That output format doesn't make sense to me. I don't think it's going to be practical at all.

Anyway, just write it per line, then transpose (or better, leave it per line):

tr '\n' ' ' < example | tr 'N' '\n'

gives

A 4 3 5 7 8 3 
A 
A 
A 3 4 5 2 
A 2 7 4 6 9 
A 

That output format doesn't make sense to me. I don't think it's going to be practical at all.

Anyway, just write it per line, then transpose (or better, leave it per line):

tr '\n' ' ' < example | tr 'N' '\n' | sed 's/^A //; /^$/d'

gives

4 3 5 7 8 3 
3 4 5 2 
2 7 4 6 9