TABLE 2.

Nucleotide sequences of primers used for amplification of flagellin genes, sequencing analysis of gene fljB, and construction of overlapping fragments

Primer functionc and name	Sequencea	Primer positionb	Gene
FS E1	5′AAGGAATTCATCATGGCACAAG-3′	>−12	fliC or fljB
F E2	5′-GAAGAATTCAACGCAGTAAAGAGAG-3′	<1471	fliC
F P1	5′-AAAGTCCTGGCGCAGGACAACA-3′	>406	fliC or fljB
F P2	5′-ATAGCGGAGTTGAAACGGTTCT-3′	<1289	fliC
		<1322	fliB
S S1,2	5′-TGGATGGAGTCGAGGTCAGACT-3′	<317	fljB
O ST i-191D2	5′-TGTGAATTCATATGCCGATACTACGATTG-3′	>561	fliC
O ST i-197D	5′-TACGAATTCTGCTTTAGACAATAGTACTT-3′	>582	fliC
O ST i-202D	5′-GACGAATTCACTTTTAAAGCCTCGGCT-3′	>595	fliC
O ST i-238R	5′-CCAGTCGACCCCGTAACGGTAACTTT-3′	<697	fliC
O ST i-274R	5′-TTTGTCGACTCCTCAGTTGCTGTCGCAGGTAGT-3′	<810	fliC
O ST i-282R	5′-AACGTCGACATTTTTCACATCCTCAGT-3′	<826	fliC
O ST i-314R	5′-ACCGTCGACATCAGTATAAGACATCTTAAC-3′	<922	fliC
O ST1,2-190D	5′-ACAGAATTCGCTTATGCCAATAATGGT-3′	>559	fljB
O ST1,2-224R	5′-TTTGTCGACACCACCGGTTACAGAAGC-3′	<655	fljB
O ST1,2-258R	5′-ACCGTCGACAGCAACGTTAACTTCATA-3′	<757	fljB
O ST1,2-291R	5′-ACAGTCGACGGTGTATCTTTTAACTC-3′	<856	fljB

^aThe EcoRI (GAATTC) and SalI (GTCGAC) sites are indicated in bold. Start or stop codons are underlined. 

^bNumbering refers to position of the 5′ end of the last perfect matching nucleotide in forward primers (indicated by >) or the last matching nucleotide in the 3′ end in reverse primers (indicated by <) and is according to an alignment performed with Clustal-W (15) with sequence D13689 from the NCBI database. 

^cPrimers were used for amplification of flagellin genes (F), sequencing analysis of gene fljB (S), and construction of overlapping fragments (O). All primers were ordered from Pharmacia.