GENES 2867:::H37Ra..Sauton.s.media.replicate.1 2867:::H37Ra..Sauton.s.media.replicate.2 2867:::H37Ra..Sauton.s.media.replicate.4 2885:::H37Ra..7H9.roll.replicate.1 4060:::H37Rv.0.05..SDS.exposure.for.1h.rep.1 4062:::MTB.strain.1254.Ctrl.vs.0.005.mM.DETA.NO.40min.rep.4 4062:::MTB.strain.1254.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.1 4062:::MTB.strain.1254.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.7 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.16hrs.rep.1 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.16hrs.rep.4 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.20min.rep.3 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN.1hr.rep.1 4062:::MTB.strain.1254.Ctrl.vs.high.aeration...0.001.mM.DETA.NO.rep.1 4062:::MTB.strain.1254.Ctrl.vs.high.aeration.rep1 4062:::MTB.strain.1254.Ctrl.vs.high.aeration.rep2 4062:::MTB.strain.1254.Ctrl.vs.low.aeration..0.2..oxygen..2hr.rep.1 4062:::MTB1254.Day.0.rep.1 4089:::H37Rv.wild.type.vs..H37Rv.whiB7.null.rep.4 4089:::MTB1254.control.vs..0.5.ug.ml.Streptomycin.for.15.min.rep.3 4089:::MTB1254.control.vs..25.ug.ml.Streptomycin.for.15.min.rep.3 4089:::MTB1254.control.vs..25.ug.ml.Streptomycin.for.15.min.rep.4 4089:::MTB1254.control.vs..5.0.ug.ml.Streptomycin.for.15.min.rep.1 4089:::MTB1254.ethanol.vs..100.ug.ml.Tetracyclin.for.30.min.rep.3 4089:::MTB1254.ethanol.vs..100.ug.ml.Tetracyclin.for.30.min.rep.4 4089:::MTB1254.vs..MTB1254.rep4 4101:::NRP.Day14..1 4101:::NRP.Day14..4 4107:::DIPED..100ug.mL..DMSO..12h..1 4107:::DIPED..100ug.mL..DMSO..12h..2 4107:::DIPED..100ug.mL..DMSO..12h..3 4107:::DIPED..50ug.mL..DMSO..12h 4107:::DIPED.50ug.mL.vs.DMSO.12h.1 4107:::EMB..10ug.mL..DMSO..12h 4107:::pH4.8vspH6.8..2h.B 4107:::X.241..0.1ug.mL..DMSO..12h..1..GEO.acc.GSM28046. 4107:::X0.12mg.mL.BZA.pH5.6..2h. 4107:::X0.12mg.mL.BZAvspH5.6..7h. 4107:::X0.1mg.mLTriclosanvsEtOH.6hB 4107:::X0.1mM.GSNOvsDMSO..4h 4107:::X0.1mMGSNO.10ug.mLmdvsDMSO.6hA 4107:::X0.1mMGSNO.20ug.mLCPZvsDMSO.6h 4107:::X0.1mMGSNO.5ug.mLKCNvsDMSO.6h 4107:::X0.1mMGSNO.5ug.mLKCNvsDMSO.6h.A 4107:::X0.1ug.mL.Mtmvsctrl..0.33h. 4107:::X0.1ug.mL.Mtmvsctrl..0.75h. 4107:::X0.2mg.mL.AmpvsEtOH..6hC 4107:::X0.2ug.mL.INH.EtOH..6h 4107:::X0.2ug.mL.Mtmvsctrl..0.75h. 4107:::X0.2ug.mL.PA824.DMSO..6h..2 4107:::X0.4ug.mL.INHvsEtOH..6hA 4107:::X0.4ug.mL.PA824.DMSO..6h..3 4107:::X0.4ug.mL.PA824.DMSO..6h..4 4107:::X0.5ug.mL..111891vsDMSO.6h 4107:::X0.5ug.mL..111891vsDMSO.6hA 4107:::X0.5ug.mL..121940vsDMSO.6h 4107:::X0.5ug.mL..124196vsDMSO..6hA 4107:::X0.5ug.mL.CeruleninvsDMSO..6hC 4107:::X0.5uMValinomycin.70mMKClvsDMSO.6h 4107:::X1.2mg.mL.PZAvspH5.6..10.5h. 4107:::X1.2mg.mL.PZAvspH5.6..4h.B 4107:::X1.ug.mL..111891vsDMSO..6h 4107:::X100ug.mL.TriclosanvsEtOH..6hA 4107:::X100ug.mLCephalexinvsEtOH.6hA 4107:::X100uM.DCCD.DMSO..6h 4107:::X100uM.Dipyridylvsctrl..6h 4107:::X100uM.DipyridylvsCtrl..6hA 4107:::X10ug.mL..109.DMSO..6h 4107:::X10ug.mL..241.DMSO..6h 4107:::X10ug.mL.clofazimine.DMSO..6h 4107:::X10ug.mL.EMBvsDMSO..6hA 4107:::X10ug.mL.menadionevsDMSO..6h 4107:::X10ug.mL.methoxatinvsDMSO..6h.A 4107:::X10ug.mL.Nvb.DMSO..6h..2 4107:::X10ug.mL.PA.1vsDMSO..6hA 4107:::X10ug.mL.TriclosanvsDMSO..6h 4107:::X10ug.mL.TriclosanvsDMSO..6hA 4107:::X10ug.mL.TRZ.DMSO..6h..1 4107:::X10ug.mLchlorpromazinevsctrl.6h 4107:::X10ug.mLchlorpromazinevsctrl.6hA 4107:::X10ug.mLMethoxatinvsDMSO.6h 4107:::X13ug.mL.clfzine.DMSO..6h..1 4107:::X13ug.mL.clfzine.DMSO..6h..2 4107:::X150uM.Deferroxaminevsctrl..6hA 4107:::X150uM.Deferroxaminevsctrl..6hB 4107:::X1mM.DNP.DMSO..6h..2 4107:::X1ug.mL..109vsDMSO..6h 4107:::X1ug.mL..111891vsDMSO..6h 4107:::X1ug.mL..111895vsDMSO..6hA 4107:::X1ug.mL..121940.DMSO..12h 4107:::X1ug.mL..124196vsDMSO..6h 4107:::X1ug.mL..124196vsDMSO..6hA 4107:::X1ug.mL..241vsDMSO..6h 4107:::X1ug.mL..59vsDMSO..6h 4107:::X1ug.mL..59vsDMSO..6hA 4107:::X1uM.ValinomycinvsDMSO..6h 4107:::X1uM.ValinomycinvsDMSO..6h.B 4107:::X2.5mM.Dinitrophenol.DMSO..6h 4107:::X20ug.mL.chlorprmz.DMSO..6h..1 4107:::X20ug.mL.chlorprmz.DMSO..6h..2 4107:::X20ug.mL.CPZvsDMSO..6h 4107:::X20ug.mL.CPZvsDMSO..6h.A 4107:::X20ug.mL.KCN.DMSO..6h 4107:::X20ug.mL.methoxatinvsDMSO..6h 4107:::X20ug.mLProcept6778vsDMSO.6h 4107:::X20ug.mLProcept6778vsDMSO.6hB 4107:::X20uM.DCCD.DMSO..6h..1 4107:::X20uM.DCCD.DMSO..6h..2 4107:::X250uM.DeferroxaminevsDMSO..6h 4107:::X25J.UVvs.ctrl..6h. 4107:::X25ug.mL.AntimycinvsDMSO..6h 4107:::X25ug.mL.TRZ.DMSO..6h 4107:::X2mM.DTTvsDMSO..6h.A 4107:::X2ug.mL.PA824.DMSO..6h..1 4107:::X2ug.mL.PA824.DMSO..6h..2 4107:::X40ug.mL.5CL.pH5.6..2h..2 4107:::X50ug.mL.Thioridazine.DMSO..6h 4107:::X50ug.mL.Triclosan.EtOH 4107:::X50ug.mLAntimycinAvsDMSO..6hB 4107:::X50uM.CCCP.DMSO..6h..2 4107:::X50uM.CCCPvsDMSO..6h 4107:::X50uM.NigericinvsDMSO..6h.A 4107:::X5ug.mLProcept.6778vsDMSO.6hA 4107:::X9ug.mLAscidideminNpvsDMSO.6h 4364:::H37dosR.mutant.hypoxia.12hr.rep.3 4365:::H37Rv.diamide.1h.rep.5 4365:::H37Rv.sigma.H.null.mutant.diamide.1h.rep.1 4489:::MTB1254.WT.vs.Rv3662c.3665c.KO.in.7H9OADC.Exp2..OD1.5.1 4523:::H37Rv.sigB.null.mutant.control.vs.0.05..SDS.for.60.min.rep.4 4523:::H37Rv.sigB.null.mutant.control.vs.5mM.Diamide.for.60.min.rep.2 4523:::H37Rv.wild.type.control.vs.0.05..SDS.for.60.min.rep.1 4523:::H37Rv.wild.type.control.vs.0.05..SDS.for.60.min.rep.2 4523:::H37Rv.wild.type.control.vs.0.05..SDS.for.60.min.rep.3 4523:::H37Rv.wild.type.control.vs.0.05..SDS.for.60.min.rep.6 4523:::H37Rv.wild.type.control.vs.5mM.Diamide.for.60.min.rep.3 4523:::H37Rv.wild.type.vs.H37Rv.sigB.null.mutant.rep.2 4523:::H37Rv.wild.type.vs.H37Rv.sigB.null.mutant.rep.4 4523:::H37Rv.wild.type.Vs.H37Rv.wild.type.rep.2 4583:::X0.2mg.ml.TLM.vs.Ethanol.6hrs.rep.1 4583:::X0.2ug.ml.Isoniazid.vs.Ethanol.6hrs.rep.2 4583:::X0.5ug.mL.Cerulenin.vs.DMSO..6hrs.rep.3 4583:::X0.5ug.mL.Cerulenin.vs.DMSO..6hrs.rep.4 4583:::X40ug.ml.Ethionamide.vs.Ethanol.6hrs.rep.2 4615:::AA_30uM_10.min_07 4615:::AA_30uM_24h_03 4615:::AA_30uM_2h_09 4615:::CHP.AA.24h.1 4615:::CHP25uM_24h.50uMOA_30min_01 4615:::CK.for.OA.PA.Na.4h 4615:::MDGCy3.7H9Cy5.02 4615:::MTB1254_FA5_10min_01 4615:::MTB1254_INH_20MIN 4615:::MTB1254_Pellicle_14D_02 4615:::MTB1254_Pellicle_21D_04 4615:::MTB1254_SDS_90MIN_01 4615:::MTB1254_SDS_90MIN_02 4615:::MTB1254_SDS_90MIN_04 4615:::MTB1254.0465.4._SDS_60MIN_01 4615:::MTB1254.0485.1._AA_10m_01 4615:::MTB1254.0485.1._OA_10m_04 4615:::MTB1254.0485.1._PA_10m_01 4615:::MTB1254.0485.1._PA_10m_02 4615:::MTB1254.0485.1._PA_30m_03 4615:::MTB1254.0485.1._PA_30m_04 4615:::MTB1254.3524.1._INH_20MIN 4615:::MTB1254.3524.1.T0_WtT0_02 4615:::MTB1254whiB4_SDS_90MIN_01 4615:::MTB1254whiB4_SDS_90MIN_02 4615:::MTB1254whiB4_SDS_90MIN_04 4615:::OA_50uM_10min_01 4615:::OA_50uM_10min_06 4615:::OA_50uM_1h_03 4615:::OA_50uM_24h_03 4615:::OA_50uM_2h.1.0..BSA_30min_01 4615:::OA_50uM_2h.1.5..BSA_30min_01 4615:::OA_50uM_4h_08 4615:::PA_100uM_2h_03 4615:::PA_50uM_10.min_03 4615:::PA_50uM_10min_10 4615:::PA_50uM_24h_09 4615:::PA_50uM_24h_10 4615:::PA_50uM.OA_10uM_4h_01 4615:::PA_50uM.OA_10uM_4h_04 4615:::Rv.MT71_100803_01 4615:::Rv.pMV0481.2. 4615:::SDS_3h_01 4615:::Starvation_OA50_24h_04 4615:::Starvation_OA50_6h_03 4615:::TBD041 4615:::TBD1137 4615:::TBD816 4615:::TBE058 4615:::TBE735 4615:::WT_65.4_SDS_01 4615:::WT_85.1_OA_10min_01 4615:::WT_85.1_PA_10min_01 4615:::X2.2..Dipyridyl_0.2mM.Dpd.AA_50uM_01 4615:::X2.BA.1 4615:::X7H9MTB1254_SDS_90MIN_01 4615:::X7H9MTB1254.0465.4._SDS_90MIN_01 4630:::H37Rv.wild.type.Cy5.vs.Rv0485.Tn.mutant.Cy3..DS..rep.1 4696:::H37Rv.wt.vs.dosS.dosT.null.dosT.complemented.rapid.anaerobic.dormancy.day.6.rep.1 4696:::H37Rv.wt.vs.dosS.dosT.null.dosT.complemented.rapid.anaerobic.dormancy.day.6.rep.3 4696:::H37Rv.wt.vs.dosS.dosT.null.rapid.anaerobic.dormancy.day.6.rep.1 4696:::H37Rv.wt.vs.dosS.dosT.null.rapid.anaerobic.dormancy.day.6.rep.2 4696:::H37Rv.wt.vs.dosS.dosT.null.rapid.anaerobic.dormancy.day.6.rep.3 4696:::H37Rv.wt.vs.dosT.null.rapid.anaerobic.dormancy.day.6.rep.1 4699:::CDC1551.Ctrl.vs.clinical.isolate.2169.99_Uganda.rep.1 4699:::CDC1551.Ctrl.vs.clinical.isolate.2333.99_Uganda.rep.2 4699:::CDC1551.Ctrl.vs.clinical.isolate.5468.02_Afri2.rep.2 4699:::CDC1551.Ctrl.vs.clinical.isolate.5468.02_Afri2.rep.3 4699:::CDC1551.Ctrl.vs.clinical.isolate.947.01_EAI.rep.3 4703:::Clinical.isolate.4130.02_Haarlem.extra.vs.intracellular.in.resting.macrophages.rep.2 4704:::Clinical.isolate.10514.01_Afri2.extra.vs.intracellular.in.activated.macrophages.rep.2 4704:::Clinical.isolate.10517.01_Afri2.extra.vs.intracellular.in.activated.macrophages.rep.1 4704:::Clinical.isolate.10517.01_Afri2.extra.vs.intracellular.in.activated.macrophages.rep.2 4704:::Clinical.isolate.12954.03_Beijing.extra.vs.intracellular.in.activated.macrophages.rep.2 4704:::Clinical.isolate.1797.03_EAI.extra.vs.intracellular.in.activated.macrophages.rep.1 4704:::Clinical.isolate.1934.03_Beijing.extra.vs.intracellular.in.activated.macrophages.rep.2 4704:::Clinical.isolate.2191.99_Uganda.extra.vs.intracellular.in.activated.macrophages.rep.1 4704:::H37Rv.extra.vs.intracellular.in.activated.macrophages.rep.1 4704:::H37Rv.extra.vs.intracellular.in.activated.macrophages.rep.2 4731:::X2ug.ml.PA.824.vs.DMSO.6hrs.rep.1 4735:::BCG.wild.type.vs.BCG.with.pMFdosR.at.OD.0.4.rep.3 4795:::CDC1551.ctrl.vs.10.ug.ml.Thioridazine.2hr.rep.2 4795:::CDC1551.ctrl.vs.10.ug.ml.Thioridazine.4hr.rep.2 4795:::CDC1551.ctrl.vs.40.ug.ml.Thioridazine.2hr.rep.1 4795:::CDC1551.ctrl.vs.40.ug.ml.Thioridazine.2hr.rep.2 4795:::CDC1551.ctrl.vs.40.ug.ml.Thioridazine.4hr.rep.1 4799:::H37Rv.mouse.hallow.fiber..ctrl.vs.25mg.kg.Isoniazid.3rd.dose.6hrs.rep.1 4802:::H37Rv.ctrl.vs.relE1.overexpression.24.hr.rep.1 4802:::H37Rv.ctrl.vs.relE1.overexpression.72.hr.rep.2 4802:::H37Rv.ctrl.vs.relE2.overexpression.24.hr.rep.3 4802:::H37Rv.ctrl.vs.relE2.overexpression.6.hr.rep.3 4802:::H37Rv.ctrl.vs.relE2.overexpression.72.hr.rep.3 4815:::H37Rv.reaeration.for.1hrs.rep.6 4860:::CDC1551.nadABC.null.nicotinamide.starvation.rep.3 Provvedi_Microbiology2009:::H37Rv.Control.vs.400.ug.ml.vancomycin.for.4.hrs.DS.rep.1 Rohde_CellHostMicrobe2007:::CDC1551.ctrl..vs.2.hr.after.macrophage.infection RV0421C 0.1 0.45 0.35 NA -0.8 0.915380316432522 0.240889556955927 0.481779113911854 -0.915380316432522 -0.0963558227823707 0.578134936694224 -0.722668670867781 0.62631284808541 0.62631284808541 1.30080360756201 0.529957025303039 0.385423291129483 -0.348124262955662 -0.565701927302951 -0.58745969373768 -0.522186394433493 0.435155328694578 -1.47952811756156 -1.8058946140825 -0.348124262955662 -0.182674580691578 -0.660438868654166 -0.457690158216261 1.85484958856064 1.90302749995182 -0.168622689869149 -0.457690158216261 -0.0240889556955927 -1.39715943034438 -0.409512246825076 0.62631284808541 -0.0240889556955927 1.20444778477963 1.27671465186641 0.481779113911854 0.770846582258966 -0.62631284808541 -1.61396003160471 0.0963558227823707 -0.26497851265152 -0.120444778477963 0.289067468347112 0.0481779113911854 1.03582509491049 0.481779113911854 0.939469272128115 1.30080360756201 0.26497851265152 0.409512246825076 0.505868069607446 0.0481779113911854 0.216800601260334 -1.27671465186641 0.26497851265152 -0.0481779113911854 0.289067468347112 -2.79431886068875 0.0963558227823707 -3.6133433543389 -0.289067468347112 -0.505868069607446 -0.963558227823707 -1.44533734173556 0.794935537954559 0.240889556955927 -1.44533734173556 0.867202405041337 0.602223892389817 0.0963558227823707 -1.37307047464878 -1.54169316451793 0.770846582258966 -0.120444778477963 0.120444778477963 0.36133433543389 1.51760420882234 1.54169316451793 -0.578134936694224 0.337245379738298 -0.433601202520668 0.963558227823707 0.120444778477963 0.891291360736929 0.337245379738298 0.313156424042705 -0.216800601260334 0.770846582258966 0.602223892389817 0.409512246825076 -3.2760979746006 -3.13156424042705 -0.915380316432522 1.01173613921489 0.794935537954559 0.0963558227823707 1.03582509491049 -0.168622689869149 0.62631284808541 -0.289067468347112 -0.385423291129483 -0.674490759476595 -0.505868069607446 0.843113449345744 0.168622689869149 -0.433601202520668 -3.42063170877416 -1.20444778477963 0.144533734173556 0.915380316432522 0.144533734173556 -4.02285560116398 -2.52934034803723 0.0963558227823707 -2.79431886068875 -0.746757626563373 1.27671465186641 0.385423291129483 0.26497851265152 1.32048190939784 -1.30401546832142 -0.089932101263546 -0.125 -0.620531498718468 0.539592607581276 -3.69620936193174 -0.485633346823149 -1.78065560501821 -1.02522595440442 0.161877782274383 -0.242816673411574 0.323755564548766 0.78240928099285 -0.0936792721495271 0.393452943028014 -0.0187358544299054 0.993000284784987 -0.24356610758877 0.207535618300491 0 0.700432711764157 -1.11550394836514 0.441013188888543 NA 1.40086542352831 -0.103767809150245 0.57072295032635 0.155651713725368 0.856084425489525 -0.415071236600982 -0.518839045751227 0.38912928431342 -0.311303427450736 -0.103767809150245 -0.259419522875613 -0.544780998038788 -0.466955141176104 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POSITION A C G T 1 0.2 0.8 0 0 2 0.3 0 0.7 0 3 0 0 0 1 4 0 0.5 0.3 0.2 5 0.7 0 0 0.3 6 0.2 0.5 0 0.3 7 0 0.6 0.4 0 8 0.4 0 0 0.6 9 0.2 0.2 0 0.6 10 0.1 0.9 0 0 11 1 0 0 0 12 0 0.3 0 0.7 13 0 0.8 0.2 0 14 0.2 0 0.8 0 15 0 0.3 0 0.7

POSITION A C G T 1 0 0 1 0 2 0.166667 0 0 0.833333 3 0 0 0 1 4 0 0 0 1 5 0 0 0 1 6 0 1 0 0 7 0.166667 0.5 0.166667 0.166667 8 1 0 0 0