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Will the lower CTR have any effect on the quality or price of the Adsense ads displayed on the site?
Will the lower CTR have any effect on the ads displayed on my other site?
Any help will be appreciated.
One thing we do know is that likelihood of conversion (as projected by Google's "smart pricing" formula) can have a direct impact on the actual price paid by the advertiser and--as a consequence--on the amount received by the publisher. As long as the clicks on your new site convert decently for advertisers (or seem likely to do so, according to Google's "black box"), you shouldn't have to worry too much about the quality or price of the AdSense ads displayed on the site.