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. 2004 Aug 19;5:113. doi: 10.1186/1471-2105-5-113

Figure 12.

Figure 12

Problem dimer pair. The aligned dimer pair -X ↔ -- causes a problem because its gap penalty contribution cannot be computed without additional information. Note that the first column of indels is external; after this column is discarded, different penalties may be needed, as these two examples show.