Scatter Plots and Quadratic Fits on Average GC% for Substitution Rate, Branch Length, K2 Distances, INDEL/10 kb, SINE% and LINE%. Scatter plots of substitution rate, branch length, K2 distance, INDEL/10 kb, SINE% and LINE% against average GC% in three-way alignments among cattle (C), dog (D), and human (H). Substitution rates (the top left panel) and branch lengths (the top right panel) were estimated for each species by the PAML package (Methods). For each pairwise comparison in three-way alignments, K2 distances (the middle left panel) and large indel frequency (>100 bp insertion/deletion event count per 10 kb, the middle right panel) were calculated. Other sequence properties in each species such as SINE% (the bottom left panel), LINE% (the bottom right panel) were also plotted. Quadratic fit curves are derived on each plot and their formulas are provided on the top of each panel.