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They appear depending on trade values, location etc. But there is a random chance as well. So the best thing you can do is hope, and maybe build up Manhattan a little...
 
Playing as Russia, a CoT appeared in Massachusetts almost immediately after the colony was upgraded to a city. In the same game, Portugal has a CoT in southern Africa.

Is there a limit to the number of CoTs which may be active in a game?
 
There is a value in province.csv for every province in the game (829 of them) which ranges from -3 to +5 called CoT historical modifier.
Thus, CoT placement is somewhat random but certain places are more common then others.

Having a well developed city in an almost deserted area, increases the chance for a CoT to pop up there dramatically too.