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
ME.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.19
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.6
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.16
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.18
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.21
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.15.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.15.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.18
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.5
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.14
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.20
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.17
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.8
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.10
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
JN.1.39.3
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
JN.1.50.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.21.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.11
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.17.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
XF
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.13.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.7
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
XS
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
B.1.258.22
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.22
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BC.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
XBB.1.5.78
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-13486.5
China
B.1.1.61
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-13529.3
Hong Kong
B.19
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-13571.9
China
BA.5.1.17
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-13571.9
China
B.1.177.89
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-13584.2
South Korea
AY.14 (Delta)
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-13584.2
South Korea
BA.2.33
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-13604.1
Singapore
B.1.393
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13628.2
China
JN.1.8.2
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13628.2
China
CH.1.1.12
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13628.2
China
AY.46.6 (Delta)
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13628.2
China
B.1.1.265
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13628.2
China
CH.1.1.27
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13628.2
China
BA.5.2.27
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13628.2
China
B.1.36.22
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-13632.4
China
B.1.267
E
Charité-E
ACAGGTACGTTAATAGTTAATAGCGT
26
34.62
26269
26294
F
-13655.5
Germany
B.1.1.327
E
Charité-E
ACAGGTACGTTAATAGTTAATAGCGT
26
34.62
26269
26294
F
-13655.5
Germany
BA.5.2.14
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-13663.4
Japan
B.1.540
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-13723.7
Germany
B.1.1.261
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-13747.9
China
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 467 of 5293
Go to page:
Prev
1
442
883
1324
1765
2206
2647
3088
3529
3970
4411
4852
5293
Next