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Need a help re Blastn against short (~50 nt seq)

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Hi Evevryone,

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!

 


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