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

C4 Alignment:
------------
         Query: SPP00000019_1.0 # Protein # Selenoprotein O (SelO) # Homo sapiens # Complete
        Target: gi|398923956|gb|JH767738.1|:subseq(9143947,124819) Ceratotherium simum simum unplaced genomic scaffold scaffold00016, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 198
   Query range: 167 -> 259
  Target range: 49999 -> 53392

   168 : GlyGluArgTrpGluLeuGlnLeuLysGlyAlaGlyProThrProPheSer{Ar}  >>> :   185
         ||||||!:!|||||||||||||||||||||:!!|||  !||||||!:!|||{||}     
         GlyGluLysTrpGluLeuGlnLeuLysGlySerGlyLysThrProTyrSer{Ar}++   
 50000 : GGTGAAAAGTGGGAGCTCCAATTAAAAGGCTCAGGAAAGACCCCATACTCT{CG}gt... : 50055

   186 : > Target Intron 1 >>>>  {g}GlnAlaAspGlyArgLysValLeuArgSerSer :   196
                90 bp            {|}.!.!.!|||||||||   |||||||||||||||
                               ++{g}AspGlyAspGlyArgAlaValLeuArgSerSer
 50056 : ......................ag{A}GATGGTGATGGCAGAGCTGTACTTCGCTCCTCA : 50174

   197 : IleArgGluPheLeuCysSerGluAlaMetPheHisLeuGlyValProThrThrArgAla :   216
         :!:|||||||||||||||||||||||||||  !:!!||||||:!!||||||!:!||||||
         ValArgGluPheLeuCysSerGluAlaMetHisTyrLeuGlyIleProThrSerArgAla
 50175 : GTGAGAGAATTTTTGTGTAGTGAGGCTATGCACTATCTTGGGATTCCAACCAGCAGAGCT : 50234

   217 : Gly{Al}  >>>> Target Intron 2 >>>>  {a}CysValThrSerGluSerThr :   225
         !.!{  }           3027 bp           {!}   !.!  !! !!  ! !  !
         Ala{Ar}++                         ++{g}LysAlaTyrTyrAlaIlePhe
 50235 : GCG{AG}gt.........................ag{A}AAAGCATATTATGCTATATTT : 53288

   226 : ValValArgAspValPheTyrAspGlyAsnProLysTyrGluGlnCysThrValValLeu :   245
         !.!  !  ! ! :!! !!|||! !  !!    !   ! !   ..! !!.!!|||||||||
         Ala***PheLysIleValTyrAlaLysIleAsnValSerPheSerGlyAlaValValLeu
 53289 : GCATAGTTTAAAATAGTTTATGCTAAAATAAATGTTTCTTTTTCAGGTGCAGTAGTGCTG : 53348

   246 : ArgValAlaSerThrPheIleArgPheGlySerPheGluIle :   259
         |||||||||!.!:!!!::.!!||||||||||||!!.||||||
         ArgValAlaLysSerTrpPheArgPheGlySerLeuGluIle
 53349 : CGTGTTGCAAAATCATGGTTTAGATTTGGATCGTTAGAAATT : 53392

vulgar: SPP00000019_1.0 167 259 . gi|398923956|gb|JH767738.1|:subseq(9143947,124819) 49999 53392 + 198 M 17 51 S 0 2 5 0 2 I 0 86 3 0 2 S 1 1 M 32 96 S 0 2 5 0 2 I 0 3023 3 0 2 S 1 1 M 41 123
# --- 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|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	gene	50000	53392	198	+	.	gene_id 1 ; sequence SPP00000019_1.0 ; gene_orientation +
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	cds	50000	50052	.	+	.	
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	exon	50000	50052	.	+	.	insertions 0 ; deletions 0
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	splice5	50053	50054	.	+	.	intron_id 1 ; splice_site "GT"
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	intron	50053	50142	.	+	.	intron_id 1
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	splice3	50141	50142	.	+	.	intron_id 0 ; splice_site "AG"
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	cds	50143	50241	.	+	.	
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	exon	50143	50241	.	+	.	insertions 0 ; deletions 0
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	splice5	50242	50243	.	+	.	intron_id 2 ; splice_site "GT"
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	intron	50242	53268	.	+	.	intron_id 2
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	splice3	53267	53268	.	+	.	intron_id 1 ; splice_site "AG"
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	cds	53269	53392	.	+	.	
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	exon	53269	53392	.	+	.	insertions 0 ; deletions 0
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	similarity	50000	53392	198	+	.	alignment_id 1 ; Query SPP00000019_1.0 ; Align 50000 168 51 ; Align 50144 186 96 ; Align 53270 219 123
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000019_1.0 # Protein # Selenoprotein O (SelO) # Homo sapiens # Complete
        Target: gi|398923956|gb|JH767738.1|:subseq(9143947,124819) Ceratotherium simum simum unplaced genomic scaffold scaffold00016, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 115
   Query range: 332 -> 360
  Target range: 59121 -> 59205

   333 : GlyValLeuAsnThrAspAsnMetSerIleLeuGlyLeuThrIleAspTyrGlyProPhe :   352
         ||||||! !||||||||||||.!.|||:!:|||..!:!!|||||||||||||||||||||
         GlyValCysAsnThrAspAsnPheSerLeuLeuSerIleThrIleAspTyrGlyProPhe
 59122 : GGTGTTTGTAATACTGATAACTTCAGTTTGTTATCCATTACAATTGACTATGGTCCCTTT : 59179

   353 : GlyPheLeuAspArgTyrAspPro :   360
         ||||||:!!!!:  !|||:!!|||
         GlyPheMetGluAlaTyrAsnPro
 59180 : GGTTTTATGGAGGCCTATAATCCA : 59205

vulgar: SPP00000019_1.0 332 360 . gi|398923956|gb|JH767738.1|:subseq(9143947,124819) 59121 59205 + 115 M 28 84
# --- 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|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	gene	59122	59205	115	+	.	gene_id 2 ; sequence SPP00000019_1.0 ; gene_orientation .
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	cds	59122	59205	.	+	.	
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	exon	59122	59205	.	+	.	insertions 0 ; deletions 0
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	similarity	59122	59205	115	+	.	alignment_id 2 ; Query SPP00000019_1.0 ; Align 59122 333 84
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000019_1.0 # Protein # Selenoprotein O (SelO) # Homo sapiens # Complete
        Target: gi|398923956|gb|JH767738.1|:subseq(9143947,124819) Ceratotherium simum simum unplaced genomic scaffold scaffold00016, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 101
   Query range: 588 -> 617
  Target range: 74732 -> 74819

   589 : AlaAsnAsnProLysTyrValLeuArgAsnTyrIleAlaGlnAsnAlaIleGluAlaAla :   608
         |||  !||||||!:!|||||||||!:!|||!::!!:|||:!!::!|||:!::!!  !|||
         AlaValAsnProArgTyrValLeuLysAsnTrpMetAlaGluSerAlaValGlnLysAla
 74733 : GCTGTTAATCCCAGATATGTGCTGAAGAACTGGATGGCAGAGTCTGCAGTGCAAAAAGCA : 74790

   609 : GluArgGlyAspPheSerGluValArg :   617
         ||||||..!||||||||||||||||||
         GluArgAsnAspPheSerGluValArg
 74791 : GAAAGGAATGATTTTTCAGAGGTAAGG : 74819

vulgar: SPP00000019_1.0 588 617 . gi|398923956|gb|JH767738.1|:subseq(9143947,124819) 74732 74819 + 101 M 29 87
# --- 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|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	gene	74733	74819	101	+	.	gene_id 3 ; sequence SPP00000019_1.0 ; gene_orientation .
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	cds	74733	74819	.	+	.	
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	exon	74733	74819	.	+	.	insertions 0 ; deletions 0
gi|398923956|gb|JH767738.1|:subseq(9143947,124819)	exonerate:protein2genome:local	similarity	74733	74819	101	+	.	alignment_id 3 ; Query SPP00000019_1.0 ; Align 74733 589 87
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
