Table 3. Clustered k-mers from S1 Fig used for validation of their biological function and reported riboswitch motifs.

Nucleotide location designated refers to match with their position reported in reference.

Rfam ID	K-mers	Position	Riboswitch function and motifs	Ref
RF00168	UCAU	U57-U60	Motifs predicted to interact with the Nova-1 protein	[40]
RF01051	CAAAG	C22-G26	Secondary structure representation of the crystallized c-di-GMP aptamer, necessary for c-di-GMP binding pocket formation	[41]
	GGUC	G8-C11	Found in Helices P1 area beginning of 5′UTR	[41]
RF00522	AAAAAA AAAC	A27-A31 A30-C33	Overlaying K-mers in the 3′ aptamer domain, rich in A, which has unique folding pseudoknot that compresses PreQ1	[42]
	UCCCA	U24-A18	Found in P2 of preQ1 riboswitch aptamer structure	[42]
RF00504	CCGAAG	C168-G173	The glycine-mediated changes in spontaneous cleavage (GAA)	[43]
	CUCU	C204-U207	In glycine riboswitch, secondary structure and in-line decreasing cleavage pattern	[43]
RF00059	UGAGA	U39-A43	The pyrimidine part of TPP is bound by bulge J3-2 located in the pyrimidine-sensor helix P2-P3	[44]
RF00162	GAGGGA	G19-A24	It is a kink-turn motif that allows pseudoknot interaction. It interacts with SAM which helps to make stable formation, can cause the downstream expression platform to form a rho-independent TT (transcriptional terminator), turning off gene expression	[45]
RF00634	CAACC CCCUC	C54-C58 C57-C61	Overlapping k-mers in SAM-IV RNA binds SAM, last C in cleavage increased by SAM	[46]
RF01057	AGGCUC	A61-C66	In P1 SAH riboswitch control reporter gene Expression, ahcY 5'UTR	[47]
	CGCU	C28-U31	In SAH riboswitch hairpin loops of P4	[47]
RF00521	GCUAAA	G42-A47	Secondary structure of the Env12 metX SAM-II riboswitch its base-pairing reflecting the tertiary structure of the SAM-bound RNA	[48]
RF00050	AGUC	A126-C129	In the secondary structure of FMN, the first three AGU make hairpin loops and identified from B. cleavage.	[49]
	ACAGU GGCGGU	A137-U141 G56-U61	Form Secondary-structure model of the 165 ribD RNA and side hairpin between P2 and 165 ribD RNA and side hairpin	[49]
RF00174	CCCGC AGUCAG	C70-C74	Predicted secondary structure of the cobalamin riboswitch in the btuB leader region of Synechococcus sp. Strain. The boxed bases represent the B12 box-P1 helix interface, where a CC-to-TT (UU in the RNA structure	[50]
RF01055	GAAAGG	G120-G125	Containing AGG at the site of Ribosomal Binding Site (RBS) located at multiple junction site. Region of the central multi-stem junction in Sequence of the 138 moaA Moco RNA.	[51]
	GCCU	G18-U21	Found in a Moco RNA at left multiple junction site	[51]
	GCCUCC	G106-C111	In Moco RNA, the last UCC makes parts of multiple junctions in P4.	[51]
RF00380	UGAGG	U28-G32	k-mers that found in part of a conserved bulge-stem region of Secondary structure of the 5`M-box portion	[52]
RF01054	AAAGG	A83-G87	Structural modulation and nucleotides comprise a conserved Shine–Dalgarno (SD)	[53]
	AGCAU	A58-U62	Unpaired Structural modulation containing constant cleavage	[53]
	AGAAAA	A88-A93	Structural modulation, AGAA in decreasing cleavage and AA in constant cleavage	[53]
RF00234	AGCGC	A12-C16	Downstream of the ribozyme cleavage site Ribozyme core site P2a	[54]
	ACGAGG	A53-G56	Ribozyme core region (Unpaired)
RF00167	CUAC	C50-C53	structural features of the guanine aptamer domain and critical for metabolite binding	[55]