Research Article

Family-Specific Degenerate Primer Design: A Tool to Design Consensus Degenerated Oligonucleotides

Table 1

List of sequences used in the test of FAS-DPD. Accession numbers and brief description are presented.

Acc. number Sequence description Acc. number Sequence description

Arenaviral sequences

AY129248.1 Machupo v. st. Carvallo U41071.1 Sabia v.
AF485260.1 Machupo v. st. Carvallo EU260463.1 Chapare v. st. 810419
AY924206.1 Machupo v. st. MARU-216606 AY081210.1 Allpahuayo v. CLHP-2098
AY924202.1 Machupo v. st. Chicava AY012686.1 Allpahuayo v. from Peru
AY624355.1 Machupo v. st. Chicava AY012687.1 Allpahuayo v. st. CLHP-2472
AY924205.1 Machupo v. st. 9301012 AF485262.1 Pirital v. st. VAV-488
AY619645.1 Machupo v. st. Mallele AF277659.1 Pirital v.
AY924203.1 Machupo v. st. 9430084 M16735.1 Pichinde v.
AY924208.1 Machupo v. st. MARU 249121 AF485261.1 Parana v. st. 12056
AY924204.1 Machupo v. st. 200002427 AF512829.1 Parana v. st. 10256
AY924207.1 Machupo v. st. MARU 222688 AF512831.1 Flexal v. st. BeAn 293022
AY571959.1 Machupo v. st. 9530537 AF485257.1 Flexal v. st. Pinheiro
AY746353.1 Junin v. st. Candid-1 AF512831.1 Flexal v. st. BeAn 293022
AY358023.2 Junin v. st. XJ13 AF512830.1 Latino v. st. MARU 10924
AY619641.1 Junin v. st. Rumero AF485259.1 Latino v. st. Maru 10924
D10072.2 Junin v. st. MC2 U34248.1 Oliveros v.
M20304.1 Tacaribe v. AY847350.1 LCM v. st. Armstrong 53b
AF485256.1 Amapari v. st. BeAn 70563 M20869.1 LCM v. st. Armstrong 53b
AF512834.1 Amapari v. st. BeAn 70563 EU136038.1 Dandenong v. is. 0710-2678
AF512832.1 Cupixi v. st. BeAn 119303 DQ328874.1 Mopeia v. st. Mozambique
AY129247.1 Guanarito v. st. INH-95551 DQ328877.1 Ippy v. st. Dak-An-B-188-d
AF485258.1 Guanarito v. st. INH-95551 X52400.1 Nigeria Lassa v.
AY497548.1 Guanarito v. st. CVH-960101 AY628206.1 Lassa v. st. Weller
AY924392.1 Bear Canyon v. st. AV 98470029 AY628201.1 Lassa v. st. Macenta
AY924391.1 Bear Canyon v. st. AV A0070039 AY628205.1 Lassa v. st. Z148
AF512833.1 Bear canyon v. st. A0060209 J04324.1 Lassa v. st. Josiah
DQ865244.1 Catarina v. st. AV A0400135 AY772168.1 Mopeia Lassa reassortant 29
DQ865245.1 Catarina v. st. AV A0400212 AY628203.1 Lassa v. st. Josiah
EU123328.1 Skinner Tank v. st. AV D1000090 AF181853.1 Lassa v. st. LP
EU123331.1 North American arenav. st. AV 96010024 AY628207.1 Lassa v. st. Pinneo
EU123330.1 North American arenav. st. AV 96010151 AY628208.1 Lassa v. st. Acar-3080
AF228063.1 Whitewater Arroyo v. st. 9310135, AF181854.1 Lassa v. st. 803213
AF485264.1 Whitewater Arroyo v. st. 9310141 AY342390.1 Mobala v. st. ACAR-3080-MRC5-P2
EU123329.1 North American arenav. st. AV D1240007 M33879.1 Mopeia v. st. AN-21366
AF485263.1 Tamiami v. st. CDC W-10777 AY772170.1 Mopeia v. st. AN-20410
AF512828.1 Tamiami v. st. W 10777

Baculoviral sequences

AP006270.1 Adoxophyes honmai nucleopolyhedrovirus DNA X77048.1 Cryptophlebia leucotreta granulosis
AF547984.1 Adoxophyes orana granulovirus X79569.1 Cryptophlebia leucotreta granulosis
NC_005839.2 Agrotis segetum granulovirus NC_002816.1 Cydia pomonella granulovirus
L22858.1 Autographa californica nucleopolyhedrovirus clone C6 NC_003083.1 Epiphyas postvittana NPV
L33180.1 Bombyx mori nuclear polyhedrosis virus isolate T3 NC_002654.2 Helicoverpa armigera
NC_005137.2 Choristoneura fumiferana DEF MNPV AF081810.1 Lymantria dispar
NC_004778.3 Choristoneura fumiferana MNPV NC_003529.1 Mamestra configurata NPV-A
AY864330.1 Chrysodeixis chalcites NPV U75930.2 Orgyia pseudotsugata MNPV
AY456389.1 Chrysodeixis chalcites NPV AF499596.1 Phthorimaea operculella granulovirus
AY456390.1 Chrysodeixis chalcites NPV NC_002593.1 Plutella xylostella granulovirus
AY545786.1 Chrysodeixis chalcites NPV NC_004323.1 Rachiplusia ou MNPV
AY545787.1 Chrysodeixis chalcites NPV NC_002169.1 Spodoptera exigua MNPV
AY229987.1 Cryptophlebia leucotreta granulovirus NC_003102.1 Spodoptera litura NPV
AY096241.1 Cryptophlebia leucotreta granulovirus NC_007383.1 Trichoplusia ni SNPV
AY096242.1 Cryptophlebia leucotreta granulovirus

Pseudomonas sp. sequences

NC_007492.2 Pseudomonas fluorescens Pf0-1 NC_004578.1 Pseudomonas syringae
NC_005773.3 Pseudomonas syringae NC_002947.3 Pseudomonas putida
NC_004129.6 Pseudomonas fluorescens NC_002516.2 Pseudomonas aeruginosa
NC_007005.1 Pseudomonas syringae

Lactobacillus sp. sequences

NC_005362.1 Lactobacillus johnsonii NC_002662.1 Lactococcus lactis subsp.
NC_007576.1 Lactobacillus sakei subsp. NC_004567.1 Lactobacillus plantarum