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
JN.1.16.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
JN.1.16.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
JN.1.16.1
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
LW.1
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-20262.1
Germany
LW.1
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
LW.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
LW.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-19646.7
China
LW.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
LW.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
LW.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
LW.1
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
LP.1
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-20262.1
Germany
LP.1
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
LP.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
LP.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-19646.7
China
LP.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
LP.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
LP.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
LP.1
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
LB.1.2.1
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-20262.1
Germany
LB.1.2.1
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
LB.1.2.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
LB.1.2.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-19646.7
China
LB.1.2.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
LB.1.2.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
LB.1.2.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
LB.1.2.1
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
KP.3.3.3
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-20262.1
Germany
KP.3.3.3
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
KP.3.3.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17351.3
China
KP.3.3.3
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-19646.7
China
KP.3.3.3
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
KP.3.3.3
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
KP.3.3.3
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
KP.3.3.3
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
ML.2
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-20262.1
Germany
ML.2
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
ML.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17351.3
China
ML.2
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-19646.7
China
ML.2
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
ML.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
ML.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
ML.2
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
KP.2.1
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-20262.1
Germany
KP.2.1
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
KP.2.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
KP.2.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-19646.7
China
KP.2.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
KP.2.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
KP.2.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
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 3825 of 5293
Go to page:
Prev
1
442
883
1324
1765
2206
2647
3088
3529
3970
4411
4852
5293
Next