6 ; splice_site "GT"
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	intron	16678	17477	.	+	.	intron_id 6
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	splice3	17476	17477	.	+	.	intron_id 5 ; splice_site "AG"
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	cds	17478	17663	.	+	.	
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	exon	17478	17663	.	+	.	insertions 0 ; deletions 0
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	splice5	17664	17665	.	+	.	intron_id 7 ; splice_site "GT"
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	intron	17664	17806	.	+	.	intron_id 7
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	splice3	17805	17806	.	+	.	intron_id 6 ; splice_site "AG"
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	cds	17807	17963	.	+	.	
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	exon	17807	17963	.	+	.	insertions 0 ; deletions 0
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	splice5	17964	17965	.	+	.	intron_id 8 ; splice_site "GC"
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	intron	17964	18066	.	+	.	intron_id 8
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	splice3	18065	18066	.	+	.	intron_id 7 ; splice_site "AG"
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	cds	18067	18237	.	+	.	
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	exon	18067	18237	.	+	.	insertions 9 ; deletions 0
GL192526.1:subseq(1683744,28237)	exonerate:protein2genome:local	similarity	6419	18237	2347	+	.	alignment_id 1 ; Query SPP00000019_1.0 ; Align 6419 117 198 ; Align 9997 183 210 ; Align 11385 254 180 ; Align 12255 314 129 ; Align 12820 358 279 ; Align 16529 452 147 ; Align 17479 502 183 ; Align 17808 564 156 ; Align 18067 616 105 ; Align 18181 651 57
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
