TABLE 1.

Characteristics of subtype-specific probes

Probe	Subtype(s) identified	Oligonucleotide sequencea	Tm (°C)
SAG1	CRF02_AG	5′-ATA TTT TGG ATA ATG ATA ATT TGT AAT GC-3′	53.7
SA2	CRF02_AG, A, CRF01_AE	5′-AAA GAY GCA GAG ACC ACC C-3′	55.2
SAE1	CRF01_AE	5′-AGA CAC AGA TGA ATT GGC CAA-3′	53.9
SB2	B	5′-GAM GGR GAY CAG GAA GAA TT-3′	51.2
SBD3	B, BD, D	5′-ATG CTC CTT GGG ATR TTR ATG-3′	52
SD1.1	D	5′-AGA GTG AGG GRG ATA GAG AGG AAT T-3′	59.5
SC1	C	5′-ATC TTA GGC TTT TGG ATG ITA ATG-3′	54
SF6	F	5′-GGG AAA TGG GGC CTT TTA TT-3′	53.2
SG1	G	5′-CAT ATA GTA CTG AAA GCC ATA ATG T-3′	54.6

^aDegenerate bases (in boldface)are defined as follows: Y, C + T; R, = A + G; M, A + C; I, inosine.