General
Give -2 if motif is 2 basepair or closer to closing basepair.
Give -1 if motif starts in closing basepair
Give + 2 for motif in stems in stems 7 bp and longer.
Give + 1 if open base is complementary to motif base. (Only + one if that creates an extra GU)
Motif specific
Give -1 if open base is non-complementary for motif 1a and 1d + 2a and 2d
Give + 1 if open base is non complementary C, for motif 1b and 1 c + 2b and 2c
Give +1⁄2 if open base is any other non complementary base for 1b and 1 c + 2b and 2c.
For the idea behind this, check THIS forum post.