New Grower Question/theory about when root start growing out of starter cup.

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I always start my seedlings in 16 oz cups.By rule of thumb when i start to see root poking out the drain holes, i try to transplant into there final containers.It seems this happens somewhere around 1 1/2- 2 weeks from sprouting.This last time around i was at about 10 days from sprouting, thinking i was ok.I noticed some yellowing of the older leaves.I looked at the bottom of the cups and the worst plants, had the most root coming out.I transplanted and they looked better in a few days.Thinking this might be from root drying out or sitting on osb board.What do you other growers do as far as transplanting? I see some put the complete cup into the final pot.I use a cup and make a perfect hole in the final pot before placing seedling into it.That way there is limited damage if any to the roots.Also when root start to come out the bottom.How long before they start to get root locked or tangled up enough to slow down the growth rate of the plant?
 
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