Often people want to do this to check for the presence of a nucleotide primer sequence in a database, but the same principles will hold for searching with short peptide sequences.
Blast is generally unsuitable for most searching with very short nucleotide sequences.
This means that Blast needs a perfect match of at least 7 nucleotides before it will even register a hit and try to expand on it. There is documentation on using Blast for short sequence searching. 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.