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Thanks for the response Martin. From what I understand, webmaster tools will not show those links still pointing to the old domain but the search engines will pass the link juice to the new domain. What's the best strategy to get back links on those sites (in hundreds) to point to a new domain?

I have a popular page on one domain and I did 301 redirect of it to another domain. Just one single page. Both the sites are very related to each other. Will the backlinks get transferred? Its been more than a week but nothing shows up in webmaster tools.