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Secondary structure model of the RSE RNA. RSE RNA corresponding to nt 2597 to 2885 (nt 4 to 292 in this figure) was folded in silico using the Mfold RNA structure prediction program (41). The RNase T1 and A cuts as well as SHAPE modifications (1M7) shown in Fig. 1 and 2 were used as constraints for this prediction and are indicated on the structure. Natural pause sites and RNase V1 were not included in the prediction but are indicated on this figure.
