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
GG.1
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
GG.1
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
GG.1
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
GG.1
ORF1ab
CN-CDC-ORF1ab
ACGATTGTGCATCAGCTGA
19
47.37
13460
13442
R
-20306.2
China
GG.1
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-20695.4
Singapore
GG.1
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
GG.1
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-5786.4
Germany
GG.1
ORF1ab
Charité-ORF1b
CARATGTTAAASACACTATTAGCATA
26
23.08
15530
15505
R
-5057.65
Germany
GG.1
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-2052.38
South Korea
GG.1
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
GG.1
ORF1ab
Chan-ORF1ab
CGCATACAGTCTTRCAGGCT
20
50
16220
16239
F
-11502.5
China
GG.1
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-17292.3
China
GG.1
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
GG.1
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-17655.9
Hong Kong
GG.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
GG.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-22070.7
Singapore
GG.1
S
Chan-S
CCTACTAAATTAAATGATCTCTGCTTTACT
30
30
22712
22741
F
-27219.1
China
GG.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
GG.1
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-22142.8
South Korea
GG.1
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-21965.9
South Korea
GG.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
GG.1
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19261.4
South Korea
GG.1
E
Charité-E
ACAGGTACGTTAATAGTTAATAGCGT
26
34.62
26269
26294
F
-19379.1
Germany
GG.1
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
GG.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
GG.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
GG.1
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
GG.1
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
GG.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GG.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
GG.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
GG.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
GG.1
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-20656.7
US
GG.1
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-25148.4
US
GG.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
GG.1
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
GG.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
GG.1
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
GG.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
GG.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
GG.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
GG.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
GG.1
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-22388.1
South Korea
GG.1
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
GG.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
GG.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
GG.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
GG.1
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
GG.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
GG.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
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 3640 of 5293
Go to page:
Prev
1
442
883
1324
1765
2206
2647
3088
3529
3970
4411
4852
5293
Next