TABLE 3.

Primers used in this study

Oligonucleotide	Specificity	Orientation	Sequencea
Δ1124-a	PGN_1124 upstream flanking sequence	Forward	AGACTCAATAGCAGATCGACG
Δ1124-b	PGN_1124 upstream flanking sequence	Reverse	TTCATACCGCCCAAGgatCCTGTTGCTGTCATA
Δ1124-c	PGN_1124 downstream flanking sequence	Forward	TATGACAGCAACAGGatcCTTGGGCGGTATGAA
Δ1124-d	PGN_1124 downstream flanking sequence	Reverse	GACCCAAACATCCATTCGG
Δ1124-confirm	PGN_1124	Reverse	TCTCATACATGGCACGCAT
Δ1123-a	PGN_1123 upstream flanking sequence	Forward	ATGCGTGCCATGTATGAGA
Δ1123-b	PGN_1123 upstream flanking sequence	Reverse	GGACTGTCAAAGGAGgatcCTAAGCACAGCAGG
Δ1123-c	PGN_1123 downstream flanking sequence	Forward	CCTGCTGTGCTTAGgatcCTCCTTTGACAGTCC
Δ1123-d	PGN_1123 downstream flanking sequence	Reverse	CCGTAACCGGGTACGAT
Δ1123-confirm	PGN_1123	Reverse	GACCCAAACATCCATTCGG
Δkgp-a	kgp upstream flanking sequence	Forward	atccatggACGCCCGATACCCATACTC
Δkgp-b	kgp upstream flanking sequence	Reverse	CACAAAGTCTCCGAGTggatccATTCAGAGAACCACG
Δkgp-c	kgp downstream flanking sequence	Forward	CGTGGTTCTCTGAATggatccACTCGGAGACTTTGTG
Δkgp-d	kgp downstream flanking sequence	Reverse	tatgtcgacAACAGGTTGTCCGTCAGC
Δkgp-confirm	kgp	Reverse	AACTTCCTAACTGCTGGCAC
ΔTn1-a	Tn1 upstream flanking sequence	Forward	AAGGCTTGATGCTGAAGACC
ΔTn1-b	Tn1 upstream flanking sequence	Reverse	GTCATTTCTTATTAAGAATAggatccTATTTACGTTGCGAGC
ΔTn1-c	Tn1 downstream flanking sequence	Forward	GCTCGCAACGTAAATAggatccTATTCTTAATAAGAAATGAC
ΔTn1-d	Tn1 downstream flanking sequence	Reverse	TCTTTGCCGGCATCTTTGC
1123-start	PGN_1123	Forward	ataggcctATGAGATTCTCTGCCATTATTATCG
1123-stop	PGN_1123	Reverse	attctaGAGGAATCCACTCGCAAATATC
SJ59	ermF promoter	Forward	ggaattcggccgCCGATAGCTTCCGCTATTG
SJ60	ermF promoter	Reverse	taggtaccaggcctGTAACTTCTTACAGGTGAATAC

^aLowercase indicates bases that add or complete a restriction site.