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.19
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
JN.19
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
JN.19
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
JN.19
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
JN.19
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-20656.7
US
JN.19
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.19
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-20812.9
Japan
KU.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
KU.1
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
KU.1
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
KU.1
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
KU.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
KU.1
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-20656.7
US
KU.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KU.1
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-20812.9
Japan
KZ.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
KZ.1
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
KZ.1
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
KZ.1
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
KZ.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
KZ.1
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-20656.7
US
KZ.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KZ.1
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-20812.9
Japan
JN.1.36
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
JN.1.36
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
JN.1.36
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
JN.1.36
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
JN.1.36
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
JN.1.36
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-20656.7
US
JN.1.36
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.36
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-2648.21
Japan
JQ.2.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
JQ.2.1
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-18080
China
JQ.2.1
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
JQ.2.1
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
JQ.2.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
JQ.2.1
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-20656.7
US
JQ.2.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JQ.2.1
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-20812.9
Japan
KT.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
KT.1
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
KT.1
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
KT.1
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
KT.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
KT.1
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-20656.7
US
KT.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KT.1
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-2648.21
Japan
LA.2
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
LA.2
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
LA.2
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
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 3047 of 5293
Go to page:
Prev
1
442
883
1324
1765
2206
2647
3088
3529
3970
4411
4852
5293
Next