Table 5 Genetic diversity observed at each locus. Amplicon lengths with external or internal primers were obtained with Primer-BLAST (NCBI), apart from the PCR products with recG external primers, and polA external and internal primers, which were estimated on agarose gels
typA | ctrA | msp4 | pleD | recG | polA | |
|---|---|---|---|---|---|---|
No. of complete sequences | 40 | 39 | 36 | 36 | 35 | 37 |
No. of sequences without ambiguities | 31 | 39 | 28 | 33 | 33 | 31 |
No. of sequences with ambiguities (%) | 9 (22.5) | 0 (0) | 8 (22.2) | 3 (8.3) | 2 (5.7) | 6 (16.2) |
Amplicon length with external primers (bp) | 1455 | 1453 | 558 | 1102 | 515 | ~490 |
Amplicon length with internal primers (bp) | 550 | 574 | 471 | na | ~480 | ~460 |
Alignment length (bp) | 385 | 317 | 337 | 597 | 309 | 331 |
No. of polymorphic sites | 5 | 6 | 11 | 20 | 6 | 7 |
Proportion of polymorphic sites | 1.30 | 1.89 | 3.26 | 3.35 | 1.94 | 2.11 |
No. of alleles at each locus | 7 | 6 | 7 | 3 | 8 | 8 |