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Hello Mike,
Good question! SQL Compare uses standard Microsoft connection strings, so the (rather non-intuitive) way to specify the port number is to follow the server name in SQL Compare's server box with a comma, then the port number.myserver.example.com,1454
You can also do some other interesting things with the server box, such as specify a protocol to connect with:TCP:myserver.example.com,1454
We'll be improving the connection dialogue in the future so that you can more easily figure out how to put the port number in. We have already added this information into the next version of our help file as well.
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What is the correct way of connection to a different SQL-Server port:
This is not working: 69.241.177.66:6660