I think it is fair to say they all markup and it is expected that you will negotiate. They, of course, hope you don't.... but it is assumed you will try.
There is no way for you to know what they bought it for, but it is fair to assume they either got it on trade or bought at auction; both well below what you see from ANY of the pricing websites. The beauty of the "trade in" is because so much about a new car purchase is variable in terms of financing and hold back that you can say your giving someone 3k for a trade in, when in reality they managed to get the car from you for 1k.
In general, expect the sticker price to be around 20-30% higher than what you would call their "bottom dollar" price. I sey, in general, some may be higher and some lower.
Your typical used lot that has cars from 3 to 5k usually have no car worth more than 2 or 3 at auction. A 3k car on their lot they managed to pick up at auto auction for 1k, maybe 1500. I have heard from friends that this lot offers the highest profit point. People easily accept 3k as a price and don't get how the dealer got it.
These cars, the 3 to 5k range are usually in crappy condition. But, I was just making a point that 50% markup isn't out of the realm of possibility.
It works like this. For every sucker who doesn't negotiate and buys it at sticker, you have s savvy person pushing the price down. A normal dealership manages to make money by knowing that you will get some willing to pay sticker (well ABOVE what it cost to get it) and those that don't.
How low they are willing to go depends on how the dealership is doing. I manged to pick up my 05 that had a sticker of 15.9 for 12.5..... that was a substantial move down.
It was a tough though and I had to leave the lot. Getting him to shed 3k, plus add in tax and tag (which is worth 1500 alone) was a tough fight and I could tell he couldn't go any lower and still make a profit. I manged to get a car that was KBB'ed for 15-17k for around 11k.....
So. If you are willing to stick your ground and WALK AWAY... you can do really well.