The best replacement for cipher is code.

The best alternatives to cipher are rated as following:
★★★★★  code
★★★★★  cypher
★★★  stream cipher
★  hash
★  block cipher
★  encryption
★  sdelete
  mobius one
  transposition cipher
  block

Your alternative for cipher is not listed? Suggest!
Speaking about cipher, one probably shouldn't forget about double strike.

Other search terms related to cipher and their ratings are:
★★★★★ double strike
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Google Trends

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cipher
code
cypher