GENES 2867:::H37Ra..7H9.shake.replicate.1 2867:::H37Ra..7H9.shake.replicate.3 2867:::H37Rv..Dubos.media.replicate.1 2867:::H37Rv..Dubos.media.replicate.2 2867:::H37Rv..Youman.media.replicate.1 2885:::Strain.9700665..replicate.1 2885:::Strain.9802501..replicate.2 2885:::Strain.H37Ra..replicate.4 2885:::Strain.M3061a..replicate.4 4062:::CDC1551.Ctrl.vs.0.05.mM.DETA.NO.40.min.rep.2 4062:::H37Rv.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.4 4062:::H37Rv.ctrl.vs.Rv3132.3134.KO..0.05.mM.DETA.NO.40min.rep.2 4062:::H37Rv.ctrl.vs.Rv3132.3134.KO..0.05.mM.DETA.NO.40min.rep.4 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.16hrs.rep.3 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.1hr.rep.4 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.24hrs...0.5.mM.DNO.40min.rep.4 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.2hrs.rep.2 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.2hrs.rep.3 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.2hrs.rep.4 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.40min.rep.2 4062:::MTB.strain.1254.Ctrl.vs.2hr.Hypoxia.rep.2 4062:::MTB.strain.1254.Ctrl.vs.low.aeration...0.001.mM.DETA.NO.rep.3 4062:::MTB.strain.1254.Ctrl.vs.low.aeration...0.05.mM.DETA.NO.rep.3 4068:::H37Rv.delta.mprAB.mutant.vs..H37Rv.delta.mprAB.mutant.SDS.treated.rep.4 4068:::H37Rv.delta.mprAB.mutant.vs..H37Rv.delta.mprAB.mutant.SDS.treated.rep.6 4089:::H37Rv.whiB7.null.ethanol.vs..1.0.ug.ml.Tetracyclin.for.15.min.rep.1 4089:::MTB1254.control.vs..0.5.ug.ml.Streptomycin.for.15.min.rep.5 4089:::MTB1254.control.vs..1.0.ug.ml.Streptomycin.for.15.min.rep.1 4089:::MTB1254.control.vs..1.0.ug.ml.Streptomycin.for.2.hr..ref..rep.3 4089:::MTB1254.control.vs..100.ug.ml.Streptomycin.for.15.min.rep.4 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.control.vs..5.0.ug.ml.Streptomycin.for.15.min.rep.2 4089:::MTB1254.ethanol.vs..0.5.ug.ml.Erythromycin.for.15.min.rep.2 4089:::MTB1254.ethanol.vs..0.5.ug.ml.Erythromycin.for.30.min.rep.4 4089:::MTB1254.ethanol.vs..0.5.ug.ml.Tetracyclin.for.30.min.rep.2 4089:::MTB1254.ethanol.vs..1.0.ug.ml.Erythromycin.for.15.min.rep.3 4089:::MTB1254.ethanol.vs..100.ug.ml.Tetracyclin.for.15.min.rep.4 4089:::MTB1254.ethanol.vs..25.ug.ml.Erythromycin.for.30.min.rep.4 4089:::MTB1254.ethanol.vs..25.ug.ml.Tetracyclin.for.15.min.rep.2 4089:::MTB1254.ethanol.vs..25.ug.ml.Tetracyclin.for.15.min.rep.4 4089:::MTB1254.ethanol.vs..25.ug.ml.Tetracyclin.for.30.min.rep.1 4089:::MTB1254.ethanol.vs..25.ug.ml.Tetracyclin.for.30.min.rep.2 4089:::MTB1254.ethanol.vs..5.0.ug.ml.Erythromycin.for.30.min.rep.1 4089:::MTB1254.ethanol.vs..5.0.ug.ml.Tetracyclin.for.15.min.rep.4 4089:::MTB1254.vs..MTB1254.rep2 4100:::H37Rv.0.2..Oxygen..2h..1 4101:::NRP.Day14..5 4101:::NRP.Day14..7 4107:::EMB.10ug.mL.vs.DMSO.12h.1 4107:::X.241..1ug.mL..DMSO..12h..1 4107:::X0.12mg.mL.BZA.pH5.6..4h..2 4107:::X0.12mg.mL.BZAvspH5.6..5h. 4107:::X0.12mg.mL.PZAvspH5.6..6h. 4107:::X0.15mg.mL.TricvsEtOH..6hA 4107:::X0.1mMGSNO.20ug.mLCPZvsDMSO.6hA 4107:::X0.2mg.mL.TLMvsEtOH..6h 4107:::X0.2mg.mL.TLMvsEtOH..6hA 4107:::X0.2ug.mL.INH.EtOH..6h 4107:::X0.2ug.mL.Mtmvsctrl..2h.B 4107:::X0.32ug.mL.CervsEtOH..6h 4107:::X0.32ug.mL.CervsEtOH..6hA 4107:::X0.4ug.mL.INHvsEtOH..6hA 4107:::X0.5ug.mL.CeruleninvsDMSO..6hA 4107:::X0.5ug.mL.CeruleninvsDMSO..6hB 4107:::X0.5ug.mL.CeruleninvsDMSO..6hC 4107:::X0.5ug.mL.CervsEtOH..6hA 4107:::X1.2mg.mL.NamvspH5.6..5h. 4107:::X100uM.Dipyridylvsctrl..6h 4107:::X100uM.DipyridylvsCtrl..6hA 4107:::X10ug.mL..109vsDMSO..6h 4107:::X10ug.mL.ChlorprovsEtOH 4107:::X10ug.mL.PA.1vsDMSO..6h 4107:::X10ug.mL.PA.21vsDMSO..6h 4107:::X10ug.mL.PA.21vsDMSO..6hA 4107:::X10ug.mL.TRZ.DMSO..6h..1 4107:::X130ug.mL.TLMvsDMSO..6h 4107:::X130ug.mL.TLMvsDMSO..6hA 4107:::X1ug.mL..111891.DMSO..12h..1 4107:::X1ug.mL..59vsDMSO..6h 4107:::X1ug.mL..59vsDMSO..6hA 4107:::X25ug.mL.CPZvsDMSO..6h.A 4107:::X25ug.mLCPZ.0.1mMGSNO.DMSO..1 4107:::X25ug.mLCPZ.0.1mMGSNO.DMSO..2 4107:::X25ug.mLCPZ.0.1mMGSNO.DMSO..3 4107:::X2ug.mL.SMvsEtOH..6h 4107:::X40ug.mL.EtavsEtOH..6h 4107:::X4mM.H2O2vsctrl..2h. 4363:::H37Rv.hypoxia.1.day.rep.10 4363:::H37Rv.hypoxia.1.day.rep.2 4363:::H37Rv.hypoxia.1.day.rep.3 4363:::H37Rv.hypoxia.1.day.rep.6 4363:::H37Rv.hypoxia.12hr.rep.1 4363:::H37Rv.hypoxia.12hr.rep.2 4363:::H37Rv.hypoxia.12hr.rep.3 4363:::H37Rv.hypoxia.4.day.rep.2 4363:::H37Rv.hypoxia.4.day.rep.5 4363:::H37Rv.hypoxia.4hr.rep.3 4363:::H37Rv.hypoxia.4hr.rep.5 4363:::H37Rv.hypoxia.7.day.rep.1 4363:::H37Rv.hypoxia.8hr.rep.3 4364:::H37dosR.mutant.hypoxia.1.day.rep.2 4364:::H37dosR.mutant.hypoxia.1.day.rep.6 4364:::H37dosR.mutant.hypoxia.12hr.rep.4 4364:::H37dosR.mutant.hypoxia.4.day.rep.1 4364:::H37dosR.mutant.hypoxia.4hr.rep.1 4364:::H37dosR.mutant.hypoxia.8hr.rep.2 4365:::H37Rv.sigma.H.null.mutant.diamide.1h.rep.4 4396:::Strain.27.cDNA.Cy5.vs.H37Rv.gDNA.Cy3.rep.1 4489:::MTB1254.Opp.KO.complemented.vs.Opp.KO.in.7H9OADC..OD..1.0.3 4489:::MTB1254.WT.vs.Rv3662c.3665c.KO.in.7H9OADC..OD.1.0.5 4489:::MTB1254.WT.vs.Rv3662c.3665c.KO.in.7H9OADC.Exp2..OD.0.3.1 4489:::MTB1254.WT.vs.Rv3662c.3665c.KO.in.7H9OADC.Exp2..OD.0.3.2 4489:::MTB1254.WT.vs.Rv3662c.3665c.KO.in.7H9OADC.Exp2..OD.0.3.3 4489:::MTB1254.WT.vs.Rv3662c.3665c.KO.in.7H9OADC.Exp2..OD.0.3.4 4489:::MTB1254.WT.vs.Rv3662c.3665c.KO.in.7H9OADC.Exp2..OD1.3 4523:::H37Rv.sigB.null.mutant.control.vs.5mM.Diamide.for.60.min.rep.2 4523:::H37Rv.wild.type.vs.H37Rv.sigB.null.mutant.rep.1 4523:::H37Rv.wild.type.vs.H37Rv.sigB.null.mutant.rep.2 4570:::MTB.strain.TB294.Ctrl.vs.SigA.overexpression.rep2 4575:::Extracted.Lung.Surfactant.30min.rep.1 4575:::Whole.Lung.Surfactant.30min.rep.4 4575:::Whole.Lung.Surfactant.30min.rep.5 4583:::X0.13mg.ml.TLM.vs.DMSO.6hrs.rep.2 4583:::X0.32ug.mL.Cerulenin.vs.Ethanol.6hrs.rep.1 4583:::X0.5ug.mL.Cerulenin.vs.Ethanol..6hrs.rep.2 4599:::H37Rv.vs.SigE.mutant.24hrs.after.macrophage.infection.rep.2 4599:::H37Rv.wild.type.vs.sigE.mutant.in.7H9.media..DS..rep.2 4599:::H37Rv.wild.type.vs.sigE.mutant.in.7H9.media..DS..rep.3 4615:::AA_30uM_1h_07 4615:::AA_30uM_1h_08 4615:::AA_30uM_24h.AA_60uM_1h_01 4615:::AA_30uM_30min_01 4615:::AA_30uM_30min_06 4615:::AA_30uM_30min_08 4615:::Acetate.3mM.2h.03 4615:::Acetate.3mM.30m.06 4615:::CA_50uM_10min_01 4615:::CK.1.2h.for.AA.NA.and.LA.NA 4615:::CK.AA0.03.2h.02 4615:::ETYA_10uM.AA_1h_02 4615:::ETYA_30uM_10min.02 4615:::Glycerol_1._30M_01 4615:::L2A_30uM_1h_06 4615:::L2A_30uM_1h_08 4615:::L2A_30uM_30min_01 4615:::L2A_30uM_30min_03 4615:::MAPP_5uM_4h_01 4615:::MDA_1254.pMV261.3524_02 4615:::MDG_1254.pMV261_01 4615:::MDG_1254.pMV261_02 4615:::MDG_1254.pMV261_04 4615:::MDG_1254.pMV261.3524_02 4615:::MTB1254_Pellicle_14D_04 4615:::MTB1254.0485.1._OA_30m_01 4615:::MTB1254.0494.4._OA_30MIN_01 4615:::MTB1254.B4.1._OA_30MIN_03 4615:::MTB1254.B4.1._OA_30MIN_04 4615:::MTB1254.B4.1.Compl._OA_30MIN_01 4615:::MTB1254.B4.1.Compl._OA_30MIN_02 4615:::MTB1254.B4.1.Compl._OA_30MIN_03 4615:::MTB1254.B4.1.Compl._OA_30MIN_04 4615:::MTB1254.Rv3524.2._PA50.OA30_2h_01 4615:::MTB1254.Rv3524.2._PA50.OA30_2h_02 4615:::MTB1254.Rv3524.2._PA50.OA30_30m_02 4615:::MTB1254.whiB4_SDS_90MIN_01 4615:::MTB1254TA1_OA.30min_03 4615:::MTB1254TA1_OA.30min_04 4615:::OA_50uM_10min_03 4615:::OA_50uM_1h_01 4615:::OA_50uM_1h_04 4615:::OA_50uM_1h_05 4615:::OA_50uM_1h_06 4615:::OA_50uM_1h_08 4615:::OA_50uM_1h_10 4615:::OA_50uM_30min_01 4615:::OA_50uM_30min_03 4615:::OA_50uM_30min_08 4615:::OA_50uM_4h_04 4615:::PA_50uM_10min_T0_01 4615:::PA_50uM_1h_01 4615:::PA_50uM_1h_11 4615:::PA_50uM_24h_07 4615:::PA_50uM_30.min_06 4615:::PA_50uM.AA_30uM_2h_04 4615:::PA_50uM.OA_10uM_2h_03 4615:::PA_50uM.OA_10uM_2h_04 4615:::PA_50uM.OA_30uM_24h_02 4615:::PA_50uM.OA_30uM_2h_03 4615:::Rv_OA30_30mim_03 4615:::Rv.MT106_100503_02 4615:::Rv.MT106_100603_01 4615:::Rv.p0485.1. 4615:::Rv.p0485.1._OK 4615:::Starvation_1254_6h_07 4615:::TBD1115 4615:::TBD1266 4615:::TBD1275 4615:::TBD622 4615:::TBE058 4615:::TBE059 4615:::TBE736 4615:::Test.1 4615:::Tet_50ng_30M_01 4615:::X2.BA_100uM_30min_01 4615:::X7H9Cy3.MDGCy5.01 4637:::H37Rv.control.vs.1mg.ml.cholesterol.for.24.hrs.rep.3 4637:::H37Rv.control.vs.1mg.ml.cholesterol.for.3.hrs.rep.1 4696:::H37Rv.wt.vs.dosS.dosT.null.anaerobic.Gaspak.4hr.rep.1 4696:::H37Rv.wt.vs.dosS.dosT.null.anaerobic.Gaspak24hr.rep.3 4696:::H37Rv.wt.vs.dosS.null.anaerobic.Gaspak.24hr.rep.2 4696:::H37Rv.wt.vs.dosS.null.anaerobic.Gaspak.24hr.rep.3 4696:::H37Rv.wt.vs.dosS.null.nitric.oxide.treatment.1hr.rep.3 4696:::H37Rv.wt.vs.dosT.null.anaerobic.Gaspak.4hr.rep.1 4696:::H37Rv.wt.vs.dosT.null.nitric.oxide.treatment.1hr.rep.1 4696:::H37Rv.wt.vs.dosT.null.nitric.oxide.treatment.1hr.rep.2 4696:::H37Rv.wt.vs.dosT.null.rapid.anaerobic.dormancy.day.6.rep.3 4699:::CDC1551.Ctrl.vs.clinical.isolate.10514.01_Afri2.rep.1 4699:::CDC1551.Ctrl.vs.clinical.isolate.10514.01_Afri2.rep.3 4699:::CDC1551.Ctrl.vs.clinical.isolate.12954.03_Beijing.rep.1 4699:::CDC1551.Ctrl.vs.clinical.isolate.1797.03_EAI.rep.3 4699:::CDC1551.Ctrl.vs.clinical.isolate.4130.02_Haarlem.rep.2 4703:::Clinical.isolate.12954.03_Beijing.extra.vs.intracellular.in.resting.macrophages.rep.1 4703:::Clinical.isolate.1500.03_Beijing.extra.vs.intracellular.in.resting.macrophages.rep.2 4703:::Clinical.isolate.2169.99_Uganda.extra.vs.intracellular.in.resting.macrophages.rep.1 4703:::Clinical.isolate.2169.99_Uganda.extra.vs.intracellular.in.resting.macrophages.rep.2 4703:::Clinical.isolate.2191.99_Uganda.extra.vs.intracellular.in.resting.macrophages.rep.1 4703:::Clinical.isolate.4850.03_EAI.extra.vs.intracellular.in.resting.macrophages.rep.1 4735:::BCG.wild.type.vs.BCG.with.pMFdosR.at.OD.0.4.rep.1 4795:::CDC1551.ctrl.vs.40.ug.ml.Thioridazine.2hr.rep.2 4799:::H37Rv.O2.depleted..ctrl.vs.1ug.ml.Isoniazid.for.2hrs.rep.2 4802:::H37Rv.ctrl.vs.relE1.overexpression.6.hr.rep.2 4802:::H37Rv.ctrl.vs.relE1.overexpression.6.hr.rep.4 4802:::H37Rv.ctrl.vs.relE2.overexpression.6.hr.rep.1 4802:::H37Rv.ctrl.vs.relE3.overexpression.6.hr.rep.1 4815:::H37Rv.reaeration.for.12hrs.rep.3 4815:::H37Rv.reaeration.for.24hrs.rep.3 4928:::Mtb.Erdman.strain.200.ppm.CO.rep.2 Maciag_JBacteriol2007:::H37Rv.wild.type.vs.H37Rv.FurB.null.rep.2 Milano_Tuberculosis2009:::H37Rv.wild.type.vs.H37Rv.Bif1.mutant.rep.1 Provvedi_Microbiology2009:::H37Rv.Control.vs.subinhibitory.conc..5.ug.ml..vancomycin.DS.rep.2 Rohde_CellHostMicrobe2007:::CDC1551.ctrl.vs.pH.5.5.7H9.broth.for.2.hr Rohde_CellHostMicrobe2007:::M..bovis.ctrl..vs.2.hr.after.macrophage.infection Schnappinger_JEM2003:::MTB.in.Wild.type.macrophages.for.4hrs RV0186 0.424679367077856 0.474641645557604 0.374717088598108 0.524603924037352 -0.674490759476595 -1.10541541136442 0.674490759476595 0.918056867065365 -0.749434177196217 0.608686782942293 1.15156958935028 -0.263215906137208 0.477078829873689 2.43474713176917 3.75082666245521 2.87892397337571 2.43474713176917 0.674490759476595 1.36543251308677 2.97762993817716 -1.46413847788822 -0.444176841606538 1.51349146028895 0.112415126579432 -0.281037816448582 0.141998054626652 0.319495622909966 0.709990273133258 1.17148395066988 0.603491732163269 -0.816488814103247 -0.177497568283314 0.638991245819932 0.958486868729898 0.319495622909966 -1.34898151895319 0.887487841416573 -2.37846741499641 -1.17148395066988 -1.59747811454983 -1.63297762820649 -2.66246352424972 -1.17148395066988 0.0354995136566629 -0.603491732163269 0.177497568283315 0.305126772144174 0.304906781681201 1.48757551062646 -0.832350298928564 0.545332954470439 -1.03326244004925 NA 0.0861052033374377 0.574034688916251 NA -0.315719078903938 -0.574034688916251 -0.200912141120688 -1.00456070560344 -1.377683253399 -1.377683253399 -0.574034688916251 -0.430526016687188 -0.717543361145314 0.0574034688916251 -0.889753767820189 1.20547284672413 0.172210406674875 0.401824282241376 -0.430526016687188 -0.574034688916251 0 -0.717543361145314 0.430526016687188 NA -1.29157805006157 -0.975858971157627 NA 0.574034688916251 0.545332954470439 -0.746245095591127 NA NA 1.32027978450738 -1.40638498784482 -1.17677111227831 -0.258315610012313 -0.212339683538928 -0.549585063277226 -2.00473642399988 1.86734015818057 -0.674490759476595 -2.54183091765717 0 1.44266079110272 0.930547436685302 0.193603829109023 0.0499622784797478 NA NA 1.40518908224291 -0.99129702529136 -1.53293354426499 -1.81908113919445 0.143073797464732 0.337245379738298 NA NA -2.14610696197098 -3.92430987331837 1.13437082275609 0.827784113903094 1.13437082275609 0.674490759476595 0.429221392394197 -0.0613173417705996 -0.0459880063279497 -0.229940031639748 0.433601202520668 -1.07169087339059 -1.16162297465414 -0.951781405039196 1.31525698097936 -0.708215297450425 -0.134898151895319 0.0634136611473722 -0.397776601742607 -0.294008792592362 -1.03767809150245 -0.933910282352209 -1.16738785294026 0.0259419522875614 -0.492897093463666 0.207535618300491 -0.441013188888543 -0.441013188888543 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POSITION A C G T 1 0 0 0 1 2 0.5 0 0 0.5 3 0 0 0 1 4 0 1 0 0 5 0.166667 0.333333 0.5 0 6 0.166667 0.166667 0 0.666667 7 0 0.166667 0.833333 0 8 0 0.833333 0.166667 0 9 0.166667 0.666667 0.166667 0 10 0 0.833333 0 0.166667 11 0.166667 0 0.666667 0.166667 12 0.666667 0 0.333333 0 13 0.333333 0 0.666667 0 14 0 0.333333 0 0.666667 15 0.333333 0 0.666667 0 16 0 0 0 1 17 0 0.666667 0.333333 0 18 1 0 0 0 19 1 0 0 0 20 0 0.166667 0.5 0.333333 21 0.666667 0.333333 0 0 22 0 0.166667 0 0.833333

POSITION A C G T 1 0 1 0 0 2 1 0 0 0 3 1 0 0 0 4 0 0 0 1 5 0.4 0 0.6 0 6 0 0 0.2 0.8 7 0 1 0 0 8 1 0 0 0 9 0 0 0.6 0.4 10 0 0 0.8 0.2 11 0.8 0 0.2 0 12 0 0.4 0 0.6 13 0.6 0.4 0 0 14 0 1 0 0