Figure 5.

These fold envelopes (triangular grids) and alignment envelope (rectangular grid) limit the subsequences (black dots) and cutpoints (short diagonal lines) to those consistent with a given alignment and consensus secondary structure (shown). The alignment path is also shown on the alignment envelope as a solid black line, broken by cutpoints.

Holmes BMC Bioinformatics 2005 6:73   doi:10.1186/1471-2105-6-73
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