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On a Google Groups thread, Barry asks whether Google Universal search will impact user-created Google Custom Search Engines.
It's a good question, according to Christine of Google. She says that it will not affect your custom search engines.
Good question. The integrated search results you're referring to won't be available on your Custom Search Engine or any other syndicated search feature.
What this means is that while the main Google search engine is displaying embedded results (local, news, video, etc.), these results will not appear within your own custom search engine results.
Discussion continues at Google Groups.
