Scans your target for the PAM sites of the chosen nuclease, scores every protospacer, and searches the sequences you supply for off-targets. Mark the change you want as [C/T] (substitution), [/ATG] (insertion) or [ATG/] (deletion) the first allele is what the genome has, the second is what you install and the tool also builds the HDR/ssODN donor with a silent PAM-blocking change, the primers that screen the edit, a prime-editing pegRNA with the PBS length picked by Tm, and the base-editing window with its bystander bases. Leave the brackets out to simply tile guides across the sequence.
Off-target scoring: Hsu et al. (Nat Biotechnol 2013). Prime editing: Anzalone et al. (Nature 2019). Donor geometry: Richardson et al. (Nat Biotechnol 2016). Scope: the off-target search covers only the sequences you paste — it is not a genome-wide index — and the activity score is a transparent composite of published sequence rules, not Rule Set 2 / Azimuth. Both are spelled out in the Warnings tab.
One target sequence, 5′→3′, with or without a FASTA header. Mark the edit as [C/T], [/ATG] or [ATG/], or [C] to mark a site without an edit. Paste 600–1000 nt around the site so the donor arms and the screening primers have room.
Extra sequences to search for off-targets: paralogues, pseudogenes, the donor plasmid, the vector backbone, other members of a gene family — as many FASTA records as you like. The target itself is always searched as well. Nothing is uploaded: the search runs in this browser, over exactly these sequences and no others.
Custom nuclease
Reject on
Constructs
Export: use Copy / Download above each report, or click inside a result area → Ctrl+A → Ctrl+C.