Alignments of chloroplast noncoding regions for context-dependency analysis

Brian Morton
Substitutions between closely related noncoding chloroplast DNA sequences are studied with respect to the composition of the three bases on each side of the substitution, that is the hexanucleotide context. There is about 100-fold variation in rate, amongst the contexts, particularly on substitutions of A and T. Rate heterogeneity of transitions differs from that of transversions, resulting in a more than 200-fold variation in the transitions:transversion bias. The data are consistent with a CpG effect,...
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