I bought 15 Blueberry Autoflower seeds, I was able to get 2 out of 3 to germinate. They have been growing well for 3 months but now they look like completely different strains. Any thoughts?

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Much like siblings, there are frequently genetic differences between seeds.
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Drinkslinger nailed it. I recently grew 2 Blue Cheese autos from the same batch of seeds. Both got exactly the same everything. One finished at 28" and the other finished at 17" BUT both produced about the same amount of bud.
The best chance for the same traits would be clones and even then they can be different.
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