Command line: [exonerate -m p2g --showtargetgff -q /homes/users/U63741/seqaahsx/selP.hs.fa -t selp..hs.subseq.fa]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000020_1.0 # Protein # Selenoprotein P (SelP) # Homo sapiens # Complete
        Target: GL192850.1:subseq(509759,22653) dna:scaffold scaffold:ailMel1:GL192850.1:1:1293473:1 REF:[revcomp]
         Model: protein2genome:local
     Raw score: 1371
   Query range: 0 -> 380
  Target range: 10000 -> 2503

     1 : MetTrpArgSerLeuGlyLeuAlaLeuAlaLeuCysLeuLeuProSerGlyGlyThrGlu :    20
         |||||||||||||||||||||||||||||||||||||||||||||!!!||||||||||||
         MetTrpArgSerLeuGlyLeuAlaLeuAlaLeuCysLeuLeuProTrpGlyGlyThrGlu
 10000 : ATGTGGAGAAGCTTGGGGCTTGCCCTGGCTCTCTGTCTCCTCCCCTGGGGAGGAACAGAG :  9943

    21 : SerGlnAspGlnSerSerLeuCysLysGlnProProAlaTrpSerIleArgAspGlnAsp :    40
         ||||||!  |||||||||!!!||||||||||||||||||||||||||||||||||||..!
         SerGlnGlyGlnSerSerPheCysLysGlnProProAlaTrpSerIleArgAspGlnSer
  9942 : AGCCAGGGACAAAGCTCCTTCTGCAAGCAACCTCCAGCCTGGAGCATAAGGGATCAAAGT :  9883

    41 : ProMetLeuAsnSerAsnGlySerValThrValValAlaLeuLeuGlnAlaSerUnkTyr :    60
         |||||||||||||||..!||||||||||||||||||||||||||||||||||||   |||
         ProMetLeuAsnSerGlyGlySerValThrValValAlaLeuLeuGlnAlaSer***Tyr
  9882 : CCAATGCTGAACTCGGGTGGGTCCGTGACCGTGGTCGCTCTTCTTCAAGCCAGCTGATAC :  9823

    61 : LeuCysIleLeuGlnAlaSer{Ly}  >>>> Target Intron 1 >>>>  {s}Leu :    69
         |||||||||||||||||||||{!:}            870 bp           {!}|||
         LeuCysIleLeuGlnAlaSer{Ar}++                         ++{g}Leu
  9822 : CTGTGCATTCTGCAGGCATCC{AG}gt.........................ag{A}TTG :  8926

    70 : GluAspLeuArgValLysLeuLysLysGluGlyTyrSerAsnIleSerTyrIleValVal :    89
         |||||||||||||||||||||:!!||||||||||||! !||||||||||||:!:||||||
         GluAspLeuArgValLysLeuGluLysGluGlyTyrLeuAsnIleSerTyrValValVal
  8925 : GAAGACCTGCGAGTAAAACTGGAGAAAGAAGGATACTTGAACATCTCTTATGTGGTTGTT :  8866

    90 : AsnHisGlnGlyIleSerSerArgLeuLysTyrThrHisLeuLysAsnLysValSerGlu :   109
         ||||||||||||:!! !!|||!:!|||||||||! !||||||||||||||||||||||||
         AsnHisGlnGlyLeuProSerGlnLeuLysTyrMetHisLeuLysAsnLysValSerGlu
  8865 : AATCATCAAGGACTTCCTTCTCAATTAAAATATATGCATCTTAAAAATAAGGTTTCAGAG :  8806

   110 : HisIleProValTyrGlnGlnGluGluAsnGlnThrAspValTrpThrLeuLeuAsnGly :   129
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         HisIleProValTyrGlnGlnGluGluAsnGlnThrAspValTrpThrLeuLeuAsnGly
  8805 : CATATTCCTGTTTATCAACAAGAAGAAAACCAAACAGATGTCTGGACGCTCTTAAATGGG :  8746

   130 : SerLysAspAspPheLeuIleTyrAsp{Ar}  >>>> Target Intron 2 >>>>   :   139
         !.!|||||||||||||||:!:||||||{||}           1253 bp           
         LysLysAspAspPheLeuValTyrAsp{Ar}++                         ++
  8745 : AAAAAGGATGACTTCCTCGTGTATGAC{AG}gt.........................ag :  7463

   140 : {g}CysGlyArgLeuValTyrHisLeuGlyLeuProPheSerPheLeuThrPheProTyr :   158
         {|}|||||||||||||||:!!|||||||||||||||!:!|||||||||||||||||||||
         {g}CysGlyArgLeuValHisHisLeuGlyLeuProTyrSerPheLeuThrPheProTyr
  7462 : {A}TGTGGCCGTCTCGTGCATCACCTTGGTTTGCCTTACTCCTTCCTAACTTTCCCGTAT :  7406

   159 : ValGluGluAlaIleLysIleAlaTyrCysGluLysLysCysGlyAsnCysSerLeuThr :   178
         |||||||||||||||||||||||||||||||||:!!|||||||||||||||||||||! !
         ValGluGluAlaIleLysIleAlaTyrCysGluGluLysCysGlyAsnCysSerLeuMet
  7405 : GTCGAAGAAGCCATTAAGATTGCTTACTGTGAAGAGAAATGTGGAAACTGCTCTCTCATG :  7346

   179 :   >>>> Target Intron 3 >>>>  ThrLeuLysAspGluAspPheCysLysArgV :   189
                    4207 bp           |||! !:!!! !|||||||||||||||! !|
         ++                         ++ThrGlnGluAlaGluAspPheCysLysMetV
  7345 : gt.........................agACCCAGGAAGCTGAAGACTTCTGTAAAATGG :  3106

   190 : alSerLeuAlaThrValAspLysThrValGluThrProSerPro<-><-><-><-><->H :   204
         |||||! !|||||||||!  !  |||..!|||.!!||| !!|||               |
         alSerSerAlaThrValGlyThrThrThrGluAlaProProProHisHisHisHisHisH
  3105 : TATCTTCGGCTACTGTGGGAACCACAACAGAGGCTCCCCCGCCACATCACCACCACCACC :  3046

   205 : isTyrHis<->HisGluHisHisHisAsnHisGlyHisGlnHisLeuGlySerSerGluL :   223
         ||:!!|||   |||..!|||||||||!!.|||||||||! !|||! !|||!:!..!||||
         isHisHisHisHisArgHisHisHisLysHisGlyHisProHisHisGlyAsnAspGluL
  3045 : ACCACCACCACCACCGGCACCATCACAAACACGGGCATCCGCATCATGGGAACGATGAGC :  2986

   224 : euSerGluAsnGlnGlnProGlyAlaProAsnAlaProThrHisProAlaProProGlyL :   243
         ||||||||:!!|||||||||! !|||  !.!.|||! !  !||||||||||||! !||||
         euSerGluAspGlnGlnProGluAlaGluGlnAlaArgGluHisProAlaProArgGlyL
  2985 : TTTCAGAGGATCAGCAACCAGAAGCAGAACAGGCTCGGGAGCATCCCGCTCCTCGAGGCC :  2926

   244 : euHisHisHisHisLysHisLysGlyGlnHisArgGlnGlyHisProGluAsnArgAspM :   263
         |||||!.!|||||||||! !|||..!!!.!!.||||||||||||||||||||| !!||||
         euHisArgHisHisLysLeuLysAsnHisGlnArgGlnGlyHisProGluAsn***AspM
  2925 : TTCATCGCCACCATAAGCTCAAGAACCACCAAAGACAGGGCCACCCTGAGAACTGAGATA :  2866

   264 : etProAla<->SerGluAspLeuGln<-><->AspLeuGlnLysLysLeuCysArgLysA :   280
         ||||||||   ||||||:!!||||||      ! !! !||||||:!!|||!! |||||| 
         etProAlaGlySerGluAsnLeuGlnLeuProValProGlnLysGlnLeu***ArgLysG
  2865 : TGCCAGCCGGAAGTGAAAATTTACAACTTCCGGTCCCACAAAAGCAGCTCTGACGAAAGG :  2806

   281 : rgCysIleAsnGlnLeuLeuCysLysLeuProThrAspSerGluLeuAlaProArgSerU :   300
         !!|||||||||!:!||||||||||||||||||! !! !|||! !|||||||||!!!||| 
         lyCysIleAsnArgLeuLeuCysLysLeuProLysValSerGlyLeuAlaProSerSer*
  2805 : GCTGTATAAATCGGTTACTCTGCAAATTGCCTAAAGTTTCAGGGTTGGCCCCTAGCAGCT :  2746

   301 : nkCysCysHisCysArgHisLeuIlePheGluLysThrGlySerAlaIleThrUnkGlnC :   320
           |||!! |||||||||||||||||||||||||||||||||||||||||||||   ||||
         **Cys***HisCysArgHisLeuIlePheGluLysThrGlySerAlaIleThr***GlnC
  2745 : GATGCTGACACTGTCGACATCTGATATTTGAAAAAACAGGGTCTGCAATCACCTGACAAT :  2686

   321 : ysLysGluAsnLeuProSerLeuCysSerUnkGlnGlyLeuArgAlaGluGluAsnIleT :   340
         ||||||||!.!||||||||||||||||||   |||||||||! !||||||||||||:!!!
         ysLysGluThrLeuProSerLeuCysSer***GlnGlyLeuLeuAlaGluGluAsnValI
  2685 : GTAAAGAAACCCTCCCCTCTTTATGCAGCTGACAGGGACTTCTGGCAGAGGAGAACGTCA :  2626

   341 : hrGluSerCysGlnUnkArgLeuProProAlaAlaUnkGlnIleSerGlnGlnLeuIleP :   360
          !||||||!! |||   ||||||||||||||||||   |||  !||||||||||||   |
         leGluSer***Gln***ArgLeuProProAlaAla***GlnAlaSerGlnGlnLeuGlnP
  2625 : TTGAATCCTGACAGTGACGTTTGCCTCCAGCTGCCTGACAAGCAAGTCAGCAGCTTCAGC :  2566

   361 : roThrGluAlaSerAlaSerUnkArgUnkLysAsnGlnAlaLysLysUnkGluUnkProS :   380
         ||||||||||||||.!!!:!   !!!   ||||||:!!||||||! !   :!!   ||||
         roThrGluAlaSerThrAsn***Ser***LysAsnLysAlaLysMet***Lys***ProS
  2565 : CCACGGAAGCCAGCACCAATTGAAGCTGAAAAAATAAGGCCAAAATGTGAAAATGACCTT :  2506

   381 : er :   380
         ||
         er
  2505 : CA :  2504

vulgar: SPP00000020_1.0 0 380 . GL192850.1:subseq(509759,22653) 10000 2503 - 1371 M 67 201 S 0 2 5 0 2 I 0 866 3 0 2 S 1 1 M 70 210 S 0 2 5 0 2 I 0 1249 3 0 2 S 1 1 M 39 117 5 0 2 I 0 4203 3 0 2 M 25 75 G 0 15 M 3 9 G 0 3 M 59 177 G 0 3 M 5 15 G 0 6 M 110 330
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2012-12-03
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	gene	2504	10000	1371	-	.	gene_id 1 ; sequence SPP00000020_1.0 ; gene_orientation +
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	cds	9798	10000	.	-	.	
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	exon	9798	10000	.	-	.	insertions 0 ; deletions 0
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	splice5	9796	9797	.	-	.	intron_id 1 ; splice_site "GT"
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	intron	8928	9797	.	-	.	intron_id 1
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	splice3	8928	8929	.	-	.	intron_id 0 ; splice_site "AG"
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	cds	8715	8927	.	-	.	
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	exon	8715	8927	.	-	.	insertions 0 ; deletions 0
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	splice5	8713	8714	.	-	.	intron_id 2 ; splice_site "GT"
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	intron	7462	8714	.	-	.	intron_id 2
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	splice3	7462	7463	.	-	.	intron_id 1 ; splice_site "AG"
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	cds	7344	7461	.	-	.	
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	exon	7344	7461	.	-	.	insertions 0 ; deletions 0
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	splice5	7342	7343	.	-	.	intron_id 3 ; splice_site "GT"
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	intron	3137	7343	.	-	.	intron_id 3
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	splice3	3137	3138	.	-	.	intron_id 2 ; splice_site "AG"
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	cds	2504	3136	.	-	.	
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	exon	2504	3136	.	-	.	insertions 27 ; deletions 0
GL192850.1:subseq(509759,22653)	exonerate:protein2genome:local	similarity	2504	10000	1371	-	.	alignment_id 1 ; Query SPP00000020_1.0 ; Align 10001 1 201 ; Align 8927 69 210 ; Align 7461 140 117 ; Align 3137 179 75 ; Align 3047 204 9 ; Align 3035 207 177 ; Align 2855 266 15 ; Align 2834 271 330
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
