LV-909 or LV-N for Interplanetary Travels?

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Engine mass is significant, so if you want to minimize mass you should look at total mass, fuel plus tanks plus engines.

And the fact that fuel tanks aren't infinitely divisible means most of the designs your program spits out won't be realizable with integer numbers of stock parts. The smaller tanks (oscar-B and round-8) don't have the same wet/dry mass ratio as the larger tanks.