For a full explanation of the code, visit http://en.wikipedia.org/wiki/Vigenère_cipher
In this instructable, I'll lay out a method by which the cleartext (the initial message, before encryption) can be disguised to help prevent decryption using either of the methods, since even decrypted it would read as gobbledygook.
The concept of rotating cleartext I got from Dan Brown's book Digital Fortress.
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However, you could choose any cleartext you want, you can usually play with it to get a square number of letters.






































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Is it? From what I remember of my crypto course, for a Vigenere-style cipher you want the key to be as long as possible, preferably the same length as the cleartext with no repeating patterns. The "secret weapon" against Vigenere ciphers (or more broadly, substitution ciphers) is frequency analysis, and if the key is only a few letters long you can quite easily do multiple periodic frequency analyses (every 6th letter with varying offsets from the beginning of the ciphertext) and deduce the key providing the message is long enough.
Ideally, I think, you want an aperiodic key that never repeats, at which point I think you have a one-time pad which is a slightly stronger class of encryption than Vigenere. Can you tell me why an overly long key is a bad thing?