Read this post: http://codijuana.blogspot.com/2013/10/case-2-alpha-pad
Remix of the permutation ciphers' design for better security. I tried to solve the issue of frequency analysis and brute force attacks by joining padding and the alphabet matching (I called it the alpha-padding)
View a demo here: http://igenda.netau.net/codijuana/alphapadding_permutation/