In stand-alone blast, I'm blasting several thousands of ~450nt long sequences against one short ~50nt long motif sequence to find the sequences that has this ~50nt motif. In blastn output I get couple of hits with >90% (and alignment length = 50) So my questions are-
1. Why I'm not getting the hits below 90% identity (like sequences that has 85 or 70% identity to the motif seq)?
2. Is there other efficient way/tool available to find the sequences from the data that has my seq of interest in it?
I'm new to blast and bioinfo in general so any help/inputs would be highly appreciated!
Thanks very much!