PCI Express® allows “Up-plugging” where a card with fewer lanes can be plugged into larger connectors that will accommodate more lanes. A card with more lanes cannot be plugged into a slot with fewer lanes (“Down-plugging”). This is prevented by the connector keying. If you want to plug the Stratix® II GX card into a x4/x1 slot, you will need to use a x8-to-x4/x8-to-x1 lane converter. Lane converters are extender cards that are designed for have higher channel connectors and lower channel PCB gold fingers.
You will also need a lane converter when the card is plugged into a x8/x16 slot, but the card is programmed with a x4/x1 PCI Express MegaCore. In this case, the card presents a x8 PCI Express electrical load but only 4 lanes (1 lane for a x1 operation) are active and the use of a lane converter will mitigate any potential BIOS issues.