$ perl 1140433.pl
Report by RNA:
  rna1 has:
    dna1 = 1111
    dna2 = 1111
  rna2 has:
    dna1 = 2222
    dna3 = 3333
  rna3 has:
    dna1 = 2222
    dna2 = 4444

Report by DNA:
  dna1 is in:
    rna1 with 1111
    rna2 with 2222
    rna3 with 2222
  dna2 is in:
    rna1 with 1111
    rna3 with 4444
  dna3 is in:
    rna2 with 3333

$