Note on redrawing the 'Nucleotide-by-nucleotide' plots:

In the current 'Nucleotide-by-nucleotide' and zoomed-in 'Nucleotide-by-nucleotide' plots, the running mean of the log likelihood scores summed over the input phylogenetic tree (i.e. the input pairs file) skips regions that are gapped (or have ambiguous nt codes) in any of the sequences in the pairs file. On the 'Redraw plots' page, you will also have the option to extend this track into gapped regions, provided the summed divergence of the contributing sequence pairs in the region is greater than some user-defined threshold value (details).