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

C4 Alignment:
------------
         Query: SPP00000103_2.0 # Protein # Selenoprotein S (SelS) # Human (Homo sapiens)
        Target: gi|398922816|gb|JH767761.1|:subseq(4189089,106698) Ceratotherium simum simum unplaced genomic scaffold scaffold00039, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 757
   Query range: 0 -> 219
  Target range: 49357 -> 56707

     1 : MetMetGlyGlySerSerAlaAlaAlaProGlyAlaGlyAlaTrpGluAlaTrpGluArg :    20
         |||   ||||||||||||:!!||||||! ! !!|||||| !! !!! !!.!|||  !  !
         MetSerGlyGlySerSerSerAlaAlaArgArgAlaGlyProGlyValValTrpProAla
 49358 : ATGTCCGGTGGGTCGTCCTCCGCGGCGCGCCGGGCCGGGCCTGGGGTGGTCTGGCCGGCA : 49415

    21 : SerGlyValGlyAlaTyrAlaAspLeuGlyGlnGlnAlaArgThrLeuArgGlyGlyPhe :    40
         :!! !!|||||||||     !   ! !|||!:!!:!||||||!:!  !||| !!|||.!!
         AlaArgValGlyAlaAlaArgArgSerGlyArgArgAlaArgSerAlaArgArgGlyLeu
 49416 : GCCCGTGTTGGCGCGGCACGCAGGTCCGGGCGGCGGGCCCGGAGCGCGCGCCGAGGCCTC : 49475

    41 : SerGlyAlaAlaLeuProTrpAlaAlaArgLeuSerLeuValCysAlaSerLeuPheCys :    60
          !!   |||||||||||||||||||||! !! !.!!! !|||!    !!.!!!!|||  !
         Arg---AlaAlaLeuProTrpAlaAlaProSerGlyProValLeuArgLysPhePheAsn
 49476 : CGA---GCCGCACTTCCCTGGGCGGCGCCCTCGGGCCCTGTTTTGCGCAAATTTTTTAAT : 49532

    61 : GluProSerProSer{L}  >>>> Target Intron 1 >>>>  {eu}GlySerLeu :    69
           !  !!.!! !:!!{:}            453 bp           {!!}|||||||||
         LeuTrpLysGlnAla{V}-+                         ++{al}GlySerLeu
 49533 : TTGTGGAAGCAAGCC{G}tt.........................ag{TG}GGCTCTCTG : 50012

    70 : LeuAlaThrTyrGlyTrpTyrIleValPheSerCysIleLeuLeuTyrValValPheGln :    89
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         LeuAlaThrTyrGlyTrpTyrIleValPheSerCysIleLeuLeuTyrValValPheGln
 50013 : CTGGCCACCTATGGCTGGTACATCGTCTTCAGCTGCATCCTTCTCTACGTGGTTTTCCAG : 50072

    90 : LysLeuSerAlaArgLeuArgAlaLeuArgGlnArgGlnLeuAspArgAlaAlaAlaAla :   109
         |||||||||.!!||||||||||||||||||||||||||||||||||||||||||||||||
         LysLeuSerThrArgLeuArgAlaLeuArgGlnArgGlnLeuAspArgAlaAlaAlaAla
 50073 : AAGCTGTCCACCCGCCTGAGGGCCTTGAGGCAGAGGCAGCTAGACCGAGCTGCGGCTGCC : 50132

   110 : Val{G}  >>>> Target Intron 2 >>>>  {lu}ProAspValValValLysArg :   118
         |||{|}           1781 bp           {||}||||||:!!||||||||||||
         Val{G}++                         ++{lu}ProAspIleValValLysArg
 50133 : GTG{G}gt.........................ag{AA}CCTGATATTGTTGTTAAACGG : 51940

   119 : GlnGluAlaLeuAlaAlaAlaArgLeuLysMetGlnGluGluLeuAsnAlaGlnValGlu :   138
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         GlnGluAlaLeuAlaAlaAlaArgLeuLysMetGlnGluGluLeuAsnAlaGlnValGlu
 51941 : CAAGAAGCTTTAGCAGCTGCTCGTTTGAAAATGCAAGAGGAACTAAATGCACAAGTTGAA : 52000

   139 : LysHisLysGluLysLeuLysGln  >>>> Target Intron 3 >>>>  LeuGluG :   149
         ||||||||||||||||||!:!|||           2585 bp           |||||||
         LysHisLysGluLysLeuArgGln++                         ++LeuGluG
 52001 : AAGCATAAGGAGAAACTAAGACAGgt.........................agCTTGAAG : 54618

   150 : luGluLysArgArgGlnLysIleGluMetTrpAspSerMetGlnGluGlyLysSerTyrL :   169
         ||||||||||||||!:!|||||||||||||||||||||||||||||||||||||||||||
         luGluLysArgArgArgLysIleGluMetTrpAspSerMetGlnGluGlyLysSerTyrL
 54619 : AAGAGAAAAGGAGACGGAAGATTGAAATGTGGGACAGCATGCAAGAAGGAAAAAGTTACA : 54678

   170 : ysGlyAsnAlaLysLysProGln  >>>> Target Intron 4 >>>>  GluGluAs :   179
         || !!||||||  !!:!||||||            100 bp           ||||||||
         ysArgAsnAlaGlyArgProGln++                         ++GluGluAs
 54679 : AAAGAAATGCAGGAAGGCCTCAGgt.........................agGAAGAAGA : 54808

   180 : pSerProGlyProSerThrSerSerValLeu<->LysArgLysSerAspArgLysProLe :   198
         ||||||||||||||||||||||||||||:!!   ||||||||||||||||||||||||||
         pSerProGlyProSerThrSerSerValIleProLysArgLysSerAspArgLysProLe
 54809 : CAGTCCTGGGCCTTCTACTTCCTCAGTCATCCCGAAACGAAAATCTGACAGAAAGCCTTT : 54868

   199 : uArgGlyGly{G}  >>>> Target Intron 5 >>>>  {ly}TyrAsnProLeuSe :   207
         ||||||||||{|}           1774 bp           {||}||||||||||||||
         uArgGlyGly{G}++                         ++{ly}TyrAsnProLeuSe
 54869 : GCGGGGAGGT{G}gt.........................ag{GT}TACAACCCTTTGTC : 56669

   208 : rGlyGluGlyGlyGlyAlaCysSerTrpArgProGly :   219
         |||||||||||||||||||||||||||||||||||||
         rGlyGluGlyGlyGlyAlaCysSerTrpArgProGly
 56670 : TGGTGAAGGAGGTGGAGCCTGCTCCTGGAGACCTGGT : 56707

vulgar: SPP00000103_2.0 0 219 . gi|398922816|gb|JH767761.1|:subseq(4189089,106698) 49357 56707 + 757 M 41 123 G 1 0 M 23 69 S 0 1 5 0 2 I 0 449 3 0 2 S 1 2 M 44 132 S 0 1 5 0 2 I 0 1777 3 0 2 S 1 2 M 35 105 5 0 2 I 0 2581 3 0 2 M 30 90 5 0 2 I 0 96 3 0 2 M 13 39 G 0 3 M 12 36 S 0 1 5 0 2 I 0 1770 3 0 2 S 1 2 M 17 51
# --- 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|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	gene	49358	56707	757	+	.	gene_id 1 ; sequence SPP00000103_2.0 ; gene_orientation +
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	cds	49358	49550	.	+	.	
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	exon	49358	49550	.	+	.	insertions 0 ; deletions 1
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	splice5	49551	49552	.	+	.	intron_id 1 ; splice_site "TT"
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	intron	49551	50003	.	+	.	intron_id 1
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	splice3	50002	50003	.	+	.	intron_id 0 ; splice_site "AG"
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	cds	50004	50138	.	+	.	
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	exon	50004	50138	.	+	.	insertions 0 ; deletions 0
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	splice5	50139	50140	.	+	.	intron_id 2 ; splice_site "GT"
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	intron	50139	51919	.	+	.	intron_id 2
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	splice3	51918	51919	.	+	.	intron_id 1 ; splice_site "AG"
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	cds	51920	52026	.	+	.	
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	exon	51920	52026	.	+	.	insertions 0 ; deletions 0
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	splice5	52027	52028	.	+	.	intron_id 3 ; splice_site "GT"
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	intron	52027	54611	.	+	.	intron_id 3
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	splice3	54610	54611	.	+	.	intron_id 2 ; splice_site "AG"
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	cds	54612	54701	.	+	.	
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	exon	54612	54701	.	+	.	insertions 0 ; deletions 0
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	splice5	54702	54703	.	+	.	intron_id 4 ; splice_site "GT"
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	intron	54702	54801	.	+	.	intron_id 4
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	splice3	54800	54801	.	+	.	intron_id 3 ; splice_site "AG"
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	cds	54802	54880	.	+	.	
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	exon	54802	54880	.	+	.	insertions 3 ; deletions 0
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	splice5	54881	54882	.	+	.	intron_id 5 ; splice_site "GT"
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	intron	54881	56654	.	+	.	intron_id 5
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	splice3	56653	56654	.	+	.	intron_id 4 ; splice_site "AG"
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	cds	56655	56707	.	+	.	
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	exon	56655	56707	.	+	.	insertions 0 ; deletions 0
gi|398922816|gb|JH767761.1|:subseq(4189089,106698)	exonerate:protein2genome:local	similarity	49358	56707	757	+	.	alignment_id 1 ; Query SPP00000103_2.0 ; Align 49358 1 123 ; Align 49481 43 69 ; Align 50006 67 132 ; Align 51922 112 105 ; Align 54612 147 90 ; Align 54802 177 39 ; Align 54844 190 36 ; Align 56657 203 51
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
