How this works

Your sequence is checked and aligned with Infernal's cmalign to the bacterial and the archaeal Rfam model for its rRNA, as on the Your sequence page. Every clade at the chosen rank is then tallied in its own domain's model columns, one sequence per species (the top rRNA hit in its representative genome), or with All hits under Advanced settings, every rRNA copy in each species' genome, so a species is scored on all its operons.

At each position, q is the share of the clade's species (at species rank, of its rRNA copies) that have your base there (only A, U, G and C are counted, as for entropy: deletions, ambiguity codes, missing sequence and bases below the PP cutoff are left out). A clade's identity is q averaged over the positions where it has data: the identity your sequence would have to a typical member. JSD is the clade deviation page's measure with your sequence in place of the domain; with one sequence it is a function of q alone, 0 at q = 1 and 1 at q = 0.

Positions where your own sequence has a deletion, an ambiguous base or a base below the PP cutoff are not scored. A small clade can top the list on one genome; the species count and the lineage column help tell a real relative from a contaminated assembly.