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. 2017 Jun 20;8(4):205–219. doi: 10.1080/21541264.2017.1318811

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© 2017 The Author(s). Published with license by Taylor & Francis

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way.

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Figure 8. — Breaking the 17-nt D loop microhelix into TAGCC₄ repeats. In the sequence logo, different modes of folding the D loop microhelix are indicated (TAGCCTAGCCTAGCCTA repeat folding; folding in a 17-nt microhelix or a 31-nt minihelix (mH); folding in the cloverleaf tRNA (CL)). Parentheses indicate base pairing. Asterisks indicate unpaired bases. Tests A–I are predicted to test as similar for a perfect repeat. Degeneracy in the third repeat (invariant A14 vs. invariant G19) causes the test in Fig. 9H to test as negative for similarity.