In the MapRRCon pipeline, ChIP-seq data are first aligned to the human reference sequence hg38. Both unique (filled gray boxes) and multiply aligned reads (hollow gray boxes) are then extracted and mapped to the 1620 annotated L1HS sites based on their genome coordinates. We exclude reads with partial alignment (soft clipping), more than 3 mismatches and any indels (boxes with red lines). Filtered reads are subsequently mapped to L1HS consensus sequence to obtain compiled reads. Finally, we generate coverage profiles for both ChIP and INPUT data and then perform median-based normalization. We then call peaks from the normalized data using a self-developed algorithm that is specifically designed for short consensus sequences.