Sequence alignments of representative informative loci. Two representative, multispecies alignments of phylogenetically informative L1MB insertions supporting the Exafroplacentalia (markers 1b and 1d), Epitheria (markers 2a and 2c), and Atlantogenata (markers 3b and 3c) hypotheses. For full species sampling see Supplemental Material 1. Potential direct repeats are boxed. The sequences above each set of alignments represent the RepeatMasker consensus elements; w corresponds to a or t. Subscript numbers indicate serial identical nucleotides. Note that the 5′ ends of the L1MB elements are truncated. The 5′ and 3′ ends of the retroposed insertions are partially shown in lowercase letters.
