Command line: [/mnt/NFS_UPF/soft/exonerate/exonerate-2.2.0-x86_64/bin/exonerate -m p2g --showtargetgff -q /home/u137251/Desktop/SelH_cow.fa -t genomic_SJYR01002415.1]
Hostname: [am33123-116042u]

C4 Alignment:
------------
         Query: SPP00000258_2.0  Protein  Selenoprotein H (SELENOH)  Cow 
        Target: SJYR01002415.1:subseq(46098,200000) Kobus ellipsiprymnus isolate DFW-375 scaffold2420_size300438, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 575
   Query range: 0 -> 123
  Target range: 99564 -> 100140

      1 : MetAlaSerArgGlyArgLysArgLysAlaGluAlaAlaLeuAlaAlaAlaAlaGluL :     20
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          MetAlaSerArgGlyArgLysArgLysAlaGluAlaAlaLeuAlaAlaAlaAlaGluL
  99565 : ATGGCGTCCCGCGGGAGGAAGCGGAAGGCCGAGGCGGCGCTGGCCGCTGCGGCCGAGA :  99622

     21 : ysArgGluLysProAlaGlyGlyGlnGluGlyGlyValGluGlyProSerValValIl :     39
          ||||||||||||||||||||||||||||| !!||||||||||||||||||||||||||
          ysArgGluLysProAlaGlyGlyGlnGluArgGlyValGluGlyProSerValValIl
  99623 : AGCGGGAGAAGCCGGCCGGCGGCCAGGAGAGGGGAGTGGAGGGGCCGAGCGTCGTCAT :  99679

     40 : eGluHis{Cy}  >>>> Target Intron 1 >>>>  {s}ThrSerUnkArgVal :     47
          |||||||{||}            85 bp            {|}||||||   ||||||
          eGluHis{Cy}++                         ++{s}ThrSer***ArgVal
  99680 : CGAGCAC{TG}gt.........................ag{C}ACGAGCTGACGAGTC :  99788

     48 : TyrGlyArgAsnAlaAlaAlaLeuSerGlnAlaLeuArgLeuGlnAlaProGluLeuT :     67
          |||||||||:!!|||||||||||||||||||||||||||||||||  !|||||||||.
          TyrGlyArgHisAlaAlaAlaLeuSerGlnAlaLeuArgLeuGlnAsnProGluLeuA
  99789 : TACGGGCGCCACGCCGCGGCCCTGAGCCAGGCGCTGCGCCTGCAGAATCCCGAGCTGG :  99848

     68 : hrValLysValAsnProAlaArgProArgArgGlySerPheGluValThrLeuLeuAr :     86
          !!|||! !||||||||||||||||||||||||||||||||||||||||||||||||||
          laValThrValAsnProAlaArgProArgArgGlySerPheGluValThrLeuLeuAr
  99849 : CGGTGACGGTGAACCCCGCCAGGCCGCGGAGGGGCAGCTTCGAGGTGACGCTGCTGCG :  99905

     87 : gAlaAspGlySer{S}  >>>> Target Intron 2 >>>>  {er}AlaGluLeu :     94
          |||||||||||||{|}            122 bp           {||}|||||||||
          gAlaAspGlySer{S}++                         ++{er}AlaGluLeu
  99906 : CGCCGACGGCAGC{A}gt.........................ag{GC}GCGGAGCTC : 100051

     95 : TrpThrGlyLeuLysLysGlyProProArgLysLeuLysPheProGluProHisValV :    114
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          TrpThrGlyLeuLysLysGlyProProArgLysLeuLysPheProGluProHisValV
 100052 : TGGACGGGTCTTAAGAAGGGGCCCCCACGCAAACTCAAGTTTCCAGAGCCTCACGTGG : 100111

    115 : alLeuGluGluLeuLysLysTyrLeuSer :    123
          |||||||||||||||||||||||||||||
          alLeuGluGluLeuLysLysTyrLeuSer
 100112 : TGCTGGAGGAGCTGAAGAAGTACCTTTCG : 100140

vulgar: SPP00000258_2.0 0 123 . SJYR01002415.1:subseq(46098,200000) 99564 100140 + 575 M 41 123 S 0 2 5 0 2 I 0 81 3 0 2 S 1 1 M 48 144 S 0 1 5 0 2 I 0 118 3 0 2 S 1 2 M 32 96
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2019-11-21
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	gene	99565	100140	575	+	.	gene_id 1 ; sequence SPP00000258_2.0 ; gene_orientation +
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	cds	99565	99689	.	+	.	
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	exon	99565	99689	.	+	.	insertions 0 ; deletions 0
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	splice5	99690	99691	.	+	.	intron_id 1 ; splice_site "GT"
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	intron	99690	99774	.	+	.	intron_id 1
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	splice3	99773	99774	.	+	.	intron_id 0 ; splice_site "AG"
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	cds	99775	99920	.	+	.	
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	exon	99775	99920	.	+	.	insertions 0 ; deletions 0
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	splice5	99921	99922	.	+	.	intron_id 2 ; splice_site "GT"
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	intron	99921	100042	.	+	.	intron_id 2
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	splice3	100041	100042	.	+	.	intron_id 1 ; splice_site "AG"
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	cds	100043	100140	.	+	.	
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	exon	100043	100140	.	+	.	insertions 0 ; deletions 0
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	similarity	99565	100140	575	+	.	alignment_id 1 ; Query SPP00000258_2.0 ; Align 99565 1 123 ; Align 99776 43 144 ; Align 100045 92 96
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000258_2.0  Protein  Selenoprotein H (SELENOH)  Cow 
        Target: SJYR01002415.1:subseq(46098,200000) Kobus ellipsiprymnus isolate DFW-375 scaffold2420_size300438, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 575
   Query range: 0 -> 123
  Target range: 100796 -> 101372

      1 : MetAlaSerArgGlyArgLysArgLysAlaGluAlaAlaLeuAlaAlaAlaAlaGluL :     20
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          MetAlaSerArgGlyArgLysArgLysAlaGluAlaAlaLeuAlaAlaAlaAlaGluL
 100797 : ATGGCGTCCCGCGGGAGGAAGCGGAAGGCCGAGGCGGCGCTGGCCGCTGCGGCCGAGA : 100854

     21 : ysArgGluLysProAlaGlyGlyGlnGluGlyGlyValGluGlyProSerValValIl :     39
          ||||||||||||||||||||||||||||| !!||||||||||||||||||||||||||
          ysArgGluLysProAlaGlyGlyGlnGluArgGlyValGluGlyProSerValValIl
 100855 : AGCGGGAGAAGCCGGCCGGCGGCCAGGAGAGGGGAGTGGAGGGGCCGAGCGTCGTCAT : 100911

     40 : eGluHis{Cy}  >>>> Target Intron 1 >>>>  {s}ThrSerUnkArgVal :     47
          |||||||{||}            85 bp            {|}||||||   ||||||
          eGluHis{Cy}++                         ++{s}ThrSer***ArgVal
 100912 : CGAGCAC{TG}gt.........................ag{C}ACGAGCTGACGAGTC : 101020

     48 : TyrGlyArgAsnAlaAlaAlaLeuSerGlnAlaLeuArgLeuGlnAlaProGluLeuT :     67
          |||||||||:!!|||||||||||||||||||||||||||||||||  !|||||||||.
          TyrGlyArgHisAlaAlaAlaLeuSerGlnAlaLeuArgLeuGlnAsnProGluLeuA
 101021 : TACGGGCGCCACGCCGCGGCCCTGAGCCAGGCGCTGCGCCTGCAGAATCCCGAGCTGG : 101080

     68 : hrValLysValAsnProAlaArgProArgArgGlySerPheGluValThrLeuLeuAr :     86
          !!|||! !||||||||||||||||||||||||||||||||||||||||||||||||||
          laValThrValAsnProAlaArgProArgArgGlySerPheGluValThrLeuLeuAr
 101081 : CGGTGACGGTGAACCCCGCCAGGCCGCGGAGGGGCAGCTTCGAGGTGACGCTGCTGCG : 101137

     87 : gAlaAspGlySer{S}  >>>> Target Intron 2 >>>>  {er}AlaGluLeu :     94
          |||||||||||||{|}            122 bp           {||}|||||||||
          gAlaAspGlySer{S}++                         ++{er}AlaGluLeu
 101138 : CGCCGACGGCAGC{A}gt.........................ag{GC}GCGGAGCTC : 101283

     95 : TrpThrGlyLeuLysLysGlyProProArgLysLeuLysPheProGluProHisValV :    114
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          TrpThrGlyLeuLysLysGlyProProArgLysLeuLysPheProGluProHisValV
 101284 : TGGACGGGTCTTAAGAAGGGGCCCCCACGCAAACTCAAGTTTCCAGAGCCTCACGTGG : 101343

    115 : alLeuGluGluLeuLysLysTyrLeuSer :    123
          |||||||||||||||||||||||||||||
          alLeuGluGluLeuLysLysTyrLeuSer
 101344 : TGCTGGAGGAGCTGAAGAAGTACCTTTCG : 101372

vulgar: SPP00000258_2.0 0 123 . SJYR01002415.1:subseq(46098,200000) 100796 101372 + 575 M 41 123 S 0 2 5 0 2 I 0 81 3 0 2 S 1 1 M 48 144 S 0 1 5 0 2 I 0 118 3 0 2 S 1 2 M 32 96
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2019-11-21
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	gene	100797	101372	575	+	.	gene_id 2 ; sequence SPP00000258_2.0 ; gene_orientation +
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	cds	100797	100921	.	+	.	
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	exon	100797	100921	.	+	.	insertions 0 ; deletions 0
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	splice5	100922	100923	.	+	.	intron_id 1 ; splice_site "GT"
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	intron	100922	101006	.	+	.	intron_id 1
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	splice3	101005	101006	.	+	.	intron_id 0 ; splice_site "AG"
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	cds	101007	101152	.	+	.	
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	exon	101007	101152	.	+	.	insertions 0 ; deletions 0
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	splice5	101153	101154	.	+	.	intron_id 2 ; splice_site "GT"
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	intron	101153	101274	.	+	.	intron_id 2
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	splice3	101273	101274	.	+	.	intron_id 1 ; splice_site "AG"
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	cds	101275	101372	.	+	.	
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	exon	101275	101372	.	+	.	insertions 0 ; deletions 0
SJYR01002415.1:subseq(46098,200000)	exonerate:protein2genome:local	similarity	100797	101372	575	+	.	alignment_id 2 ; Query SPP00000258_2.0 ; Align 100797 1 123 ; Align 101008 43 144 ; Align 101277 92 96
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
