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. 2012 May 31;40(18):e138. doi: 10.1093/nar/gks475

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© The Author(s) 2012. Published by Oxford University Press.

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

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Figure 5. — Free energy penalty for focus mismatch (m = A, x = 10) derived from experimental intensities according to Equation (8) as a function of the location x + Δx of the second mismatch (n, x + Δx). For each |Δx > 4| the three values, one per possible mismatch, are indicated by the letter representing the mismatching nucleotide n of the probe. The target sequence is written in top of the x-axis in 3′ – 5′ notation, t₁ in left pane, t₂ in right pane. The dotted line corresponds to the median value of the 48 estimates. The circled point is the estimate without second mismatch coming from Equation (4). For this particular mismatch, the free energy penalty for both t₁ and t₂ is identical and corresponds to .

Inline graphic — Free energy penalty for focus mismatch (m = A, x = 10) derived from experimental intensities according to Equation (8) as a function of the location x + Δx of the second mismatch (n, x + Δx). For each |Δx > 4| the three values, one per possible mismatch, are indicated by the letter representing the mismatching nucleotide n of the probe. The target sequence is written in top of the x-axis in 3′ – 5′ notation, t₁ in left pane, t₂ in right pane. The dotted line corresponds to the median value of the 48 estimates. The circled point is the estimate without second mismatch coming from Equation (4). For this particular mismatch, the free energy penalty for both t₁ and t₂ is identical and corresponds to .