Table S3. sRNAs that overlap ORFs,,,,,,,,
sRNA,Bacterium*,Genome Accession,sRNA left end,sRNA right end,Strand,ORF left end,ORF right end,ORF annotation
Ysr110,Salmonella enterica subsp. enterica serovar Typhi str. CT18,NC_003198.1,"2,464,479","2,464,681",+,"2,462,589","2,464,511",Acyltransferase
Tpke70,Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150,NC_006511.1,"526,978","527,376",+,"525,741","526,979",Alanine transaminase
STnc3160,Cronobacter turicensis z3032,NC_013282.2,"1,378,128","1,378,197",+,"1,376,498","1,378,138",Alpha-D-glucose phosphate-specific phosphoglucomutase
Ysr218,Pectobacterium atrosepticum SCRI1043,NC_004547.2,"67,444","67,658",-,"65,657","67,552",Bifunctional metallophosphatase
Ysr121,Enterobacter cloacae subsp. cloacae ATCC 13047,NC_014121.1,"3,321,968","3,322,134",-,"3,321,147","3,322,089",Chemotaxis protein MotA
sR054,Yersinia pestis CO92,NC_003143.1,"2,621,033","2,621,097",+,"2,620,043","2,621,035",D-lactate dehydrogenase
OxyS,Serratia proteamaculans 568,NC_009832.1,"5,291,115","5,291,225",+,"5,290,442","5,291,173",Glutathione peroxidase
STnc4100,Salmonella enterica subsp. enterica serovar Typhi str. CT18,NC_003198.1,"4,119,259","4,119,374",+,"4,118,018","4,119,334",Glycerol-3-phosphate ABC transporter substrate-binding protein
IsrC,"Salmonella enterica subsp. enterica serovar Schwarzengrund str.
CVM19633",NC_011094.1,"1,295,886","1,296,087",+,"1,295,746","1,295,910",Hypothetical protein
MgrR,"Salmonella enterica subsp. arizonae serovar 62:z4,z23:-",NC_010067.1,"1,414,640","1,414,737",+,"1,414,477","1,414,672",Hypothetical protein
PsrO/SraG,Klebsiella pneumoniae subsp. pneumoniae MGH 78578,NC_009648.1,"3,934,707","3,934,873",+,"3,934,604","3,934,817",Hypothetical protein
RprA,Edwardsiella ictaluri 93-146,NC_012779.2,"1,847,642","1,847,753",-,"1,847,421","1,847,688",Hypothetical protein
STnc100,Escherichia coli CFT073,NC_004431.1,"1,343,250","1,343,439",+,"1,343,177","1,343,270",Hypothetical protein
STnc3060,Klebsiella pneumoniae subsp. pneumoniae MGH 78578,NC_009648.1,"3,989,172","3,989,267",+,"3,988,991","3,989,195",Hypothetical protein
STnc3170,Cronobacter turicensis z3032,NC_013282.2,"30,028","30,130",+,"29,623","30,048",Hypothetical protein
STnc3390,Citrobacter koseri ATCC BAA-895,NC_009792.1,"1,953,689","1,953,756",+,"1,953,499","1,953,718",Hypothetical protein
STnc4080,Erwinia pyrifoliae Ep1/96,NC_012214.1,"170,918","171,029",-,"170,762","170,956",Hypothetical protein
STnc500,"Salmonella enterica subsp. arizonae serovar 62:z4,z23:-",NC_010067.1,"1,795,953","1,796,237",-,"1,795,873","1,796,110",Hypothetical protein
Ysr101,Klebsiella pneumoniae subsp. pneumoniae MGH 78578,NC_009648.1,"4,951,859","4,952,000",+,"4,951,724","4,951,946",Hypothetical protein
Ysr131,Citrobacter koseri ATCC BAA-895,NC_009792.1,"3,959,670","3,959,839",+,"3,959,470","3,959,746",Hypothetical protein
Ysr138,Yersinia enterocolitica subsp. enterocolitica 8081,NC_008800.1,"1,085,896","1,086,022",-,"1,085,777","1,086,008",Hypothetical protein
Ysr79,Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67,NC_006905.1,"2,715,673","2,715,856",-,"2,715,555","2,715,756",Hypothetical protein
Ysr192,Yersinia enterocolitica subsp. enterocolitica 8081,NC_008800.1,"4,278,843","4,278,980",+,"4,278,667","4,278,882",Protein SlyX
STnc3230,"Salmonella enterica subsp. arizonae serovar 62:z4,z23:-",NC_010067.1,"2,870,439","2,870,563",+,"2,869,795","2,870,520",Sugar-binding protein
Ysr224,Yersinia enterocolitica subsp. enterocolitica 8081,NC_008800.1,"3,539,609","3,539,748",+,"3,539,206","3,539,646",Thioredoxin TrxC
Ysr129,Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150,NC_006511.1,"2,078,010","2,078,134",-,"2,078,059","2,078,161",Addiction module toxin RelE
Ysr212,Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044,NC_012731.1,"2,742,147","2,742,209",-,"2,742,176","2,743,237",Cell division protein ZapE
IsrA/McaS,Escherichia coli HS,NC_009800.1,"1,451,904","1,452,056",-,"1,451,972","1,452,083",Glutamate decarboxylase
Ysr206,Yersinia enterocolitica subsp. enterocolitica 8081,NC_008800.1,"4,188,318","4,188,522",-,"4,188,489","4,189,160",Glutathione-S-transferase
STnc480,Salmonella enterica subsp. enterica serovar Typhi str. Ty2,NC_004631.1,"2,399,960","2,400,030",-,"2,400,031","2,401,179",Glycerate 3-kinase
Ysr187,Yersinia enterocolitica subsp. enterocolitica 8081,NC_008800.1,"4,561,702","4,561,836",-,"4,561,809","4,562,282",Heat shock chaperone IbpB
FnrS,Yersinia pestis KIM10+,NC_004088.1,"2,195,786","2,195,903",+,"2,195,793","2,196,003",Hypothetical protein
GcvB,Sodalis glossinidius str. 'morsitans',NC_007712.1,"3,365,794","3,365,981",+,"3,365,867","3,366,083",Hypothetical protein
GlmZ,Yersinia pestis KIM10+,NC_004088.1,"420,943","421,165",+,"421,139","421,319",Hypothetical protein
IsrM,Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853,NC_011205.1,"2,958,409","2,958,670",+,"2,958,633","2,958,822",Hypothetical protein
PsrN/sraF,Sodalis glossinidius str. 'morsitans',NC_007712.1,"424,363","424,537",-,"424,524","425,102",Hypothetical protein
RydC,Klebsiella pneumoniae subsp. pneumoniae MGH 78578,NC_009648.1,"2,580,741","2,580,803",+,"2,580,746","2,580,938",Hypothetical protein
STnc4150,"Salmonella enterica subsp. arizonae serovar 62:z4,z23:-",NC_010067.1,"2,465,779","2,465,908",+,"2,465,825","2,466,004",Hypothetical protein
STnc470,"Salmonella enterica subsp. arizonae serovar 62:z4,z23:-",NC_010067.1,"2,862,303","2,862,522",-,"2,862,523",2862945),Hypothetical protein
Ysr192,Serratia proteamaculans 568,NC_009832.1,"3,109,745","3,110,106",-,"3,109,916","3,110,108",Hypothetical protein
Ysr195,Yersinia pestis Angola,NC_010159.1,"2,737,116","2,737,415",+,"2,737,409","2,737,652",Hypothetical protein
Ysr207,Serratia proteamaculans 568,NC_009832.1,"3,045,931","3,046,158",-,"3,046,070","3,046,277",Hypothetical protein
Ysr43,Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853,NC_011205.1,"3,150,322","3,150,437",+,"3,150,369","3,150,585",Hypothetical protein
Esr2,Shigella dysenteriae Sd197,NC_007606.1,"1,424,982","1,425,168",+,"1,425,128","1,425,401",Insertion element iso-IS1N protein InsA
Ysr232,Erwinia tasmaniensis Et1/99,NC_010694.1,"2,996,135","2,996,565",-,"2,996,183","2,996,707",Integrase
STnc240,Shigella flexneri 2a str. 301,NC_004337.2,"2,092,778","2,092,853",-,"2,092,844","2,093,827",LysR family transcriptional regulator
StyR-3,Klebsiella pneumoniae subsp. pneumoniae MGH 78578,NC_009648.1,"622,751","622,895",+,"622,801","623,916",MBL fold metallo-hydrolase
Ysr81,Shigella flexneri 2a str. 301,NC_004337.2,"3,024,536","3,024,788",-,"3,024,688","3,024,939",Membrane protein
STnc280,Cronobacter sakazakii ATCC BAA-894,NC_009778.1,"424,395","424,481",-,"424,460","425,638",Oligogalacturonate lyase
sR077,Yersinia pestis CO92,NC_003143.1,"2,311,814","2,311,957",+,"2,311,957","2,312,541",Ribosomal-protein-S5-alanine N-acetyltransferase
Esr4,Escherichia coli CFT073,NC_004431.1,"2,568,797","2,569,034",-,"2,568,937","2,569,072",Transposase
IsrL,Pectobacterium atrosepticum SCRI1043,NC_004547.2,"3,885,836","3,886,048",-,"3,885,899","3,886,357",Xanthine phosphoribosyltransferase
Ysr38,Enterobacter cloacae subsp. cloacae ATCC 13047,NC_014121.1,"187,283","187,384",-,"187,348","187,815",YhcH/YjgK/YiaL family protein
Esr6,Citrobacter rodentium ICC168,NC_013716.1,"4,862,315","4,862,416",-,"4,862,245","4,862,425",Hypothetical protein
RyhB,Yersinia pestis KIM10+,NC_004088.1,"4,314,252","4,314,317",+,"4,314,193","4,314,405",Hypothetical protein
sR055,Erwinia tasmaniensis Et1/99,NC_010694.1,"1,225,140","1,225,251",-,"1,225,093","1,225,344",Hypothetical protein
sR070,Cronobacter sakazakii ATCC BAA-894,NC_009778.1,"2,349,839","2,349,929",+,"2,349,753","2,349,942",Hypothetical protein
STnc1690,Escherichia fergusonii ATCC 35469,NC_011740.1,"2,805,595","2,805,685",+,"2,805,569","2,805,767",Hypothetical protein
STnc1870,Escherichia coli O157:H7 str. EC4115,NC_011353.1,"314,321","314,406",+,"314,260","314,413",Hypothetical protein
STnc3340,Klebsiella pneumoniae subsp. pneumoniae MGH 78578,NC_009648.1,"898,629","898,691",-,"898,575","898,755",Hypothetical protein
STnc380,Escherichia coli CFT073,NC_004431.1,"4,211,456","4,211,558",-,"4,211,420","4,211,604",Hypothetical protein
Tp2,Escherichia coli CFT073,NC_004431.1,"133,248","133,361",-,"133,199","133,382",Hypothetical protein
,,,,,,,,
*Best hit,,,,,,,,