TABLE 1.

PCR primers and oligonucleotide probes used in this study

Oligonucleotide	Sequence (5′-3′)	Position in gene	Function	Reference
MUCAP1	CAGTGTTGACGCATCCAGGTCATGATCGCA	981–952	5′ BIOTIN-LABELED CAPTURE PROBE FOR IS2404	THIS STUDY
MUCAP3	AGGACCTGTCCGAGCGCCTTGGATATGACC	270–299	5′ BIOTIN-LABELED CAPTURE PROBE FOR IS2606	THIS STUDY
MYC16SCAP	ATGCACCACCTGCACACAGGCCACAAGGGA	1056–1027	5′ BIOTIN-LABELED CAPTURE PROBE FOR MYCOBACTERIAL 16S RDNA	THIS STUDY
MU5	AGCGACCCCAGTGGATTGGT	392–411	MU5 AND MU6; 492-BP PCR PRODUCT FROM IS2404	30
MU6	CGGTGATCAAGCGTTCACGA	862–881
MU7	GGCCTGGCGGATTGCTCAAGG	213–233	MU7 AND MU8: 332-BP PCR PRODUCT FROM IS2606	30
MU8	CGTAGATGTGGGCGAAATGG	542–523
MUNEST2	TGATCGTCAAGTCCAACCAA	664–683	MU5 AND MUNEST2: 206-BP SEMINESTED PCR PRODUCT FROM IS2404	THIS STUDY
MUNEST3	CGGTGCTCACTGATGGGTGC	357–376	MU7 AND MUNEST3: 200-BP SEMINESTED PCR PRODUCT FROM IS2606	THIS STUDY
MYCGENF	AGAGTTTGATCCTGGCTCAG	16–35	MYCGENF AND MYCGENR: 1,030-BP PCR PRODUCT FROM 16S RRNA IN ALL MYCOBACTERIA	6
MYCGENR	TGCACACAGGCCACAAGGGA	1046–1027
UPS-IPCF	GCGGTCCCAAAAGGGTCAGTATGACAGCCACTCCT		IPCF AND IPCR: 331-BP PRODUCT FROM IPC DNA	12
UPS-IPCR	GCGGTCCCAAAAGGGTCAGTATGTCAGTTGTGACCACGAA