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No spark in one cylinder

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Port side engine want's to start but is only getting spark in one of the cyclinders. It ran fine for about 5 minutes and then took on some water at speed when the engine died. I got it out of the water and pulled the plugs and cranked the moter until there wasn't any water coming out of the exhaust or the cylinders. The spark plug wire goes directly to the coil. Could the spark plug boot or wire short out? or maybe the coil is bad. How do I test without taking to a shop?
 
The 720 engine's coil fires both plugs together. I would check the spark plug wire on the bad side. Take it off, and cut it back a little. They are known to burn inside, right where the boot connects, because of a poor connection.
 
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