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CPU slots are directly connected to the CPU, a PCH slot shares the DMI link (same bandwidth as a x4 PCIE 2.0 slot) to the CPU with all other PCH slots, onboard SATA, NICs, etc, Supermicro usually identifies which are which so you don't even need to look at the block diagram, notice on the image you posted CPU slot 3, PCH slot 2, etc.

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