Table 3.

Classification of sequences in the final alignment

Genotype	C..*	CN.*	C.W*	CNW*	S..*	SN.*	S.W*	SNW*	Total	C**U	S**U
A	424	9	87	3	4676	64	596	9	5868	0	149
B	458	5	119	2	2957	60	986	43	4630	7	8
C	868	4	210	5	5684	92	916	41	7820	2	130
D	544	1	127	6	6276	61	1257	28	8300	35	163
E	165	0	41	0	1594	8	234	1	2043	0	0
F	104	2	37	2	722	49	63	6	985	2	5
G	17	0	1	0	157	0	14	0	189	0	4
H	11	0	5	0	76	0	16	0	108	0	0
I	5	0	0	0	14	0	4	0	23	0	0
Total	2596	21	627	18	22,156	334	4086	128	29,966	46	459

“C” in the first position represents “Complete” sequences, “S” in the first position represents “Subgenomic” sequences, “N” in the second position indicates at least one “N” character in the sequence, otherwise “.”; “W” in the third position indicates at least one wobble in the sequence, otherwise “.”, “U” in the last position indicates an “Unverified” sequence, otherwise “.”, “*” indicates that either value for that position is included whereas "**" indicates either value for two adjoining columns, the “Total” column is the total of the first eight columns