I also suggest that you read about the split() function. The default split uses /\s+/. Basically that means that when a sequence of one or more "whitespace" characters are found, they are thrown away and the token to that point is returned. Your split is highly unlikely to return anything of interest.

my @genpepts = split(/^\w{5}/,$in);
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Probably is not going to do what you want.

You seem to be describing a file like:

LOCAL
asrdf asfd afd asdf aafd
qwer qwer qre qwre qrew
//
LOCAL
asrdf asfd afd asdf aafd
qwer qwer qre qwre qrew
//
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I doubt that this is what you actually have.

use split() when you know what to throw away.
use match global when you know what you want to keep.