When you say that the sequences cannot bind to each other, do you mean that they cannot be complementary to each other? Also, could you clarify what you mean by "harmful secondary structures"? If 7 orthogonal sequences will suffice, then it should be fairly easy to write some code yourself to do the job.

 Hi Khan, 

Thanks. When I say the sequences cannot bind to each other, I mean they don't have too many base pairs complementary, say less than 4. Harmful secondary structures means no hairpin, palindromic sequence et al. As for the code, can you give me some hints on that? Thanks.

Gang

the attached paper may be of use