Figure 4.

Sequence alignment of sodium-bisulfite-modified palindrome clones. (A) Central portion of sequence from five clones of the bisulfite-modified PCR fragment of one of the independent pAL300 candidates. Only one strand is represented for each clone. The bracket at the top of the sequence alignment indicates the central non-palindromic bases. The clone designations indicate the pAL300 candidate number sequenced (i.e. clone 3) with the primers (A–E) used for amplification as designated in Figure 2, followed by the designated number of the particular Topo clone sequenced. A consensus sequence derived from the alignment of the various clones is shown below (consensus). By aligning the consensus with the reverse complement of the consensus sequence, we were able to correctly deduce the starting sequence of the palindrome. (B) Central portion of sequence from independent Topo clones for pAL301 candidate 1 aligned as described in (A). The arrow defines the center of symmetry.