What does "large file" mean in your context? Of what file sizes are you speaking?

I think this could be a solution for files less than 100 MB. Didn't test it... (with large files)

#!/usr/bin/perl
use strict;
use warnings;

{
    local $/;
    my $data = <DATA>;

    $data =~ s/((?:n+\n?)+n+)/replace($1)/gme;

    print $data, "\n";

    sub replace {
        my $s = shift;

        substr( $s, 0, 1, '^' );
        substr( $s, -1, 1, '^' );

        return $s;
    }
}
__DATA__
acacccacacacaccacacccacacaccacacccacacccacacaccaca
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
cccacaccacacccacacaccacacaccacacccacacccacacacacca
cacccacacaccacacccacacacaccctaaccctaacccctaaccccta
accctaacccnnnnnnnnnnnnnnnnnnnnnnnnnnnccctaaccctaac
ccctaaccctaaccctaaccgtaaccctaaccctttaccctaacccgaac
ccctaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggggg
gaccctgaccgtgaccctgaccctaacccgaacccgaacccgaaccccga
accccgaaccccgaaccccaaccccaaccccaaccccaaccctaacccct
caccctcaccctcgacccccgacccccgacccccgacccccaccccgaac
ggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnaccctaaccctaaaaccctaaccctagcc
ctagccctagccctagccctaacccctaacccctaaccctaagccgaagc
[download]

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