Note: "checkout" is all one word. "Check out" is a phrasal verb.
If you really want to keep your word order, you need a couple of commas: "Cigarettes, at supermarkets, are usually sold by the checkout". Otherwise it sounds as if "cigarettes at supermarkets" is a recognised common term.
For info, in the UK, it depends on the layout of the supermarket. In smaller ones, the cigarettes are usually on a wall display behind the tills so you take your shopping to the checkout and then ask the assistant to add the cigarettes to your shopping. At larger supermarkets, there are separate areas where you can buy cigarettes and, sometimes, sweets, newspapers and other small items.
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