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They are basiclly the same, but shear numbers is what changes. When naruto uses his regular chakra he can summon about a few hundred. But when he uses the nine-tails chakra he can make several thousand. And also if he is in Nine-Tails form without the cloak they become super-charged (so to speak) with nine-tails chakra making them as strong as the orignal Naruto. BUt while he has the cloak on he is incapable of creating the clones, he has never been shown with the cloak on and making shadow clones.

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