Yep their all x16 but then the first and the 4th are the 2 primary slots the others downgrade to x8 and x4 depending how many slots you fill I think. Any how there's an order to which it's best to fill them and the first two are the 1st (the one at the top) and the 4th, then the 2nd and the 5th and so on.
Having removed it from the 4th due to ongoing problems that's stopped my PC working and having no more Ideas what was wrong I started moving things about and the card went into the 1st slot, this is right up against the bottom of the RAM and on the right it's up against the 20-1 pin socket for the front panel, or close to and I mentioned this as I noticed when i tried to check the plug as I had to take the GPU out first to get to it.
If your looking at the board or a picture of it you can see the top PCI slot it quite high up and my GPU is long and the end of it sits across the top SATA ports with the USB3 front port just above the plug sits almost flush with the top of the GPU. The point being that when I move the GPU my shut downs stopped but then it would not boot and when in the end i got it working again I lost all my front panel and a Ghost drive started appering when i use the other rear USB posrd, which is a lot odviously, this is an nother thread:
http://answers.microsoft.com/en-us/windows/forum/windows8_1-system/windows-has-encountered-a-problem-with-a-device/913e914c-75d6-4acc-ad9b-b1f4c66c7186?page=3&tm=1401117703947#LastReply
I have had problems with this PC ever since i turned it on 6 week ago and I have many threads about the varying problems many of which involved constant shut downs and Blue screens, most problems have gone away for the last few days but non were ever identified or solved, many people have said there are hardware problems but without knowing what it's not much use. Right now it's the lost front panel and ghost drive. This is why I am becoming paranoid about things and the fact it died on me due to the front panel when i moved the GPU next to it short of any other ideas I start to wonder about things.
I am having to work on it now and am in a constant state of fear evey time i turn it on or off i will lose everything and have to start again reinstalling and taking it all apart again.