CRISPR MultiTargeter is a web-based tool for automatic searches of CRISPR guide RNA targets. It can find highly similar or identical target sites in multiple genes or transcripts or design targets unique to particular genes or transcripts. The search for common targets is based on generating a multiple sequence alignment, and unique targets are found using a string comparison algorithm among all possible targets for each sequence. The basic algorithm implemented in CRISPR MultiTargeter is versatile and can accommodate almost any possible target specificity of CRISPR/Cas system, which is important because new target specificities are discovered and will be used in applied studies in different model systems.

Simple CRISPR guide RNA target search in an input sequence	Find common and unique CRISPR guide RNA targets in multiple sequences	Find common and unique CRISPR guide RNA targets for similar genes or transcripts	Find common and unique CRISPR guide RNA targets for transcripts of one gene