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. 2017 Oct 24;7:13892. doi: 10.1038/s41598-017-14108-2

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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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Bootscanning analysis of the recombination structures for newly identified URFs. Recombination patterns of CRF01_AE/B and CRF01_AE/CRF07_BC are shown in Figure A and Figure B, respectively. Unless otherwise specified, the general conditions for bootscanning analysis were as follows: Window: 300 bp, Step: 20 bp; GapStrip: on, Reps: 100, Kimura (2-parameter), T/t: 2.0, Neighbor-joining. Some analyses were performed after slight adjustments to the Window and Step sizes. The exception sequences include NB130937 (Window: 350 bp), NB132624 (Window: 350 bp), HZ130947 (Window: 250 bp) and HZ130198 (Window: 400 bp, Step: 30 bp). The reference sequences, including CRF01_AE, B, B’, CRF07_BC and K (outlier), are shown at the bottom left of the figure.