gag F1 / TCACCTAGAACTTTAAATGCATGGGTAAAAGT / 32
gag F2 / AATGCATGGGTAAAAGTAGTAGAAGAGAAGGC / 32
gag F3 / AAGGCTTTCAGCCCAGAAGTGATACCCATGTT / 32
gag R1 / TATTTGTTCCTGAAGGGTACTAGTAGTTCCTG / 32
gag R2 / TACTAGTAGTTCCTGCTATGTCACTTCCCCTT / 32
gag R3 / CCTGCTATGTCACTTCCCCTTGGTTCTCTCAT / 32
gag R4 / TTGATGGTCTCTTTTAACATTTGCATGGCTGC / 32
gag R44 / CCCATTCTGCAGCTTCCTCATTGATGGTCTC / 31
gag R55 / TCATTGATGGTCTCTTTTAACATTTGCATGGC / 32
gag Fpg probe / FAM-CAGCA-dR-[T(BHQ-1)]TATCAGAAGGAGCCACCCCACAAGATTTA-SpacerC3 / 36
LTR F1 / CCCTCAGATGCTGCATATAAGCAGCTGCTTT / 31
LTR F2+ / CATATAAGCAGCTGCTTTTTGCCTGTACTGGGT / 33
LTR F3 / CCTGTACTGGGTCTCTCTGGTTAGACCAGAT / 31
LTR F4 / CTGGGTCTCTCTGGTTAGACCAGATTTGAGCCTG / 34
LTR F5 / TTAGACCAGATTTGAGCCTGGGAGCTCTCTGGC / 33
LTR F6 / CCTGGGAGCTCTCTGGCTAACTAGGGAACCCA / 32
LTR R1+ / CCCTGTTCGGGCGCCACTGCTAGAGATTTT / 30
LTR R2 / TCTGAGGGATCTCTAGTTACCAGAGTCACACAA / 33
LTR R3 / ATCTCTAGTTACCAGAGTCACACAACAGACGG / 32
LTR R4 / CCAGAGTCACACAACAGACGGGCACACACTAC / 32
LTR Fpg probe / FAM-CACTG-dR-[T(BHQ-1)]TTAAGCCTCAATAAAGCTTGCCTTGAGTG-SpacerC3 / 36
LTR Exo probe+ / GCTTAAGCCTCAATAAAGCTTGCCTTGAG[T(FAM)]G-[dSpacer]T-[T(BHQ-1)]CAAGTAGTGTGTGC-SpacerC3 / 48
pol F1 / CCCTACAATCCCCAAAGTCAAGGAGTAGTAGAA / 33
pol F2 / CCCAAAGTCAAGGAGTAGTAGAATCTATGAATA / 33
pol F3 / TAGTAGAATCTATGAATAAAGAATTAAAGAAAAT / 34
pol F4 / ACAGCAGTACAAATGGCAGTATTCATCCACAAT / 33
pol F5* / TGGCAGTATTCATTCACAATTTTAAAAGAAAAGG / 34
pol R1 / TGTATTACTACTGCCCCTTCACCTTTCCAGAG / 32
pol R2 / CTGTAATAAACCCGAAAATTTTGAATTTTTG / 31
pol R3*¥ / CCCGAAAATTTTGAATTTTTGTAATTTGTTTTTG / 34
pol R4 / TAATTCTTTAGTTTGTATGTCTGTTGCTATTAT / 33
pol Fpg probe / FAM-GTCTA-dR-[T(BHQ-1)]ATTCTTTCCCCTGCACTGTACCCCCCAA-SpacerC3 / 35
pol F5BIO¥ / BIO-TGGCAGTATTCATTCACAATTTTAAAAGAAAAGG
pol Exo probe*¥ / TGCTATTATGTCTACTATTCTTTCCCC[T(FAM)]GC-[dSpacer]C-[T(BHQ1)]GTACCCCCCAATCCCC-SpacerC3 / 48
+ Primers and probe sequences used for further development of the LTR RPA assay.
* Primers and probe sequences used for further development of the pol RPA assay.
¥ Primers and probe used for the ICS format of the RPA assay.
bp = nucleotide base pair; FAM = fluorescein amidite; dR = an abasic residue with a fluorophore attached to the ribose via a C-O-C linker; [dSpacer] = abasic site; [T(BHQ-1)] = Black Hole Quencher-1 bound to an internal Thymine residue; Spacer C3 = a moiety that replaces the 3’-OH group preventing nucleotide extension from an intact probe.