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I've been looking at the new Extreme11 X99 mobo for a new rig, and to be honest I love the x16/x16/x16/x16 configuration. My only problem is that whichever way you want to use the PCIe ports, the 3rd port is never used. How come?
Your answer is pretty much yes. While it can be used, it's mostly in the way shares it's resources with the M.2 slots. This also applies to one of the SATA ports. Depending on what, if anything, you connect to the M.2 port, this will change. I wouldn't attempt SLI on the port (which is possible with an extension) due to possible conflicts and lane limits. I may be mistaken, but I believe it is limited to 4x.
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