Every clade at the chosen rank is compared with its whole domain. At each position, the clade's distribution over A/U/G/C is measured against the domain's distribution by Jensen–Shannon divergence (JSD, in bits): 0 means the clade looks exactly like the domain there, and 1 means they share no state at all. For several positions the per-position values are averaged, so a high score means the clade is unusual across the region, not at a single site.
Counts use one sequence per species: the top rRNA hit in its representative genome, or every rRNA copy in it with All hits under Advanced settings. Only A, U, G and C are counted, the same states as Shannon entropy: deletions, ambiguity codes, missing sequence (~) and calls below the PP threshold are left out. A clade with no A/U/G/C at a position has no score there.
The PTC and decoding-center regions are 3D shells from the E. coli 70S structure 7K00. They include every nucleotide with any heavy atom within the radius of any heavy atom of the center, as in "Find positions near…" on the Positions page.
