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I have created two similar websites (relating to monetary systems). So far, one appears to be loved by Google and the other hated. I'm struggling to work out why.

This is a mystery to me because both sites were created by me with the same design philosophy, both in pure html. Both are packed to the rafters with references to, and information about, their respective subjects.

One issue I'm worried may be the cause is to do with the location of the sites. I got a web hosting package from hostmonster.com for the successful one, but less liked one is just an "add-on" which sits on a subdirectory of the successful one. I wonder if Google somehow detects this and treats it as a less significant website?

EDIT: Just to clarify, even though one site is an add-on that sits on a subdirectory of the other, the URL is arranged to look like it is a root. I.e. the unpopular site can be accessed directly with a simple www.myunpopularsite.com name, without specifying any subdirectory.

EDIT: Just in case its important... say the popular site is called pop.com and the unpopular one unpop.com. In the webspace I've purchased, there is a directory called public_html. This is where I put the index.htm and all the other files of my popular site. When I purchased the add-on unpop.com. I made a subdirectory of public_html called unpop. It is within this "public_html\unpop\" that I place the index.htm and all the other files of my unpopular site. Typing www.unpop.com into the address bar of a browser links directly to the contents of "public_html\unpop\" and the user is not aware that this site is sitting on a subdirectory of another site. BUT if you type "www.pop.com/unpop" into the address bar of a browser you DO see the unpopular site.

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Make sure that the 'unpopular site' cannot be accessed by the subdirectory, only by the add-on domain name. –  w3d Oct 14 '12 at 15:11
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There is a link from the popular site to the unpopular one on its subdirectory, but its done via <a href="www.just_the_site_with_no_subdirectory_mentioned.com">text</a>. –  Mick Oct 14 '12 at 15:26
    
@w3d: See edit to OP. Is this a problem? –  Mick Oct 14 '12 at 15:39
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www.pop.com/unpop should not be accessible over HTTP. It should only be accessible via www.unpop.com. The subdirectory should be blocked in .htaccess. This is potentially a problem if Google was able to somehow find the content via the subdirectory. But otherwise, as John Conde states in his answer, an add-on domain should not impose an SEO penalty - no more so than hosting two sites on the same server (same IP). –  w3d Oct 14 '12 at 16:14
    
@wd3: Interesting. I'd never even heard of .htaccess before. Just looking it up now... –  Mick Oct 14 '12 at 16:20
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Google can't see the directory structure for your website. It is not a ranking factor. (As it shouldn't be this since in no way indicates quality of content).

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This seems open to misinterpretation. Would it be a bit better/more accurate to say Google can't see the dir structure of the server (/filesystem) as opposed to site? –  Su' Oct 14 '12 at 11:41
    
Yes, your clarification is a better explanation. –  John Conde Oct 14 '12 at 15:45
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