FIG. 4.

Alignment of the consensus bacterial CIRCE sequence (29) and the sequences of CIRCE elements from C. trachomatis strain MoPn (51), C. trachomatis serovar D (47), C. pneumoniae strain CWL029 (17), and C. caviae strain GPIC (37). The heavy underlining indicates the CIRCE region; the lowercase letters indicate mismatches with the consensus CIRCE sequence; the light underlining indicates a region of extended complementarity; the arrows indicate the maximum extent of extended complementarity; and the asterisks indicate mismatches with the consensus sequence which are complemented in the inverted repeat.