colour ambiguous nucleotides and report residue statistics in alignment properties

As part of the Scottish daffodil project, it would be useful to be able to (i) colour the ambiguous nucleotide bases in an assembled sequence, (ii) count the number of ambiguous nucleotide bases and give the assembled sequence some sort of quality score.
KEY:
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