Table 1. The sequences and discrimination factors (DF) of duplexes containing different types of 5′,3′ mismatches.

Probe a	Type of mismatched base pair (N:M)	Discrimination factor (DF) b
P-3FAM-4C	C:C	320
	C:A	165
	C:T	140
P-3FAM-4G	G:T	52
	G:A	35
	G:G	17
P-3FAM-4T	T:C	38
	T:T	25
	T:G	4.0
P-3FAM-4A	A:C	7.2
	A:A	5.6
	A:G	4.2

^aThe probe sequence is 5′PO₄-TCT(-FAM)NCACAGACACATACTCCA-BHQ1; the target sequences are 5′GTTTTAAA TTATGGAGTATGTGTCTGTTMAAACGAGAGTAAG; the two purposefully inserted mismatched bases are underlined. M represents the SNP site. N is the base opposite M in the probe, which is C, G, T and A for P-3FAM-4C, P-3FAM-4G, P-3FAM-4T and P-3FAM-4A, respectively.

^b1× ThermoPol Reaction Buffer with additional (NH₄)₂SO₄ and KCl was used as the reaction buffer. For reactions with P-3FAM-4G, the concentration of (NH₄)₂SO₄ and KCl was 30 mM. For the other three probes, the concentration of (NH₄)₂SO₄ and KCl was 20 mM.