What the tool does
The finder scans a DNA sequence for the recognition sites of 32 common Type II restriction enzymes, reports every site with its position and the overhang the enzyme leaves, and simulates a digest with the enzymes you select. Fragment sizes are shown in a table and on a virtual agarose gel against a ladder.
Linear and circular DNA
A plasmid is circular, so n cuts give n fragments, while a linear molecule such as a PCR product gives n + 1. Sites that span the end of a circular sequence are found as well. Choose the topology that matches your molecule.
Planning a cloning digest
Enzymes that cut only once in a vector and not at all in the insert are candidates for directional cloning. Check that the overhangs of the two enzymes are compatible with your strategy, and remember that methylation and star activity are not modelled here.