Your hit will be where you aim.
So if you have your target locked in your scope (L-key), and fire on the solution you get there, then you will hit approx. midships...everytime.
To hit a different spot, still get the solution for midships, but then unlock, and aim for the area you want, and fire immeadiatly (torpedoe-tube should already be opened).
You can read depth of rudder/scew, by taking a look at the recognition-manual.
Set the torp on magnetic impact, just to be sure.
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