>VHC781 (VHC781Q) /CSM/VH/VHC7-D/VHC781Q.Seq.d/
AAAATGTCGAAGGTAAACGTATTCCATTTGGTTTCCAAAGTAGAACATTACCACATTTCA
CCAAGGATGATTATGGTCCAGAGAGTCGTGGTTTCGTAGAGAATTCATATCTTCGTGGTT
TAACTCCTCAAGAATTCTTTTTCCATGCTATGGGTGGTAGAGAAGGTTTAATTGATACTG
CCGTAAAAACATCTGAAACCGGTTATATTCAACGTCGTCTTGTAAAAGCAATGGAGGATG
TCTCAATTAAATATGATGCCACAGTTAGAAATTCATTGGGTGATGTTATTCAATTTGCCT
ATGGTGAAGATGGTATAGATGGTTGTTTTGTTGAGAATCAATCCATTGATTCCCTTAGAA
AAGATAATACCGAATTGGAACGTATGTATCGTCATCAAGTTGATAAACCAGACTATGGTG
ATGGTTGGATGGATCCATTGGTAATTGAACATGTTAGAAACGATTCATTAACTCGTGATA
CATTGGAGAAAGAATTTGAACGTATTAAATCGGATCGXXXXXXXXXX

NVEGKRIPFGFQSRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTA
VKTSETGYIQRRLVKAMEDVSIKYDATVRNSLGDVIQFAYGEDGIDGCFVENQSIDSLRK
DNTELERMYRHQVDKPDYGDGWMDPLVIEHVRNDSLTRDTLEKEFERIKSD---

Frame A:
kmskvnvfhlvskvehyhisprmimvqrvvvs*rihifvv*llknsfsmlwvvekv*lil
p*khlkpvifnvvl*kqwrmsqlnmmpqleihwvmlfnlpmvkmv*mvvllrinpliple
kiipnwnvciviklinqtmvmvgwihw*lnmletih*lvihwrknlnvlnri---


Frame B:
kcrr*tysiwfpk*nittfhqg*lwsreswfrrefisswfnssrilfpcygw*rrfn*yc
rkni*nrlystsscksnggcln*i*chs*kfig*cysiclw*rwyrwlfc*esih*fp*k
r*yrigtyvssss**trlw*wldgsign*tc*krfins*yigeri*ty*ig---


Frame C:
NVEGKRIPFGFQSRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTA
VKTSETGYIQRRLVKAMEDVSIKYDATVRNSLGDVIQFAYGEDGIDGCFVENQSIDSLRK
DNTELERMYRHQVDKPDYGDGWMDPLVIEHVRNDSLTRDTLEKEFERIKSD---

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

VHC781 (VHC781Q) /CSM/VH/VHC7-D/VHC781Q.Seq.d/                       1025   0.0
CHP723 (CHP723Q) /CSM/CH/CHP7-A/CHP723Q.Seq.d/                        892   0.0
SHD675 (SHD675Q) /CSM/SH/SHD6-D/SHD675Q.Seq.d/                        815   0.0
CHM760 (CHM760Q) /CSM/CH/CHM7-C/CHM760Q.Seq.d/                        613   e-174
VHM557 (VHM557Q) /CSM/VH/VHM5-C/VHM557Q.Seq.d/                        111   1e-23
SHG344 (SHG344Q) /CSM/SH/SHG3-B/SHG344Q.Seq.d/                         84   2e-15
SHE878 (SHE878Q) /CSM/SH/SHE8-D/SHE878Q.Seq.d/                         84   2e-15
SHE423 (SHE423Q) /CSM/SH/SHE4-A/SHE423Q.Seq.d/                         84   2e-15
SHA179 (SHA179Q) /CSM/SH/SHA1-D/SHA179Q.Seq.d/                         84   2e-15
CHJ412 (CHJ412Q) /CSM/CH/CHJ4-A/CHJ412Q.Seq.d/                         84   2e-15

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

S52651|S52651.1 RNA polymerase II largest subunit [Dictyostelium discoideum, mRNA Partial, 2874 nt].   726   0.0    1
AF058710|AF058710.1 Dictyostelium discoideum RNA polymerase II largest subunit (RPB1) gene, partial cds.   289   4e-74  1
DQ294611|DQ294611.1 Neocallimastix sp. GE13 RNA polymerase II largest subunit (RPB1) gene, partial cds.   200   1e-57  3
EF014394|EF014394.1 Neocallimastix frontalis RNA polymerase II largest subunit (RPB1) gene, partial cds.   200   3e-57  3
X52494|X52494.1 Arabidopsis thaliana RPB1 gene for the largest subunit of RNA polymerase II.   141   5e-43  3
X52954|X52954.1 Arabidopsis thaliana rpII gene for RNA polymerase large subunit (EC 2.7.7.6).   141   6e-43  3
AV530018|AV530018.1 Arabidopsis thaliana cDNA clone:APZL56b03R, 5' end.   141   6e-43  2
U10336|U10336.1 Helobdella stagnalis RNA polymerase II largest subunit mRNA, partial cds.   119   6e-42  3
AF519537|AF519537.1 Welwitschia mirabilis RNA polymerase II largest subunit (RPB1) mRNA, partial cds.   155   8e-41  3
AL031986|AL031986.1 Arabidopsis thaliana DNA chromosome 4, BAC clone F4B14 (ESSA  project).   141   2e-40  4

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

DQ223185_1(DQ223185|pid:none) Glaucocystis nostochinearum strain...   248   7e-65
AF519541_1(AF519541|pid:none) Amborella trichopoda RNA polymeras...   244   9e-64
EU543188_1(EU543188|pid:none) Nicotiana tabacum RNA polymerase I...   243   2e-63
DQ020644_1(DQ020644|pid:none) Lycopersicon esculentum RNA polyme...   243   2e-63
X52494_1(X52494|pid:none) Arabidopsis thaliana RPB1 gene for the...   243   2e-63
X52954_1(X52954|pid:none) Arabidopsis thaliana rpII gene for RNA...   243   2e-63
JDMU1(T04690;S12071;S27346;S11960)DNA-directed RNA polymerase (E...   243   2e-63
U90210_1(U90210|pid:none) Spirogyra sp. RNA polymerase II larges...   241   6e-63
AY490550_1(AY490550|pid:none) Thuja occidentalis RNA polymerase ...   241   1e-62
AY490551_1(AY490551|pid:none) Taxus canadensis RNA polymerase II...   241   1e-62

 psg: 0.71  gvh: 0.34  alm: 0.51  top: 0.53  tms: 0.00  mit: 0.28  mip: 0.04
 nuc: 0.00  erl: 0.00  erm: 0.20  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 

	 48.0 %: nuclear
	 28.0 %: cytoplasmic
	 12.0 %: mitochondrial
	  8.0 %: cytoskeletal
	  4.0 %: extracellular, including cell wall

>> prediction for VHC781 is nuc

>VHC781F.Seq
AAAATGTCGAAGGTAAACGTATTCCATTTGGTTTCCAAAGTAGAACATTACCACATTTCA
CCAAGGATGATTATGGTCCAGAGAGTCGTGGTTTCGTAGAGAATTCATATCTTCGTGGTT
TAACTCCTCAAGAATTCTTTTTCCATGCTATGGGTGGTAGAGAAGGTTTAATTGATACTG
CCGTAAAAACATCTGAAACCGGTTATATTCAACGTCGTCTTGTAAAAGCAATGGAGGATG
TCTCAATTAAATATGATGCCACAGTTAGAAATTCATTGGGTGATGTTATTCAATTTGCCT
ATGGTGAAGATGGTATAGATGGTTGTTTTGTTGAGAATCAATCCATTGATTCCCTTAGAA
AAGATAATACCGAATTGGAACGTATGTATCGTCATCAAGTTGATAAACCAGACTATGGTG
ATGGTTGGATGGATCCATTGGTAATTGAACATGTTAGAAACGATTCATTAACTCGTGATA
CATTGGAGAAAGAATTTGAACGTATTAAATCGGATCGNNNNNNNNNN