Command line: [exonerate -m p2g --showtargetgff -q 1B.query.dir/E.SelP.1.fa.x.fa -t 3B.fastasub.dir/1.E.SelP.1.fa.x.fa]
Hostname: [ws116063]

C4 Alignment:
------------
         Query: SPP00000876_2.0 # Protein # Selenoprotein P (SelP) # Horse (Equus caballus)
        Target: gi|398924304|gb|JH767731.1|:subseq(22294808,105799) Ceratotherium simum simum unplaced genomic scaffold scaffold00009, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 1703
   Query range: 0 -> 385
  Target range: 55799 -> 49999

     1 : MetTrpArgSerLeuGlyLeuAlaLeuAlaLeuCysLeuLeuProTrpGlyGlyThrGlu :    20
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         MetTrpArgSerLeuGlyLeuAlaLeuAlaLeuCysLeuLeuProTrpGlyGlyThrGlu
 55799 : ATGTGGAGAAGCCTGGGGCTTGCCCTGGCTCTCTGTCTCCTTCCATGGGGAGGAACAGAG : 55742

    21 : SerGlnGlyGlnSerSerPheCysLysGlnProProAlaTrpSerIleArgAspGlnAsp :    40
         |||||||||:!!|||||||||||||||:!!||||||||||||!:!|||||||||||||||
         SerGlnGlyGluSerSerPheCysLysLysProProAlaTrpAsnIleArgAspGlnAsp
 55741 : AGCCAGGGGGAAAGCTCCTTTTGTAAGAAACCTCCAGCCTGGAACATAAGGGATCAAGAT : 55682

    41 : ProMetLeuAsnSerTyrGlySerValThrValValAlaLeuLeuGlnAlaSerUnkTyr :    60
         |||||||||||||||||||||||||||! !||||||||||||||||||||||||   |||
         ProMetLeuAsnSerTyrGlySerValIleValValAlaLeuLeuGlnAlaSer***Tyr
 55681 : CCAATGCTGAACTCCTATGGTTCAGTGATTGTGGTTGCTCTTCTTCAAGCCAGCTGATAC : 55622

    61 : LeuCysLeuLeuGlnAlaSer{Ar}  >>>> Target Intron 1 >>>>  {g}Leu :    69
         ||||||:!!||||||||||||{||}            783 bp           {|}|||
         LeuCysIleLeuGlnAlaSer{Ar}++                         ++{g}Leu
 55621 : CTGTGCATTCTGCAGGCATCT{AG}gt.........................ag{A}TTG : 54812

    70 : GluAspLeuArgValLysLeuGluLysGluGlyTyrSerAsnIleSerTyrValValVal :    89
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         GluAspLeuArgValLysLeuGluLysGluGlyTyrSerAsnIleSerTyrValValVal
 54811 : GAAGACCTGAGAGTAAAACTGGAGAAAGAAGGATATTCTAACATCTCCTATGTTGTTGTT : 54752

    90 : AsnHisGlnGluIleSerAlaArgLeuLysTyrIleHisLeuLysAsnLysValSerGlu :   109
         |||||||||! !||||||:!!!:!||||||||||||||||||||||||||||||||||||
         AsnHisGlnGlyIleSerSerGlnLeuLysTyrIleHisLeuLysAsnLysValSerGlu
 54751 : AATCATCAAGGAATCTCTTCTCAATTAAAATACATACATCTTAAAAATAAGGTTTCAGAG : 54692

   110 : TyrIleAlaValTyrGlnGlnGluGluAsnGlnThrAspIleTrpThrLeuLeuAsnGly :   129
         |||||| !!||||||||||||||||||||||||||||||:!!||||||||||||||||||
         TyrIleProValTyrGlnGlnGluGluAsnGlnThrAspValTrpThrLeuLeuAsnGly
 54691 : TATATTCCTGTTTATCAACAAGAAGAAAACCAAACAGATGTCTGGACTCTCTTAAATGGA : 54632

   130 : SerLysAspAspPheLeuIleTyrAsp{Ar}  >>>> Target Intron 2 >>>>   :   139
         ..!|||||||||||||||:!!||||||{||}           1284 bp           
         AspLysAspAspPheLeuValTyrAsp{Ar}++                         ++
 54631 : GACAAAGATGACTTCCTCGTATATGAC{AG}gt.........................ag : 53318

   140 : {g}CysGlyArgLeuValTyrHisLeuGlyLeuProTyrSerPheLeuThrPheProTyr :   158
         {|}|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         {g}CysGlyArgLeuValTyrHisLeuGlyLeuProTyrSerPheLeuThrPheProTyr
 53317 : {A}TGTGGCCGTCTTGTATATCATCTTGGTTTGCCTTACTCCTTCCTAACTTTCCCATAT : 53261

   159 : ValGluGluAlaIleLysIleAlaTyrCysGluLysLysCysGlyAsnCysSerLeuMet :   178
         ||||||||||||||||||! !||||||||||||||||||||||||!!.|||||||||! !
         ValGluGluAlaIleLysSerAlaTyrCysGluLysLysCysGlyLysCysSerLeuThr
 53260 : GTAGAAGAAGCCATTAAGAGTGCTTACTGTGAAAAGAAATGTGGAAAGTGCTCTCTCACG : 53201

   179 :   >>>> Target Intron 3 >>>>  ThrLeuGluAspGluAspPheCysLysThrL :   189
                    2581 bp           ||||||||||||||||||||||||||||||:
         ++                         ++ThrLeuGluAspGluAspPheCysLysThrI
 53200 : gt.........................agACACTGGAAGATGAAGACTTCTGTAAAACTA : 50587

   190 : euSerLeuAlaThrValGluLysThrThrGluAspSerGlnProHisHisHisHisHisH :   209
         !!:!!||||||||||||!!:! !|||||||||||||||||||||||||||||||||!!.|
         leAlaLeuAlaThrValAspThrThrThrGluAspSerGlnProHisHisHisHisGlnH
 50586 : TAGCTTTGGCTACTGTGGATACAACAACTGAGGATTCGCAGCCACATCACCATCACCAGC : 50527

   210 : isGlnHisHisHisLysHisGlyHisGlnHisValGlyAsnSerGlnLeuSerGluAsnG :   229
         ||   |||||||||||||||||||||||||||||||||||||||||||||||||||||||
         is---HisHisHisLysHisGlyHisGlnHisValGlyAsnSerGlnLeuSerGluAsnG
 50526 : AT---CATCATCACAAGCATGGGCACCAGCATGTTGGGAACAGTCAGCTTTCAGAGAATC : 50470

   230 : lnGlnProGluAlaThrGlyAlaProGluHisProProProProGlyLeuHisHisHisH :   249
         |||||||||||||| !!! !|||||||||||||||||||||! !||||||||||||||||
         lnGlnProGluAlaProAspAlaProGluHisProProProLeuGlyLeuHisHisHisH
 50469 : AGCAACCAGAAGCACCAGATGCTCCTGAGCATCCCCCTCCTCTAGGCCTTCATCACCACC : 50410

   250 : isLysHisLysGlyGlnGlnArgArgGlyHisProGluAsnUnkAspMetProGlyGlyG :   269
         |||||||||||||||||||||||!:!! !||||||||||||   |||||||||||| !!|
         isLysHisLysGlyGlnGlnArgGlnAspHisProGluAsn***AspMetProGlyArgG
 50409 : ATAAGCACAAGGGCCAACAAAGACAGGATCACCCAGAGAACTGAGACATGCCAGGAAGGG : 50350

   270 : luSerLeuGlnLeuSerLeuProGlnLysLysLeuUnkGlnLysGlyCysIleAsnGlnL :   289
         ||||||||||||||||||||||||||!!.||||||   !:!||| !!|||||||||||||
         luSerLeuGlnLeuSerLeuProGlnAsnLysLeu***ArgLysArgCysIleAsnGlnL
 50349 : AAAGTTTACAACTTTCTCTTCCACAAAATAAGCTCTGACGAAAGAGGTGTATAAATCAGT : 50290

   290 : euLeuCysLysMetProLysAspSerLysLeuAlaProSerSerUnkCysUnkHisCysA :   309
         |||||||||||:!!||||||||||||:!!|||||||||||||||   |||   |||||||
         euLeuCysLysLeuProLysAspSerGluLeuAlaProSerSer***Cys***HisCysA
 50289 : TACTCTGCAAGTTGCCCAAAGATTCAGAATTGGCCCCTAGTAGCTGATGCTGACATTGTC : 50230

   310 : rgHisLeuIlePheGluAsnThrArgSerAlaIleThrUnkGlnCysThrGluAsnLeuP :   329
         |||||||||||||||||!!.||| !!||||||||||||   ||||||! !||||||||||
         rgHisLeuIlePheGluLysThrGlySerAlaIleThr***GlnCysLysGluAsnLeuP
 50229 : GACATCTGATATTTGAAAAAACAGGGTCTGCAATCACCTGACAGTGTAAAGAAAACCTCC : 50170

   330 : roSerLeuCysSerUnkGlnGlyLeuTrpAlaGluGluAsnValIleGluSerCysGlnU :   349
         ||||||||||||||   ||||||! !|||||||||||||||||||||||||||!! ||| 
         roSerLeuCysSer***GlnGlyArgTrpAlaGluGluAsnValIleGluSer***Gln*
 50169 : CCTCTTTATGTAGCTGACAGGGACGTTGGGCAGAGGAGAATGTCATTGAATCTTGACAGT : 50110

   350 : nkArgLeuProProAlaAlaUnkGlnProSerGlnGlnLeuLysProThrGluAlaSerT :   369
           ||||||||||||||||||   |||||||||||||||||||||||||||||||||||||
         **ArgLeuProProAlaAla***GlnProSerGlnGlnLeuLysProThrGluAlaSerT
 50109 : GACGTTTGCCTCCAGCTGCCTGACAGCCAAGTCAGCAGCTCAAACCCACAGAAGCCAGCA : 50050

   370 : hrAsnUnkSerUnkLysTyrLysAlaAlaMetUnkLysUnkProSerAsn :   385
         |||||    !!   ||| !!||||||! !|||   |||   |||||||||
         hrAsn***Arg***LysAsnLysAlaGluMet***Lys***ProSerAsn
 50049 : CCAATTGACGCTGAAAAAATAAGGCAGAAATGTGAAAATGACCTTCAAAC : 50000

vulgar: SPP00000876_2.0 0 385 . gi|398924304|gb|JH767731.1|:subseq(22294808,105799) 55799 49999 - 1703 M 67 201 S 0 2 5 0 2 I 0 779 3 0 2 S 1 1 M 70 210 S 0 2 5 0 2 I 0 1280 3 0 2 S 1 1 M 39 117 5 0 2 I 0 2577 3 0 2 M 31 93 G 1 0 M 175 525
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2014-11-25
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	gene	50000	55799	1703	-	.	gene_id 1 ; sequence SPP00000876_2.0 ; gene_orientation +
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	cds	55597	55799	.	-	.	
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	exon	55597	55799	.	-	.	insertions 0 ; deletions 0
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	splice5	55595	55596	.	-	.	intron_id 1 ; splice_site "GT"
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	intron	54814	55596	.	-	.	intron_id 1
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	splice3	54814	54815	.	-	.	intron_id 0 ; splice_site "AG"
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	cds	54601	54813	.	-	.	
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	exon	54601	54813	.	-	.	insertions 0 ; deletions 0
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	splice5	54599	54600	.	-	.	intron_id 2 ; splice_site "GT"
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	intron	53317	54600	.	-	.	intron_id 2
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	splice3	53317	53318	.	-	.	intron_id 1 ; splice_site "AG"
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	cds	53199	53316	.	-	.	
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	exon	53199	53316	.	-	.	insertions 0 ; deletions 0
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	splice5	53197	53198	.	-	.	intron_id 3 ; splice_site "GT"
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	intron	50618	53198	.	-	.	intron_id 3
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	splice3	50618	50619	.	-	.	intron_id 2 ; splice_site "AG"
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	cds	50000	50617	.	-	.	
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	exon	50000	50617	.	-	.	insertions 0 ; deletions 1
gi|398924304|gb|JH767731.1|:subseq(22294808,105799)	exonerate:protein2genome:local	similarity	50000	55799	1703	-	.	alignment_id 1 ; Query SPP00000876_2.0 ; Align 55800 1 201 ; Align 54813 69 210 ; Align 53316 140 117 ; Align 50618 179 93 ; Align 50525 211 525
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
