Alignment of internal ribosomal entry sites (IRES) from CrP-like viruses . Subfigures A-C are created by means of CONSTRUCT using the RNAALIFOLD covariation score including stacking and parameters wTD = 0.5, wCV = 0.5, tTD = 0.03, and tCV = 0.15. Colored bars and labels are added in a graphics program according to the nomenclature given in . The used color-coding is explained in Table S4 in Additional file 1. Sensitivity and specificity are above 90 % compared to the structures given in  and ; falsely predicted are only a few additional, non-contradictory base pairs, for example those labelled by "j" in figure part C. A: Dotplot; note that base pairs, which give rise to the pseudoknots (PK I-III), are present not only in the covariation plot (lower triangle) but also, with low probability, in the thermodynamics plot (upper triangle); i. e., they are part of suboptimal secondary structures. B: Circles plot. C: Structural alignment output.