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

C4 Alignment:
------------
         Query: SPP00000871_2.0 # Protein # Selenoprotein M (SelM) # Horse (Equus caballus)
        Target: gi|398923055|gb|JH767752.1|:subseq(1482093,102239) Ceratotherium simum simum unplaced genomic scaffold scaffold00030, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 636
   Query range: 0 -> 142
  Target range: 49936 -> 52239

     1 : MetHisLeuProLeuProProProProLeuLeuLeuLeuValAlaAlaValAlaAlaAla :    20
         |||||||||||||||||||||! !|||||||||||||||:!!||||||:!!|||||||||
         MetHisLeuProLeuProProArgProLeuLeuLeuLeuLeuAlaAlaLeuAlaAlaAla
 49937 : ATGCATCTCCCGCTGCCTCCGCGGCCCCTACTGCTGCTTCTCGCGGCACTCGCGGCCGCC : 49994

    21 : AlaThrThrPheArgProAspTrpAsnArgLeuHisArgLeuAlaArgAlaArgValGlu :    40
         .!!||||||||||||||||||||||||||||||||| !!|||||||||||||||||||||
         ThrThrThrPheArgProAspTrpAsnArgLeuHisGlyLeuAlaArgAlaArgValGlu
 49995 : ACCACCACCTTCCGGCCCGACTGGAACCGTCTGCACGGCCTGGCCCGAGCCCGGGTAGAG : 50054

    41 :   >>>> Target Intron 1 >>>>  ThrCysGlyGlyUnkGlnLeuAsnArgLeuL :    51
                    1231 bp           ||||||||||||   |||||||||||||||!
         ++                         ++ThrCysGlyGly***GlnLeuAsnArgLeuA
 50055 : gt.........................agACCTGTGGGGGATGACAGCTGAATCGCCTGA : 51318

    52 : ysGlu  >>>> Target Intron 2 >>>>  ValLysAlaPheValThrGluAspIl :    61
         :!|||            203 bp           ||||||||||||||||||:!!|||||
         rgGlu++                         ++ValLysAlaPheValThrGlnAspIl
 51319 : GGGAGgt.........................agGTGAAGGCCTTTGTCACCCAGGACAT : 51551

    62 : eProPhe{Ty}  >>>> Target Intron 3 >>>>  {r}HisAsnLeuValMetLy :    70
         |||||||{||}            364 bp           {|}|||||||||||||||||
         eProPhe{Ty}++                         -+{r}HisAsnLeuValMetLy
 51552 : CCCATTC{TA}gt.........................tg{T}CACAACCTGGTAATGAA : 51942

    71 : sHisLeuProGlyAlaAspProGluLeuValLeuLeuGlyHisArgTyrGluGluLeuGl :    90
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         sHisLeuProGlyAlaAspProGluLeuValLeuLeuGlyHisArgTyrGluGluLeuGl
 51943 : ACACCTCCCGGGGGCCGACCCAGAGCTCGTGCTGCTGGGCCACCGCTACGAGGAACTGGA : 52002

    91 : u  >>>> Target Intron 4 >>>>  ArgIleProLeuSerGluMetThrArgGlu :   100
         |            79 bp            ||||||||||||||||||||||||||||||
         u++                         ++ArgIleProLeuSerGluMetThrArgGlu
 52003 : Ggt.........................agCGAATCCCACTCAGCGAAATGACCCGCGAG : 52111

   101 : GluIleAsnAlaLeuValGlnGluLeuGlyPheTyrArgLysAlaAlaProAspAspPro :   120
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         GluIleAsnAlaLeuValGlnGluLeuGlyPheTyrArgLysAlaAlaProAspAspPro
 52112 : GAGATCAACGCGCTGGTGCAGGAGCTCGGCTTCTACCGCAAGGCGGCGCCGGACGATCCT : 52171

   121 : ValProProGluPheLeuArgAlaProAlaArgProAlaLysGlySerProAlaArgAla :   140
         ||||||||||||!:!|||||||||||||||!:!||||||:!!|||:!!||||||||| !!
         ValProProGluTyrLeuArgAlaProAlaLysProAlaGluGlyAlaProAlaArgPro
 52172 : GTGCCCCCCGAGTACCTGCGGGCGCCCGCTAAGCCCGCCGAAGGCGCTCCGGCCCGCCCT : 52231

   141 : AspLeu :   142
         ||||||
         AspLeu
 52232 : GACCTG : 52239

vulgar: SPP00000871_2.0 0 142 . gi|398923055|gb|JH767752.1|:subseq(1482093,102239) 49936 52239 + 636 M 40 120 5 0 2 I 0 1227 3 0 2 M 12 36 5 0 2 I 0 199 3 0 2 M 11 33 S 0 2 5 0 2 I 0 360 3 0 2 S 1 1 M 26 78 5 0 2 I 0 75 3 0 2 M 52 156
# --- 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|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	gene	49937	52239	636	+	.	gene_id 1 ; sequence SPP00000871_2.0 ; gene_orientation +
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	cds	49937	50056	.	+	.	
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	exon	49937	50056	.	+	.	insertions 0 ; deletions 0
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	splice5	50057	50058	.	+	.	intron_id 1 ; splice_site "GT"
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	intron	50057	51287	.	+	.	intron_id 1
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	splice3	51286	51287	.	+	.	intron_id 0 ; splice_site "AG"
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	cds	51288	51323	.	+	.	
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	exon	51288	51323	.	+	.	insertions 0 ; deletions 0
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	splice5	51324	51325	.	+	.	intron_id 2 ; splice_site "GT"
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	intron	51324	51526	.	+	.	intron_id 2
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	splice3	51525	51526	.	+	.	intron_id 1 ; splice_site "AG"
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	cds	51527	51561	.	+	.	
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	exon	51527	51561	.	+	.	insertions 0 ; deletions 0
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	splice5	51562	51563	.	+	.	intron_id 3 ; splice_site "GT"
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	intron	51562	51925	.	+	.	intron_id 3
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	splice3	51924	51925	.	+	.	intron_id 2 ; splice_site "TG"
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	cds	51926	52004	.	+	.	
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	exon	51926	52004	.	+	.	insertions 0 ; deletions 0
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	splice5	52005	52006	.	+	.	intron_id 4 ; splice_site "GT"
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	intron	52005	52083	.	+	.	intron_id 4
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	splice3	52082	52083	.	+	.	intron_id 3 ; splice_site "AG"
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	cds	52084	52239	.	+	.	
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	exon	52084	52239	.	+	.	insertions 0 ; deletions 0
gi|398923055|gb|JH767752.1|:subseq(1482093,102239)	exonerate:protein2genome:local	similarity	49937	52239	636	+	.	alignment_id 1 ; Query SPP00000871_2.0 ; Align 49937 1 120 ; Align 51288 41 36 ; Align 51527 53 33 ; Align 51927 65 78 ; Align 52084 91 156
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
