To my understanding, some clones where used for special squads and missions, most where murdered or (since there clones) got rid off, in ep3 you can see obi talking about: 'its gonna take a while for the clones to understand what happended", i think the emperor used his clones to colonize planets, get new recruits, and when he got himself a army, he got rid of em, since if they found out the emperor whas the real traitor, they would turn on him. So imo he just mass-murdered 'em, tis a shame.
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