Command line: [exonerate -m p2g --showtargetgff -q ./proteins/SPP00000029_1.0.fa -t ./exonerate/SPP00000029_1.0_1_genomic.fa_exonerate.fa]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000029_1.0 # Protein # Selenoprotein V (SelV) # Homo sapiens # Complete
        Target: gi|357434082|gb|JH378281.1|:subseq(870235,302809) Saimiri boliviensis boliviensis unplaced genomic scaffold scaffold00177, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 986
   Query range: 0 -> 346
  Target range: 153245 -> 149999

      1 : MetAsnAsnGlnAlaArgThrProAlaProSerSerAlaArgThrSerThrSerValA :     20
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          MetAsnAsnGlnAlaArgThrProAlaProSerSerAlaArgThrSerThrSerValA
 153245 : ATGAATAACCAGGCGCGGACCCCCGCCCCCTCCTCGGCCCGGACCTCAACGTCGGTCC : 153188

     21 : rgAlaSerThrProThrArgThrProThrProLeuArgThrProThrProValArgTh :     39
          ||||||||||||||||||||||||||||||||:!!|||||||||||| !!!.!|||||
          rgAlaSerThrProThrArgThrProThrProValArgThrProThrAlaAlaArgTh
 153187 : GGGCTTCTACCCCGACCCGGACACCGACTCCAGTCCGGACTCCGACCGCGGCCCGGAC : 153131

     40 : rArgThrProIleArgThrLeuThrProValLeuThrProSerProAlaGlyThrSer :     58
          ||||||||||||||||||||||||||||  !|||            ||||||||| !!
          rArgThrProIleArgThrLeuThrProSerLeu------------AlaGlyThrPro
 153130 : TCGGACCCCCATCCGGACCCTGACCCCATCTCTG------------GCCGGGACTCCC : 153086

     59 : ProLeuValLeuThrProAlaProAlaGlnIleProThrLeuValProThrProAlaL :     78
           !!||||||! !|||||||||||||||!:!||| !!  !! !||||||||||||!.!!
          AlaLeuValProThrProAlaProAlaArgIleSerArgProValProThrProValP
 153085 : GCTCTGGTCCCGACTCCAGCTCCGGCCCGGATCTCCCGTCCGGTCCCAACTCCAGTTC : 153026

     79 : euAlaArgIleProArgLeuValProProProAlaProAlaTrpIleProThrProVa :     97
           !.!!! !  !|||  !! !..!||| !!|||  !||||||  !:!!! !|||! !..
          roThrProAlaProAlaArgThrProThrProIleProAlaLeuValArgThrLeuTh
 153025 : CGACTCCTGCTCCCGCCCGGACCCCAACTCCGATCCCGGCTCTGGTTCGGACCCTGAC : 152969

     98 : lProThrProValProValArgAsn{Pr}  >>>> Target Intron 1 >>>>   :    106
          !|||..!! !:!!|||!.!! !  !{! }            52 bp            
          rProValArgLeuProAlaProAla{Ar}+-                         --
 152968 : TCCAGTCCGGCTCCCAGCCCCCGCC{CG}gn.........................nn : 152890

    107 : {o}ThrProValProThrProAlaArgThrLeuThrProProValArgValProAlaP :    125
          { }...         ...   ...   ...   ...                  ..!|
          {g}UnkUnkUnkUnkUnkUnkUnkUnkUnkUnkUnkUnkUnkUnkUnkUnkUnkUnkP
 152889 : {N}NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCC : 152833

    126 : roAlaProAlaGlnLeuLeuAlaGlyIleArgAlaAlaLeuProValLeuAspSerTy :    144
          |||||||||||! !:!!||||||||||||||||||  !|||||| !!|||||||||||
          roAlaProAlaLeuValLeuAlaGlyIleArgAlaMetLeuProPheLeuAspSerTy
 152832 : CAGCCCCAGCTCTAGTACTGGCCGGGATTCGGGCCATGCTCCCCTTCTTGGACTCCTA : 152776

    145 : rLeuAlaProAlaLeuProLeuAspProProProGluProAlaProGluLeuPro<-> :    163
          |! !||| !!|||||||||! !||||||! !||||||||||||||||||! !|||   
          rProAlaSerAlaLeuProTrpAspProLeuProGluProAlaProGluProProVal
 152775 : CCCGGCCTCGGCCCTGCCTTGGGATCCGCTCCCGGAACCTGCTCCGGAGCCGCCTGTG : 152719

    164 : <->LeuLeuProGluGluAspProGluProAlaProSerLeuLysLeuIleProSerV :    181
             :!!! ! !!||||||||||||||||||||||||||||||||||||:!!|||||||
          SerValSerSerGluGluAspProGluProAlaProSerLeuLysLeuValProSerV
 152718 : TCTGTGTCATCCGAGGAGGACCCTGAGCCGGCGCCGAGCCTGAAGCTCGTCCCGTCGG : 152659

    182 : alSerSerGluAlaGlyProAlaProGlyProLeuProThrArgThrProLeuAlaAl :    200
          |||||.!!|||.!!||||||||||||! !|||||||||.!!|||||||||||||||.!
          alSerGlyGluThrGlyProAlaProGluProLeuProAlaArgThrProLeuAlaTh
 152658 : TCTCCGGCGAGACTGGGCCCGCCCCGGAGCCCCTTCCCGCGCGCACCCCACTGGCCAC : 152602

    201 : aAsnSerProGlyProThrLeuAspPheThrPheArgAlaAspProSerAlaIleGly :    219
          !||| !!||||||||||||||||||      |||!:!|||||||||||||||! !|||
          rAsnProProGlyProThrLeuAsp------PheLysAlaAspProSerAlaThrGly
 152601 : GAACCCACCCGGGCCCACGCTAGAC------TTCAAGGCAGACCCGTCGGCCACTGGG : 152551

    220 : LeuAlaAspProProIleProSerProValProSerProIleLeuGlyThrIleProS :    239
          |||||||||! ! !!||||||.!! !!||||||:!!||||||! !|||||||||||||
          LeuAlaAspHisThrIleProGlySerValProAlaProIleProGlyThrIleProS
 152550 : CTGGCGGATCACACCATTCCCGGCTCTGTCCCTGCGCCCATCCCGGGGACCATCCCGT : 152491

    240 : erAlaIleSerLeuGlnAsnCysThrGluThrPheProSerSerSerGluAsnPheAl :    258
          |||||  !||||||! !|||! !.!!|||!:!|||  !|||:!!||||||||||||||
          erAlaAlaSerLeuProAsnSerAlaGluSerPheValSerAlaSerGluAsnPheAl
 152490 : CGGCCGCCTCCTTACCGAATTCTGCCGAAAGCTTCGTCTCCGCCAGCGAGAACTTCGC : 152434

    259 : aLeuAspLysArgValLeuIleArgValThrTyr{Cy}  >>>> Target Intron :    270
          ||||||||||||||||! !|||||||||||||||{||}           1985 bp  
          aLeuAspLysArgValProIleArgValThrTyr{Cy}++                  
 152433 : GCTGGACAAGAGGGTCCCTATTCGAGTGACTTAC{TG}gt.................. : 152394

    271 :  2 >>>>  {s}GlyLeuUnkSerTyrSerLeu-----ArgTyrIleLeuLeuLysLy :    284
                   {|}! !! !   !!!   |||:!!#####!:!|||||||||||||||||
                 -+{s}AspProMetThrProSerVal#####GlnTyrIleLeuLeuLysLy
 152393 : .......tg{C}GACCCCATGACCCCATCTGTGCCCCTCAGTACATTCTACTGAAAAA : 150366

    285 : sSerLeuGluGlnGlnPheProAsnHisLeuLeuPhe  >>>> Target Intron  :    297
          |||||||||||||!:!||||||:!!!.!|||||||||            85 bp    
          sSerLeuGluGlnArgPheProAspArgLeuLeuPhe++                   
 150365 : GAGCCTGGAGCAGCGATTTCCAGATCGCCTACTCTTTgt................... : 150325

    298 : 3 >>>>  GluGluAspArgAlaAlaGlnAlaThrGlyGluPheGluValPheValAs :    313
                  ||||||||||||||||||||||||||||||!!:|||||||||||||||:!
                ++GluGluAspArgAlaAlaGlnAlaThrGlyAspPheGluValPheValAs
 150324 : ......agGAGGAAGACAGAGCTGCCCAGGCTACAGGGGATTTTGAAGTGTTTGTAGA : 150194

    314 : nGlyArgLeuValHisSerLysLys  >>>> Target Intron 4 >>>>  ArgG :    323
          !||||||||||||||||||||||||            93 bp            ||||
          pGlyArgLeuValHisSerLysLys++                         ++ArgG
 150193 : TGGGAGACTGGTCCATTCCAAAAAGgt.........................agAGGG : 150071

    324 : lyAspGlyPheValAsnGluSerArgLeuGlnLysIleValSerValIleAspGluGl :    342
          ||||||||||||||:!!|||:!!!:!||||||||||||||||||||||||||||||! 
          lyAspGlyPheValAspGluAlaLysLeuGlnLysIleValSerValIleAspGluVa
 150070 : GTGACGGCTTTGTGGATGAGGCCAAGCTGCAGAAAATTGTGAGCGTTATTGATGAGGT : 150014

    343 : uIleLysLysArg :    346
          !||||||||||||
          lIleLysLysArg
 150013 : GATCAAGAAGAGG : 150000

vulgar: SPP00000029_1.0 0 346 . gi|357434082|gb|JH378281.1|:subseq(870235,302809) 153245 149999 - 986 M 50 150 G 4 0 M 51 153 S 0 2 5 0 2 I 0 48 3 0 2 S 1 1 M 56 168 G 0 6 M 46 138 G 2 0 M 59 177 S 0 2 5 0 2 I 0 1981 3 0 2 S 1 1 M 7 21 F 0 5 M 19 57 5 0 2 I 0 81 3 0 2 M 25 75 5 0 2 I 0 89 3 0 2 M 25 75
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2012-11-14
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	gene	150000	153245	986	-	.	gene_id 1 ; sequence SPP00000029_1.0 ; gene_orientation +
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	cds	152941	153245	.	-	.	
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	exon	152941	153245	.	-	.	insertions 0 ; deletions 4
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	splice5	152939	152940	.	-	.	intron_id 1 ; splice_site "GN"
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	intron	152889	152940	.	-	.	intron_id 1
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	splice3	152889	152890	.	-	.	intron_id 0 ; splice_site "NN"
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	cds	152397	152888	.	-	.	
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	exon	152397	152888	.	-	.	insertions 6 ; deletions 2
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	splice5	152395	152396	.	-	.	intron_id 2 ; splice_site "GT"
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	intron	150412	152396	.	-	.	intron_id 2
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	splice3	150412	150413	.	-	.	intron_id 1 ; splice_site "TG"
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	cds	150328	150411	.	-	.	
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	exon	150328	150411	.	-	.	insertions 0 ; deletions 0 ; frameshifts 5
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	splice5	150326	150327	.	-	.	intron_id 3 ; splice_site "GT"
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	intron	150243	150327	.	-	.	intron_id 3
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	splice3	150243	150244	.	-	.	intron_id 2 ; splice_site "AG"
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	cds	150168	150242	.	-	.	
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	exon	150168	150242	.	-	.	insertions 0 ; deletions 0
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	splice5	150166	150167	.	-	.	intron_id 4 ; splice_site "GT"
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	intron	150075	150167	.	-	.	intron_id 4
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	splice3	150075	150076	.	-	.	intron_id 3 ; splice_site "AG"
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	cds	150000	150074	.	-	.	
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	exon	150000	150074	.	-	.	insertions 0 ; deletions 0
gi|357434082|gb|JH378281.1|:subseq(870235,302809)	exonerate:protein2genome:local	similarity	150000	153245	986	-	.	alignment_id 1 ; Query SPP00000029_1.0 ; Align 153246 1 150 ; Align 153096 55 153 ; Align 152888 107 168 ; Align 152714 163 138 ; Align 152576 211 177 ; Align 150411 271 21 ; Align 150385 278 57 ; Align 150243 297 75 ; Align 150075 322 75
# --- END OF GFF DUMP ---
#