Program to align big DNA sequences (100000 bases) and look at conserved regions among them?

Question

[DanielC]

Dear Friends,

I have to align 20 DNA sequences of about 100,000 bases each and manually look at a conserved region (tail region; phages) in the alignment to see differences in that region if any. Could you please suggest what tool would be the best for this purpose? As visualization of the region in the alignment is also important. Thanks so much!