Can open site explorer miss incoming links?
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In open site explorer I only see one linking domain, eventhough I know of at least 1 other. Why is that?
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Due to the size of the internet as a whole, you'll find that all of those type of tools have indexed different content.
If you really want to see as many as possible, do a direct Google search on your domain in quotes "yoursite.com" and "www.yoursite.com" Then use Webmasters Tools, Open Site Explorer, Majestic and AHrefs as a starting point.
See Rand's blog on the size of the OSE database here: http://www.seomoz.org/blog/octobers-mozscape-update
Moz crawled 55 billion URLs. In May they were indexing 150 billion but have had issues with that. Most importantly, on the crawl updates, they said:
"**This bit is important: **Next index, we're going back down to between 70-90 billion URLs, and focusing on getting back to much fresher updates (we're even aiming to get to updates every 2 weeks, though this is a challenging goal, not a guarantee). The 150 billion+ page indices are an awesome milestone, but as you've likely noticed, the extra data does not equate with hugely better correlations nor even with massively higher amounts of data on the URLs most of our customers care about (as an example, in index 50, we had ~53 billion pages and 82.09% of URLs requested had data). That said, once our architecture is more stable, we will be aiming to get to both huge index sizes and dramatically better freshness."
So Mozscape/OSE index, Ahrefs, Majestic, Google and WMT will all show different URLs - try to check them all once in awhile and definitely stick with Google, WMT and Moz for the big databases.
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