Command line: [exonerate -m p2g --showtargetgff -q ./selenoproteines/TR2.fa -t contigmodTR1.fa]
Hostname: [portatil]

C4 Alignment:
------------
         Query: SPP00000035_1.0 # Protein # Thioredoxin reductase 2 (TR2) # Homo sapiens # Complete
        Target: gi|56500783|emb|CAAI01000787.1| Plasmodium berghei whole genome shotgun assembly, contig PB_RP0892, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 1031
   Query range: 38 -> 524
  Target range: 8595 -> 7107

   39 : AspTyrAspLeuLeuValValGlyGlyGlySerGlyGlyLeuAlaCysAlaLysGluAlaAl :   59
        |||||||||! !:!!|||:!!||||||||| !!||||||:!!|||!  ||||||||||||||
        AspTyrAspTyrIleValIleGlyGlyGlyProGlyGlyMetAlaSerAlaLysGluAlaAl
 8595 : GACTATGATTATATAGTTATTGGTGGAGGCCCTGGAGGTATGGCATCAGCTAAAGAAGCTGC : 8535

   60 : aGlnLeuGlyArgLysValAlaValValAspTyrValGluProSerProGlnGlyThrArgT :   80
        |..!! !|||  !||||||  !:!! !!|||!:!|||:!!||||||  !|||||||||!:!|
        aSerHisGlyAlaLysValLeuLeuPheAspPheValLysProSerSerGlnGlyThrLysT
 8534 : TTCACACGGAGCTAAAGTTTTGCTATTTGATTTTGTTAAACCGAGTAGTCAAGGAACAAAAT : 8472

   81 : rpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHisGlnAla :  100
        |||||:!!|||||||||||||||||||||||||||:!!|||||||||||||||||| ! |||
        rpGlyIleGlyGlyThrCysValAsnValGlyCysValProLysLysLeuMetHisTyrAla
 8471 : GGGGTATTGGAGGTACATGTGTAAATGTCGGATGTGTACCGAAAAAGTTAATGCACTATGCA : 8412

  101 : AlaLeuLeuGlyGlyLeuIleGln<->AspAlaProAsnTyrGlyTrpGluValAlaGlnPr :  120
        !.!  !:!!|||  !|||.!!:!!   |||:!!  !!!.||||||||||||   ..!.!.  
        GlyAsnMetGlyThrLeuPheLysAsnAspSerAspLysTyrGlyTrpGlu---CysAsnAs
 8411 : GGAAATATGGGAACATTATTTAAAAATGATTCGGATAAATATGGATGGGAA---TGTAATAA : 8352

  121 : oValProHisAspTrpArgLysMetAlaGluAlaValGlnAsnHisValLysSerLeuAsnT :  141
        !:!!  !|||||||||!.!|||:!:!.!....!!||||||::!|||:!!:::|||||||||!
        nLeuLysHisAspTrpAsnLysLeuValSerThrValGlnSerHisIleArgSerLeuAsnP
 8351 : TTTAAAACATGATTGGAATAAATTAGTTAGTACTGTTCAGTCTCATATACGTTCATTAAATT : 8289

  142 : rpGlyHisArgValGlnLeuGlnAspArgLysValLysTyrPheAsnIleLysAlaSerPhe :  161
        ::.!!:!!! !:!!  !|||:!!...!:!||||||||||||.!!|||  !  !|||!.!!!.
        heSerTyrMetIleGlyLeuLysSerLysLysValLysTyrIleAsnGlyLeuAlaLysLeu
 8288 : TTAGTTATATGATAGGATTAAAATCAAAAAAAGTTAAATATATTAATGGATTAGCAAAATTA : 8229

  162 : ValAspGluHisThrValCysGlyValAlaLysGly<-><->GlyLysGluIleLeuLeuSe :  180
          !:!!:!!:!!||||||!    !  !  !||||||      ..!||||||  !! !:!!!!
        LysAsnLysAsnThrValSerTyrTyrLeuLysGlyAspSerSerLysGluAspCysValTh
 8228 : AAAAATAAAAATACAGTATCATATTATTTAAAAGGTGATTCATCTAAAGAAGATTGTGTAAC : 8166

  181 : rAlaAspHisIleIleIleAlaThrGlyGlyArgProArgTyrProThrHisIleGluGlyA :  201
        !!.! ! :!!|||:!!|||||||||||| !!||||||!.!   |||  ! !!:!!  !||||
        rGlyLysTyrIleLeuIleAlaThrGlyCysArgProAsnIleProAspAspValIleGlyA
 8165 : AGGCAAATATATTTTAATTGCAACAGGATGTCGACCAAATATACCAGATGATGTTATAGGTG : 8103

  202 : laLeuGluTyrGlyIleThrSerAspAspIlePheTrpLeuLysGluSerProGlyLysThr :  221
        ||  !|||   .!!|||||||||||||||||||||!  ||||||.!...!||||||||||||
        laLysGluLeuSerIleThrSerAspAspIlePheSerLeuLysAsnAspProGlyLysThr
 8102 : CTAAAGAACTAAGTATAACTTCTGATGATATATTTTCTTTAAAAAATGATCCTGGAAAAACG : 8043

  222 : LeuValValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPheLeuThrGlyIleGlyLe :  242
        ||||||||||||||||||||||||||||||||||||||||||||||||!.!..!:!!|||! 
        LeuValValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPheLeuAsnSerLeuGlyTy
 8042 : CTAGTTGTTGGTGCTTCTTATGTAGCTTTAGAATGTGCTGGATTTTTAAATTCATTAGGATA : 7980

  243 : uAspThrThrIleMetMetArgSerIleProLeuArgGlyPheAspGlnGlnMetSerSerM :  263
        !|||||||||:!!   :!:|||||||||  !|||||||||||||||||||||   :!!!:!!
        rAspThrThrValSerValArgSerIleIleLeuArgGlyPheAspGlnGlnCysAlaAsnL
 7979 : TGATACAACTGTATCTGTACGTTCAATAATATTAAGAGGTTTTGATCAACAATGTGCAAATA : 7917

  264 : etValIleGluHisMetAlaSerHisGlyThrArgPheLeuArgGlyCysAlaProSerArg :  283
          :!!! !  !:!!|||! !..!!!.|||..!! !|||:!! !!|||     !|||!.!!:!
        ysIleLysLeuTyrMetGluGluGlnGlyValThrPheMetCysGlyIleLeuProLysLys
 7916 : AAATAAAATTATATATGGAAGAACAAGGTGTAACATTTATGTGTGGTATATTACCTAAAAAA : 7857

  284 : ValArgArgLeuProAspGlyGlnLeuGlnValThrTrpGluAspSerThrThrGlyLysGl :  304
        :!!! !!:!  !  !|||   :!!:!!  !|||  !!::.!.:!!!:!||||||! !  !  
        LeuThrLysGluAsnAsp---LysIleLeuValHisPheAsnAsnAsnThrThrGluLeuPh
 7856 : CTAACTAAAGAAAATGAC---AAAATTTTAGTTCATTTTAATAATAATACTACAGAATTATT : 7797

  305 : uAspThrGlyThrPheAspThrValLeuTrpAlaIleGlyArgValProAspThrArgSerL :  325
         ||||||               ||||||!::||||||||||||  !  !|||! !  !.!!|
        eAspThr---------------ValLeuTyrAlaIleGlyArgLysGlyAspIleAspGlyL
 7796 : TGATACT---------------GTTTTATATGCAATAGGTAGAAAAGGAGATATTGATGGAT : 7749

  326 : euAsnLeuGluLysAlaGlyValAspThrSerProAspThrGlnLysIleLeuValAspSer :  345
        ||||||||||||||  !..!:!!:!!! !!:!  !:!!!.!.!.||||||:!!..!|||..!
        euAsnLeuGluLysLeuAsnIleAsnIleAsnSerAsnAsnAsnLysIleIleThrAspGlu
 7748 : TAAATTTAGAAAAATTAAATATAAATATAAATAGTAATAATAATAAAATTATAACAGATGAA : 7689

  346 : ArgGluAlaThrSerValProHisIleTyrAlaIleGlyAspValValGluGlyArgProGl :  366
          !.....!|||!:!:!!|||:!!|||!:!|||:!!||||||:!!!.!|||..!  !|||||
        PheSerCysThrAsnIleProAsnIlePheAlaValGlyAspIleAlaGluAsnValProGl
 7688 : TTTAGTTGTACAAATATTCCTAACATTTTTGCAGTTGGCGACATTGCTGAAAATGTACCTGA : 7626

  367 : uLeuThrProIleAlaIleMetAlaGlyArgLeuLeuValGlnArgLeuPheGlyGlySerS :  387
        ||||.!!|||:!!||||||! !||||||..!:!!|||!.!!:!|||||||||  !..!|||!
        uLeuAlaProValAlaIleLysAlaGlyGluIleLeuAlaArgArgLeuPheLysAsnSerA
 7625 : GCTAGCTCCAGTAGCTATAAAGGCAGGTGAAATATTAGCTCGAAGATTATTTAAAAATTCGA : 7563

  388 : erAspLeuMetAspTyrAspAsnValProThrThrValPheThrProLeuGluTyrGlyCys :  407
        :!!!::!!||| ! |||:!!  !:!!||||||:!!:!!!:!||||||:!!|||||||||!  
        snGluIleMetLysTyrAsnPheIleProThrSerIleTyrThrProIleGluTyrGlySer
 7562 : ATGAAATTATGAAATATAATTTTATACCAACATCTATTTATACACCTATTGAATATGGATCA : 7503

  408 : ValGlyLeuSerGluGluGluAlaValAlaArgHisGlyGlnGluHisValGluValTyrHi :  428
          !|||! !|||||||||:!!|||  !! !  !  !|||:!!.!.:!!:!!|||:!!!:!  
        CysGlyTyrSerGluGluLysAlaTyrGluLeuPheGlyLysAsnAsnIleGluIlePheLe
 7502 : TGTGGATATTCTGAAGAAAAAGCATATGAATTATTTGGAAAAAATAATATTGAAATATTTTT : 7440

  429 : sAlaHisTyrLysProLeuGluPheThrValAlaGlyArgAspAla{S}  >>>> Target :  444
           !.!.!:!!!.  !||||||.!.:!!!.!!.!  !|||     !{ }            4
        uGlnGluPheAsnAsnLeuGluIleSerAlaValHisArgThrLys{A}-+           
 7439 : ACAAGAATTTAATAATTTAGAAATATCAGCAGTTCACAGAACAAAA{C}at........... : 7389

  445 :  Intron 1 >>>>  {er}GlnCysTyrValLysMetValCysLeuArgGluProProGln :  458
        2 bp            {!!}   |||!    !|||:!:|||||||||!:!.!.  !  !.!.
                      +-{rg}ThrCysLeuSerLysLeuValCysLeuLysAsnGluAspAsn
 7388 : ..............aa{GT}ACTTGTTTATCGAAACTTGTTTGTTTAAAAAATGAAGATAAT : 7308

  459 : LeuValLeuGlyLeuHisPheLeuGlyProAsnAlaGlyGluValThrGlnGlyPheAlaLe :  479
        ! !|||:!!|||!!!|||!:!:!!||||||||||||||||||||||||||||||.!.|||||
        ArgValValGlyPheHisTyrValGlyProAsnAlaGlyGluValThrGlnGlyMetAlaLe
 7307 : CGAGTTGTTGGTTTTCATTATGTTGGACCTAATGCAGGTGAAGTCACTCAAGGAATGGCATT : 7245

  480 : uGlyIleLysCysGlyAlaSerTyrAlaGlnValMetArgThrValGlyIleHisProThrC :  500
        |!.!:!!|||!  ..!|||!.! ! :!!.!. !!   !.!  !:!!||||||||||||||| 
        uAlaLeuLysLeuAsnAlaLysLysSerAspPheAspAsnCysIleGlyIleHisProThrA
 7244 : GGCTTTAAAATTAAATGCAAAGAAATCCGATTTTGATAACTGTATTGGAATTCATCCAACAG : 7182

  501 : ysSerGluGluValValLysLeuArgIleSerLysArgSerGlyLeuAspProThrValThr :  520
         !:!!|||..! !!:!!!!.|||  !|||!!!  !  !|||||||||..!  !.!!!.!! !
        spAlaGluSerPheMetAsnLeuSerIleThrLeuSerSerGlyLeuSerTyrAlaAlaLys
 7181 : ATGCAGAATCATTTATGAATCTATCAATTACTTTATCATCGGGTTTGTCTTATGCAGCAAAA : 7122

  521 : GlyCysUnkGly :  524
        ||| !    |||
        GlyGlyCysGly
 7121 : GGTGGATGTGGT : 7108

vulgar: SPP00000035_1.0 38 524 . gi|56500783|emb|CAAI01000787.1| 8595 7107 - 1031 M 70 210 G 0 3 M 8 24 G 1 0 M 56 168 G 0 6 M 116 348 G 1 0 M 16 48 G 5 0 M 132 396 S 0 1 5 0 2 I 0 38 3 0 2 S 1 2 M 80 240
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2009-02-27
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|56500783|emb|CAAI01000787.1|	exonerate:protein2genome:local	gene	7108	8595	1031	-	.	gene_id 1 ; sequence SPP00000035_1.0 ; gene_orientation +
gi|56500783|emb|CAAI01000787.1|	exonerate:protein2genome:local	cds	7392	8595	.	-	.	
gi|56500783|emb|CAAI01000787.1|	exonerate:protein2genome:local	exon	7392	8595	.	-	.	insertions 9 ; deletions 7
gi|56500783|emb|CAAI01000787.1|	exonerate:protein2genome:local	splice5	7390	7391	.	-	.	intron_id 1 ; splice_site "AT"
gi|56500783|emb|CAAI01000787.1|	exonerate:protein2genome:local	intron	7350	7391	.	-	.	intron_id 1
gi|56500783|emb|CAAI01000787.1|	exonerate:protein2genome:local	splice3	7350	7351	.	-	.	intron_id 0 ; splice_site "AA"
gi|56500783|emb|CAAI01000787.1|	exonerate:protein2genome:local	cds	7108	7349	.	-	.	
gi|56500783|emb|CAAI01000787.1|	exonerate:protein2genome:local	exon	7108	7349	.	-	.	insertions 0 ; deletions 0
gi|56500783|emb|CAAI01000787.1|	exonerate:protein2genome:local	similarity	7108	8595	1031	-	.	alignment_id 1 ; Query SPP00000035_1.0 ; Align 8596 39 210 ; Align 8383 109 24 ; Align 8359 118 168 ; Align 8185 174 348 ; Align 7837 291 48 ; Align 7789 312 396 ; Align 7348 445 240
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
