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Hi Julius,
The malware may have been uploaded to one of your pages thanks to an infected FTP client or editor. You can probably find it just by looking first at any page of your site that has the maleware warning, then look for a script or iframe that doesn't belong.
If you don't find it, remove all of the advertising from your site and check for malware again. If its now clear, replace the ads one at a time until you find the culprit.
Good luck!
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