Why are you sorting s in s=sort(s)?
There's no need to manually eliminate the NaN values and there's no need to use a loop.
Here's a demo. bci is 2*n for n columns of s showing the [lower; upper] CIs.
u = rand(6,500) .* (1:6)';
s=u';
% s=sort(s);
nBoot=2000;
[bci,bmeans] = bootci(nBoot,{@(v)mean(v,'omitnan'),s},'alpha',.1,'type','per')
bmu = mean(bmeans)
Plot CIs to see if they make sense. The red lines within each boxplot show the median values. The light blue error bars are the CIs around the mean values.
clf()
boxplot(s)
hold on
errorbar(1:numel(bmu), bmu, bmu-bci(1,:), bmu-bci(2,:), 'LineStyle', 'none')
