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What kind of traffic are you getting, simply providing a small percentage CTR is not an accurate representation. If that's the percentage of 10 visitors or 2,000 visitors it kind of makes a difference.
My recommendation would be to forget CTR right now, if you are only getting a few visitors. Focus on getting more visitors, quality content, backlinks, general marketing mumbo jumbo, then get to work on ad placement. With a larger sample it's easier to do CTR studies to find out where your hot spots would be. Otherwise it's just a shot in the dark and guess work.
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