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. 2018 Aug 13;19(Suppl 6):566. doi: 10.1186/s12864-018-4920-6

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© The Author(s) 2018

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 2 — Illustration of two example repeats that are not fully constructed by the original REPdenovo. Highly frequent 30-mers of one human individual NA19230 are aligned to the human consensus repeats in Repbase. The left part (a) shows the alignments on repeat “LTR2B”. Two gaps are formed when 30-mers originated from highly divergent regions have low frequencies due to repeat copy divergence. The right part (b) shows the alignments on repeat “LTR10C”. The colored bars are variations on copies. The assembled contigs are fragmented because the 30-mers are of highly divergence