Command line: [exonerate -m p2g --showtargetgff -q ../Exonerate/querysambX/TR2.fa -t ../fastasubseq/fastasubseqexit/2011_tblastn/H.arabidopsidis/TR2/h1/fastasubseq_TR2_H.ara_h1.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query: SPP00000035_1.0 # Protein # Thioredoxin reductase 2 (TR2) # Homo sapiens # Complete
        Target: gi|199611737|gb|ABWE01000075.1|:subseq(6040,30000) Hyaloperonospora parasitica strain Emoy2 v-7.0.1_Cont51.5, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 1117
   Query range: 38 -> 524
  Target range: 19999 -> 21472

    39 : AspTyrAspLeuLeuValValGlyGlyGlySerGlyGlyLeuAlaCysAlaLysGluAla :    58
         ||||||||||||:!!|||:!!|||||||||||||||||||||||||||:!!|||||||||
         AspTyrAspLeuValValIleGlyGlyGlySerGlyGlyLeuAlaCysSerLysGluAla
 20000 : GACTACGACCTGGTGGTAATTGGTGGGGGTTCCGGGGGCTTGGCATGCTCTAAGGAGGCT : 20057

    59 : AlaGlnLeuGlyArgLysValAlaValValAspTyrValGluProSerProGlnGlyThr :    78
         |||..!!!!|||!:!||||||..!|||:!!|||||||||:!!|||||||||!!.||||||
         AlaSerPheGlyLysLysValCysValLeuAspTyrValLysProSerProHisGlyThr
 20058 : GCTTCATTCGGGAAAAAGGTGTGTGTGCTCGACTACGTGAAACCGTCTCCTCACGGAACG : 20117

    79 : ArgTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHis :    98
           !|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         SerTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHis
 20118 : TCATGGGGTCTTGGCGGCACGTGTGTCAATGTTGGCTGCATTCCAAAGAAACTGATGCAC : 20177

    99 : GlnAlaAlaLeuLeuGlyGlyLeuIle<->GlnAspAlaProAsnTyrGlyTrpGluVal :   117
         |||::!:!!|||:!!|||! !:!!:!:   !!.|||..! !!!:!!:!||||||.!.|||
         GlnSerSerLeuIleGlyGluIleLeuHisHisAspCysAlaSerPheGlyTrpAsnVal
 20178 : CAAAGCTCATTGATCGGTGAGATACTGCATCATGACTGCGCGAGCTTTGGTTGGAACGTC : 20237

   118 : <-><-><-><->AlaGlnProValProHisAspTrpArgLysMetAlaGluAlaValGln :   133
                     !.!|||  !  ! !!  !||||||!:!:!!:!:!.!..!  !|||...
         GlySerValAsnGlyGlnValProThrPheAspTrpLysGlnLeuValSerAsnValSer
 20238 : GGGAGTGTGAATGGGCAGGTCCCGACGTTTGATTGGAAGCAGCTCGTGTCGAACGTTAGC : 20297

   134 : AsnHisValLysSerLeuAsnTrpGlyHisArgValGlnLeuGlnAspArgLysValLys :   153
         ::!:!!:!!||||||:!!!:!!::  !:!!!:!|||:!!|||!::..!!:!:!!||||||
         SerTyrIleLysSerIleSerPheLysTyrLysValGluLeuArgSerLysGlnValLys
 20298 : TCTTACATTAAGAGCATCAGCTTTAAGTACAAGGTAGAGCTTCGCAGCAAGCAAGTCAAG : 20357

   154 : TyrPheAsnIleLysAlaSerPheValAspGluHisThrValCysGlyValAlaLysGly :   173
         |||   |||:!!   !.!||||||||||||  !||||||:!!     !  !  !  !  !
         TyrGluAsnValLeuGlySerPheValAspProHisThrLeuLysLeuTrpHisProLys
 20358 : TACGAGAATGTCCTCGGCTCGTTCGTGGATCCACACACACTGAAGTTGTGGCACCCAAAG : 20417

   174 : GlyLysGluIleLeuLeuSerAlaAspHisIleIleIleAlaThrGlyGlyArgProArg :   193
           !     !!    !:!!!!!.!!   |||:!::!!||||||..!|||||||||||||||
         LysGlyThrLysGluIleThrThrArgHisValValIleAlaValGlyGlyArgProArg
 20418 : AAAGGTACGAAGGAGATCACTACCCGGCATGTGGTCATCGCTGTGGGTGGACGACCTAGG : 20477

   194 : TyrProThrHisIleGluGlyAlaLeuGluTyrGlyIleThrSerAspAspIlePheTrp :   213
          ! ! !.!!  !:!:!  |||      |||  !!.!:!!:!!||||||||||||||||||
         GlnLeuAlaCysLeuGlyGly------GluLeuAlaValSerSerAspAspIlePheTrp
 20478 : CAGCTGGCGTGTCTGGGCGGC------GAGCTTGCAGTTTCGAGTGATGACATCTTCTGG : 20531

   214 : LeuLysGlu<->SerProGlyLysThrLeuValValGlyAlaSerTyrValAlaLeuGlu :   232
         :!!|||:!!   ..!|||||||||||||||||||||||||||||||||||||||||||||
         MetLysGlnLysGluProGlyLysThrLeuValValGlyAlaSerTyrValAlaLeuGlu
 20532 : ATGAAGCAGAAGGAACCTGGCAAGACATTGGTCGTGGGCGCTTCGTATGTAGCGCTCGAG : 20591

   233 : CysAlaGlyPheLeuThrGlyIleGlyLeuAspThrThrIleMetMetArgSerIlePro :   252
         |||||||||||||||! !|||!!:|||! !! !..!! !:!:|||:!!|||||||||  !
         CysAlaGlyPheLeuLysGlyMetGlyTyrAlaValLysValMetValArgSerIleLeu
 20592 : TGTGCGGGCTTCCTGAAGGGGATGGGCTACGCTGTGAAGGTGATGGTGCGCTCCATCTTG : 20651

   253 : LeuArgGlyPheAspGlnGlnMetSerSerMetValIleGluHisMet<->AlaSerHis :   271
         ||||||||||||||||||.!.|||:!!|||! !:!!  !|||:!!|||     !..!   
         LeuArgGlyPheAspGlnAspMetAlaSerLysIleGlyGluTyrMetGluMetGlnSer
 20652 : CTTCGTGGCTTTGATCAGGATATGGCTAGCAAGATTGGAGAGTACATGGAGATGCAATCA : 20711

   272 : GlyThrArgPheLeuArgGlyCysAlaProSerArgValArgArgLeuProAspGlyGln :   291
         |||! !..!|||:!!|||  !   !.!|||..!  !:!!! !!:!|||  !..!||||||
         GlyIleGluPheIleArgLysThrValProGlnSerIleThrLysLeuAspSerGlyGln
 20712 : GGCATCGAGTTCATTCGCAAGACGGTTCCACAATCCATCACAAAGCTCGATAGCGGCCAG : 20771

   292 : LeuGlnValThrTrpGluAspSerThrThrGlyLysGluAspThrGlyThrPheAspThr :   311
         |||! !|||! !|||      !!!  !  !||| !      !  !! !||||||||||||
         LeuLeuValLysTrp---IleThrGluAspGlyAspCysPheGluGluThrPheAspThr
 20772 : CTACTGGTGAAGTGG---ATAACAGAAGATGGTGATTGCTTTGAGGAAACGTTCGACACA : 20828

   312 : ValLeuTrpAlaIleGlyArgValProAspThrArgSerLeuAsnLeuGluLysAlaGly :   331
         ||||||   |||!  ||||||! !||||||..!  !!.!|||..!|||!!::!!||||||
         ValLeuAsnAlaThrGlyArgAspProAspValAlaLysLeuGlyLeuAspGluAlaGly
 20829 : GTCCTGAATGCGACGGGCCGTGATCCGGACGTTGCCAAGCTTGGCTTGGATGAGGCTGGT : 20888

   332 : ValAspThrSerProAspThrGlnLysIleLeuValAspSerArgGluAlaThrSerVal :   351
         ||| !   !!:!  ! ! |||   :::|||! !|||:!!!:!   |||  !|||!!!..!
         ValLysLeuAsnGluLysThrGlyArgIleTrpValAsnAsn---GluGlnThrThrThr
 20889 : GTAAAGCTGAACGAGAAGACGGGTCGCATCTGGGTGAATAAT---GAGCAGACCACGACA : 20945

   352 : ProHisIleTyrAlaIleGlyAspValValGluGlyArgProGluLeuThrProIleAla :   371
         |||:!!:!!||||||||||||||||||:!!!!:!.!   |||||||||||||||:!!|||
         ProAsnValTyrAlaIleGlyAspValIleAspAla---ProGluLeuThrProValAla
 20946 : CCGAACGTCTATGCCATTGGCGATGTCATTGACGCG---CCAGAGCTCACACCAGTAGCG : 21002

   372 : IleMetAlaGlyArgLeuLeuValGlnArgLeuPheGlyGlySerSerAspLeuMetAsp :   391
         |||...|||||||||||||||  !!::||||||!:!..!! !.!!!!!!  ! !||||||
         IleGlnAlaGlyArgLeuLeuSerArgArgLeuTyrAsnGluGlyThrValGlnMetAsp
 21003 : ATCCAAGCAGGGCGTCTACTTTCTCGTCGCCTGTACAACGAAGGTACTGTGCAGATGGAC : 21062

   392 : TyrAspAsnValProThrThrValPheThrProLeuGluTyrGlyCysValGlyLeuSer :   411
         ||||||!!.:!!  !|||.!!||||||||||||:!!||||||||||||  !|||||||||
         TyrAspLysIleCysThrAlaValPheThrProIleGluTyrGlyCysCysGlyLeuSer
 21063 : TACGACAAGATTTGCACGGCGGTGTTCACGCCGATTGAATACGGCTGCTGCGGTTTATCG : 21122

   412 : GluGluGluAlaValAlaArgHisGlyGlnGluHisValGluValTyrHisAlaHisTyr :   431
         ||||||!!:::!  !! !..!:!!|||.!.!!:  !|||||||||||||||  !:!!!:!
         GluGluAspSerLysGluGluTyrGlyAspAspSerValGluValTyrHisLysAsnPhe
 21123 : GAGGAGGACAGCAAGGAAGAGTACGGCGATGACAGTGTGGAGGTGTACCACAAGAACTTT : 21182

   432 : LysProLeuGluPheThrValAlaGlyArgAsp<-><-><->AlaSerGlnCysTyrVal :   448
            |||||||||!:::!!:!!|||! !!:!  !         |||..!...|||||||||
         ValProLeuGluTrpSerLeuAlaGluGlnThrArgIleAlaAlaGluSerCysTyrVal
 21183 : GTTCCGTTGGAATGGTCGCTCGCTGAGCAGACCCGCATCGCAGCTGAGTCCTGCTACGTG : 21242

   449 : LysMetValCysLeuArgGluProProGlnLeuValLeuGlyLeuHisPheLeuGlyPro :   468
         |||:!!||||||  !!:!   ! !  !.!.!!!|||||||||!!!|||!:!|||||||||
         LysValValCysAspLysThrArgAsnAsnPheValLeuGlyPheHisTyrLeuGlyPro
 21243 : AAGGTGGTTTGCGACAAGACCCGTAATAATTTCGTGCTGGGCTTTCATTACCTGGGACCG : 21302

   469 : AsnAlaGlyGluValThrGlnGlyPheAlaLeuGlyIleLysCysGlyAlaSerTyrAla :   488
         |||||||||||||||||||||!.!.!.!.!|||!.!!!:|||  !|||  !!!!|||! !
         AsnAlaGlyGluValThrGlnAlaMetGlyLeuAlaMetLysLeuGlyPheThrTyrAsp
 21303 : AATGCGGGCGAAGTGACGCAGGCCATGGGTCTGGCAATGAAGCTTGGTTTTACGTACGAC : 21362

   489 : GlnValMetArgThrValGlyIleHisProThrCysSerGluGluValValLysLeuArg :   508
         |||:!!:!:  !|||||||||||||||||||||   :!!|||! ! !!..!! !|||..!
         GlnLeuValAspThrValGlyIleHisProThrThrAlaGluAlaPheThrThrLeuGlu
 21363 : CAATTGGTCGACACCGTGGGCATTCATCCGACGACGGCCGAGGCATTCACGACGCTAGAG : 21422

   509 : IleSerLysArgSerGlyLeuAspProThrValThrGlyCysUnkGly :   524
         !  !!!|||!!!||||||  !... !!|||! !  !||||||   |||
         ThrThrLysSerSerGlyAspSerThrThrGlyGlyGlyCys***Gly
 21423 : ACGACGAAGAGCAGTGGCGACTCGACGACTGGCGGAGGATGCTGAGGC : 21472

vulgar: SPP00000035_1.0 38 524 . gi|199611737|gb|ABWE01000075.1|:subseq(6040,30000) 19999 21472 + 1117 M 69 207 G 0 3 M 10 30 G 0 12 M 83 249 G 2 0 M 14 42 G 0 3 M 52 156 G 0 3 M 28 84 G 1 0 M 48 144 G 1 0 M 17 51 G 1 0 M 78 234 G 0 9 M 82 246
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-03-14
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|199611737|gb|ABWE01000075.1|:subseq(6040,30000)	exonerate:protein2genome:local	gene	20000	21472	1117	+	.	gene_id 1 ; sequence SPP00000035_1.0 ; gene_orientation .
gi|199611737|gb|ABWE01000075.1|:subseq(6040,30000)	exonerate:protein2genome:local	cds	20000	21472	.	+	.	
gi|199611737|gb|ABWE01000075.1|:subseq(6040,30000)	exonerate:protein2genome:local	exon	20000	21472	.	+	.	insertions 30 ; deletions 5
gi|199611737|gb|ABWE01000075.1|:subseq(6040,30000)	exonerate:protein2genome:local	similarity	20000	21472	1117	+	.	alignment_id 1 ; Query SPP00000035_1.0 ; Align 20000 39 207 ; Align 20210 108 30 ; Align 20252 118 249 ; Align 20501 203 42 ; Align 20546 217 156 ; Align 20705 269 84 ; Align 20789 298 144 ; Align 20933 347 51 ; Align 20984 365 234 ; Align 21227 443 246
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
