Table 1. Numbers of predicted regulatory RNAs with supporting evidence by RSSVM, RNAz and QRNA in the 1002 orthologous 5′-UTRs of five Shewanella species.

	RSSVM (FPR = 0.01)	RNAz (FPR = 0.01)	QRNA
Total number of predicted regulatory RNAs	166	109	112
False positives on shuffled sequences	0	0	13
Matching known RNA motifs in Rfam a (19)d	17	16	11
Overlapping with predicted transcription terminators or attenuators	72	49	40
Overlapping with predicted transcription terminators b (106)d	62	42	31
Overlapping with predicted transcription attenuators c (123)d	56	37	32
With literature support	21	11	7

^aWe searched all the orthologous UTRs with Infernal using all bacterial RNA motif models from Rfam, and 19 known RNA motifs gave Infernal scores higher than 10 bits and occurred in at least two orthologous sequences of a UTR set. 6 of the 19 RNA motifs have orthologous sequences from S. oneidensis and E. coli in the Rfam seed alignments.

^bPutative transcription terminators predicted by Rnall [43].

^cPutative transcription attenuators predicted by a previous comparative genomics study [44].

^dNumbers in the parentheses are the total numbers of known RNA motifs or predicted transcription terminators/attenuators in the 1002 Shewanella 5′-UTR sequence sets.