Fig. 1

Experimental protocol design. a Scheme of SVA element structure. b Sequence alignment of SVA_1 and SVA_2 primer binding sites and SVA, Alu subfamily consensuses. The SVA_1 and SVA_2 primer sequences are shown above of the alignment and the amplification directions are indicated by arrows. Top row of the sequence alignment shows the sequences of the primer binding sites of SVA_1 and SVA_2. SVA_1 binding site includes the SVA characteristic deletion as compared to Alu sequences. Dots in the alignment represent the same nucleotides as the primer binding site sequences. Deletions are shown as dashes and mutations are shown as the correct base for the consensus. c SVA-specific amplifications during ME-Scan-SVA library construction and the final DNA fragment structure. The DNA library after second-round amplification is size-selected at ~500 bp (an example electropherogram image is shown). White box: adaptor; grey box: index; dark green box: flanking genomic region; yellow box: TSD; orange box: (CCCTCT)_n hexamer simple repeat; light green box: SVA Alu-like region