I use CopyScape but it's more of a plagiarism tool then an actual duplicate content identifier tool. I say that because just because a few lines of text are the same on a page, that doesn't mean Google will remove it from the SERPs. Generally duplicate content has to be a substantial portion of a webpage to be considered duplicate content.
I would first dig into Moz Analytics and see WHY you are generating duplicate content before I would worry about what part of the page is duplicate.
- Have you set canonicals on your pages?
- Does your site produce session IDs?
- Do you have pagination?
- Are you copying and pasting text from page to page to fill up your site?
Google has said time and time again, duplicate content issues are rarely a penalty. It is more about Google knowing which page they should rank and which page they should not. Take a look at why you are getting the duplicate content issue and then we can help you resolve it or give advice on what to do next.