How can I modify your code such that it simply gives: ...

Quite simple:

my @results;
my %seen;

for (1 .. $#nsub)
{
    my $current = $nsub[$_];
    my $previous = $nsub[$_ -1];
    if ( "$previous#$current" =~ /(\w+)#\1/ )
    {
        my $found = $1;
        printf "%d -> %s (%s) %d -> %s \n",
            $_ -1,
            $previous,
            $found,
            $_,
            $current;
        $current =~ s/^$found/"-" x length($found)/e;
        $previous =~ s/$found$/"-" x length($found)/e;
        push @results, [ $_ -1, $previous] unless $seen{$_ -1}++;
        push @results, [ $_, $current] unless $seen{$_}++;
    }
    else
    {
        printf "%d -> no overlap\n", $_
    }
}

print Data::Dumper->Dump([ \@results], ['result']);
[download]