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. 2013 Aug 22;41(21):9610–9621. doi: 10.1093/nar/gkt733

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© The Author(s) 2013. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 2. — Average transition probabilities as functions of base pair location are shown for a set of 12 841 mouse genes that were aligned at their TSS (located at position 0) and oriented to transcribe to the right. These calculations were performed at T = 310 K and superhelix density σ = −0.06. Each panel shows results for a transition when it is analyzed in isolation, and when it competes with all others. Panel (a) shows denaturation, (b) shows the B–Z transition and (c) shows cruciform extrusion. The vertical scale is different for cruciforms compared with the other two transitions.