Fig. 1

Summary of GECKO’s modular design. The branches on the top represent dictionary computation using the binary tree for each sequence. Once the dictionaries are calculated, perfect matches between words produce a set of seed points (hits). Afterwards, hits are sorted (by diagonal and offset inside the diagonal) and filtered. Finally, the hits are extended to generate a set of HSPs (FragHits). An additional figure with a real example is provided in Section 2.1 of the Additional file 1