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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
LF.4.1	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
LF.4.1	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-22762.7	Japan
XDK.1.2	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
XDK.1.2	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
XDK.1.2	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
XDK.1.2	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
XDK.1.2	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
XDK.1.2	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
XDK.1.2	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-22762.7	Japan
XBB.1.5.20	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
XBB.1.5.20	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
XBB.1.5.20	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-17292.3	China
XBB.1.5.20	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
XBB.1.5.20	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
XBB.1.5.20	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
XBB.1.5.20	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
LB.1.7.3	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
LB.1.7.3	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
LB.1.7.3	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
LB.1.7.3	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
LB.1.7.3	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
LB.1.7.3	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
LB.1.7.3	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-22762.7	Japan
JN.1.18.5	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
JN.1.18.5	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
JN.1.18.5	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
JN.1.18.5	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
JN.1.18.5	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
JN.1.18.5	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
JN.1.18.5	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-22762.7	Japan
JN.1.16.3	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
JN.1.16.3	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
JN.1.16.3	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
JN.1.16.3	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
JN.1.16.3	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
JN.1.16.3	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
JN.1.16.3	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	1233.44	Japan
JN.1.1.10	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
JN.1.1.10	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
JN.1.1.10	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-13317.5	China
JN.1.1.10	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
JN.1.1.10	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
JN.1.1.10	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
JN.1.1.10	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-22762.7	Japan
HK.3.4	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
HK.3.4	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
HK.3.4	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-17292.3	China
HK.3.4	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
HK.3.4	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
HK.3.4	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