So far, DotKnot derived a set of regular stems, interrupted stems and multiloops in a heuristic fashion from the probability dot plot (Figure 2 ). There is no guarantee to find the structure element with local minimum free energy for a given sequence stretch. However, dictionaries D L s and D M s will contain structures with free energy value close or equal to the local minimum free energy. These elements will be of great benefit for the elimination of false positive pseudoknots.