freak takes one or more sequences as input and a set of bases or residues to search for. It then calculates the frequency of these bases/residues in a window as it moves along the sequence. The frequency is output to a data file or (optionally) plotted.
Here is a sample session with freak:
% freak embl:hsfau Residue/base frequency table or plot Residue letters [gc]: Output file [hsfau.freak]:
Mandatory qualifiers (bold if not always prompted):