I want to know if Atom Processor E3815 PCIe(version 2.0) is compatible with PCIe end device with Version 1.0 or 1.1. If so then how it can be configured for the same.
In this case there is no manual option to configure the PCI Express. Depending on the card that you will be adapting to your board the configuration will be automatically done but this done if the card handles parameters of PCI Express 1.0 or 1.1.
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