Notes on the zoomed in 'Nucleotide-by-nucleotide' plot:

This is a plot of the likelihood ratio, summed over the input phylogenetic tree (details), at single nucleotide resolution. The five panels show the following information:

1. This panel displays the raw likelihood ratio scores, summed over the phylogenetic tree, at each column position in the input alignment.
   
   
2. This panel displays the running mean (i.e. sliding window mean) of the likelihood ratio scores. The sliding window width is annotated on the plot, and can be changed via the 'Redraw plot' link.
   
   
3. This panel shows the input Query, or alternate model, CDS(s) (red bars), the input Known, or null model, CDS(s) (blue bars), and the reference sequence nucleotide sequence.
   
   
4. This panel shows the phylogenetic sum of sequence divergences (mean number of mutations per nucleotide) for the sequence pairs that contribute to the likelihood ratio sum at each position in the alignment. In any particular column, some sequences may be omitted from the likelihood ratio calculations due to gaps or stop to non-stop transitions. Statistics in regions with lower summed divergence (i.e. partially gapped regions) have a lower signal-to-noise ratio.
   
   
5. This panel shows the alignment and reference sequence coordinates of each position.
   
   

Notes:

• For panel 2, any columns with gaps (or ambiguous nt codes) in any sequence in the input list of sequence pairs are omitted. Such columns are omitted before taking the running mean. Thus where gaps occur a, for example, 21 nt window includes a total of 21 columns taken from either side of the gap but none from within the gap. On the 'Redraw plots' page, you may choose to extend the plot into partially gapped regions, provided the summed divergence of the contributing sequence pairs in the region is greater than some user-defined threshold value (details).