Find existing CRISPR sites in bacteria and archaea
Requires Geneious 7.0+
CRT is a tool for rapidly finding clustered regularly interspaced palindromic repeats (CRISPRs) in bacteria and archaea. This plugin runs CRT and saves the results as annotations on your genome.
Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).
Once installed, run the plugin by selecting a nucleotide sequence and choosing Annotate & Predict - Find CRISPR loci from the menu. Results are saved as annotations on your sequence.
Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P: CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007 Jun 18;8(1):209