TABLE 5.
Summary of allelic subtypes and polymorphisms in actA, inlA, prs, sigB, recA, hly-mpl, and plcA-hly
| Gene or intergenic region | Full sequence
|
Optimal window with PROSEQ (highest no. of polymorphisms)
|
Optimal window with WINDOWMIN (best descrimination)
|
||||||
|---|---|---|---|---|---|---|---|---|---|
| Length (bp) | No. of allelic subtypesa | No. of polymorphic sitesb | Location (nt)c | No. of allelic subtypesa | No. of polymorphic sitesb | Location (nt)c | No. of allelic subtypesa | No. of polymorphic sitesb | |
| actA | 1,929 | 15 (14) | 276 (14.3) | 1,330-1,929 | 13 (9) | 104 (17.3) | 316-915 | 15 (14) | 86 (14.3) |
| inlA | 2,235 | 14 (14) | 186 (8.3) | 964-1,563 | 13 (11) | 66 (11.0) | 1,090-1,690 | 13 (13) | 65 (10.8) |
| sigB | 780 | 10 (10) | 79 (10.1) | 13-612 | 9 (8) | 74 (12.3) | 150-749 | 10 (10) | 58 (9.7) |
| recA | 1,047 | 8 (7) | 107 (10.2) | 264-863 | 8 (7) | 67 (11.1) | 238-837 | 8 (7) | 66 (11.0) |
| prs | 957 | 10 (7) | 47 (4.9) | 316-915 | 10 (7) | 42 (7.0) | 313-912 | 10 (7) | 41 (6.8) |
| hly-mpl | 335 | 8 (7) | 28 (8.4) | NAd | NA | NA | NA | NA | NA |
| plcA-hly | 242 | 12 (8) | 26 (10.7) | NA | NA | NA | NA | NA | NA |
a
Total number of allelic subtypes distinguished within the specified region by a difference of 1 nt. Numbers in parentheses denote the total number of alleles distinguished by using the criteria of 2 nt differences.
b
Number of polymorphic sites within the specified region. Values in parentheses are the percentages of polymorphic sites out of all nucleotides for that specific region.
c
Locations are nucleotide (nt) positions (nucleotide 1 is the first nucleotide of the coding sequence).
d
NA, not available.