Although basis is usually apportioned by square footage, you can use the comparable values if you think it is more accurate.
Unit 1 would be $45,000 and unit 2 would be $55,000. Just make sure you apportion the closing costs the same way, so unit 1 is 45% and unit 2 is 55%.
The IRS allows you to use any reasonable method to allocate basis, but you need to make sure your are consistent.
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