Command line: [exonerate -E -m p2g --showtargetgff -q SecS_musmusculus.fa -t SecS_musmusculus_Esiliculosus_fastasubseq.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query: SecS;tr|Q3U597|Q3U597 Mus musculus #QUERY
        Target: gi|299508041|emb|FN649742.1|:subseq(93831,10203) Ectocarpus siliculosus strain Ec 32, whole genome shotgun sequence assembly, chromosome LG17
         Model: protein2genome:local
     Raw score: 664
   Query range: 0 -> 339
  Target range: 5191 -> 9659

    1 : MetAlaThr{Gl}  >>>> Target Intron 1 >>>>  {y}MetSerLeuThrLeuCy :   10
        |||||||||{||}            343 bp           {|}|||||||||.!!|||  
        MetAlaThr{Gl}++                         ++{y}MetSerLeuAlaLeuTh
 5192 : ATGGCCACC{GG}gt.........................ag{C}ATGTCCTTGGCTCTAAC : 5562

   11 : sPheLeuThrLeuArgHisLysArgProLysAlaLysTyrIleIleTrpProArgIleAspG :   31
         |||  !.!!||||||  !   !:!|||   ||||||   |||:!!|||||||||!!:||||
        rPheAlaAlaLeuArgAlaAlaLysProAlaAlaLysThrIleValTrpProArgMetAspG
 5563 : GTTCGCAGCCTTGCGGGCTGCCAAGCCCGCCGCCAAGACGATCGTCTGGCCGAGGATGGACC : 5625

   32 : lnLysSerCysPheLysSerMetValThrAlaGlyPheGluProValValIleGluAsnVal :   51
        |||||||||||!!.|||:!!!!:|||.!!|||||||||  !|||:!!|||:!:||||||:!!
        lnLysSerCysLeuLysAlaIleValAlaAlaGlyPheThrProIleValValGluAsnLeu
 5626 : AGAAGTCCTGTTTGAAAGCCATCGTGGCCGCCGGGTTCACGCCGATTGTTGTGGAAAACCTC : 5685

   52 : LeuGlu  >>>> Target Intron 2 >>>>  GlyAspGluLeuArgThrAspLeuLys :   62
        :!!:!!            248 bp           ||||||! !:!!  !||||||:!! ! 
        IleGln++                         ++GlyAspAlaValAlaThrAspValAsp
 5686 : ATCCAGgt.........................agGGCGACGCGGTTGCGACAGACGTGGAC : 5966

   63 : AlaValGluAlaLysIleGlnGluLeuGlyProGluHisIleLeuCysLeuHisSerThrTh :   83
        !.!|||..!|||  !:!::!!...! !||| !!|||:!!:!!||||||:!!  !!!!|||||
        GlyValArgAlaAlaValGluSerCysGlyAlaGluAsnValLeuCysValValThrThrTh
 5967 : GGCGTGAGAGCGGCGGTGGAAAGCTGCGGCGCGGAAAACGTCTTGTGTGTTGTCACGACAAC : 6029

   84 : rAlaCysPheAlaProArgValProAspArg  >>>> Target Intron 3 >>>>  Le :   94
        |::!|||||||||||||||:!!||||||!:!           1274 bp           :!
        rSerCysPheAlaProArgLeuProAspLys++                         ++Va
 6030 : CAGCTGCTTCGCGCCTCGCCTGCCCGACAAGgt.........................agGT : 7336

   95 : uGluGluLeuAlaValIleCysAlaAsnTyrAspIleProHisValValAsnAsnAlaTyrG :  115
        !!!:|||:!!|||  !|||||||||     !!  :!!  !||||||:!!|||||||||||||
        lAspGluValAlaArgIleCysAlaAlaSerGlyValGlyHisValIleAsnAsnAlaTyrG
 7337 : CGACGAGGTTGCCCGCATATGCGCTGCGAGCGGGGTAGGGCACGTCATCAACAACGCCTACG : 7399

  116 : lyLeuGlnSerSerLysCysMetHisLeuIleGln{Gl}  >>>> Target Intron 4  :  127
        ||:!!|||!!!||||||      !..|||:!!.!.{::}            285 bp     
        lyValGlnCysSerLysThrCysArgLeuValAsn{Ar}++                     
 7400 : GAGTTCAATGTTCCAAGACATGCCGGCTCGTCAAC{AG}gt..................... : 7439

  128 : >>>>  {n}GlyAlaArgValGlyArgIleAspAlaPheValGlnSerLeuAspLysAsnPh :  145
              {!}!.!  !  !|||||||||:!!|||||| ! |||||||||  !|||||||||||
            ++{g}AlaMetAlaValGlyArgValAspAlaValValGlnSerThrAspLysAsnPh
 7440 : ....ag{G}GCGATGGCGGTAGGGAGGGTCGACGCCGTGGTCCAGAGCACGGACAAGAACTT : 7774

  146 : eMetValProValGlyGlyAlaIleIleAlaGlyPheAsnGluProPheIleGlnAsp  >> :  165
        |:!!||||||||||||||||||:!::!:..!|||   :!!!   !!||||||:!!.!.    
        eLeuValProValGlyGlyAlaValValCysGlyProAspAlaThrPheIleGluGln+-  
 7775 : CTTGGTTCCCGTCGGCGGAGCGGTGGTGTGCGGACCGGACGCCACCTTTATCGAGCAGgc.. : 7836

  166 : >> Target Intron 5 >>>>  IleSerLysMetTyrProGlyArgAlaSerAlaSerP :  177
                282 bp           :!!.!!|||!  ||| !!||||||||||||:!!.!!|
                               ++ValGlyLysSerTyrAlaGlyArgAlaSerSerGlyP
 7837 : .......................agGTAGGTAAGAGCTACGCCGGGCGTGCAAGCTCTGGGC : 8152

  178 : roSerLeuAspValLeuIleThrLeuLeuSerLeuGlyCysSerGlyTyrArgLysLeuLeu :  197
        ||!!!||||||:!!!!!|||||||||||||||:!!|||   ..!|||!::|||::!||||||
        roCysLeuAspLeuPheIleThrLeuLeuSerMetGlyGlnGluGlyTrpArgArgLeuLeu
 8153 : CTTGCCTAGATCTCTTCATCACGCTCCTCAGCATGGGACAAGAGGGGTGGAGGCGATTGTTG : 8212

  198 : LysGluArgLysGluMetPheValTyrLeu{Se}  >>>> Target Intron 6 >>>>  :  208
          !||||||:!!   :!! ! ! !  !!!!{ !}            321 bp          
        AlaGluArgGluThrLeuValGluProPhe{Ar}++                         +
 8213 : GCGGAGCGCGAGACTTTGGTAGAGCCTTTT{CG}gt.........................a : 8566

  209 :  {r}ThrGlnLeuLysLysLeuAlaGluAlaHisAsnGluArgLeuLeuGlnThrProHisA :  228
         {!}  !!::|||::!:!!:!!||||||::!:!!...||||||||||||:!!:!!  !  !|
        +{g}ArgArgLeuArgGluValAlaGluSerAsnGlyGluArgLeuLeuGluSerSerGlyA
 8567 : g{A}CGGCGCTTACGAGAGGTGGCGGAGAGCAACGGAGAGCGCCTGCTCGAGTCAAGTGGTA : 8626

  229 : snProIleSerLeuAlaMetThrLeuLysThrIleAspGlyHis  >>>> Target Intr :  243
        || !!||||||!!!|||:!!|||||| ! !:!:!:! ! !! !             560 bp
        snThrIleSerPheAlaValThrLeuAspSerLeuValArgLys++                
 8627 : ACACCATCTCCTTCGCCGTGACTCTCGACAGCCTGGTTCGCAAGgt................ : 8673

  244 : on 7 >>>>  HisAspLys{Al}  >>>> Target Intron 8 >>>>  {a}ValThr :  248
                   :!!|||!!.{  }            138 bp           {!}!.!.!!
                 ++TyrAspAsn{Ar}++                         --{g}AlaAla
 8674 : .........agTATGACAAC{AG}gt.........................tc{G}GCGGCC : 9384

  249 : GlnLeuGlySerMetLeuPheThrArgGlnValSerGlyAlaArgAlaValProLeuGlyAs :  269
           !!!|||||||||||||||||||||   |||||||||.!!|||!.!||||||! !! !.!
        PhePheGlySerMetLeuPheThrArgCysValSerGlyThrArgValValProArgGluGl
 9385 : TTCTTCGGGTCTATGCTCTTCACGCGATGCGTGTCTGGCACCCGGGTCGTCCCGCGTGAACA : 9447

  270 : nValGlnThrValSerGlyHisThrPheArgGlyPheMetSerHisAlaAspAsnTyrProC :  290
        .  !:!!  !|||.!!|||  !  !|||!.!|||!:!  !:!!  !!.!  !..!|||||| 
        nHisLysCysValGlyGlyIleAspPheAsnGlyTyrGlyAlaSerValThrGlyTyrProH
 9448 : GCACAAGTGCGTGGGCGGCATCGATTTTAACGGCTACGGGGCGAGCGTGACCGGCTATCCGC : 9510

  291 : ysAlaTyrLeuAsnAlaAlaAlaAlaIleGlyMetLysMetGlnAspValAspLeuPheIle :  310
         !! !||||||!..||||||..!|||  !|||:!!...! !:!!!!::!!|||  !|||:!:
        isAspTyrLeuThrAlaAlaCysAlaAlaGlyLeuSerThrGluGluLeuAspGluPheLeu
 9511 : ACGACTACTTGACGGCGGCGTGTGCCGCAGGATTGTCCACGGAGGAACTTGACGAGTTTTTG : 9570

  311 : LysArgLeuAspLysCysLeuAsnIleValArgLysGluGlnThrArgAlaSerValValSe :  331
        !  ||||||||||||..!|||...!  !.!!:!   |||::!.!!..!|||! !!.!!.! !
        IleArgLeuAspLysAlaLeuArgLysAlaLysAlaGluArgAlaGluAlaLeuAlaAlaPr
 9571 : ATCCGGCTGGACAAAGCCCTTCGAAAGGCCAAGGCCGAGAGAGCAGAGGCGTTGGCAGCGCC : 9633

  332 : rGlyAlaAspArgAsnLysAlaGlu :  339
        ! !!:!!.!.  !...|||.!!|||
        oArgSerGlnAspGlyLysThrGlu
 9634 : TCGGTCACAAGATGGGAAAACGGAG : 9659

vulgar: SecS;tr|Q3U597|Q3U597 0 339 . gi|299508041|emb|FN649742.1|:subseq(93831,10203) 5191 9659 + 664 M 3 9 S 0 2 5 0 2 I 0 339 3 0 2 S 1 1 M 49 147 5 0 2 I 0 244 3 0 2 M 40 120 5 0 2 I 0 1270 3 0 2 M 33 99 S 0 2 5 0 2 I 0 281 3 0 2 S 1 1 M 37 111 5 0 2 I 0 278 3 0 2 M 43 129 S 0 2 5 0 2 I 0 317 3 0 2 S 1 1 M 34 102 5 0 2 I 0 556 3 0 2 M 3 9 S 0 2 5 0 2 I 0 134 3 0 2 S 1 1 M 93 279
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-03-16
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	gene	5192	9659	664	+	.	gene_id 1 ; sequence SecS;tr|Q3U597|Q3U597 ; gene_orientation +
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	cds	5192	5202	.	+	.	
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	exon	5192	5202	.	+	.	insertions 0 ; deletions 0
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	splice5	5203	5204	.	+	.	intron_id 1 ; splice_site "GT"
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	intron	5203	5545	.	+	.	intron_id 1
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	splice3	5544	5545	.	+	.	intron_id 0 ; splice_site "AG"
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	cds	5546	5693	.	+	.	
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	exon	5546	5693	.	+	.	insertions 0 ; deletions 0
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	splice5	5694	5695	.	+	.	intron_id 2 ; splice_site "GT"
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	intron	5694	5941	.	+	.	intron_id 2
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	splice3	5940	5941	.	+	.	intron_id 1 ; splice_site "AG"
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	cds	5942	6061	.	+	.	
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	exon	5942	6061	.	+	.	insertions 0 ; deletions 0
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	splice5	6062	6063	.	+	.	intron_id 3 ; splice_site "GT"
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	intron	6062	7335	.	+	.	intron_id 3
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	splice3	7334	7335	.	+	.	intron_id 2 ; splice_site "AG"
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	cds	7336	7436	.	+	.	
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	exon	7336	7436	.	+	.	insertions 0 ; deletions 0
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	splice5	7437	7438	.	+	.	intron_id 4 ; splice_site "GT"
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	intron	7437	7721	.	+	.	intron_id 4
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	splice3	7720	7721	.	+	.	intron_id 3 ; splice_site "AG"
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	cds	7722	7833	.	+	.	
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	exon	7722	7833	.	+	.	insertions 0 ; deletions 0
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	splice5	7834	7835	.	+	.	intron_id 5 ; splice_site "GC"
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	intron	7834	8115	.	+	.	intron_id 5
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	splice3	8114	8115	.	+	.	intron_id 4 ; splice_site "AG"
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	cds	8116	8246	.	+	.	
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	exon	8116	8246	.	+	.	insertions 0 ; deletions 0
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	splice5	8247	8248	.	+	.	intron_id 6 ; splice_site "GT"
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	intron	8247	8567	.	+	.	intron_id 6
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	splice3	8566	8567	.	+	.	intron_id 5 ; splice_site "AG"
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	cds	8568	8670	.	+	.	
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	exon	8568	8670	.	+	.	insertions 0 ; deletions 0
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	splice5	8671	8672	.	+	.	intron_id 7 ; splice_site "GT"
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	intron	8671	9230	.	+	.	intron_id 7
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	splice3	9229	9230	.	+	.	intron_id 6 ; splice_site "AG"
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	cds	9231	9241	.	+	.	
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	exon	9231	9241	.	+	.	insertions 0 ; deletions 0
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	splice5	9242	9243	.	+	.	intron_id 8 ; splice_site "GT"
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	intron	9242	9379	.	+	.	intron_id 8
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	splice3	9378	9379	.	+	.	intron_id 7 ; splice_site "TC"
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	cds	9380	9659	.	+	.	
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	exon	9380	9659	.	+	.	insertions 0 ; deletions 0
gi|299508041|emb|FN649742.1|:subseq(93831,10203)	exonerate:protein2genome:local	similarity	5192	9659	664	+	.	alignment_id 1 ; Query SecS;tr|Q3U597|Q3U597 ; Align 5192 1 9 ; Align 5547 5 147 ; Align 5942 54 120 ; Align 7336 94 99 ; Align 7723 128 111 ; Align 8116 165 129 ; Align 8569 209 102 ; Align 9231 243 9 ; Align 9381 247 279
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
