% canonical_loop(n) makes a loop of n RNA bases with canonical base pairs

function [Pi] = canonical_loop(n)

Pair = ['AU'; 'UA'; 'CG'; 'GC'];     % canonical base pairs
Freq = [1 1 1 1]/4;                  % base pair frequencies

Loop = ['AAAG'; 'GGGA'];             % possible loop ends
L    = length(Loop(:,1));            % number of possible loops

Pi   = Loop(rando(ones(L,1)/L),:);   % start with a random loop end

for i=1:round(n/2),
  b = rando(Freq);
  Pi = [Pair(b,1) Pi Pair(b,2)];     % add this pair to front and back of Pi
end