Table 2.
PCR primers.
| Gene or genomic region affected by deletion | Primer | Sequence (5′–3′) |
|---|---|---|
| Rv1519 | CM1518F | TTCTCACCTGGTTGATCGTG |
| CM1520R | GTCCAGTAATCGTCGCCTTC | |
| CM1518Fb | CGTTTTGAGGATCCCAGTGT | |
| CM1520Rb | GGAATGCCAAATACCGTGAG | |
| RD3 region8 | RD3 intF | TTATCTTGGCGTTGACGATG |
| RD3 intR | CATATAAGGGTGCCCGCTAC | |
| plcD/cut1 and Rvd2 region | CM1755exF | CAGTTCGCTGATGTGACGAT |
| CM1758R | ATTGCCTCCGCTAGAACAGA | |
| ORF3Rvd3F | GATTGCGTTTGTTTTGCTGA | |
| ORF1Rvd2R | TGGTCGCAGTGTTTCCAATA | |
| Rv1917c | CM1916F | ATGACCCTGATCCACCTCTG |
| CM1917exR | TCGATTCCTAAAGCGGCTAA | |
| CM1917R | CCACCAGAGATCAACTC | |
| CM1917F | CGCCACTGTTGAAGAAG | |
| Rv3017c→22c region | CM3017exF | TGGCTGTTCGTCAGTAGGTG |
| CM3022exR | GGAACCTTCACTCGTACACCA | |
| CM3022R | TTGCAGAGTGCGGTGGGGTTT | |
| CM3019exF | CGCTAGCGGAATCAATGTG | |
| IS-R | AGTTTGGTCATCAGCCGTTC | |
| ISup | TACCTCCTCGATGAACCACC | |
| ISdown | CTCTACCAGTACTGCGGCGACG | |
| ISdw | CTGCCTACTACGCTCAAC | |
| Rv3135 | CM3135F | CATATCGCTTGACCCACAGA |
| CM3136R | TCGCTGTTTGCTGTGTCTTT | |
| Rv3516-17 | CM3515F | CCTTGTGTTTGTGGATCGTG |
| CM3518R | TTCGCATGTGTCTCAAGAGG | |
| CM3515Fc | ACCTTGTCGTCCTTTTGCAC | |
| CM3515Rb | CGAAATCCAAACAGCCACTT | |
| Rv3738c-39c | CM3737F | GAGTTCCTCGCCTCACCAT |
| CM3739exR | TCAGTTGACTGACCGGCTTT |
The primers were used to confirm the deletions and polymorphism by PCR and sequencing.