Use Structure Superposition (using POSA)
to find common part for all motifs for supermotifs (6 main supermotifs).

to find the common core for all supermotifs.

Some times A and B share some common part, B and C share some common part, C and A share some common part, BUT, if you try to find common part of A and B and C, you'll fail, because they don't have common part.
(just an Idea, not sure yet.)

using statistics to find common and difference between and within strandon.
ex:
1265
8734
is there any thing in common between 1-2, 3-4, 5-6, 7-8?
is there any thing in common between 2-6,3-7?