Table 1.

Primer and Probe Sequences and Concentrations Used in the Study

Primer/Probe ID [3]	Sequence (5′ – 3′) [3]	Probe Dye [3]	Probe Special Chemistry [3]	Quencher (3′) [3]	Traditional PCR, nM [3]	Direct PCR, nM
1-F	TTTCATCCCTATGTGTGGTATAG				300	600
1-R	GCTTTAGAAGGTAGAGTTAACAAC				300	600
1-Probe	TGCCAAAGCCAGCCAT	FAM	LNAa	BHQ1	100	200
2-F	TGTTATCCCATATAAGAACCGAGTGT				300	600
2-R	AAAATTACCCCAAAAGCTATCCAA				300	600
2-Probe	TTGCAATT“T”CAATTTTTTTGCCCCAATCTC	FAM	“T” b= BHQ1	BHQ1	200	400
3-F	CCACTAAAGCTTTGGCAAAAGAAA				300	600
3-R	CCCGAACGTAAAGCTTCTTCA				300	600
3-Probe	TTGTAGACCGCCCCACAA“T”TCATTTTGT	HEX	“T” b= BHQ1	BHQ1	200	400
4F	GCTTCTGCTGTAACTGTTGTGC				300	600
4-R	CACCACCATAGTAACCAAAGTTCC				300	600
4-Probe	TTCCACAAAAGAAGAGCCTACAGGTAACCCCA	ROX		BHQ2	100	200
5-F	CATGATTTATGCCCTCTTGCAA				300	600
5-R	GACAGTATAAGAAAAAGCAAGGGCTAA				300	600
5-Probe	TCTTCTTCTCA“T”CGTTTCCGCATGCTTTT	HEX	“T” b= BHQ1	BHQ1	200	400
6A/6B/6C/6D-F	GTTTGCACTAGAGTATGGGAAGG				200	400
6A/6B/6C/6D-R	TAGCCTTTCTGAAAACATTTAGCG				200	400
6A/6B/6C/6D-Probe	TGTTCTGCCC“T”GAGCAACTGGTCTTGTATC	FAM	“T” b= BHQ1	BHQ1	200	400
6C/6D-F	TTGGGATGATTGGTCGTATTAG				200	400
6C/6D-R	CTCTTCAATTAGTTCTTCAGTTCG				200	400
6C/6D-Probe	CCACGCAATTCGCCATC	FAM	LNAa	BHQ1	100	200
7F/7A-F	ATGAAGGCTTTGGTTTGACAGG				200	400
7F/7A-R	ATTCTCGCCATCAATTGCATATTC				200	400
7F/7A-Probe	ACACCACTATAGGCTGTTGAGACTAACGCACA	ROX		BHQ2	100	200
9V/9A-F	AGGTATCCTATATACTGCTTTAGG				300	600
9V/9A-R	CGAATCTGCCAATATCTGAAAG				300	600
9V/9A-Probe	ACACATTGACAACCGCT	HEX	LNAa	BHQ1	100	200
11A/11D-F	AAATGGTTTGGATATGGTTTGTTTGG				300	600
11A/11D-R	AAATGGTTTGGATATGGTTTGTTTGG				300	600
11A/11D-Probe	ATTCCAACTTCTCCCAATTTCTGCCACGG	ROX		BHQ2	100	200
12F/12A/12B/44/46-F	GCACCCACGGGTAAATATTCTAC				300	600
12F/12A/12B/44/46-R	CAACTAAGAACCAAGGATCCACAG				300	600
12F/12A/12B/44/46-Probe	TGCCCACCAACACCAGGTCCAGGT	ROX		BHQ2	200	400
14-F	AGAGTGTATGAGGAATCC				300	600
14-R	ATATATCTACTGTAGAGGGAAT				300	600
14-Probe	CGCCAAGTAACA“T”TTCCATTCCATT	FAM	“T” b= BHQ1	BHQ1	100	200
15A/15F-F	AATTGCCTATAAACTCATTGAGATAG				200	400
15A/15F-R	CCATAGGAAGGAAATAGTATTTGTTC				200	400
15A/15F-Probe	CCCGCAAACTCTGTCCT	FAM	LNAa	BHQ1	100	200
16F-F	TAATGTTATGACCTTGGTAATCTTCCC				300	600
16F-R	TCCCAAAGGATAATCAATAACTTTTAGAAG				300	600
16F-Probe	AGCCATAAGTCT“T”CCAAATGCTTAACCGCT	HEX	“T” b= BHQ1	BHQ1	100	200
18C/18A/18B//18F-F	TCGATGGCTAGAACAGATTTATGG				200	400
18C/18A/18B/18F-R	CCATTGTCCCTGTAAGACCATTG				200	400
18C/18A/18B/18F-Probe	AGGGAGTTGAATCAACCTATAATTTCGCCCC	HEX		BHQ1	100	200
19A-F	CGCCTAGTCTAAATACCA				200	400
19A-R	GAGGTCAACTATAATAGTAAGAG				200	400
19A-Probe	TATCAATGAGCCGATCCGTCACTT	FAM		BHQ1	100	200
19F-F	TGAGGTTAAGATTGCTGATCG				300	600
19F-R	CACGAATGAGAACTCGAATAAAAG				300	600
19F-Probe	CGCACTGTCAATTCACCTTC	ROX	LNAa	BHQ2	100	200
22F/22A-F	TCTATTAAATAACCCATTGGAATTGAAACG				200	400
22F/22A-R	TCGCAATTGAAGACCACATAAACTG				200	400
22F/22A-Probe	TCCGTAAT“T”CGCTTATGGGCACATTCTCCA	HEX	“T” b= BHQ1	BHQ1	200	400
23A-F	CTCCCCTCCATTACCCATTTGG				200	400
23A-R	TGAAGAAAGTGCTGTTTGTGAACC				200	400
23A-Probe	AGCTAGAAC“T”CCCACACTCCCTACTCCCA	ROX	“T” b= BHQ2	BHQ2	100	200
23F-F	GACAGCAACGACAATAGTCATCTC				300	600
23F-R	TCCATCCCAACCTAACACACTTC				300	600
23F-Probe	ATTGTGTCCA“T”AACCCTTCGTCGTATTTCCAAAG	ROX	“T” b= BHQ2	BHQ2	200	400
33F/33A/37-F	GGAACTGGTTCAGCAACTATACG				200	400
33F/33A/37-R	GGTTCTAAGACCGTCTGAAATAC				200	400
33F/33A/37-Probe	CCCCAAATAGGAC“T”TTTCTGCCATGCCAAA	HEX	“T” b= BHQ1	BHQ1	200	400

^aLocked nucleic acid nucleotides are underlined.

^b“T” indicates a black hole quencher placed internally on the thymidine base.