Figure 1.

Screenshot of VisualRepbase graphical display. The interface contains three sections. The top section permits selection of families of TEs and eukaryotic genomes, or individual chromosomes. The middle section displays a variety of options for graphical presentation, the help menu, and output format options. The third section displays chromosomes with a graphical representation of TEs and other annotated features, tables of occurrences, and sequence information. This figure illustrates an example of two TE families from Repbase (AtREP1; AtREP3) on chromosome 2 of Arabidopsis thaliana. On the first line the selected families are displayed, including sequence orientation. On the second line other repeats from Repbase are displayed in orange, and their orientation is indicated. On the third line, other genomic annotations are displayed in addition to the selected families. The annotations include exons (in red), introns and UTRs (in framed white), and other annotated non-coding regions (in pink). Their orientations are also indicated. The table of occurrences lists the names of selected families, colors they are displayed in, chromosome name, species, number of elements on this particular chromosome, and the total number in all chromosomes displayed in the window (in this case all chromosomes of the Arabidopsis thaliana genome). The sequence is displayed in the bottom text window in FASTA format, and appears after clicking on the red rectangle which represents an exon.