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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
JN.1.34	S	WuhanCoV-spk1	TGTGGTTCATAAAAATTCCTTTGTG	25	32	24900	24876	R	-23857.7	Japan
JN.1.34	S	NIID WH-1 F24381R24873	TCAAGACTCACTTTCTTCCAC	21	42.86	24364	24384	F	-16362.7	Japan
JN.1.34	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
JN.1.34	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	-16797.4	Japan
JN.1.34	S	NIID WH-1 Seq F24383R24865	CAAAGACACCTTCACGAGG	19	52.63	24848	24830	R	-20677.6	Japan
HK.3.2	ORF1ab	Yip-ORF1ab	ATGCATTTGCATCAGAGGCT	20	45	1866	1885	F	-21402.5	China
HK.3.2	ORF1ab	Yip-ORF1ab	TTGTTATAGCGGCCTTCTGT	20	45	1970	1951	R	-21075.5	China
HK.3.2	ORF1ab	Pasteur-ORF1ab-1	ATGAGCTTAGTCCTGTTG	18	44.44	12690	12707	F	-17837.6	France
HK.3.2	ORF1ab	Pasteur-ORF1ab-1	CTCCCTTTGTTGTGTTGT	18	44.44	12797	12780	R	-15630.5	France
HK.3.2	ORF1ab	Pasteur-ORF1ab-2	GGTAACTGGTATGATTTCG	19	42.11	14080	14098	F	-18581.4	France
HK.3.2	ORF1ab	Pasteur-ORF1ab-2	CTGGTCAAGGTTAATATAGG	20	40	14186	14167	R	-18348.8	France
HK.3.2	ORF1ab	CN-CDC-ORF1ab	CCCTGTGGGTTTTACACTTAA	21	42.86	13342	13362	F	-20516.2	China
HK.3.2	ORF1ab	CN-CDC-ORF1ab	ACGATTGTGCATCAGCTGA	19	47.37	13460	13442	R	-20306.2	China
HK.3.2	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
HK.3.2	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
HK.3.2	ORF1ab	Charité-ORF1b	GTGARATGGTCATGTGTGGCGG	22	54.55	15431	15452	F	-17266.7	Germany
HK.3.2	ORF1ab	Charité-ORF1b	CARATGTTAAASACACTATTAGCATA	26	23.08	15530	15505	R	-9191.15	Germany
HK.3.2	ORF1ab	Won-ORF1ab	CATGTGTGGCGGTTCACTAT	20	50	15441	15460	F	-19758.2	South Korea
HK.3.2	ORF1ab	Won-ORF1ab	TGCATTAACATTGGCCGTGA	20	45	15558	15539	R	-21175.8	South Korea
HK.3.2	ORF1ab	Chan-ORF1ab	CGCATACAGTCTTRCAGGCT	20	50	16220	16239	F	-11502.5	China
HK.3.2	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-17292.3	China
HK.3.2	ORF1ab	HKU-ORF1b	TGGGGYTTTACRGGTAACCT	20	45	18778	18797	F	-7043.36	Hong Kong
HK.3.2	ORF1ab	HKU-ORF1b	AACRCGCTTAACAAAGCACTC	21	42.86	18909	18889	R	-17655.9	Hong Kong
HK.3.2	S	Young-S	TATACATGTCTCTGGGACCA	20	45	21763	21782	F	-19121.1	Singapore
HK.3.2	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
HK.3.2	S	Chan-S	CCTACTAAATTAAATGATCTCTGCTTTACT	30	30	22712	22741	F	-27219.1	China
HK.3.2	S	Chan-S	CAAGCTATAACGCAGCCTGTA	21	47.62	22869	22849	R	-22073.5	China
HK.3.2	S	Won-S	CTACATGCACCAGCAACTGT	20	50	23114	23133	F	-22142.8	South Korea
HK.3.2	S	Won-S	CACCTGTGCCTGTTAAACCA	20	50	23213	23194	R	-21965.9	South Korea
HK.3.2	E	Won-E	TTCGGAAGAGACAGGTACGTT	21	47.62	26259	26279	F	-15016.3	South Korea
HK.3.2	E	Won-E	CACACAATCGATGCGCAGTA	20	50	26365	26346	R	-19261.4	South Korea
HK.3.2	E	Charité-E	ACAGGTACGTTAATAGTTAATAGCGT	26	34.62	26269	26294	F	-19379.1	Germany
HK.3.2	E	Charité-E	ATATTGCAGCAGTACGCACACA	22	45.45	26381	26360	R	-23527.6	Germany
HK.3.2	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-25022.8	China
HK.3.2	E	Huang-E	GCAGCAGTACGCACACAATC	20	55	26376	26357	R	-23540.5	China
HK.3.2	E	Niu-E	TTCTTGCTTTCGTGGTATTC	20	40	26303	26322	F	-19913.4	China
HK.3.2	E	Niu-E	CACGTTAACAATATTGCAGC	20	40	26391	26372	R	-20723.8	China
HK.3.2	N	CN-CDC-N	GGGGAACTTCTCCTGCTAGAAT	22	50	28881	28902	F	-17926.1	China
HK.3.2	N	CN-CDC-N	CAGACATTTTGCTCTCAAGCTG	22	45.45	28979	28958	R	-23140.2	China
HK.3.2	N	NIH-TH_N	CGTTTGGTGGACCCTCAGAT	20	55	28320	28339	F	-22019.3	Thailand
HK.3.2	N	NIH-TH_N	CCCCACTGCGTTCTCCATT	19	57.89	28376	28358	R	-3370.08	Thailand
HK.3.2	N	US-CDC-N-1	GACCCCAAAATCAGCGAAAT	20	45	28287	28306	F	-18526.8	US
HK.3.2	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
HK.3.2	N	US-CDC-N-2	TTACAAACATTGGCCGCAAA	20	40	29164	29183	F	-21115.5	US
HK.3.2	N	US-CDC-N-2	GCGCGACATTCCGAAGAA	18	55.56	29230	29213	R	-21404.2	US
HK.3.2	N	US-CDC-N-3	GGGAGCCTTGAATACACCAAAA	22	45.45	28681	28702	F	-22824.1	US
HK.3.2	N	US-CDC-N-3	TGTAGCACGATTGCAGCATTG	21	47.62	28752	28732	R	-23779.6	US
HK.3.2	N	Young-N	CTCAGTCCAAGATGGTATTTCT	22	40.91	28583	28604	F	-21953.9	Singapore
HK.3.2	N	Young-N	AGCACCATAGGGAAGTCC	18	55.56	28648	28631	R	-19874.5	Singapore
HK.3.2	N	Corman-N	CACATTGGCACCCGCAATC	19	57.89	28706	28724	F	-23131.5	Germany
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