I have problems with pop up windows after earlier today I updated the software

I have a macbook pro, and I updated the software today, I have OS X 10.9
After I did this I started having problems in safari with pop up windows, before it only happened with some sites, but now almost every site I try to open it also opens 
pop up windows, and some sites have underlined words that link to other sites for advertising.
I really don't know what to do and I've read several posts of people that also have had my problem but I don't the solutions.

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