Table 2.

Comparison of conserved optimal codon numbers at paired and unpaired sites.

	RNAfold (S. cerevisiae)		ALIfold
	MFE	Mc	MFE	Mc
Amino acids with GC-ending optimal codons
LeuTTG	1.380 ***	1.273 ***	1.811 ***	1.456 ***
LysAAG	1.772 ***	1.654 ***	2.019 ***	1.654 ***
PheTTC	1.075 ***	1.120 ***	0.786 NS	0.864 **
TyrTAC	0.809 NS	0.720 NS	0.741 NS	0.631 NS
HisCAC	0.707 NS	0.600 NS	0.568 NS	0.657 *
AspGAC	0.813 NS	0.838 NS	0.656 ***	0.746 **
AsnAAC	0.891 *	0.831 NS	0.725 **	0.637 NS
Amino acids with one GC- and one AT-ending optimal codon
IleATC	1.318 ***	1.254 ***	1.555 ***	1.049 ***
IleATT	1.272 ***	0.978 ***	1.561 ***	1.009 ***
ValGTC	0.585 NS	0.852 ***	0.734 ***	0.560 ***
ValGTT	0.705 *	0.794 NS	0.806 *	0.686 NS
ThrACC	0.838 **	0.921 ***	0.811 ***	0.750 ***
ThrACT	0.940 ***	0.876 ***	0.932 ***	0.655 ***
SerTCC	0.614 NS	0.668 NS	0.583 NS	0.591 NS
SerTCT	0.794 NS	0.816 NS	0.816 ***	0.985 ***
Amino acids with AT-ending optimal codons
AlaGCT	0.968 **	0.904 ***	1.073 ***	0.883 ***
ArgAGA,CGT	0.588 ***	0.545 ***	0.518 ***	0.460 ***
GlyGGT	0.894 NS	0.779 NS	0.901 ***	0.752 NS
GlnCAA	0.442 ***	0.353 ***	0.293 ***	0.278 ***
GluGAA	0.946 ***	0.350 ***	0.386 ***	0.315 ***
ProCCA	0.851 NS	0.734 NS	0.729 **	0.689 *
CysTGT	0.500 NS	0.382 NS	0.755 ***	0.403 NS

Separately for each amino acid, I combine contingency tables of the different genes. Mantel Haenzsel estimators and significances are presented, with W_MH <1 = lower optimal codon use at paired than at unpaired sites. Structure prediction is based on ALIfold and RNAfold using MFE and McCaskill's (Mc) algorithm.

* < 0.05, ** < 0.01, *** < 0.005, NS = not significant