Variant-aware Cas-OFFinder

Off-target search that accounts for an individual’s genetic variants

Variant-aware Cas-OFFinder is a web-based tool for identifying potential CRISPR off-target sites across different genomes. It accounts for both reference genomes and individual genetic variants to improve accuracy in diverse populations. This addresses limitations caused by incomplete representation of genetic variation in reference genomes. Variant-aware Cas-OFFinder is freely available under GNU AGPL.

Citation Mekonnen, A. M., Seong, K., Kim, H., & Park, J. (2025). Variant-aware Cas-OFFinder: web-based in silico variant-aware potential off-target site identification for genome editing applications. Nucleic Acids Research, gkaf389.

Result will be notified by e-mail if provided.

PAM Type

52 PAM types available

Target Genome

Genomes

159 assemblies across 84 species

Variant File

The VCF must be phased and contain a single sample. Chromosome names have to match the indexed reference genome exactly.

Download an example VCF file

Query Sequences

Please input your RNA, DNA, or sequence tag (one sequence per line, up to 10 sequences per run).

Please enter each DNA sequence on a new line. PAM sequence (e.g., NGG) must NOT be included. The length of each query sequence should be between 17 and 23 bp, or it will be the same length!