Word size
Change of the word size has a great impact on the seeded sequence space as described above. But one can change the word size to find sequence matches which would otherwise not be found using the default parameters. For instance the word size can be decreased when searching for primers or short nucleotides. For blastn a suitable setting would be to decrease the default word size of 11 to 7, increase the E-value significantly (1000) and turn off the complexity filtering.For blastp a similar approach can be used. Decrease the word size to 2, increase the E-value and use a more stringent substitution matrix, e.g. a PAM30 matrix.
Fortunately, the optimal search options for finding short, nearly exact matches can already be found on the BLAST web pages http://www.ncbi.nlm.nih.gov/BLAST/.