Command line: [exonerate -m p2g --showtargetgff -q SPS_1.fa.U_to_X -t gi|511782584|gb|CM001949.1|.fastasubseq]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00001330_2.0 # Protein # Selenophosphate synthetase (SPS) # Macaque (Macaca mulatta) 
        Target: gi|511782584|gb|CM001949.1|:subseq(13249704,219541) Chlorocebus sabaeus isolate 1994-021 chromosome 9, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 1346
   Query range: 113 -> 434
  Target range: 119556 -> 99999

    114 : ThrPheProAlaLeuGlyIleGlyMetAspSerCysValIleProLeuArgHisGlyG :    133
          |||! !  !:!!  !|||||||||||||||!!!|||||||||||||||||||||||||
          ThrSerIleSerThrGlyIleGlyMetAspThrCysValIleProLeuArgHisGlyG
 119556 : ACTTCCATCTCCACAGGCATTGGAATGGATACTTGTGTCATTCCTTTGAGGCACGGTG : 119499

    134 : lyLeuSerLeuValGlnThrThrAspPhePheTyrProLeuValGluAspProTyrMe :    152
          ||||||||||||||||||||||||||!:!.!!||||||:!!|||!!:|||||||||||
          lyLeuSerLeuValGlnThrThrAspTyrIleTyrProIleValAspAspProTyrMe
 119498 : GGCTTTCCTTGGTTCAAACCACAGATTACATTTACCCGATCGTAGACGACCCTTACAT : 119442

    153 : tMet  >>>> Target Intron 1 >>>>  GlyArgIleAlaCysAlaAsnValL :    162
          ||||           2356 bp           |||||||||||||||||||||||||
          tMet++                         ++GlyArgIleAlaCysAlaAsnValL
 119441 : GATGgt.........................agGGCAGGATAGCATGTGCCAATGTCC : 117056

    163 : euSerAspLeuTyrAlaMetGlyIleThrGluCysAspAsnMetLeuMetLeuLeuSe :    181
          |||||||||||||||||||||||:!!||||||||||||||||||||||||||||||.!
          euSerAspLeuTyrAlaMetGlyValThrGluCysAspAsnMetLeuMetLeuLeuGl
 117055 : TCAGTGACCTCTACGCAATGGGGGTCACGGAATGTGACAATATGCTGATGCTCCTTGG : 116999

    182 : rValSerGlnSerMetSerGluGlu  >>>> Target Intron 2 >>>>  GluA :    191
          !||||||.!.!.!|||!!!!!:..!           1948 bp           ||||
          yValSerAsnLysMetThrAspArg++                         ++GluA
 116998 : AGTCAGTAATAAAATGACTGACAGGgt.........................agGAAA : 115021

    192 : rgGluLysValThrProLeuMetValLysGlyPheArgAspAla{A}  >>>> Targ :    206
          ||!!:||||||! !||||||!!::!!:!!||||||!:!||||||{|}           
          rgAspLysValMetProLeuIleIleGlnGlyPheLysAspAla{A}-+         
 115020 : GGGATAAAGTGATGCCTCTGATTATCCAAGGTTTTAAAGACGCA{G}ct......... : 114973

    207 : et Intron 3 >>>>  {la}GluGluGlyGlyThrAlaValThrGlyGlyGlnThr :    218
          2271 bp           {||}||||||!.!||||||:!!||||||||||||||||||
                          ++{la}GluGluAlaGlyThrSerValThrGlyGlyGlnThr
 114972 : ................ag{CT}GAGGAAGCAGGAACGTCTGTAACGGGCGGCCAAACA : 112669

    219 : ValValAsnProTrpIleIleIleGlyGlyValAlaThrValValCysGlnProAsnG :    238
          |||:!!||||||||||||:!!:!:|||||||||||||||..!||||||||||||||||
          ValLeuAsnProTrpIleValLeuGlyGlyValAlaThrThrValCysGlnProAsnG
 112668 : GTACTAAACCCCTGGATTGTCCTGGGAGGAGTTGCTACCACTGTCTGTCAGCCCAATG : 112609

    239 : luPheIle{Me}  >>>> Target Intron 4 >>>>  {t}ProAspSerAlaVa :    246
          ||||||||{||}           2583 bp           {|}||||||!:!|||||
          luPheIle{Me}++                         ++{t}ProAspAsnAlaVa
 112608 : AATTTATC{AT}gt.........................ag{G}CCGGACAATGCAGT : 110002

    247 : lValGlyAspValLeuValLeuThrLysProLeuGlyThrGlnValAlaValAsnAla :    265
          |  !||||||||||||||||||||||||||||||||||||||||||||||||  !!.!
          lProGlyAspValLeuValLeuThrLysProLeuGlyThrGlnValAlaValAlaVal
 110001 : ACCAGGGGATGTGCTGGTGTTGACAAAACCCCTGGGGACACAGGTGGCAGTGGCTGTG : 109945

    266 : HisGlnTrpLeuAspAsn  >>>> Target Intron 5 >>>>  ProGluArgTr :    275
          |||||||||||||||! !           1442 bp           ||||||!:!||
          HisGlnTrpLeuAspIle++                         ++ProGluLysTr
 109944 : CACCAGTGGCTGGATATTgt.........................agCCTGAGAAATG : 108473

    276 : pAsnLysValLysMetValValSerArgGluGluValGluLeuAlaTyrGlnGluAla :    294
          |||||||:!!|||:!:||||||!!!!:!|||!!:||||||||||||||||||||||||
          pAsnLysIleLysLeuValValThrGlnGluAspValGluLeuAlaTyrGlnGluAla
 108472 : GAATAAGATCAAACTAGTGGTCACCCAAGAAGACGTAGAGCTGGCCTACCAGGAGGCA : 108416

    295 : MetPheAsnMetAlaThrLeuAsnArgThr{A}  >>>> Target Intron 6 >> :    305
          |||.!.|||||||||! !||||||||||||{|}           4813 bp       
          MetMetAsnMetAlaArgLeuAsnArgThr{A}-+                       
 108415 : ATGATGAACATGGCGAGGCTCAACAGGACA{G}ct....................... : 108380

    306 : >>  {la}AlaGlyLeuMetHisThrPheAsnAlaHisAlaAlaThrAspIleThrGl :    322
              {||}||||||||||||||||||||||||||||||||||||||||||||||||||
            ++{la}AlaGlyLeuMetHisThrPheAsnAlaHisAlaAlaThrAspIleThrGl
 108379 : ..ag{CT}GCAGGACTCATGCACACGTTCAATGCCCACGCGGCCACTGACATCACGGG : 103519

    323 : yPheGlyIleLeuGlyHisSerGlnAsnLeuAlaLysGlnGlnArgAsnGluValSer :    341
          |||||||||||||||||||:!!||||||||||||||||||||||||||||||||||||
          yPheGlyIleLeuGlyHisAlaGlnAsnLeuAlaLysGlnGlnArgAsnGluValSer
 103518 : CTTTGGGATTTTGGGCCACGCACAGAACCTGGCCAAGCAGCAGAGGAACGAGGTGTCA : 103462

    342 : PheValIleHisAsnLeuProValIleAlaLysMetAlaAlaValSerLysAlaSerG :    361
          ||||||||||||||||||||||||:!:|||||||||||||||||||||||||||!!!|
          PheValIleHisAsnLeuProValLeuAlaLysMetAlaAlaValSerLysAlaCysG
 103461 : TTTGTAATTCACAACCTCCCGGTGCTGGCCAAGATGGCTGCGGTGAGCAAGGCCTGCG : 103402

    362 : lyArg<->PheGlyLeuLeuGlnGlyThrSerAlaGluThrSer{G}  >>>> Targ :    375
          ||!.!   |||||||||:!!!!.||||||!!! !!|||||||||{|}           
          lyAsnMetPheGlyLeuMetHisGlyThrCysProGluThrSer{G}++         
 103401 : GAAACATGTTCGGCCTCATGCACGGGACCTGCCCGGAGACCTCA{G}gt......... : 103354

    376 : et Intron 7 >>>>  {ly}GlyLeuLeuIleCysLeuProArgGluGlnAlaAla :    387
          3178 bp           {||}||||||||||||||||||||||||||||||||||||
                          ++{ly}GlyLeuLeuIleCysLeuProArgGluGlnAlaAla
 103353 : ................ag{GC}GGCCTTCTGATCTGTTTACCACGTGAGCAAGCAGCT : 100143

    388 : ArgPheCysSerGluIleLysSerSerLysTyrGlyGluGlyHisGlnAlaTrpIleV :    407
          |||||||||:!!|||||||||||| !!||||||||||||||||||||||||||||||:
          ArgPheCysAlaGluIleLysSerProLysTyrGlyGluGlyHisGlnAlaTrpIleI
 100142 : CGGTTCTGTGCAGAGATAAAGTCCCCCAAATATGGTGAAGGCCACCAAGCATGGATTA : 100083

    408 : alGlyIleValGluLysGlyAsnArgThrAlaArgIleIleAspLysProArgValIl :    426
          !!|||||||||||||||||||||||||||||||||||||||||||||||||||:!!||
          leGlyIleValGluLysGlyAsnArgThrAlaArgIleIleAspLysProArgIleIl
 100082 : TTGGGATTGTAGAGAAGGGCAACCGCACAGCCAGAATCATAGACAAACCCCGGATCAT : 100026

    427 : eGluValLeuProArgGlyAlaThr :    434
          |||||||  !|||!:!! !||||||
          eGluValAlaProGlnValAlaThr
 100025 : CGAGGTCGCACCACAAGTGGCCACT : 100000

vulgar: SPP00001330_2.0 113 434 . gi|511782584|gb|CM001949.1|:subseq(13249704,219541) 119556 99999 - 1346 M 40 120 5 0 2 I 0 2352 3 0 2 M 36 108 5 0 2 I 0 1944 3 0 2 M 16 48 S 0 1 5 0 2 I 0 2267 3 0 2 S 1 2 M 34 102 S 0 2 5 0 2 I 0 2579 3 0 2 S 1 1 M 30 90 5 0 2 I 0 1438 3 0 2 M 33 99 S 0 1 5 0 2 I 0 4809 3 0 2 S 1 2 M 57 171 G 0 3 M 12 36 S 0 1 5 0 2 I 0 3174 3 0 2 S 1 2 M 59 177
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-06
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	gene	100000	119556	1346	-	.	gene_id 1 ; sequence SPP00001330_2.0 ; gene_orientation +
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	cds	119437	119556	.	-	.	
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	exon	119437	119556	.	-	.	insertions 0 ; deletions 0
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	splice5	119435	119436	.	-	.	intron_id 1 ; splice_site "GT"
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	intron	117081	119436	.	-	.	intron_id 1
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	splice3	117081	117082	.	-	.	intron_id 0 ; splice_site "AG"
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	cds	116973	117080	.	-	.	
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	exon	116973	117080	.	-	.	insertions 0 ; deletions 0
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	splice5	116971	116972	.	-	.	intron_id 2 ; splice_site "GT"
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	intron	115025	116972	.	-	.	intron_id 2
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	splice3	115025	115026	.	-	.	intron_id 1 ; splice_site "AG"
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	cds	114976	115024	.	-	.	
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	exon	114976	115024	.	-	.	insertions 0 ; deletions 0
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	splice5	114974	114975	.	-	.	intron_id 3 ; splice_site "CT"
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	intron	112705	114975	.	-	.	intron_id 3
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	splice3	112705	112706	.	-	.	intron_id 2 ; splice_site "AG"
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	cds	112599	112704	.	-	.	
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	exon	112599	112704	.	-	.	insertions 0 ; deletions 0
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	splice5	112597	112598	.	-	.	intron_id 4 ; splice_site "GT"
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	intron	110016	112598	.	-	.	intron_id 4
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	splice3	110016	110017	.	-	.	intron_id 3 ; splice_site "AG"
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	cds	109925	110015	.	-	.	
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	exon	109925	110015	.	-	.	insertions 0 ; deletions 0
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	splice5	109923	109924	.	-	.	intron_id 5 ; splice_site "GT"
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	intron	108483	109924	.	-	.	intron_id 5
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	splice3	108483	108484	.	-	.	intron_id 4 ; splice_site "AG"
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	cds	108383	108482	.	-	.	
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	exon	108383	108482	.	-	.	insertions 0 ; deletions 0
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	splice5	108381	108382	.	-	.	intron_id 6 ; splice_site "CT"
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	intron	103570	108382	.	-	.	intron_id 6
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	splice3	103570	103571	.	-	.	intron_id 5 ; splice_site "AG"
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	cds	103357	103569	.	-	.	
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	exon	103357	103569	.	-	.	insertions 3 ; deletions 0
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	splice5	103355	103356	.	-	.	intron_id 7 ; splice_site "GT"
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	intron	100179	103356	.	-	.	intron_id 7
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	splice3	100179	100180	.	-	.	intron_id 6 ; splice_site "AG"
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	cds	100000	100178	.	-	.	
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	exon	100000	100178	.	-	.	insertions 0 ; deletions 0
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	similarity	100000	119556	1346	-	.	alignment_id 1 ; Query SPP00001330_2.0 ; Align 119557 114 120 ; Align 117081 154 108 ; Align 115025 190 48 ; Align 112703 207 102 ; Align 110015 242 90 ; Align 108483 272 99 ; Align 103568 306 171 ; Align 103394 363 36 ; Align 100177 376 177
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00001330_2.0 # Protein # Selenophosphate synthetase (SPS) # Macaque (Macaca mulatta) 
        Target: gi|511782584|gb|CM001949.1|:subseq(13249704,219541) Chlorocebus sabaeus isolate 1994-021 chromosome 9, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 114
   Query range: 32 -> 79
  Target range: 125838 -> 125697

     33 : ArgSerPheSerAsnTyrArgProPheGluProGlnAlaLeuGlyLeuSerProSerT :     52
          |||!!!.!.|||!..   ..! !!|||.!.|||:!!::!! !! !|||..!  !|||!
          ArgThrMetSerThrArgGluSerPheAsnProGluSerTyrGluLeuAspLysSerP
 125838 : AGAACCATGTCTACGCGGGAGTCCTTTAACCCGGAAAGTTACGAATTGGACAAAAGCT : 125781

     53 : rpArgLeuThrGlyPheSerGlyMetLysGlyUnkGlyCysLysValProGlnGluTh :     71
          ::||||||||| !!|||!!!! !:!!||||||...||||||||||||||||||!!:..
          heArgLeuThrArgPheThrGluLeuLysGlyThrGlyCysLysValProGlnAspVa
 125780 : TCCGGCTAACCAGATTCACTGAACTGAAGGGCACAGGCTGCAAAGTGCCCCAAGATGT : 125724

     72 : rLeuLeuLysLeuLeuAlaGlyLeu :     79
          !|||! !|||||||||! !..!|||
          lLeuGlnLysLeuLeuGluSerLeu
 125723 : CCTGCAAAAATTGCTGGAATCTTTA : 125698

vulgar: SPP00001330_2.0 32 79 . gi|511782584|gb|CM001949.1|:subseq(13249704,219541) 125838 125697 - 114 M 47 141
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-06
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	gene	125698	125838	114	-	.	gene_id 2 ; sequence SPP00001330_2.0 ; gene_orientation .
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	cds	125698	125838	.	-	.	
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	exon	125698	125838	.	-	.	insertions 0 ; deletions 0
gi|511782584|gb|CM001949.1|:subseq(13249704,219541)	exonerate:protein2genome:local	similarity	125698	125838	114	-	.	alignment_id 2 ; Query SPP00001330_2.0 ; Align 125839 33 141
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis