If you get a message like this 

You should try to use the Web Engine with Auto-Detect Base Code, this will ignore duplicated after 50. The issue may lie that your check is producing a large amount of duplicates, this could be the case if your code base is using a popular library it will be detected in a lot of web matches, so the Auto-Detect Base Code will ignore the duplicates (which tend to be the really popular code found online). 

You can change the check settings by clicking on the settings tab, and selecting the option highlighted below:
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