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  1. or download this
    ref     atgtagctagctagctaacgagcgctagctagctagtgatg
    substr      agctagctagctaac
    
  2. or download this
    $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;
    
  3. or download this
    ref    agctagctagctagcatgctagctagctgatcgatgctagctagctgactgacgacg
    out1       atctagcat                    agctagcgatcga    gactgacagc
    out2                             tagctagctgctagc
    out3                       agtcgatcgatgctagc
    
  4. or download this
    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