First Section: If I undestand the question correctly, you are looking for compare multiple arrays, is this?
a1= [0 0 0 1 0 1];
a2=[0 1 1 1 0 1];
a3=[1 0 1 0 0 0];
r1=sum(a1==a2);
r2=sum(a2==a3);
r3=sum(a3==a1);
The maximum result of r is more related to each other, in this example r1=4, hence it might be more related (a1 and a2)
Second question, to hold the scaler value, you can use array indexing in this case, like r(i) , if the result is vector you have to look for cell array to hold the data.
