Fig. 1

ME-specific amplification during ME-Scan library construction. For each ME type library, two rounds of nested amplification are performed. The ME-specific amplification primers (ME1 and ME2) are shown as thin arrows above the ME consensus and the amplification directions are indicated by the arrows. First-round amplification primers (ME1) are biotinylated (green star) for enrichment, and the second-round nested primers (ME2) include the Illumina sequencing adaptor (orange box). Different components of AluYb, SVA, and L1HS consensuses are labelled. The final paired-end sequencing reads from the resulting sequencing libraries are represented with blue arrows (ME Reads) and black arrows (Flanking Reads), respectively. Blue box: ME sequence; grey box: flanking genomic region; green star: biotin; orange box: Illumina sequencing adaptor