Table 2.

List of selected asRNAs. The asRNA identifier, location in prophages, strand, putative target genes and coverage (number of cDNA reads calculated using SAMtools) are indicated. Classification: asRNAs from 3 different families were retrieved from the sRNA sequencing data. asRNAs are depicted in red and putative target mRNAs are indicated in purple. 5' UTR and 3' UTR correspond to asRNAs that are complementary to the 5' and 3' UTRs of their putative target mRNAs, respectively. CDS corresponds to asRNAs that are complementary to the coding sequences of their putative target mRNAs. UTR: untranslated region; CDS: coding sequence.

Classification	Name	Phage	Strand	mRNA putative target gene	Coverage
	Spy_sRNA392987		+	SPy_0481: transposase	220
	Spy_sRNA480642		+	SPy_0598: phosphoglycerate mutase	108
	Spy_sRNA480696		−	SPy_0596: hypothetical protein	71
	Spy_sRNA477741		−	SPy_0593: hypothetical protein	100
	Spy_sRNA531081	370.1	+	SPy_0656: hypothetical protein	140
	Spy_sRNA532788	370.1	−	SPy_0658: hypothetical protein	68
	Spy_sRNA800369	370.3	−	SPy_0978: hypothetical protein	878
	Spy_sRNA1221370	370.2	−	SPy_1487: hypothetical protein	136
	Spy_sRNA1718031		−	SPy_2063: hypothetical protein	46
	Spy_sRNA1778807		−	SPy_2129: hypothetical protein	334
	Spy_sRNA728180		+	SPy_0880: mvaS.1, 3-hydroxy-3-0methylglutaryl-coenzyme A	21
	Spy_sRNA924338		−	SPy_1128: eutD phosphotransacetylase	29
	Spy_sRNA1032107		+	SPy_1251: tRNA pseudouridine synthase B	37
	Spy_sRNA1063616		−	SPy_1287: ABC transporter permease	155
	Spy_sRNA1167444		+	SPy_1408: comEC, competence protein	68