In the help text for E (Expectation) values it says "any small RNA-target pair with an expectation less than the cutoff will be discarded in the final result.". Can you confirm that results with an E value below the cutoff are excluded? As E value increases with increasing miss-matches I would expect results with an E value above the threshold to be excluded.
In the help text for E (Expectation) values it says "any small RNA-target pair with an expectation less than the cutoff will be discarded in the final result.". Can you confirm that results with an E value below the cutoff are excluded? As E value increases with increasing miss-matches I would expect results with an E value above the threshold to be excluded.