Command line: [exonerate -m p2g --showtargetgff -q msraseq.fa -t genomicmsra.fa]
Hostname: [ws101061]

C4 Alignment:
------------
         Query: SPP00001613_2.0 # Protein # Methionine sulfoxide reductase A (MsrA) # Microbat (Myotis lucifugus)
        Target: gi|411115890|gb|JH977673.1|:subseq(7046454,490578) Eptesicus fuscus unplaced genomic scaffold scaffold00063, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 1205
   Query range: 0 -> 233
  Target range: 49999 -> 440578

      1 : MetLeuSerAlaThrArgArgAlaArgGlnLeuPheHisSerLeuIleProValProG :     20
          |||:!!||||||||||||||||||||||||||||||||||||||||||||||||||| 
          MetIleSerAlaThrArgArgAlaArgGlnLeuPheHisSerLeuIleProValProA
  50000 : ATGATCTCGGCCACCAGGCGGGCTCGCCAACTCTTCCACAGCCTGATTCCTGTTCCGA :  50057

     21 : lyMetGlyAspSerAlaSerLysMetIleSerProGlnGluAlaLeuProGlyArgLy :     39
          !!||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          rgMetGlyAspSerAlaSerLysMetIleSerProGlnGluAlaLeuProGlyArgLy
  50058 : GAATGGGCGACTCCGCTTCTAAGATGATCAGCCCCCAGGAGGCCTTGCCGGGCCGGAA :  50114

     40 : sAspProIleAlaValAla{A}  >>>> Target Intron 1 >>>>  {la}Lys :     47
          |||||||||||||||||||{|}          157435 bp          {||}|||
          sAspProIleAlaValAla{A}++                         ++{la}Lys
  50115 : GGACCCGATCGCTGTGGCG{G}gt.........................ag{CC}AAA : 207573

     48 : HisHisValAsnGlyAsnArgThrValGluProPheProGluGlyThrGlnMetAlaV :     67
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          HisHisValAsnGlyAsnArgThrValGluProPheProGluGlyThrGlnMetAlaV
 207574 : CATCATGTCAATGGCAACAGAACAGTTGAACCTTTCCCAGAGGGAACACAGATGGCTG : 207633

     68 : alPhe{G}  >>>> Target Intron 2 >>>>  {ly}MetGlyCysPheTrpGl :     75
          |||||{|}           39878 bp          {||}|||||||||||||||||
          alPhe{G}++                         ++{ly}MetGlyCysPheTrpGl
 207634 : TATTT{G}gt.........................ag{GA}ATGGGCTGTTTCTGGGG : 247535

     76 : yAlaGluArgLysPheTrpThrLeuLysGlyValTyrSerThrGlnValGlyTyrAla :     94
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          yAlaGluArgLysPheTrpThrLeuLysGlyValTyrSerThrGlnValGlyTyrAla
 247536 : AGCGGAGAGGAAATTTTGGACCCTGAAAGGAGTATATTCAACTCAAGTTGGCTATGCA : 247592

     95 : GlyGlyTyrThrSerAsnProThrTyrGlnGluValCysSer{G}  >>>> Target :    109
          ||||||||||||||||||||||||||||||||||||||||||{|}           75
          GlyGlyTyrThrSerAsnProThrTyrGlnGluValCysSer{G}++           
 247593 : GGAGGCTACACTTCCAATCCGACTTACCAAGAAGTCTGCTCA{G}gt........... : 247640

    110 :  Intron 3 >>>>  {ly}LysThrGlyHisAlaGluValValArgValValTyrGl :    122
          284 bp          {||}||||||||||||||||||||||||||||||||||||||
                        ++{ly}LysThrGlyHisAlaGluValValArgValValTyrGl
 247641 : ..............ag{GA}AAAACTGGGCATGCCGAAGTAGTCCGGGTGGTGTACCA : 322960

    123 : nProGluHisIleSerPheGluGluLeuLeuLysValPheTrpGluAsnHisAspPro :    141
          |||||||!.!||||||||||||||||||||||||||||||||||||||||||||||||
          nProGluArgIleSerPheGluGluLeuLeuLysValPheTrpGluAsnHisAspPro
 322961 : GCCAGAGCGCATCAGCTTTGAGGAGCTGCTCAAGGTCTTCTGGGAGAATCATGACCCG : 323017

    142 : ThrGln{G}  >>>> Target Intron 4 >>>>  {ly}MetArgGlnGlyAsnA :    150
          ||||||{|}           31545 bp          {||}||||||||||||||||
          ThrGln{G}++                         ++{ly}MetArgGlnGlyAsnA
 323018 : ACCCAA{G}gt.........................ag{GC}ATGCGCCAAGGCAATG : 354589

    151 : spHisGlySerGlnTyrArgSerAlaIleTyrProThrLeuAlaSerHisMetGluVa :    169
          ||||||||||||||||||||||||||||||||||||||! !|||!!!|||||||||!.
          spHisGlySerGlnTyrArgSerAlaIleTyrProThrSerAlaThrHisMetGluAl
 354590 : ACCATGGCTCTCAGTACCGGTCAGCCATCTATCCGACCTCTGCTACGCACATGGAGGC : 354646

    170 : lAlaLeuArgSerLysGluAspTyrGlnLys  >>>> Target Intron 5 >>>> :    180
          !||||||||||||||||||||||||||||||           85738 bp        
          aAlaLeuArgSerLysGluAspTyrGlnLys++                         
 354647 : GGCCCTGCGATCCAAAGAGGACTACCAGAAGgt......................... : 354681

    181 :   ValLeuSerGluAsnGlyTyrGlyProIleThrThrAspIleArgGluGlyGlnTh :    198
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          ++ValLeuSerGluAsnGlyTyrGlyProIleThrThrAspIleArgGluGlyGlnTh
 354682 : agGTCCTGTCAGAGAATGGCTACGGCCCGATCACAACCGACATCCGGGAGGGACAAAC : 440471

    199 : rPheTyrTyrAlaGluAspTyrHisGlnGlnTyrLeuSerLysAsnProAspGlyTyr :    217
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          rPheTyrTyrAlaGluAspTyrHisGlnGlnTyrLeuSerLysAsnProAspGlyTyr
 440472 : ATTCTACTACGCCGAGGACTACCACCAGCAGTACCTGAGCAAGAACCCTGACGGCTAC : 440528

    218 : CysGlyLeuGlyGlyThrGlyValSerCysProLeuGlyIleLysLys :    233
          ||||||||||||||||||||||||||||||||||||||||||||||||
          CysGlyLeuGlyGlyThrGlyValSerCysProLeuGlyIleLysLys
 440529 : TGCGGCCTGGGGGGCACCGGGGTGTCCTGCCCTCTGGGCATTAAAAAG : 440578

vulgar: SPP00001613_2.0 0 233 . gi|411115890|gb|JH977673.1|:subseq(7046454,490578) 49999 440578 + 1205 M 45 135 S 0 1 5 0 2 I 0 157431 3 0 2 S 1 2 M 22 66 S 0 1 5 0 2 I 0 39874 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 75280 3 0 2 S 1 2 M 34 102 S 0 1 5 0 2 I 0 31541 3 0 2 S 1 2 M 35 105 5 0 2 I 0 85734 3 0 2 M 54 162
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-05
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	gene	50000	440578	1205	+	.	gene_id 1 ; sequence SPP00001613_2.0 ; gene_orientation +
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	cds	50000	50135	.	+	.	
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	exon	50000	50135	.	+	.	insertions 0 ; deletions 0
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	splice5	50136	50137	.	+	.	intron_id 1 ; splice_site "GT"
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	intron	50136	207570	.	+	.	intron_id 1
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	splice3	207569	207570	.	+	.	intron_id 0 ; splice_site "AG"
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	cds	207571	207639	.	+	.	
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	exon	207571	207639	.	+	.	insertions 0 ; deletions 0
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	splice5	207640	207641	.	+	.	intron_id 2 ; splice_site "GT"
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	intron	207640	247517	.	+	.	intron_id 2
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	splice3	247516	247517	.	+	.	intron_id 1 ; splice_site "AG"
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	cds	247518	247637	.	+	.	
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	exon	247518	247637	.	+	.	insertions 0 ; deletions 0
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	splice5	247638	247639	.	+	.	intron_id 3 ; splice_site "GT"
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	intron	247638	322921	.	+	.	intron_id 3
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	splice3	322920	322921	.	+	.	intron_id 2 ; splice_site "AG"
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	cds	322922	323026	.	+	.	
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	exon	322922	323026	.	+	.	insertions 0 ; deletions 0
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	splice5	323027	323028	.	+	.	intron_id 4 ; splice_site "GT"
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	intron	323027	354571	.	+	.	intron_id 4
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	splice3	354570	354571	.	+	.	intron_id 3 ; splice_site "AG"
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	cds	354572	354678	.	+	.	
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	exon	354572	354678	.	+	.	insertions 0 ; deletions 0
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	splice5	354679	354680	.	+	.	intron_id 5 ; splice_site "GT"
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	intron	354679	440416	.	+	.	intron_id 5
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	splice3	440415	440416	.	+	.	intron_id 4 ; splice_site "AG"
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	cds	440417	440578	.	+	.	
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	exon	440417	440578	.	+	.	insertions 0 ; deletions 0
gi|411115890|gb|JH977673.1|:subseq(7046454,490578)	exonerate:protein2genome:local	similarity	50000	440578	1205	+	.	alignment_id 1 ; Query SPP00001613_2.0 ; Align 50000 1 135 ; Align 207573 47 66 ; Align 247520 70 117 ; Align 322924 110 102 ; Align 354574 145 105 ; Align 440417 180 162
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
