A chain of hits meeting CRISPR criteria. CRISPR arrays are identified by following chains of hits. Starting with a given pile, each hit that connects this pile to another pile later in the genome is a potential link in the chain. All possible chains are explored, abandoning the search each time the chain violates the criteria used for CRISPR array recognition (see Table 2). These criteria include maximum and minimum repeat length, maximum and minimum spacer length, and measures of the variance in repeat and spacer lengths. Shorter links are explored before longer links as regularly spaced arrays will be obtained by skipping every second, third... repeat. The figure shows the correct chain (arrows) for the example array from Fig. 3.