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
ED.2	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
ED.2	E	Huang-E	GCAGCAGTACGCACACAATC	20	55	26376	26357	R	-23540.5	China
ED.2	E	Niu-E	TTCTTGCTTTCGTGGTATTC	20	40	26303	26322	F	-19913.4	China
ED.2	E	Niu-E	CACGTTAACAATATTGCAGC	20	40	26391	26372	R	-20723.8	China
ED.2	N	CN-CDC-N	GGGGAACTTCTCCTGCTAGAAT	22	50	28881	28902	F	-17926.1	China
ED.2	N	CN-CDC-N	CAGACATTTTGCTCTCAAGCTG	22	45.45	28979	28958	R	-23140.2	China
ED.2	N	NIH-TH_N	CGTTTGGTGGACCCTCAGAT	20	55	28320	28339	F	-22019.3	Thailand
ED.2	N	NIH-TH_N	CCCCACTGCGTTCTCCATT	19	57.89	28376	28358	R	-3370.08	Thailand
ED.2	N	US-CDC-N-1	GACCCCAAAATCAGCGAAAT	20	45	28287	28306	F	-20656.7	US
ED.2	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
ED.2	N	US-CDC-N-2	TTACAAACATTGGCCGCAAA	20	40	29164	29183	F	-21115.5	US
ED.2	N	US-CDC-N-2	GCGCGACATTCCGAAGAA	18	55.56	29230	29213	R	-21404.2	US
ED.2	N	US-CDC-N-3	GGGAGCCTTGAATACACCAAAA	22	45.45	28681	28702	F	-21956.6	US
ED.2	N	US-CDC-N-3	TGTAGCACGATTGCAGCATTG	21	47.62	28752	28732	R	-23779.6	US
ED.2	N	Young-N	CTCAGTCCAAGATGGTATTTCT	22	40.91	28583	28604	F	-21953.9	Singapore
ED.2	N	Young-N	AGCACCATAGGGAAGTCC	18	55.56	28648	28631	R	-19874.5	Singapore
ED.2	N	Corman-N	CACATTGGCACCCGCAATC	19	57.89	28706	28724	F	-23131.5	Germany
ED.2	N	Corman-N	GAGGAACGAGAAGAGGCTTG	20	55	28833	28814	R	-22527.5	Germany
ED.2	N	Won-N	CAATGCTGCAATCGTGCTAC	20	50	28732	28751	F	-22388.1	South Korea
ED.2	N	Won-N	GTTGCGACTACGTGATGAGG	20	55	28849	28830	R	-23088.1	South Korea
ED.2	N	NIID-JP-N	AAATTTTGGGGACCAGGAAC	20	45	29125	29144	F	-20489.8	Japan
ED.2	N	NIID-JP-N	TGGCAGCTGTGTAGGTCAAC	20	55	29282	29263	R	-20522.3	Japan
ED.2	N	HKU-N	TAATCAGACAAGGAACTGATTA	22	31.82	29145	29166	F	-18800.2	Hong Kong
ED.2	N	HKU-N	CGAAGGTGTGACTTCCATG	19	52.63	29254	29236	R	-20936.4	Hong Kong
ED.2	N	Chan-N	GCGTTCTTCGGAATGTCG	18	55.56	29210	29227	F	-21207.6	China
ED.2	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	China
ED.2	N	SC2	CTGCAGATTTGGATGATTTCTCC	23	43.48	29463	29485	F	-23117.2	US
ED.2	N	SC2	CCTTGTGTGGTCTGCATGAGTTTAG	25	48	29554	29530	R	-26482.3	US
ED.2	ORF1ab	NIID WH-1 F501R913	TTCGGATGCTCGAACTGCACC	21	57.14	484	504	F	-24908.9	Japan
ED.2	ORF1ab	NIID WH-1 F501R913	CTTTACCAGCACGTGCTAGAAGG	23	52.17	896	874	R	-25657.5	Japan
ED.2	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-21969.5	Japan
ED.2	ORF1ab	NIID WH-1 F509R854	CAGAAGTTGTTATCGACATAGC	22	40.91	837	816	R	-21257.9	Japan
ED.2	ORF1ab	NIID WH-1 Seq F519R840	ACCTCATGGTCATGTTATGG	20	45	502	521	F	-20812.9	Japan
ED.2	ORF1ab	NIID WH-1 Seq F519R840	GACATAGCGAGTGTATGCC	19	52.63	823	805	R	-20165.2	Japan
ED.2	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
ED.2	S	WuhanCoV-spk1	TGTGGTTCATAAAAATTCCTTTGTG	25	32	24900	24876	R	-23857.7	Japan
ED.2	S	NIID WH-1 F24381R24873	TCAAGACTCACTTTCTTCCAC	21	42.86	24364	24384	F	-20966	Japan
ED.2	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
ED.2	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	-21400.8	Japan
ED.2	S	NIID WH-1 Seq F24383R24865	CAAAGACACCTTCACGAGG	19	52.63	24848	24830	R	-20677.6	Japan
ED.1	N	HKU-N	TAATCAGACAAGGAACTGATTA	22	31.82	29145	29166	F	-18800.2	Hong Kong
ED.1	N	HKU-N	CGAAGGTGTGACTTCCATG	19	52.63	29254	29236	R	-20936.4	Hong Kong
ED.1	N	Chan-N	GCGTTCTTCGGAATGTCG	18	55.56	29210	29227	F	-21207.6	China
ED.1	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	China
ED.1	N	SC2	CTGCAGATTTGGATGATTTCTCC	23	43.48	29463	29485	F	-23117.2	US
ED.1	N	SC2	CCTTGTGTGGTCTGCATGAGTTTAG	25	48	29554	29530	R	-26482.3	US
ED.1	ORF1ab	NIID WH-1 F501R913	TTCGGATGCTCGAACTGCACC	21	57.14	484	504	F	-24908.9	Japan
ED.1	ORF1ab	NIID WH-1 F501R913	CTTTACCAGCACGTGCTAGAAGG	23	52.17	896	874	R	-25657.5	Japan
ED.1	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-21969.5	Japan
ED.1	ORF1ab	NIID WH-1 F509R854	CAGAAGTTGTTATCGACATAGC	22	40.91	837	816	R	-21257.9	Japan
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