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I've recently looked up the exact format of a transaction and came up with this (source with explanation):

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However, this seems not to include transaction fees. Are they not part of the transaction? Or do they have a special output lock script that basically makes it available to everybody?

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The transaction fee is implicitly specified. It is given to the miner as the remainder of the transaction: the difference between the sum of all transaction inputs and the sum of all transaction outputs is left free to be collected by the miner.

See also: collecting block reward and transaction fees

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