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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
XAF	N	SC2	CTGCAGATTTGGATGATTTCTCC	23	43.48	29463	29485	F	-23117.2	US
XAF	ORF1ab	NIID WH-1 F501R913	TTCGGATGCTCGAACTGCACC	21	57.14	484	504	F	-24908.9	Japan
XAF	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-21969.5	Japan
XAF	ORF1ab	NIID WH-1 Seq F519R840	ACCTCATGGTCATGTTATGG	20	45	502	521	F	-20812.9	Japan
XAF	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
XAF	S	NIID WH-1 F24381R24873	TCAAGACTCACTTTCTTCCAC	21	42.86	24364	24384	F	-20966	Japan
XAF	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	-21400.8	Japan
BC.2	ORF1ab	Yip-ORF1ab	ATGCATTTGCATCAGAGGCT	20	45	1866	1885	F	-21402.5	China
BC.2	ORF1ab	Pasteur-ORF1ab-1	ATGAGCTTAGTCCTGTTG	18	44.44	12690	12707	F	-17837.6	France
BC.2	ORF1ab	Pasteur-ORF1ab-2	GGTAACTGGTATGATTTCG	19	42.11	14080	14098	F	-18581.4	France
BC.2	ORF1ab	CN-CDC-ORF1ab	CCCTGTGGGTTTTACACTTAA	21	42.86	13342	13362	F	-20516.2	China
BC.2	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
BC.2	ORF1ab	Charité-ORF1b	GTGARATGGTCATGTGTGGCGG	22	54.55	15431	15452	F	-20262.1	Germany
BC.2	ORF1ab	Won-ORF1ab	CATGTGTGGCGGTTCACTAT	20	50	15441	15460	F	-22753.7	South Korea
BC.2	ORF1ab	Chan-ORF1ab	CGCATACAGTCTTRCAGGCT	20	50	16220	16239	F	-11502.5	China
BC.2	ORF1ab	HKU-ORF1b	TGGGGYTTTACRGGTAACCT	20	45	18778	18797	F	-7043.36	Hong Kong
BC.2	S	Young-S	TATACATGTCTCTGGGACCA	20	45	21763	21782	F	-13443.5	Singapore
BC.2	S	Chan-S	CCTACTAAATTAAATGATCTCTGCTTTACT	30	30	22712	22741	F	-613.77	China
BC.2	S	Won-S	CTACATGCACCAGCAACTGT	20	50	23114	23133	F	-2729.83	South Korea
BC.2	E	Won-E	TTCGGAAGAGACAGGTACGTT	21	47.62	26259	26279	F	-18253.7	South Korea
BC.2	E	Charité-E	ACAGGTACGTTAATAGTTAATAGCGT	26	34.62	26269	26294	F	-11626.3	Germany
BC.2	E	Huang-E	ACTTCTTTTTCTTGCTTTCGTGGT	24	37.5	26295	26318	F	-3064.43	China
BC.2	E	Niu-E	TTCTTGCTTTCGTGGTATTC	20	40	26303	26322	F	-4083.33	China
BC.2	N	CN-CDC-N	GGGGAACTTCTCCTGCTAGAAT	22	50	28881	28902	F	-17926.1	China
BC.2	N	NIH-TH_N	CGTTTGGTGGACCCTCAGAT	20	55	28320	28339	F	-22019.3	Thailand
BC.2	N	US-CDC-N-1	GACCCCAAAATCAGCGAAAT	20	45	28287	28306	F	-20656.7	US
BC.2	N	US-CDC-N-2	TTACAAACATTGGCCGCAAA	20	40	29164	29183	F	-21115.5	US
BC.2	N	US-CDC-N-3	GGGAGCCTTGAATACACCAAAA	22	45.45	28681	28702	F	-22824.1	US
BC.2	N	Young-N	CTCAGTCCAAGATGGTATTTCT	22	40.91	28583	28604	F	-21953.9	Singapore
BC.2	N	Corman-N	CACATTGGCACCCGCAATC	19	57.89	28706	28724	F	-18248.7	Germany
BC.2	N	Won-N	CAATGCTGCAATCGTGCTAC	20	50	28732	28751	F	-22388.1	South Korea
BC.2	N	NIID-JP-N	AAATTTTGGGGACCAGGAAC	20	45	29125	29144	F	-20489.8	Japan
BC.2	N	HKU-N	TAATCAGACAAGGAACTGATTA	22	31.82	29145	29166	F	-18800.2	Hong Kong
BC.2	N	Chan-N	GCGTTCTTCGGAATGTCG	18	55.56	29210	29227	F	-21207.6	China
BC.2	N	SC2	CTGCAGATTTGGATGATTTCTCC	23	43.48	29463	29485	F	-23117.2	US
BC.2	ORF1ab	NIID WH-1 F501R913	TTCGGATGCTCGAACTGCACC	21	57.14	484	504	F	-24908.9	Japan
BC.2	ORF1ab	NIID WH-1 F509R854	CTCGAACTGCACCTCATGG	19	57.89	492	510	F	-21969.5	Japan
BC.2	ORF1ab	NIID WH-1 Seq F519R840	ACCTCATGGTCATGTTATGG	20	45	502	521	F	-20812.9	Japan
BC.2	S	WuhanCoV-spk1	TTGGCAAAATTCAAGACTCACTTT	24	33.33	24354	24377	F	-23366.4	Japan
BC.2	S	NIID WH-1 F24381R24873	TCAAGACTCACTTTCTTCCAC	21	42.86	24364	24384	F	-20966	Japan
BC.2	S	NIID WH-1 Seq F24383R24865	AAGACTCACTTTCTTCCACAG	21	42.86	24366	24386	F	-21400.8	Japan
P.1.17.1 (Gamma)	ORF1ab	Yip-ORF1ab	ATGCATTTGCATCAGAGGCT	20	45	1866	1885	F	-21402.5	China
P.1.17.1 (Gamma)	ORF1ab	Pasteur-ORF1ab-1	ATGAGCTTAGTCCTGTTG	18	44.44	12690	12707	F	-17837.6	France
P.1.17.1 (Gamma)	ORF1ab	Pasteur-ORF1ab-2	GGTAACTGGTATGATTTCG	19	42.11	14080	14098	F	-18581.4	France
P.1.17.1 (Gamma)	ORF1ab	CN-CDC-ORF1ab	CCCTGTGGGTTTTACACTTAA	21	42.86	13342	13362	F	-20516.2	China
P.1.17.1 (Gamma)	ORF1ab	Young-ORF1ab	TCATTGTTAATGCCTATATTAACC	24	29.17	14155	14178	F	-20695.4	Singapore
P.1.17.1 (Gamma)	ORF1ab	Charité-ORF1b	GTGARATGGTCATGTGTGGCGG	22	54.55	15431	15452	F	-20262.1	Germany
P.1.17.1 (Gamma)	ORF1ab	Won-ORF1ab	CATGTGTGGCGGTTCACTAT	20	50	15441	15460	F	-22753.7	South Korea
P.1.17.1 (Gamma)	ORF1ab	Chan-ORF1ab	CGCATACAGTCTTRCAGGCT	20	50	16220	16239	F	-11502.5	China
P.1.17.1 (Gamma)	ORF1ab	HKU-ORF1b	TGGGGYTTTACRGGTAACCT	20	45	18778	18797	F	-7043.36	Hong Kong
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