TABLE 3.

PCR primers used to screen for deletions at the indicated loci

AES, allelic exchange substrate.

Locus	Flank	Primer name	Binding site	Primer sequence
Rv1151c	Left	1151c L Flank F = P7	Upstream of L flank, in wild-type and mutant	CAT GCC GTT CAG CAT GTC
		sacBout_LR = P10	Within AES construct, mutant only	GAT GTC TCA CTG AGG TCT CT
		1151c L Flank R = P8	Within deleted region, wild-type only	GGT GAT GAC GCT GAC CTC
	Right	1151c R Flank F = P5	Within deleted region, wild-type only	CGT CAT CAC CCA GAA TGT C
		hygout_RR = P9	Within AES construct, mutant only	CGA GTG TCT GGT CTC GTA G
		1151c R Flank R = P6	Downstream of R flank, in wild-type and mutant	GGC ACT GTC GGA TTA CAA G
Rv0998	Left	0998 L Flank F = P1	Upstream of L flank, in wild-type and mutant	CGT TGT GTC TAC TGC TCG AC
		sacBout_LR = P9	Within AES construct, mutant only	GAT GTC TCA CTG AGG TCT CT
		0998 L Flank R = P2	Within deleted region, wild-type only	GAT GAT CGC AAC ACC ATC
	Right	0998 R Flank F = P3	Within deleted region, wild-type only	CGG TTC ATG TCG GCT CGT GTT C
		hygout_RR = P10	Within AES construct, mutant only	CGA GTG TCT GGT CTC GTA G
		0998 R Flank R = P4	Downstream of R flank, in wild-type and mutant	TGT GCG GTA CAT CGA CCA CCT C