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As a reminder, supplemental results aren’t something to be afraid of; I’ve got pages from my site in the supplemental results, for example. A complete software rewrite of the infrastructure for supplemental results launched in Summer o’ 2005, and the supplemental results continue to get fresher. Having urls in the supplemental results doesn’t mean that you have some sort of penalty at all; the main determinant of whether a url is in our main web index or in the supplemental index is PageRank.
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That statement still holds. It’s perfectly normal for a website to have pages in our main web index and our supplemental index. If a page doesn’t have enough PageRank to be included in our main web index, the supplemental results represent an additional chance for users to find that page, as opposed to Google not indexing the page.