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PCIe Slot Numbers

Hi RJC, its a Gigabyte GA-Z97X-Gaming GT.
I went for this board because it has good slot spacing's as my GPU's are 2 1/2 slots wide.
I have 2 Sapphire Vapor X 290X's.
The GPU's are in slots PCIEX16_1 & PCIEX16_2 which are 3 slots apart to help with the cooling.
PCIEX8_1 & PCIE8_2 are empty.
The GPU in PCIEX16_1 has been given the ident GPU2 in both CCC and AB.
I can see its not a mix up as as you would expect this is the card that gets the hotter of the two and is the one that does most work when just in Windows or playing a non xfire game for example.
I just expected that the GPU in slot 1 would be designated as GPU1.
I've done a bit of Googling and there seems to be a similar issue with folding / mining but I don't do either of them.
 
I can only assume that with 2 cards in place in makes the 2nd PCI_16x slot the master.
 
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