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
BQ.1.1.73
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
DW.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
BR.5.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
BA.2.75.3
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XAK
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XAA
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
BQ.1.30
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
BQ.1.1.50
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
BA.5.1.36
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XBB.1.23
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XBB.1.38.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
N/A
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
A.23
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
1233.44
Japan
B.1.596.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.473
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.595.2
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19188.3
Japan
BA.2.76.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
BA.2.38.4
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
BA.2.38.3
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
BM.4
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.1.357
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
BP.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.348
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.428.2
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
AJ.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-1403.3
Japan
B.1.459
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.160.29
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.415.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.243.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.1.98
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.566
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.1.480
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.579
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
N.10
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
P.1.11 (Gamma)
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.435
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.445
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.124
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.384
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XAQ
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
BA.2.3.8
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.569
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.524
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XAY
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
DJ.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XAE
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.467
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.1.484
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
B.1.476
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
A.19
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
1233.44
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 113 of 5293
Go to page:
Prev
1
442
883
1324
1765
2206
2647
3088
3529
3970
4411
4852
5293
Next