>VSJ228 (VSJ228Q) /CSM/VS/VSJ2-B/VSJ228Q.Seq.d/
CAACAATGGAAGGAGAACAATTACAAACTGCACCATACAACCCAAGATTCCCACAACAAA
ACCAAACTAAACATTGTTGGGCTAACTACGTTGATTACTATGGTTGTGTCAAACATTACA
ATGGTGACAACTCAAAATGTCAAACTTTTTTCAACTCAATGAACTCATTATGTCCAGCTG
CCTGGATTTCAGAATGGGATGAACAAAAAGCCGCTGATCTCTTCCCATCAGACAGAGTTT
AAATATATAATATAAATAATTAATAGTAGTATCAATAATTTATTCAAAAAAAAAGAAAAA
AAAAAXXXXXXXXXXCCATNATTTATTCNAAAAAAAAGAAAAAAAAAAAAGAACATAATG
ATATAAATAAAAAAAATAGAAAATTTTAAAAAAAATAAAATAACCCCCACTTGCTGTTCA
CTTT

qqwkennyklhhttqdshnktklnivglttlitmvvsnitmvttqnvklfstq*thyvql
pgfqngmnkkplisshqtefkyii*IINSSINNLFKKKEKK---

---XIYSKKKKKKKEHNDINKKNRKF*kk*nnphllft

Frame A:
qqwkennyklhhttqdshnktklnivglttlitmvvsnitmvttqnvklfstq*thyvql
pgfqngmnkkplisshqtefkyii*IINSSINNLFKKKEKK---

---pxfixkkrkkkknimi*ikkienfkknkitptccsl

Frame B:
nngrrtitnctiqpkipttkpn*tllg*lr*llwlcqtlqw*qlkmsnffqlnelimssc
ldfrmg*tksr*slpirqslni*yk*livvsiiyskkkkkk---

---hxlfxkkekkkrt**yk*kk*kilkkik*pplavhf

Frame C:
tmegeqlqtapynprfpqqnqtkhcwanyvdyygcvkhyngdnskcqtffnsmnslcpaa
wisewdeqkaadlfpsdrv*iyninn***yq*fiqkkrkkk---

---XIYSKKKKKKKEHNDINKKNRKF*kk*nnphllft

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

VSJ228 (VSJ228Q) /CSM/VS/VSJ2-B/VSJ228Q.Seq.d/                        565   e-160
VSI263 (VSI263Q) /CSM/VS/VSI2-C/VSI263Q.Seq.d/                        565   e-160
VSH265 (VSH265Q) /CSM/VS/VSH2-C/VSH265Q.Seq.d/                        565   e-160
VSF762 (VSF762Q) /CSM/VS/VSF7-C/VSF762Q.Seq.d/                        565   e-160
VSD559 (VSD559Q) /CSM/VS/VSD5-C/VSD559Q.Seq.d/                        565   e-160
VSA196 (VSA196Q) /CSM/VS/VSA1-D/VSA196Q.Seq.d/                        565   e-160
VHK558 (VHK558Q) /CSM/VH/VHK5-C/VHK558Q.Seq.d/                        565   e-160
SSE738 (SSE738Q) /CSM/SS/SSE7-B/SSE738Q.Seq.d/                        565   e-160
SSF773 (SSF773Q) /CSM/SS/SSF7-D/SSF773Q.Seq.d/                        561   e-159
VSH131 (VSH131Q) /CSM/VS/VSH1-B/VSH131Q.Seq.d/                        551   e-156

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

AC122291|AC122291.4 Mus musculus chromosome 15 clone RP23-255N20, complete sequence.    42  0.013  2
AX537130|AX537130.1 Sequence 731 from Patent WO02064766.          44  0.021  2
AL404156|AL404156.1 T7 end of clone AT0AA013E12 of library AT0AA from strain CBS 4311 of Saccharomyces servazzii.    40  0.066  2
AC118594|AC118594.3 Mus musculus clone RP24-479J20, WORKING DRAFT SEQUENCE, 7 unordered pieces.    54  0.13  3
AC117576|AC117576.3 Mus musculus clone RP23-34E15, WORKING DRAFT SEQUENCE, 14 unordered pieces.    50  0.16  4
AX537066|AX537066.1 Sequence 667 from Patent WO02064766.          44  0.26  3
AE003549|AE003549.4 Drosophila melanogaster chromosome 3L, section 36 of 83 of the complete sequence.    46  0.34  1
AL133247|AL133247.1 BAC sequence from the SPG4 candidate region at 2p21-2p22 BAC 11B22  of library CITB_978_SKB from chromosome 2 of Homo sapiens (Human).    46  0.34  1
AJ303666|AJ303666.1 Plasmodium chabaudi genome survey sequence, clone PC10c1.p1t.    46  0.34  1
AC093550|AC093550.3 Drosophila melanogaster 3L BAC RP98-24K7 (Roswell Park Cancer Institute Drosophila BAC Library) complete sequence.    46  0.34  1

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q01519) RecName: Full=Cytochrome c oxidase polypeptide VIb;    ...    89   6e-17
AM920427_744(AM920427|pid:none) Penicillium chrysogenum Wisconsi...    87   1e-16
AM269997_1(AM269997|pid:none) Aspergillus niger contig An02c0020...    87   2e-16
CR382131_683(CR382131|pid:none) Yarrowia lipolytica strain CLIB1...    86   4e-16
CR382126_746(CR382126|pid:none) Kluyveromyces lactis strain NRRL...    86   4e-16
CP000497_298(CP000497|pid:none) Pichia stipitis CBS 6054 chromos...    84   2e-15
AE017346_138(AE017346|pid:none) Cryptococcus neoformans var. neo...    84   2e-15
(P14854) RecName: Full=Cytochrome c oxidase subunit VIb isoform ...    82   5e-15
(Q5RCT0) RecName: Full=Cytochrome c oxidase subunit VIb isoform ...    82   5e-15
(P00429) RecName: Full=Cytochrome c oxidase subunit VIb isoform ...    80   2e-14

 psg: 0.33  gvh: -0.04  alm: 0.74  top: 0.53  tms: 0.00  mit: 0.25  mip: 0.00
 nuc: 0.93  erl: 0.00  erm: 0.40  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 

	 80.0 %: nuclear
	 16.0 %: cytoplasmic
	  4.0 %: mitochondrial

>> prediction for VSJ228 is nuc

>VSJ228F.Seq
CAACAATGGAAGGAGAACAATTACAAACTGCACCATACAACCCAAGATTCCCACAACAAA
ACCAAACTAAACATTGTTGGGCTAACTACGTTGATTACTATGGTTGTGTCAAACATTACA
ATGGTGACAACTCAAAATGTCAAACTTTTTTCAACTCAATGAACTCATTATGTCCAGCTG
CCTGGATTTCAGAATGGGATGAACAAAAAGCCGCTGATCTCTTCCCATCAGACAGAGTTT
AAATATATAATATAAATAATTAATAGTAGTATCAATAATTTATTCAAAAAAAAAGAAAAA
AAAAA----------

>VSJ228Z.Seq
----------CCATNATTTATTCNAAAAAAAAGAAAAAAAAAAAAGAACATAATGATATA
AATAAAAAAAATAGAAAATTTTAAAAAAAATAAAATAACCCCCACTTGCTGTTCACTTT

>VSJ228P.Seq
CAACAATGGAAGGAGAACAATTACAAACTGCACCATACAACCCAAGATTCCCACAACAAA
ACCAAACTAAACATTGTTGGGCTAACTACGTTGATTACTATGGTTGTGTCAAACATTACA
ATGGTGACAACTCAAAATGTCAAACTTTTTTCAACTCAATGAACTCATTATGTCCAGCTG
CCTGGATTTCAGAATGGGATGAACAAAAAGCCGCTGATCTCTTCCCATCAGACAGAGTTT
AAATATATAATATAAATAATTAATAGTAGTATCAATAATTTATTCAAAAAAAAAGAAAAA
AAAAA----------CCATNATTTATTCNAAAAAAAAGAAAAAAAAAAAAGAACATAATG
ATATAAATAAAAAAAATAGAAAATTTTAAAAAAAATAAAATAACCCCCACTTGCTGTTCA
CTTT