Table 2.

Pairs of primers used in the PCR mapping assay analyzing the pKpQIL-like plasmids

Primer	Sequence (5′ → 3′)	Annealing positionsa	Product size (bp)	pKpQIL fragment analyzeda	Resultb
RepAF	GCTGAGCGTAAATCTCAC	4439–4456	159	IncFIIK replicon region (FIIKrepA gene)	+
RepAR	CTCAACCTCACGCTTCAG	4580–4597
RepAF	GCTGAGCGTAAATCTCAC	4439–4456	1,497	Junction between the FIIK replicon region and the pNYC-derived region	+
ORF8R	CAGACGTGATTTTCTGACCAC	5915–5935
ORF11R	GCATGTTTGAACTGGTCAG	8347–8365	682	Junction between Tn4401 and its 5′ flank within the pNYC region	+
tnpRF	CGACGTCGATGTATTTGCATG	9008–9028
IS26LF	GTCGGTGGTGATAAAC	25556–25571	2,847	IS26 insertion within 1331 the pKPN4-derived Tn	+/−
TEM-F	TTACTGTCATGCCATCC	28386–28402
OXA-9F	CTGCTGCATATGTTGGTG	26542–26559	1,861	Junction between blaOXA-9 and blaTEM-1 within the pKPN4 Tn1331	+/−
TEM-F	TTACTGTCATGCCATCC	28386–28402
rep2R	TCTGCTGGTTATTGGGTGAG	53337–53356	312	FIB-like repA gene within the pKPN4 region	+
rep2F	GTCTTCGCAGCACAACTATC	53629–53648
TraXF	CGCAATGTTCTATGCTGTG	112918–112936	1,576	Junction between the pKPN4 region (traX gene) and the FIIK replicon region	+/−
ORF2R	CAGAATAACTGCTGCTCAG	838–856

^aPosition numbering and the description of plasmid regions is according to reference 25 and the pKpQIL sequence (GenBank accession no. GU595196).

^bSymbols: +, PCR worked with all plasmids analyzed; +/−, PCR worked, but not with all plasmids analyzed.