Table 4.

Predicted novel antisense RNA (asRNA) candidates

	Peaka (nt)	Start	End	cDNA #	Opposite gene	Overlapb	asRNA direction	Name
ncr2706	47	3738263	3738309	114	ywqA	N	−
ncr1430	70	4035606	4035675	58	bglP	5′	+
ncr1687	24	1154737	1154760	26	wprA	G	−
ncr1296	236	3460215	3460450	26	opuBD	G	+	shd102
ncr1207	231	2997369	2997599	15	ytoI	G	+	shd84
ncr1334	103	3669968	3670070	12	ggaA	3′	+	shd112
ncr1812	239	1915034	1915272	11	yndL	5′	−	SurA
ncr1265	218	3307602	3307819	10	yutK	G	+
ncr1193	130	2892567	2892696	10	leuA	G	+	shd83
ncr2153	101	2641931	2642031	9	comER	G	−
ncr1383	204	3862340	3862543	8	ywfM	3′	+	shd115
ncr1135	160	2600156	2600315	7	sigA	3′	+	shd77
ncr1186	17	2849374	2849390	7	nadB	G	+
ncr1006	219	2002176	2002394	6	yoeA	5′	+
ncr1799	25	1775732	1775756	6	mutS	5′	−
ncr1479	232	4213213	4213444	6	jag	G	+	shd127
ncr1046	71	2190676	2190746	5	yoqZ	G	+	shd60
ncr1557	159	519216	519374	5	ndoA	3′	−	shd23
ncr2058	110	2483671	2483780	5	yqzJ	G	−
ncr394	76	646225	646300	5	ydiF	G	+	shd26
ncr2160	259	2647405	2647663	3	sda	G	−
ncr1351	227	3747160	3747386	2	mbl	3′	+
ncr1565	61	554497	554557	2	yddR	3′	−
ncr2885	106	4186388	4186493	2	yyaQ	3′	−
ncr1546	50	452734	452783	2	mtlD	3′	−
ncr507	30	924181	924210	2	yfhD	3′	+
ncr2410	249	3123766	3124014	2	ytoA	3′	−

^aCandidates for antisense RNA are selected based on cDNA signals (of the enriched sample) that either start within genes with the opposite orientation or end within 50 nt away from such genes. The length is measured from the start to the end of cDNA signals.

^bOverlapping region is classified as follows: G = asRNA is fully complementary to the opposite gene. 5′ = asRNA 5′ end is complementary to the 5′ region of the opposite gene. 3′ = asRNA 3′ end is complementary to the 3′ region of the opposite gene. N = no overlap; the distance between 3′-end of the asRNA and the opposite gene is less than 50 nt and there is no predicted intrinsic terminator.