Table 1 List and characteristics of primers designed in this study
Primer type | Primer name | Sequence 5′–3’ | Cluster specificitya | Melting temperature (°C) | Amplicon size (bp) |
|---|---|---|---|---|---|
External primers | Ana-Ext-F2 | TCTGMAAGCCATTATCAYAG | I, II, III, IV | 58 | 1609 |
Ana-Ext-R1 | TGCTTCACGAARCGCATA | ||||
Internal primers | Ana-Int-F1 | CATCKAGCAKGTRTTGAAGG | I, II, III, IV | 58 | 731–737 |
Ana-Int-R3 | TGTARAGGRGCARMACC | ||||
Sequencing primers | Ana-Int-F2 | GCGAGTGTGCAGASKCACTA | I, II, III, IV | 58 | 328 |
Ana-Int-R3 | TGTARAGGRGCARMACC | ||||
Internal cluster-specific primers | Ana-F-Cl2 | GTGACAATTTTGRGACATTAC | II | 60 | 1512 |
Ana-R-Cl2 | TCCTAGTCCGCGAGCTAAGT | ||||
Ana-F-Cl3 | GTGAGAATTTTGAGTCATTG | III | 60 | 1512 | |
Ana-R-Cl3 | TCCGAACCCGRGCGCTCAT | ||||
Ana-F-Cl4b | GAGGTATCTAGGAAGTGCC | IV | 61 | 1286 | |
Ana-R-Cl4 | TCAAGTTCCGTGCGGTTAGG |