16S rRNA and 5S rRNA datasets
RNA STRAND v2.0 - The RNA secondary STRucture and statistical ANalysis Database
http://www.rnasoft.ca/strand/ 

16S rRNA: secondary structure file in ct format

http://www.rnasoft.ca/strand/show_file.php?format=CT&amp;molecule_ID=CRW_00111&amp;check_out_the=View+the+RNA+sequence+and+secondary+structure+for+molecule+CRW_00111

5S rRNA: secondary structure file in ct format

http://www.rnasoft.ca/strand/show_file.php?format=CT&amp;molecule_ID=CRW_00573&amp;check_out_the=View+the+RNA+sequence+and+secondary+structure+for+molecule+CRW_00573