Figure 5.

Helitron2 subgroup and its terminal structure. (A) Structural features of Helitron1 and Helitron2 groups. Helitron1 has only 3^′-subterminal hairpin structure [2]. The dark arrows in Helitron2 represent the asymmetric terminal inverted repeats (ATIRs). (B) Phylogeny of the RepHel proteins encoded by Heliron1 and Helitron2 groups. The black square indicates Helitrons in which both termini are known. The alignment of the RepHel proteins is shown in Additional file 9. (C) Terminal sequences from the selected examples of Helitron2 elements. The bases in bold font represent the ATIRs. Pairing nucleotides in the hairpins are shaded in gray. The 5^′-end sequences of CRe-1, 2, 3 are similar to that of Helitron-1_CRe (not shown). Note that the RepHel protein is encoded in the opposite direction in Helitron-2_CRe and Helitron-1_DR (marked with #). The compensatory mutations in the complementary segments are highlighted by asterisks at the bottom in the alignment of Helitron-1N1_CQu and Helitron-1N2_CQu.