Additional file 17.

CR3 pattern, Alignment based figure. The pattern and the transcription factor binding sites found in the murine CR3 region. In principle, the elements of this figure correspond to those in Figure 7. Obviously, the alignment-based figures are much larger than their homology-based version. In contrast to the homology-based figure type, the leaves of the species tree on the left are corresponding to the sequences of the extant species on the right. The sequences are shown in a sequence alignment and the transcription factor binding site predictions are plotted below the sequences. Because the species belonging to each prediction is obviously determined by its vertical position (the leaves are not color coded here), only the thicker part of the colored overlays (see Figure 7) is informative and thus it is shown; it denotes the pattern by referring to its color. To keep the figures readable, by default only the first 10 patterns (ordered by branch length score) are shown in the alignment-based figures.

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Struckmann et al. BMC Evolutionary Biology 2011 11:267   doi:10.1186/1471-2148-11-267