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ref     atgtagctagctagctaacgagcgctagctagctagtgatg
substr      agctagctagctaac

$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;

ref    agctagctagctagcatgctagctagctgatcgatgctagctagctgactgacgacg
out1       atctagcat                    agctagcgatcga    gactgacagc
out2                             tagctagctgctagc
out3                       agtcgatcgatgctagc

create one blank line of output
foreach substring
   take the first blank line
...
      if there is overlap
         create a new blank line
         substr the new blank line