Table 1.

Allele-specific oligonucleotide probes used for typing 10 intragenic polymorphic sites (loci) in the P. falciparum msp1 gene

Locus*	Allele	Oligonucleotide sequence
aa 44	S	aca	ggt	tat	agt	tta	ttt
	G	aca	ggt	tat	ggt	tta	ttt
block 2	MAD-like	aca	agt	gga	aca	gct	gtt
	K1-like	gca	tca	gct	gga	ggg	ctt
	RO33-like	gtt	gtt	gca	aag	cct	gca
aa 160	Q	cat	aga	gtt	caa	aat	tac
	R	cac	aga	gta	cga	aat	tac
aa 222	A	gca	tgt	gcc	aat	agt	tat
	V	gta	tgt	gct	aat	gat	tat
aa 297-8	TK	gca	act	aaa	gaa	gaa	gaa
	DN	gca	gat	aat	gaa	gaa	gga
aa 320	E	aaa	caa	tta	gaa	gaa	gca
	Q	aaa	caa	tta	caa	gaa	gca
block 4 b	Kl-like	ctt	gat	aag	aac	aaa	aaa
	MAD-like	cct	gag	aat	aag	aaa	aaa
block 6-16	Kl-like	agt	tca	gga	tcc	aca	aaa
	MAD-like	tcc	gac	aca	tta	gaa	caa
aa 1644	E	caa	tgt	cca	gaa	aat	tct
	Q	caa	tgt	cca	caa	aat	tct
aa 1700-1	SR	ggt	agc	agc	aga	aag	aaa
	NG	ggt	agc	aac	gga	aag	aaa

^*Loci are given either as polymorphic amino acid position(s) in the deduced protein sequence [numbered as in the alignment of Miller et al. (21)] or as polymorphic blocks of sequence (following the scheme of Tanabe et al. (17)] Bases that differ between allelic probes are in bold and underlined. Previously described very rare alleles at block 4b (RO33-like) and aa 1700-01 (SG) were absent (in the case of the former) or extremely rare (in the case of the latter) in a large subsample of more than half the total number of isolates, and hybridization patterns for all of the other intragenic loci did not suggest the existence of any previously undescribed additional alleles of these sequences.