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So I'm breeding my first team in X and Y, and I'm trying to get a Deino with perfect IV's. My only ditto is one with 6 perfect IV's, and it holds Destiny Knot, which transfers 5 IV's. However, none of the Deinos I have gotten so far has even 1 perfect IV! I checked, the little perfect IV markers are there. I know the ditto has perfect IV's also. I'm just straight breeding those two until I get one with perfect IV's in HP, Def, SAk, SDf, and Spd. What am I missing here?

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you have to mark the iv markers. they dont get marked on thier own.

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Remember, Destiny Knot only transfers 5 of the 12 possible IVs to offspring. I explain this in more elaborate detail here. IV Breeding requires patience and luck, so you will get that 5 IV Deino sooner or later.

Source: Above link and Experience

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Thanks
You mean 5 of the 6. It takes 5 random IVs from either Pokemon and puts them in the offspring.
I think you might be mistaken -- the mechanic is simply that the offspring inherits 5 IVs from its parents. It's not one parent specifically, so the answer is correct in saying that that there are twelve possible IVs because between the two parents because there are twelve different values that could be passed down. Serebii supports this: http://www.serebii.net/itemdex/destinyknot.shtml