Command line: [exonerate -m p2g --showtargetgff -q SelU2.fa.U_to_X -t gi|511782562|gb|CM001951.1|.fastasubseq]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000114_2.0 # Protein # Selenoprotein U2 (SelU2) # Human (Homo sapiens) 
        Target: gi|511782562|gb|CM001951.1|:subseq(2858954,52671000) Chlorocebus sabaeus isolate 1994-021 chromosome X, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 964
   Query range: 0 -> 219
  Target range: 99999 -> 100652

      1 : MetAlaAlaProAlaProValThrArgGlnValSerGlyAlaAlaAlaLeuValProA :     20
          |||||||||||||||||||||||||||||||||||||||!.!||||||! !|||||||
          MetAlaAlaProAlaProValThrArgGlnValSerGlyGlyAlaAlaProValProA
 100000 : ATGGCCGCGCCTGCCCCGGTCACACGGCAGGTTAGCGGCGGCGCCGCCCCGGTCCCGG : 100057

     21 : laProSerGlyProAspSerGlyGlnProLeuAlaAlaAlaValAlaGluLeuProVa :     39
          ||||||||||||||||| !!|||||||||||||||.!!|||..!||||||||||||||
          laProSerGlyProAspArgGlyGlnProLeuAlaThrAlaThrAlaGluLeuProVa
 100058 : CCCCGAGCGGCCCAGACCGCGGGCAGCCCCTGGCAACCGCCACGGCCGAGCTGCCGGT : 100114

     40 : lLeuAspAla--ArgGlyGlnArgValProPheGlyAlaLeuPheArgGluArgArgA :     58
          ||||||||||##|||   ||||||||||||||||||||||||||||||||||||||||
          lLeuAspAla##Arg---GlnArgValProPheGlyAlaLeuPheArgGluArgArgA
 100115 : GCTGGACGCCGCAGG---CAGCGGGTACCGTTCGGCGCGCTGTTCCGGGAGCGCCGCG : 100170

     59 : laValValValPheValArgHisPheLeuCysTyrIleCysLysGluTyrValGluAs :     77
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          laValValValPheValArgHisPheLeuCysTyrIleCysLysGluTyrValGluAs
 100171 : CCGTGGTGGTGTTCGTGCGGCATTTCCTGTGTTACATCTGCAAGGAATACGTAGAGGA : 100227

     78 : pLeuAlaLysIleProArgSerPheLeuGlnGluAlaAsnValThrLeuIleValIle :     96
          ||||||||||||||||..!||||||||||||||||||||||||||||||! !||||||
          pLeuAlaLysIleProGluSerPheLeuGlnGluAlaAsnValThrLeuThrValIle
 100228 : TCTGGCCAAAATCCCCGAGAGTTTCTTACAAGAAGCAAATGTCACCCTTACAGTGATT : 100284

     97 : GlyGlnSerSerTyrHisHisIleGluProPheCysLysLeuThrGlyTyrSerHisG :    116
          ||| !!|||||||||||||||||||||||||||||||||! !||||||||||||||||
          Gly***SerSerTyrHisHisIleGluProPheCysLysProThrGlyTyrSerHisG
 100285 : GGATAGTCATCCTACCATCATATTGAGCCTTTTTGCAAACCGACTGGATATTCTCATG : 100344

    117 : luIleTyrValAspProGluArgGluIleTyrLysArgLeuGlyMetLysArgGlyGl :    135
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          luIleTyrValAspProGluArgGluIleTyrLysArgLeuGlyMetLysArgGlyGl
 100345 : AAATCTATGTCGATCCTGAGAGAGAAATTTATAAAAGATTGGGAATGAAAAGAGGTGA : 100401

    136 : uGluIleAlaSerSerGlyGlnSerProHisIleLysSerAsnLeuLeuSerGlySer :    154
          ||||||||||:!!||| !!||||||||||||:!!||||||||||||||||||||||||
          uGluIleAlaAlaSerArgGlnSerProHisValLysSerAsnLeuLeuSerGlySer
 100402 : AGAAATTGCCGCCTCACGACAGAGCCCCCACGTAAAATCAAATCTGCTCTCAGGAAGC : 100458

    155 : LeuGlnSerLeuTrpArgAlaValThrGlyProLeuPheAspPheGlnGlyAspProA :    174
          |||||||||||||||||||||||||||||||||! !||||||||||||||||||||||
          LeuGlnSerLeuTrpArgAlaValThrGlyProGlnPheAspPheGlnGlyAspProA
 100459 : CTTCAGAGCCTGTGGCGGGCAGTGACTGGCCCTCAGTTTGATTTTCAAGGAGACCCAG : 100518

    175 : laGlnGlnGlyGlyThrLeuIleLeuGlyProGlyAsnAsnIleHisPheIleHisAr :    193
          ||||||||||||||! !||||||||||||! !     !|||||||||||||||||| !
          laGlnGlnGlyGlyIleLeuIleLeuGlyLeu---ValAsnIleHisPheIleHisCy
 100519 : CTCAGCAAGGTGGAATCCTCATTTTAGGTCTA---GTTAACATCCATTTTATACACTG : 100572

    194 : gAspArgAsnArgLeuAspHisLysProIleAsnSerValLeuGlnLeuValGlyVal :    212
          !|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          sAspArgAsnArgLeuAspHisLysProIleAsnSerValLeuGlnLeuValGlyVal
 100573 : TGATAGGAATAGGTTGGATCACAAACCTATCAACTCTGTTTTACAGCTTGTAGGAGTT : 100629

    213 : GlnHisValAsnPheThrAsn :    219
          |||||||||||||||||||||
          GlnHisValAsnPheThrAsn
 100630 : CAGCATGTGAACTTTACAAAC : 100652

vulgar: SPP00000114_2.0 0 219 . gi|511782562|gb|CM001951.1|:subseq(2858954,52671000) 99999 100652 + 964 M 42 126 F 0 2 M 1 3 G 1 0 M 140 420 G 1 0 M 34 102
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-04
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	gene	100000	100652	964	+	.	gene_id 1 ; sequence SPP00000114_2.0 ; gene_orientation .
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	cds	100000	100652	.	+	.	
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	exon	100000	100652	.	+	.	insertions 0 ; deletions 2 ; frameshifts 2
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	similarity	100000	100652	964	+	.	alignment_id 1 ; Query SPP00000114_2.0 ; Align 100000 1 126 ; Align 100128 43 3 ; Align 100131 45 420 ; Align 100551 186 102
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000114_2.0 # Protein # Selenoprotein U2 (SelU2) # Human (Homo sapiens) 
        Target: gi|511782562|gb|CM001951.1|:subseq(2858954,52671000) Chlorocebus sabaeus isolate 1994-021 chromosome X, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 485
   Query range: 9 -> 171
  Target range: 52571637 -> 52514696

       10 : GlnValSerGlyAlaAlaAlaLeuValProAlaProSerGlyProAspSerGly :       27
            :!! !!||||||!.!!.!|||! !|||  !|||! !|||||||||!!:  !|||
            LysPheSerGlyGlyValAlaProVal***AlaLeuSerGlyProGluHisGly
 52571637 : AAGTTCAGTGGTGGTGTTGCCCCTGTCTAGGCCCTGAGTGGCCCTGAGCATGGG : 52571586

       28 : GlnProLeuAlaAlaAlaValAlaGluLeuProValLeuAspAlaArgGlyGln :       45
            ||| !!|||!.!||||||:!!|||||||||||||||||||||:!!!.!||||||
            GlnSerLeuValAlaAlaIleAlaGluLeuProValLeuAspSerHisGlyGln
 52571585 : CAGTCCCTGGTGGCTGCCATAGCCGAGCTACCAGTGCTGGACTCCCATGGGCAG : 52571532

       46 : ArgValProPheGlyAlaLeuPheArgGluArgArgAlaValValValPheVal :       63
             !!||||||||||||||||||.!!||||||||| !!|||:!!|||:!!||||||
            TrpValProPheGlyAlaLeuLeuArgGluArgCysAlaMetValLeuPheVal
 52571531 : TGGGTGCCGTTTGGAGCTCTCCTCCGGGAGCGCTGTGCCATGGTACTGTTTGTG : 52571478

       64 : ArgHisPheLeuCysTyrIleCysLysGluTyrValGluAspLeuAlaLysIle :       81
            !:!|||||||||! !|||||||||!!.||||||||||||||||||  !||||||
            GlnHisPheLeuPheTyrIleCysAsnGluTyrValGluAspLeu***LysIle
 52571477 : CAGCATTTCCTGTTTTACATTTGCAACGAATATGTAGAGGATCTGTGAAAAATC : 52571424

       82 : ProArgSerPheLeuGlnGluAlaAsnValThrLeuIleValIleGlyGlnSer :       99
            ! !!:!|||||||||||||||||||||||||||||||||||||||! !||||||
            LeuLysSerPheLeuGlnGluAlaAsnValThrLeuIleValIleGluGlnSer
 52571423 : CTGAAGAGTTTCTTACAAGAAGCAAATGTCACCCTTATAGTGATTGAACAGTCA : 52571370

      100 : SerTyrHisHisIleGluProPheCysLysLeuThrGlyTyrSerHisGluIle :      117
            |||||||||! !||||||||||||||||||||| !!||||||||||||||||||
            SerTyrHisProIleGluProPheCysLysLeuProGlyTyrSerHisGluIle
 52571369 : TCCTACCATCCTATTGAGCCTTTTTGCAAACTGCCTGGATATTCTCATGAAATC : 52571316

      118 : Tyr--ValAspProGluArgGluIleTyrLysArgLeuGlyMetLysArgGlyG :      135
            |||##    !!|||||||||||||||||||||! !|||||||||||||||||||
            Tyr##---HisProGluArgGluIleTyrLysIleLeuGlyMetLysArgGlyG
 52571315 : TATTT---CATCCTGAGAGGGAAATTTATAAAATATTGGGAATGAAAAGAGGTG : 52571263

      136 : luGluIleAlaSerSerGlyGlnSerProHisIleLysSerAsnLeuLeuSerG :      153
            |||||!!:||||||||||||||||||||||||:!!!!.|||.!.  !  !! !|
            luGluMetAlaSerSerGlyGlnSerProHisValAsnSerGlnGluAlaPheG
 52571262 : AAGAAATGGCCTCATCAGGACAGAGCCCCCACGTAAACTCTCAGGAAGCCTTTG : 52571209

      154 : lySerLeuGlnSer  >>>> Target Intron 1 >>>>  LeuTrpArgAl :      161
            ||:!!! !   .!!           56456 bp          |||||| !!||
            lyAlaCysGlyGly--                         ++LeuTrpGlyAl
 52571208 : GAGCTTGTGGTGGGca.........................agCTCTGGGGGGC : 52514729

      162 : aValThrGlyProLeuPheAspPheGlnGly :      171
            |!.!||||||||||||  !  !|||...|||
            aAlaThrGlyProLeuAlaPhePheSerGly
 52514728 : TGCTACAGGGCCCCTGGCTTTTTTCTCTGGC : 52514697

vulgar: SPP00000114_2.0 9 171 . gi|511782562|gb|CM001951.1|:subseq(2858954,52671000) 52571637 52514696 - 485 M 109 327 F 0 2 G 1 0 M 38 114 5 0 2 I 0 56452 3 0 2 M 14 42
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-04
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	gene	52514697	52571637	485	-	.	gene_id 1 ; sequence SPP00000114_2.0 ; gene_orientation +
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	cds	52571195	52571637	.	-	.	
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	exon	52571195	52571637	.	-	.	insertions 0 ; deletions 1 ; frameshifts 2
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	splice5	52571193	52571194	.	-	.	intron_id 1 ; splice_site "CA"
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	intron	52514739	52571194	.	-	.	intron_id 1
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	splice3	52514739	52514740	.	-	.	intron_id 0 ; splice_site "AG"
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	cds	52514697	52514738	.	-	.	
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	exon	52514697	52514738	.	-	.	insertions 0 ; deletions 0
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	similarity	52514697	52571637	485	-	.	alignment_id 1 ; Query SPP00000114_2.0 ; Align 52571638 10 327 ; Align 52571309 120 114 ; Align 52514739 158 42
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000114_2.0 # Protein # Selenoprotein U2 (SelU2) # Human (Homo sapiens) 
        Target: gi|511782562|gb|CM001951.1|:subseq(2858954,52671000) Chlorocebus sabaeus isolate 1994-021 chromosome X, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 298
   Query range: 150 -> 226
  Target range: 52571225 -> 52570999

      151 : LeuSerGlySerLeuGlnSerLeuTrpArgAlaValThrGlyProLeuPheAsp :      168
            |||||||||||||||  !||||||||| !!||||||||||||||||||||||||
            LeuSerGlySerLeuTrpSerLeuTrpTrpAlaValThrGlyProLeuPheAsp
 52571225 : CTCTCAGGAAGCCTTTGGAGCTTGTGGTGGGCAGTGACTGGCCCTCTCTTTGAT : 52571174

      169 : PheGlnGlyAspProAlaGlnGlnGlyGlyThrLeuIleLeuGlyProGlyAsn :      186
            ||||||||||||||||||||||||||||||||||||||||||||| !!||||||
            PheGlnGlyAspProAlaGlnGlnGlyGlyThrLeuIleLeuGlySerGlyAsn
 52571173 : TTTCAAGGAGATCCAGCTCAGCAAGGTGGAACTCTCATTTTAGGTTCAGGTAAC : 52571120

      187 : AsnIleHisPheIleHisArgAspArgAsnArgLeuAspHisLysProIleAsn :      204
            ||||||||||||||||||!.!!!:||||||! !|||||||||||||||||||||
            AsnIleHisPheIleHisHisGluArgAsnThrLeuAspHisLysProIleAsn
 52571119 : AACATCCATTTTATACACCATGAAAGGAATACGTTGGATCACAAACCTATCAAC : 52571066

      205 : -SerValLeuGlnLeuValGlyValGlnHisValAsnPheThrAsnArgProSe :      222
            #   ||||||||||||||||||||| !!|||||||||||||||||||||! !||
            #---ValLeuGlnLeuValGlyVal***HisValAsnPheThrAsnArgLeuSe
 52571065 : T---GTTTTACAGCTTGTAGGAGTTTAACATGTGAACTTTACAAACAGACTTTC : 52571014

      223 : rValIleHisVal :      226
            |||||||||||||
            rValIleHisVal
 52571013 : AGTTATCCATGTG : 52571000

vulgar: SPP00000114_2.0 150 226 . gi|511782562|gb|CM001951.1|:subseq(2858954,52671000) 52571225 52570999 - 298 M 54 162 F 0 1 G 1 0 M 21 63
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-04
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	gene	52571000	52571225	298	-	.	gene_id 2 ; sequence SPP00000114_2.0 ; gene_orientation .
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	cds	52571000	52571225	.	-	.	
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	exon	52571000	52571225	.	-	.	insertions 0 ; deletions 1 ; frameshifts 1
gi|511782562|gb|CM001951.1|:subseq(2858954,52671000)	exonerate:protein2genome:local	similarity	52571000	52571225	298	-	.	alignment_id 2 ; Query SPP00000114_2.0 ; Align 52571226 151 162 ; Align 52571063 206 63
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis