CRISPR Indel Analysis & Frameshift Caller
Aligns an edited clone against its reference to call indel size, position and reading-frame consequence.
How it works
An edited sequence is aligned against its unedited reference using Needleman-Wunsch with affine gap penalties, so a single clean deletion scores better than several scattered ones — which matters because NHEJ repair produces the former. The alignment gives the net indel size, where the first difference falls, and whether the length change is a multiple of three, from which the reading-frame consequence follows directly.
Frequently asked questions
Can you measure CRISPR editing efficiency from two sequences?
No, and any tool that reports one from plain sequence text is not measuring it. Editing efficiency describes the mixture of alleles across a population of cells, and that information lives in the superimposed peaks of a Sanger chromatogram downstream of the cut site — not in a consensus sequence, which has already collapsed the mixture to one base per position. Comparing two sequences tells you what edit a clone carries; for population efficiency you need the .ab1 trace and a deconvolution tool such as ICE or TIDE.
Does an in-frame indel still knock out the gene?
Often not. A deletion that is a multiple of three removes residues without shifting the reading frame, so translation continues to the normal stop and produces a shortened protein that may retain partial or full function. This is why frameshift status matters more than indel size for a knockout: a clean 3 bp or 6 bp deletion can look like a successful edit on a gel and still leave the gene working. Confirm loss of protein by western blot rather than inferring it from the sequence alone.