Command line: [exonerate -m p2g --showtargetgff -q queryANOPHA.fa -t fastasubseqanophaVSchabaudi.fa]
Hostname: [ws101088.aulescm.upf.edu]

C4 Alignment:
------------
         Query: TR1 #anophagefferens # scaffold_11:subseq(783554,7436).pep  
        Target: gi|56525189|emb|CAAJ01002935.1|:subseq(3556,1893) Plasmodium chabaudi whole genome shotgun assembly, contig PC_RP3210, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 811
   Query range: 0 -> 397
  Target range: 1696 -> 511

    1 : GlyPheAspTyrAspValValValValGlyGlyGlySerGlyGlyLeuAlaCysSerLysGl :   21
        ..!!:!|||||||||  !:!!|||:!!||||||||| !!||||||:!!|||! !:!!|||||
        AsnTyrAspTyrAspTyrIleValIleGlyGlyGlyProGlyGlyMetAlaSerAlaLysGl
 1696 : AATTACGACTATGATTATATAGTTATTGGTGGAGGACCTGGTGGTATGGCATCCGCTAAAGA : 1636

   22 : uCysAlaLysLeuGlyAlaLysValAlaValLeuAspPheValLysProSerProAlaGlyS :   42
        |..!|||..!! !||||||||||||  !:!!!!!|||||||||||||||||| !!  !|||!
        uAlaAlaSerHisGlyAlaLysValLeuLeuPheAspPheValLysProSerThrGlnGlyT
 1635 : AGCTGCTTCACATGGAGCTAAAGTTTTGCTATTTGATTTTGTTAAGCCAAGTACCCAAGGAA : 1573

   43 : erThrTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHis :   62
        !!! !||||||:!!|||||||||||||||||||||||||||:!!||||||||||||||||||
        hrLysTrpGlyIleGlyGlyThrCysValAsnValGlyCysValProLysLysLeuMetHis
 1572 : CAAAATGGGGTATTGGAGGTACATGCGTAAATGTAGGATGTGTACCAAAAAAGTTAATGCAT : 1513

   63 : ThrAlaSerIleIleGlyGluThrLeuLysAspAspAlaAlaAlaPheGlyTrpLysAspAl :   83
          !|||.!!! !!!:|||     !!!!|||:!!|||:!!! !  !!:!||||||   |||..
        TyrAlaGlyAsnMetGlyThrLeuPheLysAsnAspSerGluLysTyrGlyTrp---AspCy
 1512 : TATGCAGGAAATATGGGAACCTTATTTAAAAATGATTCAGAGAAATATGGATGG---GATTG : 1453

   84 : aAlaAlaGlyAlaHisAspTrpGluSerMetLysSerThrValGlnAspHisIleLysSerL :  104
        !! !  !  !  !|||||||||.!.!.!:!:   ||||||||||||..!||||||:::||||
        sAspAsnLeuLysHisAspTrpAsnLysLeuValSerThrValGlnSerHisIleArgSerL
 1452 : TGATAATCTAAAACATGATTGGAATAAATTAGTTAGCACTGTTCAGTCTCATATACGTTCAT : 1390

  105 : euAsnPheLysTyrArgValAlaLeuArgGluAlaGlyIleThrTyrLeuAsnArgLeuGly :  124
        ||||||||!..|||! !|||!.!|||!:!...:!!  !:!!! !|||:!!||| !!|||!.!
        euAsnPheSerTyrMetValGlyLeuLysSerSerLysValLysTyrIleAsnGlyLeuAla
 1389 : TAAATTTTAGTTATATGGTAGGATTAAAATCTTCGAAAGTAAAATATATTAACGGGTTAGCT : 1330

  125 : GluPheGluAspLysAsnThrIleSer<-><->LeuThrAspLysLysGlyAsnLysThrSe :  143
        :!!!!.:!!||||||||||||:!:|||      |||! !! ! ! !  ..!!!.:!!  !!!
        LysLeuLysAspLysAsnThrValSerTyrTyrLeuLysGlyAspThrSerLysGluGluCy
 1329 : AAATTAAAAGATAAAAATACAGTGTCATATTATTTAAAAGGTGATACTTCTAAAGAAGAATG : 1267

  144 : rValThrAlaAlaArgPheIleValAlaValGlyGlyArgProAsnLysLeuGlyCysProG :  164
        !||||||!.!  !  !.!!:!!||||||..!||| !!|||||||||! !! !! !  !  ! 
        sValThrGlyLysTyrIleLeuValAlaThrGlyCysArgProAsnIleProAspAspValI
 1266 : TGTAACAGGAAAATATATTTTAGTTGCAACAGGATGTAGACCAAATATACCAGATGATGTTA : 1204

  165 : lyGly<-><->GluHisAlaIleAspSerAspAspLeuPheSerLeuProLysAlaProGly :  182
         !|||      |||!  ::!|||  !|||||||||:!!|||||||||  !!:!..!||||||
        leGlyAlaLysGluLeuSerIleThrSerAspAspIlePheSerLeuLysArgCysProGly
 1203 : TAGGTGCTAAAGAACTAAGTATAACTTCTGATGATATATTCTCTTTAAAAAGATGTCCAGGA : 1144

  183 : ArgValLeuCysValGlyGlyGlyTyrIleAlaLeuGluCysGlyGlyPheThrAlaGlyMe :  203
        !:!..!|||  !||||||!.!..!|||:!!||||||||||||!.!||||||  !  !..!:!
        LysThrLeuValValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPheLeuAsnSerLe
 1143 : AAAACATTAGTTGTTGGTGCTTCATATGTAGCTTTAGAATGTGCTGGTTTTTTAAATTCATT : 1081

  204 : tGlyTyrProThrThrCysMetValArgSerIleLeuLeuArgGlyPheAspArgGluCysV :  224
        :||||||  !..!|||      ||||||||||||:!!|||||||||||||||!:!:!!|||!
        uGlyTyrAspValThrIleSerValArgSerIleIleLeuArgGlyPheAspGlnGlnCysA
 1080 : AGGTTATGATGTAACAATATCAGTACGTTCGATAATATTAAGAGGCTTTGATCAACAGTGTG : 1018

  225 : alGlyLysIleGluAlaHisIleLysHisHisGlyValGlnLeuGlnValGlyValThrPro :  244
        .!..!||||||:!!  !:!!!!::!!.!.!!.||||||  !!!!..!..!||||||  !|||
        laAsnLysIleLysLeuTyrMetGluGluGlnGlyValThrPheMetThrGlyValLeuPro
 1017 : CAAATAAAATAAAATTATATATGGAAGAACAAGGTGTAACATTTATGACTGGTGTGTTACCT :  958

  245 : AlaLysIleGluLysAspAlaAlaThrGlyValLeuThrValThrAspSerGlyGlyGlyVa :  265
          !|||:!!  !|||!!:      !.!! !  !:!!  !|||  !  !!:!..!! !  !..
        LysLysLeuThrLysGlu------AsnAspLysIleLeuValHisPheAsnAsnAspThrTh
  957 : AAAAAACTAACAAAAGAA------AATGATAAAATCCTCGTCCATTTTAATAATGATACTAC :  901

  266 : lHisGluTyrAspThrValLeuValAlaThrGlyArgTyrAlaAspThrAlaAlaLeuGlyI :  286
        !.!.! !!:!||||||||||||  !|||! !|||||| ! !.!|||! !! !!.!|||..!:
        rGluValPheAspThrValLeuTyrAlaIleGlyArgLysGlyAspIleAspGlyLeuAsnL
  900 : AGAAGTATTTGATACTGTTTTATATGCAATAGGTAGAAAGGGAGATATCGATGGTTTAAATT :  838

  287 : leAspAsnValProGlyAlaSerAlaAsnValAsnAlaLysThrLysLysLeuGluCysVal :  306
        !!!!:!!.:!!         !:!  !|||:!!|||  !!!.!.!||||||:!!  !...! !
        euGluLysLeu---------AsnIleAsnIleAsnAsnAsnAsnLysLysIleIleAlaAsp
  837 : TAGAAAAATTA---------AATATAAATATAAATAATAATAATAAAAAAATAATAGCAGAT :  787

  307 : AspGluGlnLeuProGlyAlaProHisValTyrAlaIleGlyAspValValGluGlyArgPr :  327
        .!.   ...! ! !!..!  !|||:!!:!!!:!|||:!!||||||:!!!.!|||..!  !||
        GlnPheSerCysThrAsnIleProAsnIlePheAlaValGlyAspIleAlaGluAsnValPr
  786 : CAATTTAGCTGTACAAATATTCCTAATATTTTTGCAGTTGGAGATATTGCTGAAAATGTACC :  724

  328 : oGluLeuThrProValAlaIleGluAlaGlyLeuArgLeuAlaArgArgLeuPheGlyGlyL :  348
        |||||||.!!||||||||||||:!!||||||  !! !||||||||||||||||||  !..!.
        oGluLeuAlaProValAlaIleLysAlaGlyGluIleLeuAlaArgArgLeuPheLysAsnS
  723 : TGAGCTAGCACCAGTAGCTATAAAAGCAGGAGAAATATTGGCTAGACGATTATTTAAAAATT :  661

  349 : ysThrGluProMetAspTyrGluCysValAlaThrThrIlePheThrProLeuGluTyrGly :  368
        .!!.!|||  !||| ! |||!!:! !:!! !!|||:!!|||!:!||||||:!!|||||||||
        erAsnGluIleMetLysTyrAspPheIleProThrSerIleTyrThrProIleGluTyrGly
  660 : CAAATGAAATTATGAAATATGATTTTATACCAACATCAATTTATACACCTATTGAATATGGA :  601

  369 : ThrIleGlyLeuSerGluAspAspAlaLysAlaGlnLeuGlyGluCysAsnValGluSerTy :  389
        :!!  !|||! !||||||!!: ! ||| ! ! !  !!!!|||:!!  !|||:!!|||  !!:
        SerCysGlyTyrSerGluGluLysAlaTyrGluIlePheGlyLysAsnAsnIleGluValPh
  600 : TCATGTGGATACTCAGAAGAAAAAGCATATGAAATATTTGGAAAAAATAATATCGAAGTATT :  538

  390 : rIleSerGluPheAlaProLeuGlu :  397
        !:!!..!||||||  !  !||||||
        eLeuGlnGluPheAsnAsnLeuGlu
  537 : TTTACAAGAATTTAATAATTTAGAA :  512

vulgar: TR1 0 397 . gi|56525189|emb|CAAJ01002935.1|:subseq(3556,1893) 1696 511 - 811 M 80 240 G 1 0 M 52 156 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 2010-03-10
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|56525189|emb|CAAJ01002935.1|:subseq(3556,1893)	exonerate:protein2genome:local	gene	512	1696	811	-	.	gene_id 1 ; sequence TR1 ; gene_orientation .
gi|56525189|emb|CAAJ01002935.1|:subseq(3556,1893)	exonerate:protein2genome:local	cds	512	1696	.	-	.	
gi|56525189|emb|CAAJ01002935.1|:subseq(3556,1893)	exonerate:protein2genome:local	exon	512	1696	.	-	.	insertions 12 ; deletions 6
gi|56525189|emb|CAAJ01002935.1|:subseq(3556,1893)	exonerate:protein2genome:local	similarity	512	1696	811	-	.	alignment_id 1 ; Query TR1 ; Align 1697 1 240 ; Align 1457 82 156 ; Align 1295 134 96 ; Align 1193 166 255 ; Align 938 253 111 ; Align 827 293 315
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: TR1 #anophagefferens # scaffold_11:subseq(783554,7436).pep  
        Target: gi|56525189|emb|CAAJ01002935.1|:subseq(3556,1893) Plasmodium chabaudi whole genome shotgun assembly, contig PC_RP3210, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 216
   Query range: 410 -> 488
  Target range: 439 -> 199

 411 : CysPheAlaLysLeuValValAspLysSer<->ThrGlyLysValValGlyPheHisTyrLeuG : 431
       ||||||:!!|||||||||  !   |||!:!     !..!::!||||||||||||||||||:!!|
       CysPheSerLysLeuValCysLeuLysAsnGluAspAsnArgValValGlyPheHisTyrValG
 439 : TGCTTTTCTAAACTTGTATGTTTAAAAAACGAAGATAATCGAGTTGTTGGTTTTCATTATGTTG : 376

 432 : lyProAsnAlaGlyGluIleThrGlnGlyPheSerIleAlaMetArgLysGlyAlaThrTyrAl : 452
       |||||||||||||||||:!!|||||||||.!.:!!:!!|||:!:!:!  !..!|||! ! ! :!
       lyProAsnAlaGlyGluValThrGlnGlyMetAlaLeuAlaLeuLysLeuAsnAlaLysLysSe
 375 : GACCTAATGCAGGTGAAGTTACTCAAGGAATGGCATTAGCTTTAAAATTAAATGCAAAGAAATC : 313

 453 : aAspPheIleSerThrValGlyIleHisProThrValAlaGluGluPheThrSerMetThrVal : 473
       !||||||  !!:!  !:!!|||||||||||||||! !||||||..!|||! !!:!:!:|||:!!
       rAspPheAspAsnCysIleGlyIleHisProThrAspAlaGluSerPheMetAsnLeuThrIle
 312 : CGATTTTGATAACTGTATTGGAATACATCCAACAGATGCAGAATCATTTATGAATCTAACAATT : 250

 474 : ThrLysSerSerGlyGluSer<->AlaAlaLysGlyGlyCysUnkGly : 488
       |||  !|||||||||  !|||   ||||||||||||||||||   |||
       ThrLeuSerSerGlyLeuSerTyrAlaAlaLysGlyGlyCysGlyGly
 249 : ACTTTATCATCTGGTTTGTCTTATGCTGCTAAAGGTGGATGTGGTGGA : 200

vulgar: TR1 410 488 . gi|56525189|emb|CAAJ01002935.1|:subseq(3556,1893) 439 199 - 216 M 10 30 G 0 3 M 60 180 G 0 3 M 8 24
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2010-03-10
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|56525189|emb|CAAJ01002935.1|:subseq(3556,1893)	exonerate:protein2genome:local	gene	200	439	216	-	.	gene_id 2 ; sequence TR1 ; gene_orientation .
gi|56525189|emb|CAAJ01002935.1|:subseq(3556,1893)	exonerate:protein2genome:local	cds	200	439	.	-	.	
gi|56525189|emb|CAAJ01002935.1|:subseq(3556,1893)	exonerate:protein2genome:local	exon	200	439	.	-	.	insertions 6 ; deletions 0
gi|56525189|emb|CAAJ01002935.1|:subseq(3556,1893)	exonerate:protein2genome:local	similarity	200	439	216	-	.	alignment_id 2 ; Query TR1 ; Align 440 411 30 ; Align 407 421 180 ; Align 224 481 24
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
