For most restriction enzymes, this is the short (typically a half-dozen or so bases long) sequence of DNA or RNA which is recognised and consequently within which the DNA is restricted (cut)

eg. that for EcoRI is GAATTC, with cleavage occurring between the G and A on each strand to leave sticky ends.

For type IIs restriction enzymes, the recognition site and cleavage site are separated by a number of bases characteristic to the particular enzyme.

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