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At the moment in google Analytics when I view the in-page analytics section it shows the % of what's clicked on a page.

Different links that go to the same page are currently registered as the 'same' link, for obvious reasons.

What's the best way to separate the two so I can see which link is being used more? Is there any way to do this with GA without changing any code?

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Good news! Analytics now comes with just such an option (Enhanced Link Attribution). When you get the code snippet from Analytics you can now choose to add in this extra tracking code. This is enabled under the Properties tab.

See https://support.google.com/analytics/bin/answer.py?hl=en&utm_id=ad&answer=2558867

And the blog article from Google announcing it:

http://analytics.blogspot.ie/2012/11/announcing-enhanced-link-attribution.html

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In-page analytics has or was in beta for a while and that is one draw back, links on a page leading to the same target show the same stats.

You should use event tracking on the links to track clicks, and conversions

https://developers.google.com/analytics/devguides/collection/gajs/eventTrackerGuide

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