TABLE 5.

PCR primer sets, amplicons, and sizes

Primer	Primer sequence (5′–3′)a	Amplicon	Amplicon size (bp)
AfpX-derived amplicons
AFPF	AAAAAGCTTTTGTGAAATTGCTGGCTCAG	AFPX17CH	1,439
AFPR	AAAAAGCTTGAATTCGCGTTAGATACCCCCA
AFP15F	CCAAACGGCTTGCACTACCGCGGG	AFPX1516	4,539
AFP16R	TGAGACTCATGAGGTCAAGCGTTCC
18MFEF	AAACAATTGGGGCATCTCGCCTCATGAGGG	18MFE	2,219
18MFER	AAACAATTGGCGAGCGATATACTCCAACGC
17BGLF	AAAAGATCTGGGTGGAGCAGCGATAACGCG	17BGL	2,329
17BGLR	AAAAGATCTGCAGTGCGTCATCCATCGCCTC
Antibiotic cassettes
KNRVF	AAAGATATCGTAAGCCAGTATACACTCCGCTAGCGC	KNRV	1,201
KNRVR	AAAGATATCAGTGTTACAACCAATTAACCAATTC
KNBGLF	AAAAGATCTGTAAGCCAGTATACACTCCGCTAGCGC	KNBGL	1,201
KNBGLR	AAAAGATCTGAGTGTTACAACCAATTAACCAATTC
KNNAEF	AAAGCCGGCTAAGCCAGTATACACTCCGCTAGCGC	KNNAE	1,201
KNNAER	AAAGCCGGCAGTGTTACAACCAATTAACCAATTC
KNMFEF	AAACAATTGTAAGCCAGTATACACTCCGCTAGCGC	KNMFE	1,201
KNMFER	AAACAATTGGAGTGTTACAACCAATTAACCAATTC
SPBGLF	AAAAGATCTATGCCCGTTCCATACAGAAGCT	SPBGL	1,379
SPBGLR	AAAAGATCTGACATTATTTGCCGACTACCT
SPMFEF	AAACAATTGATGCCCGTTCCATACAGAAGCT	SPMFE	1,379
SPMFER	AAACAATTGCGACATTATTTGCCGACTACCT
Primers for validation of homologous recombination
1516F	GAGTCGTTGTTTACAACGCCAGG		4,814
1516R	GTGCGCATCTGCATTTACCGG
18F	GTTAGATTACTCCCACCTTCCGGATG		2,441
18R	GATAATTAGACATCCTCGTTCCTC
17F	TTAACCACTTGGGTAACGACCTCC		2,632
17R	ACTGGTACTGATTGCGGGTCCAAGG
Diagnostic primers
AFP8F	CTGGACATAGCGGGACAGCGCAGCAC		909
AFP8R	ACTCAGGGTGATACTCTCGCCCG
AFPX17F	GCCGACTAACACACCACAGTTACAGC		2,600
AFPX17R	TTAACGCATGATCATTTGCGCTTCCGG
AFPX18F	CAACTGGAGCAGTTCGAGCTGGC		805
AFPX18R	GTCATAAGACTCATGCCAAGAGTC
REPA	TGCAGGGGAACGATCTTCTTGAGG		893
REPR	GCCCCACTTTCTTGTACCATCCAG
BOXA1R	CTACGGCAAGGCGACGCTGACG

^aUnderlining denotes the restriction enzyme site.