A frequently used method of comparing large RNA molecules employs the two-dimensional display of oligonucleotides generated through the action of specific RNases (oligonucleotide mapping, fingerprinting). Using computer simulations and simple analytic expressions the number of large RNase T1-resistant oligonucleotides obtained from random RNA sequences can be estimated. The computer simulations also permit estimation of the number of large oligonucleotides which remain unchanged as random variations are introduced into a random RNA sequence. In addition, computer analysis also provides a means of estimating statistical confidence limits to be used in a quantitative comparison of fingerprints of different RNA molecules. The model shows that two RNA sequences which differ overall by 1%, 5% or 10% share, on average, only 85%, 50% or 25%, respectively, of their large oligonucleotides. Thus, the use of fingerprint analysis is recommended only when closely related RNAs or regions of RNAs are compared (sequence homology greater than 90%).