Google uses the index they've created for the web search engine, and limits by domain name, host, and/or URLs. When someone enters a query in the search form on your site, the Google server application receives the query, formats the results, and sends them back in either HTML or XML (for the business version) with links directly to the pages on your site.
See also: Google Search Appliance
Platforms: all Internet-accessible web servers indexed by the Googlebot
A support document (cached copy) for the Google CSE and CSBE notes that some results may be different than those found in the same search on Google.com. It attributes this to including more than three sites in the CSE, and says that the CSE is using a subset of the Google.com index.
They recommend limiting the CSE to three sites, changing the behavior to 'Search the entire web but emphasize included sites', or adding refinements that have the same effect.
As of August 16, 2007, the support note says "We're working to bring more complete results to all Custom Search Engines."
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