495904.fig.004
Figure 4: Secondary structure of PSTVd and location of miRNA/miRNA* complexes as predicted by NOVOMIR. The structure scheme is based on a consensus structure of 45 ( + )-stranded circular PSTVd sequence variants [32]; the sequence is given for the PSTVd variant Intermediate [33]. The five homology domains of pospiviroids are marked as proposed by Keese and Symons [34]: terminal left and right (TL,TR), pathogenicity-modulating (P), central conserved (C), and variable (V) domain. The transcription start site for ( )-strand synthesis is marked by “polII” [35]. The predicted miRNA/miRNA* complexes are shown as larger italic characters. The complex in the P domain is predicted using default parameters; the complex in the TR domain is additionally predicted with a normalized energy threshold 𝑡 Δ 𝐺 / 𝐿 / 𝑓 G C = 0 . 6 9 (instead of 0.75).