. 2016 Feb 15;7:135. doi: 10.3389/fmicb.2016.00135

Table 1.

Primers and probes for real-time PCR detection of E. coli flagellar types H1 and H12.

Target gene	Forward primer, reverse primer and probe sequences (5′–3 ′)^a	Length and location within 21 sequences listed in Table 2 (5′ –3′)
fliC_H1	AGGACGAAATCAAATCCCGTCT	338–359^b
	ACGGTTCGATGAAAATTCAGGTT	422–444^c
	[6FAM]- GACCGCGTATCC GGTCA-[BHQ1]^a	370–386^d
fliC_H12	TCCATTCAGGACGAAATCAAATC	331–353^b
	CGTGAACGTACTGGCGAAAG	402–421^e
	[6FAM] -GTATCTGGCC AGACCCA-[BHQ1]^a	376–392^f
fliC_H1∕H12	TGATGGTGAAATGACTACAATTGGT	1329–1353^g
	GGTAACTGTTGATTCTGGAACTGGT	1395–1419^g
	[6FAM]–CGAAGTATTCAATCG ATGCTAACAACGGCA–[BHQ1]	1363–1393^g

XS probes (MGB-replacement) were used for fliC_H1 and fliC_H12 specific real-time PCRs.

Forward primer conserved in all analyzed fliC_H1 and fliC_H12 sequences.

FliC_H1 reverse primer: one mismatch at position 429: fliC_H1 = G, fliC_H12 = A (underlined).

FliC_H1 probe: one mismatch at position 381: fliC_H1 = C, fliC_H12 = T; and position 384: fliC_H1 = T, fliC_H12 = C (underlined).

FliC_H12 reverse primer: one mismatch at position 402 with fliC_H1 = T (4/13 strains), fliC_H12 = C (underlined).

FliC_H12probe: one mismatch at position 381: fliC_H12 = T, fliC_H1 = C; and position 384: fliC_H12 = C, fliC_H1 = T (underlined).

Conserved in all 21 fliC_H1 and fliC_H12 sequences from Table 2.