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Example of a matched helical region. (a) shows pairing of nucleotides where bold lines represent hydrogen bonds. The fragments that make up matched helical regions are enclosed by dashed rectangles in (a). (b) shows the alignment of nucleotides in matched helical region, pairing of nucleotides are also shown in (b) by bold lines connecting base paired nucleotides. (b) illustrates alignment of base pairs, insertion of base pairs and alignment of base pairs to unpaired nucleotides.
