Perl substrings

Hello everybody,
I have been dealing with this problem in PERL a few days now, and it has get into my nerves, so, if anyone has a hint on how to procceed, it would be more than welcome.
Say you have one file that contains a sequence of letters, eg :
SGFEFHGYARSGVIMNDSGASTKSGAYITPAGETGGAIGRLGNQADTYVEMNLEHKQTLDN [file 1]

the same sequence is also in the [file 2], but, with "." and "-" in it, like:
...---SGFEF....HG-.--YARSGVI---MNDSGAS..--TKSGAY--....--ITPAG--ETGGAI..GRLGN--Q..AD---TY--V..EMNL--EHKQTLDN [file 2]

Let's say I want to check how two substrings (namely SGASTK and GNQADT) have become in file 2 compared to what they were in file1.

I see that SGASTK, that was substring 19-24 in file1 is now SGAS..--TK and substring 36-41.
GNQADT which was substring 42-48 in file1 is now GN--Q..AD---T and substring 76-82.

My question is how can i find the old substrings from file 1 in file 2 and how can i store the new begginings and endings of the new substrings in file2...