GENES 2867:::H37Ra..7H9.shake.replicate.3 2867:::H37Ra..7H9.shake.replicate.4 2867:::H37Ra..Youman.media.replicate.2 2885:::Strain.3160...replicate.3 2885:::Strain.9700665..replicate.4 2885:::Strain.9802501..replicate.3 2885:::Strain.CDC1551..replicate.2 2885:::Strain.M3061a..replicate.2 2885:::Strain.M3061a..replicate.4 4060:::H37Rv.sigE.null.0.05..SDS.exposure.for.1h.rep.5 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN...2hr.hypoxia.rep.1 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN...2hr.hypoxia.rep.2 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN...2hr.hypoxia.rep.3 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN.20min...0.05.mM.DETA.NO.40min.rep.1 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN.20min...0.05.mM.DETA.NO.40min.rep.2 4062:::MTB.strain.1254.Ctrl.vs.high.aeration...0.001.mM.DETA.NO.rep.3 4062:::MTB1254.Day.0.rep.2 4084:::High.iron.wt.vs.high.iron.ideR.Complement.3b 4089:::H37Rv.wild.type.vs..H37Rv.whiB7.null.with.whiB7.over.expression.rep.1 4101:::H37Rv.Day6.3 4101:::H37Rv.Day8.3 4107:::DIPED..50ug.mL..DMSO..12h 4107:::DIPED.10ug.mL.vs.DMSO.12h.1 4107:::DIPED.10ug.mL.vs.DMSO.12h.2 4107:::DIPED.50ug.mL.vs.DMSO.12h.1 4107:::DIPED.50ug.mL.vs.DMSO.12h.2 4107:::DIPED.5ug.mL.vs.DMSO.12h.2 4107:::EMB.10ug.mL.vs.DMSO.12h.2 4107:::EMB.10ug.mL.vs.DMSO.12h.3 4107:::EMB.10ug.mL.vs.DMSO.12h.4 4107:::H2O2.4mM.vs.ctrl.8h.1 4107:::pH5.6vspH6.8..11h. 4107:::pH5.6vspH6.8..4h. 4107:::pH5.6vspH6.8..4h.B 4107:::WT.t.6h.WT.t.0h..2 4107:::X.109..0.1ug.mL..vs.DMSO..12h..GEO.acc.GSM28050. 4107:::X.109..1ug.mL..vs.DMSO..12h..replicate.2..GEO.acc.GSM28052. 4107:::X0.12mg.mL.BZAvspH5.6..7h. 4107:::X0.12mg.mL.Nam.pH5.6..2h..1 4107:::X0.12mg.mL.Nam.pH5.6..4h..1 4107:::X0.12mg.mL.Nam.pH5.6..4h..2 4107:::X0.12mg.mL.NamvspH5.6..4h. 4107:::X0.12mg.mL.NamvspH5.6..5.5h. 4107:::X0.12mg.mL.PZA.pH5.6..2h. 4107:::X0.12mg.mL.PZA.pH5.6..5h. 4107:::X0.12mg.mL.PZAvspH5.6..11h. 4107:::X0.12mg.mL.PZAvspH5.6..4h. 4107:::X0.12mg.mL.PZAvspH5.6..5.5h. 4107:::X0.13mg.mL.TLMvsDMSO..6h 4107:::X0.13mg.mL.TLMvsDMSO..6hA 4107:::X0.15mg.mL.TricvsEtOH..6hA 4107:::X0.1mMGSNO.5ug.mLKCNvsDMSO.6h 4107:::X0.2mg.mL.AmpvsEtOH..6h 4107:::X0.2ug.mL.Mtmvsctrl..0.33h. 4107:::X0.4mM.NaN3vsDMSO..4h 4107:::X0.4ug.mL.PA824.DMSO..6h..3 4107:::X0.4ug.mL.PA824.DMSO..6h..4 4107:::X0.5mM.DNP.DMSO..6h 4107:::X0.5ug.mL..111895vsDMSO.6h 4107:::X0.5uMValinomycin.70mMKClvsDMSO.6h 4107:::X1.2mg.mL.PZA.pH5.6..2h.. 4107:::X1.2mg.mL.PZA.pH5.6..5h. 4107:::X1.2mg.mL.PZAvspH5.6..16h. 4107:::X1.2mg.mL.PZAvspH5.6..4h. 4107:::X1.2mg.mL.PZAvspH5.6..4h.A 4107:::X1.2mg.mL.PZAvspH5.6..4h.B 4107:::X1.2mg.mL.PZAvspH5.6..6h. 4107:::X1.2mg.mL.PZAvspH5.6..6h.A 4107:::X1.2mg.mL.PZAvspH5.6..7h. 4107:::X1.2mg.mL.PZAvspH5.6..7h.A 4107:::X100ug.mLCephalexinvsEtOH.6h 4107:::X100ug.mLCephalexinvsEtOH.6hA 4107:::X10ug.mL..241.DMSO..6h 4107:::X10ug.mL.EconazolevsEtOH..6hA 4107:::X10ug.mL.menadionevsDMSO..6h 4107:::X10ug.mL.Nvb.DMSO..6h..1 4107:::X10ug.mL.Nvb.DMSO..6h..3 4107:::X10ug.mL.PA.1vsDMSO..6hA 4107:::X10ug.mL.PA.1vsDMSO..6hB 4107:::X10ug.mL.PA.21vsDMSO..6h 4107:::X10ug.mL.PA.21vsDMSO..6hA 4107:::X10ug.mL.TriclosanvsDMSO..6hB 4107:::X10ug.mLmnd.Dubos.vsDMSO.6h 4107:::X1uM.ValinomycinvsDMSO..6h 4107:::X1uM.ValinomycinvsDMSO..6h.A 4107:::X20ug.mL.ethambutol.DMSO 4107:::X20ug.mL.Prcp.6778.DMSO..6h..2 4107:::X20uM.DCCD.DMSO..6h..1 4107:::X20uM.DCCD.DMSO..6h..2 4107:::X25ug.mL.AntimycinvsDMSO..6h 4107:::X2mM.DTTvsDMSO..6h.A 4107:::X2ug.mL..111895vsDMSO..6hA 4107:::X2ug.mL.PA824.DMSO..6h..2 4107:::X30ug.mLProcept6776vsDMSO.6h 4107:::X40ug.mL.5CL.pH5.6..2h..1 4107:::X40ug.mL.5CL.pH5.6..4h..2 4107:::X40ug.mL.5CL.pH5.6..4h..3 4107:::X40ug.mL.EtavsEtOH..6hA 4107:::X40ug.mLProcept6778vsDMSO.6h 4107:::X40ug.mLProcept6778vsDMSO.6hA 4107:::X4mM.H2O2vsctrl..1h. 4107:::X50ug.mL.PA.1vsDMSO..6h 4107:::X50ug.mL.PA.21vsDMSO..6h 4107:::X50ug.mL.PA.21vsDMSO..6hA 4107:::X50ug.mLAntimycinAvsDMSO..6h 4107:::X50ug.mLAntimycinAvsDMSO..6hA 4107:::X5ug.mL.KCN.DMSO..6h..1 4107:::X5ug.mL.KCN.DMSO..6h..2 4107:::X7d.Dubos.NRP.1vsDubos.log.phase.A 4363:::H37Rv.hypoxia.4hr.rep.1 4363:::H37Rv.hypoxia.4hr.rep.2 4363:::H37Rv.hypoxia.4hr.rep.3 4363:::H37Rv.hypoxia.4hr.rep.6 4364:::H37dosR.mutant.hypoxia.7.day.rep.1 4365:::H37Rv.diamide.1h.rep.5 4396:::Strain.27.cDNA.Cy5.vs.H37Rv.gDNA.Cy3.rep.1 4396:::Strain.49.cDNA.Cy3.vs.H37Rv.gDNA.Cy5..DS..rep.1 4396:::Strain.49.cDNA.Cy3.vs.H37Rv.gDNA.Cy5..DS..rep.2 4396:::Strain.49.cDNA.Cy3.vs.H37Rv.gDNA.Cy5..DS..rep.3 4489:::MTB1254.Opp.KO.complemented.vs.Opp.KO.in.7H9OADC..OD..1.0.3 4489:::MTB1254.WT.vs.Rv3662c.3665c.KO.in.7H9OADC.Exp2..OD1.1 4523:::H37Rv.sigB.null.mutant.control.vs.0.05..SDS.for.60.min.rep.2 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.6 4523:::H37Rv.wild.type.control.vs.5mM.Diamide.for.60.min.rep.3 4523:::H37Rv.wild.type.control.vs.5mM.Diamide.for.60.min.rep.4 4575:::Purified.Human.SP.A.Uncoated.2hrs.rep1 4575:::Purified.Surfactant.Lipids.30min.rep.1 4581:::H37Rv.Ctrl.vs.5.ug.ml.garlic.extract.6hrs 4583:::X0.13mg.ml.TLM.vs.DMSO.6hrs.rep.1 4583:::X0.13mg.ml.TLM.vs.DMSO.6hrs.rep.2 4583:::X0.2mg.ml.TLM.vs.Ethanol.6hrs.rep.2 4583:::X12ug.ml.Ethionamide.vs.Ethanol.6hrs.rep.2 4583:::X40ug.ml.Ethionamide.vs.Ethanol.6hrs.rep.1 4583:::X5ug.ml.KCN.vs.DMSO.6hrs.rep.1 4583:::X5ug.ml.KCN.vs.DMSO.6hrs.rep.2 4599:::H37Rv.wild.type.vs.sigE.mutant.in.RPMI.media.for.2.hrs.rep.3 4599:::SigE.mutant.grown.in.7H9.vs.24hrs.after.infection.in.macrophages.rep.2 4615:::AA_30uM_10.min_05 4615:::AA_30uM_10min_02 4615:::AA_30uM_1h_04 4615:::AA_30uM_24h_T0_01 4615:::aceatate.induction.1 4615:::Acetate.3mM.10m.01 4615:::Acetate.3mM.30m.02 4615:::CK.for.MDG.OA.4h 4615:::L2A_30uM_2h_02 4615:::L2A_30uM_2h_03 4615:::L2A_30uM_30min_04 4615:::L2A_30uM_30Min_06 4615:::MTB1254_Bottom_21D_01 4615:::MTB1254_Bottom_21D_03 4615:::MTB1254_Bottom_42D_03 4615:::MTB1254_Pellicle_56D_02 4615:::MTB1254.0485.1._PA_10m_04 4615:::MTB1254.0485.1._PA_12h_02 4615:::MTB1254.0485.1._PA_4h_01 4615:::MTB1254.0485.1._PA_4h_02 4615:::MTB1254.0485.1._PA_4h_03 4615:::MTB1254.0485.1._PA_4h_04 4615:::MTB1254.3219.1._01 4615:::MTB1254.3219.2._01 4615:::MTB1254.3524.1._INH_20MIN 4615:::MTB1254.B4.1._PA_4h_02 4615:::MTB1254.B4.1._PA_4h_04 4615:::MTB1254.B4.1.Compl._OA_30MIN_04 4615:::MTB1254.B4.1.Compl._PA_4h_03 4615:::OA_50uM_10min_01 4615:::OA_50uM_2h_06 4615:::OA_50uM_2h_08 4615:::OA_50uM_4h_07 4615:::OA_50uM_4h_08 4615:::PA_300uM_2h_T0_01 4615:::PA_50uM_10.min_02 4615:::PA_50uM_10min_01 4615:::PA_50uM_1h_05 4615:::PA_50uM_24h_02 4615:::PA_50uM_2h_03 4615:::PA_50uM_30min_01 4615:::PA_50uM_4h 4615:::Rv.3524.1._01 4615:::Rv.3524.2._01 4615:::Rv.MT106_100503_02 4615:::Rv.p0485.1. 4615:::Rv.p0485.1._300uM.PA_10m 4615:::Rv.p0485.1._OK 4615:::Rv.pMV0481.1. 4615:::Spe_100uM_30M_01 4615:::Starvation_1254_3d_04 4615:::Starvation_1254_PA50_6h_02 4615:::TBD817 4615:::TBE055 4615:::TBE057 4615:::WM_1254_10d_02 4615:::WT_65.4_SDS_02 4615:::X2.2..Dipyridyl_0.2mM.Dpd.AA_50uM_01 4615:::X2.BA.OA.1 4615:::X7H9_MTB1254_OA50_10M_01 4615:::X7H9_PA_50uM_4h_T0_02 4630:::H37Rv.wild.type.Cy5.vs.Rv0485.Tn.mutant.Cy3..DS..rep.3 4696:::H37Rv.wt.vs.dosT.null.anaerobic.Gaspak24hr.rep.2 4699:::CDC1551.Ctrl.vs.clinical.isolate.10517.01_Afri2.rep.2 4699:::CDC1551.Ctrl.vs.clinical.isolate.12954.03_Beijing.rep.2 4699:::CDC1551.Ctrl.vs.clinical.isolate.1934.03_Beijing.rep.2 4699:::CDC1551.Ctrl.vs.clinical.isolate.2336.02_Haarlem.rep.3 4699:::CDC1551.Ctrl.vs.clinical.isolate.4130.02_Haarlem.rep.2 4699:::CDC1551.Ctrl.vs.clinical.isolate.4130.02_Haarlem.rep.3 4699:::CDC1551.Ctrl.vs.clinical.isolate.4850.03_EAI.rep.1 4699:::CDC1551.Ctrl.vs.clinical.isolate.4850.03_EAI.rep.2 4699:::CDC1551.Ctrl.vs.clinical.isolate.947.01_EAI.rep.3 4699:::CDC1551.Ctrl.vs.clinical.isolate.9532.03_Haarlem.rep.1 4699:::CDC1551.Ctrl.vs.H37Rv.rep.2 4703:::Clinical.isolate.10514.01_Afri2.extra.vs.intracellular.in.resting.macrophages.rep.1 4703:::Clinical.isolate.10517.01_Afri2.extra.vs.intracellular.in.resting.macrophages.rep.1 4703:::Clinical.isolate.12954.03_Beijing.extra.vs.intracellular.in.resting.macrophages.rep.1 4703:::Clinical.isolate.12954.03_Beijing.extra.vs.intracellular.in.resting.macrophages.rep.2 4703:::Clinical.isolate.1500.03_Beijing.extra.vs.intracellular.in.resting.macrophages.rep.1 4703:::Clinical.isolate.1934.03_Beijing.extra.vs.intracellular.in.resting.macrophages.rep.2 4703:::Clinical.isolate.2336.02_Haarlem.extra.vs.intracellular.in.resting.macrophages.rep.1 4703:::Clinical.isolate.5468.02_Afri2.extra.vs.intracellular.in.resting.macrophages.rep.1 4704:::CDC1551.extra.vs.intracellular.in.activated.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.12954.03_Beijing.extra.vs.intracellular.in.activated.macrophages.rep.1 4704:::Clinical.isolate.1500.03_Beijing.extra.vs.intracellular.in.activated.macrophages.rep.2 4704:::Clinical.isolate.1797.03_EAI.extra.vs.intracellular.in.activated.macrophages.rep.2 4704:::Clinical.isolate.1934.03_Beijing.extra.vs.intracellular.in.activated.macrophages.rep.1 4704:::Clinical.isolate.2333.99_Uganda.extra.vs.intracellular.in.activated.macrophages.rep.1 4704:::Clinical.isolate.2336.02_Haarlem.extra.vs.intracellular.in.activated.macrophages.rep.2 4704:::Clinical.isolate.9532.03_Haarlem.extra.vs.intracellular.in.activated.macrophages.rep.1 4735:::BCG.wild.type.vs.BCG.with.pMFdosR.at.OD.0.4.rep.1 4795:::CDC1551.ctrl.vs.10.ug.ml.Thioridazine.1hr.rep.1 4799:::H37Rv.ctrl.vs.1ug.ml.Isoniazid.for.2hrs.rep.2 4802:::H37Rv.ctrl.vs.relE1.overexpression.72.hr.rep.1 4802:::H37Rv.ctrl.vs.relE1.overexpression.72.hr.rep.2 4802:::H37Rv.ctrl.vs.relE2.overexpression.6.hr.rep.3 4802:::H37Rv.ctrl.vs.relE3.overexpression.6.hr.rep.2 4815:::H37Rv.reaeration.for.12hrs.rep.3 Raghavan_Nature2008:::espR.mutant.complemented.with.N.terminal.Flag.espR..RFL..rep1 Rohde_CellHostMicrobe2007:::CDC1551.ctrl..vs.2.hr.after.macrophage.infection RV1037C 1.47473403343188 1.17750081739134 1.13177263030818 1.23656639237376 0.75231661633928 -0.458307823746918 -1.25386102723213 -0.527486363180415 -0.804200520914402 0 -2.23808297462688 -0.981077468329593 -3.37245379738298 -1.28766417718259 -1.16502949364139 -0.0919760126558993 0.398562721508897 -1.23656639237376 1.86609110121858 -0.320659541390513 -0.221144511303802 0.457413273668036 1.41875642510594 0.643479690075372 0.829546106482709 0.488424343069259 1.18617340459677 0.984601453488823 0.9535903840876 1.15516233519555 0.0852804408533626 1.51178963330961 1.24819554339922 0.255841322560088 1.68235051501633 0.379885600164979 0.240335787859476 -2.25605529893896 -1.31021768220166 -2.4576272500469 -2.67470473585546 -3.21739845037686 -1.86841693142367 -2.27156083363957 -1.75987818851939 -2.51964938884935 -2.28706636834018 -1.68235051501633 0.674490759476595 0.674490759476595 -2.16302209073529 NA 0.488424343069259 0.829546106482709 NA NA NA NA 0.472918808368647 -1.68235051501633 -2.19403316013651 -1.46527302920778 -1.72886711911817 -2.44212171534629 -2.76773794405913 -3.37245379738298 -2.4576272500469 -1.74437265381878 -0.752018432979652 -1.97695567432795 0.0077527673503057 0.0077527673503057 -0.209324718458254 -0.317863461362533 -0.0077527673503057 NA NA 1.10864573109371 0.61246862067415 0.829546106482709 1.31021768220166 1.00010698818943 NA 0.178313649057031 -0.116291510254585 0.240335787859476 NA NA NA 1.34122875160288 0.209324718458254 1.71336158441756 NA -0.457413273668036 -3.01582649926891 -2.92279329106525 -1.03111805759066 0.550446481871704 -3.32593719328114 -2.39560511124446 -1.60482284151328 0.876062710584543 0.271346857260699 1.06212912699188 1.86841693142367 1.62032837621389 NA NA NA NA NA NA NA NA 1.25262569617082 -2.30120376762603 1.66638893517747 2.61861118385031 0.634814832448561 -0.80296518985309 0.0642372151882472 1.96395838788773 2.22185191356996 -0.0198379635140175 -0.734004650018648 -1.26962966489712 0.251280871177555 -0.119027781084105 -0.654356706954906 0.69135302846351 0.69135302846351 0.303520841764468 0.961149332254148 0.741939835424255 NA NA NA NA 1.75367597463915 0.96677008858312 0.0449660506317731 -0.607041683528936 -1.77615899995503 -0.0224830253158865 0.179864202527092 0.0449660506317731 -0.427177481001844 -0.562075632897163 0.696973784792482 1.34898151895319 -2.1583704303251 -1.61877782274383 -2.51809883537929 -2.54058186069518 1.46139664553262 -0.764422860740141 -0.831871936687801 -1.03421916453078 -0.809388911371914 -1.28153244300553 1.01173613921489 0.427177481001844 0.134898151895319 0.157381177211206 -0.562075632897163 0.764422860740141 0.472143531633617 2.20333648095688 -1.23656639237376 -0.539592607581276 0 0.89932101263546 -0.359728405054184 1.6637438733756 1.3264984936373 -0.382211430370071 -1.59629479742794 -0.921804037951347 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POSITION A C G T 1 0.333333 0.666667 0 0 2 0.222222 0.777778 0 0 3 0.888889 0.111111 0 0 4 0.666667 0 0.333333 0 5 0 1 0 0 6 0.888889 0 0.111111 0 7 0.555556 0.333333 0 0.111111 8 0 0.666667 0 0.333333 9 0.444444 0 0.111111 0.444444 10 0.555556 0.111111 0.111111 0.222222 11 0 0.888889 0.111111 0 12 0 0 0.777778 0.222222 13 0.777778 0.222222 0 0 14 0.444444 0.111111 0.333333 0.111111 15 0 1 0 0 16 0.888889 0 0 0.111111 17 0 0 1 0 18 0.111111 0.888889 0 0 19 0.777778 0 0 0.222222 20 0.888889 0 0.111111 0 21 0.111111 0 0.888889 0 22 1 0 0 0 23 0 0 1 0 24 0.222222 0.777778 0 0

POSITION A C G T 1 0 0.666667 0 0.333333 2 1 0 0 0 3 0.333333 0 0 0.666667 4 0 1 0 0 5 0 0 0.666667 0.333333 6 0 0 0 1 7 0 0 1 0 8 0.666667 0 0.333333 0 9 0.666667 0.333333 0 0 10 0 1 0 0 11 1 0 0 0 12 0 0 0.333333 0.666667 13 0 0 1 0 14 0 0.666667 0 0.333333 15 0 0 0 1 16 0 0 1 0 17 0 1 0 0 18 0.666667 0.333333 0 0 19 0 1 0 0 20 0 0 1 0 21 0 0.333333 0.666667 0 22 0 0 1 0 23 0 0 1 0 24 0 0 0 1