Each selection is tallied one sequence per species: the top rRNA hit in its representative genome (or every rRNA copy in it, under Advanced settings). Positions are matched by the number you type, translated into each side's own alignment, so an archaeal clade lines up with a bacterial one through E. coli or H. marismortui numbering.
Divergence is the Jensen–Shannon divergence between the two sides' A/U/G/C distributions at each position (deletions and ambiguity codes are not counted, as for entropy): 0 means identical, 1 means no base in common. A conserved difference is a position where each side is at least 90% one state (adjustable under Advanced settings) and the two states differ.
Position by position
On the secondary structure
R2DT diagram (E. coli or H. marismortui), shaded by divergence — click to show
