Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures

Table 3 Similarity of predicted structures for species pairs.

Species comparison	Prediction Method	(P+U)/all	P/all	U/all
Genes shorter than 800 bp
Across all 4 yeasts	MFE	27% ± 0.6	17% ± 0.3	10% ± 0.5
	Mc	27% ± 0.4	9% ± 0.2	18% ± 0.3
*S. cerevisiae – S. paravensis*	MFE	63% ± 0.6	36% ± 0.3	27% ± 0.3
	Mc	64% ± 0.5	22% ± 0.4	42% ± 0.5
*S. cerevisiae – S. mikitae*	MFE	59% ± 0.3	34% ± 0.2	25% ± 0.2
	Mc	61% ± 0.4	20% ± 0.4	41% ± 0.6
*S. cerevisiae – S. bayanus*	MFE	42% ± 0.4	23% ± 0.5	19% ± 0.1
	Mc	59% ± 0.3	20% ± 0.0	40% ± 0.5
All genes
Across all 4 yeasts	MFE	25% ± 0.3	8% ± 0.1	16% ± 0.2
	Mc	25% ± 0.4	16% ± 0.2	9% ± 0.1
*S. cerevisiae – S. paravensis*	MFE	61% ± 0.4	36% ± 0.2	25% ± 0.2
	Mc	63% ± 0.3	22% ± 0.3	41% ± 0.4
*S. cerevisiae – S. mikitae*	MFE	58% ± 0.2	35% ± 0.2	23% ± 0.1
	Mc	60% ± 0.3	20% ± 0.3	40% ± 0.4
*S. cerevisiae – S. bayanus*	MFE	57% ± 0.2	34% ± 0.1	23% ± 0.1
	Mc	58% ± 0.2	20% ± 0.2	39% ± 0.4

The average percentages of sites (± variances) unambiguously predicted to be paired (P/all) and/or unpaired ((P+U)/all, U/all) for the respective species comparison using RNAfold MFE and McCaskill's (Mc) algorithm are presented.

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