Additional file 1: Figure S1. of Virus-like attachment sites as structural landmarks of plants retrotransposons

Sequence logos and PlotCon of U3 and U5 vl-att putative sites of 9 LTR-retrotransposon lineages divided by genome and plant group. Sequence logos of the first and last 40 bases of the LTR from 9 LTR-RT lineages divided by genome or plant group (eudicot - monocot species). Sequence logo is a graphical representation of nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each nucleic acid at that position. Behind each logo it is the PlotCon analysis, where the X-axis for all plots refers to the relative residue position in each alignment and the Y-axis to their similarity, indicated as the pairwise scores that are taken from the specified similarity matrix. The PlotCon graphics are based on an algorithm that shows, along the alignment, the regions with significant similarity (above 0 mark of similarity), giving a strong view of the vl-att sites candidates. (PDF 8527 kb)