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1. This is a region that is quite regular with thunderstorms. The captain probably assumed this was like any other storm in this area any other day of the week.

2. This route is at the upperlimit this plane configuration can fly. If they had to reroute they would need to stop and refuel in another country, possibly Spain, Senegal or Morocco. I assume the captain didn't want to do this and soldiered ahead.

You simply don't fly through a thunderstorm, as you simply don't drive through A concrete wall at 100mph. No matter how short you are on fuel.

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