Command line: [exonerate -m p2g --showtargetgff -q 1B.query.dir/MM.SelU1.1.fa.x.fa -t 3B.fastasub.dir/1.MM.SelU1.1.fa.x.fa]
Hostname: [ws101145]

C4 Alignment:
------------
         Query: SPP00001587_2.0 # Protein # Selenoprotein U1 (SelU1) # Mouse (Mus musculus)
        Target: gi|398922712|gb|JH767764.1|:subseq(20398377,110088) Ceratotherium simum simum unplaced genomic scaffold scaffold00042, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 1027
   Query range: 0 -> 226
  Target range: 60088 -> 49999

     1 : MetSerPheLeuGlnAspProSerPhePheSerMetGlyMetTrpSerIleGlyValGly :    20
         ||||||||||||||||||||||||||||||!!!:!!||||||||||||:!!|||!.!|||
         MetSerPheLeuGlnAspProSerPhePheThrValGlyMetTrpSerValGlyAlaGly
 60088 : ATGTCTTTCCTGCAGGATCCAAGTTTCTTCACCGTGGGGATGTGGTCCGTTGGCGCGGGG : 60031

    21 : AlaValGlyAlaAlaAlaValAlaLeuLeuLeuAlaAsnThrAspMetPheLeuSerLys :    40
         |||:!!||||||||||||:!!||||||||||||||||||||||||:!!|||||| !!:!!
         AlaLeuGlyAlaAlaAlaLeuAlaLeuLeuLeuAlaAsnThrAspValPheLeuProGlu
 60030 : GCTCTGGGGGCTGCTGCCTTGGCTCTGCTCCTGGCCAACACAGACGTGTTCCTGCCTGAG : 59971

    41 : ProArgLysAlaAlaLeuGluTyrLeuGluAspIleAspLeuLysThrLeuGluLys{G} :    60
          !!!:!:!!||||||||||||||||||||||||:!!|||||||||||||||||||||{|}
         SerGlnGluAlaAlaLeuGluTyrLeuGluAspValAspLeuLysThrLeuGluLys{G}
 59970 : TCCCAGGAAGCAGCGCTGGAGTATCTGGAGGATGTAGACCTGAAGACACTGGAGAAG{G} : 59911

    61 :   >>>> Target Intron 1 >>>>  {lu}ProArgThrPheLysAlaLysGluLeu :    69
                    2076 bp           {||}|||||||||||||||||||||||||||
         ++                         ++{lu}ProArgThrPheLysAlaLysGluLeu
 59910 : gt.........................ag{AA}CCAAGGACTTTCAAAGCAAAGGAGCTC : 57808

    70 : TrpGluLysAsnGlyAlaValIleMetAlaValArgArgProGlyCysPheLeuCysArg :    89
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         TrpGluLysAsnGlyAlaValIleMetAlaValArgArgProGlyCysPheLeuCysArg
 57807 : TGGGAAAAAAATGGAGCTGTGATTATGGCTGTGCGGAGGCCAGGCTGTTTCCTCTGTCGA : 57748

    90 : Ala  >>>> Target Intron 2 >>>>  GluAlaAlaAspLeuMetSerLeuLysP :   100
         ! !           3187 bp           |||||||||! !|||   ||||||||||
         Glu++                         ++GluAlaAlaGlyLeuSerSerLeuLysP
 57747 : GAGgt.........................agGAGGCTGCGGGCCTGTCCTCCCTGAAGC : 54528

   101 : roLysLeuAspGluLeuGlyValProLeuTyrAlaValValLysGluGlnValLysArgG :   120
         ||||||||||||||||||||||||||||||||||||||||||||||||||:!!  !! !|
         roLysLeuAspGluLeuGlyValProLeuTyrAlaValValLysGluGlnIleGlyThrG
 54527 : CCAAGCTGGACGAGTTGGGTGTCCCCCTCTATGCAGTAGTGAAGGAGCAGATCGGGACTG : 54468

   121 : luValGluAspPheGlnProTyrPheLysGlyGluIlePheLeuAspGluLys  >>>>  :   138
         |||||:!!|||||||||||||||||||||||||||||||||||||||||||||       
         luValLysAspPheGlnProTyrPheLysGlyGluIlePheLeuAspGluLys++     
 54467 : AAGTGAAGGACTTCCAGCCTTATTTCAAAGGAGAAATCTTCCTGGATGAGAAGgt..... : 54412

   139 : Target Intron 3 >>>>  LysLysPheTyrGlyProGluArgArgLysMetMetPh :   150
              948 bp           ||||||||||||||||||:!!|||||||||||||||||
                             ++LysLysPheTyrGlyProGlnArgArgLysMetMetPh
 54411 : ....................agAAAAAATTCTACGGTCCCCAGAGGCGGAAGATGATGTT : 53430

   151 : eMetGlyLeuIleArgLeuGlyValTrpTyrAsnSerPheArgAlaTrpAsnGlyGlyPh :   170
         |||||||!!!:!!|||||||||||||||||||||! !|||||||||||||||||||||||
         eMetGlyPheValArgLeuGlyValTrpTyrAsnPhePheArgAlaTrpAsnGlyGlyPh
 53429 : TATGGGATTTGTCCGCCTGGGTGTCTGGTACAACTTCTTCCGGGCCTGGAACGGAGGCTT : 53370

   171 : eSerGlyAsnLeuGluGlyGluGlyPheIleLeuGlyGlyValPheValIleGlySerGl :   190
         |||||||||||||||||||||||||||||||||||||||||||||||||:!:||||||||
         eSerGlyAsnLeuGluGlyGluGlyPheIleLeuGlyGlyValPheValValGlySerGl
 53369 : CTCTGGAAACCTGGAAGGCGAAGGCTTCATCCTTGGGGGAGTTTTTGTGGTGGGGTCAGG : 53310

   191 : yLysGln  >>>> Target Intron 4 >>>>  GlyIleLeuLeuGluHisArgGlu :   200
         |||||||           3200 bp           ||||||||||||||||||||||||
         yLysGln++                         ++GlyIleLeuLeuGluHisArgGlu
 53309 : AAAGCAGgt.........................agGGCATTCTTCTTGAGCACCGAGAA : 50080

   201 : LysGluPheGlyAspArgValAsnProLeuSerValLeuGluAlaValLysLysIleLys :   220
         |||||||||||||||!:!|||||||||:!!|||||||||||||||!.!  !|||||||||
         LysGluPheGlyAspLysValAsnProValSerValLeuGluAlaAlaGlyLysIleLys
 50079 : AAAGAATTTGGAGACAAAGTAAACCCAGTTTCTGTTCTGGAAGCTGCTGGAAAGATCAAG : 50020

   221 : LeuGlnThrProAlaSer :   226
         ! !|||||| !!||||||
         ProGlnThrSerAlaSer
 50019 : CCACAGACTTCGGCCTCA : 50000

vulgar: SPP00001587_2.0 0 226 . gi|398922712|gb|JH767764.1|:subseq(20398377,110088) 60088 49999 - 1027 M 59 177 S 0 1 5 0 2 I 0 2072 3 0 2 S 1 2 M 30 90 5 0 2 I 0 3183 3 0 2 M 47 141 5 0 2 I 0 944 3 0 2 M 55 165 5 0 2 I 0 3196 3 0 2 M 34 102
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2014-11-26
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	gene	50000	60088	1027	-	.	gene_id 1 ; sequence SPP00001587_2.0 ; gene_orientation +
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	cds	59911	60088	.	-	.	
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	exon	59911	60088	.	-	.	insertions 0 ; deletions 0
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	splice5	59909	59910	.	-	.	intron_id 1 ; splice_site "GT"
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	intron	57835	59910	.	-	.	intron_id 1
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	splice3	57835	57836	.	-	.	intron_id 0 ; splice_site "AG"
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	cds	57743	57834	.	-	.	
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	exon	57743	57834	.	-	.	insertions 0 ; deletions 0
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	splice5	57741	57742	.	-	.	intron_id 2 ; splice_site "GT"
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	intron	54556	57742	.	-	.	intron_id 2
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	splice3	54556	54557	.	-	.	intron_id 1 ; splice_site "AG"
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	cds	54415	54555	.	-	.	
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	exon	54415	54555	.	-	.	insertions 0 ; deletions 0
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	splice5	54413	54414	.	-	.	intron_id 3 ; splice_site "GT"
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	intron	53467	54414	.	-	.	intron_id 3
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	splice3	53467	53468	.	-	.	intron_id 2 ; splice_site "AG"
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	cds	53302	53466	.	-	.	
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	exon	53302	53466	.	-	.	insertions 0 ; deletions 0
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	splice5	53300	53301	.	-	.	intron_id 4 ; splice_site "GT"
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	intron	50102	53301	.	-	.	intron_id 4
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	splice3	50102	50103	.	-	.	intron_id 3 ; splice_site "AG"
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	cds	50000	50101	.	-	.	
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	exon	50000	50101	.	-	.	insertions 0 ; deletions 0
gi|398922712|gb|JH767764.1|:subseq(20398377,110088)	exonerate:protein2genome:local	similarity	50000	60088	1027	-	.	alignment_id 1 ; Query SPP00001587_2.0 ; Align 60089 1 177 ; Align 57833 61 90 ; Align 54556 91 141 ; Align 53467 138 165 ; Align 50102 193 102
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
