>SSJ346 (SSJ346Q) /CSM/SS/SSJ3-B/SSJ346Q.Seq.d/
GGAATTGGCCTTATGCCAATTTTCTTTAGGCCCCCTTACTGGTAGGCCTTCCCCTCGAGG
TTGAAGTTCTGATTAACTTTGAAAATGTTAAGCCCAAATCCCAGATAAAGAGGTATCCCC
CCCGGTTCACCAAGATTAATCTTGCCGGTAAACCATTTGGAAGCCGGTCGTACTCTTTCC
GATTCCATTTCCCAAAAGGATCAACTCTCCCCCTTAGTCTTAGATTAAGAGTTGTTGGTG
TTAAAAGGAGGAGGAGGAGGCCCTAGGTTCCCCCAAGGGTTCCCAGGGGAAATTTGGGAA
AGTTTAATTTCCCCGCCCTCAAATCCTACAAATTCGACGAAACCGGTAAAATCAAACGTT
TCTTAAGAGAATTTCCAGCTGAAACCTGTGGTGCTGGTGTCTTCATGGCTCAACATGCTA
ATCGTCAATACTGTGGTAAATGTCACTCAACTTTAGTTAAAAAATCCAAATAAACAATTT
TCTTGAAAATATCATAATGCTTATCTAGTATGTGTTTTTCATGATTAGAGGACGTACTAT
GCCATACCCAATTAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

nwpyanfl*APLLVGLPLEVEVLINFENVKPKSQIKRYPPRFTKINLAGKPFGSRSYSFR
FHFPKGSTLPLSLRLRVVGVKRRRRRP*vpprvprgnlgkfnfpalksykfdetgkikrf
lrefpaetcgagvfmaqhanrqycgkchstlvkksk*tiflkis*clssmcfs*ledvlc
htqlkqkkkkkkkkkkkkk

Frame A:
giglmpiffrppyw*afpsrlkf*ltlkmlspnpr*rgippgsprlilpvnhleagrtls
dsisqkdqlsplvld*ellvlkgggggprfpqgfpgeiweslisppsnptnstkpvksnv
s*enfqlkpvvlvsswlnmlivntvvnvtql*lknpnkqfs*kyhnaylvcvfhd*rtyy
aipn*nkkkkkkkkkkkkkk


Frame B:
elalcqfslgpltgrpsprg*ssd*l*kc*aqipdkevsppvhqd*scr*tiwkpvvlfp
ipfpkrinspp*s*ikscwc*keeeealgspkgsqgkfgkv*fprpqilqirrnr*nqtf
lkriss*nlwcwclhgstc*ssilw*mslnfs*kiqinnfleniimli*yvffmirgrtm
pypiktkkkkkkkkkkkkk


Frame C:
nwpyanfl*APLLVGLPLEVEVLINFENVKPKSQIKRYPPRFTKINLAGKPFGSRSYSFR
FHFPKGSTLPLSLRLRVVGVKRRRRRP*vpprvprgnlgkfnfpalksykfdetgkikrf
lrefpaetcgagvfmaqhanrqycgkchstlvkksk*tiflkis*clssmcfs*ledvlc
htqlkqkkkkkkkkkkkkk

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

SSJ346 (SSJ346Q) /CSM/SS/SSJ3-B/SSJ346Q.Seq.d/                       1065   0.0
VSG649 (VSG649Q) /CSM/VS/VSG6-C/VSG649Q.Seq.d/                        484   e-136
VHJ458 (VHJ458Q) /CSM/VH/VHJ4-C/VHJ458Q.Seq.d/                        484   e-136
VHD646 (VHD646Q) /CSM/VH/VHD6-B/VHD646Q.Seq.d/                        484   e-136
VHB117 (VHB117Q) /CSM/VH/VHB1-A/VHB117Q.Seq.d/                        484   e-136
VFK618 (VFK618Q) /CSM/VF/VFK6-A/VFK618Q.Seq.d/                        484   e-136
SSI244 (SSI244Q) /CSM/SS/SSI2-B/SSI244Q.Seq.d/                        484   e-136
FC-AT06 (FC-AT06Q) /CSM/FC/FC-AT/FC-AT06Q.Seq.d/                      484   e-136
FC-AJ24 (FC-AJ24Q) /CSM/FC/FC-AJ/FC-AJ24Q.Seq.d/                      484   e-136
VSH239 (VSH239Q) /CSM/VS/VSH2-B/VSH239Q.Seq.d/                        482   e-135

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

M23750|M23750.1 D.discoideum ubiquitin mRNA, complete cds, clone DCUBV20.   448   e-132  5
AC115584|AC115584.2 Dictyostelium discoideum chromosome 2 map complement(3622543-3568102) strain AX4, complete sequence.   448   e-124  5
AX364512|AX364512.1 Sequence 519 from Patent WO0208410.            42   0.002  2
AC126037|AC126037.2 Mus musculus chromosome UNK clone RP24-223I19, WORKING DRAFT SEQUENCE, 2 unordered pieces.    36   0.076  4
AL669969|AL669969.14 Mouse DNA sequence from clone RP23-254J18 on chromosome 11.    36   0.097  4
BQ476381|BQ476381.1 curculio4b06.b Curculio glandium cDNA Curculio glandium cDNA clone curculio4b06 5', mRNA sequence.    38   0.17   2
AC107706|AC107706.4 Mus musculus clone RP24-218L20, WORKING DRAFT SEQUENCE, 8 ordered pieces.    36   0.19   6
BQ476658|BQ476658.1 curculio4b06.g Curculio glandium cDNA Curculio glandium cDNA clone curculio4b06 3', mRNA sequence.    38   0.21   2
AF462552|AF462552.1 Hemibagrus nemurus clone PCTE4 microsatellite sequence.    36   0.28   2
AC132931|AC132931.3 Mus musculus clone RP24-77C19, WORKING DRAFT SEQUENCE, 6 unordered pieces.    32   0.30   7

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

M23750_1(M23750|pid:none) D.discoideum ubiquitin mRNA, complete ...   114   2e-24
AC115584_9(AC115584|pid:none) Dictyostelium discoideum chromosom...   114   2e-24
(P14797) RecName: Full=40S ribosomal protein S27a;                    102   6e-21
AY752793_1(AY752793|pid:none) Culicoides sonorensis clone CsARU ...    80   4e-14
EZ000373_1(EZ000373|pid:none) TSA: Culex tarsalis Ctar-169 ribos...    73   2e-13
AY552058_1(AY552058|pid:none) Aedes aegypti ribosomal protein S2...    77   3e-13
EU139195_1(EU139195|pid:none) Flustra foliacea ubiquinated putat...    77   4e-13
EU558350_1(EU558350|pid:none) Phoronis muelleri putative ubiquit...    75   1e-12
DQ517325_1(DQ517325|pid:none) Pectinaria gouldii ubiquitin/ribos...    74   2e-12
EU558303_1(EU558303|pid:none) Novocrania anomala putative ubiqui...    74   2e-12

 psg: 0.75  gvh: 0.39  alm: 0.36  top: 0.53  tms: 0.00  mit: 0.11  mip: 0.07
 nuc: 0.28  erl: 0.00  erm: 0.00  pox: 0.00  px2: 0.00  vac: 0.00  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 

	 60.0 %: nuclear
	 20.0 %: cytoplasmic
	 12.0 %: cytoskeletal
	  4.0 %: Golgi
	  4.0 %: vesicles of secretory system

>> prediction for SSJ346 is nuc

>SSJ346E.Seq
GGAATTGGCCTTATGCCAATTTTCTTTAGGCCCCCTTACTGGTAGGCCTTCCCCTCGAGG
TTGAAGTTCTGATTAACTTTGAAAATGTTAAGCCCAAATCCCAGATAAAGAGGTATCCCC
CCCGGTTCACCAAGATTAATCTTGCCGGTAAACCATTTGGAAGCCGGTCGTACTCTTTCC
GATTCCATTTCCCAAAAGGATCAACTCTCCCCCTTAGTCTTAGATTAAGAGTTGTTGGTG
TTAAAAGGAGGAGGAGGAGGCCCTAGGTTCCCCCAAGGGTTCCCAGGGGAAATTTGGGAA
AGTTTAATTTCCCCGCCCTCAAATCCTACAAATTCGACGAAACCGGTAAAATCAAACGTT
TCTTAAGAGAATTTCCAGCTGAAACCTGTGGTGCTGGTGTCTTCATGGCTCAACATGCTA
ATCGTCAATACTGTGGTAAATGTCACTCAACTTTAGTTAAAAAATCCAAATAAACAATTT
TCTTGAAAATATCATAATGCTTATCTAGTATGTGTTTTTCATGATTAGAGGACGTACTAT
GCCATACCCAATTAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA