Secondary structure consequences of the deletion in ITS2. A) Predicted secondary structure of Phalaris arundinacea ITS2, based on the common variant (ITS2-long). B) Detail of helix I; DEL = the bases (GGGATGC) deleted in the ITS2-short variant; HR – C5 = 5 cytosine homopolymer repeat; asterisk T – position of the T/C single nucleotide polymorphism (aligned position 413). C) Possible alternative structure of helix I in the ITS2-short variant, based on homology modelling using Arctagrostis latifolia as the template; the cytosine homopolymer repeat is now C6 (6 cytosines); the arrow shows the position of the deleted sequence.