Note that using a loop is likely to be quite slow. Instead, as long as the number of rows is a multiple of the number of elements that you wish to flip, then this is easy without any loops using reshape and flipud :
N = 5; % number of elements in each group
A = (1:4*N).'; fake data
B = reshape(A,N,[]);
B = flipud(B);
B = reshape(B,[],1);
If the number of elements of A is not a multiple of the then you will need to pad A to become a multiple. You can rearrange the whole code to fit on one line:
B = reshape(flipud(reshape(A,N,[])),[],1);
