Command line: [exonerate -m p2g --showtargetgff -q queryanno.fa -t fastasubseqbernou.fa]
Hostname: [ws101144.aulescm.upf.edu]

C4 Alignment:
------------
         Query: TR1 #anophagefferens # scaffold_11:subseq(783554,7436).pep  
        Target: gi|56500783|emb|CAAI01000787.1|:subseq(5105,5495) Plasmodium berghei whole genome shotgun assembly, contig PB_RP0892, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 753
   Query range: 0 -> 397
  Target range: 3495 -> 2311

    1 : GlyPheAspTyrAspValValValValGlyGlyGlySerGlyGlyLeuAlaCysSerLysGl :   21
        ..!!:!|||||||||  !:!!|||:!!||||||||| !!||||||:!!|||!  :!!|||||
        AsnTyrAspTyrAspTyrIleValIleGlyGlyGlyProGlyGlyMetAlaSerAlaLysGl
 3495 : AATTATGACTATGATTATATAGTTATTGGTGGAGGCCCTGGAGGTATGGCATCAGCTAAAGA : 3435

   22 : uCysAlaLysLeuGlyAlaLysValAlaValLeuAspPheValLysProSerProAlaGlyS :   42
        |..!|||..!! !||||||||||||  !:!!!!!||||||||||||||||||  !  !|||!
        uAlaAlaSerHisGlyAlaLysValLeuLeuPheAspPheValLysProSerSerGlnGlyT
 3434 : AGCTGCTTCACACGGAGCTAAAGTTTTGCTATTTGATTTTGTTAAACCGAGTAGTCAAGGAA : 3372

   43 : erThrTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHis :   62
        !!! !||||||:!!|||||||||||||||||||||||||||:!!||||||||||||||||||
        hrLysTrpGlyIleGlyGlyThrCysValAsnValGlyCysValProLysLysLeuMetHis
 3371 : CAAAATGGGGTATTGGAGGTACATGTGTAAATGTCGGATGTGTACCGAAAAAGTTAATGCAC : 3312

   63 : ThrAlaSerIleIleGlyGluThrLeuLysAspAspAlaAlaAlaPheGlyTrpLysAspAl :   83
          !|||.!!! !!!:|||  !  !!!!|||:!!|||:!!! !  !!:!||||||   !!:..
        TyrAlaGlyAsnMetGlyThrLeuPheLysAsnAspSerAspLysTyrGlyTrp---GluCy
 3311 : TATGCAGGAAATATGGGAACATTATTTAAAAATGATTCGGATAAATATGGATGG---GAATG : 3252

   84 : aAlaAlaGlyAlaHisAspTrpGluSerMetLysSerThrValGlnAspHisIleLysSerL :  104
        !  !  !  !  !|||||||||.!.!.!:!:   ||||||||||||..!||||||:::||||
        sAsnAsnLeuLysHisAspTrpAsnLysLeuValSerThrValGlnSerHisIleArgSerL
 3251 : TAATAATTTAAAACATGATTGGAATAAATTAGTTAGTACTGTTCAGTCTCATATACGTTCAT : 3189

  105 : euAsnPheLysTyrArgValAlaLeuArgGluAla--GlyIleThrTyrLeuAsnArgLeuG :  124
        ||||||||!..|||! !:!!!.!|||!:!..!:!!##   :!!! !|||:!!||| !!|||!
        euAsnPheSerTyrMetIleGlyLeuLysSerSer##---ValLysTyrIleAsnGlyLeuA
 3188 : TAAATTTTAGTTATATGATAGGATTAAAATCATCAAA---GTTAAATATATTAATGGATTAG : 3130

  125 : lyGluPheGluAspLysAsnThrIleSer<-><->LeuThrAspLysLysGlyAsnLysThr :  142
        .!:!!!!.:!!:!!|||||||||:!!|||      |||! !! ! ! ..!..!!!.:!!  !
        laLysLeuLysAsnLysAsnThrValSerTyrTyrLeuLysGlyAspSerSerLysGluAsp
 3129 : CAAAATTAAAAAATAAAAATACAGTATCATATTATTTAAAAGGTGATTCATCTAAAGAAGAT : 3070

  143 : SerValThrAlaAlaArgPheIleValAlaValGlyGlyArgProAsnLysLeuGlyCysPr :  163
        !!!||||||!.!  !  !.!!:!!:!!|||..!||| !!|||||||||! !! !! !  !  
        CysValThrGlyLysTyrIleLeuIleAlaThrGlyCysArgProAsnIleProAspAspVa
 3069 : TGTGTAACAGGCAAATATATTTTAATTGCAACAGGATGTCGACCAAATATACCAGATGATGT : 3007

  164 : oGlyGly<-><->GluHisAlaIleAspSerAspAspLeuPheSerLeuProLysAlaProG :  182
        !  !|||      |||!  ::!|||  !|||||||||:!!|||||||||  !!!.! !||||
        lIleGlyAlaLysGluLeuSerIleThrSerAspAspIlePheSerLeuLysAsnAspProG
 3006 : TATAGGTGCTAAAGAACTAAGTATAACTTCTGATGATATATTTTCTTTAAAAAATGATCCTG : 2944

  183 : lyArgValLeuCysValGlyGlyGlyTyrIleAlaLeuGluCysGlyGlyPheThrAlaGly :  202
        ||!:!..!|||  !||||||!.!..!|||:!!||||||||||||!.!||||||  !  !..!
        lyLysThrLeuValValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPheLeuAsnSer
 2943 : GAAAAACGCTAGTTGTTGGTGCTTCTTATGTAGCTTTAGAATGTGCTGGATTTTTAAATTCA : 2884

  203 : MetGlyTyrProThrThrCysMetValArgSerIleLeuLeuArgGlyPheAspArgGluCy :  223
        :!:||||||  !||||||      ||||||||||||:!!|||||||||||||||!:!:!!||
        LeuGlyTyrAspThrThrValSerValArgSerIleIleLeuArgGlyPheAspGlnGlnCy
 2883 : TTAGGATATGATACAACTGTATCTGTACGTTCAATAATATTAAGAGGTTTTGATCAACAATG : 2821

  224 : sValGlyLysIleGluAlaHisIleLysHisHisGlyValGlnLeuGlnValGlyValThrP :  244
        |!.!..!||||||:!!  !:!!!!::!!.!.!!.||||||  !!!!..!  !|||:!!  !|
        sAlaAsnLysIleLysLeuTyrMetGluGluGlnGlyValThrPheMetCysGlyIleLeuP
 2820 : TGCAAATAAAATAAAATTATATATGGAAGAACAAGGTGTAACATTTATGTGTGGTATATTAC : 2758

  245 : roAlaLysIleGluLysAspAlaAlaThrGlyValLeuThrValThrAspSerGlyGlyGly :  264
        ||  !|||:!!   |||!!:      !.!! !  !:!!  !|||  !  !!:!..!..!  !
        roLysLysLeuThrLysGlu------AsnAspLysIleLeuValHisPheAsnAsnAsnThr
 2757 : CTAAAAAACTAACTAAAGAA------AATGACAAAATTTTAGTTCATTTTAATAATAATACT : 2704

  265 : ValHisGluTyrAspThrValLeuValAlaThrGlyArgTyrAlaAspThrAlaAlaLeuGl :  285
        ..!.!.  !!:!||||||||||||  !|||! !|||||| ! !.!|||! !! !!.!|||..
        ThrGluLeuPheAspThrValLeuTyrAlaIleGlyArgLysGlyAspIleAspGlyLeuAs
 2703 : ACAGAATTATTTGATACTGTTTTATATGCAATAGGTAGAAAAGGAGATATTGATGGATTAAA : 2641

  286 : yIleAspAsnValProGlyAlaSerAlaAsnValAsnAlaLysThrLysLysLeuGluCysV :  306
        !:!!!!:!!.:!!         !:!  !|||:!!|||::!!!.!.!!!.|||:!!  !   !
        nLeuGluLysLeu---------AsnIleAsnIleAsnSerAsnAsnAsnLysIleIleThrA
 2640 : TTTAGAAAAATTA---------AATATAAATATAAATAGTAATAATAATAAAATTATAACAG : 2587

  307 : alAspGluGlnLeuProGlyAlaProHisValTyrAlaIleGlyAspValValGluGlyArg :  326
         !!!:   ...! ! !!..!  !|||:!!:!!!:!|||:!!||||||:!!!.!|||..!  !
        spGluPheSerCysThrAsnIleProAsnIlePheAlaValGlyAspIleAlaGluAsnVal
 2586 : ATGAATTTAGTTGTACAAATATTCCTAACATTTTTGCAGTTGGCGACATTGCTGAAAATGTA : 2527

  327 : ProGluLeuThrProValAlaIleGluAlaGlyLeuArgLeuAlaArgArgLeuPheGlyGl :  347
        |||||||||.!!||||||||||||:!!||||||  !! !||||||||||||||||||  !..
        ProGluLeuAlaProValAlaIleLysAlaGlyGluIleLeuAlaArgArgLeuPheLysAs
 2526 : CCTGAGCTAGCTCCAGTAGCTATAAAGGCAGGTGAAATATTAGCTCGAAGATTATTTAAAAA : 2464

  348 : yLysThrGluProMetAspTyrGluCysValAlaThrThrIlePheThrProLeuGluTyrG :  368
        !..!!.!|||  !||| ! |||.!.! !:!! !!|||:!!|||!:!||||||:!!|||||||
        nSerAsnGluIleMetLysTyrAsnPheIleProThrSerIleTyrThrProIleGluTyrG
 2463 : TTCGAATGAAATTATGAAATATAATTTTATACCAACATCTATTTATACACCTATTGAATATG : 2401

  369 : lyThrIleGlyLeuSerGluAspAspAlaLysAlaGlnLeuGlyGluCysAsnValGluSer :  388
        ||:!!  !|||! !||||||!!: ! ||| ! ! !  !!!!|||:!!  !|||:!!|||! !
        lySerCysGlyTyrSerGluGluLysAlaTyrGluLeuPheGlyLysAsnAsnIleGluIle
 2400 : GATCATGTGGATATTCTGAAGAAAAAGCATATGAATTATTTGGAAAAAATAATATTGAAATA : 2341

  389 : TyrIleSerGluPheAlaProLeuGlu :  397
        !:!:!!..!||||||  !  !||||||
        PheLeuGlnGluPheAsnAsnLeuGlu
 2340 : TTTTTACAAGAATTTAATAATTTAGAA : 2312

vulgar: TR1 0 397 . gi|56500783|emb|CAAI01000787.1|:subseq(5105,5495) 3495 2311 - 753 M 80 240 G 1 0 M 34 102 F 0 2 G 1 0 M 17 51 G 0 6 M 32 96 G 0 6 M 85 255 G 2 0 M 37 111 G 3 0 M 105 315
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2010-03-15
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|56500783|emb|CAAI01000787.1|:subseq(5105,5495)	exonerate:protein2genome:local	gene	2312	3495	753	-	.	gene_id 1 ; sequence TR1 ; gene_orientation .
gi|56500783|emb|CAAI01000787.1|:subseq(5105,5495)	exonerate:protein2genome:local	cds	2312	3495	.	-	.	
gi|56500783|emb|CAAI01000787.1|:subseq(5105,5495)	exonerate:protein2genome:local	exon	2312	3495	.	-	.	insertions 12 ; deletions 7 ; frameshifts 2
gi|56500783|emb|CAAI01000787.1|:subseq(5105,5495)	exonerate:protein2genome:local	similarity	2312	3495	753	-	.	alignment_id 1 ; Query TR1 ; Align 3496 1 240 ; Align 3256 82 102 ; Align 3152 117 51 ; Align 3095 134 96 ; Align 2993 166 255 ; Align 2738 253 111 ; Align 2627 293 315
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: TR1 #anophagefferens # scaffold_11:subseq(783554,7436).pep  
        Target: gi|56500783|emb|CAAI01000787.1|:subseq(5105,5495) Plasmodium berghei whole genome shotgun assembly, contig PB_RP0892, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 205
   Query range: 410 -> 488
  Target range: 2239 -> 1999

  411 : CysPheAlaLysLeuVal<->ValAspLysSerThrGlyLysValValGlyPheHisTyrLe :  430
        |||!!.:!!|||||||||   :!! ! !!...!  !..!::!||||||||||||||||||:!
        CysLeuSerLysLeuValCysLeuLysAsnGluAspAsnArgValValGlyPheHisTyrVa
 2239 : TGTTTATCGAAACTTGTTTGTTTAAAAAATGAAGATAATCGAGTTGTTGGTTTTCATTATGT : 2179

  431 : uGlyProAsnAlaGlyGluIleThrGlnGlyPheSerIleAlaMetArgLysGlyAlaThrT :  451
        !||||||||||||||||||:!!|||||||||.!.:!!:!:|||:!:!:!  !..!|||! ! 
        lGlyProAsnAlaGlyGluValThrGlnGlyMetAlaLeuAlaLeuLysLeuAsnAlaLysL
 2178 : TGGACCTAATGCAGGTGAAGTCACTCAAGGAATGGCATTGGCTTTAAAATTAAATGCAAAGA : 2116

  452 : yrAlaAspPheIleSerThrValGlyIleHisProThrValAlaGluGluPheThrSerMet :  471
        ! :!!||||||  !!:!  !:!!|||||||||||||||! !||||||..!|||! !!:!:!:
        ysSerAspPheAspAsnCysIleGlyIleHisProThrAspAlaGluSerPheMetAsnLeu
 2115 : AATCCGATTTTGATAACTGTATTGGAATTCATCCAACAGATGCAGAATCATTTATGAATCTA : 2056

  472 : ThrValThrLysSerSerGlyGluSer<->AlaAlaLysGlyGlyCysUnkGly :  488
        :!!:!!|||  !|||||||||  !|||   ||||||||||||||||||   |||
        SerIleThrLeuSerSerGlyLeuSerTyrAlaAlaLysGlyGlyCysGlyGly
 2055 : TCAATTACTTTATCATCGGGTTTGTCTTATGCAGCAAAAGGTGGATGTGGTGGA : 2000

vulgar: TR1 410 488 . gi|56500783|emb|CAAI01000787.1|:subseq(5105,5495) 2239 1999 - 205 M 6 18 G 0 3 M 64 192 G 0 3 M 8 24
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2010-03-15
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|56500783|emb|CAAI01000787.1|:subseq(5105,5495)	exonerate:protein2genome:local	gene	2000	2239	205	-	.	gene_id 2 ; sequence TR1 ; gene_orientation .
gi|56500783|emb|CAAI01000787.1|:subseq(5105,5495)	exonerate:protein2genome:local	cds	2000	2239	.	-	.	
gi|56500783|emb|CAAI01000787.1|:subseq(5105,5495)	exonerate:protein2genome:local	exon	2000	2239	.	-	.	insertions 6 ; deletions 0
gi|56500783|emb|CAAI01000787.1|:subseq(5105,5495)	exonerate:protein2genome:local	similarity	2000	2239	205	-	.	alignment_id 2 ; Query TR1 ; Align 2240 411 18 ; Align 2219 417 192 ; Align 2024 481 24
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
