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As you may be aware already (since you obviously have behaved rather astutely in this matter): A pop-up message is *not* a reliable authority about anything, on your computer... unless it definitely comes from your security software or your anti-virus software.
(Do you have anti-virus software of a good degree? Windows Defender, nor MalwareBytes, despite their good name in some ways, are neither of them anything like adequate overall.)
I suggest that, to eliminate anything that GoToAssist *might* have put on your computer, that you do a System Restore, back about a week for instance, to get the system back to where it was previous to this event.
System Restore can be done by the following:
Start - [All] Programs - Accessories - System Tools - System Restore
and choose to Restore system to a previous [etc.], then from the calendar-like interface, choose the first restore point *before* the problem started, then do the restoring.
(Warning: it may help to first disconnect from the internet, then also disable - temporarily, i.e. turn Off - your anti-virus utility, since they can often interfere with the Restore operation completing successfully.... before doing a System Restore.)
The computer will grind away for a while, then restart automatically, then grind away some more, and hopefully will come up with a message that the Restore operation was fully successful.
And hopefully that will cure the problem.
(PS: Do not choose to do a System Restore if you have recently installed any Microsoft software of any considerable cost. Its installation may be reversed, and you may lose money that way. Let me know if you think that's the case, and I will advise you further as to what to do.)