It comes down to the most obvious common sense things, like easy-to-understand website structure, well-written relevant copy carefully picked descriptive page titles, etc. Some more complicated problems may occur from time to time, but in most cases, you can identify and fix things with tools. It will also calculate your website internal Page Rank allowing you to see if each important page of your website gets enough attention. The tool will automatically identify your competitors and find the keywords they rank and even suggest one of your site pages which could rank for that term.
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