A recognition sequence is a DNA sequence to which a structural motif of a DNA-binding domain exhibits binding specificity.
[1] The transcription factor Sp1 for example, binds the sequences 5'-(G/T)GGGCGG(G/A)(G/A)(C/T)-3', where (G/T) indicates that the domain will bind a guanine or thymine at this position.
The restriction endonuclease PstI recognizes, binds, and cleaves the sequence 5'-CTGCAG-3'.
A given recognition sequence can occur one or more times, or not at all, on a specific DNA fragment.
For example, there are two PstI recognition sites in the following DNA sequence fragment, starting at base 9 and 31 respectively.