A Simple Solution for Oligonucleotide Design


Click here for a list of viruses in the database


Two search options:
1. Search by virus name and/or primer data
2. Search by PMID, VirOligoID, or taxonomy ID;

Virus name:

Oligo Sequence:

Tm:
°C± °C
Oligo length:
bp± bp



PMID:

Common Data ID:

Taxonomy ID:

GI Number:



Oligonucleotide information
Forward(324) primer
Oligo ID:MP00442
Oligo type: PCR Denegeracy: 2
Target: 59-79 Tm: 73.9 C at salt 1000.0mMLength: 21
Sequence: ATGCCC(A/T)TAGTAGGACTAGCA
(6 other experimental conditions)
Note: Used with 326 detected virus only 10.5%

Experimental condition used for the oligonucleotide

Common Data ID: MP0044 Publication date: 03/00
PMID: 10730955 GI: 14113964 Taxonomy ID:144353
Virus Name: bovine viral diarrhea virus, BVDV Product size (PCR):
bp
MgCl2: 1.5 mM dNTPs: 0.23 mM Type: RT-PCR
Temp (PCR cycle):95C 4min>(95C 1min>56C 1.5min>74C 1min)*40
Buffer: 1x PCR buffer (Promega), 0.03U/microL Taq Extender (Stratagene)
Polymerase: 0.03U/microL Taq poly (Promega)Cycler: N/A
Note: Used with 326 detected virus only 10.5%



Oligonucleotide information
Forward(PN00246) primer
Oligo ID:PN00246
Oligo type: Denegeracy: 2
Target: 109-129 Tm: 73.9 C at salt 1000.0mMLength: 21
Sequence: ATGCCC(A/T)TAGTAGGACTAGCA
(6 other experimental conditions)
Note:

Experimental condition used for the oligonucleotide

Common Data ID: SK0053 Publication date: 11/00
PMID: 11042401 GI: 3661565 Taxonomy ID:11096
Virus Name: Classical swine fever virus, CSFV Product size (PCR):
bp
MgCl2: 6.0 mM dNTPs: 0.4 mM Type: RT-Nested PCR 1
Temp (PCR cycle):42C 30min>95C 3min>(94C 1min>60C 1min>72C 1min)*20
Buffer: 1x Buffer (Promega), 0.2% Triton X-100, 0.2U/microL RNAsin, 2U/microL MMLV RTase
Polymerase: 0.05U/microL Taq poly (Promega)Cycler:
Note:



Oligonucleotide information
Forward(BVD324) primer
Oligo ID:pn00291
Oligo type: Denegeracy: 2
Target: 108-128 Tm: 73.9 C at salt 1000.0mMLength: 21
Sequence: ATGCCC(A/T)TAGTAGGACTAGCA
(6 other experimental conditions)
Note:

Experimental condition used for the oligonucleotide

Common Data ID: SK0064 Publication date: 11/00
PMID: 11085469 GI: 7960753 Taxonomy ID:11100
Virus Name: bovine viral diarrhea virus (isolate NADL), NADL; pestivirus type 1 strain CS8644, CS8644 Product size (PCR):
bp
MgCl2: N/A mM dNTPs: 0.2 mM Type: Universal RT-PCR
Temp (PCR cycle):50C 45min>94C 2min>50C 4min>72C 5min>(94C 0.5min>50C 2min>72C 5min)*35>72C 15min
Buffer: 20mM Tris-HCl (pH 8.8), 10mM KCl, 10mM (NH4)2SO4, 2.0mM MgSO4, 0.1% Triton X-100, 10ng/microL BSA, 5mM DTT
Polymerase: 0.02U/microL AmpliTaq DNA poly (Perkin-Elmer Biosystems)Cycler: 2400, 9600 or 9700 thermocycler (Perkin-Elmer Biosystems)
Note:



Oligonucleotide information
Forward(PN00285) primer
Oligo ID:PN00285
Oligo type: Denegeracy: 2
Target: 108-128 Tm: 73.9 C at salt 1000.0mMLength: 21
Sequence: ATGCCC(A/T)TAGTAGGACTAGCA
(6 other experimental conditions)
Note:

Experimental condition used for the oligonucleotide

Common Data ID: SK0065 Publication date: 08/01
PMID: 11390104 GI: 9626649 Taxonomy ID:11099
Virus Name: Pestivirus type 1 Product size (PCR): 288 bp
MgCl2: N/A mM dNTPs: 0.3 mM Type: RT-PCR
Temp (PCR cycle):60C 30min>94C 1min>(94C 15sec>63C 40sec)*40>63C 7min
Buffer: 2.5mM Mn(OAc)2
Polymerase: 0.1U/microL rTth DNA poly (Perkin-Elmer)Cycler: GeneAmp PCR system 2400 (Perkin-Elmer)
Note:



Oligonucleotide information
Forward(324) primer
Oligo ID:pb00364
Oligo type: Denegeracy: 2
Target: 108-128 Tm: 73.9 C at salt 1000.0mMLength: 21
Sequence: ATGCCC(A/T)TAGTAGGACTAGCA
(6 other experimental conditions)
Note: Specific to 5' noncoding region.

Experimental condition used for the oligonucleotide

Common Data ID: BM0050 Publication date: 04/97
PMID: 9129644 GI: 7960755 Taxonomy ID:61010
Virus Name: Border disease virus strain Moredun cp, BDV cp; Border disease virus strain Moredun ncp, BDV ncp; Hog cholera virus (strain Brescia), CSFV; bovine viral diarrhea virus (isolate NADL), BVDV NADL Product size (PCR):
bp
MgCl2: 2.5 mM dNTPs: 0.2 mM Type: RT-PCR
Temp (PCR cycle):(94C 1min>56C 1min>72C 1min)*35>72C 7min
Buffer: 10mM Tris-HCl (pH 8.3), 50mM KCl, 0.1mg/mL BSA
Polymerase: 0.02U/microL Taq poly (Perkin Elmer-Cetus)Cycler: Perkin Elmer-Cetus thermocycler
Note: Specific to 5' noncoding region.



Oligonucleotide information
Forward(primer 324) primer
Oligo ID:PL00064
Oligo type: Denegeracy: 2
Target: 108-128 Tm: 73.9 C at salt 1000.0mMLength: 21
Sequence: ATGCCC(A/T)TAGTAGGACTAGCA
(6 other experimental conditions)
Note:

Experimental condition used for the oligonucleotide

Common Data ID: MP0264 Publication date: 04/97
PMID: 9129644 GI: 7960753 Taxonomy ID:11100
Virus Name: bovine viral diarrhea virus (isolate NADL), BVDV Product size (PCR): 288 bp
MgCl2: 2.5 mM dNTPs: 0.2 mM Type: RT-PCR
Temp (PCR cycle):(94C 1min>56C 1min>72C 1min)*35>72C 7min
Buffer: 1x PCR buffer (10mM Tris-HCl, pH 9.0, 50mM KCl, 0.1mg/ml BSA)
Polymerase: 0.02U/microL Taq poly (Perkin Elmer-Cetus)Cycler: Perkin Elmer Cetus Thermocycler
Note:



Oligonucleotide information
Forward(324) primer
Oligo ID:SG005601
Oligo type: Forward Primer Denegeracy: 2
Target: 108-128 Tm: 72.5C at salt 1000.0 mMLength: 21
Sequence: ATGCCC(A/T)TAGTAGGACTAGCA
(6 other experimental conditions)
Note: Primer 324 is located in the 5' UTR.

Experimental condition used for the oligonucleotide

Common Data ID: SG0056 Publication date: 2004
PMID: 14991444 GI: 7960753 Taxonomy ID:11099
Virus Name: Bovine viral diarrhea virus 1 Product size (PCR): 5959 bp
MgCl2: mM dNTPs: mM Type: RT-PCR
Temp (PCR cycle):(94C 1min>55C 1min>72C 2min)*30>72C 7min
Buffer:
Polymerase: Taq poly (Promega)Cycler:
Note: Primer 324 is located in the 5' UTR.

Total 7 Oligos
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