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. 2017 Jun;27(6):1039–1049. doi: 10.1101/gr.214973.116

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© 2017 Löytynoja and Goldman; Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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Figure 2. — Example events detected in human. (A) A near-perfect inverted repeat in chimp (dashed black arrows, the one mismatch indicated with asterisks) has been converted into a perfect inverted repeat (red arrows) in human (top). The cluster of six additional dissimilarities (dotted line) in fact represents perfect inversion of the 6-bp spacer sequence and makes the template switch (bottom) a likely explanation (Original data: http://grch37.ensembl.org/Homo_sapiens/Location/Compara_Alignments?align=548;r=2:85464419-85464489). (B) Predicted DNA secondary structure before (chimp; bottom) and after (human; top) the template switch event. The dotted arrows indicate the reverse-complemented spacer region, which the four-point model explains with a single event. (C,D) Additional complex mutation patterns (mismatches in lower case) that can be explained by a single template switch event. (C) Event “1-3-2-4” only converts the spacer sequence (http://grch37.ensembl.org/Homo_sapiens/Location/Compara_Alignments?align=548;r=9:113151972-113152067). (D) Event “3-1-4-2” converts the spacer sequence and creates two inverted repeats (red and magenta arrows) (http://grch37.ensembl.org/Homo_sapiens/Location/Compara_Alignments?align=548;r=2:135684492-135684613).