Command line: [exonerate -m p2g --showtargetgff -q querytannulata.fa -t fastafetchannulataVSparamecium.fa]
Hostname: [ws101145.aulescm.upf.edu]

C4 Alignment:
------------
         Query: gi|85000191|ref|XP_954814.1| thioredoxin reductase [Theileria annulata strain Ankara]
        Target: gi|71533066|emb|CR940352.2| Theileria annulata strain Ankara isolate clone C9, *** SEQUENCING IN PROGRESS ***, 3 ordered pieces
         Model: protein2genome:local
     Raw score: 2923
   Query range: 0 -> 604
  Target range: 222621 -> 227575

      1 : MetLeuPheLysLysArgAsnLeuIleThrIleThrValProLysIlePheLeuSerS :     20
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          MetLeuPheLysLysArgAsnLeuIleThrIleThrValProLysIlePheLeuSerS
 222622 : ATGTTGTTTAAAAAGCGTAATCTTATTACAATTACTGTTCCAAAGATTTTTTTATCTT : 222679

     21 : erTyrLeuIlePheArgGlnSerAspPheLeuSerTyrSerPheCysTyrAsnPheAs :     39
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          erTyrLeuIlePheArgGlnSerAspPheLeuSerTyrSerPheCysTyrAsnPheAs
 222680 : CTTATTTAATTTTTAGACAATCTGATTTTCTTTCATATTCTTTTTGTTATAATTTTAA : 222736

     40 : nHisLeuThrAspTyrArgAsnPhePheHisLysIleAsnSerAsnAsnSerTyrSer :     58
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          nHisLeuThrAspTyrArgAsnPhePheHisLysIleAsnSerAsnAsnSerTyrSer
 222737 : TCATTTAACTGATTATCGAAATTTTTTTCATAAAATCAATTCCAACAATTCTTATTCT : 222793

     59 : AsnSerSerAsnSerTyrSerIleAsnThrSerLeuGlnSerSerGlnSerAsnSerT :     78
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          AsnSerSerAsnSerTyrSerIleAsnThrSerLeuGlnSerSerGlnSerAsnSerT
 222794 : AATTCTTCCAATTCTTATTCTATTAACACGAGTTTACAGTCCAGTCAATCCAATTCCT : 222853

     79 : yrSerThrAsnThrAsnSerGlnSerAsnHisThrAsnThrAsnSerAsnHisThrAs :     97
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          yrSerThrAsnThrAsnSerGlnSerAsnHisThrAsnThrAsnSerAsnHisThrAs
 222854 : ATTCCACTAATACCAACTCACAATCCAATCACACCAACACAAATTCCAATCACACTAA : 222910

     98 : nThrAsnThrAsnPheGluLysAsnSerPheArgIleLysAsnMetIleHisTyrAsp :    116
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          nThrAsnThrAsnPheGluLysAsnSerPheArgIleLysAsnMetIleHisTyrAsp
 222911 : TACTAATACTAATTTTGAAAAAAATTCATTTAGAATAAAAAATATGATACATTATGAT : 222967

    117 : LeuIleValLeuGlyGlyGlyProAlaGlyMetAlaAlaAlaLysGluAlaSerArgL :    136
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          LeuIleValLeuGlyGlyGlyProAlaGlyMetAlaAlaAlaLysGluAlaSerArgL
 222968 : TTAATAGTTTTGGGTGGTGGTCCAGCTGGTATGGCAGCAGCAAAAGAAGCATCACGTT : 223027

    137 : eu{G}  >>>> Target Intron 1 >>>>  {ly}LysArgThrValLeuPheAs :    144
          ||{|}            58 bp            {||}||||||||||||||||||||
          eu{G}++                         ++{ly}LysArgThrValLeuPheAs
 223028 : TA{G}gt.........................ag{GT}AAAAGAACAGTATTATTTGA : 223109

    145 : pTyrValThrProSerAlaArgGlyThrSerTrpGlyValGlyGlyThrCysValAsn :    163
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          pTyrValThrProSerAlaArgGlyThrSerTrpGlyValGlyGlyThrCysValAsn
 223110 : TTATGTAACACCATCTGCAAGAGGTACAAGTTGGGGTGTTGGTGGTACATGTGTTAAT : 223166

    164 : ValGlyCysIleProLysLysLeuMetHisTyrAlaSerLeuLeuArgSerSerAsnT :    183
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          ValGlyCysIleProLysLysLeuMetHisTyrAlaSerLeuLeuArgSerSerAsnT
 223167 : GTCGGTTGTATACCTAAAAAATTAATGCATTATGCAAGTTTATTAAGAAGTTCTAATT : 223226

    184 : yrAspLysPheGlnTyrGlyLeuThrAsnThrGlnGluLeuThrProIleAsnTrpAs :    202
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          yrAspLysPheGlnTyrGlyLeuThrAsnThrGlnGluLeuThrProIleAsnTrpAs
 223227 : ATGATAAATTTCAATATGGTCTAACTAATACACAGGAATTAACACCAATCAATTGGAA : 223283

    203 : nLysLeuIleGln  >>>> Target Intron 2 >>>>  ThrIleGlnAsnTyrI :    212
          |||||||||||||            549 bp           ||||||||||||||||
          nLysLeuIleGln++                         ++ThrIleGlnAsnTyrI
 223284 : TAAATTAATACAAgt.........................agACAATACAGAATTATA : 223862

    213 : leLysMetLeuAsnPheSerTyrArgSerSerLeuLeuThrSerGlyValAspTyrIl :    231
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          leLysMetLeuAsnPheSerTyrArgSerSerLeuLeuThrSerGlyValAspTyrIl
 223863 : TAAAGATGTTGAATTTTTCATATCGTTCGAGTTTATTAACTTCTGGTGTTGATTATAT : 223919

    232 : eAsnAlaPheGlyIleLeuLysHisAsnLysIleIleGluTyrAsnLeuAsnAsnGlu :    250
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          eAsnAlaPheGlyIleLeuLysHisAsnLysIleIleGluTyrAsnLeuAsnAsnGlu
 223920 : TAATGCATTTGGTATTTTAAAACATAATAAAATTATTGAATATAATCTTAATAATGAA : 223976

    251 : IleLys  >>>> Target Intron 3 >>>>  TyrValSerGlyAspLysIleIl :    260
          ||||||            468 bp           |||||||||||||||||||||||
          IleLys++                         ++TyrValSerGlyAspLysIleIl
 223977 : ATTAAGgt.........................agTATGTGAGTGGTGATAAAATAAT : 224474

    261 : eIleAlaIleGlyGluArgProTyrIleProSerAspValGluGlyAlaAsnGluTyr :    279
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          eIleAlaIleGlyGluArgProTyrIleProSerAspValGluGlyAlaAsnGluTyr
 224475 : AATAGCAATTGGTGAAAGACCATATATACCATCAGATGTTGAAGGTGCTAATGAATAT : 224531

    280 : AlaIleThrSerAspAspLeuPheGlnLeuAsnThrAsnProGlyLys{Th}  >>>> :    296
          ||||||||||||||||||||||||||||||||||||||||||||||||{||}      
          AlaIleThrSerAspAspLeuPheGlnLeuAsnThrAsnProGlyLys{Th}++    
 224532 : GCTATTACTTCTGATGATTTATTTCAATTAAATACTAATCCAGGCAAA{AC}gt.... : 224586

    297 :  Target Intron 4 >>>>  {r}LeuIleValGlyAlaSerTyrValAlaLeuGl :    307
                108 bp           {|}||||||||||||||||||||||||||||||||
                               ++{r}LeuIleValGlyAlaSerTyrValAlaLeuGl
 224587 : .....................ag{A}TTAATTGTTGGTGCAAGTTATGTAGCATTAGA : 224723

    308 : uCysAlaGlyPheLeuThrGlyLeuGlyTyrAsn  >>>> Target Intron 5 > :    319
          ||||||||||||||||||||||||||||||||||            203 bp      
          uCysAlaGlyPheLeuThrGlyLeuGlyTyrAsn++                      
 224724 : ATGTGCTGGTTTTCTAACAGGTTTAGGTTATAATgt...................... : 224761

    320 : >>>  ValAspValSerValArgSerIleLeuLeuArgGlyPheAspArgGlnCysVa :    336
               |||||||||||||||||||||||||||||||||||||||||||||||||||||
             ++ValAspValSerValArgSerIleLeuLeuArgGlyPheAspArgGlnCysVa
 224762 : ...agGTTGATGTATCAGTTCGAAGTATATTATTAAGAGGATTTGATAGACAATGTGT : 225013

    337 : lLysLysValGluGluLeuMetGluAlaSerGlyValLeuPheLeuTyrHisLysLeu :    355
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          lLysLysValGluGluLeuMetGluAlaSerGlyValLeuPheLeuTyrHisLysLeu
 225014 : AAAGAAAGTTGAAGAACTTATGGAAGCTTCTGGTGTTTTATTTCTATATCATAAACTT : 225070

    356 : ProIleLysIleGluLysHisAsnGlnGlnLeuLys  >>>> Target Intron 6 :    368
          ||||||||||||||||||||||||||||||||||||            484 bp    
          ProIleLysIleGluLysHisAsnGlnGlnLeuLys++                    
 225071 : CCAATCAAAATTGAAAAACATAATCAACAACTTAAAgt.................... : 225111

    369 :  >>>>  ValThrPheAsnAspGlnSerValAsnTyrTyrAspThrValLeuTyrAla :    384
                 |||||||||||||||||||||||||||||||||||||||||||||||||||
               ++ValThrPheAsnAspGlnSerValAsnTyrTyrAspThrValLeuTyrAla
 225112 : .....agGTTACATTTAATGATCAAAGTGTAAATTATTATGATACTGTATTATATGCC : 225641

    385 : IleGlyArgIleProSerGlnTyrThrGln{H}  >>>> Target Intron 7 >> :    395
          ||||||||||||||||||||||||||||||{|}            176 bp       
          IleGlyArgIleProSerGlnTyrThrGln{H}++                       
 225642 : ATTGGACGTATACCATCACAATATACACAA{C}gt....................... : 225677

    396 : >>  {is}LeuLysGluValGlyIleGluPheAspGlyAsnGlyAsnIleLeuValTh :    412
              {||}||||||||||||||||||||||||||||||||||||||||||||||||||
            ++{is}LeuLysGluValGlyIleGluPheAspGlyAsnGlyAsnIleLeuValTh
 225678 : ..ag{AT}TTGAAAGAAGTTGGAATAGAATTTGATGGGAATGGAAATATATTAGTAAC : 225901

    413 : rAsnGluGluThrAsnIleLysAspIleTyrAlaValGlyAspIleValSerLysVal :    431
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          rAsnGluGluThrAsnIleLysAspIleTyrAlaValGlyAspIleValSerLysVal
 225902 : GAATGAAGAGACAAATATAAAAGATATTTATGCTGTTGGTGACATAGTATCAAAAGTA : 225958

    432 : ProLysLeuAlaProValAlaIleLysSerSerGluLeuLeuIleGlnArgLeuTyrS :    451
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          ProLysLeuAlaProValAlaIleLysSerSerGluLeuLeuIleGlnArgLeuTyrS
 225959 : CCAAAATTAGCACCAGTCGCTATCAAATCTTCCGAATTATTAATTCAACGTTTATATT : 226018

    452 : erAsnAsnAsnThrGln  >>>> Target Intron 8 >>>>  MetAsnTyrGlu :    460
          |||||||||||||||||            133 bp           ||||||||||||
          erAsnAsnAsnThrGln++                         ++MetAsnTyrGlu
 226019 : CCAATAATAATACACAAgt.........................agATGAATTATGAA : 226178

    461 : AsnValProLysCysValTyrThrProPheGluTyrSerSerCysGlyLeuThrGluG :    480
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          AsnValProLysCysValTyrThrProPheGluTyrSerSerCysGlyLeuThrGluG
 226179 : AATGTACCGAAATGTGTTTATACACCATTTGAATATTCTTCATGTGGATTAACAGAAG : 226238

    481 : luGluAlaIle  >>>> Target Intron 9 >>>>  GluLysTyrGlyGluAsp :    489
          |||||||||||            864 bp           ||||||||||||||||||
          luGluAlaIle++                         ++GluLysTyrGlyGluAsp
 226239 : AAGAAGCCATAgt.........................agGAAAAATATGGAGAAGAC : 227129

    490 : AsnLeuGluIleTyrLeuLysGluTyrAsnAsnLeuGluIleSerProValHisArgI :    509
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          AsnLeuGluIleTyrLeuLysGluTyrAsnAsnLeuGluIleSerProValHisArgI
 227130 : AATTTGGAAATATATTTAAAGGAATATAATAATTTGGAAATTTCACCTGTACATCGAA : 227189

    510 : leAsnLysLysThrAsnAsp{G}  >>>> Target Intron 10 >>>>  {lu}P :    517
          ||||||||||||||||||||{|}             99 bp            {||}|
          leAsnLysLysThrAsnAsp{G}++                          ++{lu}P
 227190 : TTAATAAAAAAACTAATGAT{G}gt..........................ag{AA}T : 227312

    518 : heAspTyrProMetThrCysLeuSerLysValIleCysLeuLysAspGlyLysIleIl :    536
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          heAspTyrProMetThrCysLeuSerLysValIleCysLeuLysAspGlyLysIleIl
 227313 : TTGATTATCCAATGACATGTTTAAGTAAAGTAATATGTTTAAAAGATGGAAAGATAAT : 227369

    537 : eGlyMetHisPheValGlyProAsnAlaGlyGluIleMetGlnGlyPheSerValLeu :    555
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          eGlyMetHisPheValGlyProAsnAlaGlyGluIleMetGlnGlyPheSerValLeu
 227370 : TGGAATGCATTTTGTAGGACCAAATGCAGGTGAAATAATGCAAGGATTTTCAGTATTA : 227426

    556 : LeuThrLeuAsnAlaLysLysSerAspLeuAspLysThrValGlyIleHisProThrA :    575
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          LeuThrLeuAsnAlaLysLysSerAspLeuAspLysThrValGlyIleHisProThrA
 227427 : CTTACACTAAACGCAAAGAAAAGTGATTTGGATAAAACAGTAGGAATTCATCCAACTG : 227486

    576 : spAlaGluSerPheValAsnLeuThrValThrLysSerSerGlyLysSerTrpIleAl :    594
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          spAlaGluSerPheValAsnLeuThrValThrLysSerSerGlyLysSerTrpIleAl
 227487 : ATGCTGAAAGCTTTGTTAACTTAACCGTTACTAAATCTAGTGGAAAATCATGGATTGC : 227543

    595 : aThrGlyGlyCysAlaGlyGlyLysCysGly :    604
          |||||||||||||||||||||||||||||||
          aThrGlyGlyCysAlaGlyGlyLysCysGly
 227544 : TACTGGTGGATGTGCAGGTGGTAAATGTGGT : 227575

vulgar: gi|85000191|ref|XP_954814.1| 0 604 . gi|71533066|emb|CR940352.2| 222621 227575 + 2923 M 136 408 S 0 1 5 0 2 I 0 54 3 0 2 S 1 2 M 69 207 5 0 2 I 0 545 3 0 2 M 46 138 5 0 2 I 0 464 3 0 2 M 43 129 S 0 2 5 0 2 I 0 104 3 0 2 S 1 1 M 22 66 5 0 2 I 0 199 3 0 2 M 49 147 5 0 2 I 0 480 3 0 2 M 27 81 S 0 1 5 0 2 I 0 172 3 0 2 S 1 2 M 61 183 5 0 2 I 0 129 3 0 2 M 27 81 5 0 2 I 0 860 3 0 2 M 32 96 S 0 1 5 0 2 I 0 95 3 0 2 S 1 2 M 88 264
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2010-03-11
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	gene	222622	227575	2923	+	.	gene_id 1 ; sequence gi|85000191|ref|XP_954814.1| ; gene_orientation +
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	cds	222622	223030	.	+	.	
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	exon	222622	223030	.	+	.	insertions 0 ; deletions 0
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice5	223031	223032	.	+	.	intron_id 1 ; splice_site "GT"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	intron	223031	223088	.	+	.	intron_id 1
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice3	223087	223088	.	+	.	intron_id 0 ; splice_site "AG"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	cds	223089	223297	.	+	.	
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	exon	223089	223297	.	+	.	insertions 0 ; deletions 0
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice5	223298	223299	.	+	.	intron_id 2 ; splice_site "GT"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	intron	223298	223846	.	+	.	intron_id 2
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice3	223845	223846	.	+	.	intron_id 1 ; splice_site "AG"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	cds	223847	223984	.	+	.	
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	exon	223847	223984	.	+	.	insertions 0 ; deletions 0
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice5	223985	223986	.	+	.	intron_id 3 ; splice_site "GT"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	intron	223985	224452	.	+	.	intron_id 3
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice3	224451	224452	.	+	.	intron_id 2 ; splice_site "AG"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	cds	224453	224583	.	+	.	
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	exon	224453	224583	.	+	.	insertions 0 ; deletions 0
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice5	224584	224585	.	+	.	intron_id 4 ; splice_site "GT"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	intron	224584	224691	.	+	.	intron_id 4
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice3	224690	224691	.	+	.	intron_id 3 ; splice_site "AG"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	cds	224692	224758	.	+	.	
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	exon	224692	224758	.	+	.	insertions 0 ; deletions 0
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice5	224759	224760	.	+	.	intron_id 5 ; splice_site "GT"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	intron	224759	224961	.	+	.	intron_id 5
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice3	224960	224961	.	+	.	intron_id 4 ; splice_site "AG"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	cds	224962	225108	.	+	.	
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	exon	224962	225108	.	+	.	insertions 0 ; deletions 0
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice5	225109	225110	.	+	.	intron_id 6 ; splice_site "GT"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	intron	225109	225592	.	+	.	intron_id 6
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice3	225591	225592	.	+	.	intron_id 5 ; splice_site "AG"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	cds	225593	225674	.	+	.	
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	exon	225593	225674	.	+	.	insertions 0 ; deletions 0
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice5	225675	225676	.	+	.	intron_id 7 ; splice_site "GT"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	intron	225675	225850	.	+	.	intron_id 7
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice3	225849	225850	.	+	.	intron_id 6 ; splice_site "AG"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	cds	225851	226035	.	+	.	
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	exon	225851	226035	.	+	.	insertions 0 ; deletions 0
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice5	226036	226037	.	+	.	intron_id 8 ; splice_site "GT"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	intron	226036	226168	.	+	.	intron_id 8
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice3	226167	226168	.	+	.	intron_id 7 ; splice_site "AG"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	cds	226169	226249	.	+	.	
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	exon	226169	226249	.	+	.	insertions 0 ; deletions 0
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice5	226250	226251	.	+	.	intron_id 9 ; splice_site "GT"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	intron	226250	227113	.	+	.	intron_id 9
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice3	227112	227113	.	+	.	intron_id 8 ; splice_site "AG"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	cds	227114	227210	.	+	.	
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	exon	227114	227210	.	+	.	insertions 0 ; deletions 0
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice5	227211	227212	.	+	.	intron_id 10 ; splice_site "GT"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	intron	227211	227309	.	+	.	intron_id 10
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	splice3	227308	227309	.	+	.	intron_id 9 ; splice_site "AG"
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	cds	227310	227575	.	+	.	
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	exon	227310	227575	.	+	.	insertions 0 ; deletions 0
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	similarity	222622	227575	2923	+	.	alignment_id 1 ; Query gi|85000191|ref|XP_954814.1| ; Align 222622 1 408 ; Align 223091 138 207 ; Align 223847 207 138 ; Align 224453 253 129 ; Align 224693 297 66 ; Align 224962 319 147 ; Align 225593 368 81 ; Align 225853 396 183 ; Align 226169 457 81 ; Align 227114 484 96 ; Align 227312 517 264
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: gi|85000191|ref|XP_954814.1| thioredoxin reductase [Theileria annulata strain Ankara]
        Target: gi|71533066|emb|CR940352.2| Theileria annulata strain Ankara isolate clone C9, *** SEQUENCING IN PROGRESS ***, 3 ordered pieces
         Model: protein2genome:local
     Raw score: 109
   Query range: 58 -> 101
  Target range: 222774 -> 222903

     59 : AsnSerSerAsnSerTyrSerIleAsnThrSerLeuGlnSerSerGlnSerAsnSerT :     78
          ||||||!:!||||||||||||! !::!:!!!:!! ! ! |||! !.!.!!!!:!! ! 
          AsnSerAsnAsnSerTyrSerAsnSerSerAsnSerTyrSerIleAsnThrSerLeuG
 222775 : AATTCCAACAATTCTTATTCTAATTCTTCCAATTCTTATTCTATTAACACGAGTTTAC : 222832

     79 : yrSerThrAsnThrAsnSerGlnSerAsnHisThrAsnThrAsnSerAsnHisThrAs :     97
          ! |||!:!.!.:!!|||||| ! |||!.!:!!||||||:!!.!.||||||||||||||
          lnSerSerGlnSerAsnSerTyrSerThrAsnThrAsnSerGlnSerAsnHisThrAs
 222833 : AGTCCAGTCAATCCAATTCCTATTCCACTAATACCAACTCACAATCCAATCACACCAA : 222889

     98 : nThrAsnThrAsn :    101
          |||||||:!!|||
          nThrAsnSerAsn
 222890 : CACAAATTCCAAT : 222903

vulgar: gi|85000191|ref|XP_954814.1| 58 101 . gi|71533066|emb|CR940352.2| 222774 222903 + 109 M 43 129
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2010-03-11
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	gene	222775	222903	109	+	.	gene_id 2 ; sequence gi|85000191|ref|XP_954814.1| ; gene_orientation .
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	cds	222775	222903	.	+	.	
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	exon	222775	222903	.	+	.	insertions 0 ; deletions 0
gi|71533066|emb|CR940352.2|	exonerate:protein2genome:local	similarity	222775	222903	109	+	.	alignment_id 2 ; Query gi|85000191|ref|XP_954814.1| ; Align 222775 59 129
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
