Kenneth,

Am I right that the percentage is kept in some qualifiers of BLAST annotations? In this case, you can use sequence marker element. You just need to create a new marker group and set it up to mark data using a qualifier value. For the needed values you should create a special marker name (e.g. "needed") and set the Filter element up to filter the data flow using this value "needed".

So, you scheme should be:
... -> BLAST -> Sequence Marker -> Filter (by "needed") -> ...