Command line: [/mnt/NFS_UPF/soft/exonerate/exonerate-2.2.0-x86_64/bin/exonerate -m p2g --showtargetgff -q /home/u137834/Desktop/TR2.fa -t genomic_SJYR01003863.1]
Hostname: [am32944-116076u]

C4 Alignment:
------------
         Query: SPP00000035_1.0  Protein  Thioredoxin reductase 2 (TR2)  Homo sapiens  Complete
        Target: SJYR01003863.1:subseq(0,142278) Kobus ellipsiprymnus isolate DFW-375 scaffold3876_size142061, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 2099
   Query range: 34 -> 524
  Target range: 94531 -> 69685

    35 : AlaGlyGlnArgAspTyrAspLeuLeuValValGlyGlyGlySerGlyGlyLeuAlaCys :    54
         ||||||!:!!:!  !|||||||||||||||:!!|||||||||||||||||||||||||||
         AlaGlyArgGlnCysTyrAspLeuLeuValIleGlyGlyGlySerGlyGlyLeuAlaCys
 94531 : GCAGGCCGGCAGTGCTACGACCTCCTGGTGATCGGAGGCGGATCCGGCGGCCTGGCCTGC : 94474

    55 : AlaLysGlu{A}  >>>> Target Intron 1 >>>>  {la}AlaGlnLeuGlyArg :    63
         |||||||||{|}           3574 bp           {||}||||||||||||!:!
         AlaLysGlu{A}++                         ++{la}AlaGlnLeuGlyLys
 94473 : GCCAAGGAA{G}gt.........................ag{CC}GCCCAGCTGGGGAAG : 90873

    64 : LysValAlaValValAspTyrValGluProSerProGln{G}  >>>> Target Intr :    77
         ||||||||||||:!!|||||||||||||||||||||!:!{|}            120 bp
         LysValAlaValLeuAspTyrValGluProSerProArg{G}++                
 90872 : AAGGTGGCCGTGCTGGACTACGTGGAGCCTTCCCCCCGA{G}gt................ : 90828

    78 : on 2 >>>>  {ly}ThrArgTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIle :    92
                    {||}|||||||||||||||||||||||||||||||||||||||||||||
                  ++{ly}ThrArgTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIle
 90827 : .........ag{gc}acCAGGTGGGGCCTCGGCGGTACCTGCGTGAACGTTGGCTGCATC : 90666

    93 : ProLysLysLeuMetHisGlnAlaAlaLeuLeuGlyGlyLeuIleGlnAspAlaProAsn :   112
         |||||||||||||||||||||||||||||||||||||||:!!|||!::|||||||||:!!
         ProLysLysLeuMetHisGlnAlaAlaLeuLeuGlyGlyMetIleArgAspAlaProHis
 90665 : CCCAAGAAGCTGATGCACCAGGCGGCGCTGCTGGGGGGCATGATCCGCGATGCCCCCCAC : 90606

   113 : TyrGlyTrpGluValAlaGlnProValProHisAsp{Tr}  >>>> Target Intron :   125
         |||||||||...|||||||||   !.!|||||||||{||}            376 bp  
         TyrGlyTrpArgValAlaGln---AlaProHisAsp{Tr}++                  
 90605 : TACGGCTGGCGCGTGGCCCAG---GCCCCGCACGAC{TG}gt.................. : 90566

   126 :  3 >>>>  {p}ArgLysMetAlaGluAlaValGlnAsnHisValLysSerLeuAsnTrp :   141
                  {|}  !! !||||||!!:|||:!!|||||||||||||||||||||||||||
                ++{p}AlaThrMetAlaAspAlaIleGlnAsnHisValLysSerLeuAsnTrp
 90565 : .......ag{G}GCGACGATGGCGGACGCCATTCAGAACCACGTGAAGTCCCTGAACTGG : 90146

   142 : GlyHisArgValGlnLeuGlnAsp{Ar}  >>>> Target Intron 4 >>>>  {g} :   150
         ||||||||||||||||||||||||{||}            633 bp           {|}
         GlyHisArgValGlnLeuGlnAsp{Ar}++                         ++{g}
 90145 : GGCCACCGCGTCCAGCTGCAGGAC{AG}gt.........................ag{G} : 89484

   151 : LysValLysTyrPheAsnIleLysAlaSerPheValAspGluHisThrValCysGlyVal :   170
         ||||||||||||||||||:!!||||||||||||||||||  !||||||||||||||||||
         LysValLysTyrPheAsnValLysAlaSerPheValAspThrHisThrValCysGlyVal
 89483 : AAAGTCAAGTATTTTAACGTCAAGGCCAGCTTTGTCGACACGCACACGGTTTGCGGTGTC : 89426

   171 : AlaLysGlyGlyLysGlu  >>>> Target Intron 5 >>>>  IleLeuLeuSerA :   181
         :!!|||||||||:::|||            398 bp           ! !||||||||||
         SerLysGlyGlyGluGlu++                         ++ThrLeuLeuSerA
 89425 : TCCaaaggtggggaggaggt.........................agACTCTGCTTTCGG : 88995

   182 : laAspHisIleIleIleAlaThrGlyGlyArgProArgTyrProThrHis  >>>> Tar :   198
         ||!!:||||||:!!||||||||||||||||||||||||||||||||||||          
         laGluHisIleValIleAlaThrGlyGlyArgProArgTyrProThrHis++        
 88994 : CCGAGCACATTGTCATTGCCACCGGAGGTCGGCCGCGGTATCCCACGCACgt........ : 88942

   199 : get Intron 6 >>>>  IleGluGlyAlaLeuGluTyrGlyIleThrSerAspAspIl :   211
           856 bp           |||||||||||||||||||||||||||||||||||||||:!
                          ++IleGluGlyAlaLeuGluTyrGlyIleThrSerAspAspLe
 88941 : .................agATCGAAGGCGCTTTGGAGTACGGGATCACGAGCGATGACCT : 88049

   212 : ePheTrpLeuLysGluSerProGlyLys{Th}  >>>> Target Intron 7 >>>>  :   221
         !|||||||||||||||||||||||||||{||}           6282 bp          
         uPheTrpLeuLysGluSerProGlyLys{Th}++                         +
 88048 : CTTCTGGCTGAAGGAATCCCCTGGAAAA{AC}gt.........................a : 81737

   222 :  {r}LeuValValGlyAlaSer{T}  >>>> Target Intron 8 >>>>  {yr}Va :   229
          {|}||||||||||||||||||{|}            594 bp           {||}||
         +{r}LeuValValGlyAlaSer{T}++                         ++{yr}Va
 81736 : g{G}TTGGTGGTTGGGGCCAGC{T}gt.........................ag{AC}GT : 81119

   230 : lAlaLeuGluCysAlaGlyPheLeuThrGlyIleGlyLeuAspThrThrIleMetMetAr :   249
         |||||||||||||||||||.!!|||||||||:!!|||||||||||||||:!!|||!!:||
         lAlaLeuGluCysAlaGlyLeuLeuThrGlyLeuGlyLeuAspThrThrValMetIleAr
 81118 : AGCCCTGGAGTGCGCGGGCCTCCTCACCGGGCTCGGCTTGGACACCACCGTCATGATACG : 81059

   250 : gSerIleProLeuArgGlyPheAspGln  >>>> Target Intron 9 >>>>  Gln :   259
         ||||:!:|||||||||!.!|||||||||           1091 bp           |||
         gSerValProLeuArgAlaPheAspGln++                         ++Gln
 81058 : CAGCGTGCCCCTCCGGGCCTTCGACCAGgt.........................agCAA : 79938

   260 : MetSerSerMetValIleGluHisMetAlaSerHisGlyThrArgPheLeuArgGlyCys :   279
         |||:!!  !:!!|||! !||||||||||||.!!|||||||||||| !!||||||||||||
         MetAlaLeuLeuValThrGluHisMetAlaGlyHisGlyThrArgValLeuArgGlyCys
 79937 : ATGGCCCTGCTGGTCACCGAGCACATGGCTGGCCACGGCACCCGGGTCCTGCGGGGCTGC : 79878

   280 : AlaProSerArgValArgArgLeuProAspGlyGlnLeuGlnValThrTrpGluAspSer :   299
         ||||||..!!:!|||..!!:!||||||! !  !||||||!::|||||||||! !|||  !
         AlaProGluLysValGluLysLeuProGlyGlnGlnLeuArgValThrTrpValAspLeu
 79877 : GCCCCCGAGAAGGTGGAGAAGCTCCCAGGCCAGCAGCTCCGCGTCACCTGGGTGGACCTC : 79818

   300 : ThrThrGlyLysGluAspThrGlyThrPheAspThrValLeuTrpAlaIle{G}  >>>> :   317
         .!!:!!! !::!:!!||||||||||||||||||||||||||||||||||||{|}      
         AlaSerAspArgLysAspThrGlyThrPheAspThrValLeuTrpAlaIle{G}++    
 79817 : GCCTCGGACCGAAAGGACACAGGCACCTTTGACACCGTGCTCTGGGCCATA{G}gt.... : 79761

   318 :  Target Intron 10 >>>>  {ly}ArgValProAspThrArgSerLeuAsnLeuGl :   328
               6006 bp           {||}|||||||||!!:|||   ||||||||||||||
                               ++{ly}ArgValProGluThrAlaSerLeuAsnLeuGl
 79760 : ......................ag{GC}CGAGTTCCAGAAACCGCgagtctgaatttgga : 73725

   329 : uLysAlaGlyValAspThrSerProAspThrGlnLysIleLeuValAspSerArgGluAl :   348
         |||||||||||||  !|||!:!|||! !|||  !|||||||||||||||:!!!:!|||||
         uLysAlaGlyValArgThrAsnProValThrGlyLysIleLeuValAspAlaGlnGluAl
 73724 : aaaggCTGGTGTGCGTACGAACCCTGTCACTGGGAAGATCCTCGTTGATGCCCAGGAAGC : 73665

   349 : aThrSerValProHisIleTyrAlaIleGlyAspValValGlu  >>>> Target Int :   363
         |||||||:!!|||||||||||||||||||||||||||!.!|||            1054 
         aThrSerIleProHisIleTyrAlaIleGlyAspValAlaGlu++               
 73664 : CACCTCCATCCCCCACATCTACGCCATCGGCGATGTTGCAGAGgt............... : 73618

   364 : ron 11 >>>>  GlyArgProGluLeuThrProIleAlaIleMetAlaGlyArgLeuLe :   378
         bp           |||||||||||||||||||||! !|||||||||||||||||||||||
                    ++GlyArgProGluLeuThrProThrAlaIleMetAlaGlyArgLeuLe
 73617 : ...........agGGGCGGCCGGAGCTGACACCCACAGCCATCATGGCCGGGCGGCTCCT : 72521

   379 : uValGlnArgLeuPheGlyGlySerSerAspLeuMetAspTyrAspAsn  >>>> Targ :   395
         |!.!|||||||||  !||| !!!!!||||||||||||||||||..!!:!           
         uAlaGlnArgLeuSerGlyArgThrSerAspLeuMetAspTyrSerSer++         
 72520 : GGCCCAGCGGCTGAGTGGCAGGACCTCAGACCTGATGGACTACAGCAGCgt......... : 72468

   396 : et Intron 12 >>>>  ValProThrThrValPheThrProLeuGluTyrGlyCysVa :   408
          474 bp            |||||||||||||||||||||||||||||||||||||||||
                          ++ValProThrThrValPheThrProLeuGluTyrGlyCysVa
 72467 : .................agGTCCCCACGACCGTCTTCACCCCGCTGGAGTACGGCTGCGT : 71957

   409 : lGlyLeuSerGluGluGluAlaValAlaArgHisGlyGlnGluHisValGlu  >>>> T :   426
         ||||||||||||||||! !||||||||||||||||||:!!||||||||||||        
         lGlyLeuSerGluGluAlaAlaValAlaArgHisGlyGluGluHisValGlu++      
 71956 : GGGGCTGTCAGAGGAGGCGGCCGTGGCTCGCCATGGAGAAGAGCACGTGGAGgt...... : 71901

   427 : arget Intron 13 >>>>  ValTyrHisAlaHisTyrLysProLeuGluPheThrVa :   438
             1211 bp           ||||||||||||  !|||||||||||||||||||||||
                             ++ValTyrHisAlaPheTyrLysProLeuGluPheThrVa
 71900 : ....................agGTTTACCACGCGTTCTACAAACCGCTGGAGTTCACTGT : 70656

   439 : lAlaGlyArgAspAlaSerGlnCysTyrValLys  >>>> Target Intron 14 >> :   450
         | !!  !|||||||||||||||||||||||||||             70 bp        
         lProGlnArgAspAlaSerGlnCysTyrValLys++                        
 70655 : CCCCCAGCGGGATGCCTCTCAGTGCTACGTGAAGgt........................ : 70618

   451 : >>  MetValCysLeuArgGluProProGlnLeuValLeuGlyLeuHisPheLeuGlyPr :   468
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
           ++MetValCysLeuArgGluProProGlnLeuValLeuGlyLeuHisPheLeuGlyPr
 70617 : ..agATGGTGTGTCTGCGGGAGCCCCCGCAGCTGGTGCTGGGCCTGCACTTCCTCGGCCC : 70496

   469 : oAsnAlaGlyGluValThrGlnGlyPheAlaLeuGlyIle{Ly}  >>>> Target In :   482
         ||||||||||||||||||||||||||||||||||||||||{||}            640 
         oAsnAlaGlyGluValThrGlnGlyPheAlaLeuGlyIle{Ly}++              
 70495 : CAACGCAGGCGAAGTTACTCAGGGATTTGCCCTGGGGATC{AA}gt.............. : 70450

   483 : tron 15 >>>>  {s}CysGlyAlaSerTyrAlaGlnValMetArgThrValGlyIleH :   497
         bp            {|}||||||||||||!:!  !|||||||||||||||||||||||||
                     ++{s}CysGlyAlaSerPheGlnGlnValMetArgThrValGlyIleH
 70449 : ............ag{G}TGTGGGGCCTCCTTCCAGCAGGTGATGCGCACAGTGGGCATCC : 69769

   498 : isProThrCysSerGluGluValValLysLeuArgIleSerLysArgSerGlyLeuAspP :   517
         |||||||||||:!!|||||||||!.!||||||||||||||||||||||||||||||||||
         isProThrCysAlaGluGluValAlaLysLeuArgIleSerLysArgSerGlyLeuAspP
 69768 : ACCCCACCTGTGCGGAGGAGGTGGCCAAGCTCCGCATCTCCAAGCGCTCCGGCCTGGACC : 69709

   518 : roThrValThrGlyCysUnkGly :   524
         |||||||||||||||||   |||
         roThrValThrGlyCys***Gly
 69708 : CCACGGTGACCGGCTGCTGAGGC : 69686

vulgar: SPP00000035_1.0 34 524 . SJYR01003863.1:subseq(0,142278) 94531 69685 - 2099 M 23 69 S 0 1 5 0 2 I 0 3570 3 0 2 S 1 2 M 18 54 S 0 1 5 0 2 I 0 116 3 0 2 S 1 2 M 42 126 G 1 0 M 4 12 S 0 2 5 0 2 I 0 372 3 0 2 S 1 1 M 24 72 S 0 2 5 0 2 I 0 629 3 0 2 S 1 1 M 26 78 5 0 2 I 0 394 3 0 2 M 21 63 5 0 2 I 0 852 3 0 2 M 23 69 S 0 2 5 0 2 I 0 6278 3 0 2 S 1 1 M 6 18 S 0 1 5 0 2 I 0 590 3 0 2 S 1 2 M 30 90 5 0 2 I 0 1087 3 0 2 M 58 174 S 0 1 5 0 2 I 0 6002 3 0 2 S 1 2 M 45 135 5 0 2 I 0 1050 3 0 2 M 32 96 5 0 2 I 0 470 3 0 2 M 31 93 5 0 2 I 0 1207 3 0 2 M 24 72 5 0 2 I 0 66 3 0 2 M 32 96 S 0 2 5 0 2 I 0 636 3 0 2 S 1 1 M 42 126
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2019-11-20
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	gene	69686	94531	2099	-	.	gene_id 1 ; sequence SPP00000035_1.0 ; gene_orientation +
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	94462	94531	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	94462	94531	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice5	94460	94461	.	-	.	intron_id 1 ; splice_site "GT"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	intron	90888	94461	.	-	.	intron_id 1
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice3	90888	90889	.	-	.	intron_id 0 ; splice_site "AG"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	90831	90887	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	90831	90887	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice5	90829	90830	.	-	.	intron_id 2 ; splice_site "GT"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	intron	90711	90830	.	-	.	intron_id 2
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice3	90711	90712	.	-	.	intron_id 1 ; splice_site "ag"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	90569	90710	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	90569	90710	.	-	.	insertions 0 ; deletions 1
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice5	90567	90568	.	-	.	intron_id 3 ; splice_site "GT"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	intron	90193	90568	.	-	.	intron_id 3
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice3	90193	90194	.	-	.	intron_id 2 ; splice_site "AG"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	90118	90192	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	90118	90192	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice5	90116	90117	.	-	.	intron_id 4 ; splice_site "GT"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	intron	89485	90117	.	-	.	intron_id 4
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice3	89485	89486	.	-	.	intron_id 3 ; splice_site "ag"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	89406	89484	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	89406	89484	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice5	89404	89405	.	-	.	intron_id 5 ; splice_site "gt"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	intron	89008	89405	.	-	.	intron_id 5
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice3	89008	89009	.	-	.	intron_id 4 ; splice_site "AG"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	88945	89007	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	88945	89007	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice5	88943	88944	.	-	.	intron_id 6 ; splice_site "GT"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	intron	88089	88944	.	-	.	intron_id 6
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice3	88089	88090	.	-	.	intron_id 5 ; splice_site "AG"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	88018	88088	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	88018	88088	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice5	88016	88017	.	-	.	intron_id 7 ; splice_site "GT"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	intron	81736	88017	.	-	.	intron_id 7
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice3	81736	81737	.	-	.	intron_id 6 ; splice_site "AG"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	81716	81735	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	81716	81735	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice5	81714	81715	.	-	.	intron_id 8 ; splice_site "GT"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	intron	81122	81715	.	-	.	intron_id 8
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice3	81122	81123	.	-	.	intron_id 7 ; splice_site "AG"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	81030	81121	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	81030	81121	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice5	81028	81029	.	-	.	intron_id 9 ; splice_site "GT"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	intron	79939	81029	.	-	.	intron_id 9
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice3	79939	79940	.	-	.	intron_id 8 ; splice_site "AG"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	79764	79938	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	79764	79938	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice5	79762	79763	.	-	.	intron_id 10 ; splice_site "GT"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	intron	73758	79763	.	-	.	intron_id 10
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice3	73758	73759	.	-	.	intron_id 9 ; splice_site "AG"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	73621	73757	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	73621	73757	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice5	73619	73620	.	-	.	intron_id 11 ; splice_site "GT"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	intron	72567	73620	.	-	.	intron_id 11
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice3	72567	72568	.	-	.	intron_id 10 ; splice_site "AG"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	72471	72566	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	72471	72566	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice5	72469	72470	.	-	.	intron_id 12 ; splice_site "GT"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	intron	71997	72470	.	-	.	intron_id 12
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice3	71997	71998	.	-	.	intron_id 11 ; splice_site "AG"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	71904	71996	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	71904	71996	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice5	71902	71903	.	-	.	intron_id 13 ; splice_site "GT"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	intron	70693	71903	.	-	.	intron_id 13
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice3	70693	70694	.	-	.	intron_id 12 ; splice_site "AG"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	70621	70692	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	70621	70692	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice5	70619	70620	.	-	.	intron_id 14 ; splice_site "GT"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	intron	70551	70620	.	-	.	intron_id 14
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice3	70551	70552	.	-	.	intron_id 13 ; splice_site "AG"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	70453	70550	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	70453	70550	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice5	70451	70452	.	-	.	intron_id 15 ; splice_site "GT"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	intron	69813	70452	.	-	.	intron_id 15
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice3	69813	69814	.	-	.	intron_id 14 ; splice_site "AG"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	69686	69812	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	69686	69812	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	similarity	69686	94531	2099	-	.	alignment_id 1 ; Query SPP00000035_1.0 ; Align 94532 35 69 ; Align 90886 59 54 ; Align 90709 78 126 ; Align 90583 121 12 ; Align 90192 126 72 ; Align 89484 151 78 ; Align 89008 177 63 ; Align 88089 198 69 ; Align 81735 222 18 ; Align 81120 229 90 ; Align 79939 259 174 ; Align 73756 318 135 ; Align 72567 363 96 ; Align 71997 395 93 ; Align 70693 426 72 ; Align 70551 450 96 ; Align 69812 483 126
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000035_1.0  Protein  Thioredoxin reductase 2 (TR2)  Homo sapiens  Complete
        Target: SJYR01003863.1:subseq(0,142278) Kobus ellipsiprymnus isolate DFW-375 scaffold3876_size142061, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 230
   Query range: 149 -> 198
  Target range: 98412 -> 97867

   150 : ArgLysValLysTyrPheAsnIleLysAlaSerPheValAspGluHisThrValCysGly :   169
         |||||||||||||||||||||:!!||||||||||||||||||  !|||||||||||||||
         ArgLysValLysTyrPheAsnValLysAlaSerPheValAspThrHisThrValCysGly
 98412 : agGAAAGTCAAGTATTTTAACGTCAAGGCCAGCTTTGTCGACACGCACACGGTTTGCGGT : 98355

   170 : ValAlaLysGlyGlyLysGlu  >>>> Target Intron 1 >>>>  IleLeuLeuS :   180
         |||:!!|||||||||:::|||            398 bp           ! !|||||||
         ValSerLysGlyGlyGluGlu++                         ++ThrLeuLeuS
 98354 : GTCTCCaaaggtggggaggaggt.........................agACTCTGCTTT : 97924

   181 : erAlaAspHisIleIleIleAlaThrGlyGlyArgProArgTyrProThrHisIle :   198
         |||||!!:||||||:!!||||||||||||||||||||||||||||||||||||:!:
         erAlaGluHisIleValIleAlaThrGlyGlyArgProArgTyrProThrHisVal
 97923 : CGGCCGAGCACATTGTCATTGCCACCGGAGGTCGGCCGCGGTATCCCACGCACGTG : 97868

vulgar: SPP00000035_1.0 149 198 . SJYR01003863.1:subseq(0,142278) 98412 97867 - 230 M 27 81 5 0 2 I 0 394 3 0 2 M 22 66
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2019-11-20
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	gene	97868	98412	230	-	.	gene_id 2 ; sequence SPP00000035_1.0 ; gene_orientation +
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	98332	98412	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	98332	98412	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice5	98330	98331	.	-	.	intron_id 1 ; splice_site "gt"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	intron	97934	98331	.	-	.	intron_id 1
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	splice3	97934	97935	.	-	.	intron_id 0 ; splice_site "AG"
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	97868	97933	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	97868	97933	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	similarity	97868	98412	230	-	.	alignment_id 2 ; Query SPP00000035_1.0 ; Align 98413 150 81 ; Align 97934 177 66
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000035_1.0  Protein  Thioredoxin reductase 2 (TR2)  Homo sapiens  Complete
        Target: SJYR01003863.1:subseq(0,142278) Kobus ellipsiprymnus isolate DFW-375 scaffold3876_size142061, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 106
   Query range: 34 -> 59
  Target range: 96299 -> 96224

    35 : AlaGlyGlnArgAspTyrAspLeuLeuValValGlyGlyGlySerGlyGlyLeuAlaCys :    54
         ||||||!:!!:!  !|||||||||||||||:!!|||||||||||||||||||||||||||
         AlaGlyArgGlnCysTyrAspLeuLeuValIleGlyGlyGlySerGlyGlyLeuAlaCys
 96299 : GCAGGCCGGCAGTGCTACGACCTCCTGGTGATCGGAGGCGGATCCGGCGGCCTGGCCTGC : 96242

    55 : AlaLysGluAlaAla :    59
         |||||||||!.!|||
         AlaLysGluGlyAla
 96241 : GCCAAGGAAGGTGCG : 96225

vulgar: SPP00000035_1.0 34 59 . SJYR01003863.1:subseq(0,142278) 96299 96224 - 106 M 25 75
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2019-11-20
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	gene	96225	96299	106	-	.	gene_id 3 ; sequence SPP00000035_1.0 ; gene_orientation .
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	cds	96225	96299	.	-	.	
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	exon	96225	96299	.	-	.	insertions 0 ; deletions 0
SJYR01003863.1:subseq(0,142278)	exonerate:protein2genome:local	similarity	96225	96299	106	-	.	alignment_id 3 ; Query SPP00000035_1.0 ; Align 96300 35 75
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
