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

C4 Alignment:
------------
         Query: SPP00000034_1.0 # Protein # Thioredoxin reductase 1 (TR1)
        Target: scaffold_11:subseq(784530,5460) [revcomp]
         Model: protein2genome:local
     Raw score: 692
   Query range: 9 -> 258
  Target range: 3463 -> 2716

   10 : SerTyrAspTyrAspLeuIleIleIleGlyGlyGlySerGlyGlyLeuAlaAlaAlaLysGl :   30
        ...:::|||||||||::::::::::::||||||||||||||||||||||||..!:!!|||||
        GlyPheAspTyrAspValValValValGlyGlyGlySerGlyGlyLeuAlaCysSerLysGl
 3463 : ggcttcgactacgacgtcgtcgtcgtcggcggcggctccggcggcCTCGCCTGCTCCAAGGA : 3403

   31 : uAlaAlaGlnTyrGlyLysLysValMetValLeuAspPheValThrProThrProLeuGlyT :   51
        |..!|||:!!  !|||   ||||||   |||||||||||||||! !|||:!!|||  !|||:
        uCysAlaLysLeuGlyAlaLysValAlaValLeuAspPheValLysProSerProAlaGlyS
 3402 : GTGCGCGAAGCTCGGCGCCAAGGTCGCCGTGCTCGACTTCGTGAAGCCGTCGCCGGCGGGGT : 3340

   52 : hrArgTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHis :   71
        !!! !|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        erThrTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHis
 3339 : CGACGTGGGGCCTCGGCGGCACGTGCGTCAACGTCGGCTGCATCCCGAAGAAGCTCATGCAC : 3280

   72 : GlnAlaAlaLeuLeuGlyGlnAlaLeuGln<->AspSerArgAsnTyrGlyTrpLysValGl :   91
          !|||:!!:!!:!!|||:!!.!!|||:!!   |||:!!  !  !!:!|||||||||! !! 
        ThrAlaSerIleIleGlyGluThrLeuLysAspAspAlaAlaAlaPheGlyTrpLysAspAl
 3279 : ACGGCGTCCATCATCGGCGAGACGCTCAAGGACGACGCCGCCGCCTTCGGGTGGAAGGACGC : 3217

   92 : uGluThrValLysHisAspTrpAspArgMetIleGluAlaValGlnAsnHisIleGlySerL :  112
         !  .!!! !  !|||||||||!!:  !|||!  ..!.!!||||||:!!||||||  !||||
        aAlaAlaGlyAlaHisAspTrpGluSerMetLysSerThrValGlnAspHisIleLysSerL
 3216 : CGCCGCGGGCGCGCACGACTGGGAGTCGATGAAGTCGACGGTGCAGGACCACATCAAGTCGC : 3154

  113 : euAsnTrpGlyTyrArgValAlaLeuArgGluLysLysValValTyrGluAsnAlaTyrGly :  132
        |||||!::  !|||||||||||||||||||||  !   :!!..!|||  !|||  !  !|||
        euAsnPheLysTyrArgValAlaLeuArgGluAlaGlyIleThrTyrLeuAsnArgLeuGly
 3153 : TCAACTTCAAGTACCGCGTCGCGCTCCGCGAGGCGGGCATCACCTACCTGAACCGCCTCGGC : 3094

  133 : GlnPheIleGlyProHisArgIleLysAlaThrAsnAsnLysGlyLysGluLysIleTyrSe :  153
        :!!|||   ! !  !:!!! !|||...  !|||:!!!!.||||||!!.:!!! !  !  !!!
        GluPheGluAspLysAsnThrIleSerLeuThrAspLysLysGlyAsnLysThrSerValTh
 3093 : GAGTTCGAGGACAAGAACACCATCTCCCTCACGGACAAGAAGGGCAACAAGACGTCCGTCAC : 3031

  154 : rAlaGluArgPheLeuIleAlaThrGlyGluArgProArgTyrLeuGlyIleProGlyAspL :  174
        !|||! !||||||:!!:!!|||..!|||!  ||||||!.! ! ||||||  !||||||! ! 
        rAlaAlaArgPheIleValAlaValGlyGlyArgProAsnLysLeuGlyCysProGlyGly-
 3030 : GGCCGCGCGGTTCATCGTCGCCGTCGGCGGCCGCCCGAACAAGCTCGGCTGCCCCGGCGGC- : 2968

  175 : ysGluTyrCysIleSerSerAspAspLeuPheSerLeuProTyrCysProGlyLysThrLeu :  194
          |||:!!..!|||..!|||||||||||||||||||||||| ! ...||||||:::..!|||
        --GluHisAlaIleAspSerAspAspLeuPheSerLeuProLysAlaProGlyArgValLeu
 2967 : --GAGCACGCCATCGACAGCGACGACCTGTTCTCCCTGCCCAAGGCGCCGGGCCGCGTGCTC : 2911

  195 : ValValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPheLeuAlaGlyIleGlyLeuAs :  215
          !||||||!.!.!!|||:!!||||||||||||!.!||||||  !||||||!!:|||! !  
        CysValGlyGlyGlyTyrIleAlaLeuGluCysGlyGlyPheThrAlaGlyMetGlyTyrPr
 2910 : TGCGTCGGCGGCGGCTACATCGCGCTCGAGTGCGGCGGCTTCACGGCCGGCATGGGCTACCC : 2848

  216 : pValThrValMetValArgSerIleLeuLeuArgGlyPheAspGlnAspMetAlaAsnLysI :  236
         ..!|||  !|||||||||||||||||||||||||||||||||!::!!:   !.!..!||||
        oThrThrCysMetValArgSerIleLeuLeuArgGlyPheAspArgGluCysValGlyLysI
 2847 : GACGACGTGCATGGTCCGGTCCATCCTCCTCCGCGGCTTCGACCGCGAGTGCGTCGGCAAGA : 2785

  237 : leGlyGluHisMetGluGluHisGlyIleLysPheIleArgGlnPheValProIleLysVal :  256
        ||! !!  |||!!::!!.!.||||||:!!:!!.!!     !    !!..!|||   |||:!!
        leGluAlaHisIleLysHisHisGlyValGlnLeuGlnValGlyValThrProAlaLysIle
 2784 : TCGAGGCCCACATCAAGCACCACGGCGTCCAGCTCCAGGTCGGCGTCACGCCCGCGAAGATC : 2725

  257 : GluGln :  258
        |||:!!
        GluLys
 2724 : GAGAAG : 2717

vulgar: SPP00000034_1.0 9 258 . scaffold_11:subseq(784530,5460) 3463 2716 - 692 M 72 216 G 0 3 M 92 276 G 1 0 M 84 252
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2010-03-08
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_11:subseq(784530,5460)	exonerate:protein2genome:local	gene	2717	3463	692	-	.	gene_id 1 ; sequence SPP00000034_1.0 ; gene_orientation .
scaffold_11:subseq(784530,5460)	exonerate:protein2genome:local	cds	2717	3463	.	-	.	
scaffold_11:subseq(784530,5460)	exonerate:protein2genome:local	exon	2717	3463	.	-	.	insertions 3 ; deletions 1
scaffold_11:subseq(784530,5460)	exonerate:protein2genome:local	similarity	2717	3463	692	-	.	alignment_id 1 ; Query SPP00000034_1.0 ; Align 3464 10 216 ; Align 3245 82 276 ; Align 2969 175 252
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000034_1.0 # Protein # Thioredoxin reductase 1 (TR1)
        Target: scaffold_11:subseq(784530,5460) [revcomp]
         Model: protein2genome:local
     Raw score: 487
   Query range: 282 -> 499
  Target range: 2665 -> 1999

  283 : GluTyrAsnThrValMetLeuAlaIleGlyArgAspAlaCysThrArgLysIleGlyLeuGl :  303
        ||||||:!!||||||:!::!!|||!  |||||| !!|||  !|||  !   :!!|||:!!!!
        GluTyrAspThrValLeuValAlaThrGlyArgTyrAlaAspThrAlaAlaLeuGlyIleAs
 2665 : GAGTACGACACGGTGCTCGTCGCGACGGGCCGCTACGCGGACACGGCGGCCCTCGGCATCGA : 2605

  304 : uThrVal<-><-><->GlyValLysIleAsnGluLysThrGlyLysIleProValThrAspG :  321
        :!.!|||         ..!!.!!!.:!:|||! !||||||  !|||:!!  !  !..!||||
        pAsnValProGlyAlaSerAlaAsnValAsnAlaLysThrLysLysLeuGluCysValAspG
 2604 : CAACGTGCCCGGCGCGTCGGCGAACGTGAACGCGAAGACGAAGAAGCTCGAGTGCGTCGACG : 2542

  322 : luGluGlnThrAsnValProTyrIleTyrAlaIleGlyAspIleLeuGluAspLysValGlu :  341
        ||:!!! ! !!..!!.!|||:!!:!!|||||||||||||||:!!:!!|||! !::!  !|||
        luGlnLeuProGlyAlaProHisValTyrAlaIleGlyAspValValGluGlyArgProGlu
 2541 : AGCAGCTGCCCGGCGCGCCGCACGTCTACGCGATCGGCGACGTCGTCGAGGGCCGGCCCGAG : 2482

  342 : LeuThrProValAlaIleGlnAlaGlyArgLeuLeuAlaGlnArgLeuTyrAlaGlySerTh :  362
        ||||||||||||||||||:!!||||||! !! !||||||!:!||||||!:!!.!|||!.!||
        LeuThrProValAlaIleGluAlaGlyLeuArgLeuAlaArgArgLeuPheGlyGlyLysTh
 2481 : CTCACGCCCGTCGCCATCGAGGCGGGCCTGCGCCTCGCGCGGCGCCTCTTCGGCGGCAAGAC : 2419

  363 : rValLysCysAspTyrGluAsnValProThrThrValPheThrProLeuGluTyrGlyAlaC :  383
        |! !      |||||||||  !||| !!||||||:!!|||||||||||||||||||||.!! 
        rGluProMetAspTyrGluCysValAlaThrThrIlePheThrProLeuGluTyrGlyThrI
 2418 : CGAGCCCATGGACTACGAGTGCGTCGCGACGACGATCTTCACGCCGCTCGAGTACGGCACGA : 2356

  384 : ysGlyLeuSerGluGluLysAlaValGluLysPheGlyGluGluAsnIleGluValTyrHis :  403
         !||||||||||||!!: ! |||  !!  :!!.!!||||||   |||:!!|||  !|||  !
        leGlyLeuSerGluAspAspAlaLysAlaGlnLeuGlyGluCysAsnValGluSerTyrIle
 2355 : TCGGGCTGAGCGAGGACGACGCCAAGGCCCAGCTCGGCGAGTGCAACGTCGAGTCCTACATC : 2296

  404 : SerTyrPheTrpProLeuGluTrpThrIlePro<-><-><->SerArgAspAsnAsnLysCy :  421
        ||| ! |||  !|||||||||!::.!!:!!  !         |||..!  !..!:!!   ||
        SerGluPheAlaProLeuGluTyrAlaLeuSerGluThrArgSerGluArgGlyAspGlyCy
 2295 : AGCGAGTTCGCGCCCCTCGAGTACGCCCTCAGCGAGACGCGCAGCGAGCGCGGCGACGGCTG : 2233

  422 : sTyrAlaLysIleIleCysAsnThrLysAspAsnGluArgValValGlyPheHisValLeuG :  442
        |!:!||||||:!!:!!  !:!!   |||..!!..!  !:!|||||||||||||||  !||||
        sPheAlaLysLeuValValAsp---LysSerThrGlyLysValValGlyPheHisTyrLeuG
 2232 : CTTCGCCAAGCTCGTCGTCGAC---AAGAGCACGGGCAAGGTCGTCGGCTTCCACTACCTCG : 2173

  443 : lyProAsnAlaGlyGluValThrGlnGlyPheAlaAlaAlaLeuLysCysGlyLeuThrLys :  462
        |||||||||||||||||:!!||||||||||||:!!  !|||:!!:::   |||  !||| ! 
        lyProAsnAlaGlyGluIleThrGlnGlyPheSerIleAlaMetArgLysGlyAlaThrTyr
 2172 : GCCCCAACGCCGGCGAGATCACCCAGGGCTTCTCCATCGCCATGCGCAAGGGCGCGACCTAC : 2113

  463 : LysGlnLeuAspSerThrIleGlyIleHisProValCysAlaGluValPheThrThrLeuSe :  483
           .!.!!!  !||||||:!!||||||||||||..!  !||||||! !||||||:!!:!!!!
        AlaAspPheIleSerThrValGlyIleHisProThrValAlaGluGluPheThrSerMetTh
 2112 : GCCGACTTCATCTCCACCGTCGGCATCCACCCGACGGTCGCCGAGGAGTTCACGTCCATGAC : 2050

  484 : rValThrLysArgSerGlyAlaSerIleLeuGlnAlaGlyCysUnkGly :  499
        !|||||||||  !||||||! !|||  !  !:!!!.!||||||   |||
        rValThrLysSerSerGlyGluSerAlaAlaLysGlyGlyCys***Gly
 2049 : CGTGACCAAGTCGAGCGGCGAGTCCGCAGCCAAGGGCGGCTGCTGAGGC : 2000

vulgar: SPP00000034_1.0 282 499 . scaffold_11:subseq(784530,5460) 2665 1999 - 487 M 23 69 G 0 9 M 109 327 G 0 9 M 14 42 G 1 0 M 70 210
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2010-03-08
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_11:subseq(784530,5460)	exonerate:protein2genome:local	gene	2000	2665	487	-	.	gene_id 2 ; sequence SPP00000034_1.0 ; gene_orientation .
scaffold_11:subseq(784530,5460)	exonerate:protein2genome:local	cds	2000	2665	.	-	.	
scaffold_11:subseq(784530,5460)	exonerate:protein2genome:local	exon	2000	2665	.	-	.	insertions 18 ; deletions 1
scaffold_11:subseq(784530,5460)	exonerate:protein2genome:local	similarity	2000	2665	487	-	.	alignment_id 2 ; Query SPP00000034_1.0 ; Align 2666 283 69 ; Align 2588 306 327 ; Align 2252 415 42 ; Align 2210 430 210
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
