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. 2017 Apr 6;7:711. doi: 10.1038/s41598-017-00764-x

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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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A motif from Thermus thermophilus 16S ribosomal RNA. (a) Nucleotides 932–936 and 1379–1385 are similar in sequence to IL2 of PSTVd; interactions are extracted by x3dna-dssr from PDB 1FJG⁷⁸. (b) A logo of the motif (a) from an alignment of 23,500 bacterial 16S ribosomal RNAs⁵⁴. (c) A logo of the motif (a) for 1850 sequences from the same alignment as used in (b), but sequences identical to the consensus 5′ CGCAC/GUUCCCG 3′ were removed. Columns with less then 1% of nucleotides and sequences not fully spanning the motif or containing nucleotides other then [AUCG] were removed from the alignments used for the logos.