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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
BN.1.2.2	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
BN.1.2.2	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
BN.1.2.2	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
BN.1.2.2	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
CQ.2	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
CQ.2	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
CQ.2	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
CQ.2	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
CQ.2	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
CQ.2	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
CQ.2	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
CH.1.1.24	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
CH.1.1.24	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
CH.1.1.24	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
CH.1.1.24	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
CH.1.1.24	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
CH.1.1.24	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
CH.1.1.24	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
BA.5.2.43	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
BA.5.2.43	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
BA.5.2.43	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
BA.5.2.43	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
BA.5.2.43	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
BA.5.2.43	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
BA.5.2.43	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
BA.5.2.19	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
BA.5.2.19	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
BA.5.2.19	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
BA.5.2.19	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
BA.5.2.19	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
BA.5.2.19	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
BA.5.2.19	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
BF.38.3	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
BF.38.3	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
BF.38.3	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
BF.38.3	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
BF.38.3	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
BF.38.3	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
BF.38.3	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
BF.7.19.1	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
BF.7.19.1	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
BF.7.19.1	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
BF.7.19.1	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
BF.7.19.1	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
BF.7.19.1	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
BF.7.19.1	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
BQ.1.1.43	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
BQ.1.1.43	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
BQ.1.1.43	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
BQ.1.1.43	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
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