Helical regions correspond with missing data or possible foreign DNA. 1a: Possible chimerical patterns in previously published sequences (yellow bars) match with regions of double stranded DNA forming helical regions (blue bars) in newly generated sequences. Epimenia sp. (Ep_sp) and Helicoradomenia sp. (He_sp) sequences have been aligned to the nucleotide positions (represented by the scale bar) of the sequences from this study, Wirenia argentea (Wi_ar) and Simrothiella margaritacea (Si_ma). The simplified schematic alignments (green bars) show high similarity (>90%) whereas other regions (yellow bars) possess lower similarity and point to contamination issues. BLASTn searches of yellow domains indicate high similarity with polychaetes (PI to III) or cnidarians (C), or resulted in no significant hit, indicated as Helicoradomenia only (H). Detailed BLASTn results are given in additional file 1: Blast result table. Below the scale bar, the double stranded helical regions of 18S sequences are indicated containing 66-82% GC islands. 1b and c: Close-up views of single stranded regions of helix 1 (1b) and helix 2 (1c) of S. margaritacea 18S. These stems have strong adhesive forces probably hampering PCR. Secondary structures were calculated using mfold, applying 72°C. G-C hydrogen bonds are indicated in red.