Table 1.

Predicted cis-regulatory elements in the 5’-UTRs. The predictions were obtained by using Infernal 1.1.2 with the Rfam 12.1 database and compared with the primary 5′-end data set. The list is sorted by Bit Score in descending order. Abbreviation: n.a., not applicable

Infernal prediction with Rfam						RNA-Seq detection
Name	ID	Start	End	Bit Score	Strand	Status	Start	End	Gene
Cobalamin riboswitch	RF00174	1,066,117	1,066,317	90.8	+	observed	1,066,117	1,066,317	DIP1084
Cobalamin riboswitch	RF00174	862,214	862,414	81.8	+	not observeda	n.a.	n.a.	n.a.
cspA	RF01766	285,506	285,923	64.8	+	observed	285,506	285,923	DIP0320 / cspA
mraW	RF01746	1,640,095	1,639,987	70.2	–	observedb	1,640,095	1,639,987	DIP1606 / mraW
TPP riboswitch	RF00059	924,778	924,890	60.8	+	observedc	924,778	924,890	DIP0953
TPP riboswitch	RF00059	922,838	922,969	60.0	+	observedc	922,838	922,969	DIP0951
msiK	RF01747	509,334	509,277	48.2	–	observed	509,334	509,277	DIP0539
TPP riboswitch	RF00059	27,456	27,566	57.6	+	not observeda	n.a.	n.a.	n.a.

^aNo TSS detected and insufficient read coverage in that area

^bMotif of the mraW region is located upstream of the TSS of DIP1606 / mraW

^cLast base of TPP riboswitch is located in the respective CDS