TABLE 5.

Primers for the PCR analyses of the M. avium subsp. avium 197K locus and the M. avium subsp. paratuberculosis 19K locus

Primer location and sequence	Position in M. avium subsp. avium genome (TIGR strain 104, contig 3294)	Position in M. avium subsp. paratuberculosis genome (UMN strain K-10, contig 16)	PCR results for:
			M. avium subsp. avium S2/S4	M. avium subsp. paratuber- culosis type I	M. avium subsp. paratuber- culosis type II
Left transition side of M. avium subsp. avium 197K
p12 (5′-TGA TCC GGG CGA CGA TCT GG-3′)	1,794,970-1,794,989 and     2,073,405-2,073,422	3,430,140-3,430,159	−/+	−	−
p13 (5′-TGG CGT TGA TAT CGC GAC TGG-3′)	1,795,236-1,795,256
Right-hand end of M. avium subsp. avium 197K
p14 (5′-TCG TCC AGG TAG CCG TTC AAC TC-3′)	1,991,916-1,991,938		+/+	+	−
p15 (5′-TGC AGC AGG TGT TCG GGA TGG-3′)	1,992,400-1,992,420 and     2 other hits, 2,449,453-2,449,472 and     4,813,981-4,814,000
Left transition side of M. avium subsp. paratuberculosis 19K
p12 (5′-TGA TCC GGG CGA CGA TCT GG-3′)	1,794,970-1,794,989	3,430,140-3,430,159	−/−	+	+
p16 (5′-TGT CGT CAA CGC GGT TGG CG-3′)		3,430,532-3,430,551
Right-hand end of M. avium subsp. paratuberculosis 19K
p17 (5′-TAC TAC GCC TAC GCA CCG CG-3′)		3,448,574-3,448,593	−/−	+	+
p18 (5′-TAG ATC AGG ATG TGC CCG GCC-3′)		3,448,995-3,448,975
Right-hand end of M. avium subsp. paratuberculosis 19K plus left-hand end of M. avium subsp. avium 197K
p17 (5′-TAC TAC GCC TAC GCA CCG CG-3′)		3,448,574-3,448,593	−/−	−	−
p13 (5′-TGG CGT TGA TAT CGC GAC TGG-3′)	1,795,236-1,795,256