Table 2. Primers used in bisulfite sequencing.

Primers	Structure (5′–3′)
LTR11bisfor1	TATAAGTTGGATTTGTATTAGAGGATTTG
LTR11bisfor2	GGTTTAGAGTTTAGGAGTTTTGGTTGTTAG
LTR11bisrev1	CTTACTCACACTAAACCTAACAATAAATACTC
LTR11bisrev2	ACATCCCCAACCTACATCTCCCTC
LTR12bisfor1	GTAGGATATGAAGTATGGAGAATAGGTAAG
LTR12bisfor2	TATTTTTGTAGGGATGTATAGTGTTGGG
LTR12bisrev1	CACCTATAAACCATCCTTTACTATTATAAAC
LTR12bisrev2	AAAATCCTTTTACCTCCATTCATCTTC
LTR27bisfor1	TTTTGTTATTGAGAAGTATATAGTTTAGTGG
LTR27bisfor2	GGAAGAAGAGTTAATTGGTGGTATAAGG
LTR27bisrev1	AAATCTCTAATACCATTCCTCCTACC
LTR27bisrev2	ATAAAAATCCCAATATTAAAATCACATCC

The PCR primers were designed to be fully complementary to the deaminated DNA strand and did not include CG dinucleotides. First round amplifications (with primers for1 and rev1) were performed in 25 µl of PCR buffer for Taq DNA polymerase (Promega) containing 200 µM of each dNTP, 1.5 mM MgCl₂, 0.4 µM of each primer and 1 U of Taq DNA polymerase (Promega), with individual 3 µl beads in a thermal cycler (MJ Research) as follows: 35 cycles at 95°C for 20 s, 63°C for 30 s, and 72°C for 1.5 min. Amplifications using nested primers (for2 and rev2) were performed using 1 µl of the PCR mixture after the first round under PCR conditions as follows: 22 cycles at 95°C for 20 s, 60°C for 30 s, and 72°C for 1.5 min.