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

C4 Alignment:
------------
         Query: SecS;tr|Q3U597|Q3U597 Mus musculus #QUERY
        Target: gi|288565305|gb|GG743892.1|:subseq(236720,10866) Saprolegnia parasitica CBS 223.65 genomic scaffold supercont1.10, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 634
   Query range: 30 -> 317
  Target range: 4919 -> 6126

   31 : GlnLysSerCysPheLysSerMetValThrAla{G}  >>>> Target Intron 1 >>> :   42
        |||||||||||||||||||||||||||||||||{|}            47 bp         
        GlnLysSerCysPheLysSerMetValThrAla{G}++                        
 4920 : CAAAAGTCATGCTTCAAGTCCATGGTCACCGCC{G}gt........................ : 4956

   43 : >  {ly}PheGluProValValIleGluAsnValLeuGluGlyAspGluLeuArgThrAspL :   61
           {||}.!!|||||||||||||||||||||||||||!!:||||||||||||||||||||||
         ++{ly}LeuGluProValValIleGluAsnValLeuAspGlyAspGluLeuArgThrAspL
 4957 : .ag{GC}CTCGAGCCCGTTGTGATCGAGAACGTCTTGGACGGCGACGAGCTGCGCACGGACC : 5057

   62 : euLysAlaValGluAlaLysIleGlnGluLeuGlyProGluHisIleLeuCysLeuHisSer :   81
        ||  !|||:!!|||||||||!!:!::|||||||||||||||:!!|||||||||:!!! !|||
        euAlaAlaLeuGluAlaLysMetArgGluLeuGlyProGluAsnIleLeuCysValLeuSer
 5058 : TCGCAGCGCTTGAAGCCAAGATGCGCGAACTCGGGCCCGAGAACATTCTGTGCGTGCTCTCG : 5117

   82 : ThrThrAlaCysPheAlaProArgValProAspArgLeuGluGluLeuAlaValIleCysAl :  102
        ||||||::!|||||||||||||||! !  !||||||:!!!!:|||:!!|||  !:!!|||  
        ThrThrSerCysPheAlaProArgGlyTyrAspArgValAspGluIleAlaGlnLeuCysAr
 5118 : ACCACGAGCTGCTTTGCGCCGCGCGGCTACGACCGCGTCGACGAGATCGCGCAGCTCTGCCG : 5180

  103 : aAsnTyrAspIle{P}  >>>> Target Intron 2 >>>>  {ro}HisValValAsnA :  112
        !.!.|||||||||{ }            51 bp            { !}||||||:!!||||
        gGlnTyrAspIle{G}++                         ++{ly}HisValIleAsnA
 5181 : GCAATACGATATT{G}gt.........................ag{GG}CACGTCATCAACA : 5261

  113 : snAlaTyrGlyLeuGlnSerSerLysCysMetHisLeuIleGlnGln  >>>> Target I :  128
        |||||||||||||||||||||||||||||! !||||||:!:.!.|||            51 
        snAlaTyrGlyLeuGlnSerSerLysCysThrHisLeuValAsnGln++             
 5262 : ATGCCTACGGACTCCAGTCGTCCAAGTGCACGCACCTCGTGAATCAAgt............. : 5311

  129 : ntron 3 >>>>  GlyAlaArgValGlyArgIleAspAlaPheValGlnSerLeuAspLys :  143
        bp            !.!  !|||:!!||||||:!!||||||! !:!!||||||  !||||||
                    ++AlaPheArgLeuGlyArgValAspAlaCysIleGlnSerThrAspLys
 5312 : ............agGCATTTCGGCTCGGGCGCGTCGACGCGTGCATCCAGAGCACGGACAAG : 5405

  144 : AsnPheMetValProValGlyGlyAlaIleIleAlaGlyPheAsn-GluProPheIleGlnA :  164
        ||||||:!:||||||||||||||||||:!!|||:!!    !!!.!#:!! !!|||:!!|||!
        AsnPheLeuValProValGlyGlyAlaValIleSer---ValThr#GlnAlaPheValGlnA
 5406 : AACTTTCTCGTGCCCGTCGGTGGCGCCGTCATCTCA---GTCACCTCAGGCCTTTGTACAAG : 5466

  165 : spIleSerLysMetTyrPro{G}  >>>> Target Intron 4 >>>>  {ly}ArgAla :  173
          |||.!!||||||||||||{|}            59 bp            {||}||||||
        laIleGlyLysMetTyrPro{G}++                         ++{ly}ArgAla
 5467 : CGATCGGCAAGATGTACCCA{G}gt.........................ag{GC}CGCGCG : 5552

  174 : SerAlaSerProSerLeuAspValLeuIleThrLeuLeuSerLeuGlyCysSerGlyTyrAr :  194
        |||  !:!!|||:!!||||||:!!!!!||||||:!!|||  !|||||| !  !!||||||!:
        SerAsnAlaProAlaLeuAspLeuPheIleThrMetLeuHisLeuGlyArgArgGlyTyrLy
 5553 : AGCAACGCGCCAGCGCTGGACCTTTTCATTACGATGCTGCACCTTGGCCGACGCGGGTACAA : 5615

  195 : gLysLeuLeuLysGluArgLysGluMetPheValTyrLeuSerThrGlnLeuLysLysLeuA :  215
        !  !|||||| ! |||||||||...:!: !   !|||!!!|||.!!  !|||! !..!:!!|
        sAlaLeuLeuAspGluArgLysArgLeuValProTyrPheSerAlaAlaLeuThrSerValA
 5616 : GGCGCTTCTGGACGAACGCAAGCGCCTCGTGCCCTACTTTTCCGCGGCGCTCACGTCGGTCG : 5678

  216 : laGluAlaHisAsnGluArgLeuLeuGlnThrProHisAsnPro  >>>> Target Intr :  230
        ||  !||||||..!||||||:!!|||   |||! !||||||  !            51 bp 
        laThrAlaHisGlyGluArgValLeuValThrArgHisAsnAsp++                
 5679 : CGACGGCCCACGGCGAACGCGTCCTCGTCACGCGGCACAACGATgt................ : 5725

  231 : on 5 >>>>  IleSerLeuAlaMetThrLeuLysThrIleAspGlyHisHisAspLysAla :  246
                   ||||||!!!..!:!!||||||!..  !:!:! !|||:!! !!         
                 ++IleSerPheCysLeuThrLeuSerHisValGlyGlyAsnAsp---------
 5726 : .........agATTTCGTTTTGCTTGACATTGAGCCACGTGGGCGGCAACGAC--------- : 5816

  247 : ValThrGlnLeuGlySerMetLeuPheThrArgGlnValSerGlyAla{Ar}  >>>> Tar :  263
        !.!|||   ||||||||||||||||||:!!|||   |||||||||.!!{||}          
        AlaThrPheLeuGlySerMetLeuPheSerArgGlyValSerGlyThr{Ar}++        
 5817 : GCGACGTTCCTCGGCTCGATGCTCTTTTCGCGCGGCGTCTCGGGCACG{CG}gt........ : 5868

  264 : get Intron 6 >>>>  {g}AlaValProLeuGlyAsnValGlnThrValSerGlyHisT :  277
          47 bp            {|}!.!||| !!  !  !:::  !  !|||:!!  !||||||.
                         ++{g}ValValThrGlyThrSerArgAlaThrIleValGlyHisA
 5869 : .................ag{C}GTCGTCACCGGCACATCGCGCGCGACGATCGTGGGCCACG : 5953

  278 : hrPheArgGlyPheMetSerHisAlaAspAsnTyrProCysAlaTyrLeuAsnAlaAlaAla :  297
        !!|||..!||||||   :!!|||:!!!  !..||||||  !|||||||||:::||||||..!
        laPheGluGlyPheGlyAlaHisSerAlaThrTyrProThrAlaTyrLeuSerAlaAlaCys
 5954 : CGTTTGAGGGCTTTGGCGCGCACTCGGCGACGTACCCGACCGCGTACCTCTCGGCGGCCTGC : 6013

  298 : AlaIleGlyMetLysMetGln  >>>> Target Intron 7 >>>>  AspValAspLeu :  308
        ||||||||||||!  ....!.            51 bp            !!::!!|||:!!
        AlaIleGlyMetThrGlnAsp++                         ++GluIleAspVal
 6014 : GCGATTGGCATGACCCAAGACgt.........................agGAAATCGACGTC : 6097

  309 : PheIleLysArgLeuAspLysCysLeu :  317
        ||||||  !||||||:!!|||  !|||
        PheIleAlaArgLeuAsnLysThrLeu
 6098 : TTCATCGCGCGGCTCAACAAGACTCTC : 6126

vulgar: SecS;tr|Q3U597|Q3U597 30 317 . gi|288565305|gb|GG743892.1|:subseq(236720,10866) 4919 6126 + 634 M 11 33 S 0 1 5 0 2 I 0 43 3 0 2 S 1 2 M 64 192 S 0 1 5 0 2 I 0 47 3 0 2 S 1 2 M 20 60 5 0 2 I 0 47 3 0 2 M 28 84 G 1 0 M 2 6 F 0 1 M 12 36 S 0 1 5 0 2 I 0 55 3 0 2 S 1 2 M 58 174 5 0 2 I 0 47 3 0 2 M 14 42 G 3 0 M 16 48 S 0 2 5 0 2 I 0 43 3 0 2 S 1 1 M 41 123 5 0 2 I 0 47 3 0 2 M 13 39
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-03-15
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	gene	4920	6126	634	+	.	gene_id 1 ; sequence SecS;tr|Q3U597|Q3U597 ; gene_orientation +
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	cds	4920	4953	.	+	.	
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	exon	4920	4953	.	+	.	insertions 0 ; deletions 0
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	splice5	4954	4955	.	+	.	intron_id 1 ; splice_site "GT"
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	intron	4954	5000	.	+	.	intron_id 1
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	splice3	4999	5000	.	+	.	intron_id 0 ; splice_site "AG"
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	cds	5001	5195	.	+	.	
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	exon	5001	5195	.	+	.	insertions 0 ; deletions 0
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	splice5	5196	5197	.	+	.	intron_id 2 ; splice_site "GT"
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	intron	5196	5246	.	+	.	intron_id 2
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	splice3	5245	5246	.	+	.	intron_id 1 ; splice_site "AG"
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	cds	5247	5308	.	+	.	
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	exon	5247	5308	.	+	.	insertions 0 ; deletions 0
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	splice5	5309	5310	.	+	.	intron_id 3 ; splice_site "GT"
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	intron	5309	5359	.	+	.	intron_id 3
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	splice3	5358	5359	.	+	.	intron_id 2 ; splice_site "AG"
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	cds	5360	5487	.	+	.	
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	exon	5360	5487	.	+	.	insertions 0 ; deletions 1 ; frameshifts 1
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	splice5	5488	5489	.	+	.	intron_id 4 ; splice_site "GT"
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	intron	5488	5546	.	+	.	intron_id 4
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	splice3	5545	5546	.	+	.	intron_id 3 ; splice_site "AG"
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	cds	5547	5722	.	+	.	
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	exon	5547	5722	.	+	.	insertions 0 ; deletions 0
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	splice5	5723	5724	.	+	.	intron_id 5 ; splice_site "GT"
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	intron	5723	5773	.	+	.	intron_id 5
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	splice3	5772	5773	.	+	.	intron_id 4 ; splice_site "AG"
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	cds	5774	5865	.	+	.	
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	exon	5774	5865	.	+	.	insertions 0 ; deletions 3
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	splice5	5866	5867	.	+	.	intron_id 6 ; splice_site "GT"
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	intron	5866	5912	.	+	.	intron_id 6
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	splice3	5911	5912	.	+	.	intron_id 5 ; splice_site "AG"
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	cds	5913	6036	.	+	.	
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	exon	5913	6036	.	+	.	insertions 0 ; deletions 0
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	splice5	6037	6038	.	+	.	intron_id 7 ; splice_site "GT"
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	intron	6037	6087	.	+	.	intron_id 7
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	splice3	6086	6087	.	+	.	intron_id 6 ; splice_site "AG"
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	cds	6088	6126	.	+	.	
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	exon	6088	6126	.	+	.	insertions 0 ; deletions 0
gi|288565305|gb|GG743892.1|:subseq(236720,10866)	exonerate:protein2genome:local	similarity	4920	6126	634	+	.	alignment_id 1 ; Query SecS;tr|Q3U597|Q3U597 ; Align 4920 31 33 ; Align 5003 43 192 ; Align 5249 108 60 ; Align 5360 128 84 ; Align 5444 157 6 ; Align 5451 159 36 ; Align 5549 172 174 ; Align 5774 230 42 ; Align 5816 247 48 ; Align 5914 264 123 ; Align 6088 305 39
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
