They define base pairing rules, and by their physical nature also the strengths of the base pair interactions.
All quantities presented here depend strongly on the particular alphabet chosen.
RNA secondary structues are partitioned into structural elements, such as stacks, loops, joints and free ends. The results obtained from the statistics of random ensembles are compared with the data derived from natural RNA molecules with similar base frequencies. Secondary structures are represented as trees. Two different, but formally equivalent tree representations are introduced and compared in actual computations of RNA structures. Nearly the entire range of tree distances is covered with considerable probability already at small Hamming distances from a typical sequence.