Figure 3

Cases of unpaired interval [ i , j ] within a loop enclosed by p · q while [ k , l ] remains unpaired. In case (x), interval [k, l] is outside of substructure [p, q], but its effect on the probability of base pair p·q should be considered. For the other cases substructure [p, q] contains interval [k, l]. Base pair p·q can close different loop types (a) hairpin, (b-b"') internal loop, and (c-e) multiloop. Cases (b-b"') refer to the four possibilities for the position of interior base pair k 1·k 2 and unpaired intervals [k, l] and [i, j]. If base pair p·q closes a multiloop, unpaired intervals [k, l] and [i, j] can have three different conformations (c-e).