Figure 1

Possible results of treating gaps as bases. The consensus structure of the alignment in the middle is predicted once with gaps treated as if they were bases (old), and once by removing them before computing the energies (new). The predicted structures (highlighted in red) are shown to the left. As can be seen in 1, sequence 1 can form a perfect hairpin. In 2, the sterically impossible hairpin for the other two sequences is shown. Two of the three sequences cannot form the predicted structure. On the other hand, the new version of RNAalifold predicts a stem that has a bulge (3), but only in one sequence, the other two sequences can form the perfect stem shown in 4.