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Whenever it comes time to terminate Cat6 lines into an RJ-45 connector, there is an expected way of lining up the colors in each end. This differs somewhat between Cat5 and Cat6 but the principle remains the same: there is a standard order in which to feed the wires into the connector.

My question is, why is this order used? Is there a specific reason why it is done this way?

The way I see it, since all 8 wires inside the cable are the same, it shouldn't matter which order you use, as long as it is the same on both ends...

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The wires are not all the same, firstly, pairs are twisted together. Twisting of pairs used for signalling has an important effect on the way external noise is picked up. If you used for a signal pair, two wires that were from different twist-pairs the signal would be degraded.

The colours and pin-ordering follow T568A or T568B as specified in TIA/EIA-568. So far as I know, the same ordering is used for Cat5/5E as for Cat6.

The ordering for 8P8C connectors was initially established for voice communications where each pair carried a separate voice channel. The innermost pair carried one signal, the next wire to the left and right formed the next pair and so on. This makes sense when you remember that there are a variety of modular connectors used for voice comms with different total numbers of pins. In theory you could plug a 6p4c plug into an 8p8c receptacle and have it work (in practice this is not a good idea). Ethernet termination varies from this to keep the pairs closer together but the idea of keeping a pair on the central positions for compatibility with voice applications means that some compromise has to be made.

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Okay that makes sense, but why do we terminate them in that specific order? Why do we break up the green pair? Wouldn't it be simpler to have each color pair right next to each other, O,OW,B,BW,G,GW,Br,BrW? –  Jared Tritsch Nov 22 '12 at 9:13
    
Answer updated. –  RedGrittyBrick Nov 22 '12 at 9:28
    
Thanks!This explains what I was looking for. So it purely legacy networking for telecoms. Makes sense. –  Jared Tritsch Nov 22 '12 at 19:40

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