I'd like to search for sites that contain homo-pyrimidine sequences. Is there any way to incorporate a feature which allows searching for ambiguous bases using standard nomenclature (see below)?

                       R = G or A
                       Y = C or T
                       M = A or C
                       K = G or T
                       S = G or C
                       W = A or T
                       B = not A (C or G or T)
                       D = not C (A or G or T)
                       H = not G (A or C or T)
                       V = not T (A or C or G)
                       N = A or C or G or T

To some degree, this is possible by using the restriction digest analysis coupled with custom sequences. However, I'd like to also be able to make use of the % match feature in the "find pattern" function.

One CAN search for ambiguous bases using Find Pattern dialog, just make sure to check corresponding option (see screenshot attached)

Also Smith-Waterman based search is also supposed to support ambiguous bases but there is currently an open issue related to this problem.

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