Table 1.

Palindromic pairs within instances of SDR1 found by pattern

^aA sequence found by the pattern . . . . (. . . .)GCGAG.AG.CGA(. . . .), where a period is satisfied by any nucleotide, is counted as “paired” if the two tetranucleotides within the parentheses can base pair with each other either using conventional base pairing or allowing GT or AC pairing. No instance with GT or AC pairing had more than one such pair.

^bThe number expected is: length (s⁷ w³), where length is the length of the N. punctiforme genome (9.1 Mbp), s is the fraction of G and the fraction of C in the genome (0.21), and w is the fraction of A and the fraction of T (0.29). The probability that a random tetramer pairs exactly with another random tetramer is 0.4%. The same probability allowing for GT pairing at any position or AT pairi006Eg at any position is 2.0%.

^cSDR1 instances found by the pattern were divided into two groups: (1) those that had previously been found by overall similarity, as described in the Methods section, and (2) those that had not been found by this means.