I am looking for a sequence similarity search tool, preferably
web-based, but anything will do, that will search nucleotide sequence
databases and return relatively long matches ( +- 100 nt ) that may have
relatively low sequence identity ( +- 50%).
My problem is, when I enter my sequence of interest (102 nt) in BLASTn,
it returns only short, high identity sequences (ie, 15 bp, 95%
identity). Even by significantly increasing my expect value and
allowing a large number of hits, BLAST won't return long sequences
unless they have very high sequence identity.
TIA for any advice -