Command line: [/mnt/NFS_UPF/soft/exonerate/exonerate-2.2.0-x86_64/bin/exonerate -m p2g --showtargetgff -q /home/u137834/Desktop/SelM_cow.fa -t genomic_SJYR01000283.1]
Hostname: [am30754-101102u]

C4 Alignment:
------------
         Query: SPP00000261_2.0  Protein  Selenoprotein M (SELENOM)  Cow 
        Target: SJYR01000283.1:subseq(647078,200000) Kobus ellipsiprymnus isolate DFW-375 scaffold292_size1023160, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 696
   Query range: 0 -> 142
  Target range: 102423 -> 99954

      1 : MetHisLeuProLeuProProProProLeuLeuLeuLeuLeuAlaAlaValAlaAlaA :     20
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          MetHisLeuProLeuProProProProLeuLeuLeuLeuLeuAlaAlaValAlaAlaA
 102423 : ATGCACCTCCCGCTGCCTCCGCCGCCCTTGCTGCTCCTCCTCGCGGCAGTCGCGGCCG : 102366

     21 : laThrThrThrPheArgProAspTrpAsnArgLeuGlnGlyLeuAlaArgAlaArgVa :     39
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          laThrThrThrPheArgProAspTrpAsnArgLeuGlnGlyLeuAlaArgAlaArgVa
 102365 : CCACCACCACCTTCCGGCCCGACTGGAACCGTCTACAAGGCCTGGCCCGAGCCCGGGT : 102309

     40 : lGlu  >>>> Target Intron 1 >>>>  ThrCysGlyGlyUnkGlnLeuAsnA :     49
          ||||           1414 bp           ||||||||||||   ||||||||||
          lGlu++                         ++ThrCysGlyGly***GlnLeuAsnA
 102308 : AGAGgt.........................agACATGTGGAGGATGACAGCTTAATC : 100865

     50 : rgLeuLysGlu  >>>> Target Intron 2 >>>>  ValLysAlaPheValThr :     58
          |||||||||||            197 bp           ||||||||||||||||||
          rgLeuLysGlu++                         ++ValLysAlaPheValThr
 100864 : GCCTGAAGGAGgt.........................agGTGAAGGCCTTCGTCACC : 100641

     59 : GlnAspIleProLeu{Ty}  >>>> Target Intron 3 >>>>  {r}HisAsnL :     67
          |||||||||||||||{||}            355 bp           {|}|||||||
          GlnAspIleProLeu{Ty}++                         ++{r}HisAsnL
 100640 : CAGGACATTCCACTC{TA}gt.........................ag{C}CACAACC : 100259

     68 : euValMetLysHisLeuProGlyAlaAspProGluLeuValLeuLeuGlyHisArgPh :     86
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          euValMetLysHisLeuProGlyAlaAspProGluLeuValLeuLeuGlyHisArgPh
 100258 : TGGTGATGAAACACCTGCCGGGGGCCGACCCAGAGCTCGTGTTGCTGGGCCACCGCTT : 100202

     87 : eGluGluLeuGlu  >>>> Target Intron 4 >>>>  ArgIleProLeuSerA :     96
          |||||||||||||            77 bp            ||||||||||||||||
          eGluGluLeuGlu++                         ++ArgIleProLeuSerA
 100201 : TGAGGAACTGGAGgt.........................agCGAATTCCACTCAGCG : 100095

     97 : spMetThrArgGluGluIleAsnAlaLeuValGlnGluLeuGlyPheTyrArgLysAl :    115
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          spMetThrArgGluGluIleAsnAlaLeuValGlnGluLeuGlyPheTyrArgLysAl
 100094 : ACATGACCCGCGAGGAGATCAACGCGCTGGTGCAGGAGCTCGGCTTCTACCGCAAGGC : 100038

    116 : aSerProAspGluProValProProGluTyrLeuArgAlaProAlaArgProAlaGly :    134
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          aSerProAspGluProValProProGluTyrLeuArgAlaProAlaArgProAlaGly
 100037 : GTCGCCCGACGAGCCTGTGCCCCCGGAGTACCTTCGGGCGCCCGCTAGGCCCGCCGGA :  99981

    135 : AspAlaProAspHisAlaAspLeu :    142
          ! !|||||||||||||||||||||
          GlyAlaProAspHisAlaAspLeu
  99980 : GGCGCTCCTGACCACGCAGACCTG :  99955

vulgar: SPP00000261_2.0 0 142 . SJYR01000283.1:subseq(647078,200000) 102423 99954 - 696 M 40 120 5 0 2 I 0 1410 3 0 2 M 12 36 5 0 2 I 0 193 3 0 2 M 11 33 S 0 2 5 0 2 I 0 351 3 0 2 S 1 1 M 26 78 5 0 2 I 0 73 3 0 2 M 52 156
# --- 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
#
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	gene	99955	102423	696	-	.	gene_id 1 ; sequence SPP00000261_2.0 ; gene_orientation +
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	cds	102304	102423	.	-	.	
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	exon	102304	102423	.	-	.	insertions 0 ; deletions 0
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	splice5	102302	102303	.	-	.	intron_id 1 ; splice_site "GT"
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	intron	100890	102303	.	-	.	intron_id 1
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	splice3	100890	100891	.	-	.	intron_id 0 ; splice_site "AG"
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	cds	100854	100889	.	-	.	
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	exon	100854	100889	.	-	.	insertions 0 ; deletions 0
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	splice5	100852	100853	.	-	.	intron_id 2 ; splice_site "GT"
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	intron	100657	100853	.	-	.	intron_id 2
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	splice3	100657	100658	.	-	.	intron_id 1 ; splice_site "AG"
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	cds	100622	100656	.	-	.	
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	exon	100622	100656	.	-	.	insertions 0 ; deletions 0
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	splice5	100620	100621	.	-	.	intron_id 3 ; splice_site "GT"
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	intron	100267	100621	.	-	.	intron_id 3
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	splice3	100267	100268	.	-	.	intron_id 2 ; splice_site "AG"
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	cds	100188	100266	.	-	.	
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	exon	100188	100266	.	-	.	insertions 0 ; deletions 0
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	splice5	100186	100187	.	-	.	intron_id 4 ; splice_site "GT"
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	intron	100111	100187	.	-	.	intron_id 4
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	splice3	100111	100112	.	-	.	intron_id 3 ; splice_site "AG"
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	cds	99955	100110	.	-	.	
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	exon	99955	100110	.	-	.	insertions 0 ; deletions 0
SJYR01000283.1:subseq(647078,200000)	exonerate:protein2genome:local	similarity	99955	102423	696	-	.	alignment_id 1 ; Query SPP00000261_2.0 ; Align 102424 1 120 ; Align 100890 41 36 ; Align 100657 53 33 ; Align 100266 65 78 ; Align 100111 91 156
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
