Command line: [/mnt/NFS_UPF/soft/exonerate/exonerate-2.2.0-x86_64/bin/exonerate -m p2g --showtargetgff -q /home/u137251/Desktop/selenop_cow.fa -t genomic_SJYR01002566.1]
Hostname: [am30372-101055u]

C4 Alignment:
------------
         Query: SPP00000267_2.0  Protein  Selenoprotein P (SELENOP)  Cow 
        Target: SJYR01002566.1:subseq(259241,200000) Kobus ellipsiprymnus isolate DFW-375 scaffold2569_size522084, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 884
   Query range: 0 -> 178
  Target range: 106192 -> 102439

      1 : MetTrpArgGlyLeuGlyLeuAlaLeuAlaLeuCysLeuLeuLeuThrGlyGlyThrG :     20
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          MetTrpArgGlyLeuGlyLeuAlaLeuAlaLeuCysLeuLeuLeuThrGlyGlyThrG
 106192 : ATGTGGAGAGGCCTGGGGCTGGCTCTGGCTCTCTGCCTCCTCCTAACCGGAGGAACAG : 106135

     21 : luSerGlnGlyGlnSerSerTyrCysLysGlnProProProTrpSerIleLysAspGl :     39
          |||||||||||||||||||||||||||||||||||||| !!|||||||||||||||||
          luSerGlnGlyGlnSerSerTyrCysLysGlnProProAlaTrpSerIleLysAspGl
 106134 : AGAGCCAGGGCCAAAGCTCCTATTGTAAGCAACCTCCAGCCTGGAGCATAAAGGATCA : 106078

     40 : nAspProMetLeuAsnSerTyrGlySerValThrValValAlaLeuLeuGlnAlaSer :     58
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          nAspProMetLeuAsnSerTyrGlySerValThrValValAlaLeuLeuGlnAlaSer
 106077 : AGACCCTATGTTGAACTCCTATGGTTCAGTGACCGTGGTTGCTCTTCTTCAAGCCAGC : 106021

     59 : UnkTyrLeuCysIleLeuGlnAlaSer{Ar}  >>>> Target Intron 1 >>>> :     68
             ||||||||||||||||||||||||{||}           1158 bp         
          ***TyrLeuCysIleLeuGlnAlaSer{Ar}++                         
 106020 : TGATACCTGTGCATTCTGCAGGCATCT{AG}gt......................... : 105987

     69 :   {g}LeuGluAspLeuArgValLysLeuGluLysGluGlyTyrSerAsnIleSerTy :     86
            {|}||||||||||||||||||||||||||||||||||||||||||!!.||||||||
          ++{g}LeuGluAspLeuArgValLysLeuGluLysGluGlyTyrSerLysIleSerTy
 105986 : ag{a}tTGGAAGACCTGCGAGTAAAACTGGAGAAAGAAGGATATTCTAAGATCTCCTA : 104779

     87 : rValValValAsnHisGlnGlyIleSerSerArgLeuLysTyrValHisLeuLysAsn :    105
          |||||||||||||||||||! !|||||||||||||||||||||! !||||||||||||
          rValValValAsnHisGlnGluIleSerSerArgLeuLysTyrGluHisLeuLysAsn
 104778 : TGTTGTTGTTAATCATCAAGAAATCTCTTCTCGATTAAAATATGAGCATCTTAAAAAT : 104722

    106 : LysValSerGluHisIleProValTyrGlnGlnGluGluAsnGlnProAspValTrpT :    125
          ||||||||||||||||||||||||||||||||||||:!!:!!||||||||||||||||
          LysValSerGluHisIleProValTyrGlnGlnGluLysAspGlnProAspValTrpT
 104721 : AAGGTTTCAGAACATATTCCTGTTTACCAACAAGAAAAAGACCAACCAGATGTCTGGA : 104662

    126 : hrLeuLeuAsnGlyAsnLysAspAspPheLeuIleTyrAsp{Ar}  >>>> Target :    139
          |||||||||||||||||||||||||||||||||||||||||{||}           20
          hrLeuLeuAsnGlyAsnLysAspAspPheLeuIleTyrAsp{Ar}++           
 104661 : CTCtcttaaatggaaataaagatgACTTCCTCATATATGAC{AG}gt........... : 104616

    140 :  Intron 2 >>>>  {g}CysGlyArgLeuValTyrHisLeuGlyLeuProTyrSer :    152
          61 bp           {|}|||||||||||||||||||||||||||||||||||||||
                        ++{g}CysGlyArgLeuValTyrHisLeuGlyLeuProTyrSer
 104615 : ..............ag{A}TGTGGCCGCCTTGTATATCATCTTGGTTTGCCTTATTCC : 102520

    153 : PheLeuThrPheThrTyrValGluAspSerIleLysThrValTyrCysGluAspLysC :    172
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          PheLeuThrPheThrTyrValGluAspSerIleLysThrValTyrCysGluAspLysC
 102519 : TTCCTAACTTTCACATATGTAGAAGATTCCATTAAGACTGTTTACTGTGAAGATAAAT : 102460

    173 : ysGlyAsnCysSerLeuLys :    178
          ||||||||||||||||||||
          ysGlyAsnCysSerLeuLys
 102459 : GTGGAAACTGCTCTCTCAAG : 102440

vulgar: SPP00000267_2.0 0 178 . SJYR01002566.1:subseq(259241,200000) 106192 102439 - 884 M 67 201 S 0 2 5 0 2 I 0 1154 3 0 2 S 1 1 M 70 210 S 0 2 5 0 2 I 0 2057 3 0 2 S 1 1 M 39 117
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2019-11-22
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	gene	102440	106192	884	-	.	gene_id 1 ; sequence SPP00000267_2.0 ; gene_orientation +
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	cds	105990	106192	.	-	.	
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	exon	105990	106192	.	-	.	insertions 0 ; deletions 0
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	splice5	105988	105989	.	-	.	intron_id 1 ; splice_site "GT"
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	intron	104832	105989	.	-	.	intron_id 1
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	splice3	104832	104833	.	-	.	intron_id 0 ; splice_site "ag"
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	cds	104619	104831	.	-	.	
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	exon	104619	104831	.	-	.	insertions 0 ; deletions 0
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	splice5	104617	104618	.	-	.	intron_id 2 ; splice_site "GT"
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	intron	102558	104618	.	-	.	intron_id 2
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	splice3	102558	102559	.	-	.	intron_id 1 ; splice_site "AG"
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	cds	102440	102557	.	-	.	
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	exon	102440	102557	.	-	.	insertions 0 ; deletions 0
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	similarity	102440	106192	884	-	.	alignment_id 1 ; Query SPP00000267_2.0 ; Align 106193 1 201 ; Align 104831 69 210 ; Align 102557 140 117
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000267_2.0  Protein  Selenoprotein P (SELENOP)  Cow 
        Target: SJYR01002566.1:subseq(259241,200000) Kobus ellipsiprymnus isolate DFW-375 scaffold2569_size522084, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 711
   Query range: 246 -> 402
  Target range: 100467 -> 99999

    247 : ThrProAspThrProGluAsnProProProSerGlyLeuHisHisHisHisHisArgH :    266
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          ThrProAspThrProGluAsnProProProSerGlyLeuHisHisHisHisHisArgH
 100467 : ACACCAGACACCCCTGAGAATCCCCCTCCTTCAGGtcttcatcaccaccaccataggC : 100410

    267 : isLysGlyProGlnArgGlnGlyHisSerAspAsnCysAspThrProValGlySerGl :    285
          ||||||||! !|||||||||||||||||||||||||||||||||||||||||||||||
          isLysGlyHisGlnArgGlnGlyHisSerAspAsnCysAspThrProValGlySerGl
 100409 : ACAAGGGTCACCAAAGACAGGGTCACTCAGATAACTGTGATACACCAGTAGGAAGTGA : 100353

    286 : uSerLeuGlnProSerLeuProGlnLysLysLeuUnkArgLysArgCysIleAsnGln :    304
          |!:!||||||! !|||||||||||||||||||||   |||||||||||||||||||||
          uAsnLeuGlnLeuSerLeuProGlnLysLysLeu***ArgLysArgCysIleAsnGln
 100352 : AAATTTACAACTTTCTCTTCCACAAAAGAAGCTCTGACGAAAGAGATGCATAAATCAG : 100296

    305 : LeuLeuUnkGlnPheProLysAspSerGluSerAlaLeuSerSerCysCysCysHisC :    324
          ||||||   |||||||||||||||||||||||||||||||||||||||||||||||||
          LeuLeu***GlnPheProLysAspSerGluSerAlaLeuSerSerCysCysCysHisC
 100295 : TTACTCTGACAGTTTCCCAAAGATTCAGAATCTGCTTTGAGTAGCTGCTGTTGCCACT : 100236

    325 : ysArgHisLeuValPheGluLysThrGlySerAlaIleThrUnkGlnCysThrGluLy :    343
          |||||||||||||||||||||||||||||||||||||||||   ||||||||||||!!
          ysArgHisLeuValPheGluLysThrGlySerAlaIleThr***GlnCysThrGluAs
 100235 : GTCGACATCTGGTATTTGAAAAAACAGGGTCTGCAATCACCTGACAGTGTACAGAAAA : 100179

    344 : sLeuProSerLeuCysSerUnkGlnGlyLeuLeuAlaGluGluAsnValIleGluSer :    362
          .||||||||||||||||||   ||||||||||||||||||||||||||||||||||||
          nLeuProSerLeuCysSer***GlnGlyLeuLeuAlaGluGluAsnValIleGluSer
 100178 : CCTCCCCTCTTTATGTAGCTGACAGGGCCTTTTGGCAGAGGAGAACGTCATTGAATCT : 100122

    363 : UnkGlnUnkArgLeuProProAlaAlaUnkGlnAlaAlaGlyGlnGlnLeuAsnProT :    382
             |||   ||||||||||||||||||   ||||||||||||||||||||||||||||
          ***Gln***ArgLeuProProAlaAla***GlnAlaAlaGlyGlnGlnLeuAsnProT
 100121 : TGACAGTGACGTTTGCCTCCAGCTGCCTGACAGGCAGCAGGTCAGCAGCTCAACCCCA : 100062

    383 : hrGluAlaSerThrLysUnkSerUnkLysAsnLysAlaLysMetUnkLysUnkProSe :    401
          ||! !||||||||||||   |||   ||||||||||||||||||   |||   |||||
          hrGlyAlaSerThrLys***Ser***LysAsnLysAlaLysMet***Lys***ProSe
 100061 : CAGGAGCCAGCACCAAATGAAGCTGAAAAAATAAGGCCAAAATGTGAAAATGACCTtc : 100005

    402 : rAsn :    402
          ||||
          rAsn
 100004 : aaat : 100000

vulgar: SPP00000267_2.0 246 402 . SJYR01002566.1:subseq(259241,200000) 100467 99999 - 711 M 156 468
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2019-11-22
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	gene	100000	100467	711	-	.	gene_id 2 ; sequence SPP00000267_2.0 ; gene_orientation .
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	cds	100000	100467	.	-	.	
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	exon	100000	100467	.	-	.	insertions 0 ; deletions 0
SJYR01002566.1:subseq(259241,200000)	exonerate:protein2genome:local	similarity	100000	100467	711	-	.	alignment_id 2 ; Query SPP00000267_2.0 ; Align 100468 247 468
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
