The statistics produced when searching databases with short sequences may not be reliable . The following article has some comments on the statitics of searching with nucleic acid sequences less than 200 base pairs long. Fuzznuc will search for patterns in nucleotide sequences and fuzzpro looks for patterns in amino acid sequences. They are able to search for patterns and allow for mismatching. These programs use different algorithms to do the search depending on the pattern you are searching with and should thus be more efficient than Findpatterns.
More information is available here .
Patterns for searching with Fuzznuc and Fuzzpro are specified in the same manner as Prosite patterns. If you want to search for degenerate primer sequences, we suggest you try Fuzznuc before Findpatterns. GCG's Findpatterns Findpatterns looks for short patterns in a database of sequences. It can look for absolute patterns, or search for patterns that include degeneracies. If you are going to use findpatterns, we recommend you refer to the official documentation .