Table 2.

Influenza hemagglutinin gene primers

Forward primer	5′–3′ Sequencea	Alignment percentageb	Mismatches to templatec	Reverse primer	5′–3′ Sequence	Alignment percentage	Mismatches to template
HA5F1	GTYACTGTBACACAYGCCCAAG			HA5R1	CCGAGGAGCCATCCAGCTACACTA
	GTtACTGTtACACAtGCCCAAG	85.0	0		CCGAGGAGCCATCCAGCTACACTA	93.8	0
	GTcACTGTtACACAcGCCCAAG	4.3	0		CCAAGGAGCCATCCAGCTACACTA	1.2	1
	GTcACTGTtACACAtGCCCAAG	3.2	0		CCGAGGAGCCATCCAGCTCCACTA	0.5	1
	GTtACTGTcACACAtGCCCAAG	2.0	0		CCGAGGAGCCATCCGGCTACACTA	0.5	1
	GTgACTGTcACACAcGCCCAAG	0.3	0		CCGAGGAGCCATCCAGCCACACTA	0.5	1
	GTtACTGTtACACAcGCCCAAG	0.3	0		CCGAGGGGCCATCCAGCTACACTA	0.2	1
	GTtACTGTcACGCAtGCCCAAG	0.3	0		CCCAGGAGCCATCCAGCTACACTA	0.2	1
	GTtACTGTgACACAtGCCCAAG	0.3	0		CCGAGAAGCCATCCAGCTACACTA	0.2	1
	GTtACTGCtACACAtGCCCAAG	0.3	0		CCGAGGAGCCACCCAGCTACACTA	0.2	1
	GTtACTGTtACACAtACCCAAG	0.3	1		CCGAGGAGCCAACCAGCTACACTA	0.2	1
HA5F2	GTGACGGTCACACATGCTCAGG				CCGAGGAGCCATCCAGCGACACTA	0.2	1
	GTGACGGTCACACATGCTCAGG	1.2	0	HA5R2	CCGAGGAGCCATCCAGCTACGCTA
HA5F3	GTTACTGTTACACATGCCCAAA				CCGAGGAGCCATCCAGCTACGCTA	1.0	0
	GTTACTGTTACACATGCCCAAA	1.2	0	HA5R3	CCAAGAAGCCATCCAGCCACACTG
HA5F4	GTTACTGTTACACATGCTCAAG				CCAAGAAGCCATCCAGCCACACTG	0.7	0
	GTTACTGTTACACATGCTCAAGd	1.4	0		CCAAGAAGCCACCCAGCTACACTG	0.2	2
					CCGAGGAGCCATCCAGCTACACTG	0.2	3

^aDegenerate positions are in lower case; primers are in boldface.

^bUnique template sequences and their representation in the alignment.

^cPrimer mismatches to each template sequence, nucleotide is indicated in boldface.

^dDark bar represents the 3′ pentamer where no mismatches are allowed.