Command line: [exonerate -m p2g --showtargetgff -q ../Exonerate/querysambX/TR2.fa -t ../fastasubseq/fastasubseqexit/2011_tblastn/B.hominis/TR2/h2/fastasubseq_TR2_B.hom_h2.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query: SPP00000035_1.0 # Protein # Thioredoxin reductase 2 (TR2) # Homo sapiens # Complete
        Target: gi|300123462|emb|FN668689.1|:subseq(386486,30000) Blastocystis hominis, Singapore isolate B (sub-type 7) whole genome shotgun sequence assembly, scaffold_7:[revcomp]
         Model: protein2genome:local
     Raw score: 1098
   Query range: 38 -> 524
  Target range: 21514 -> 19999

    39 : AspTyrAspLeuLeuValValGlyGlyGlySerGly{G}  >>>> Target Intron  :    51
         ||||||||||||:!!|||:!!|||||||||||||||{|}            34 bp    
         AspTyrAspLeuIleValIleGlyGlyGlySerGly{G}++                   
 21514 : GATTATGATTTGATTGTAATTGGTGGTGGTTCTGGA{G}gt................... : 21475

    52 : 1 >>>>  {ly}LeuAlaCysAlaLysGluAlaAlaGlnLeuGlyArgLysValAlaVal :    67
                 {||}||||||..!:!!||||||||||||.!.||||||  !!  ||||||:!!
               ++{ly}LeuAlaAlaSerLysGluAlaAlaAspLeuGlyAlaThrValAlaLeu
 21474 : ......ag{GT}CTGGCTGCCTCAAAGGAGGCCGCGGATCTCGGAGCCACTGTCGCTCTA : 21396

    68 : ValAspTyrValGluProSerProGlnGlyThrArgTrpGlyLeuGlyGlyThrCysVal :    87
          !!|||||||||:!!|||||||||||||||:!!! !||||||||||||||||||||||||
         PheAspTyrValLysProSerProGlnGlySerThrTrpGlyLeuGlyGlyThrCysVal
 21395 : TTTGATTATGTAAAGCCCTCTCCTCAGGGATCCACTTGGGGTCTCGGAGGTACGTGCGTG : 21336

    88 : AsnValGlyCysIleProLysLysLeuMetHisGlnAlaAlaLeuLeuGlyGlyLeuIle :   107
         ||||||||||||||||||||||||||||||||||||||||||:!!:!!|||! !!!!:!!
         AsnValGlyCysIleProLysLysLeuMetHisGlnAlaAlaIleIleGlyGluPheVal
 21335 : AATGTCGGTTGCATTCCCAAGAAGCTGATGCACCAAGCCGCCATCATCGGCGAGTTTGTT : 21276

   108 : GlnAspAlaProAsnTyrGlyTrpGluValAlaGlnProValProHisAspTrpArgLys :   127
         !::|||||| !!::!!:!||||||!!:||| !!:!!   |||! !||| !!|||!.!! !
         ArgAspAlaSerSerPheGlyTrpAspValProGlu---ValHisHisHisTrpAsnThr
 21275 : CGCGACGCTTCCTCTTTCGGCTGGGACGTTCCCGAG---GTTCACCACCACTGGAACACG : 21219

   128 : MetAlaGluAlaValGlnAsnHisValLysSerLeuAsnTrpGlyHisArgValGlnLeu :   147
         :!!!.!!!:  !||||||:!!:!!:!!:::.!!||||||!::..!:!!||||||...|||
         LeuValAspAsnValGlnAspTyrIleArgGlyLeuAsnTyrAsnTyrArgValSerLeu
 21218 : CTGGTGGACAACGTGCAGGACTACATCCGCGGCTTGAATTACAACTACCGCGTGTCTCTG : 21159

   148 : GlnAspArgLysValLysTyrPheAsnIleLysAlaSerPheValAspGluHisThrVal :   167
         ..!...!:! ! |||!  |||!:!|||     !|||! ! !   !|||! !|||||||||
         MetSerLysHisValThrTyrTyrAsnGlnLeuAlaTyrValLysAspAlaHisThrVal
 21158 : ATGTCGAAGCACGTCACCTACTACAACCAGCTGGCCTACGTAAAGGACGCGCACACCGTG : 21099

   168 : CysGlyValAlaLysGlyGlyLys  >>>> Target Intron 2 >>>>  GluIleL :   178
            |||..!! !     !||| !             32 bp            :!!  !:
         GluGlyThrAspValPheGlyAsp++                         ++LysHisI
 21098 : GAAGGCACGGACGTTTTCGGTGATgt.........................agAAGCACA : 21034

   179 : euLeuSerAlaAspHisIleIleIleAlaThrGlyGlyArgProArgTyrProThrHisI :   198
         !!! !!!!..!  !!.!||||||:!:|||..!||||||||||||!.!     !  !  ! 
         leTyrThrCysArgArgIleIleValAlaValGlyGlyArgProAsn---LysLeuGlyC
 21033 : TCTACACGTGTCGCCGCATCATCGTGGCTGTGGGCGGTCGTCCGAAC---AAGCTGGGCT : 20977

   199 : leGluGlyAlaLeuGluTyrGlyIleThrSerAspAspIlePheTrpLeuLysGluSerP :   218
          !  !|||! !   |||   !.!:!!||||||||||||:!:|||  !||| ! .!. !!|
         ysProGlyGlu---GluLeuAlaValThrSerAspAspLeuPheMetLeuAspHisProP
 20976 : GCCCGGGAGAG---GAGCTGGCGGTCACGAGCGATGATCTGTTCATGCTGGACCATCCCC : 20920

   219 : roGlyLysThrLeuValValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPheLeuT :   238
         ||  !|||||||||:!!||||||||||||!:!:!!|||||||||||||||||||||||| 
         roLysLysThrLeuLeuValGlyAlaSerPheIleAlaLeuGluCysAlaGlyPheLeuH
 20919 : CCAAGAAGACCCTTCTGGTGGGCGCCTCGTTCATCGCTCTGGAGTGTGCCGGGTTCCTGC : 20860

   239 : hrGlyIleGlyLeuAspThrThrIleMetMetArgSerIleProLeuArgGlyPheAspG :   258
          !  !:!!|||!!!|||..!|||:!:|||:!!|||||||||! !||||||||||||||||
         isHisLeuGlyPheAspValThrValMetValArgSerIleLeuLeuArgGlyPheAspG
 20859 : ACCACCTTGGCTTCGACGTGACGGTGATGGTGCGCTCGATCCTGCTCCGCGGATTCGACC : 20800

   259 : lnGlnMetSerSerMetValIleGluHisMetAlaSerHisGlyThrArgPheLeuArgG :   278
         ||:!!   :!!!:!! !:!!  !!!:  !|||  !..!.!.|||! !!.!||||||!.!.
         lnGluCysAlaAsnLysIleGlyAspPheMetLysGluGluGlyIleHisPheLeuHisA
 20799 : AGGAATGCGCGAACAAGATCGGCGACTTCATGAAGGAGGAGGGCATCCACTTCCTCCACA : 20740

   279 : lyCysAlaProSerArgValArgArgLeuProAspGlyGlnLeuGlnValThrTrpGluA :   298
         .!   !.!|||!!!..!:!!!:!|||||||||:!!|||!:::!!! !|||! !!:::!!!
         snThrValProThrGluLeuGlnArgLeuProAsnGlyArgIleLeuValLysTyrGlnG
 20739 : ACACGGTCCCCACCGAGCTGCAGCGTCTCCCGAACGGACGCATCCTGGTGAAGTACCAGG : 20680

   299 : spSerThrThrGlyLysGluAsp<-><-><->ThrGlyThrPheAspThrValLeuTrpA :   315
          !|||  !  !!.!!!...!!!:           !! !  !||||||||||||:!! ! .
         lySerGlyPheAlaAsnSerGluLeuArgGlyGluGluGluPheAspThrValValSerC
 20679 : GCAGCGGCTTCGCGAACTCGGAGCTGCGCGGCGAGGAGGAGTTCGACACCGTGGTGAGCT : 20620

   316 : laIleGlyArgValProAspThrArgSerLeuAsnLeuGluLysAlaGlyValAspThrS :   335
         .!|||||||||  ! !!||||||..! !!|||..!|||!!::!!  !|||||| ! ||| 
         ysIleGlyArgTyrAlaAspThrGluArgLeuGlyLeuAspGlnLeuGlyValLysThrA
 20619 : GCATCGGCCGCTACGCGGACACGGAGCGCCTGGGCCTCGACCAGCTGGGCGTGAAGACGC : 20560

   336 : erProAspThrGlnLysIleLeuValAspSerArgGluAlaThrSerValProHisIleT :   355
         !!        !  !|||||||||   ...  !!:!|||  !||||||||||||:!!||||
         rg------ArgGlyLysIleLeu---SerValGlnGluGlnThrSerValProAsnIleT
 20559 : GG------CGCGGGAAGATCCTG---TCGGTGCAGGAGCAGACGAGCGTGCCGAACATCT : 20509

   356 : yrAlaIleGlyAspValValGluGlyArgProGluLeuThrProIleAlaIleMetAlaG :   375
         ||!.!||||||||||||:!! ! |||!:!! !||||||||||||:!:||||||..!.!!|
         yrGlyIleGlyAspValLeuTyrGlyLysGlnGluLeuThrProValAlaIleGlnThrG
 20508 : ACGGCATCGGCGACGTGCTCTACGGCAAGCAGGAGCTCACGCCGGTGGCCATCCAGACGG : 20449

   376 : lyArgLeuLeuValGlnArgLeuPheGlyGlySerSerAspLeuMetAspTyrAspAsnV :   395
         ||!:!||||||!.!!:!||||||!:!||||||||||||!  ! !|||||||||!!:||||
         lyLysLeuLeuAlaArgArgLeuTyrGlyGlySerSerValGlnMetAspTyrGluAsnV
 20448 : GCAAGCTGCTGGCGCGGCGGCTGTACGGCGGCAGCAGCGTGCAGATGGACTACGAGAACG : 20389

   396 : alProThrThrValPheThrProLeuGluTyrGlyCysValGlyLeuSerGluGluGluA :   415
         |||||! !|||||||||||||||||||||||||||  !  !||||||!!!||||||! !|
         alProMetThrValPheThrProLeuGluTyrGlyAsnCysGlyLeuThrGluGluAlaA
 20388 : TGCCGATGACGGTGTTCACGCCGCTGGAGTACGGAAACTGCGGCCTGACGGAGGAGGCGG : 20329

   416 : laValAlaArgHisGlyGlnGluHisValGluValTyrHisAlaHisTyrLysProLeuG :   435
         ||:!!! !|||  !|||:!!!!::!!||||||||||||   ::!!!.!:!!  |||||||
         laLeuGluArgPheGlyGluAspAsnValGluValTyrValSerGlnPheThrProLeuG
 20328 : CGCTGGAGCGGTTCGGAGAGGACAACGTGGAGGTGTACGTGAGCCAGTTCACTCCGCTGG : 20269

   436 : luPheThrValAlaGlyArgAspAlaSerGlnCysTyrValLysMetValCysLeuArgG :   455
         ||!::  !:!!:!!  !!.!     !!.!:!!   ! ! !!  !! !:!!  !  !!:!.
         luTrpGlnIleSerProHisArgArgLysGluValCysPheAlaLysLeuIleThrLysA
 20268 : AGTGGCAGATCTCGCCGCACCGGAGAAAGGAGGTGTGCTTCGCGAAGCTGATCACGAAGC : 20209

   456 : luProProGlnLeuValLeuGlyLeuHisPheLeuGlyProAsnAlaGlyGluValThrG :   475
         ..  !  !  !|||:!!||||||!!!|||.!!|||..!|||||||||||||||:!!||||
         rgAspAspGlyLeuIleLeuGlyPheHisIleLeuSerProAsnAlaGlyGluIleThrG
 20208 : GCGACGACGGACTGATCCTGGGGTTCCACATCCTGTCGCCGAACGCGGGCGAAATCACGC : 20149

   476 : lnGlyPheAlaLeuGlyIleLysCysGlyAlaSerTyrAlaGlnValMetArgThrValG :   495
         ||||||||!.!|||!.!.!!:!!  !  !|||!!!|||  !.!.:!!|||  !  !||||
         lnGlyPheGlyLeuAlaPheGlnThrLysAlaThrTyrGlnAsnLeuMetAspLeuValG
 20148 : AGGGCTTCGGACTGGCGTTCCAGACCAAGGCGACGTACCAGAATCTGATGGATCTGGTGG : 20089

   496 : lyIleHisProThrCysSerGluGluValValLysLeuArgIleSerLysArgSerGlyL :   515
         ||||||||||||||  !:!!|||||| !!..!! !|||!!!:!!!!!|||||||||||| 
         lyIleHisProThrIleAlaGluGluPheThrThrLeuSerValThrLysArgSerGlyA
 20088 : GCATCCACCCGACCATCGCGGAGGAGTTCACCACGCTGAGCGTCACGAAGCGGTCGGGAG : 20029

   516 : euAspProThrValThrGlyCysUnkGly :   524
          !..! !!! !  !  !||||||   |||
         laSerAlaLysLysGlyGlyCys***Gly
 20028 : CCTCCGCGAAGAAGGGAGGATGCTGAGGT : 20000

vulgar: SPP00000035_1.0 38 524 . gi|300123462|emb|FN668689.1|:subseq(386486,30000) 21514 19999 - 1098 M 12 36 S 0 1 5 0 2 I 0 30 3 0 2 S 1 2 M 68 204 G 1 0 M 55 165 5 0 2 I 0 28 3 0 2 M 18 54 G 1 0 M 7 21 G 1 0 M 103 309 G 0 9 M 30 90 G 2 0 M 5 15 G 1 0 M 181 543
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-03-15
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|300123462|emb|FN668689.1|:subseq(386486,30000)	exonerate:protein2genome:local	gene	20000	21514	1098	-	.	gene_id 1 ; sequence SPP00000035_1.0 ; gene_orientation +
gi|300123462|emb|FN668689.1|:subseq(386486,30000)	exonerate:protein2genome:local	cds	21478	21514	.	-	.	
gi|300123462|emb|FN668689.1|:subseq(386486,30000)	exonerate:protein2genome:local	exon	21478	21514	.	-	.	insertions 0 ; deletions 0
gi|300123462|emb|FN668689.1|:subseq(386486,30000)	exonerate:protein2genome:local	splice5	21476	21477	.	-	.	intron_id 1 ; splice_site "GT"
gi|300123462|emb|FN668689.1|:subseq(386486,30000)	exonerate:protein2genome:local	intron	21444	21477	.	-	.	intron_id 1
gi|300123462|emb|FN668689.1|:subseq(386486,30000)	exonerate:protein2genome:local	splice3	21444	21445	.	-	.	intron_id 0 ; splice_site "AG"
gi|300123462|emb|FN668689.1|:subseq(386486,30000)	exonerate:protein2genome:local	cds	21073	21443	.	-	.	
gi|300123462|emb|FN668689.1|:subseq(386486,30000)	exonerate:protein2genome:local	exon	21073	21443	.	-	.	insertions 0 ; deletions 1
gi|300123462|emb|FN668689.1|:subseq(386486,30000)	exonerate:protein2genome:local	splice5	21071	21072	.	-	.	intron_id 2 ; splice_site "GT"
gi|300123462|emb|FN668689.1|:subseq(386486,30000)	exonerate:protein2genome:local	intron	21041	21072	.	-	.	intron_id 2
gi|300123462|emb|FN668689.1|:subseq(386486,30000)	exonerate:protein2genome:local	splice3	21041	21042	.	-	.	intron_id 1 ; splice_site "AG"
gi|300123462|emb|FN668689.1|:subseq(386486,30000)	exonerate:protein2genome:local	cds	20000	21040	.	-	.	
gi|300123462|emb|FN668689.1|:subseq(386486,30000)	exonerate:protein2genome:local	exon	20000	21040	.	-	.	insertions 9 ; deletions 5
gi|300123462|emb|FN668689.1|:subseq(386486,30000)	exonerate:protein2genome:local	similarity	20000	21514	1098	-	.	alignment_id 1 ; Query SPP00000035_1.0 ; Align 21515 39 36 ; Align 21442 52 204 ; Align 21238 121 165 ; Align 21041 176 54 ; Align 20987 195 21 ; Align 20966 203 309 ; Align 20648 306 90 ; Align 20558 338 15 ; Align 20543 344 543
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
