TABLE 4.

Regions of complementarity between the sRNAs and sRNA-regulated mRNA transcripts.

sRNA sequencea	sRNA startb	sRNA endb	mRNAc	mRNA sequencea,d	mRNA starte	mRNA ende	Energyf	p-valueg
XrrA
Seed region # 1
aGUCAUUGAGAAcUUGAu	34	17	asnO2	aUAGUAACUCUUuAACU	−72	−56	−11.97	0.008
Seed region # 2
CCUCu UUUCUACCG-AUagCGa	92	72	GBAA_4468	GGAG-GGAGAUGGCaUGgaGC	−14	+7	−13.21	0.003
uAUACCUCUUUUCUaCCg	96	79	GBAA_5301	uUAUGGAGAAAAGGaGG	−27	−11	−14.83	0.001
aUACCUCUUUucUACc	95	80	GBAA_0656	gGUGGAGAAGuuAUGa	−12	+4	−11.58	0.01
Seed region # 3
aUUCCCUCAAUcAAUAUu	177	160	GBAA_3451	aGGGGGAGUUA-UUAUAu	−15	+2	−14.81	0.001
uCUUUaUUCCCUCa	182	169	hutU	uGAGAaAAGGGAGa	−21	−8	−13.72	0.002
U-CUUUAUUCCCUc	182	170	inha1	AgGAAAUAAGGGAu	−12	+2	−11.54	0.01
XrrB
AUGGUaCCCCUUUg	194	180	GBAA_2549	UACUAaGGGGGAAa	−19	−6	−13.7	0.002

^aComplementarity between sequences is shown in uppercase letters. Dashes indicate a break in the complementarity region.

^bIndicates start and end of complementarity region on the sRNA, relative to the sRNA transcriptional start site.

^cTranscripts exhibiting a fold-change of ≥4.0 in at least one sRNA-null strain were selected for analysis.

^dNucleotides that are part of the translational start codon of the mRNA are shown in bold.

^eIndicates start and end of complementarity region on the mRNA, relative to the mRNA translational start site.

^fThermodynamic energy (kcal/mol) of hybridization between sRNA and mRNA, as calculated by TargetRNA2.

^gIndicates probability that the sRNA and mRNA interaction occurs by chance (p-value cutoff was 0.05), as calculated by TargetRNA2.