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What is the difference between indexing a website with a www. and without www.

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There is no difference.
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The difference between indexing a website with "www" and without "www" is primarily a matter of preference and the way the domain name is structured.

When a website is indexed with the "www" prefix, it means that the domain name is structured as "www.example.com." The "www" stands for "World Wide Web" and has historically been used to indicate that the domain is associated with a website. Many websites have traditionally used this prefix by default, and it has become ingrained in popular usage.

On the other hand, indexing a website without the "www" prefix means that the domain name is structured as "example.com," without the additional "www" subdomain. This approach is often referred to as a "naked" or "non-www" domain. In recent years, there has been a trend towards using naked domains, with many organizations and websites opting to drop the "www" prefix to simplify their URLs and make them more concise.

From a technical standpoint, there is no inherent difference in how websites are indexed or function based on the presence or absence of the "www" prefix. It is simply a matter of configuring the domain settings and server redirects to handle requests with or without "www" correctly.

In terms of search engine optimization (SEO) and indexing, search engines generally treat the "www" and non-"www" versions of a website as separate entities. If both versions are accessible, it is advisable to set a preferred version (with or without "www") using canonicalization techniques, such as 301 redirects, to avoid potential duplicate content issues. This helps consolidate the website's authority and prevents splitting of SEO efforts between multiple versions.

Ultimately, whether to use "www" or not is a personal or organizational choice, and the most important aspect is to ensure that the chosen version is consistently used and properly configured for indexing and user access.