Identification of <i>LINE-1</i> and <i>Alu</i> consensus sequences followed by analyses on repeat masker [48] and ClustalW.

<p>(A-C) Alignment of the 5’ end region of <i>L1</i> elements. The alignments include the old <i>L1PA</i> consensus sequence (A), the young <i>L1Hs</i> consensus representative to <i>L1-Ta-0</i> (B) and <i>L1-Ta-1</i> (C). The positions of the primers used in this study are shown with arrows, indicating the primers have been well designed to target all <i>L1Hs</i> elements including the <i>L1</i> consensus sequence (accession no. X58075). (D-F) Alignment of the <i>Alu</i> sequences of young (<i>AluY</i>), intermediate (<i>AluS</i>) and old (<i>Alu J</i>) individual <i>Alu</i> repeats. Based on these <i>Alu</i> consensus sequences, the primer sets specific to methylated <i>Alu</i> sequences were designed. The positions of the primers used in this study are shown with arrows.</p> <p>(PDF)</p>