Fig. 6

Motif discovery and distinct features of the introns from atpF and ccsA. The intron features were comparison with other group II introns (mainly from rbcL and psbA) in the Bryopsidales. a The top five motifs that were found from the 40 atpF and 37 ccsA intron sequences by MEME. Height of letters in motif logos indicates the occurrence of nucleotides at specific position. The frequency pie chart represents the frequency of occurrences of each motif across the 77 intron sequences, and the E-value indicates the statistical significance of the motifs. Width represents the number of nucleotides in a particular motif. b Comparison of the consensus secondary structures of domain V among atpF ccsA, and other group II introns (rbcL and psbA). The conserved trinucleotide 5′-AGC-3′, and the 2-nt bulge in domain V, which were the two catalytically important sites of group II introns, were highlighted by boxes and double arrow curves. c Comparison of the intron boundaries (5′ and 3′ end) among atpF ccsA, and other group II introns (rbcL and psbA)