Comparison of 5′ flanking sequences between β- and δ-globin genes. (A) Alignment of the sequences between human β-and δ-globin genes. The program sim was used to compute local alignments between the 2 sequences, and positions of the alignment were plotted by the program laps. (B) Pairwise alignment of the sequences of human δ-globin and β-globin genes. Sequences were aligned using the program sim with a gap-open penalty of 4. Only the part of the alignment beginning at position −294 and ending at position +62 of the δ-globin gene is shown, but the complete alignment begins at −546 bp of the δ-globin gene and continues through exon 3. On the line between the sequences, a vertical line (‖) marks a match, a hyphen (-) indicates a gap introduced to optimize the alignment, and a space indicates a mismatch. The sequences are numbered as in the GenBank sequence file HUMHBB on the far left, and positions with respect to the cap site are given above the δ-globin gene sequence and below the β-globin gene sequence. The right-most digit in each number aligns with the numbered nucleotide. Binding sites for specific proteins are labeled above the δ-globin and below the β-globin gene sequences, as summarized in Hardison et al.29 ini, start site for translation. Periods (.) and colons (:) above the δ-globin gene sequence mark every fifth and tenth position in the alignment.