Nucleotide-by-nucleotide plot. Example output nucleotide-by-nucleotide plot for the 'Test input query CDSs' option. Luteovirus, six sequences [GenBank:NC_002160, GenBank:NC_003056, GenBank:NC_003369, GenBank:NC_003680, GenBank:NC_004666, GenBank:NC_004750], with NC_002160 as the reference sequence. NC_002160 has six annotated CDSs. CDS3 was used as the query CDS and the remaining five CDSs were taken as the known CDSs. The first panel displays the raw log(LR) statistics at each alignment position. There is a separate track for each reference – non-reference sequence pair (labelled at the right, together with the pairwise divergences). Gaps, and stop codons in each of the null and alternate model CDSs, for each sequence, are marked on the appropriate tracks. The second panel displays the ∑tree log (LR) statistic at each alignment position. The third and fourth panels display sliding window means of the statistics in the first and second panels, respectively. The fifth panel shows the locations of the null and alternate model CDSs. The sixth panel shows the summed mean sequence divergence (mutations per nt) for the sequence pairs that contribute to the ∑tree log (LR) statistic at each alignment position. This is a measure of the information available at each alignment position (e.g. partially gapped regions have lower summed mean sequence divergence). (See website for more details.) The predominantly positive values in the fourth panel show that CDS3 is functionally constrained over the majority of its length.