Table 1.
Characteristics of variable number of tandem repeats (VNTR) and Hunter–Gaston Discriminatory Index (HGDI) scores for the 16 loci of the multilocus variable number of tandem repeat analyses (MLVA) scheme.
| Locus | Position in Strain 85-10 1 |
Dominant Repeat Type | Other Repeat Types 2 | No. of Alleles 3 | Allelic Range 4 | HGDI Score 5 |
|---|---|---|---|---|---|---|
| Xe_02 | 215122..215170 | TCCCCAT | - | 4 | 4–7 # | 0.286 |
| Xe_03 | 487069..487152 | TTTGGC | TCTGGC * TTCGGC TTTGTC * | 3 | 12–14 # | 0.190 |
| Xe_04 | 624229..624277 | CGATTCC | - | 8 | 5–12# | 0.764 |
| Xe_06 | 857148..857196 | AACAGCC | - | 3 | 6–8 # | 0.317 |
| Xe_07 | 924719..924767 | CCGGGTC | CCGGGCC * | 4 | 4–7 # | 0.211 |
| Xe_09 | 1053822..1053863 | GGGATTT | GGGATTC GGGAATC | 7 | 6–18 | 0.803 |
| Xe_10 | 1222069..1222110 | AGGCGGT | AGGCGGC * | 6 | 5–12 | 0.575 |
| Xe_11 | 1504314..1504418 | CCGATTC | CCTAATC CCCAATC | 5 (6) | 11–16 | 0.455 (0.480) |
| Xe_14 | 2268785..2268850 | ACAGCG | - | 6 | 6–11 # | 0.738 |
| Xe_15 | 3198440..3198527 | GCAGACAG | GCAGGCAG GCAGAGAT * | 5 (8) | 6–10 # | 0.688 (0.779) |
| Xe_16 | 3505639..3505687 | AATGGGG | AATCGGG * | 3 | 5–9 | 0.263 |
| Xe_17 | 3514941..3514994 | TCGGCA | TCGGCG * | 5 | 9–14 | 0.437 |
| Xe_22 | 4396287..4396335 | TTGGCGG | TTGGCGC * | 3 | 5–10 | 0.190 |
| Xe_29 | 4211581..4211608 | CGATTCC | - | 2 | 4–5 # | 0.315 |
| Xe_34 | 458055..458096 | GATTCGG | GAATCGG GAATTCG * GAATCCG * | 4 (5) | 5–16 | 0.190 (0.192) |
| Xe_49 | 4410313..4410342 | TGGCCG | - | 4 | 5–8# | 0.575 |
| MLVA-16 | 36 haplotypes | 0.944 |
1 Genomic coordinates in GenBank accession number AM039952. 2 Alternative repeat types that are only found once per repeat array at its end are indicated by a *. 3 Number of alleles from the VNTR-rep dataset. Numbers in brackets take resolved cases of homoplasy, i.e., different sequence types, into account (from the VNTR-seq dataset). 4 Allelic ranges that contain all alleles are indicated by a #. 5 Hunter–Gaston discriminatory index (HGDI) scores of individual VNTR loci and of the 16-loci VNTR analysis, MLVA-16. Numbers in brackets correspond to the VNTR-seq dataset.