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Can somebody explain trigger wires to me? In relation to ignition wires? I have a wiring schematic that says two of my wires from the stator (blue and yellow) are trigger wires on the ignition coil? Anybody know how this works as far as the bike running? Do I have to hook it up to the rectifier?
 

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I'm not sure what type of engine you have there, but most often these tell the coils when to send a spark to the spark plugs using a pickup coil.

It is doubtful that the rectifier is involved.
 

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Please post the details of your bike in this thread: make, model, year. It will help us try to help you.

I'm guessing that, because there are only two trigger wires, that it is a single cylinder, or a twin with single-fire. They should be routed to the electronic ignition controller, or igniter (some call it CDI, but that's a misnomer). There is a small magnet on the rotor that passes over a pickup coil (trigger), which creates a low-level pulse in the wires; this pulse is a timing reference for the igniter, which drives the coil to create a spark. No points needed. Oh, and some twins use a single trigger for both coils, instead of one for each.
 
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