Figure 2

Pair probability computation. Computation of pair probabilities. A single base pair (i, j) either lies within another base pair or not (First term on top). Base pair (i, j) and the enclosing base pair (k, l) either form an interior loop (rightmost term on top), or a multi loop. Based on the location of the other components within the multi loop, three possibilities for the closing of a multi loop exist. Here, the contributions collected in auxiliary array are colored green, in red.