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. 2017 Oct 16;7:13202. doi: 10.1038/s41598-017-13402-3

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© The Author(s) 2017

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Design of Alu Primers and Probe. (a) Graphical representation of the Alu subfamily consensus sequences visualized by the WebLogo program. (b) The Alu model sequence and the primers and probe used in this study. The sequences of our primers and probe (101 F, 206 R, and 144RH, in red) and those of McBride et al. (98 F, 188 R, and 133FH, in blue) are depicted at the corresponding positions in the Alu model sequence (in bold). (c) The number of 19-nt sequences in the Alu model sequence that matched rodent genomic material. (d) The number of 19-nt sequences in the Alu model sequence showing a 100% match with rodent genomes. (e) Bimolecular secondary structures in homo- and heterodimers of the forward primer (101 F) and the reverse primer (206 R). (f) Bimolecular secondary structures between the primers and probe (144RH).