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

C4 Alignment:
------------
         Query: SecS;tr|Q3U597|Q3U597 Mus musculus #QUERY
        Target: gi|217409454|gb|CM000608.1|:subseq(915570,10860) Phaeodactylum tricornutum CCAP 1055/1 chromosome 5, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 648
   Query range: 17 -> 326
  Target range: 4535 -> 3441

   18 : ArgProLysAlaLysTyrIleIleTrpProArgIleAspGlnLysSerCysPheLysSerMe :   38
        !:!||| !   !!!.  !:!!:!:|||  !|||||||||||||||||||||||||||:!!!!
        LysProTyrArgAsnIleValLeuTrpSerArgIleAspGlnLysSerCysPheLysAlaIl
 4535 : AAACCGTACAGAAATATTGTCTTGTGGAGTCGGATTGATCAAAAGAGTTGTTTCAAGGCGAT : 4475

   39 : tValThrAlaGlyPheGluProValValIleGluAsnValLeuGluGlyAspGluLeuArgT :   59
        :  !:!!||||||.!.|||  !||||||:!:  !!..  !|||! !||||||! !:!!  !|
        eGlnSerAlaGlyLeuGluCysValValValProThrArgLeuAlaGlyAspAlaValValT
 4474 : CCAGTCGGCTGGCCTGGAGTGCGTTGTCGTGCCGACGCGATTGGCAGGTGACGCGGTCGTGA : 4412

   60 : hrAspLeuLysAlaValGluAlaLysIleGlnGluLeuGlyProGluHisIleLeuCysLeu :   79
        |||||||| ! ||| !!:!!|||...:!!! !   ! !|||   !!:!.!:!!|||..!:!!
        hrAspLeuAspAlaPheGlnAlaSerLeuLeuThrTyrGly---AspArgValLeuAlaVal
 4411 : CGGATTTGGATGCCTTCCAGGCGTCTCTACTGACTTACGGA---GACCGCGTTCTGGCCGTC : 4355

   80 : HisSerThrThrAlaCysPheAlaProArgValProAspArgLeuGluGluLeuAlaValIl :  100
           !!!||||||:!!||||||||||||||||||||||||!:!:!!!!:!  :!!|||  !:!
        ValThrThrThrSerCysPheAlaProArgValProAspGlnValAspAlaValAlaArgLe
 4354 : GTGACCACAACGTCCTGCTTTGCACCGCGGGTGCCCGACCAAGTGGACGCCGTGGCCAGACT : 4292

  101 : eCysAlaAsnTyrAspIleProHisValValAsnAsnAlaTyrGlyLeuGlnSerSerLysC :  121
        :||||||.!. !   !:!!|||||||||:!!||||||||||||||||||||||||||| !  
        uCysAlaGluGlnCysValProHisValIleAsnAsnAlaTyrGlyLeuGlnSerSerAspT
 4291 : GTGCGCCGAACAATGTGTACCGCACGTCATCAACAACGCGTACGGGTTGCAAAGCTCCGATA : 4229

  122 : ysMetHisLeuIleGlnGlnGlyAlaArgValGlyArgIleAspAlaPheValGlnSerLeu :  141
              ! |||:!!.!.!:!!.!..!  !|||||||||:!:||||||.!!|||   |||  !
        hrSerLysLeuLeuAsnArgAlaCysAlaValGlyArgValAspAlaIleValCysSerThr
 4228 : CGTCCAAACTCCTCAATCGGGCTTGCGCAGTCGGTCGGGTGGATGCGATTGTGTGTTCGACC : 4169

  142 : AspLysAsnPheMetValProVal{G}  >>>> Target Intron 1 >>>>  {ly}Gl :  151
        |||||||||||||||||||||:!!{|}            131 bp           {||}||
        AspLysAsnPheMetValProIle{G}++                         ++{ly}Gl
 4168 : GACAAAAACTTTATGGTGCCCATT{G}gt.........................ag{GT}GG : 4008

  152 : yAlaIleIleAlaGlyPheAsnGluProPheIleGlnAspIleSerLysMetTyrProGlyA :  172
        |||||||:!!  !..!   :!!|||  !!!.||||||:!!:!:.!!|||:!:||| !!||||
        yAlaIleValLeuSerProAspGluSerLeuIleGlnAsnValGlyLysValTyrAlaGlyA
 4007 : TGCGATTGTTCTGTCACCGGACGAAAGCTTGATCCAGAACGTGGGCAAGGTATACGCCGGTC : 3945

  173 : rgAlaSerAlaSerProSerLeuAspValLeuIleThrLeuLeuSerLeuGlyCysSerGly :  192
        |||||||||||||||||! !||||||:!!!!!|||||||||! !|||:!!|||    !!|||
        rgAlaSerAlaSerProMetLeuAspLeuPheIleThrLeuCysSerMetGlyLeuArgGly
 3944 : GTGCGTCGGCTTCACCCATGCTGGATTTGTTCATTACGTTGTGCTCCATGGGTCTACGGGGC : 3885

  193 : TyrArgLysLeuLeuLysGluArgLysGluMetPheValTyrLeuSerThrGlnLeuLysLy :  213
        |||!:!:!!||||||! !...|||:::  !:!:.!!  !   !!!!!!  !!:!||||||:!
        TyrGlnGlnLeuLeuThrSerArgArgIleLeuLeuProThrPheThrGluArgLeuLysGl
 3884 : TATCAACAATTACTGACGTCCCGGCGCATACTACTCCCTACGTTCACGGAGCGGTTAAAAGA : 3822

  214 : sLeuAlaGluAlaHisAsnGluArgLeuLeuGlnThrProHisAsnProIleSerLeuAlaM :  234
        !:!!|||.!.  !:!!..!||||||:!!|||:!!  !! !   |||  !||||||!!!!.!:
        uValAlaAsnLysTyrGlyGluArgValLeuGluCysArgThrAsnCysIleSerPheGlyV
 3821 : AGTCGCGAACAAGTACGGTGAACGGGTCCTGGAGTGTCGGACGAATTGTATCAGTTTTGGAG : 3759

  235 : etThrLeuLysThrIle  >>>> Target Intron 2 >>>>  AspGlyHisHisAspL :  245
        !:|||||| !   !:!:            39 bp                 !  !   ..!!
        alThrLeuAspGlyLeu++                         +-ArgThrSerValSerA
 3758 : TCACTTTGGATGGCTTGgt.........................atCGGACGAGTGTGAGTA : 3687

  246 : ysAlaValThrGlnLeuGlySerMetLeuPheThrArgGlnValSerGlyAlaArgAlaVal :  265
        :!! !|||:!!...||||||:!!|||||||||  !|||   |||||||||.!!|||!.!|||
        rgAspValSerSerLeuGlyAlaMetLeuPheGlnArgCysValSerGlyThrArgValVal
 3686 : GGGACGTATCCAGCTTAGGTGCTATGCTGTTCCAACGGTGCGTGAGCGGGACAAGGGTGGTA : 3627

  266 : ProLeuGlyAsnValGlnThrValSerGlyHisThrPheArgGlyPheMetSerHisAlaAs :  286
        |||! !|||!..||||||  !:!!.!!|||     !||| !!||||||  !|||  !  !||
        ProArgGlyThrValGlnArgMetGlyGlyMetGluPheCysGlyPheGlySerSerHisAs
 3626 : CCCCGGGGCACGGTGCAGCGCATGGGCGGGATGGAATTTTGCGGTTTTGGGAGTAGTCACGA : 3564

  287 : pAsnTyrProCysAlaTyrLeuAsnAlaAlaAlaAlaIleGlyMetLysMetGlnAspValA :  307
        |  !||||||  !|||||||||!..||||||..!|||||||||:!!!    !...!!:! !|
        pAlaTyrProHisAlaTyrLeuThrAlaAlaCysAlaIleGlyLeuThrAlaSerGluGlyA
 3563 : TGCCTATCCACACGCCTACTTGACGGCGGCGTGTGCGATTGGACTGACCGCGTCCGAAGGAG : 3501

  308 : spLeuPheIleLysArgLeuAspLysCysLeuAsnIleValArgLysGluGlnThrArg :  326
        ||  !|||.!!!  |||||||||:!!   |||:!!  ! !!!:!|||..!|||  !|||
        spAspPhePheThrArgLeuAspGlnThrLeuHisGluPheGlnLysArgGlnArgArg
 3500 : ACGACTTTTTTACTCGGCTCGATCAAACGCTGCACGAATTTCAAAAACGACAGCGGCGT : 3442

vulgar: SecS;tr|Q3U597|Q3U597 17 326 . gi|217409454|gb|CM000608.1|:subseq(915570,10860) 4535 3441 - 648 M 55 165 G 1 0 M 76 228 S 0 1 5 0 2 I 0 127 3 0 2 S 1 2 M 89 267 5 0 2 I 0 35 3 0 2 M 87 261
# --- 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|217409454|gb|CM000608.1|:subseq(915570,10860)	exonerate:protein2genome:local	gene	3442	4535	648	-	.	gene_id 1 ; sequence SecS;tr|Q3U597|Q3U597 ; gene_orientation +
gi|217409454|gb|CM000608.1|:subseq(915570,10860)	exonerate:protein2genome:local	cds	4142	4535	.	-	.	
gi|217409454|gb|CM000608.1|:subseq(915570,10860)	exonerate:protein2genome:local	exon	4142	4535	.	-	.	insertions 0 ; deletions 1
gi|217409454|gb|CM000608.1|:subseq(915570,10860)	exonerate:protein2genome:local	splice5	4140	4141	.	-	.	intron_id 1 ; splice_site "GT"
gi|217409454|gb|CM000608.1|:subseq(915570,10860)	exonerate:protein2genome:local	intron	4011	4141	.	-	.	intron_id 1
gi|217409454|gb|CM000608.1|:subseq(915570,10860)	exonerate:protein2genome:local	splice3	4011	4012	.	-	.	intron_id 0 ; splice_site "AG"
gi|217409454|gb|CM000608.1|:subseq(915570,10860)	exonerate:protein2genome:local	cds	3742	4010	.	-	.	
gi|217409454|gb|CM000608.1|:subseq(915570,10860)	exonerate:protein2genome:local	exon	3742	4010	.	-	.	insertions 0 ; deletions 0
gi|217409454|gb|CM000608.1|:subseq(915570,10860)	exonerate:protein2genome:local	splice5	3740	3741	.	-	.	intron_id 2 ; splice_site "GT"
gi|217409454|gb|CM000608.1|:subseq(915570,10860)	exonerate:protein2genome:local	intron	3703	3741	.	-	.	intron_id 2
gi|217409454|gb|CM000608.1|:subseq(915570,10860)	exonerate:protein2genome:local	splice3	3703	3704	.	-	.	intron_id 1 ; splice_site "AT"
gi|217409454|gb|CM000608.1|:subseq(915570,10860)	exonerate:protein2genome:local	cds	3442	3702	.	-	.	
gi|217409454|gb|CM000608.1|:subseq(915570,10860)	exonerate:protein2genome:local	exon	3442	3702	.	-	.	insertions 0 ; deletions 0
gi|217409454|gb|CM000608.1|:subseq(915570,10860)	exonerate:protein2genome:local	similarity	3442	4535	648	-	.	alignment_id 1 ; Query SecS;tr|Q3U597|Q3U597 ; Align 4536 18 165 ; Align 4371 74 228 ; Align 4009 151 267 ; Align 3703 240 261
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
