Looking at the first few numbers in the sequence we see that the remainders cycle in the order 1, 2, 2, 4, 3, 2 with period 6.
So we just need to find the remainder when 1000 is divided by 6. This is 4. The numbers above correspond to remainders of 0, 1, 2, 3, 4, 5 respectively, so the remainder when a1000 is divided by 5 is 3.