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I put the answer for my question here, if someone else need it, the right answer is: Convert before hashing and after hashing


I think you may be missing that when a node in the Merkle tree doesn't have a hashing partner it is concatenated with itself before hashing. To calculate the Merkle root of a transaction tree with a single transaction txid0, you would need to hash: Merkle root = sha256d(txid0 + txid0) I'm not sure about the endianess conversions.

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