Limitations

•  The pattern/blocks database must not have more than 10,000 entries (but several 
    databases can be used simultaneously).

•  Patterns may consist of up to 50 positions (see help topic 'PROSITE Pattern Syntax') or 
    512 characters in total.

•  Up to eight entry sets can be created. Names of sets may have up to 15 characters.

•  Sequences must not be longer than 30,000 residues.

•  The maximum number of pattern hits per sequence is 2000.

•  A maximum of 10 windows (+ one sequence window) can be open at a time.

•  Only 32K of data can be displayed in the "results window". Longer output will be 
    saved to disk.