Pips of the human–mouse comparisons from the β-globin gene cluster (HBB) and the Bruton’s tyrosine kinase (BTK) locus, and for a human-rabbit comparison of the α-globin cluster. The human and mouse sequences are first examined by RepeatMasker (A.F.A. Smit and P. Green,http://ftp.genome.washington.edu/cgi-bin/RepeatMasker) to identify known interspersed repeats. Interspersed repeats other than MIR and LINE2 (Smit 1996) are masked (marked as unalignable), and a descendent of the Sim program (Huang et al. 1990) is used to compute all the local alignments that score above a certain approximate significance. The percent identity in each gap-free aligning segment is plotted using the coordinates of the human sequence, and notable features in the human sequence, such as genes (exons are black boxes), repeated DNA sequences (SINEs other than MIR are light gray triangles pointing toward the A-rich 3′ end; L1 repeats are open arrowed boxes; MIR and LINE2 elements are black triangles and pointed boxes, respectively; and other interspersed repeats are dark gray triangles) and DNase hypersensitive sites (white boxes labeled HSn, wheren is an integer) are placed along the top of the plots. Note that the percent identity is only plotted between 50% and 100%, limiting the output to a range of mildly to strongly conserved sequences. The first two rows of panels shows the LCR and ε-globin gene and also the region from δ-globin to β-globin inHBB. The next row shows two portions of the BTKlocus. The last row shows the comparison between α-globin genes of human and rabbit; the published sequences of the mouse α-globin genes are not long enough to be effective in this analysis, and the mouse genes lack the CpG islands.
