. 2011 Dec 9;6(12):e28274. doi: 10.1371/journal.pone.0028274

Table 3. Novel B. anthracis canSNP assays developed in this report.

Assay name	A.Br.011	A.Br.011/009_3692595
Assay target	Provides resolution within A.Br.008/009 group	SNP on A.Br.011/009 branch (terminal genome is A0343)
SNP Position (bp)^a	2552486	3692595
Ancestral primer (5′-3′)^b	AAACGAATTCCCGCTGAAAATAcTG	CCCTAAAAAAGCAGAGACTATgG
Derived primer (5′-3′)^b	CGGGGCGGGGCGGGGCGGGCGAAACGAATTCCCGCTGAAAATAtTA	CCCTAAAAAAGCAGAGACTATcA
Consensus primer (5′-3′)	GATAAAAATCGGAATTGAAGCAGGA	CGCACATGAAGTGGAAGAAAGTACG
Assay format^c	meltMAMA	SYBR MAMA

Using ‘Ames ancestor’ genome (GenBank ref: AE017334).

Underlined nucleotides indicate the position of the SNP; bolded nucleotides indicate an introduced GC clamp that increases the melt temperature of the primer, thus enhancing allelic discrimination [13]; small-case nucleotides represent deliberate mismatches incorporated into the allele-specific primers.

All assays were optimized on an Applied Biosystems ABI PRISM 7900HT Sequence Detection System using default thermocycling parameters, with the addition of the dissociation curve [13], [14].