There will always be differences based on the time you perform the manual search. 

For example, if you try to manually see where your site tries to rank for any given keyword, at 1 PM, but our tool checked your rankings a day before at 2 AM, it's very likely that there will be differences. 

Google is changing the search engine results pages (SERPs) on a regular basis, and sometimes the rankings can fluctuate quite a lot in a matter of hours. Some people refer to this as the “Google dance.”
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