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Table 1 SNPs markers, primers and probes used in RT-PCR

From: A single-nucleotide-polymorphism real-time PCR assay for genotyping of Mycobacterium tuberculosis complex in peri-urban Kampala

SNP Name Primer and probes Tm-1 Tm-2 Primer annealing temperature Fragment length (bp)
Rv004c-0619n (MTB L4-U) Forward:5-ATT GCT CGA TGG CAG A-3 a62 °C 68 °C 57 °C 160
Reverse: 5-AAA CCA GGT ACT TGT CGG-3
LC Red 640-TGA TGA CGG AAA GCC GT GAA A-Pho-3
5-GTT TTC GCG GTA GGT GCC CTC GAT G-Fluo-3
Rv2962c-0711 s (MTB L4-NU) Forward: 5-GAA CGC CCT TTG CTC TTC-3 56 °C a64 °C 51 °C 181
Reverse:5-CAA GGT ACT CGT GGT TGG-3
LC Red 610- CCC GAG CTG ATG CCC ACC T-Pho-3
5-CAC ACC CTG TAT GC GAC G-Fluo-3
Rv0129c-0472n (MTB L3) Forward:5-CGA CTG GTA TCA GCC CTC-3 a58 °C 68 °C 53 ° C 191
Reverse:5-GGA ACT GCT GCG GGT AGT A-3
LC Red 610-GAC ACG CC TTG TTG GCC-Pho-3
5-CGC CGC GTT GCC TGT CG –Fluo-3
  1. Shaded and bold nucleotide denotes SNP position relative to H37Rv MTB genotype
  2. aDenotes MTB lineage specific melting temperature (Tm)