Command line: [exonerate -m p2g --showtargetgff -q 1B.query.dir/MM.SelI.1.fa.x.fa -t 3B.fastasub.dir/1.MM.SelI.1.fa.x.fa]
Hostname: [ws101159]

C4 Alignment:
------------
         Query: SPP00001577_2.0 # Protein # Selenoprotein I (SelI) # Mouse (Mus musculus)
        Target: gi|398925635|gb|JH767723.1|:subseq(46528413,140323) Ceratotherium simum simum unplaced genomic scaffold scaffold00001, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 1867
   Query range: 0 -> 398
  Target range: 90323 -> 49999

     1 : MetAlaGlyTyrGluTyrValSerProGluGlnLeuSerGlyPheAspLysTyrLys  > :    20
         ||||||||||||||||||||||||||||||||||||:!!||||||||||||||||||   
         MetAlaGlyTyrGluTyrValSerProGluGlnLeuAlaGlyPheAspLysTyrLys++ 
 90323 : ATGGCTGGTTACGAATACGTGAGCCCGGAGCAGCTGGCTGGCTTTGATAAGTACAAGgt. : 90264

    21 : >>> Target Intron 1 >>>>  TyrSerAlaLeuAspThrAsnProLeuSerLeuT :    31
                 17693 bp          ||||||||||||||||||||||||||||||||||
                                 ++TyrSerAlaLeuAspThrAsnProLeuSerLeuT
 90263 : ........................agTACAGTGCTCTGGACACCAATCCACTCTCTCTGT : 72540

    32 : yrIleMetHisProPheTrpAsnThrIleValLys  >>>> Target Intron 2 >> :    43
         ||||||||||||||||||||||||||:!!||||||            480 bp       
         yrIleMetHisProPheTrpAsnThrValValLys++                       
 72539 : ATATCATGCATCCATTTTGGAACACCGTAGTAAAGgt....................... : 72502

    44 : >>  ValPheProThrTrpLeuAlaProAsnLeuIleThrPheSerGlyPheMetLeuLe :    61
             ||||||||||||||||||||||||||||||||||||||||||||||||:!!|||:!
           ++ValPheProThrTrpLeuAlaProAsnLeuIleThrPheSerGlyPheLeuLeuVa
 72501 : ..agGTATTTCCTACTTGGCTGGCTCCAAATCTGATCACCTTTTCTGGCTTTCTGCTGGT : 71970

    62 : uValPheAsnPheLeuLeuLeuThrTyrPheAspProAspPheTyrAlaSer{A}  >>> :    79
         !||||||||||||||||||:!!.!!:!!||||||||||||||||||||||||{|}     
         lValPheAsnPheLeuLeuMetAlaHisPheAspProAspPheTyrAlaSer{A}++   
 71969 : TGTATTTAATTTCCTACTTATGGCACACTTTGATCCTGACTTTTATGCTTCA{G}gt... : 71913

    80 : > Target Intron 3 >>>>  {la}ProGlyHisLysHisValProAspTrpValTr :    90
               2222 bp           {||}||||||||||||||||||||||||||||||||
                               ++{la}ProGlyHisLysHisValProAspTrpValTr
 71912 : ......................ag{CA}CCGGGTCACAAGCACGTACCTGATTGGGTTTG : 69661

    91 : pIleValValGlyIleLeuAsnPheAlaAlaTyrThrLeu{A}  >>>> Target Int :   104
         |||||||||||||||||||||||||  !||||||||||||{|}           3837 b
         pIleValValGlyIleLeuAsnPheIleAlaTyrThrLeu{A}++               
 69660 : GATTGTAGTAGGCATCCTCAACTTCATAGCCTACACTCTA{G}gt............... : 69616

   105 : ron 4 >>>>  {sp}GlyValAspGlyLysGlnAlaArgArgThrAsnSerSerThrPr :   119
         p           {||}||||||||||||||||||||||||||||||||||||||||||||
                   ++{sp}GlyValAspGlyLysGlnAlaArgArgThrAsnSerSerThrPr
 69615 : ..........ag{AT}GGTGTGGATGGAAAGCAAGCCCGTAGAACCAATTCCAGCACCCC : 65737

   120 : oLeuGlyGluLeuPheAspHisGlyLeuAspSerTrpSerCysValTyrPheValValTh :   139
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         oLeuGlyGluLeuPheAspHisGlyLeuAspSerTrpSerCysValTyrPheValValTh
 65736 : TTTAGGGGAGCTTTTTGACCATGGCCTGGATAGTTGGTCATGTGTTTACTTTGTTGTCAC : 65677

   140 : rValTyrSerIlePheGlyArgGlyProThrGlyValSerValPheValLeuTyrLeuLe :   159
         ||||||||||||||||||||||||||||:!!|||||||||||||||||||||||||||||
         rValTyrSerIlePheGlyArgGlyProSerGlyValSerValPheValLeuTyrLeuLe
 65676 : TGTGTATTCCATCTTTGGACGAGGACCATCTGGTGTCAGTGTGTTTGTTCTTTATCTCCT : 65617

   160 : uLeuTrpValValLeuPheSerPheIleLeuSerHisTrpGluLysTyrAsnThrGlyVa :   179
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||:!
         uLeuTrpValValLeuPheSerPheIleLeuSerHisTrpGluLysTyrAsnThrGlyIl
 65616 : GCTATGGGTAGTTTTGTTTTCTTTCATCCTGTCTCACTGGGAAAAGTATAACACAGGGAT : 65557

   180 : lLeuPheLeuProTrpGlyTyrAspIleSerGlnVal  >>>> Target Intron 5  :   192
         !||||||||||||||||||||||||||||||||||||            960 bp     
         eLeuPheLeuProTrpGlyTyrAspIleSerGlnVal++                     
 65556 : TCTTTTCCTGCCATGGGGATATGACATTAGCCAGGTGgt..................... : 65516

   193 : >>>>  ThrIleSerPheValTyrIleValThrAlaValValGlyValGluAlaTrpTyr :   209
               ||||||||||||||||||||||||||||||:!!|||||||||||||||||||||
             ++ThrIleSerPheValTyrIleValThrAlaIleValGlyValGluAlaTrpTyr
 65515 : ....agACTATTTCTTTTGTCTACATAGTGACTGCGATTGTGGGAGTTGAGGCCTGGTAT : 64507

   210 : GluProPheLeuPheAsnPheLeuTyrArgAspLeuPheThrAlaMetIleIle{G}  > :   228
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||{|}   
         GluProPheLeuPheAsnPheLeuTyrArgAspLeuPheThrAlaMetIleIle{G}++ 
 64506 : GAACCTTTCCTGTTTAATTTCTTATATAGAGACCTATTCACTGCAATGATTATT{G}gt. : 64447

   229 : >>> Target Intron 6 >>>>  {ly}CysAlaLeuCysValThrLeuProMetSer :   238
                 9091 bp           {||}||||||||||||||||||||||||||||||
                                 ++{ly}CysAlaLeuCysValThrLeuProMetSer
 64446 : ........................ag{GT}TGTGCATTATGTGTGACTCTTCCAATGAGT : 55329

   239 : LeuLeuAsnPhePhe{Ar}  >>>> Target Intron 7 >>>>  {g}SerTyrLys :   247
         |||||||||||||||{||}           1405 bp           {|}|||||||||
         LeuLeuAsnPhePhe{Ar}++                         ++{g}SerTyrLys
 55328 : TTATTAAACTTTTTC{AG}gt.........................ag{A}AGCTATAAA : 53897

   248 : SerAsnThrLeuLysHisLysSerValTyrGluAlaMetValProPhePheSerProCys :   267
         !:!|||||||||||||||!  |||||||||||||||||||||||||||||||||||||||
         AsnAsnThrLeuLysHisThrSerValTyrGluAlaMetValProPhePheSerProCys
 53896 : AATAACACCTTGAAACACACTTCAGTCTATGAAGCTATGGTTCCCTTCTTTTCTCCATGT : 53837

   268 : LeuLeuPheThrLeuCysThrValTrpIleLeuTrpSerProSerAspIleLeuGluIle :   287
         |||||||||! !|||! !|||||||||||||||  !|||||||||! !||||||||||||
         LeuLeuPheIleLeuSerThrValTrpIleLeuGlnSerProSerAlaIleLeuGluIle
 53836 : TTGCTATTCATTTTGTCTACAGTATGGATCCTCCAGTCACCTTCAGCTATTTTAGAGATA : 53777

   288 : HisProArgIlePheTyrPheMetValGlyThrAlaPheAlaAsnIleThr  >>>> Ta :   305
         |||||||||:!!|||||||||||||||||||||||||||||||||||||||         
         HisProArgValPheTyrPheMetValGlyThrAlaPheAlaAsnIleThr++       
 53776 : CATCCTAGAGTATTCTACTTTATGGTTGGAACAGCCTTTGCCAATATCACAgt....... : 53721

   306 : rget Intron 8 >>>>  CysGlnLeuIleValCysGlnMetSerSerThrArgCysP :   318
           1433 bp           ||||||||||||||||||||||||||||||||||||||||
                           ++CysGlnLeuIleValCysGlnMetSerSerThrArgCysP
 53720 : ..................agTGTCAGCTGATTGTTTGTCAAATGAGCAGTACTCGGTGCC : 52251

   319 : roThrLeuAsnTrpLeuLeuLeuProLeuLeuLeuValValAlaAlaValIleValGlyA :   338
         ||||||||||||||||||||:!!||||||!!!|||||||||!.!!.!|||! !:!!|||!
         roThrLeuAsnTrpLeuLeuValProLeuPheLeuValValValValValAsnLeuGlyV
 52250 : CAACTTTGAATTGGCTGCTGGTTCCTCTCTTCTTGGTTGTCGTGGTGGTAAACTTAGGAG : 52191

   339 : laAlaThrSerArgLeuGluSerAlaLeuLeuTyrThrLeuThrAlaAlaPheThrLeuA :   358
         .!|||   |||  !  !|||!!!  !||||||||||||||||||.!!|||||||||||||
         alAla---SerTyrThrGluThrLeuLeuLeuTyrThrLeuThrThrAlaPheThrLeuA
 52190 : TAGCC---TCTTACACTGAGACCCTTCTCCTGTATACATTAACAACTGCTTTCACTCTGG : 52134

   359 : laHisIleHisTyrGlyValGlnVal  >>>> Target Intron 9 >>>>  ValLy :   368
         ||||||||||||||||||||!:!|||           2012 bp           |||||
         laHisIleHisTyrGlyValArgVal++                         ++ValLy
 52133 : CCCACATCCATTATGGAGTCCGAGTGgt.........................agGTAAA : 50092

   369 : sGlnLeuSerArgHisPheGlnIleTyrProPheSerLeuArgLysProAsnSerAspUn :   388
         |||||||||| !!|||||||||||||||||||||||||||||||||||||||||||||  
         sGlnLeuSerGlyHisPheGlnIleTyrProPheSerLeuArgLysProAsnSerAsp**
 50091 : GCAGCTGAGCGGCCATTTTCAGATTTACCCCTTCTCATTGAGGAAACCAAACTCGGATTG : 50032

   389 : kLeuGlyMetGluGluGlnAsnIleGlyLeu :   398
          |||||||||||||||::!!!.|||||||||
         *LeuGlyMetGluGluArgLysIleGlyLeu
 50031 : ACTAGGAATGGAAGAAAGGAAGATTGGCTTG : 50000

vulgar: SPP00001577_2.0 0 398 . gi|398925635|gb|JH767723.1|:subseq(46528413,140323) 90323 49999 - 1867 M 19 57 5 0 2 I 0 17689 3 0 2 M 23 69 5 0 2 I 0 476 3 0 2 M 36 108 S 0 1 5 0 2 I 0 2218 3 0 2 S 1 2 M 24 72 S 0 1 5 0 2 I 0 3833 3 0 2 S 1 2 M 87 261 5 0 2 I 0 956 3 0 2 M 36 108 S 0 1 5 0 2 I 0 9087 3 0 2 S 1 2 M 15 45 S 0 2 5 0 2 I 0 1401 3 0 2 S 1 1 M 60 180 5 0 2 I 0 1429 3 0 2 M 35 105 G 1 0 M 26 78 5 0 2 I 0 2008 3 0 2 M 32 96
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2014-11-28
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	gene	50000	90323	1867	-	.	gene_id 1 ; sequence SPP00001577_2.0 ; gene_orientation +
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	cds	90267	90323	.	-	.	
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	exon	90267	90323	.	-	.	insertions 0 ; deletions 0
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice5	90265	90266	.	-	.	intron_id 1 ; splice_site "GT"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	intron	72574	90266	.	-	.	intron_id 1
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice3	72574	72575	.	-	.	intron_id 0 ; splice_site "AG"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	cds	72505	72573	.	-	.	
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	exon	72505	72573	.	-	.	insertions 0 ; deletions 0
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice5	72503	72504	.	-	.	intron_id 2 ; splice_site "GT"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	intron	72025	72504	.	-	.	intron_id 2
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice3	72025	72026	.	-	.	intron_id 1 ; splice_site "AG"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	cds	71916	72024	.	-	.	
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	exon	71916	72024	.	-	.	insertions 0 ; deletions 0
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice5	71914	71915	.	-	.	intron_id 3 ; splice_site "GT"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	intron	69694	71915	.	-	.	intron_id 3
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice3	69694	69695	.	-	.	intron_id 2 ; splice_site "AG"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	cds	69619	69693	.	-	.	
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	exon	69619	69693	.	-	.	insertions 0 ; deletions 0
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice5	69617	69618	.	-	.	intron_id 4 ; splice_site "GT"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	intron	65782	69618	.	-	.	intron_id 4
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice3	65782	65783	.	-	.	intron_id 3 ; splice_site "AG"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	cds	65519	65781	.	-	.	
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	exon	65519	65781	.	-	.	insertions 0 ; deletions 0
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice5	65517	65518	.	-	.	intron_id 5 ; splice_site "GT"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	intron	64559	65518	.	-	.	intron_id 5
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice3	64559	64560	.	-	.	intron_id 4 ; splice_site "AG"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	cds	64450	64558	.	-	.	
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	exon	64450	64558	.	-	.	insertions 0 ; deletions 0
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice5	64448	64449	.	-	.	intron_id 6 ; splice_site "GT"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	intron	55359	64449	.	-	.	intron_id 6
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice3	55359	55360	.	-	.	intron_id 5 ; splice_site "AG"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	cds	55310	55358	.	-	.	
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	exon	55310	55358	.	-	.	insertions 0 ; deletions 0
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice5	55308	55309	.	-	.	intron_id 7 ; splice_site "GT"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	intron	53905	55309	.	-	.	intron_id 7
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice3	53905	53906	.	-	.	intron_id 6 ; splice_site "AG"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	cds	53724	53904	.	-	.	
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	exon	53724	53904	.	-	.	insertions 0 ; deletions 0
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice5	53722	53723	.	-	.	intron_id 8 ; splice_site "GT"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	intron	52291	53723	.	-	.	intron_id 8
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice3	52291	52292	.	-	.	intron_id 7 ; splice_site "AG"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	cds	52108	52290	.	-	.	
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	exon	52108	52290	.	-	.	insertions 0 ; deletions 1
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice5	52106	52107	.	-	.	intron_id 9 ; splice_site "GT"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	intron	50096	52107	.	-	.	intron_id 9
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	splice3	50096	50097	.	-	.	intron_id 8 ; splice_site "AG"
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	cds	50000	50095	.	-	.	
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	exon	50000	50095	.	-	.	insertions 0 ; deletions 0
gi|398925635|gb|JH767723.1|:subseq(46528413,140323)	exonerate:protein2genome:local	similarity	50000	90323	1867	-	.	alignment_id 1 ; Query SPP00001577_2.0 ; Align 90324 1 57 ; Align 72574 20 69 ; Align 72025 43 108 ; Align 69692 80 72 ; Align 65780 105 261 ; Align 64559 192 108 ; Align 55357 229 45 ; Align 53904 245 180 ; Align 52291 305 105 ; Align 52186 341 78 ; Align 50096 367 96
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
