Without knowing what data structure you have your start and end positions in, this is a pure guess:

my @motif = ( [30,43], [107,128], [209,254] );

# make sure it is in order by beginning position
@motif = sort { $a->[0] <=> $b->[0] } @motif;

my $last_group = 0;
for my $motif (@motif) {
    my $group = int(($motif->[0]+99)/100);
    if ($group != $last_group) {
        print "\n" if $last_group; # blank between groups
        print "group $group (", $group*100-99, "-", $group*100, "):\n"
+;
        $last_group = $group;
    }
    print "> genome.ptt_", $motif->[0], " ", $motif->[1], "\n",
        substr($string, $motif->[0]-1, $motif->[1] - $motif->[0]), "\n
+";
}
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Doesn't show group headers for groups with no motifs. Assumes you want motifs that span groups to be reported only with the first group they are part of, not the last or all. Assumes you are using 1-based offsets (yuck) based on the 1-100, 101-200, stuff.