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I recently added Enhanced Link Attribution to my site and was looking over some of the data. I noticed that the search input box had 1% of the clicks, and the submit button had 14% of the clicks. This seems like a large difference that it can't be visitors just clicking the search button without entering any search data.

The only possibility I can think of is that the 1% of clicks on the search input doesn't represent people clicking into the search input, but rather it shows the number of times someone has used the search input and used the 'Enter' button to submit.

Does Google Analytics track this as a different click than actually clicking on the submit button?

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Your explanation about hitting the enter button seems to be correct. According to the Google documentation, enhanced link attribution tries to figure out which element was responsible for navigation. This implies that if a click doesn't cause a user to navigate to a new page, then it wouldn't get counted in the link attribution report. So clicks on the search box wouldn't get counted, but hitting enter within it would.

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