Illustration of the probabilistic alignment constraint set and comparison against the true alignment and the M parameter constraint set for tRNA sequences: X57045 and X57046. The abscissa and ordinates of the plots indicate nucleotide positions n1 and n2 along the sequences X57045 and X57046, respectively, (a) Probabilistic alignment constraint set with permitted alignments (shown in dark gray). (b) Alignment constraint set with true alignment super-imposed (in black). (c) Alignment constraint set for the prior M parameter with M = 7 (shown in light gray). (d) Difference between the M parameter and the probabilistic alignment constraint sets. Light gray regions indicate nucleotide position alignments permitted by the M constraint and not by the probabilistic constraint and the situation is vice-versa for dark gray regions.