1. ab c Ahmed Supplementary Figure 1

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

3. Ahmed Supplementary Figure 3 ddc a rdd met1 b c TE start 200bp400bp600bp800bp 1kb TE end 200bp 400bp600bp800bp 1kb 3’ flank TE sequence 5’ flank Methylation density TE start 200bp400bp600bp800bp 1kb TE end 200bp 400bp600bp800bp 1kb 3’ flank TE sequence 5’ flank Methylation density TE start 200bp400bp600bp800bp 1kb TE end 200bp 400bp600bp800bp 1kb 3’ flank TE sequence 5’ flank Methylation density

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

5. ab dc e fkl ji gh Ahmed Supplementary Figure 5 3’ flankTE 5’ flankTE Methylation density 5’ flankTE Methylation density 3’ flankTE Methylation density 3’ flankTE Methylation density 3’ flankTE Methylation density 5’ flankTE Methylation density 5’ flankTE Methylation density 5’ flankTE Methylation density 3’ flankTE Methylation density 3’ flankTE Methylation density 5’ flankTE Methylation density

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