Fig. 3.

TSM-like patterns with different effects on sequence and secondary structure. Alignment shows inferred sequences for selected ancestral nodes and predicted secondary structures for the affected nodes and their immediate child nodes. The source and target regions for the inferred TSM event are highlighted, and the homologous region in the parent is framed. Sequences in Right show the reference (parent; below) and the query (child; on top) sequences and the inferred TSM processes explaining the differences. The sequence differences are shown in lowercase, and the secondary structure is given with the dots and parentheses notation. (A) TSM causing a CM with a parallel inversion of the loop sequence (Metazoa, tardigrades). (B and C) TSM causing an inversion of the loop sequence only (Bacteria, Actinobacteria; Bacteria, Firmicutes).