The Google Webmaster Central blog announced you can now use a new method to verify your site with Google Webmaster Tools.
To verify your unverified site with Google Tag Manager, go to the Webmaster Tools home page. Then, click Manage site for the site next to the site that you’d like to verify, and then select Verify this site. Click the Add a site button in the top right corner.
Then, you will be taken to the Verification page; select Google Tag Manager as the verification method and follow the steps on your screen.
Then, click on Verify and you should be all set.
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