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On my site, blending the ads in resulted in a lower CTR.
I think that what works best depends on the type of site.
but am wondering if putting them in the top, middle or side would make a difference.
Make a couple of channels and give it a test run to find out. You may be surprised.
I think it will vary from site to site, depending on how your content is organized, but it's definitely worth a test.
To be specific, almost all of my pages are black text on white backgrounds with blue links. What I had originally were highly contrasting ad colors, such as dark blue background with white text. Then I changed all the ads to light-grey border, white background, and blue links, so they look virtually like regular content. I am even considering changing the font of my website to match the Adsense font.
Unfortunately, although CTR was 20% higher, average earnings per day were 17% lower for the same period. I think this is due to other factors though, like declining relevance of the content in my pages, declining advertising expenditures, and perhaps temporary traffic spikes to high revenue pages during the prior period.