Table 2.

Hypothetical 21-state data plotted in Figure 3

	0	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18
A	420	0	0	0	0	21	0	1	4	20	14	42	400	380	340	300	260	220	180
C	0	420	0	0	21	21	17	16	16	20	16	42	1	2	4	6	8	10	12
D	0	0	420	0	21	21	19	19	24	20	24	42	1	2	4	6	8	10	12
E	0	0	0	420	21	21	15	15	22	20	22	42	1	2	4	6	8	10	12
F	0	0	0	0	21	21	26	26	18	20	18	42	1	2	4	6	8	10	12
G	0	0	0	0	21	21	18	18	26	20	26	42	1	2	4	6	8	10	12
H	0	0	0	0	21	21	21	21	24	20	24	42	1	2	4	6	8	10	12
I	0	0	0	0	21	21	23	23	19	20	17	42	1	2	4	6	8	10	12
K	0	0	0	0	21	21	25	25	17	20	17	42	1	2	4	6	8	10	12
L	0	0	0	0	21	0	16	16	22	20	20	42	1	2	4	6	8	10	12
M	0	0	0	0	21	21	27	27	21	20	21	0	1	2	4	6	8	10	12
N	0	0	0	0	21	21	20	20	25	20	25	0	1	2	4	6	8	10	12
P	0	0	0	0	21	21	21	21	22	20	22	0	1	2	4	6	8	10	12
Q	0	0	0	0	21	21	20	20	23	20	21	0	1	2	4	6	8	10	12
R	0	0	0	0	21	21	23	23	16	20	16	0	1	2	4	6	8	10	12
S	0	0	0	0	21	21	22	22	19	20	19	0	1	2	4	6	8	10	12
T	0	0	0	0	21	21	24	24	23	20	22	0	1	2	4	6	8	10	12
V	0	0	0	0	21	21	23	23	21	20	21	0	1	2	4	6	8	10	12
W	0	0	0	0	21	21	18	18	21	20	20	0	1	2	4	6	8	10	12
X	0	0	0	0	21	21	20	20	20	20	18	0	1	2	4	6	8	10	12
Y	0	0	0	0	21	21	22	22	17	20	17	0	1	2	4	6	8	10	12

A data matrix for a hypothetical dataset of functional class frequencies over 420 sequences of length 18. Logos based on this dataset are plotted in Figure 3.