Methods and systems for searching genomes for potential CRISPR off-target sites are provided. In preferred embodiments, the methods include identifying possible on- and off-target cleavage sites and/or ranking the potential off-target sites based on the number and location of mismatches, insertions, and/or deletions in the gRNA guide sequence relative to the genomic DNA sequence at a putative target site in the genome. These methods allow for the selection of better target sites and/or experimental confirmation of off-target sites and are an improvement over partial search mechanisms that fail to locate every possible target site.