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Ditto daycare question?

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a lot of times when I try to breed my ditto with another Pokemon it says that they dont seem to like each other much, does it make a difference with nature and evs and if yes what would be best?

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With breeding it goes like this

Same species and different ID number
"The two seem to get along very well"
69.87% chance of getting an egg every 255 steps

Same species, same ID number
"The two seem to get along"
49.5% chance every 255 steps

Different species same ID number
"The two don't seem to like each other"
19.81% chance of an egg every 255 steps.

Different species different ID number
"The two seem to get along"
49.5% chance ever 255 steps

Different egg group, same gender, or undiscovered egg group
"The two prefer to play with other Pokemon"
0% chance to get an egg

These are the only things that influence breeding. Also everybody can breed with Ditto unless they are legendary or baby Pokemon.

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sometimes when it said the two prefer to play with other pokemon i still get an egg sometimes
Than your game must be glitched. It's impossibly for an Egg to happen in that case. Also, Manaphy is not in the Undiscovered Egg Group - so it can breed.
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I am unsure about EV's but nature does make a difference and I always try to get Pokemon with hardy or serious natures but that is because there are no hindering stats.

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No, EVs do not make a difference, and neither do Natures. The only reason why it would not work is because the Genders or Egg Groups are an invalid combination, or you aren't giving enough time. Various combinations work faster than others - patience is important. Eggs don't happen immediately - give them some time to do... whatever they do. O_o

More information on Bulbapedia here: http://bulbapedia.bulbagarden.net/wiki/Pokémon_breeding

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