Putative novel ncRNAs in D. purpureum. The sequences and predicted structures of select class I and II ncRNAs in both D. discoideum and D. purpureum. The red dots indicate base pair positions that possess high mutual information but lack sequence identity. This region contains the 5' and 3' stem sequences, which are conserved among each species but not between both. Blue dots indicate base positions where sequences are perfectly conserved, corresponding to the non-self-binding region (NSBR). The starred positions are connected via a variable sequence (green box in alignment), which lacks primary sequence or secondary structure conservation (see Figure S8 in Additional file 1 for complete alignment).