By MIRU-VNTR 31 (45%) of the 69 patients with Beijing strains were found in altogether 7 clusters (2 11 per cluster), yielding 45 different patterns (Fig. 2).
Primers were designed to flank the entire RAD cluster, yielding products of 160-391 bp.
If the overlap conditions are met, they are clustered, yielding only one prediction for all overlapping Sox matches named "Sox".
Clusters yielding large Ka/ Ks ratios were checked manually to eliminate spurious results due to poor alignment.
Clusters yielding CM search hits with an E-value of E<10−5 were considered as known, others as novel.
Three households were excluded from the final sample because their inclusion would have resulted in oversampling of the cluster, yielding a final sample of 142 households for analysis.
For the hairpin types we defined a PWM for each cluster, yielding 2 PWMs each, of lengths 19, 20 and 21.
In addition, our data proved that the nettle associated phenotypes form a secY cluster, yielding the RFLP pattern SecY 1 after digestion with Hinf1 (Fig. 5).
For instance, of the 62 clusters yielding significant Ka/ Ks results among ingroup taxa (table 8), only 22 were included in the data set used for MK tests.
These were measured to determine the number of localizations of each color within the clusters, yielding a value for the degree of crosstalk.
