TABLE 2.
Percentage mismatches to the 23S rRNA gene dataset at each position for previously described universal primersa
| Primer (reference) | Nucleotide and % mismatch | ||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ITSReub (7) | G | C | C | A | A | - | G | G | C | A | T | C | C | A | C | C | |||||||
| 7.9 | 6.2 | 2.9 | 16.4 | 10.8 | 0.4 | 2.9 | 4.2 | 5.8 | 2.1 | 0.5 | 10.6 | 2.8 | 12.8 | 5.3 | 4.0 | ||||||||
| 66r (19) | C | A | C | G | T | C | T | T | T | C | A | T | C | G | S | C | T | ||||||
| 24.4 | 17.6 | 3.1 | 0.9 | 7.7 | 0.1 | 94.4 | 0.0 | 2.6 | 0.4 | 17.0 | 0.4 | 2.9 | 4.2 | 6.2 | 6.0 | 1.3 | |||||||
| fprimer6 (3a) | G | C | G | A | T | T | T | C | Y | G | A | A | Y | G | G | G | R | A | A | A | C | C | C |
| 50.6 | 80.3 | 7.0 | 11.7 | 0.1 | 46.9 | 5.1 | 0.2 | 0.1 | 2.4 | 0.2 | 0.5 | 0.3 | 2.4 | 2.1 | 2.0 | 0.9 | 39.3 | 0.5 | 1.1 | 2.2 | 2.4 | 7.5 | |
| 130f (9b) | C | C | G | A | A | T | G | G | G | G | V | A | A | G* | G* | G* | |||||||
| 0.3 | 8.4 | 2.4 | 0.2 | 0.5 | 0.6 | 2.4 | 2.1 | 2.0 | 9.0 | 4.0 | 0.5 | 1.1 | 100 | 99.9 | 100 | ||||||||
| 130r (9b) | C* | C* | T | T | G | C | C | C | C | A | T | T | C | G | G | ||||||||
| 99.9 | 100 | 1.1 | 0.5 | 84.5 | 9.0 | 2.0 | 2.1 | 2.4 | 0.6 | 0.5 | 0.2 | 2.4 | 8.4 | 0.3 | |||||||||
| 11A (20a) | G | G | A | A | C | T | G | A | A | A | C | A | T | C | T | A | A | G | T | A | |||
| 47.0 | 0.2 | 0.0 | 0.0 | 17.1 | 0.3 | 0.3 | 0.0 | 0.6 | 1.6 | 4.7 | 0.3 | 0.1 | 0.3 | 0.0 | 34.0 | 0.1 | 2.3 | 0.2 | 0.1 | ||||
| 242r (9b) | K | T | T | C | G | C | - | T | C | G | C | C | R | C | T | A | C | ||||||
| 2.9 | 0.2 | 0.6 | 0.8 | 0.5 | 1.7 | 0.6 | 0.0 | 0.0 | 2.2 | 5.5 | 0.0 | 0.3 | 0.2 | 0.3 | 0.0 | 0.1 | |||||||
| 256f (9b) | A | G | T | A | G | Y | G | G | C | G | A | - | G | C | G | A | A | ||||||
| 3.1 | 0.1 | 0.0 | 0.3 | 0.2 | 0.3 | 0.0 | 5.5 | 2.2 | 0.0 | 0.0 | 0.6 | 1.7 | 0.5 | 0.8 | 0.6 | 0.2 | |||||||
| 23ar (20a) | C | G | G | T | A | C | T | - | G | G | T | T | C | A | C | T | A | T | C | G | G | ||
| 0.1 | 5.2 | 0.6 | 0.0 | 0.0 | 0.2 | 0.1 | 0.4 | 38.4 | 10.6 | 0.2 | 13.0 | 0.2 | 17.2 | 0.1 | 0.2 | 0.0 | 0.1 | 1.3 | 0.0 | 2.4 | |||
| rprimer10 (3) | T | T | C | G | C | C | T | T | T | C | C | C | - | T | C | A | C | G | G | T | A | C | T |
| 0.5 | 0.3 | 0.9 | 66.5 | 3.1 | 0.1 | 4.4 | 0.1 | 0.0 | 1.3 | 0.7 | 5.5 | 0.5 | 0.2 | 1.3 | 3.7 | 0.1 | 5.2 | 0.6 | 0.0 | 0.0 | 0.2 | 0.1 | |
| 473f (10) | A | G | T | A | C | C | G | Y | G | A | - | G | G | G | A | A | A | G | |||||
| 0.1 | 0.2 | 0.0 | 0.0 | 0.6 | 5.2 | 0.1 | 0.1 | 1.3 | 0.2 | 0.5 | 5.5 | 0.7 | 1.3 | 0.0 | 0.1 | 4.4 | 0.1 | ||||||
| 559r (9b) | C | A | T | T | M | T | A | C | A | A | A | A | G | G | Y | A | C | G | C | ||||
| 0.3 | 2.5 | 0.1 | 6.2 | 0.3 | 0.7 | 25.6 | 0.2 | 0.3 | 0.1 | 4.9 | 0.3 | 4.3 | 0.1 | 0.3 | 0.1 | 6.7 | 6.6 | 4.9 | |||||
| 559r (21a) | C | A | T | T | M | T | R | C | A | A | A | A | G | G | Y | A | C | G | C | ||||
| 0.3 | 2.5 | 0.1 | 6.2 | 0.3 | 0.7 | 11.4 | 0.2 | 0.3 | 0.1 | 4.9 | 0.3 | 4.3 | 0.1 | 0.3 | 0.1 | 6.7 | 6.6 | 4.9 | |||||
| 803r (21a) | T | T | C | G | G | R | G | A | G | A | A | C | S | A | G | M | T | A | |||||
| 0.3 | 0.5 | 0.5 | 0.2 | 45.0 | 2.8 | 0.8 | 0.5 | 15.8 | 3.7 | 0.3 | 0.2 | 4.9 | 0.3 | 0.2 | 0.4 | 0.1 | 0.5 | ||||||
| 820f (20a) | T | A | G | C | T | G | G | T | T | C | T | C | Y | Y | C | G | A | A | |||||
| 0.5 | 0.1 | 10.5 | 0.2 | 0.3 | 9.5 | 0.2 | 0.3 | 3.7 | 15.8 | 0.5 | 0.8 | 2.8 | 26.7 | 0.2 | 0.5 | 0.5 | 0.3 | ||||||
| 975r (10) | T | C | T | - | G | G | G | Y | T | G | T | T | Y | C | C | C | - | T | |||||
| 0.2 | 1.6 | 6.3 | 0.3 | 0.8 | 0.2 | 2.2 | 0.1 | 0.4 | 21.0 | 0.5 | 0.5 | 1.1 | 2.3 | 0.2 | 0.4 | 0.4 | 0.7 | ||||||
| 43a (20a) | G | G | A | T | G | T | T | G | G | C | T | T | A | G | A | A | G | C | A | G | |||
| 2.0 | 4.5 | 0.4 | 55.2 | 0.2 | 0.0 | 2.4 | 5.2 | 0.0 | 0.1 | 1.6 | 2.2 | 2.7 | 0.2 | 0.0 | 2.6 | 0.0 | 0.0 | 0.0 | 0.1 | ||||
| 1075f (10) | G | T | T | G | G | C | T | T | R | G | A | R | G | C | A | G | C | ||||||
| 0.2 | 0.0 | 2.4 | 5.2 | 0.0 | 0.1 | 1.6 | 2.2 | 0.0 | 0.2 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.1 | 0.3 | |||||||
| 1091r (9b) | R | G | T | G | A | G | C | T | R | T | T | A | C | G | C | ||||||||
| 0.0 | 1.9 | 0.0 | 1.1 | 0.3 | 0.2 | 0.1 | 0.3 | 0.0 | 0.1 | 0.0 | 0.1 | 0.2 | 0.2 | 0.1 | |||||||||
| 1104f (9b) | W | G | C | G | T | A | A | Y | A | G | C | T | C | A | C | ||||||||
| 0.0 | 0.0 | 0.2 | 0.2 | 0.1 | 0.0 | 0.1 | 0.0 | 0.3 | 0.1 | 0.2 | 0.3 | 1.1 | 0.0 | 1.9 | |||||||||
| 1200f (10) | G | G | T | A | G | R | R | G | A | - | G | C | G | T | T | - | C | ||||||
| 0.6 | 2.3 | 0.6 | 0.6 | 0.3 | 25.8 | 2.6 | 1.0 | 0.8 | 0.4 | 16.7 | 1.5 | 4.6 | 0.8 | 10.2 | 0.3 | 15.0 | |||||||
| 1363f (10) | G | A | G | G | C | C | G | A | N | - | - | A | R | G | C | G | - | T | A | ||||
| 6.3 | 2.4 | 4.5 | 8.6 | 22.4 | 24.3 | 2.9 | 1.9 | 0.0 | 1.1 | 0.4 | 5.4 | 11.4 | 22.9 | 11.4 | 0.5 | 0.4 | 2.9 | 1.8 | |||||
| 53a (20a) | G | G | A | C | - | A | A | C | A | G | G | T | T | A | A | - | T | A | T | T | C | C | |
| 0.0 | 0.6 | 53.3 | 80.0 | 3.8 | 0.2 | 29.9 | 23.9 | 28.6 | 3.0 | 7.7 | 0.9 | 11.2 | 26.4 | 0.1 | 2.8 | 8.6 | 0.5 | 1.3 | 0.1 | 8.4 | 3.3 | ||
| 1623f (9b) | A | A | A | C | C | G | W | C | A | C | A | G | G | T | R | G | |||||||
| 3.1 | 0.0 | 1.7 | 0.1 | 5.5 | 3.4 | 0.1 | 0.1 | 3.0 | 0.1 | 2.5 | 4.9 | 0.0 | 0.4 | 0.6 | 5.7 | ||||||||
| 62ar (20a) | G | G | G | G | C | C | A | T | T | T | T | G | C | C | G | A | G | T | T | C | |||
| 10.8 | 8.4 | 54.9 | 42.1 | 55.9 | 27.8 | 0.2 | 26.6 | 2.9 | 0.1 | 0.0 | 0.3 | 0.2 | 8.7 | 34.4 | 0.0 | 0.2 | 0.1 | 0.0 | 0.2 | ||||
| 1685r (21a) | C | C | T | T | M | T | C | S | C | - | G | A | A | S | T | T | A | C | G | G | |||
| 8.5 | 6.6 | 0.0 | 0.0 | 0.9 | 0.1 | 21.6 | 0.1 | 2.7 | 0.9 | 4.9 | 0.0 | 0.4 | 0.1 | 5.6 | 0.1 | 0.1 | 0.0 | 10.8 | 8.4 | ||||
| 69ar (20a) | C | T | T | A | G | G | A | C | C | G | T | T | A | T | A | G | T | T | A | C | |||
| 0.3 | 0.3 | 0.3 | 1.5 | 0.8 | 2.0 | 0.3 | 5.8 | 5.9 | 0.7 | 0.1 | 3.0 | 0.0 | 0.8 | 0.6 | 0.5 | 0.3 | 0.1 | 0.0 | 0.2 | ||||
| 1930r (9b) | C | G | A | C | A | A | G | G | A | A | - | T | T | T | C | G | C | T | A | C | |||
| 3.7 | 0.0 | 0.7 | 0.5 | 0.9 | 0.1 | 0.4 | 0.3 | 1.1 | 0.0 | 0.4 | 1.1 | 0.4 | 0.2 | 0.3 | 0.3 | 0.1 | 0.1 | 0.1 | 0.1 | ||||
| 2069f (9b) | G | A | C | G | Y* | A | A | A | G | A | C | C | C | C | R | T | G | ||||||
| 0.1 | 0.0 | 0.2 | 3.1 | 99.8 | 0.5 | 0.5 | 0.3 | 0.1 | 0.1 | 0.3 | 0.0 | 0.0 | 3.5 | 0.0 | 5.8 | 1.6 | |||||||
| 2241r (9b) | A | C | C | G | C | C | C | C | A | G | T | H | A | A | A | C | T | ||||||
| 0.4 | 0.4 | 0.7 | 2.6 | 0.4 | 0.4 | 0.1 | 0.0 | 0.0 | 0.3 | 0.9 | 1.0 | 0.1 | 0.1 | 0.2 | 0.2 | 0.6 | |||||||
| 2436f (10) | T | C | - | G | C | T | C | A | A | C | G | G | A | T | A | A | A | A | G | ||||
| 0.9 | 2.7 | 0.3 | 3.0 | 1.5 | 0.3 | 4.1 | 0.3 | 3.0 | 6.1 | 0.7 | 3.5 | 1.9 | 0.8 | 0.4 | 0.2 | 0.0 | 0.3 | 0.2 | |||||
| 2498r (9b) | G | A | G | Y | C | G | A | C | A | T | C | G | A | G | G | ||||||||
| 0.3 | 0.1 | 0.3 | 0.0 | 0.3 | 0.2 | 0.2 | 0.1 | 0.1 | 0.1 | 0.2 | 0.2 | 0.2 | 0.3 | 0.2 | |||||||||
| 93ar (20a) | C | G | A | C | G | - | T | T | C | T | G | A | A | C | C | C | A | G | C | T | C | ||
| 0.2 | 0.2 | 0.1 | 0.2 | 0.2 | 0.2 | 2.0 | 0.1 | 10.7 | 0.2 | 38.6 | 0.2 | 0.2 | 0.2 | 0.2 | 0.1 | 0.1 | 2.9 | 0.2 | 0.2 | 0.2 | |||
| 2603f (21a) | A | R | A | M | - | C | G | T | C | G | T | G | A | G | A | C | A | G | |||||
| 0.2 | 0.1 | 0.1 | 0.1 | 0.2 | 0.2 | 0.2 | 0.1 | 0.2 | 0.2 | 2.0 | 0.0 | 0.0 | 0.1 | 0.1 | 0.2 | 0.2 | 0.2 | ||||||
| 2669f (9b) | A | G | T | A | C | G | A | G | - | A | G | G | A | C | C | G | G | ||||||
| 0.5 | 0.2 | 0.1 | 0.2 | 0.3 | 0.2 | 0.2 | 0.6 | 0.3 | 0.1 | 0.1 | 0.1 | 0.1 | 0.6 | 0.3 | 3.5 | 8.0 | |||||||
| 2744r (10) | C | T | T | - | A | G | A | T | G | C | Y | T | T | C | A | G | C | ||||||
| 2.2 | 0.1 | 0.2 | 0.4 | 0.1 | 5.7 | 0.1 | 0.2 | 0.2 | 0.4 | 1.5 | 0.1 | 0.0 | 0.2 | 0.2 | 2.3 | 3.2 | |||||||
| 2747r (9b) | G | Y | T | T | - | A | G | A | T | G | C | Y | T | T | C | ||||||||
| 17.4 | 0.0 | 0.1 | 0.2 | 0.4 | 0.1 | 5.7 | 0.1 | 0.2 | 0.2 | 0.4 | 1.5 | 0.1 | 0.0 | 0.2 | |||||||||
| 97ar (20a) | C | C | C | G | C | T | T | - | A | G | A | T | G | C | T | T | T | C | A | G | C | ||
| 2.3 | 35.9 | 19.0 | 17.4 | 2.2 | 0.1 | 0.2 | 0.4 | 0.1 | 5.7 | 0.1 | 0.2 | 0.2 | 0.4 | 5.6 | 0.1 | 0.0 | 0.2 | 0.2 | 2.3 | 3.2 | |||
| 2758f (9b) | Y | T | G | A | A | R | G | C | A | T | C | T | - | A | A | ||||||||
| 0.0 | 0.2 | 0.2 | 0.0 | 0.1 | 1.5 | 0.4 | 0.2 | 0.2 | 0.1 | 5.7 | 0.1 | 0.4 | 0.2 | 0.1 | |||||||||
a
Primers follow the naming convention of the original publication but are ordered according to their position along the 23S rRNA sequence. Positions shown in boldface indicate that >5% of sequences do not match the primer at that position. Degenerate positions in the sequences were assumed to equally contribute to all possible nucleotides. Hyphens indicate insertions in more than two sequences. *, probable typographic error in the published primer sequence.