The most common monitor connectors are shown here Perhaps the one at the bottom of your tower is a digital one like the one on the left and comes from a Graphics card although that sounds unusual as the location of a graphics card slot is rarely at the bottom edge of the motherboard. If the connector on the motherboard is similar to the one on the right then it is a VGA analogue connector. If you do indeed have two graphics outputs, one from onboard graphics and one from a separate graphics card, you may need to select which one to use in your BIOS. However this reply should get your thread bumped back to the top and others may be able to help.
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