Enabled by data from
assayM COVID-19: track sensitivity of RT-PCR primers on COVID-19 Variants
#last Updated:
Sunday, 15 September 2024 05:10:01 GMT+3 (Arabian Standard Time)
, based on 3892 variants (from 8.94 million sequences) and 34 primer sets.
Menu
Home
WHO Primers
New Primers
Simple Primers
LAMP Primers
Browse
NCBI
GISAID
Search
NCBI
GISAID
Genome Scan
Mutants
Substitution
Deletion
Tutorial
Contact
Browse
Prediction results retrieved after performance evaluation of WHO approved 34 primers to estimate their binding affinities for 3892 SARS-CoV-2 variants.
Lineage
(WHO label)
Target Gene
Primer Name
Primer Sequence
Primer Length
Primer GC Content (%)
Start Position
End Position
Primer Direction
ΔG (cal)
Primer first used
EG.5.1.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
EG.5.1.6
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
EG.5.1.6
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
GK.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
GK.1.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
FL.1.5.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
FL.1.5.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JF.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JF.1.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
GK.1.8
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
GK.1.8
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JD.1.1.8
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JD.1.1.8
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
HK.3
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
HK.3
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
EG.5.1.14
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
EG.5.1.14
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JN.1.7.9
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.7.9
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
KW.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KW.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
MF.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
MF.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
LF.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LF.2
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
KR.3
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KR.3
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
LQ.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LQ.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
XDK.5
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
XDK.5
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JN.1.4.8
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.4.8
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JF.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JF.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
XBB.2.3.19
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
XBB.2.3.19
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JD.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JD.1.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JN.1.52
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.52
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JN.1.42
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.42
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
KB.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KB.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JN.1.14
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.14
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
MJ.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
MJ.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JN.1.1.6
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
Lineage
(WHO label)
Target Gene
Primer Name
Primer Sequence
Primer Length
Primer GC Content (%)
Start Position
End Position
Primer Direction
ΔG (cal)
Primer first used
Page 2800 of 5293
Go to page:
Prev
1
442
883
1324
1765
2206
2647
3088
3529
3970
4411
4852
5293
Next