PlasmidLab / Free tools / Restriction sites
Find restriction sites in a DNA sequence
Paste DNA to see which of 162 restriction enzymes cut it, how many times and where. Choose circular for a plasmid, and sites that span the origin are found too.
Reading the results
A position is where the enzyme cuts the top strand: 396 means between bases 396 and 397. The bar beside each enzyme shows its cuts along the sequence. Recognition sequences with IUPAC codes, such as AccI's GTMKAC, are matched on both strands, and enzymes that cut outside their site, such as BsaI GGTCTC(1/5), are placed where they cut. Sites whose cut falls at or beyond either end of a linear sequence are not listed.
Dam and Dcm methylation are not taken into account here. The PlasmidLab app can mark the sites they block.
Recognition sites and cut positions from REBASE, the Restriction Enzyme Database (rebase.neb.com), release 611. This is the same enzyme list the PlasmidLab app uses.