You can make them equal in the following way, but you might want to assign any other value instead of "0" which best match your purpose.
fs = 40;
t1 = 0:( 1/fs ):6; S2 = [ sin( 2*pi*5*t1( t1<=2 ) ), sin( 2*pi*10*t1( 2<t1<4 ) ),sin( 2*pi*15*t1( t1>4 ) ) ];
for i = length(t1)+ 1 : length(S2)
t1(:, i) = 0;
end
plot(t1,S2)
