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In the original Keccak you would pad by adding a 1 bit proceeded by a predetermined amount of 0 bits and then another 1 bit.

When Keccak was standardized to sha3 the padding was changed. It was then (unless you needed to pad by just one character) 0x06, followed by a predetermined number of 0 bytes and then 0x80.

My question is... why was this change made?

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It accomplishes 2 things.

  1. SHA-3 hashes of the same input will be distinct from Keccak hashes with the same rate/capacity.

  2. XOFs (SHAKE) with the same rate/capacity will start also with distinct hash output, when compared to both SHA-3 and Keccak

There is no change to security or performance, although having SHAKE share a prefix with a hash of the same input would have been considered a security concern.

Also, padding conventions differ between the implementation and the code, the difference between SHA-3 padding and Keccak padding is minimal. SHA-3 still supports inputs in bits rather than bytes, and the padding is also bit based.

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