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well, they physically connect different parts of the mobo in various combinations, or create various signals which are interpreted in the running of the system. you set them by putting the jumper sleeve over the jumper pins.
They act like switches on the board to set different options. Setting a jumper open or closed will either prevent or allow electricity to flow through and thus board behaves corresponding to your selection.
To set them you use a little black piece of plastic (the jumper sleeve) and slip it over the two pins of the jumper setting you want. In general it is not a good idea to mess around with your jumper settings unless you know what you are doing.
Suppose at certain times - well it would be a pain in the backside to keep taking off the case to alter the jumpers everytime you wanted to disable a device. I expect you would be able to on some mobo's though (not sure!).
Jumpers can control whatever they are set up to do - I find that a lot of older mobo's rely on them more then modern ones, where the newer mobo's use the BIOS setup to make changes - that seems to be my experience.
For instance - on my Socket A mobo I have only one jumper I can set for using USB. Where as on an old Socket 7 one there are about 12 different ones I can change.
On my brother's old P110 there were jumpers to set how much RAM was present, and of what type (it could take about 3 different types), to set the speed of the processor (both FSB and multiplier), to enable/disable USB, etc, etc.
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