A Simple Solution for Oligonucleotide Design

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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:

CommonData ID: JX0086Publication date: 01/01
PMID: 11136755GI: 9790357 Taxonomy ID: 10243
Virus Name: Cowpox virus; Ectromelia virus; Taterapox virus; Vaccinia virus (strain Lister); Buffalopox virus; Rabbitpox virus (strain Utrecht); Variola major virus; variola minor virus; Monkeypox virus; Camelpox virusProduct size (PCR):
bp
MgCl2: N/A mMdNTPs: mMType: Universal PCR
Temp (PCR cycle):(94C 1min>55C 1min>72C 1min)*25>72C 5min
Buffer: N/A
Polymerase: N/ACycler: model 9600 thermalcycler (Perkin-Elmer Cetus)
Note: Universal PCR. This primer set amplifies the following viruses:
Cowpox virus [Taxonomy:10243]
Ectromelia virus [Taxonomy:12643]
Taterapox virus [Taxonomy:28871]
Vaccinia virus (strain Lister) [Taxonomy:10252]
Buffalopox virus [Taxonomy:32605]
Rabbitpox virus (strain Utrecht) [Taxonomy:45417]
Variola major virus [Taxonomy:12870]
variola minor virus [Taxonomy:53258]
Monkeypox virus [Taxonomy:10244]
Camelpox virus [Taxonomy:28873]

Article does not mention RT conditions.

PCR mix contains 50ng template DNA and 0.5microg each primers VL2N and VL33.
Article does not mention other PCR reagents.
Forward(VL2N) primer
Oligo type: Degeneracy: 1
Target: 5001-5016Tm: 50 CLength:
Sequence: ACATGCATGCCAGGAC
(0 other experimental conditions)
Note: Primer anneals as forward primer at positions 5001-5016 and as a reverse primer at positions 186737-186722.
Reverse(VL33) primer
Oligo type: Degeneracy: 1
Target: 6209-6191Tm: 62.9 C at salt 1000.0mMLength:
Sequence: ACCATTACAAACATTATCC
(0 other experimental conditions)
Note: There was a mismatch at position 6198.
Primer anneals as reverse primer at positions 6209-6191 and as a forward primer at positions 185529-185547.
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