ref     atgtagctagctagctaacgagcgctagctagctagtgatg
substr      agctagctagctaac
##</code><code>##

$reference_string = 'gctagctgatgctagcagcagcatgtagctagctgacga'
$substring = 'aatgctagctagc'

$output_line = qw{ } x length($reference_string);
substr $output_line, $start_position, $length, $substring;
print $reference_string, "\n", $output_line;
##</code><code>##

ref    agctagctagctagcatgctagctagctgatcgatgctagctagctgactgacgacg
out1       atctagcat                    agctagcgatcga    gactgacagc
out2                             tagctagctgctagc
out3                       agtcgatcgatgctagc    

##</code><code>##

create one blank line of output
foreach substring
   take the first blank line
      if there is no overlap
         substr the blank line
      if there is overlap
         create a new blank line
         substr the new blank line