Figure 3.

The sequence similarity space of CRISPR repeats visualized with the BioLayout (Java) program [26]. Dots denote individual repeat sequences; connecting lines represent Smith-Waterman similarities, such that closer dots represent more similar sequences. Dot colors denote cluster association as derived from MCL clustering. The 12 largest clusters are indicated by circles together with their sequence logos, coarse phylogenetic composition, and sample secondary structures where applicable.