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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
AY.90 (Delta)	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
AY.90 (Delta)	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
BF.23	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
BF.23	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
BF.23	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
BF.23	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
BF.23	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
BF.23	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
BF.23	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
BF.30	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
BF.30	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
BF.30	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
BF.30	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
BF.30	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
BF.30	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
BF.30	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
BA.1.1.12	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
BA.1.1.12	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
BA.1.1.12	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
BA.1.1.12	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
BA.1.1.12	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
BA.1.1.12	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
BA.1.1.12	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
BA.2.87	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
BA.2.87	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
BA.2.87	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
BA.2.87	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
BA.2.87	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
BA.2.87	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
BA.2.87	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
BA.5.2.33	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
BA.5.2.33	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
BA.5.2.33	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
BA.5.2.33	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
BA.5.2.33	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
BA.5.2.33	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
BA.5.2.33	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
BA.2.46	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
BA.2.46	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
BA.2.46	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
BA.2.46	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
BA.2.46	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-22590.4	China
BA.2.46	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
BA.2.46	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
AY.58 (Delta)	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
AY.58 (Delta)	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
AY.58 (Delta)	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
AY.58 (Delta)	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
AY.58 (Delta)	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
AY.58 (Delta)	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
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