With efforts from the entire genome editing communities, new CRISPR design tools are increasingly comprehensive and accurate.
Our CRISPR design tool was launched as one of first few sgRNA design tools available four years ago, when our server could barely handle concurrent sgRNA designs for 16 different organisms. In order to manage a reasonable response time to sgRNA design queries, we excluded repeat regions by using genome sequences that are repeats masked (see details in our release note). This and other performance considerations are addressed by most of today’s guide design tools, and therefore we recommend users switching to these newer tools. The comparison of different sgRNA design tools have been extensively reviewed, e.g., in Haeussler et al., Genome Biology, 2016.
However, since a number of users liked our software interface and included it into their routines, we will still keep our CRISPR design web tool available and urge users to BLA(S)T their sequences against genome repeats for duplicates that fall in the masked genomic regions.