I have a sitemap file that has been submitted to Google, and has been processed, according to Google Webmaster Tools.
As per GWT for 2013-05-31, 8255 web-pages are submitted, but only 8209 are indexed.
Which 46 of the 8255 pages are not indexed?
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ThompsonPaul wrote on moz.com about figuring out which pages are not indexed. Here is a summary of what he has to say:
site:search on Google. You can use a bookmarklet grab the search results into a list more easily.
Clearly this is a manual and time consuming task that isn't going to work well if you site has more than thousands of pages.