How do I stop my Mac from automatically opening multiple programs, ie: iMessage and Mail at startup?

I have tried unchecking the option "Open at startup" found when you higlight the program while it is in the dock.  I have also gone into Preferences/Users and Groups and none of the programs that I do not want to open at startup are in the list.
While I am familiar with other Apple products this is my first Mac, and this is just one of the many things that is taking time to figure out.

Click Restart, and uncheck  "Reopen windows when logging back in".
You can also try quitting those apps before you restart. Make sure you quit them completely (cmd-Q) and not just closing the window.
Matt

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