blastn for matching small sequences

Question

[harpreetmanku04]

hello, i stuck with the blast command, see when i do blastn for 300 bp long seq then it retains result but when i do blastn for 20-25 nucl seq then it retain no result. do you have any idea why so it is? i want to blast small sequences with my local database.

Answer 1

[zizigolu]

http://www.ncbi.nlm.nih.gov/blast/html/BLASThomehelp.html in Search for short, nearly exact sequences section you may could find some clues