I have solved the problem using reshape and con2seq: That makes the input and target of same size!
u=X(200:500,:); y=T(200:500,:);
r1=length (u); c1=size(u,2); % Taking size of Input vector r2=length (y); c2=size(y,2); % Taking size of Target vector
u=reshape(u,c1,r1); %Making cell array of Input Matrix %u=num2cell(X,1); u=con2seq(u);
y=reshape(y,c2,r2); %Making cell array of Target matrix %y=num2cell(T,1); y=con2seq(y);