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\caption{Results of the evolutionary analyses for positively selected sites for Spike ali nucl-VIRULIGN. P-values were achieved by performing chi-squared tests on twice the difference of the computed log likelihood values of the models disallowing (M7) or allowing (M8) $dN/dS>1$. The BEB column lists rapidly evolving sites with a $dN/dS>1$ and a posterior probability $>0.95$, determined by the Bayes Empirical Bayes implemented in \texttt{Codeml}. Amino acids refer to \emph{SARS-CoV|GenBank:AY278741}. Note that INDELs and the stop codon were removed from the alignment prior to evolutionary analysis, so shown positions are based on the \textbf{alignment without gaps}. Fragments arising from insignificant breakpoints (adjusted p-value $>$ 0.1) are marked with an asterisk.}\\\\
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		\bf Region &  \bf M7 vs M8 & \bf M7 vs M8 & \bf \% sites with & \bf avg($\omega$) & \bf M8 BEB \\
    & ($\chi^2$) & p-value & $\omega>1$ &  & ($PP>0.95/>\textbf{0.99}$) \\

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\multicolumn{6}{c}{{\bfseries \tablename\ \thetable{} -- continued from previous page}} \\\toprule		\bf Region &  \bf M7 vs M8 & \bf M7 vs M8 & \bf \% sites with & \bf avg($\omega$) & \bf M8 BEB \\
    & ($\chi^2$) & p-value & $\omega>1$ &  & ($PP>0.95/>\textbf{0.99}$) \\
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		%% F61
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    \multicolumn{6}{l}{\textbf{F61}}  \\
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full (aa 1--1219) &  8.51  &  $0.014$  &  4.13  &  1.0  &  none \\ 
frag1 (aa 1--842) &  4.66  &  $0.097$  &  0.91  &  1.96  &  none \\ 
frag2* (aa 843--1219) &  0.0  &  $0.999$  &  NA  &  NA  &  NA \\ 
		%% F1X4
	  \midrule
    \multicolumn{6}{l}{\textbf{F1X4}}  \\
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full (aa 1--1219) &  12.24  &  $0.002$  &  2.41  &  1.0  &  none \\ 
frag1 (aa 1--842) &  10.21  &  $0.006$  &  1.21  &  1.5  &  none \\ 
frag2* (aa 843--1219) &  0.0  &  $0.999$  &  NA  &  NA  &  NA \\ 
		%% F3X4
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    \multicolumn{6}{l}{\textbf{F3X4}}  \\
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full (aa 1--1219) &  18.62  &  $<0.001$  &  2.16  &  1.0  &  none \\ 
frag1 (aa 1--842) &  27.92  &  $<0.001$  &  1.89  &  1.15  &  none \\ 
frag2* (aa 843--1219) &  0.0  &  $0.999$  &  NA  &  NA  &  NA \\ 


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