Command line: [exonerate -m p2g --showtargetgff -q 1B.query.dir/SP.SelV.1.fa.x.fa -t 3B.fastasub.dir/1.SP.SelV.1.fa.x.fa]
Hostname: [ws116063]

C4 Alignment:
------------
         Query: SPP00000029_1.0 # Protein # Selenoprotein V (SelV) # Homo sapiens # Complete
        Target: gi|398920895|gb|JH767830.1|:subseq(1533009,102959) Ceratotherium simum simum unplaced genomic scaffold scaffold00108, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 592
   Query range: 10 -> 346
  Target range: 49441 -> 52959

    11 : SerSerAlaArgThrSerThrSerValArgAlaSerThrProThrArgThrProThrPro :    30
         :!!.!!:!!||| !!.!!:!! !!  !  !::!  !.!!|||! !!.!!.!! !.!!  !
         AlaGlySerArgProGlySerProGlnAspSerLeuAlaProMetAsnAsnGlnAlaArg
 49442 : GCGGGATCTCGACCCGGGTCACCCCAGGACAGCCTGGCCCCCATGAACAACCAGGCGAGG : 49499

    31 : LeuArgThrProThrProValArgThrArgThrProIleArgThrLeuThrProValLeu :    50
           !! !..!|||:!!|||!.!||||||  !  ! !!:!!|||.!!! !|||||||||  !
         AlaProValProSerProAlaArgThrSerGlySerValArgAlaSerThrProValArg
 49500 : GCCCCAGTCCCCTCCCCGGCCCGGACCTCGGGCTCGGTCCGGGCTTCGACCCCGGTCAGG : 49559

    51 : ThrProSerProAlaGlyThrSerProLeuValLeuThrProAlaProAlaGlnIlePro :    70
         ||| !!! !|||!.! !!|||||| !!! !|||! !||||||.!!! !!.!!:!  ! !!
         ThrSerIleProValArgThrSerThrProValArgThrProThrLeuValArgAlaSer
 49560 : ACTTCGATCCCGGTTCGGACCTCGACCCCCGTCCGGACCCCGACTCTGGTCCGGGCCTCC : 49619

    71 : ThrLeuValProThrProAlaLeuAlaArgIleProArgLeuValProProProAlaPro :    90
         |||! !|||! ! !!|||.!!! !!.!!:!! !|||! !! !|||! ! !! !!.!!|||
         ThrProValArgProProThrProValGlnThrProThrProValArgAlaSerThrPro
 49620 : ACTCCCGTCCGGCCCCCGACCCCTGTCCAGACACCGACTCCGGTCCGGGCCTCAACCCCT : 49679

    91 : AlaTrpIleProThrProValProThrProValProValArgAsnProThrProValPro :   110
         !.!|||  !||||||||||||! !||||||..!|||||| !!!.! !!||||||  !! !
         ValTrpProProThrProValArgThrProThrProValGlyThrSerThrProAsnArg
 49680 : GTCTGGCCCCCGACTCCCGTTCGGACGCCGACTCCCGTCGGGACCTCGACCCCCAACCGG : 49739

   111 : ThrProAlaArgThrLeuThrProProValArgValProAlaProAlaProAlaGlnLeu :   130
         ||||||!.!||||||! !||||||         |||  !.!!! !.!!! !!.!!:!:!!
         ThrProValArgThrProThrPro---------ValTrpThrArgThrLeuValArgIle
 49740 : ACCCCCGTCCGGACCCCGACTCCG---------GTCTGGACCCGGACCCTGGTCCGGATC : 49790

   131 : LeuAlaGlyIleArgAlaAlaLeuProValLeuAspSerTyrLeuAlaProAlaLeuPro :   150
         ! !.!!  !! !! !:!!:!!:!!|||!.!! !!!:|||!:!! !  ! !!|||! ! !!
         ProThrProThrProSerSerValProAlaSerGluSerPheSerAsnSerAlaProSer
 49791 : CCAACCCCAACCCCATCCTCGGTCCCTGCCTCGGAATCCTTCTCAAACTCCGCCCCGTCC : 49850

   151 : LeuAspProProProGluProAlaProGluLeuProLeuLeuProGluGluAspProGlu :   170
         |||||||||||||||||||||||| !!|||! !||||||! !|||.!.:!!||||||! !
         LeuAspProProProGluProAlaAlaGluProProLeuSerProAsnLysAspProAla
 49851 : TTGGATCCGCCCCCAGAACCTGCTGCGGAGCCCCCATTGTCGCCCAACAAGGACCCTGCG : 49910

   171 : ProAla<->ProSerLeuLysLeuIleProSerValSerSerGluAlaGlyProAlaPro :   189
         |||.!!   ||||||:!!|||! !:!!|||||||||:!!!.!! !  !|||||| !!! !
         ProThrProProSerValLysHisValProSerValAlaLysGlyPheGlyProProGln
 49911 : CCCACGCCGCCAAGTGTGAAGCACGTCCCCTCGGTGGCCAAGGGATTTGGGCCCCCCCAG : 49970

   190 : GlyProLeuProThrArgThrProLeuAlaAlaAsnSerProGlyProThrLeuAspPhe :   209
         !.!|||||||||.!!! ! !!|||! !|||.!!:!!! !|||||||||!.!|||!  ! !
         AlaProLeuProAlaLeuProProSerAlaThrAspLeuProGlyProAsnLeuGlySer
 49971 : GCGCCCCTTCCTGCGCTCCCTCCATCGGCCACTGATTTACCGGGGCCCAACCTGGGGTCC : 50030

   210 : ThrPheArgAlaAspProSerAlaIleGlyLeuAlaAspProProIleProSerProVal :   229
         ! !  !|||||||||||||||.!!! !  !|||.!!|||||||||   |||.!!|||:!!
         IleProArgAlaAspProSerThrThrLysLeuThrAspProPro---ProGlyProIle
 50031 : ATCCCCAGGGCAGATCCATCCACCACCAAGTTGACAGATCCCCCT---CCTGGACCCATC : 50087

   230 : ProSerProIleLeuGlyThrIleProSerAlaIleSerLeuGlnAsnCysThrGluThr :   249
              !||||||:!!||||||:!!||||||.!!! ! !!:!!...       !!... !!
         ---ValProIleValGlyThrValProSerThrThrProIleSer------ProSerPro
 50088 : ---GTGCCCATCGTGGGGACCGTCCCGTCCACCACACCGATTTCT------CCCAGCCCG : 50138

   250 : PheProSerSerSerGluAsnPheAlaLeuAspLysArgValLeuIleArgValThrTyr :   269
         !!. !!|||!!!||||||||||||  !:!!|||!..!:!:!!  !|||||||||! !|||
         LeuAlaSerThrSerGluAsnPheGlnValAspSerLysIleThrIleArgValIleTyr
 50139 : TTAGCCTCCACCAGCGAGAACTTTCAAGTGGACAGCAAGATCACGATTCGAGTGATCTAC : 50198

   270 : {Cy}  >>>> Target Intron 1 >>>>  {s}GlyLeuUnkSerTyrSerLeuArg :   278
         {||}           2311 bp           {|}!.!! !...  !  ! !!! !!:!
         {Cy}++                         +-{s}Ala***SerHisLeuProProGln
 50199 : {TG}gt.........................ac{T}GCATGATCCCATCTCCCCCCGCAG : 52536

   279 : TyrIleLeuLeuLysLysSerLeuGluGlnGlnPheProAsnHisLeuLeuPhe  >>>> :   297
         ||||||||||||||||||||||||!!:|||||||||||||||!.!|||||||||      
         TyrIleLeuLeuLysLysSerLeuAspGlnGlnPheProAsnArgLeuLeuPhe++    
 52537 : TATATTCTACTGAAAAAGAGTCTGGACCAGCAATTTCCAAATCGTCTACTCTTTgt.... : 52595

   298 :  Target Intron 2 >>>>  GluGluAspArgAlaAlaGlnAlaThrGlyGluPheG :   309
               119 bp           |||:!!|||! !:!!|||||||||:!!||||||||||
                              ++GluGlnAspIleSerAlaGlnAlaSerGlyGluPheG
 52596 : .....................agGAGCAGGACATATCCGCCCAGGCTTCAGGGGAGTTTG : 52748

   310 : luValPheValAsnGlyArgLeuValHisSerLysLys  >>>> Target Intron 3 :   322
         |||||||||||.!.|||! !||||||||||||||||||            98 bp     
         luValPheValGluGlyThrLeuValHisSerLysLys++                    
 52749 : AAGTGTTTGTGGAAGGGACACTGGTCCATTCGAAGAAGgt.................... : 52789

   323 :  >>>>  ArgGlyAspGlyPheValAsnGluSerArgLeuGlnLysIleValSerValIl :   339
                !:!|||||||||||||||:!!|||  !!!!|||!:!|||||||||||||||||
              ++LysGlyAspGlyPheValAspGluValSerLeuArgLysIleValSerValIl
 52790 : .....agAAGGGTGACGGCTTTGTGGACGAGGTCAGTCTGCGGAAAATTGTGAGCGTCAT : 52936

   340 : eAspGluGluIleLysLysArg :   346
         |:!!|||||||||!:!||||||
         eAsnGluGluIleArgLysArg
 52937 : CAACGAGGAGATCAGGAAGAGG : 52959

vulgar: SPP00000029_1.0 10 346 . gi|398920895|gb|JH767830.1|:subseq(1533009,102959) 49441 52959 + 592 M 108 324 G 3 0 M 51 153 G 0 3 M 52 156 G 1 0 M 4 12 G 1 0 M 14 42 G 2 0 M 23 69 S 0 2 5 0 2 I 0 2307 3 0 2 S 1 1 M 26 78 5 0 2 I 0 115 3 0 2 M 25 75 5 0 2 I 0 94 3 0 2 M 25 75
# --- 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|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	gene	49442	52959	592	+	.	gene_id 1 ; sequence SPP00000029_1.0 ; gene_orientation +
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	cds	49442	50202	.	+	.	
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	exon	49442	50202	.	+	.	insertions 3 ; deletions 7
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	splice5	50203	50204	.	+	.	intron_id 1 ; splice_site "GT"
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	intron	50203	52513	.	+	.	intron_id 1
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	splice3	52512	52513	.	+	.	intron_id 0 ; splice_site "AC"
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	cds	52514	52592	.	+	.	
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	exon	52514	52592	.	+	.	insertions 0 ; deletions 0
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	splice5	52593	52594	.	+	.	intron_id 2 ; splice_site "GT"
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	intron	52593	52711	.	+	.	intron_id 2
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	splice3	52710	52711	.	+	.	intron_id 1 ; splice_site "AG"
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	cds	52712	52786	.	+	.	
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	exon	52712	52786	.	+	.	insertions 0 ; deletions 0
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	splice5	52787	52788	.	+	.	intron_id 3 ; splice_site "GT"
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	intron	52787	52884	.	+	.	intron_id 3
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	splice3	52883	52884	.	+	.	intron_id 2 ; splice_site "AG"
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	cds	52885	52959	.	+	.	
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	exon	52885	52959	.	+	.	insertions 0 ; deletions 0
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	similarity	49442	52959	592	+	.	alignment_id 1 ; Query SPP00000029_1.0 ; Align 49442 11 324 ; Align 49766 122 153 ; Align 49922 173 156 ; Align 50078 226 12 ; Align 50090 231 42 ; Align 50132 247 69 ; Align 52515 271 78 ; Align 52712 297 75 ; Align 52885 322 75
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000029_1.0 # Protein # Selenoprotein V (SelV) # Homo sapiens # Complete
        Target: gi|398920895|gb|JH767830.1|:subseq(1533009,102959) Ceratotherium simum simum unplaced genomic scaffold scaffold00108, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 237
   Query range: 0 -> 169
  Target range: 49483 -> 50050

     1 : MetAsnAsnGlnAlaArgThrProAlaProSerSerAlaArgThrSerThrSerValArg :    20
         ||||||||||||||||||.!!|||!.!|||||| !!||||||||||||  !|||||||||
         MetAsnAsnGlnAlaArgAlaProValProSerProAlaArgThrSerGlySerValArg
 49484 : ATGAACAACCAGGCGAGGGCCCCAGTCCCCTCCCCGGCCCGGACCTCGGGCTCGGTCCGG : 49541

    21 : AlaSerThrPro  >>>> Target Intron 1 >>>>  ThrArgThrProThrProL :    31
         ||||||||||||            54 bp            ..!|||.!! !!||||||:
         AlaSerThrPro++                         -+ValArgAlaSerThrProV
 49542 : GCTTCGACCCCGgt.........................tgGTCCGGGCCTCCACTCCCG : 49628

    32 : euArgThrProThrProValArgThrArgThrProIleArgThrLeuThrProValLeuT :    51
         !!||| !!||||||||||||!:!|||! !||||||:!!|||.!!! !|||||||||! ! 
         alArgProProThrProValGlnThrProThrProValArgAlaSerThrProValTrpP
 49629 : TCCGGCCCCCGACCCCTGTCCAGACACCGACTCCGGTCCGGGCCTCAACCCCTGTCTGGC : 49688

    52 : hrProSerProAlaGlyThrSerProLeuValLeuThrProAlaProAlaGlnIleProT :    71
         !!|||!!!|||!.! !!||| !! !!! !|||  !||| !!.!!|||  !!:!! !|||.
         roProThrProValArgThrProThrProValGlyThrSerThrProAsnArgThrProV
 49689 : CCCCGACTCCCGTTCGGACGCCGACTCCCGTCGGGACCTCGACCCCCAACCGGACCCCCG : 49748

    72 : hrLeuValProThrProAlaLeuAlaArgIleProArgLeuValProProProAlaProA :    91
         .!! !..!|||||||||!.!! !.!!|||! !! !  !! !:!!||| !!|||.!!|||:
         alArgThrProThrProValTrpThrArgThrLeuValArgIleProThrProThrProS
 49749 : TCCGGACCCCGACTCCGGTCTGGACCCGGACCCTGGTCCGGATCCCAACCCCAACCCCAT : 49808

    92 : laTrpIleProThrProValProThrProValProValArgAsnProThrProValProT :   111
         !!! !:!!|||.!! !!! ! !!  ! !!  ! !!!.!! !::!  !  !|||  !||| 
         erSerValProAlaSerGluSerPheSerAsnSerAlaProSerLeuAspProProProG
 49809 : CCTCGGTCCCTGCCTCGGAATCCTTCTCAAACTCCGCCCCGTCCTTGGATCCGCCCCCAG : 49868

   112 : hrPro<->AlaArgThrLeuThrProProValArgValProAlaProAlaProAlaGlnL :   130
          !|||   |||..! !!! !  ! !!|||  !!:!! !|||||||||.!!||| !!...:
         luProAlaAlaGluProProLeuSerProAsnLysAspProAlaProThrProProSerV
 49869 : AACCTGCTGCGGAGCCCCCATTGTCGCCCAACAAGGACCCTGCGCCCACGCCGCCAAGTG : 49928

   131 : euLeuAlaGlyIleArgAlaAlaLeuProValLeuAspSerTyrLeu<->AlaProAlaL :   149
         !!  !  !! !  !  !!.!|||  !  ! !!  !  ! !! !   !     !|||||||
         alLysHisValProSerValAlaLysGlyPheGlyProProGlnAlaProLeuProAlaL
 49929 : TGAAGCACGTCCCCTCGGTGGCCAAGGGATTTGGGCCCCCCCAGGCGCCCCTTCCTGCGC : 49988

   150 : euProLeuAspProProProGluProAlaProGluLeuProLeuLeuProGluGluAspP :   169
         |||||! !... !! !!  !  !|||!.!|||.!.|||  !! !:!!|||..!! !||||
         euProProSerAlaThrAspLeuProGlyProAsnLeuGlySerIleProArgAlaAspP
 49989 : TCCCTCCATCGGCCACTGATTTACCGGGGCCCAACCTGGGGTCCATCCCCAGGGCAGATC : 50048

   170 : ro :   169
         ||
         ro
 50049 : CA : 50050

vulgar: SPP00000029_1.0 0 169 . gi|398920895|gb|JH767830.1|:subseq(1533009,102959) 49483 50050 + 237 M 24 72 5 0 2 I 0 50 3 0 2 M 88 264 G 0 3 M 33 99 G 0 3 M 24 72
# --- 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|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	gene	49484	50050	237	+	.	gene_id 2 ; sequence SPP00000029_1.0 ; gene_orientation +
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	cds	49484	49555	.	+	.	
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	exon	49484	49555	.	+	.	insertions 0 ; deletions 0
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	splice5	49556	49557	.	+	.	intron_id 1 ; splice_site "GT"
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	intron	49556	49609	.	+	.	intron_id 1
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	splice3	49608	49609	.	+	.	intron_id 0 ; splice_site "TG"
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	cds	49610	50050	.	+	.	
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	exon	49610	50050	.	+	.	insertions 6 ; deletions 0
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	similarity	49484	50050	237	+	.	alignment_id 2 ; Query SPP00000029_1.0 ; Align 49484 1 72 ; Align 49610 25 264 ; Align 49877 113 99 ; Align 49979 146 72
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000029_1.0 # Protein # Selenoprotein V (SelV) # Homo sapiens # Complete
        Target: gi|398920895|gb|JH767830.1|:subseq(1533009,102959) Ceratotherium simum simum unplaced genomic scaffold scaffold00108, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 177
   Query range: 10 -> 88
  Target range: 49531 -> 49765

    11 : SerSerAlaArgThrSerThrSerValArgAlaSerThrProThrArgThrProThrPro :    30
         .!!|||!.!|||.!!|||||| !!||||||.!!|||! !|||..!|||||| !!||||||
         GlySerValArgAlaSerThrProValArgThrSerIleProValArgThrSerThrPro
 49532 : GGCTCGGTCCGGGCTTCGACCCCGGTCAGGACTTCGATCCCGGTTCGGACCTCGACCCCC : 49589

    31 : LeuArgThrProThrProValArgThrArgThrProIleArgThrLeuThrProValLeu :    50
         :!!||||||||||||! !||||||.!!  !||||||:!!||| !!! !|||||||||! !
         ValArgThrProThrLeuValArgAlaSerThrProValArgProProThrProValGln
 49590 : GTCCGGACCCCGACTCTGGTCCGGGCCTCCACTCCCGTCCGGCCCCCGACCCCTGTCCAG : 49649

    51 : ThrProSerProAlaGlyThrSerProLeuValLeuThrProAlaProAlaGlnIlePro :    70
         ||||||!!!|||!.! !!.!!||| !!! !|||! ! !!|||.!!|||!.!!:!!  |||
         ThrProThrProValArgAlaSerThrProValTrpProProThrProValArgThrPro
 49650 : ACACCGACTCCGGTCCGGGCCTCAACCCCTGTCTGGCCCCCGACTCCCGTTCGGACGCCG : 49709

    71 : ThrLeuValProThrProAlaLeuAlaArgIleProArgLeuValProProPro :    88
         |||! !|||  !||| !!.!!! !  !|||! !|||  !! !..!||| !!|||
         ThrProValGlyThrSerThrProAsnArgThrProValArgThrProThrPro
 49710 : ACTCCCGTCGGGACCTCGACCCCCAACCGGACCCCCGTCCGGACCCCGACTCCG : 49765

vulgar: SPP00000029_1.0 10 88 . gi|398920895|gb|JH767830.1|:subseq(1533009,102959) 49531 49765 + 177 M 78 234
# --- 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|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	gene	49532	49765	177	+	.	gene_id 3 ; sequence SPP00000029_1.0 ; gene_orientation .
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	cds	49532	49765	.	+	.	
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	exon	49532	49765	.	+	.	insertions 0 ; deletions 0
gi|398920895|gb|JH767830.1|:subseq(1533009,102959)	exonerate:protein2genome:local	similarity	49532	49765	177	+	.	alignment_id 3 ; Query SPP00000029_1.0 ; Align 49532 11 234
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
