Fig. 4.

Example of guide matching by considering up to one mismatch and up to one RNA/DNA bulge. The search starts by visiting the left-most path of the tree, which represents the candidate sequence CT2. After the second mismatch (T versus C), the algorithm verifies that no bulges are allowed and stops the visit over the CT2 path. Back to the previous branch G, which in the example represents the first mismatch, it continues over the CT1 path. It verifies that the second mismatch cannot be considered as a DNA bulge but it can be considered as RNA bulge. It concludes the CT1 path visit to the leaf, thus identifying CT1 as an off-target with one mismatch and one RNA bulge. Similarly, the algorithm jumps back to the previous branch A and reaches the CT3 leaf, thus identifying CT3 as an off-target with one mismatch and one DNA bulge