Figure 5
Indel-based evolutionary distance q for intron pairs of different average lengths L (in bins of size 100, data points are shown at the top boundaries of bins; for each bin, its own P(δ) was used). For rat and mouse, actual data (red line) and the maximal likelihood estimate of q (black line, a = 0.46) are shown. For mouse and human, estimates of q under a = 0.46, 0.42, and 0.38 are shown. The blue line shows the ratio of mouse–human over rat–mouse estimates of q. The green line shows the same ratio, computed for only those parts of mouse and human intron sequences that are not masked by RepeatMasker, on the basis of P(δ), calculated from repeat-free parts of rat–mouse alignments.
