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
GC.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
GC.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
GC.1
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
XBB.1.5.40
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.5.40
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
XBB.1.5.40
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
BQ.1.1.5
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
BQ.1.1.5
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-18253.7
South Korea
BQ.1.1.5
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
CH.1.1.11
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
CH.1.1.11
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
CH.1.1.11
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
FJ.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
FJ.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
FJ.1
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
BN.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
BN.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
BN.1
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
DV.3.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
DV.3.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
DV.3.1
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
XBB.1.5.14
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.5.14
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
XBB.1.5.14
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
XBB.1.5.80
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.5.80
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
XBB.1.5.80
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
XBB.1.5.3
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.5.3
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
XBB.1.5.3
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
GG.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
GG.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
GG.1
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
FL.3.2
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
FL.3.2
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
FL.3.2
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
CK.1.5
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
CK.1.5
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-18253.7
South Korea
CK.1.5
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
XBB.1.5.34
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.5.34
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
XBB.1.5.34
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
GD.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
GD.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
GD.1
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
XBB.1.37.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.37.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
XBB.1.37.1
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
XBB.1.5.77
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
XBB.1.5.77
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
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 3196 of 5293
Go to page:
Prev
1
442
883
1324
1765
2206
2647
3088
3529
3970
4411
4852
5293
Next