The relation between k-mer coverage C k and standard (nucleotide-wise) coverage C is C k = C* L- k-1)/ L.
Subsequently, the resulting probabilities are used to derive two nucleotide-wise pseudo-energy weights, one for contexts where the nucleotide is considerd unpaired, and the other for situations where it is involved in a base pair.
In addition to reducing statistical power to detect CpG effects, this model property precludes formal estimation of nucleotide position-wise statistics (e.g., LRT p ).
To assess if FST values significantly differed from zero, permutation tests were performed based on the KST* estimator of pair wise nucleotide differences [64].
On the contrary, the Listeria species have diverged substantially in the primary sequence of their core genes with an average pair-wise nucleotide identity of 84.8%, compared to average pair-wise nucleotide identities within species of 99.2% in F. tularensis [ 66] and 96.7% in E. coli [ 67].
The removal of this extremely divergent transcript resulted in a maximum pair-wise nucleotide divergence of 31.0% within KUNs and a maximum pair-wise amino acid divergence of 68.0%, reflecting the diversity of this toxin class, especially in comparison to LCNs.
The percentage-wise nucleotide composition of S. commerson has been computed and are indicated in Table 2 and the same also plotted in Fig. 5.
The core regions were sorted into clusters according to their pair-wise nucleotide sequence identity using the program GROUPER (unpublished software, 2004; Armstrong, JS and Gibbs, AJ) with a clustering cut off point of 85% identity.
The pair-wise nucleotide sequence identity matrix showed 99-100% sequence identity among the isolates.
For analysis of nucleotide substitutions, pair-wise alignments were obtained using ClusterW.
The maximum number of pair-wise nucleotide differences was ten (p = 0.022, total length 450 bp).
