Command line: [exonerate -m p2g --showtargetgff -q eefsec.query.U_to_X -t gi|511782571|gb|CM001963.1|.fastasubseq]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000144_2.0 # Protein # Eukaryotic elongation factor (eEFSec) # Human (Homo sapiens) 
        Target: gi|511782571|gb|CM001963.1|:subseq(52584320,353418) Chlorocebus sabaeus isolate 1994-021 chromosome 22, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 2975
   Query range: 0 -> 596
  Target range: 303454 -> 49999

      1 : MetAlaGlyArgArgValAsnValAsnValGlyValLeuGlyHisIleAspSerGlyL :     20
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          MetAlaGlyArgArgValAsnValAsnValGlyValLeuGlyHisIleAspSerGlyL
 303454 : ATGGCAGGGCGGCGAGTTAACGTGAACGTGGGCGTGCTGGGCCACATCGACAGCGGCA : 303397

     21 : ysThrAlaLeuAlaArgAlaLeuSerThrThrAlaSerThrAlaAlaPheAspLysGl :     39
          |||||||||||||||||||||||||||||||||||||||||:!!||||||||||||||
          ysThrAlaLeuAlaArgAlaLeuSerThrThrAlaSerThrSerAlaPheAspLysGl
 303396 : AGACGGCGCTGGCGCGGGCGCTAAGCACCACAGCCTCCACTTCCGCCTTTGACAAGCA : 303340

     40 : nProGlnSerArgGluArgGlyIleThrLeuAspLeuGlyPheSerCysPheSerVal :     58
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          nProGlnSerArgGluArgGlyIleThrLeuAspLeuGlyPheSerCysPheSerVal
 303339 : GCCGCAGAGCCGCGAGCGCGGCATCACGCTAGACCTGGGCTTCTCCTGCTTCTCGGTG : 303283

     59 : ProLeuProAlaArgLeuArgSerSerLeuProGluPheGlnAlaAlaProGluAlaG :     78
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          ProLeuProAlaArgLeuArgSerSerLeuProGluPheGlnAlaAlaProGluAlaG
 303282 : CCGCTGCCCGCGCGCCTGCGGTCGTCTTTGCCCGAGTTCCAGGCAGCGCCCGAGGCCG : 303223

     79 : luProGluProGlyGluProLeuLeuGlnValThrLeuValAspCysProGlyHisAl :     97
          |||||||| !!|||||||||||||||||||||||||||||||||||||||||||||||
          luProGluAlaGlyGluProLeuLeuGlnValThrLeuValAspCysProGlyHisAl
 303222 : AGCCCGAGGCCGGCGAGCCACTGCTTCAGGTCACGCTGGTCGACTGTCCCGGGCACGC : 303166

     98 : aSerLeuIleArgThrIleIleGly{G}  >>>> Target Intron 1 >>>>  { :    106
          |||||||||||||||||||||||||{|}           92686 bp          {
          aSerLeuIleArgThrIleIleGly{G}++                         ++{
 303165 : CTCCCTCATCCGGACCATCATCGGC{G}gt.........................ag{ : 210452

    107 : ly}AlaGlnIleIleAspLeuMetMetLeuValIleAspValThrLysGlyMetGlnT :    125
          ||}|||||||||||||||||||||||||||||||||||||||||||||||||||||||
          ly}AlaGlnIleIleAspLeuMetMetLeuValIleAspValThrLysGlyMetGlnT
 210451 : GG}GCCCAGATCATTGATCTGATGATGCTGGTCATCGATGTGACCAAGGGGATGCAGA : 210396

    126 : hrGlnSerAlaGluCysLeuValIleGlyGlnIleAlaCysGlnLysLeuValValVa :    144
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          hrGlnSerAlaGluCysLeuValIleGlyGlnIleAlaCysGlnLysLeuValValVa
 210395 : CCCAGTCAGCGGAATGCCTTGTGATCGGCCAGATTGCCTGCCAGAAGCTGGTTGTGGT : 210339

    145 : lLeuAsnLysIleAspLeuLeuProGluGlyLysArgGlnAlaAlaIleAspLysMet :    163
          |||||||||||||||||||||| !!|||||||||||||||||||||:!!|||||||||
          lLeuAsnLysIleAspLeuLeuAlaGluGlyLysArgGlnAlaAlaValAspLysMet
 210338 : GCTGAACAAAATAGACCTCTTAGCTGAAGGAAAGAGACAGGCAGCAGTTGATAAAATG : 210282

    164 : ThrLysLysMetGlnLysThrLeuGluAsnThr{Ly}  >>>> Target Intron  :    175
          |||||||||||||||||||||||||||||||||{||}           14749 bp  
          ThrLysLysMetGlnLysThrLeuGluAsnThr{Ly}++                   
 210281 : ACCAAGAAAATGCAGAAGACCCTAGAGAACACC{AA}gt................... : 210242

    176 : 2 >>>>  {s}PheArgGlyAlaProIleIleProValAlaAlaLysProGlyGlyPr :    191
                  {|}|||||||||||||||||||||||||||||||||||||||||||||||
                ++{s}PheArgGlyAlaProIleIleProValAlaAlaLysProGlyGlyPr
 210241 : ......ag{G}TTCCGAGGTGCACCGATTATACCTGTGGCGGCCAAGCCAGGCGGACC : 195449

    192 : oGluAlaProGluThrGluAlaProGlnGlyIleProGluLeuIleGlu  >>>> Ta :    208
          |||||||||||||||||||||||||||||||||||||||||||||||||         
          oGluAlaProGluThrGluAlaProGlnGlyIleProGluLeuIleGlu++       
 195448 : AGAGGCCCCTGAAACTGAAGCTCCACAGGGCATTCCAGAGCTCATTGAGgt....... : 195396

    209 : rget Intron 3 >>>>  LeuLeuThrSerGlnIleSerIleProThrArgAspPr :    220
            2393 bp           |||||||||||||||||||||||||||! !||||||||
                            ++LeuLeuThrSerGlnIleSerIleProMetArgAspPr
 195395 : ..................agCTCCTGACGTCCCAGATTTCTATCCCAATGAGAGACCC : 192969

    221 : oSerGlyProPheLeuMetSerValAspHisCysPheSerIleLysGlyGlnGlyThr :    239
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          oSerGlyProPheLeuMetSerValAspHisCysPheSerIleLysGlyGlnGlyThr
 192968 : CTCGGGACCGTTCCTCATGTCTGTGGACCACTGTTTCTCCATCAAAGGCCAAGGCACT : 192912

    240 : ValMetThrGlyThrIleLeuSerGlySerIleSerLeuGlyAspSerValGluIleP :    259
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          ValMetThrGlyThrIleLeuSerGlySerIleSerLeuGlyAspSerValGluIleP
 192911 : GTGATGACAGGGACCATCCTCTCAGGCTCCATCAGCCTCGGTGACAGTGTGGAGATCC : 192852

    260 : roAlaLeuLys  >>>> Target Intron 4 >>>>  ValValLysLysValLys :    268
          |||||||||||           77196 bp          ||||||||||||||||||
          roAlaLeuLys++                         ++ValValLysLysValLys
 192851 : CTGCCCTCAAGgt.........................agGTGGTGAAGAAGGTGAAG : 115629

    269 : SerMetGlnMetPheHisMetProIleThrSerAlaMetGlnGlyAspArgLeuGlyI :    288
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          SerMetGlnMetPheHisMetProIleThrSerAlaMetGlnGlyAspArgLeuGlyI
 115628 : TCCATGCAGATGTTTCACATGCCTATCACTTCAGCCATGCAAGGAGACCGGCTGGGCA : 115569

    289 : leCysValThrGlnPheAspProLysLeuLeuGluArgGlyLeuValCysAlaProGl :    307
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          leCysValThrGlnPheAspProLysLeuLeuGluArgGlyLeuValCysAlaProGl
 115568 : TCTGCGTCACCCAGTTTGACCCCAAGCTGCTGGAGCGCGGGTTGGTGTGTGCCCCTGA : 115512

    308 : uSerLeuHisThrValHisAlaAlaLeuIleSerValGluLysIleProTyrPheArg :    326
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          uSerLeuHisThrValHisAlaAlaLeuIleSerValGluLysIleProTyrPheArg
 115511 : GTCCCTGCATACTGTCCATGCGGCCCTCATCTCTGTGGAAAAGATACCATATTTCCGG : 115455

    327 : GlyProLeuGlnThrLysAlaLysPheHisIleThrValGlyHisGluThrValMetG :    346
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          GlyProLeuGlnThrLysAlaLysPheHisIleThrValGlyHisGluThrValMetG
 115454 : GGGCCCCTGCAAACCAAGGCCAAGTTCCACATTACAGTGGGCCATGAAACAGTCATGG : 115395

    347 : lyArgLeuMetPhePheSerProAlaProAspAsnPheAspGlnGluProIleLeuAs :    365
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          lyArgLeuMetPhePheSerProAlaProAspAsnPheAspGlnGluProIleLeuAs
 115394 : GCCGGTTGATGTTCTTCAGCCCTGCTCCAGATAACTTTGACCAGGAGCCTATACTGGA : 115338

    366 : pSerPheAsnPheSerGlnGluTyrLeuPheGlnGluGlnTyrLeuSerLysAspLeu :    384
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          pSerPheAsnPheSerGlnGluTyrLeuPheGlnGluGlnTyrLeuSerLysAspLeu
 115337 : CTCTTTCAACTTCTCTCAAGAATACCTCTTCCAGGAGCAGTACCTATCCAAGGATTTG : 115281

    385 : ThrProAlaValThrAspAsnAspGluAlaAspLysLysAlaGlyGlnAlaThrGluG :    404
          .!!||||||||||||:!!||||||||||||||||||||||||||||||||||||||||
          AlaProAlaValThrAsnAsnAspGluAlaAspLysLysAlaGlyGlnAlaThrGluG
 115280 : GCACCAGCAGTGACAAATAATGATGAGGCCGACAAGAAGGCCGGCCAGGCCACAGAGG : 115221

    405 : lyHisCysProArgGlnGlnTrpAlaLeuValGluPheGluLysProValThrCysPr :    423
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          lyHisCysProArgGlnGlnTrpAlaLeuValGluPheGluLysProValThrCysPr
 115220 : GCCATTGTCCTCGGCAGCAGTGGGCCCTGGTAGAGTTTGAGAAGCCCGTCACCTGCCC : 115164

    424 : oArgLeuCysLeuValIleGlySerArgLeuAspAlaAspIleHisThrAsnThrCys :    442
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          oArgLeuCysLeuValIleGlySerArgLeuAspAlaAspIleHisThrAsnThrCys
 115163 : TCGGCTGTGCCTGGTGATTGGCTCTAGGCTAGATGCGGACATTCACACCAACACGTGC : 115107

    443 : ArgLeuAlaPheHisGlyIleLeuLeuHisGlyLeuGluAspArgAsnTyrAlaAspS :    462
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          ArgLeuAlaPheHisGlyIleLeuLeuHisGlyLeuGluAspArgAsnTyrAlaAspS
 115106 : CGGCTAGCCTTCCATGGCATCCTGCTCCATGGGCTGGAGGACAGGAACTATGCCGACA : 115047

    463 : erPheLeuProArgLeuLysValTyrLysLeuLysHisLysHisGlyLeuValGluAr :    481
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          erPheLeuProArgLeuLysValTyrLysLeuLysHisLysHisGlyLeuValGluAr
 115046 : GCTTCCTGCCCAGGCTGAAGGTGTACAAGCTGAAGCACAAGCATGGCCTCGTAGAGCG : 114990

    482 : g  >>>> Target Intron 5 >>>>  AlaMetAspAspTyrSerValIleGlyA :    491
          |           16452 bp          ||||||||||||||||||||||||||||
          g++                         ++AlaMetAspAspTyrSerValIleGlyA
 114989 : Ggt.........................agGCGATGGATGACTACAGTGTGATCGGCC :  98508

    492 : rgSerLeuPheLysLysGluThrAsnIleGlnLeuPheValGlyLeuLysValHisLe :    510
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          rgSerLeuPheLysLysGluThrAsnIleGlnLeuPheValGlyLeuLysValHisLe
  98507 : GCTCCCTGTTTAAAAAGGAGACCAACATCCAGCTCTTCGTGGGGCTCAAGGTGCACCT :  98451

    511 : uSerThrGlyGluLeuGlyIleIleAspSerAlaPheGlyGlnSerGlyLysPheLys :    529
          |||||||||||||||||||:!!||||||||||||||||||||||||||||||||||||
          uSerThrGlyGluLeuGlyValIleAspSerAlaPheGlyGlnSerGlyLysPheLys
  98450 : GTCCACTGGAGAACTGGGCGTCATCGACAGTGCCTTCGGCCAGAGCGGCAAGTTCAAG :  98394

    530 : IleHisIlePro{G}  >>>> Target Intron 6 >>>>  {ly}GlyLeuSerP :    538
          ||||||||||||{|}           48191 bp          {||}||||||||||
          IleHisIlePro{G}++                         ++{ly}GlyLeuSerP
  98393 : ATCCACATCCCA{G}gt.........................ag{GT}GGCCTCAGCC :  50176

    539 : roGluSerLysLysIleLeuThrProAlaLeuLysLysArgAlaArgAlaGlyArgGl :    557
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          roGluSerLysLysIleLeuThrProAlaLeuLysLysArgAlaArgAlaGlyArgGl
  50175 : CTGAGTCCAAGAAGATCCTGACACCTGCCCTCAAGAAGCGGGCCCGGGCCGGCCGCGG :  50119

    558 : yGluAlaThrArgGlnGluGluSerAlaGluArgSerGluProSerGlnHisValVal :    576
          |||||||||||||||||||||||||||||||||||||||||||||||||||||||!.!
          yGluAlaThrArgGlnGluGluSerAlaGluArgSerGluProSerGlnHisValAla
  50118 : GGAGGCTACCAGGCAGGAGGAGAGCGCTGAGCGGAGCGAGCCCTCACAGCATGTGGCA :  50062

    577 : LeuSerLeuThrPheLysArgTyrValPheAspThrHisLysArgMetValGlnSerP :    596
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          LeuSerLeuThrPheLysArgTyrValPheAspThrHisLysArgMetValGlnSerP
  50061 : CTCAGCCTGACTTTCAAGCGTTACGTCTTCGACACCCACAAGCGCATGGTCCAGTCTC :  50002

    597 : ro :    596
          ||
          ro
  50001 : CC :  50000

vulgar: SPP00000144_2.0 0 596 . gi|511782571|gb|CM001963.1|:subseq(52584320,353418) 303454 49999 - 2975 M 105 315 S 0 1 5 0 2 I 0 92682 3 0 2 S 1 2 M 68 204 S 0 2 5 0 2 I 0 14745 3 0 2 S 1 1 M 32 96 5 0 2 I 0 2389 3 0 2 M 55 165 5 0 2 I 0 77192 3 0 2 M 219 657 5 0 2 I 0 16448 3 0 2 M 52 156 S 0 1 5 0 2 I 0 48187 3 0 2 S 1 2 M 62 186
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-05
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	gene	50000	303454	2975	-	.	gene_id 1 ; sequence SPP00000144_2.0 ; gene_orientation +
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	cds	303139	303454	.	-	.	
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	exon	303139	303454	.	-	.	insertions 0 ; deletions 0
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	splice5	303137	303138	.	-	.	intron_id 1 ; splice_site "GT"
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	intron	210453	303138	.	-	.	intron_id 1
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	splice3	210453	210454	.	-	.	intron_id 0 ; splice_site "AG"
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	cds	210245	210452	.	-	.	
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	exon	210245	210452	.	-	.	insertions 0 ; deletions 0
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	splice5	210243	210244	.	-	.	intron_id 2 ; splice_site "GT"
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	intron	195496	210244	.	-	.	intron_id 2
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	splice3	195496	195497	.	-	.	intron_id 1 ; splice_site "AG"
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	cds	195399	195495	.	-	.	
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	exon	195399	195495	.	-	.	insertions 0 ; deletions 0
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	splice5	195397	195398	.	-	.	intron_id 3 ; splice_site "GT"
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	intron	193006	195398	.	-	.	intron_id 3
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	splice3	193006	193007	.	-	.	intron_id 2 ; splice_site "AG"
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	cds	192841	193005	.	-	.	
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	exon	192841	193005	.	-	.	insertions 0 ; deletions 0
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	splice5	192839	192840	.	-	.	intron_id 4 ; splice_site "GT"
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	intron	115645	192840	.	-	.	intron_id 4
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	splice3	115645	115646	.	-	.	intron_id 3 ; splice_site "AG"
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	cds	114988	115644	.	-	.	
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	exon	114988	115644	.	-	.	insertions 0 ; deletions 0
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	splice5	114986	114987	.	-	.	intron_id 5 ; splice_site "GT"
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	intron	98536	114987	.	-	.	intron_id 5
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	splice3	98536	98537	.	-	.	intron_id 4 ; splice_site "AG"
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	cds	98379	98535	.	-	.	
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	exon	98379	98535	.	-	.	insertions 0 ; deletions 0
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	splice5	98377	98378	.	-	.	intron_id 6 ; splice_site "GT"
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	intron	50188	98378	.	-	.	intron_id 6
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	splice3	50188	50189	.	-	.	intron_id 5 ; splice_site "AG"
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	cds	50000	50187	.	-	.	
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	exon	50000	50187	.	-	.	insertions 0 ; deletions 0
gi|511782571|gb|CM001963.1|:subseq(52584320,353418)	exonerate:protein2genome:local	similarity	50000	303454	2975	-	.	alignment_id 1 ; Query SPP00000144_2.0 ; Align 303455 1 315 ; Align 210451 107 204 ; Align 195495 176 96 ; Align 193006 208 165 ; Align 115645 263 657 ; Align 98536 482 156 ; Align 50186 535 186
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis