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.7
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
EG.7
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
EG.7
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
EG.7
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
EG.7
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
EG.7
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
EG.7
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BN.1.3.5
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BN.1.3.5
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
BN.1.3.5
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
BN.1.3.5
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-20306.2
China
BN.1.3.5
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
BN.1.3.5
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13317.5
China
BN.1.3.5
S
Chan-S
CCTACTAAATTAAATGATCTCTGCTTTACT
30
30
22712
22741
F
-27219.1
China
BN.1.3.5
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
BN.1.3.5
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
BN.1.3.5
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
BN.1.3.5
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
BN.1.3.5
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
BN.1.3.5
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BN.1.3.5
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BN.1.3.5
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
BN.1.3.5
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XCF.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
XCF.1
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
XCF.1
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-1313
China
XCF.1
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-20306.2
China
XCF.1
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
XCF.1
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-17292.3
China
XCF.1
S
Chan-S
CCTACTAAATTAAATGATCTCTGCTTTACT
30
30
22712
22741
F
-51.5687
China
XCF.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XCF.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
XCF.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
XCF.1
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
XCF.1
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
XCF.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XCF.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
XCF.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XCF.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XCC
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
XCC
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
XCC
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-18766.3
China
XCC
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-20306.2
China
XCC
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
XCC
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-17603.1
China
XCC
S
Chan-S
CCTACTAAATTAAATGATCTCTGCTTTACT
30
30
22712
22741
F
-27219.1
China
XCC
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XCC
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
XCC
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
XCC
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
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 4574 of 5293
Go to page:
Prev
1
442
883
1324
1765
2206
2647
3088
3529
3970
4411
4852
5293
Next