You mentioned in your OP that the Last PCI-E slot is at x4 but is capable of x16.
Quote: Originally Posted by Tomha
My motherboard has the following PCIe slots for graphics cards:
2 x PCIe 3.0/2.0 x16 (x16 or dual x8)
1 x PCIe 2.0 x16 (x4 mode, black)
I gather the top and middle slots will offer no benefits over each other, but with a single GPU, will I notice a decrease in performance using the last PCIe 2.0 slot rather than one of the PCIe 3.0 slots. Its no real reason, just my graphics card blocks the pretty blue lights on the south bridge and if I moved it down it would block an annoying red light instead :P
There should be an option in your BIOS that alows you to select the mode of operation for that slot, i reckon. If not, try putting the card in the slot anyway, the mode of operation will change according to the demands of the card in the slot dynamically.
If you want to be sure that you're getting the right mode of PCI-E operation for your card in Windows you can always use GPU-Z to confirm it. http://www.techpowerup.com/gpuz/
Clicking on the ? next to the interface information will allow you run a render test that will show you the true values of the PCI-E Link speed