>VSA387 (VSA387Q) /CSM/VS/VSA3-D/VSA387Q.Seq.d/
XXXXXXXXXXACACCTCAAGGAACTCAGAACTGAGCTCTCAAGTTTAAGAGTTGCCCAAG
TTAAATCACCAAACCCAAGCAAATTAGCCAAAATCGGTACCGTCCGTAAAGCTATTGCCC
GTGTTTTAACTGTTTTCAACCAAACTCAAAAGAACCATCTCCGTGCTGTCTATTCTAAAA
AATCATCAAGCAAGATCCCAACTGATCTCCGTTACAAAAAGACTAGAGCCATCAGAAGAC
GTCTCACCAACAAACAATNTAAAGTTGTCACCTTAAGAGTTTCCAAAACTGCCACCAACT
TCCCACAAAGAGTTTTCGCTGTTAAAGCCTAAATTTGCATTTAGATGATTTTAAAAAATA
AAATATATTAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAA

---HLKELRTELSSLRVAQVKSPNPSKLAKIGTVRKAIARVLTVFNQTQKNHLRAVYSKK
SSSKIPTDLRYKKTRAIRRRLTNKQXKVVTLRVSKTATNFPQRVFAVKA*ici*milknk
iy*kkekkkkkkkkkkkkkkk

Frame A:
---HLKELRTELSSLRVAQVKSPNPSKLAKIGTVRKAIARVLTVFNQTQKNHLRAVYSKK
SSSKIPTDLRYKKTRAIRRRLTNKQXKVVTLRVSKTATNFPQRVFAVKA*ici*milknk
iy*kkekkkkkkkkkkkkkkk


Frame B:
---tsrnselssqv*elpklnhqtqan*pksvpsvkllpvf*lfstklkrtisvlsilkn
hqarsqlisvtkrlepsedvsptnnxklsp*efpklpptshkefsllkpkfafr*f*kik
yikkkkkkkkkkkkkkkkkkk


Frame C:
---pqgtqn*alkfkscps*itkpkqisqnryrp*sycpcfncfqpnskepspcclf*ki
ikqdpn*splqkd*shqktshqqtx*schlksfqnchqlptksfrc*slnlhlddfkk*n
ilkkrkkkkkkkkkkkkkkk

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

VSJ543 (VSJ543Q) /CSM/VS/VSJ5-B/VSJ543Q.Seq.d/                        672   0.0
VSJ336 (VSJ336Q) /CSM/VS/VSJ3-B/VSJ336Q.Seq.d/                        672   0.0
VSI788 (VSI788Q) /CSM/VS/VSI7-D/VSI788Q.Seq.d/                        672   0.0
VSI395 (VSI395Q) /CSM/VS/VSI3-D/VSI395Q.Seq.d/                        672   0.0
VSH858 (VSH858Q) /CSM/VS/VSH8-C/VSH858Q.Seq.d/                        672   0.0
VSG886 (VSG886Q) /CSM/VS/VSG8-D/VSG886Q.Seq.d/                        672   0.0
VSG811 (VSG811Q) /CSM/VS/VSG8-A/VSG811Q.Seq.d/                        672   0.0
VSG139 (VSG139Q) /CSM/VS/VSG1-B/VSG139Q.Seq.d/                        672   0.0
VSE856 (VSE856Q) /CSM/VS/VSE8-C/VSE856Q.Seq.d/                        672   0.0
VSD708 (VSD708Q) /CSM/VS/VSD7-A/VSD708Q.Seq.d/                        672   0.0

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

AL132954|AL132954.1 Arabidopsis thaliana DNA chromosome 3, BAC clone T26I12.    46  0.34  2
AC119946|AC119946.3 Mus musculus clone RP24-406B22, WORKING DRAFT SEQUENCE, 6 unordered pieces.    46  0.35  1
Z47610|Z47610.1 A. thaliana transcribed sequence; clone TAI212; 5' end; Similar to mRNA for ribosomal protein L35 ; Oriza sativa.    46  0.35  1
CB264903|CB264903.1 24-E015021-035-004-O05-T7R MPIZ-ADIS-035 Arabidopsis thaliana cDNA clone MPIZp2000O054Q 5-PRIME, mRNA sequence.    46  0.35  1
AI996565|AI996565.1 701667462 A. thaliana, Columbia Col-0, root-1 Arabidopsis thaliana cDNA clone 701667462, mRNA sequence.    46  0.35  1
AL084068|AL084068.1 Arabidopsis thaliana genome survey sequence T7 end of BAC F8C2 of  IGF library from strain Columbia of Arabidopsis thaliana.    46  0.35  1
BE038964|BE038964.1 AB07H02 AB Arabidopsis thaliana cDNA 5' similar to ribosomal protein l35, mRNA sequence.    46  0.35  1
BT006384|BT006384.1 Arabidopsis thaliana At3g55170 gene, complete cds.    46  0.35  1
AU226410|AU226410.1 Arabidopsis thaliana cDNA clone:RAFL14-31-M09, 3'-end.    46  0.35  1
AC140378|AC140378.1 Mus musculus chromosome UNK clone RP24-84M18, WORKING DRAFT SEQUENCE, 11 unordered pieces.    36  1.6  4

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AE017341_741(AE017341|pid:none) Cryptococcus neoformans var. neo...   108   8e-23
EU958029_1(EU958029|pid:none) Zea mays clone 1664319 60S ribosom...   100   1e-20
EU959220_1(EU959220|pid:none) Zea mays clone 212376 60S ribosoma...   100   3e-20
AK059262_1(AK059262|pid:none) Oryza sativa Japonica Group cDNA c...    99   5e-20
AF548325_1(AF548325|pid:none) Branchiostoma belcheri ribosomal p...    98   1e-19
(Q9M3D2) RecName: Full=60S ribosomal protein L35-3;  &AK227739_1...    97   1e-19
(Q9SF53) RecName: Full=60S ribosomal protein L35-1;  &AC016661_7...    96   5e-19
(P17078) RecName: Full=60S ribosomal protein L35;  &(Q6ZWV7) Rec...    96   5e-19
EF634780_1(EF634780|pid:none) Pristionchus lheritieri large subu...    95   7e-19
(Q9LZ41) RecName: Full=60S ribosomal protein L35-4;  &AK226248_1...    95   7e-19

 psg: 0.70  gvh: 0.45  alm: 0.46  top: 0.53  tms: 0.00  mit: 0.23  mip: 0.00
 nuc: 0.19  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 

	 56.0 %: nuclear
	 40.0 %: cytoplasmic
	  4.0 %: mitochondrial

>> prediction for VSA387 is nuc

>VSA387Z.Seq
----------ACACCTCAAGGAACTCAGAACTGAGCTCTCAAGTTTAAGAGTTGCCCAAG
TTAAATCACCAAACCCAAGCAAATTAGCCAAAATCGGTACCGTCCGTAAAGCTATTGCCC
GTGTTTTAACTGTTTTCAACCAAACTCAAAAGAACCATCTCCGTGCTGTCTATTCTAAAA
AATCATCAAGCAAGATCCCAACTGATCTCCGTTACAAAAAGACTAGAGCCATCAGAAGAC
GTCTCACCAACAAACAATNTAAAGTTGTCACCTTAAGAGTTTCCAAAACTGCCACCAACT
TCCCACAAAGAGTTTTCGCTGTTAAAGCCTAAATTTGCATTTAGATGATTTTAAAAAATA
AAATATATTAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAA