TABLE 2.

List of primers and probes used in this work

Gene or probe	Forward primer	Reverse primer	Size (bp)	Reference or origina
Genes
aggR	5′-GTATGAAATTAAAACAA ACATCG-3′	5′-GTTTATTGGCTTTTAAAATAG TC-3′	800	This study
aggA	5′-AAATATGAGAAGAAAGAA-3′	5′-AAAAATTAATTCCGGTATGG-3′	500	This study
aafA	5′-CAGAATGTTTGCGATTGCTAC-3′	5′-TTTGTCACAAGCTCAGCATT-3′	468	This study
agg3A	5′-GTATCATTGCGAGTCTGGTAT TCAG-3′	5′-GGGCTGTTATAGAGTAACTTCC AG-3′	462	5
hdaA	5′-TCCATTATGTCAGGCTGCAA-3′	5′-GGCGTTAACGTCTGATTTCC-3′	411	This study
hdaABCD	5′-TCGCTGGGAAAGTTA AAT GG-3′	5′-TTTGCTGTGGTTTTTGTTG-3′	3,498	This study
aggC	5′-GTGATCCCCCAAGCTACAGA-3′	5′-ATCCCAATGCATTACCCTGA-3′	850	This study
aafC	5′-AACGGATACGCCAAGTGTTC-3′	5′-GCACCTGTGGTGAGAGGAAT-3′	496	This study
agg3C	5′-GTT TGGAAC CGGGAA TTA ACA TTG-3′	5′-ATACTTTAGATACCC CTC ACG CAG-3′	485	5
hdaC	5′-GGGGGAGGGAATAGATATGG-3′	5′-CTCATCAGAGCCCACACTCA-3′	700	This study
aaiC	5′-ATTGTCCTCAGGCATTTCAC-3′	5′-ACGACAACCCCTGATAAACAA-3′	215	CVD collection
pet	5′-ACTGGCGGACTCATTGCTGT-3′	5′-GCGTTTTTCCGTTCCCTATT-3′	800	CVD collection
setA	5′-CCCTGATATTCCAGGGACAT-3′	5′-ATGGAAGTCAGCGTCTTTCA-3′	134	4
astA	5′-ATGCCATCAACACAGTATAT-3′	5′-GCGAGTGACGGCTTTGTAGT-3′	110	CVD collection
aap	5′-ATGAAAAAAATTAA GTTTGTTATCTT-3′	5′-TTATTTAACCCATTCG GTTAGAGC-3′	356	56
cat	5′-CTGGATATACCACCGTTG ATATA-3′	5′-GGGTGAACACTATCCCATAT-3′	100	4
cdtABC	5′-AATTGTAAATCCTTTGGGGCG TTC-3′	5′-GATCTAGGGTGCAAGGGGCT ATT-3′	2,009	This study
aafCI	5′-TCTGACGGCGTGTAGTTCTCA CCCA-3′			This study
aafCIV	5′-GTCTATAGGGCAAGACAGCG TGAAG-3′			This study
agg3CII	5′-CATCACCCCCTAAAAGGGAC ACTG-3′			This study
agg3CIII	5′-AGGCCCGAACTCATGCACGTT AT-3′			This study
Probes
AAF/I	5′-AAATATGAGAAGAAAGAA-3′	5′-AAAAATTAATTCCGGTATGG-3′		This study
AAF/II	5′-CAGAATGTTTGCGATTGCTAC-3′	5′-TTTGTCACAAGCTCAGCATT-3′		This study
AAF/III	5′-GTATCATTGCGAGTCTGGTAT TCAG-3′	5′-GGGCTGTTATAGAGTAACTTCC AG-3′		This study

^aCVD, Center for Vaccine Development.