Did you use standard-parameters? I'd at least use -e 0.0005 or something equally low for e-values; filtering by scores is harder as they change based on how short your sequences are, in that case you have to decide based on what you see in your results.

You can also use "-b 3 -v 3" to show only the best 3 database-alignments and summaries for each query, which should reduce your output considerably.

"The "Search for short, nearly exact matches" nucleotide and protein pages no longer exist. Instead, the nucleotide and protein blast programs automatically check for short queries and adjust the search parameters accordingly. This adjustment occurs when the query, either nucleotide or amino acid, is of length 30 or less. The translating blast programs or searches on the genome blast pages do not have this auto adjust feature."

I got this information from the link http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#Short

You can adjust both the word size and the expect value on the standard BLAST pages to work with short sequences. NCBI provides a BLAST page with these values preset to give optimal results with short sequences. This page ("Search for short nearly exact matches") is linked under the nucleotide BLAST section of the main BLAST page.

"Search for short and nearly exact matches" Program Word Size DUST-Filter Setting Expect Value Standard blastn 11 On 10 Search for short nearly exact matches 7 Off 1000

This information from http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=ProgSelectionGuide