Table 2. A sample of the quantitative diversity analysis for HA protein of avian Influenza A (H5N1) subtype.

The full data is available in Table S2.¹

Protein	Aligned nonamers			H(x)c	Indexd		Variantse				Nonatypesi
		Positiona	No.b		Sequence	[%]	Total	Majorf	Minorg	Uniqueh
							%
HA	#	158–166	2353	0.6	SFFRNVVWL	92	8	5	2	<1	1
	&	159–167	2352	1.1	FFRNVVWLI	83	17	8	9	1	1
	&	160–168	2353	1.1	FRNVVWLIK	83	17	7	9	1	1
	&	161–169	2352	0.9	RNVVWLIKK	88	12	7	4	1	1
	&	162–170	2351	1.7	NVVWLIKKN	64	36	23	12	1	2
	&	163–171	2351	2.8	VVWLIKKNS	30	70	26	43	1	2
	&	164–172	2350	3.5	VWLIKKDNA	21	79	20	57	1	3
	&	165–173	2350	3.4	WLIKKDNAY	21	79	21	57	1	3
	&	166–174	2350	3.4	LIKKDNAYP	21	79	21	57	1	3
	&	167–175	2349	3.5	IKKDNAYPT	21	79	21	57	2	4
	&	168–176	2349	3.2	KKDNAYPTI	24	76	21	54	1	3
	&	169–177	2349	3.2	KDNAYPTIK	24	77	21	54	1	3
	+	170–178	2350	4.1	NSTYPTIKR	18	82	14	66	2	4

Notes.

¹All percentages are shown to the nearest whole number.

^aAmino acid number at the start and end of the nonamer position in the protein alignment. The symbol # denotes a highly conserved nonamer position (index incidence ≥ 90%), & denotes a mixed-variable position (index incidence between 90% & 20%), and + denotes a highly diverse nonamer position (index incidence ≤ 20%). See Fig. S1 for the definition of diversity motifs.

^bTotal number of protein sequences analysed at the aligned nonamer position; the difference in number between the nonamer positions was due to the inclusion of both partial and full-length sequences in the alignment.

^cShannon’s nonamer entropy, which indicates the level of diversity of the nonamer sequences at the position (H(x); see Fig. 1 for details).

^dThe index nonamer is the most prevalent sequence at the position.

^eVariants are nonamer sequences that differ by one or more amino acids from the index sequence.

^fThe major variant is the second most common sequence at the position.

^gMinor variants are multiple different repeated nonamer sequences, each occurring more than once and with an incidence of less than or occasionally equal to the major variant.

^hUnique variants are nonamer sequences that are observed only once at the position.

ⁱNonatypes are distinct sequences among the variants for a given position; for example, the position 170–178 had 103 distinct nonamer sequences (Data S1; from a total of 2,350 sequences), therefore the percentage of nonatypes for this position is ∼4.4% ((103/2,350) ×100%).