Figure 6

Phylogenetic nucleotide conservation plots for selected alphavirus within-species full-genome sequence alignments. The nucleotide conservation in a 51-nt sliding window is expressed as a p-value plot, giving the probability that the conservation in the window would be as great or greater than that observed, if a given null model (CDS annotation) was true. Here the null model was set to 'non-coding' in order to give a straightforward nucleotide conservation plot. Plots are given for alignments of (1a) 7 Sindbis virus (SINV) sequences, (2a) 9 Eastern equine encephalitis virus (EEEV) sequences, (3a) 22 Venezuelan equine encephalitis virus (VEEV) sequences, and (4a) 19 Chikungunya virus (CHIKV) sequences. Panels (1-4b) show the phylogenetically summed sequence divergence (mean number of base variations per nucleotide column) for the sequences that contribute to the statistics at each position in the alignment. In any particular column, some sequences may be omitted from the statistical calculations due to alignment gaps. Statistics in regions with lower summed divergence (i.e. partially gapped regions) have a lower signal-to-noise ratio and/or may be omitted from the plot. Panels (1-4c) show the location of the non-structural (CDS1; green) and structural (CDS2; green) CDSs, the non-coding regions (black), and the location of the overlapping -1 frame ORF (red), in the GenBank RefSeqs NC_001547 (SINV), NC_003899 (EEEV), NC_001449 (VEEV) and NC_004162 (CHIKV). The location of the U UUU UUA motif coincides with the 5' end of this ORF. Plots were produced with the CDS-plotcon webserver (Firth, unpublished).