Summary (enrichment more than 3-fold)



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Nucleoid RNAs
*in blue-annotated small RNAs (sRNAs)

*in red-annotated intergenic repetitive elements

Coordinates Annotation

______________________________________________________________________

Minus Strand

1630638-1632474 ydfK, pinQ

1049958-1052050 cspG, ymcE, gnsA entire including ***PAIR4a repeats in intergenic region between cspG and ymcE

3886350-3889554 tnaCAB

1406998-1407330 intergenic ydaN and dbpA, fnrS small RNA

939670-945210 dmsA, dmsB, dmsC and ***TERM15 upstream of dmsA

1655646-1663698 ynfDEFG, dmsD, N-terminal clcB ***REPT124 between ynfD and E and REPt125 between dmsD and clcB

2493438-2494826 b2378 (lpxP)

2350534-2354930 glpABC

2823758-2828026 srlAEBD, gutM, srlR and begining of gutQ

2848662-2854258 hypABCDE and fhlA

2347398-2350550 intergenic inaA and glpQ containing yfH pseudogene,

entire glpQ, glpT

1311910-1313402 ompW

4403910-4407570 end of purA, nsrR, rnr, beginning of rlmB

1639782-1640706 cspF entire ***including intergenic cspF and ydfT containing *** TERM25

2454253-2459021 sixA, fadJ, fadI and yfcZ

2735062-2735794 yfiA and pheL

4244710-4248514 entire malK, lamB, malM

4103742-4104442 entire cpxP

772859-774018 cydB, ybgT, ybgE, N-terminal ybgC

986238-987042 intergenic ompF and asnS, region of transcription units (OmpR, CRP, CpxR, IHF, Lrp)

2588697-2589064 ypfM

3891798-3893618 yieEF

2011710- 2017661 fliFGHIJK

1130222-1141922 flgBCDEFGHIJKL entire

19742-20634 intragenic region between nhaR and yaaY (complimentary to region of insA-1 and B-1 on the opposite strand)

2414654-2416770 C-terminal pta and entire yfcC

20001766-2005954 fliD, fliS, fliT and amyA

1644342- 1645242 flxA

728230-730034 ybfA

970766-972738 ycbJ

289806-290667 intergenic ykgS anmd yagJ, complementary to insB and insA on opposite strand

2940798- 2941570 intergenic ygdI and csdA and N-terminal of csdA

2018494-2022786 fliMNOPQR and rcsA

1257886-1258410 ychH

2802702-2806482 proV, prow, proX and ygaX including ***REP193

1935438-1937426 entire pykA and ***REPt137

1997404-2001726 fliYZAC

3086206-3087667 galP

815958-816 225 intergenic moaA 5’UTR

4327094-4328162 yjcZ

2228558-2229610 yohJ, yohK

3851342-3851730 strong peak intergenic tisB and emrD ***REP279

2763886-2765538 yfjN (rnlA) and yfjO (rnlB)

1609886-1610162 N-terminal yneG

770371-772858 cydA

1805694-1806722 entire yniA

3299430-3301538 yhbU and V

2812750-2813442 sraD sRNA and N-terminal gshA

2039294-2040186 ***REP142 and entire yodA downstream

1831302-1831626 beginning of ydjX

892318- 893074 ybjN, entire

1744526- 1745162 valV, valW, ydhR

2261790-2263426 setB

2371027-2377457 pmrD, menECBHD

2924238- 2925738 ygdH

1900518-1903498 manXYZ and yobD

1940574-1942298 znuC, znuB

2231678-2234490 yeiS, yeiT and yeiA

3352134-3358738 Lrp and Fnr binding sites, gltB and gltD

1168110-1168642 ycfR

582734-583754 appY entire

1014142-1015258 ymbA and rmf, entire

1268414-1270018 intergenic strong continuos signal, parts complementary to ldrABC on the opposite strand ***LDR REPEATS

1545350-1550034 fdnGHI

1184918-1186442 pepT

2922230-2922562 csrB sRNA

829950-831509 entire rhlE

823758-824714 entire ybhQ

404942-408090 yaiI, aroL, yaiA, aroM, yaiE and ykiA

793926-797178 entire ybhT, modA, modB, modC

831509-831869 intergenic rhlE and ybiA ***RIP75

832030-835634 dinG, ybiB, ybiC

889046-889970 ybjM

932443-936074 ftsK

936150-936738 intergenic ftsK and lolA ***REP85

989734-992610 pepN entire

1031142-1036778 hyaA, B, C, D, E and F

1037595-1041178 appC, appB, appA

1064718-1066106 entire agp

1489718- 1492682 ydcA, trg

1288102-1290578 rssA, rssB

1480814-1483138 hrpA N-terminal part

1298502-1305586 oppABCDF

1145054-1145642 intergenic rluC and ycef ***REP101

1921022-1921426 ryeA,B sRNA

2183854-2184866 yohM

2467118-2468338 yfdI

2474334-2474594 entire torI

2481598- 2485906 evgA and evgS

2535262-2536386 yfeK and yfeS

2555294-2556178 Complementary to N-terminal of eutB on opposite strand

2736150-2737082 pheA and downstram intergenic containing ***REPt190

2739742-2740530 yfiR

2748750-2751898 yfjB, recN and b2617 (bamE)

2753918-2754162 ssrA

3219430-3220634 entire ebgR

3256294-3263794 complementary to tdcGFEDCB on the opposite strand

3401374-3403218 yhdH and also yrdF’ abd yrdE’ pseudogenes

3483902-3484106 intergenic prkB and crp***REPt246

3718166-3718690 C-terminal cspA and intergenic cspA and insJ ***mokA’ 3865582-3866418 yidQ entire

3965606-3965986 intergenic rho and b3784

3980790-3982149 Entire aslB

3993438-3996026 yigA, xerC, yigB

4005678-4002500 rhtC

4006251-4066740 intergenic rhtC and rhtB ***REP289

4328262-4328538 Intergenic yjcZ and prop ***TF sites CRP and Fis

4328539-4330266 proP including downstream intergenic with basS which have***REP326

4344774-4345010 complementary to the small fragment in the middle of fumB on the opposite strand 2.1

4377414-4380354 complementary to frdCBA on the opposite strand

4395014-4397394 C-terminal amiB and entire mutL

4460798-4463610 Intergenic nrdD and treC TF bindning sites FNR, long fragment complementary treC and treB on the opposite strand

4525990-4526834 Intergenic sgcA and Q, ryjB sRNA and fragment complementary to sgcQ on the opposite strand

4543030-4543834 N-terminal fimD

4589638-4592242 entire tsr and fragment complementary to N-terminal part of yjiZ on the opposite strand

4609126-4609362 intergenic prfC and osmY, TF binding sites IHF, Lrp and CRP

4638502-4638978 Intergenic yjjY and yjtD, TF binding site FNR
Plus Strand

1638023-1639847 ydfR, essQ, cspB and ***TERM24 and 25 repeats

1430834-1433696 uspF

3256031-3265139 tdcGFEDCBA

1635745-1636901 gnsB, ynfN, cpsI and ***PAIR4b repeats

2170462-2175292 gatDCBAZY

4375949-4380475 entire ampC, frdD, frdC, frdB, frdA

2713239-2714607 yfiD

3097585-3098936 ansB

3137065-3144466 Intergenic yghU and hybG ***REP221, hybGFEDCBAO

4457129-4464246 nrdG and nrdD, treC, treB including intergenic ***IRU

18 and REP338

1050213-1050468 cspH, sold-shock protein homologue

652952-655249 complementary to citB on opposite strand, intergenic region between citB and dcuC containing ***REPt56 and entire dcuC

1959655-1975718 flhEAB, cheZYBR, tap, tar, cheWA, motBA, flhC

1746670-1752742 ydhTUXWVY

3043182-3048843 yqfF, gcvPHT

948953-954044 pflA, pflB and focA including intergenic focA and ycaO containing TF binding sites CRP, FNR, IHF, ArcA, FNR

851492-852328 ybiP and ***rybA sRNA

1119724-1120680 yceP and dinI

1956174-1956820 intergenic torY and cutC and C-terminal cutC
1019341-1020210 intergenic opaA and sulA containing ***TERM16 and

whole sulA

2705133-2708133 rseC, rseB, rseA and rpoE

787259-791351 galMKTE

1395621-1396789 uspE entire

1664399-1665366 ynfK

1487646-1488813 gapC_1 and gapC_2 including ***REPt116

887061-887349 fragment complementary to ybjK on the opposite strand and ***rybB sRNA

986270-986857 Intergenic ompF and asnS* TF binding sites OmpR, CRP, CpxR, Lrp, IHF

6370-8102 entire yaaJ

50594-53566 apaH, apaG, ksgA and pdxA

63317-65798 polB

136450-136958 yacC

183730-185174 yaeH and yaeI

239666-240246 yafV

244530-246558 yafK, yafQ and dinJ

254002-254278 intergenic prfH and pepD *** REPt20

264770-265334 ykfB and beginning of yafY

296242-296446 intergenic intF and yagP ***ptWF’ *** nc1

479618-480129 tomB and downstream intergenic tomB and acrB

484837-485358 intergenic acrA and acrR containing ***TF binding sites PhoP, MarA and SoxS

555703-556007 Intergenic ybcI and folD, there should be a small ribosome-associated protein ybcJ

640614-641136 uspG

698384-698710 Intergenic asnB and nagD containing ***RIP61

682199-683682 C-terminal hscC, rihA

812269-812616 intergenic bioD and uvrB ***DARS1

828318-832188 ybiA

836708-837392 Intergenic ybiJ and ybiC ***REP77 and entire ybiJ

847566-848185 Intergenic glnH dps including TF binfing sites IHF and NtrC and dps

927044-930219 cydC and cydD

1014598-1015195 Fragment complementary to rmf on opposite strand and intergenic rmf and fabA

1025567-1026186 mgsA

1066110-1067002 yccJ and wrbA

1113071-1114782 msyB, mdtG and intergenic mdtG and lpxL including***REPt98

1128028-1129391 flgN and flgM

1189610-1189839 Intergenic phoP and purB***REPt106

1212445-1214785 ycgEF

1239102-1241345 entire cvrA

1242814-1243786 ycgR

1259917-1260167 intergenic ychM and prsA ***TERM20

1285885-1286363 part of tpr and the region of ***tRNA repeats rTV1(TLRs)

1294351-1296276 C-terminal adhE

1310253-1310579 intergenic yciA and yciB

1314399-1321182 entire trpABCDEL

1328136-1328586 yciN

1355035-1355507 intergenic sapA and ymjA ***REP110

1358035-1359002 N-terminal puuA

1417836-1418265 racR

1426362-1426824 N-terminal insH-5

1489932-1490258 hokB, mokB and fragment complementary to sokB on the opposite strand

1553796-1554132 sra

1607586-1608759 uxaB

1630838-1631664 Intergenic ydfJ and ydfK including 5’UTR

1658340-1662975 complementary to ynfE, ynF ynfG, ynfH and dmsD on the opposite strand

1670514-1671834 mdtI and mdtJ

1734063-1735643 ydhP and ***ynhF

1762725-1763350 ydiH and ydiI *** and rydB sRNA

1789366-1790252 ydiV

1797242-1797459 pheM and intergenic pheM rplT

1816549-1819789 chbR, chbA, chbC and chbB

1821781-1823041 ydjR
1862672-1863677 yeaE

1875319-1875618 yoaF

1925036-1928591 ptrB, yebE, yebF, yebG

1931072-1932783 edd

1985772-1986103 intergenic yecJ and yecR***sRNA isrB

2078431-2079413 sbmC

2099304-2099846 wbbL_2 pseudogene

2100985-2106994 wbbL_1, wbbKJIH, glf and rfbX

2246566-2247705 yeiE

2281982-2282154 intergenic yejK and yejL

2289493-2301631 ccmHGFEDCBA and napCBHGADF

2309389-2309764 intergenic ompF and yojL

2387849-2389365 nuoN

2389491-2390960 nuoM

2391219-2400090 nuoLKJIHGFE

2407059-2409478 yfbS and intergenic yfbS aand yfbR with ***REPt168 2410711-2411371 yfbV

2425450-2426000 argT

2447172-2447430 small fragment C-terminal yfcO

2541495-2542703 intergenic cysP and b2426 (ucpA) ***RSA4 repeats and entire ucpA

2557197-2558439 complementary to infZ on the opposite strand

2580792-2583603 nudK and aegA

2595606-2595950 intergenic purC and bamC***REPt181

2637622-2637817 small fragment in hisS

2644142-2650267 pbpC, yfhM

2660147-2660370 Intergenic iscR and trmJ***REP184

2715168-2715563 intergenic ung and yfiF***REPt189

2723731-2724092 intergenic kgtP and rrfG

2734613-2737103 complementary to yfiO, yfiA, pheL and pheA on the opposite strand

2759141-2763537 yfjK, yfj and PDR-A repeats

2816686-2817059 intergenic serV and csrA

2820041-2820797 recX

2833636-2836292 hypF and hydN including intergenic ***REPt196

(Flh regulon)

2840545-2848502 hycIHGFEDCBA FhlA regulon)

2848948-2852114 complementary to hypABCDE on the opposite strand

2907656-2907879 intergenic pyrG and mazG

2922166-2922601 csrB sRNA
2940478-2940684 intergenic gcvA and ygdI, ecogene: annotated as gcvB

2948979-2949849 recD


3002231-3003868 ygeV

3010869-3013141 yqeB and C

3040475-3041236 ygqA

3297285-3299300 yhbPST

3316257-3316429 metY and intergenic with ArgR, FIS, Crp

3367054-3371645 yhcH, nanKETA

3429809-3430839 yrdD, smg, smf

3483164-3483685 yhfA and ***REPt246 in itergenic with prkB

3545718-3546004 intergenic malQ and gntT ***REP254

3546010-3550555 malQ and malP entire

3561780-3573063 yzgL, glgPACXB, asd

3581391-3582164 complementary to insA-6 and insB-6 on the opp strand

3597934-3598679 rpoH

3598690-3599085 intergenic rpoH and ftsX *TF binding sites DnaA, CRP, CytA

3654072-3654650 hdeB and hdeA

3675211-3677278 yhjG and yhjH

3706854-3708629 eptB

3739197-3739563 ysaA

3886423-3888198 Fragment complementary to entire tnaA on the opposite strand

3920671-3921037 intergenic atpI and gidB ***REP15

3923636-3923917 intergenic gidA and mioC ***oriC

3938382-3939544 yieP and intergenic with rrsC *TF binding site Fis

3960821-3962120 gpp

4108404-4108838 intergenic cdh and tpiA ***REPt303

4113543-4116228 intergenic glpX and K***REPt304, glpK and glpF

4152720-4153086 Intergenic argE and argC *TF binding site ArgR

4187574-4187924 intergenic yjaZ and thiH***sroH sRNA

4227247-4228226 pepE and intergenic with yjbB ***REP312

4295103-4297467 entire fdhF

4323826-4324408 intergenic yjdM and yjdN ***REP325

4354426-4358118 cadA, cadB

4363331-4366451 dcuA and aspA

4404050-4405116 fragment complementary to nsrR and part of rnr on the opposite strand

4414310-4414784 intergenic yjfO and yjfN and entire yjfO

4497897-4498546 yjgX_2

4516480-4517243 complementary to inA-7, insB-7_1 and insB-7_2 on the opposite strand

4562715-4563936 yjiM

4578346-4579468 hsdS

4581077-4584500 hsdR and intergenic hsdR and hsdM containing ***IRU19

4586133-4589339 yjiAXY



4638368-4638820 two intergenic peaks arcA and yjtD, annotation in Ecogene: yjjY and TF binding sites FNR
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