For anyone in the future, I solved it. Here is the code. Replace S and A with any letters
%this part constructs the matrix
square=cell(5);
alpha='A':'Y';
for i=1:25
square{i}=alpha(i);
end
square=square';
[row,col]=find(ismember(reshape(alpha,5,[])',['S' 'A'])==1); %find the corners
%of submatrix given two letters
submat=square(row(1):row(2),col(1):col(2)); %find indices of corners and construct a submatrix
if isempty(submat) %if matrix is empty, reverse rows
submat=square(row(2):row(1),col(1):col(2));
end
disp(submat)
