Virtual agarose gel: predict the bands from a digest

How this is calculated

Dam and Dcm methylation are not taken into account here; a blocked site changes the band pattern. The PlasmidLab app marks the sites they block.

The fragment sizes are exact. The cut positions come from the same enzyme list and the same site search as the restriction site finder, and the fragments are the distances between neighbouring cuts, measured around the circle when the sequence is circular. Cuts from all four enzymes go into one digest, and two enzymes that cut at the same position count once.

Where a band lands is a prediction, not a measurement. It uses the gel model from the PlasmidLab app: an empirical curve of how far DNA travels against the base-10 logarithm of its length, with the length first multiplied by the agarose percentage raised to the power 1.3, and the whole distance scaled by how far you ran the gel. Read it to tell whether two bands will separate, not to measure a size.

Uncut circular DNA does not run as a linear fragment of the same length. When the sequence is circular and nothing cuts it, that band is drawn with the supercoiled factor for TAE buffer, 0.7, so a 2,686 bp plasmid runs about where a 1,880 bp linear fragment would. Supercoiling varies with the preparation, so that band is marked approximate. A band that would run past the bottom of the gel, or that has barely left the well, is drawn at the edge and labelled, so it is never silently dropped.

Recognition sites and cut positions from REBASE, the Restriction Enzyme Database (rebase.neb.com), release 611. Ladder lengths are the 1 kb and 100 bp DNA ladders. Everything runs in your browser; the sequence is not sent anywhere.