Your code is already set up to capture a value at every iteration
C1(i)=...
There is, however, a logic flaw that I see. The equation indexes the next row of C1 before there is a value there. Perhaps try something like this?
for i=1:1000000
C1(i+1) = C1(i) + dt*(E1*K1 - R1*C1(i)*Ci - Y1*D1*C1(i)*p1);
end
