How can I locate duplicated regions in a sequence?
If you know approximately where are the duplicated regions, you can cut them out from the genome and align the two block using tools like MUMmer or Mauve.

I downloaded the sequence of ch5 you linked and extracted big regions around the genes (300bp blocks). The first block is from 70100000 - 70400000 (with SMN1 sequence at 115768 - 150839) and the second from 69200000 - 69500000 (with SMN2 sequence at 140350 - 175383).

I used progressive mauve to align the two (click on File -> align with ProgressiveMauve -> add Sequence ... -> Align). 



I found that the duplicated region is almost 200k long and maps between 44690 - 225520 of the first block and 19760 - 200940 of the second block, which we still need translate to the original genome coordinates, but I believe I can leave this to you :-).

P.S. you can also somehow upload annotations to Mauve, but I was lazy, so I "hand drawn" the arrow where I knew the genes are.