RFindPatterns identifies sequences that contain short patterns like
GAATTC or YRYRYRYR.  You can define the patterns ambiguously and allow
mismatches. You can provide the patterns in a file or simply type them
in from the terminal.

The output is a series of files called r#.rfind, each containing a single
extracted sequence.  These can be fed through Pileup or manipulated in
other ways.