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
LY.1
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
LY.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
LY.1
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
LY.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
LY.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
MD.3.1
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
MD.3.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
MD.3.1
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
MD.3.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
MD.3.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
MK.1
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
MK.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
MK.1
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
MK.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
MK.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
LZ.1
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
LZ.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
LZ.1
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
LZ.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
LZ.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
MB.1.1
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
MB.1.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
MB.1.1
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
MB.1.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
MB.1.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
KP.3.2.4
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
KP.3.2.4
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
KP.3.2.4
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
KP.3.2.4
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
KP.3.2.4
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
JN.1.50
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
JN.1.50
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
JN.1.50
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
JN.1.50
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
JN.1.50
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
KP.2.14
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
KP.2.14
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
KP.2.14
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
KP.2.14
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
KP.2.14
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
unclassifiable
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-1355.31
France
unclassifiable
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-1717.06
France
unclassifiable
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
unclassifiable
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
unclassifiable
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
KS.1.1
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
KS.1.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
KS.1.1
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
KS.1.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
KS.1.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
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 5083 of 5293
Go to page:
Prev
1
442
883
1324
1765
2206
2647
3088
3529
3970
4411
4852
5293
Next