Help with term paper

I am confused on the Works Cited List. Throughout the paper are notations (numbers) at the end of the sentences to coincide with the reference that was used. Since the Works Cited List has to be in alphabetical order, than is alright to have number 5 in the first paragraph of the paper and the number one at the end?

[Tdol]

If you're using the number system, then use numerical order in your references at the end.