RNA structure forms through complementary base pairing, resulting in stabilizing stems and destabilizing loop regions. The basic building blocks for a pseudoknot are two crossing stems. We use the probability dot plot derived from the partition function as a guide for finding such building blocks. Given an RNA sequence, the partition function Q is defined as the weighted sum over the set of all possible secondary structures S, i.e. QðTÞ ¼ P s2S e ÀÁG s =RT where R is the universal gas constant and T the temperature. Once the partition function is known, probabilities for base pairs and structure elements can be calculated. The software RNAfold returns the probability dot plot representing both base pair probabilities and stack probabilities (11) . The stack probability P ij for a base pair ði, jÞ is defined as the probability that pair ði, jÞ and the subsequent pair ði þ 1, j À 1Þ are formed simultaneously (49) .