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I have windows 7 64bit and Ubuntu 11.10 64 bit installed.

Ubuntu has 3 partitions: /swap, / and a separate /home. Windows has 4 NTFS partitions.

I to want encrypt all 3 of my Ubuntu partitions, not the entire whole disk.

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It is not that easy to do that and you should know exactly what you are doing. Writing a stepwise instruction set here is nearly impossible, but there are good official How-To's:

https://help.ubuntu.com/community/EncryptedFilesystemHowto#So_How_Do_I_Encrypt_My_Home_Directory.3F

Relatively easy will be to encrypt your home folder, if you get a partition freed, then you can move your data to the new "encrypted partition" and after that mount this new partition using the fstab file. Encrypting the wohle ubuntu installation requires much experience and should be done with care.

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