Ahmed Supplementary Figure 1

1. Ahmed Supplementary Figure 1 a b c

2. Ahmed Supplementary Figure 2 a b c CG GC d CHG GHC -log(p-value) Methylation difference

3. Ahmed Supplementary Figure 3 met1 a Methylation density ddc Methylation density b TE sequence TE sequence TE sequence 5’ flank 5’ flank 5’ flank 3’ flank 3’ flank 3’ flank TE end TE end TE end TE start TE start TE start rdd 800bp 800bp 800bp 600bp 600bp 600bp 400bp 400bp 400bp 200bp 200bp 200bp 200bp 200bp 200bp 400bp 400bp 400bp 600bp 600bp 600bp 800bp 800bp 800bp 1kb 1kb 1kb 1kb 1kb 1kb Methylation density c

4. Ahmed Supplementary Figure 4 CG Methylation density TE sequence TE sequence TE sequence CHG 3’ flank 3’ flank 3’ flank Methylation density 5’ flank 5’ flank 5’ flank TE start TE start TE start TE end TE end TE end CHH Methylation density

5. Ahmed Supplementary Figure 5 a b g h Methylation density Methylation density Methylation density Methylation density 5’ flank TE 5’ flank TE 5’ flank 5’ flank TE TE TE 3’ flank 5’ flank 5’ flank TE TE TE 3’ flank i j c d Methylation density Methylation density Methylation density Methylation density TE 3’ flank TE 3’ flank f k l e Methylation density Methylation density Methylation density Methylation density TE 3’ flank TE 3’ flank

6. Ahmed Supplementary Figure 6 Cm = methyl-cytosine N = # cytosines in context having sufficient sequencing depths CG = 100% CHG = 100% CHH = 51% Pattern Assigned = MMM (Methylated CG, Methylated CHG, Methylated CHH) x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x