use strict;

my $seq = '------------GGATCC________________GGATCC=============GGATCC+++++++++';
my @splits = (0);

push @splits, pos $seq while $seq =~ /(?=GGATCC)/ig;
push @splits, length $seq;

for my $index (0 .. $#splits) {
    my $width = $splits[$index + 1] - $splits[$index];
    print substr ($seq, $splits[$index], $width), "\n";
}