Command line: [exonerate -m p2g --showtargetgff --exhaustive yes -q proteina.fa -t SecS.1.subseq.fa]
Hostname: [ws101071]

C4 Alignment:
------------
         Query: SecS
        Target: KI537300.1:subseq(2790427,200284) Balaenoptera acutorostrata scammoni unplaced genomic scaffold scaffold124, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 2263
   Query range: 0 -> 485
  Target range: 133183 -> 99999

      1 : MetAsnArgGluSerPheAlaAlaGlyGluArgLeuValSerProAlaTyrValArgG :     20
          |||||||||||||||||||||||||||||||||||||||||||||||||||:!! !!|
          MetAsnArgGluSerPheAlaAlaGlyGluArgLeuValSerProAlaTyrMetTrpG
 133183 : ATGAACCGCGAGAGCTTCGCGGCGGGCGAGCGGCTGGTGTCGCCGGCTTACATGTGGC : 133126

     21 : lnGlyCysGluAlaArgArgSerHisGluHisLeuIleArgLeuLeuLeuGluLys   :     39
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||  
          lnGlyCysGluAlaArgArgSerHisGluHisLeuIleArgLeuLeuLeuGluLys++
 133125 : AGGGCTGTGAGGCCCGCCGCTCGCACGAGCACCTCATACGGCTGCTTCTGGAGAAGgt : 133069

     40 : >>>> Target Intron 1 >>>>  GlyLysCysProGluAspGlyTrpAspGluS :     49
                    828 bp           |||||||||||||||||||||||||||||||
                                   ++GlyLysCysProGluAspGlyTrpAspGluS
 133068 : .........................agggCAAGTGTCCAGAGGATGGTTGGGATGAAA : 132211

     50 : erThrLeuGluLeuPheLeuHisGluLeuAlaIleMetAspSerAsnAsnPheLeuGl :     68
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          erThrLeuGluLeuPheLeuHisGluLeuAlaIleMetAspSerAsnAsnPheLeuGl
 132210 : GTACACTTGAACTCTTTTTACATGAACTTGCAATTATGGATAGCAACAATTTCCTGGG : 132154

     69 : yAsnCysGlyValGlyGluArgGluGlyArgValAlaSerAlaLeuValAlaArgArg :     87
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          yAsnCysGlyValGlyGluArgGluGlyArgValAlaSerAlaLeuValAlaArgArg
 132153 : CAATTGTGGtgtgggagaaagggaagggagagtggCATCTGCATTAGTTGCTCGGCGA : 132097

     88 : HisTyr{Ar}  >>>> Target Intron 2 >>>>  {g}PhePheGlnThrLysG :     96
          ||||||{||}           1539 bp           {|}||||||||||||||||
          HisTyr{Ar}++                         ++{g}PhePheGlnThrLysG
 132096 : CATTAC{ag}gt.........................ag{A}TTCTTCCAGACCAAGC : 130531

     97 : lnValThrLysAlaSerProAspSerGlyArgGluGluLeuAspProIleSerTrpCy :    115
          |||||||||||||||||! !! !|||||||||||||||||||||||||||||||||||
          lnValThrLysAlaSerLeuAlaSerGlyArgGluGluLeuAspProIleSerTrpCy
 130530 : AAGTCACTAAGGCCAGCCTAGCTTCAGGTAGAGAGGAATTAGACCCCATCTCTTGGTG : 130474

    116 : sGly{S}  >>>> Target Intron 3 >>>>  {er}ValHisThrValThrAsn :    123
          ||||{|}            706 bp           {||}||||||||||||||||||
          sGly{S}++                         ++{er}ValHisThrValThrAsn
 130473 : TGGC{A}gt.........................ag{GT}GTCCATACGGTGACCAAC : 129744

    124 : CysPheValValProMetAlaThrGlyMetSerLeuThrLeuCysPheLeuThrLeuA :    143
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          CysPheValValProMetAlaThrGlyMetSerLeuThrLeuCysPheLeuThrLeuA
 129743 : TGCTTTGTAGTTCCGATGGCAACTGGTATGAGTCTAACCCTGTGTTTCTTAACATTAC : 129684

    144 : rgHisLysArgProLysAlaLysTyrIleIleTrpProArgIleAspGlnLysSerCy :    162
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          rgHisLysArgProLysAlaLysTyrIleIleTrpProArgIleAspGlnLysSerCy
 129683 : GACACAAAAGACCAAAAGCAAAGTACATTATATGGCCACGAATAGACCAGAAGTCCTG : 129627

    163 : sPheLysSerMetIleThrAla{G}  >>>> Target Intron 4 >>>>  {ly} :    170
          ||||||||||||||||||||||{|}           2293 bp           {||}
          sPheLysSerMetIleThrAla{G}++                         ++{ly}
 129626 : CTTTAAATCCATGATCACTGCA{G}gt.........................ag{GT} : 127309

    171 : PheGluProValValIleGluAsnValLeuGluGlyAspGluLeuArgThrAspLeuL :    190
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          PheGluProValValIleGluAsnValLeuGluGlyAspGluLeuArgThrAspLeuL
 127308 : TTTGAGCCTGTGGTGATAGAGAACGTTTTAGAAGGTGACGAACTACGCACAGACCTGA : 127250

    191 : ysAlaValGluAlaLysValHisGluLeuGlyProAspTyrValLeuCysValHisSe :    209
          ||||||||||||||||||||!!.|||||||||||||||||||||||||||||||||||
          ysAlaValGluAlaLysValGlnGluLeuGlyProAspTyrValLeuCysValHisSe
 127249 : AAGCAGTGGAGGCTAAAGTCCAGGAACTTGGGCCTGATTACGTTCTTTGTGTTCATTC : 127193

    210 : rThrThrSerCysPheAlaProArgValProAsp{Ar}  >>>> Target Intron :    221
          ||||||||||||||||||||||||||||||||||{||}           3886 bp  
          rThrThrSerCysPheAlaProArgValProAsp{Ar}++                  
 127192 : TACTACATCCTGTTTTGCTCCAAGGGTGCCTGAT{AG}gt.................. : 127153

    222 :  5 >>>>  {g}LeuGluGluLeuAlaValIleCysAlaAsnTyrAspIleProHisI :    237
                   {|}|||||||||||||||||||||||||||||||||! !||||||||||
                 ++{g}LeuGluGluLeuAlaValIleCysAlaAsnTyrGlyIleProHisI
 127152 : .......ag{A}TTAGAAGAACTGGCTGTGATTTGTGCTAATTATGGCATTCCACATA : 123223

    238 : leValAsnAsnAlaTyrGlyValGlnSerSerLysCysMetHisLeuIleGlnGln   :    256
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||  
          leValAsnAsnAlaTyrGlyValGlnSerSerLysCysMetHisLeuIleGlnGln++
 123222 : TAGTTAACAATGCTTATGGAGTGCAGTCTTCAAAGTGCATGCACCTCATTCAGCAGgt : 123166

    257 : >>>> Target Intron 6 >>>>  GlyAlaArgValGlyArgIleAspAlaPheV :    266
                   6278 bp           |||||||||||||||||||||||||||||||
                                   ++GlyAlaArgValGlyArgIleAspAlaPheV
 123165 : .........................agGGGGCTCGGGTTGGTAGAATAGACGCTTTCG : 116858

    267 : alGlnSerLeuAspLysAsnPheMetValProValGlyGlyAlaIleIleAlaGlyPh :    285
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          alGlnSerLeuAspLysAsnPheMetValProValGlyGlyAlaIleIleAlaGlyPh
 116857 : TTCAGAGCTTGGACAAAAATTTTATGGTTCCAGTAGGTGGCGCTATAATTGCTGGCTT : 116801

    286 : eAsnAspSerPheIleGlnGluIleSerLysMetTyrPro{G}  >>>> Target I :    299
          ||||||||||||||||||||||||||||||||||||||||{|}            133
          eAsnAspSerPheIleGlnGluIleSerLysMetTyrPro{G}++             
 116800 : TAATGATTCCTTCATTCAGGAAATCAGCAAGATGTATCCA{G}gt............. : 116756

    300 : ntron 7 >>>>  {ly}ArgAlaSerAlaSerProSerLeuAspValLeuIleThrL :    313
           bp           {||}||||||||||||||||||!!!|||||||||||||||||||
                      ++{ly}ArgAlaSerAlaSerProThrLeuAspValLeuIleThrL
 116755 : ............ag{GA}AGAGCTTCAGCTTCACCTACTTTAGATGTCCTTATTACTT : 116584

    314 : euLeuSerLeuGlySerAsnGlyTyrLysLysLeuLeuLysGluArgLys  >>>> T :    330
          ||||||||||||||||||||||||||||||||||||||||||||||||||        
          euLeuSerLeuGlySerAsnGlyTyrLysLysLeuLeuLysGluArgLys++      
 116583 : TATTATCACTTGGATCGAATGGCTACAAGAagctattaaaagaaagaaaggt...... : 116531

    331 : arget Intron 8 >>>>  GluMetPheSerTyrLeuSerAsnGluLeuLysLysL :    342
             12863 bp          ||||||||||||||||||||||||:!!||||||||||
                             ++GluMetPheSerTyrLeuSerAsnGlnLeuLysLysL
 116530 : ...................aggaaatgttttcatatttgtcCAACCAACTAAAGAAGC : 103634

    343 : euSerGluAlaTyrAsnGlu{Ar}  >>>> Target Intron 9 >>>>  {g}Va :    350
          ||||||||||||||||||||{! }            30 bp            { }  
          euSerGluAlaTyrAsnGlu{Un}--                         --{k}--
 103633 : TGTCAGAAGCCTACAATGAA{AN}nn.........................nn{N}-- : 103580

    351 : lLeuHisThrProHisAsnProIleSerLeu{A}  >>>> Target Intron 10  :    361
               !!||||||||||||||||||||||||{|}            1450 bp     
          -UnkUnkThrProHisAsnProIleSerLeu{A}++                      
 103579 : -NNNNATACACCTCACAATCCCATAtcttta{g}gt...................... : 103547

    362 : >>>>  {la}MetThrLeuLysThrLeuAspLysHisCysAspLysAlaValThrArg :    377
                {||}|||||||||||||||||||||||||||! !|||||||||||||||!:!
              ++{la}MetThrLeuLysThrLeuAspLysHisTyrAspLysAlaValThrGln
 103546 : ....ag{ct}atgACACTTAAAACACTAGATAAACACTATGACAAAGCTGTCACTCAG : 102052

    378 : LeuGlySerMetLeuPheThrArgGlnValSerGlyAla{Ar}  >>>> Target I :    391
          |||||||||||||||||||||||||||||||||||||||{||}            172
          LeuGlySerMetLeuPheThrArgGlnValSerGlyAla{Ar}++             
 102051 : CTTGGCTCCATGCTTTTTACCAGACAGGTTTCTGGAGCC{AG}gt............. : 102006

    392 : ntron 11 >>>>  {g}ValValProLeuGlySerValGlnThrValSerGlyTyrT :    405
          6 bp           {|}||||||||||||||||||:!!|||||||||||||||||||
                       ++{g}ValValProLeuGlySerLeuGlnThrValSerGlyTyrT
 102005 : .............ag{G}GTTGTGCCTCTTGGGTCTTTGCAGACGGTGAGTGGCTACA : 100242

    406 : hrPheArgGlyPheMetSerHisThrAsnAsnTyrProCysAlaTyrLeuAsnAlaAl :    424
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          hrPheArgGlyPheMetSerHisThrAsnAsnTyrProCysAlaTyrLeuAsnAlaAl
 100241 : CTTTCAGAGGCTTTATGTCACATACAAATAATTACCCTTGTGCTTACCTCAATGCCGC : 100185

    425 : aSerAlaIleGlyMetLysThrGlnAspValAspLeuPheIleAsnArgLeuAspLys :    443
          |||||||||||||||||||||||||||||||||||||||||||!!.||||||||||||
          aSerAlaIleGlyMetLysThrGlnAspValAspLeuPheIleLysArgLeuAspLys
 100184 : ATCAGCCATCGGTATGAAGACACAGGATGTGGACTTGTTCATAAAGAGACTTGACAAG : 100128

    444 : CysLeuLysThrValArgLysGluGlnSerLysGluSerAspValSerGlyValAspA :    463
          |||||||||||||||   |||||||||:::||||||||||||||||||||||||||||
          CysLeuLysThrValGlyLysGluGlnAsnLysGluSerAspValSerGlyValAspA
 100127 : TGTTTAAAGACagtaggaaaagaacaaaataaagagagtGATGTATCTGGAGTTGACA : 100068

    464 : snTyrAspLysThrGluAspValValIleGluGluMetAlaLeuLysProAspAsnVa :    482
          |||||||||||||||||||||||! !|||||||||||||||||||||   ||||||||
          snTyrAspLysThrGluAspValAspIleGluGluMetAlaLeuLysIleAspAsnVa
 100067 : ATTATGATAAAACTGAAGATGTGGATATAGAagaaatggctttaaaaatagataatgt : 100011

    483 : lLeuLeuGly :    485
          ||||||||||
          lLeuLeuGly
 100010 : aCTTCTTGGC : 100000

vulgar: SecS 0 485 . KI537300.1:subseq(2790427,200284) 133183 99999 - 2263 M 38 114 5 0 2 I 0 824 3 0 2 M 51 153 S 0 2 5 0 2 I 0 1535 3 0 2 S 1 1 M 26 78 S 0 1 5 0 2 I 0 702 3 0 2 S 1 2 M 52 156 S 0 1 5 0 2 I 0 2289 3 0 2 S 1 2 M 50 150 S 0 2 5 0 2 I 0 3882 3 0 2 S 1 1 M 34 102 5 0 2 I 0 6274 3 0 2 M 43 129 S 0 1 5 0 2 I 0 129 3 0 2 S 1 2 M 30 90 5 0 2 I 0 12859 3 0 2 M 19 57 S 0 2 5 0 2 I 0 26 3 0 2 S 1 1 G 1 0 M 10 30 S 0 1 5 0 2 I 0 1446 3 0 2 S 1 2 M 29 87 S 0 2 5 0 2 I 0 1722 3 0 2 S 1 1 M 94 282
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2014-11-19
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	gene	100000	133183	2263	-	.	gene_id 1 ; sequence SecS ; gene_orientation +
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	cds	133070	133183	.	-	.	
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	exon	133070	133183	.	-	.	insertions 0 ; deletions 0
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice5	133068	133069	.	-	.	intron_id 1 ; splice_site "GT"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	intron	132242	133069	.	-	.	intron_id 1
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice3	132242	132243	.	-	.	intron_id 0 ; splice_site "ag"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	cds	132087	132241	.	-	.	
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	exon	132087	132241	.	-	.	insertions 0 ; deletions 0
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice5	132085	132086	.	-	.	intron_id 2 ; splice_site "gt"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	intron	130548	132086	.	-	.	intron_id 2
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice3	130548	130549	.	-	.	intron_id 1 ; splice_site "AG"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	cds	130468	130547	.	-	.	
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	exon	130468	130547	.	-	.	insertions 0 ; deletions 0
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice5	130466	130467	.	-	.	intron_id 3 ; splice_site "GT"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	intron	129762	130467	.	-	.	intron_id 3
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice3	129762	129763	.	-	.	intron_id 2 ; splice_site "aG"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	cds	129603	129761	.	-	.	
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	exon	129603	129761	.	-	.	insertions 0 ; deletions 0
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice5	129601	129602	.	-	.	intron_id 4 ; splice_site "GT"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	intron	127310	129602	.	-	.	intron_id 4
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice3	127310	127311	.	-	.	intron_id 3 ; splice_site "AG"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	cds	127156	127309	.	-	.	
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	exon	127156	127309	.	-	.	insertions 0 ; deletions 0
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice5	127154	127155	.	-	.	intron_id 5 ; splice_site "GT"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	intron	123270	127155	.	-	.	intron_id 5
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice3	123270	123271	.	-	.	intron_id 4 ; splice_site "AG"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	cds	123167	123269	.	-	.	
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	exon	123167	123269	.	-	.	insertions 0 ; deletions 0
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice5	123165	123166	.	-	.	intron_id 6 ; splice_site "GT"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	intron	116889	123166	.	-	.	intron_id 6
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice3	116889	116890	.	-	.	intron_id 5 ; splice_site "AG"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	cds	116759	116888	.	-	.	
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	exon	116759	116888	.	-	.	insertions 0 ; deletions 0
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice5	116757	116758	.	-	.	intron_id 7 ; splice_site "GT"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	intron	116626	116758	.	-	.	intron_id 7
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice3	116626	116627	.	-	.	intron_id 6 ; splice_site "AG"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	cds	116534	116625	.	-	.	
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	exon	116534	116625	.	-	.	insertions 0 ; deletions 0
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice5	116532	116533	.	-	.	intron_id 8 ; splice_site "gt"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	intron	103671	116533	.	-	.	intron_id 8
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice3	103671	103672	.	-	.	intron_id 7 ; splice_site "ag"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	cds	103612	103670	.	-	.	
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	exon	103612	103670	.	-	.	insertions 0 ; deletions 0
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice5	103610	103611	.	-	.	intron_id 9 ; splice_site "NN"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	intron	103582	103611	.	-	.	intron_id 9
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice3	103582	103583	.	-	.	intron_id 8 ; splice_site "NN"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	cds	103550	103581	.	-	.	
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	exon	103550	103581	.	-	.	insertions 0 ; deletions 1
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice5	103548	103549	.	-	.	intron_id 10 ; splice_site "gt"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	intron	102100	103549	.	-	.	intron_id 10
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice3	102100	102101	.	-	.	intron_id 9 ; splice_site "ag"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	cds	102009	102099	.	-	.	
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	exon	102009	102099	.	-	.	insertions 0 ; deletions 0
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice5	102007	102008	.	-	.	intron_id 11 ; splice_site "GT"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	intron	100283	102008	.	-	.	intron_id 11
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	splice3	100283	100284	.	-	.	intron_id 10 ; splice_site "AG"
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	cds	100000	100282	.	-	.	
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	exon	100000	100282	.	-	.	insertions 0 ; deletions 0
KI537300.1:subseq(2790427,200284)	exonerate:protein2genome:local	similarity	100000	133183	2263	-	.	alignment_id 1 ; Query SecS ; Align 133184 1 114 ; Align 132242 39 153 ; Align 130547 91 78 ; Align 129760 118 156 ; Align 127308 171 150 ; Align 123269 222 102 ; Align 116889 256 129 ; Align 116624 300 90 ; Align 103671 330 57 ; Align 103581 351 30 ; Align 102098 362 87 ; Align 100282 392 282
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
