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It's your choice on what you catch with it. To be honest, you wouldn't even have to use it at all if you figure out your own strategy to lower the catch rate of the Pokémon you're trying to catch. But yeah, if you want to use it, use it on a Pokémon you may have a difficult time catching like the running Raikou or Entei. Like said though, it's really your choice what you use it on.
