Here's my solution to what I understood you wanted (using your definitions of $blocks and @motifs:

my @results;
while ($blocks) {
   for (my $len = 1;$len <= length $blocks;$len++) {
      my $search = substr ($blocks, 0, $len);
      push @results, grep (/$search/, @motif);
   }
   #if there is a match, we're done
   last if @results;
   #mo match at starting position - try from next pos
   $blocks = substr ($blocks, 1); 
}
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Does that do what you wanted, or did I misunderstand you?

pike