>AFJ140 (AFJ140Q) /CSM/AF/AFJ1-B/AFJ140Q.Seq.d/
GATGAATATTCAAACATCATTAATAGTTTNAAAATAAATCAAGNCACTGGNGATGATTTT
GTTTTATTTGAACAAAAAGATTATGAAACTTTATCAGTNCCTTGGAAATTTCAAAAAAAA
CTTAANGAAATACAAGGNTCTXXXXXXXXXXAATCATTGGTTAATGTCAATCCACCTGAA
AGCATTATACTTCCCAAAAAGTTTATGATTAAAACACCTCTTAGTGAACCTATAGATGGT
ACTATTGAATTGATGTATGGTGGTAGAAATATGTTTACTGGCAGTGTTACACAAGGTGAT
GCTGATCTTCCTCTAAACCTCTTGGATGGTACATTTGAGGTTATCATTAAACCCAATAAG
AGTAATTTATTACCTTTAAAGTTTAAAATGATTATACATGACTCTGTAAGAACCACTTCA
AGCCATCAAAATGTCGGTAGACCTAAAAAGCCTAAAGAAATGGATTTCGTTTTAGCTTGG
GGGGAATCACCACTGGATTTGGATTCTCATATGTGGTGTATTCATCCTAATGGTTCTATT
AGTCATGTTTATTTCGGGGGTAGGAGTGTAGATAAAATGTCCTTGGAAGCTGATACTCAA
AATGGTTTTGGTCCCGAAACCATAAGTATTATACGTTTAGATGGTTGTAAATATGTTTAT
GCAGTTCATAATTTCTCAACTGAAGGAGAAATAGCTCAATCAGGTGCCAAGCTTACAACT
TGCCCATGAAACCTCAACATTATTGAAAGATGTATCCCAAACACTCGACAAACTGGTGCA
AGATTTTGGGTAGTATGTACTATTGATGGAACATCTGGAGANATGACTTCAAAGATCATT
TNAATTCCACAATTCACAAACAGAATTCCATTA

DEYSNIINSXKINQXTGDDFVLFEQKDYETLSVPWKFQKKLXEIQGS---

---SLVNVNPPESIILPKKFMIKTPLSEPIDGTIELMYGGRNMFTGSVTQGDADLPLNLL
DGTFEVIIKPNKSNLLPLKFKMIIHDSVRTTSSHQNVGRPKKPKEMDFVLAWGESPLDLD
SHMWCIHPNGSISHVYFGGRSVDKMSLEADTQNGFGPETISIIRLDGCKYVYAVHNFSTE
GEIAQSGAKLTTCP*nlniiercipntrqtgarfwvvctidgtsgxmtskiixipqftnr
ipl

Frame A:
DEYSNIINSXKINQXTGDDFVLFEQKDYETLSVPWKFQKKLXEIQGS---

---nhwlmsihlkalyfpksl*lkhllvnl*mvlln*cmvveicllavlhkvmlifl*ts
wmvhlrlslnpirviyyl*slk*lymtl*eplqaikmsvdlkslkkwisf*lggnhhwiw
ilicgvfilmvllvmfisgvgv*ikcpwklilkmvlvpkp*vlyv*mvvnmfmqfiisql
kek*lnqvpslqlahetstllkdvsqtldklvqdfg*yvllmehlex*lqrsfxfhnsqt
efh

Frame B:
mniqtslivxk*ikxlxmilfylnkkimklyqxlgnfkknlxkykx---

---iig*cqst*khytsqkvyd*nts**tyrwyy*idvww*kyvywqcytr*c*ssskpl
gwyi*gyh*tq*e*fitfkv*ndyt*lcknhfkpskcr*t*ka*rngfrfslggittgfg
fsyvvyss*wfy*sclfrg*ecr*nvlgs*yskwfwsrnhkyytfrwl*iclcss*fln*
rrnssircqaynlpmkpqhy*kmypkhstnwckilgsmyy*wniwrxdfkdhxnstihkq
nsi

Frame C:
*ifkhh**fxnksxhwx*fcfi*tkrl*nfisxleiskkt*xntrx---

---SLVNVNPPESIILPKKFMIKTPLSEPIDGTIELMYGGRNMFTGSVTQGDADLPLNLL
DGTFEVIIKPNKSNLLPLKFKMIIHDSVRTTSSHQNVGRPKKPKEMDFVLAWGESPLDLD
SHMWCIHPNGSISHVYFGGRSVDKMSLEADTQNGFGPETISIIRLDGCKYVYAVHNFSTE
GEIAQSGAKLTTCP*nlniiercipntrqtgarfwvvctidgtsgxmtskiixipqftnr
ipl

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AFJ140 (AFJ140Q) /CSM/AF/AFJ1-B/AFJ140Q.Seq.d/                       1576   0.0
AFD590 (AFD590Q) /CSM/AF/AFD5-D/AFD590Q.Seq.d/                       1386   0.0
AFD183 (AFD183Q) /CSM/AF/AFD1-D/AFD183Q.Seq.d/                       1376   0.0
AFK163 (AFK163Q) /CSM/AF/AFK1-C/AFK163Q.Seq.d/                       1374   0.0
AFE636 (AFE636Q) /CSM/AF/AFE6-B/AFE636Q.Seq.d/                       1372   0.0
CFH243 (CFH243Q) /CSM/CF/CFH2-B/CFH243Q.Seq.d/                       1362   0.0
AFM455 (AFM455Q) /CSM/AF/AFM4-C/AFM455Q.Seq.d/                       1362   0.0
AFJ592 (AFJ592Q) /CSM/AF/AFJ5-D/AFJ592Q.Seq.d/                       1360   0.0
CFH517 (CFH517Q) /CSM/CF/CFH5-A/CFH517Q.Seq.d/                       1348   0.0
AFG278 (AFG278Q) /CSM/AF/AFG2-D/AFG278Q.Seq.d/                       1348   0.0

                                                             Score    E
Sequences producing significant alignments:                  (bits) Value  N

AX661200|AX661200.1 Sequence 3 from Patent WO0246217.              34   0.10   6
AE000788|AE000788.1 Borrelia burgdorferi plasmid lp36, complete plasmid sequence.    46   0.20   5
AC140914|AC140914.12 Medicago truncatula clone mth2-18h17, WORKING DRAFT SEQUENCE, 6 ordered pieces.    48   0.24   1
AC146714|AC146714.3 Mus musculus chromosome 6 clone RP24-175I24 map 6, *** SEQUENCING IN PROGRESS ***, 3 unordered pieces.    44   0.53   2
AC096735|AC096735.3 Homo sapiens BAC clone RP11-135M12 from 4, complete sequence.    34   0.61   9
AJ428413|AJ428413.1 Calycanthus fertilis var. ferax complete chloroplast genome.    36   0.66   4
AL031745|AL031745.8 Plasmodium falciparum DNA from MAL1P2.         34   0.71   10
AY341864|AY341864.1 Borrelia burgdorferi plasmid bbk50-like (bbk50) gene, partial cds; bbk47-like (bbk47) gene, complete cds; and bbk46-like (bbk46) gene, partial cds.    46   0.96   1
AL136366|AL136366.24 Human DNA sequence from clone RP11-413C16 on chromosome 9p22.3-23.    46   0.96   1
AY341868|AY341868.1 Borrelia burgdorferi plasmid bbk50-like (bbk50) gene, partial cds; and bbk49-like (bbk49), bbk48-like (bbk48), bbk47-like (bbk47), and bbk46-like (bbk46) genes, complete cds.    46   0.96   1

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

CP000478_3794(CP000478|pid:none) Syntrophobacter fumaroxidans MP...    68   4e-10
CP000880_2513(CP000880|pid:none) Salmonella enterica subsp. ariz...    66   1e-09
CP000112_1873(CP000112|pid:none) Desulfovibrio desulfuricans G20...    65   3e-09
CU928162_679(CU928162|pid:none) Escherichia coli ED1a chromosome...    62   2e-08
AE014075_780(AE014075|pid:none) Escherichia coli CFT073, complet...    60   1e-07
CP000243_708(CP000243|pid:none) Escherichia coli UTI89, complete...    60   1e-07
CP000247_733(CP000247|pid:none) Escherichia coli 536, complete g...    58   3e-07
AE001437_1067(AE001437|pid:none) Clostridium acetobutylicum ATCC...    57   1e-06
FM954973_832(FM954973|pid:none) Vibrio splendidus LGP32 chromoso...    56   1e-06
AE001437_1068(AE001437|pid:none) Clostridium acetobutylicum ATCC...    54   6e-06

 psg: 0.75  gvh: 0.36  alm: 0.48  top: 0.53  tms: 0.00  mit: 0.13  mip: 0.00
 nuc: 0.12  erl: 0.00  erm: 0.00  pox: 0.00  px2: 0.00  vac: 0.33  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 0.00  tyr: 0.00  leu: 0.00  gpi: 0.00  myr: 0.00
 dna: 0.00  rib: 0.00  bac: 0.00  m1a: 0.00  m1b: 0.00  m2 : 0.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 1.00 

	 48.0 %: nuclear
	 32.0 %: cytoplasmic
	  8.0 %: cytoskeletal
	  8.0 %: vacuolar
	  4.0 %: mitochondrial

>> prediction for AFJ140 is nuc

>AFJ140F.Seq
GATGAATATTCAAACATCATTAATAGTTTNAAAATAAATCAAGNCACTGGNGATGATTTT
GTTTTATTTGAACAAAAAGATTATGAAACTTTATCAGTNCCTTGGAAATTTCAAAAAAAA
CTTAANGAAATACAAGGNTCT----------

>AFJ140Z.Seq
----------AATCATTGGTTAATGTCAATCCACCTGAAAGCATTATACTTCCCAAAAAG
TTTATGATTAAAACACCTCTTAGTGAACCTATAGATGGTACTATTGAATTGATGTATGGT
GGTAGAAATATGTTTACTGGCAGTGTTACACAAGGTGATGCTGATCTTCCTCTAAACCTC
TTGGATGGTACATTTGAGGTTATCATTAAACCCAATAAGAGTAATTTATTACCTTTAAAG
TTTAAAATGATTATACATGACTCTGTAAGAACCACTTCAAGCCATCAAAATGTCGGTAGA
CCTAAAAAGCCTAAAGAAATGGATTTCGTTTTAGCTTGGGGGGAATCACCACTGGATTTG
GATTCTCATATGTGGTGTATTCATCCTAATGGTTCTATTAGTCATGTTTATTTCGGGGGT
AGGAGTGTAGATAAAATGTCCTTGGAAGCTGATACTCAAAATGGTTTTGGTCCCGAAACC
ATAAGTATTATACGTTTAGATGGTTGTAAATATGTTTATGCAGTTCATAATTTCTCAACT
GAAGGAGAAATAGCTCAATCAGGTGCCAAGCTTACAACTTGCCCATGAAACCTCAACATT
ATTGAAAGATGTATCCCAAACACTCGACAAACTGGTGCAAGATTTTGGGTAGTATGTACT
ATTGATGGAACATCTGGAGANATGACTTCAAAGATCATTTNAATTCCACAATTCACAAAC
AGAATTCCATTA

>AFJ140P.Seq
GATGAATATTCAAACATCATTAATAGTTTNAAAATAAATCAAGNCACTGGNGATGATTTT
GTTTTATTTGAACAAAAAGATTATGAAACTTTATCAGTNCCTTGGAAATTTCAAAAAAAA
CTTAANGAAATACAAGGNTCT----------AATCATTGGTTAATGTCAATCCACCTGAA
AGCATTATACTTCCCAAAAAGTTTATGATTAAAACACCTCTTAGTGAACCTATAGATGGT
ACTATTGAATTGATGTATGGTGGTAGAAATATGTTTACTGGCAGTGTTACACAAGGTGAT
GCTGATCTTCCTCTAAACCTCTTGGATGGTACATTTGAGGTTATCATTAAACCCAATAAG
AGTAATTTATTACCTTTAAAGTTTAAAATGATTATACATGACTCTGTAAGAACCACTTCA
AGCCATCAAAATGTCGGTAGACCTAAAAAGCCTAAAGAAATGGATTTCGTTTTAGCTTGG
GGGGAATCACCACTGGATTTGGATTCTCATATGTGGTGTATTCATCCTAATGGTTCTATT
AGTCATGTTTATTTCGGGGGTAGGAGTGTAGATAAAATGTCCTTGGAAGCTGATACTCAA
AATGGTTTTGGTCCCGAAACCATAAGTATTATACGTTTAGATGGTTGTAAATATGTTTAT
GCAGTTCATAATTTCTCAACTGAAGGAGAAATAGCTCAATCAGGTGCCAAGCTTACAACT
TGCCCATGAAACCTCAACATTATTGAAAGATGTATCCCAAACACTCGACAAACTGGTGCA
AGATTTTGGGTAGTATGTACTATTGATGGAACATCTGGAGANATGACTTCAAAGATCATT
TNAATTCCACAATTCACAAACAGAATTCCATTA