GENES 2867:::H37Ra..Dubos.media.replicate.2 2867:::H37Ra..Sauton.s.media.replicate.1 2867:::H37Rv..Dubos.media.replicate.4 2885:::H37Ra..7H9.roll.replicate.2 2885:::Strain.9700665..replicate.2 2885:::Strain.9800608..replicate.1 2885:::Strain.9800608..replicate.4 2885:::Strain.9802826..replicate.1 2885:::Strain.9802826..replicate.3 2885:::Strain.CDC1551..replicate.3 4060:::H37Rv.sigE.null.0.05..SDS.exposure.for.1h.rep.2 4062:::H37.Rv3132.34.KO.0.days.vs.Rv3132.34.KO..complemented..hypoxia.4.day.rep.2 4062:::H37Rv.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.1 4062:::H37Rv.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.3 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.1 4062:::H37Rv.ctrl.vs.Rv3132.3134.KO..0.05.mM.DETA.NO.40min.rep.3 4062:::H37Rv.ctrl.vs.Rv3132.34.KO..complemented...0.05.mM.DETA.NO.40min.rep.1 4062:::MTB.strain.1254.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.6 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.20min.rep.3 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.24hrs...0.5.mM.DNO.40min.rep.2 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.2hrs.rep.1 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.4 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.40min.rep.3 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.5min.rep.4 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.8hrs.rep.1 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.8hrs.rep.2 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.8hrs.rep.4 4062:::MTB.strain.1254.Ctrl.vs.high.aeration...0.001.mM.DETA.NO.rep.1 4062:::MTB.strain.1254.Ctrl.vs.high.aeration...0.01.mM.DETA.NO.rep.1 4062:::MTB.strain.1254.Ctrl.vs.low.aeration...0.005.mM.DETA.NO.rep.1 4068:::H37Rv.delta.mprAB.mutant.vs..H37Rv.delta.mprAB.mutant.SDS.treated.rep.3 4084:::High.iron.wt.vs.high.iron.ideR.Complement.2b 4084:::High.iron.wt.vs.high.iron.ideR.KO.1b 4099:::H37Rv.hypoxia.2hr.rep.3 4100:::H37Rv.0.2..Oxygen..2h..3 4107:::pH5.2vspH6.8..10.5h. 4107:::X0.12mg.mL.PZA.pH5.6..5h. 4107:::X0.2ug.mL..111891.DMSO..5.5h..1 4107:::X0.2ug.mL..111891.DMSO..5.5h..2 4107:::X0.2ug.mL.Mtmvsctrl..0.75h. 4107:::X0.2ug.mL.Mtmvsctrl..4h.A 4107:::X0.5ug.mL.CeruleninvsDMSO..6hA 4107:::X0.5ug.mL.CervsEtOH..6hA 4107:::X10ug.mL.RoxvsEtOH..6hA 4107:::X10ug.mL.TetvsEtOH..6h 4107:::X1ug.mL..111891.DMSO..12h..1 4107:::X20ug.mL.methoxatinvsDMSO..6h 4107:::X2ug.mL..111891vsDMSO..6h 4107:::X40ug.mL.5CL.pH5.6..4h..1 4107:::X50ug.mL.PA.1vsDMSO..6h 4107:::X50ug.mL.PA.21vsDMSO..6hA 4366:::H37Rv.vs.H37.sigma.H.null.mutant.rep.2 4396:::Strain.32.cDNA.Cy3.vs.H37Rv.gDNA.Cy5..DS..rep.2 4396:::Strain.32.cDNA.Cy5.vs.H37Rv.gDNA.Cy3.rep.1 4489:::MTB1254.WT.vs.Rv3662c.3665c.KO.in.7H9OADC.Exp2..OD1.2 4575:::Purified.Surfactant.Lipids.2hrs.rep.2 4575:::Purified.Surfactant.Lipids.30min.rep.2 4575:::Whole.Lung.Surfactant.2hrs.rep.1 4581:::H37Rv.Ctrl.vs.10.ug.ml.garlic.extract.6hrs 4599:::H37Rv.grown.in.7H9.vs.H37Rv.4hrs.after.infection.in.macrophages.rep.5 4615:::AA_30uM_10.min_07 4615:::AA_30uM_24h.AA_60uM_1h_01 4615:::AA_30uM_2h_06 4615:::AA_30uM_30min_02 4615:::AA_30uM_30min_03 4615:::AA_30uM_30min_09 4615:::AA_30uM_4h_07 4615:::aceatate.induction.2 4615:::Acetate.3mM.10m_04 4615:::Acetate.3mM.2h.01 4615:::Acetate.3mM.2h.02 4615:::Acetate.3mM.30m.02 4615:::Acetate.3mM.30m.04 4615:::Acetate.3mM.30m.07 4615:::Acetate.3mM.30m.08 4615:::Acetate.3mM.60m.01 4615:::Acetate.3mM.60m.02 4615:::CHP_25uM_2h_01 4615:::CK_LA_2h.2 4615:::CK.4h.for.AA.NA.0.03mM 4615:::CK.MDG.AA.Na.2h 4615:::CK.PA.NA.101801.2 4615:::ETYA_30uM_10min.03 4615:::ETYA_30uM_10min.04 4615:::ETYA_30uM_10min.05 4615:::ETYA_30uM_10min.06 4615:::ETYA_3uM_1h_02 4615:::L2A_30uM_1h_02 4615:::L2A_30uM_1h_07 4615:::L2A_30uM_30min_05 4615:::L2A_30uM_30Min_06 4615:::L2A_30uM_4h_04 4615:::MDG.MD.glycerol 4615:::MTB1248_PA50_1h_01 4615:::MTB1254_Bottom_10D_01 4615:::MTB1254_Bottom_10D_02 4615:::MTB1254_Bottom_10D_03 4615:::MTB1254_Bottom_14D_03 4615:::MTB1254_Bottom_21D_02 4615:::MTB1254_Bottom_42D_03 4615:::MTB1254_FA5_10min_01 4615:::MTB1254_Pellicle_10D_03 4615:::MTB1254_Pellicle_10D_04 4615:::MTB1254_Pellicle_14D_01 4615:::MTB1254_Pellicle_14D_02 4615:::MTB1254_Pellicle_14D_03 4615:::MTB1254_Pellicle_21D_03 4615:::MTB1254_Pellicle_21D_04 4615:::MTB1254_Pellicle_42D_01 4615:::MTB1254_Pellicle_42D_02 4615:::MTB1254_Pellicle_56D_01 4615:::MTB1254.0485.1._Act_2h_01 4615:::MTB1254.0485.1._ETYA_10m_01 4615:::MTB1254.0485.1._OA_10m_04 4615:::MTB1254.0485.1._PA_12h_03 4615:::MTB1254.3524.1._OA_10min_02 4615:::MTB1254.3524.1._OA_10min_03 4615:::MTB1254.3524.1._OA_10min_04 4615:::MTB1254.3524.1._PA_12h_03 4615:::MTB1254.B4.1._OA_10MIN_01 4615:::MTB1254.B4.1._OA_30MIN_01 4615:::MTB1254.B4.1._OA_30MIN_02 4615:::MTB1254.B4.1._PA_10MIN_02 4615:::MTB1254.B4.1._PA_4h_01 4615:::MTB1254.B4.1._PA_4h_04 4615:::MTB1254.B4.1.Compl._OA_30MIN_02 4615:::MTB1254.B4.1.Compl._OA_30MIN_03 4615:::MTB1254.B4.1.Compl._PA_4h_01 4615:::MTB1254.B4.1.Compl._PA_4h_02 4615:::MTB1254.B4.1.Compl._PA_4h_06 4615:::MTB1254.Rv3524.2._PA50.OA30_30m_01 4615:::MTB1254.Rv3524.2.compl._PA50.OA30_30m_02 4615:::MTB1254.whiB4_SDS_90MIN_01 4615:::MTB1254TA1_OA.30min_03 4615:::OA_50uM_10min_01 4615:::OA_50uM_10min_06 4615:::OA_50uM_10min_08 4615:::OA_50uM_1h_06 4615:::OA_50uM_1h_09 4615:::OA_50uM_30min_04 4615:::OA_50uM_30min_05 4615:::PA_100uM_2h_T0_05 4615:::PA_10uM_2h_T0_01 4615:::PA_25uM_2h_T0_01 4615:::PA_50uM_10min_01 4615:::PA_50uM_10min_07 4615:::PA_50uM_10min_09 4615:::PA_50uM_12h_01 4615:::PA_50uM_12h_05 4615:::PA_50uM_24h_01 4615:::PA_50uM_24h_02 4615:::PA_50uM_24h_07 4615:::PA_50uM_24h_08 4615:::PA_50uM_2h_02 4615:::PA_50uM_2h_04 4615:::PA_50uM_2h_07 4615:::PA_50uM_30.min_05 4615:::PA_50uM_30min_01 4615:::PA_50uM_30min_02 4615:::PA_50uM_30min_03 4615:::PA_50uM_3d_03 4615:::PA_50uM_4h 4615:::PA_50uM.AA_30uM_30min_01 4615:::PA_50uM.AA_30uM_30min_02 4615:::PA_50uM.AA_30uM_30min_03 4615:::PA_50uM.OA_10uM_12h_02 4615:::PA_50uM.OA_10uM_30min_02 4615:::PA_50uM.OA_10uM_30min_03 4615:::PA_50uM.OA_10uM_30min_04 4615:::PA_50uM.OA_30uM_30min_02 4615:::PA_50uM.OA_30uM_30min_03 4615:::PA_5uM_2h_T0_01 4615:::Spe_100uM_30M_01 4615:::Starvation_1254_12h_03 4615:::Starvation_1254_12h_04 4615:::Starvation_1254_24h_01 4615:::Starvation_1254_24h_02 4615:::Starvation_1254_24h_05 4615:::Starvation_1254_3d_01 4615:::Starvation_1254_3d_02 4615:::Starvation_1254_6h_03 4615:::Starvation_1254_OA50_12h_02 4615:::Starvation_1254_OA50_12h_04 4615:::Starvation_1254_OA50_24h_03 4615:::Starvation_1254_OA50_5d_01 4615:::Starvation_1254_OA50_5d_02 4615:::Starvation_1254_OA50_6h_01 4615:::Starvation_1254_OA50_6h_03 4615:::Starvation_1254_PA50_24h_03 4615:::Starvation_1254_PA50_24h_04 4615:::Starvation_1254_PA50_6h_01 4615:::Starvation_1254_PA50_6h_03 4615:::Starvation_1254_PA50.OA30_24h_03 4615:::Starvation_1254_PA50.OA30_6h_01 4615:::Starvation_1254_PA50.OA30_6h_02 4615:::Starvation_1254_PA50.OA30_6h_03 4615:::Starvation_1254_PA50.OA30_6h_04 4615:::TBD045 4615:::TBD098 4615:::TBD099 4615:::TBD1275 4615:::TBD1276 4615:::TBD426 4615:::TBD816 4615:::TBE056 4615:::TBE283 4615:::TBE734 4615:::Test.3 4615:::Tet_100uM_30M_01 4615:::X2.2..Dipyridyl_1mM.Dpd.AA_50uM_01 4637:::H37Rv.control.vs.1mg.ml.cholesterol.for.24.hrs.rep.3 4696:::H37Rv.wt.vs.dosT.null.anaerobic.Gaspak.4hr.rep.2 4696:::H37Rv.wt.vs.dosT.null.anaerobic.Gaspak24hr.rep.3 4699:::CDC1551.Ctrl.vs.clinical.isolate.2333.99_Uganda.rep.1 4699:::CDC1551.Ctrl.vs.clinical.isolate.4130.02_Haarlem.rep.1 4699:::CDC1551.Ctrl.vs.clinical.isolate.4130.02_Haarlem.rep.3 4699:::CDC1551.Ctrl.vs.clinical.isolate.4850.03_EAI.rep.2 4703:::Clinical.isolate.1797.03_EAI.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.4130.02_Haarlem.extra.vs.intracellular.in.resting.macrophages.rep.2 4704:::Clinical.isolate.2169.99_Uganda.extra.vs.intracellular.in.activated.macrophages.rep.1 4704:::Clinical.isolate.5468.02_Afri2.extra.vs.intracellular.in.activated.macrophages.rep.2 4729:::H37Rv.wild.type.vs.PepD.null.mutant.rep.3 4731:::X0.2ug.ml.Isoniazid.vs.Ethanol.6hrs.rep.3 4731:::X10ug.ml.capreomycin.vs.Ethanol..6hrs 4731:::X12ug.ml.Ethionamide.vs.Ethanol.6hrs.rep.1 4735:::BCG.wild.type.vs.BCG.with.empty.pMV361.at.OD.0.4.rep.3 4735:::BCG.wild.type.vs.BCG.with.empty.pMV361.at.OD.0.4.rep.4 4799:::H37Rv.ctrl.vs.1ug.ml.Isoniazid.for.2hrs.rep.1 4799:::H37Rv.nutrient.starved..ctrl.vs.1ug.ml.Isoniazid.for.2hrs.rep.2 4802:::H37Rv.ctrl.vs.relE1.overexpression.24.hr.rep.2 4802:::H37Rv.ctrl.vs.relE3.overexpression.72.hr.rep.5 4815:::H37Rv.reaeration.for.12hrs.rep.4 4815:::H37Rv.reaeration.for.1hrs.rep.1 RV0410C -1.50074193983542 -0.792526642384999 -0.219209496829893 0.496993191193281 -1.13598443701321 -0.354995136566629 0.638991245819932 -1.2424829779832 -0.603491732163269 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0.864731742918712 0.276714157733988 1.48733859782018 0.933910282352209 -0.069178539433497 -0.743669298910092 0.588017585184724 0.190240983442117 0.363187332025859 0.345892697167485 0.639901489759847 0.588017585184724 1.15874053551107 -1.00308882178571 0.397776601742607 -0.172946348583742 0.138357078866994 1.43545469324506 2.26559716644702 1.33168688409482 1.33168688409482 0.12106244400862 0.172946348583742 0.466955141176104 0.674490759476595 0.484249776034479 0.32859806230911 0.743669298910092 -2.50772205446426 -1.00308882178571 -1.31439224923644 -1.19332980522782 -0.588017585184724 -2.05806154814653 -2.10994545272166 1.05497272636083 -0.847437108060337 -0.89932101263546 0.0172946348583742 -0.380481966884233 -0.345892697167485 -0.882026377777086 -1.1414459006527 -2.40395424531402 -1.6084010418288 -1.90240983442117 0.103767809150245 1.41816005838669 0.89932101263546 -1.34898151895319 NA 1.00308882178571 0.345892697167485 -1.62569567668718 0.484249776034479 0.0345892697167485 0.0345892697167485 0.795553203485215 -0.985794186927331 -1.52192786753693 -0.224830253158865 -0.0172946348583742 -0.812847838343589 -1.12415126579433 -1.81593666012929 0.812847838343589 1.03767809150245 -0.57072295032635 -0.0345892697167485 0.501544410892853 -0.363187332025859 -0.0172946348583742 -0.0345892697167485 NA -0.224830253158865 1.69487421612067 -1.41816005838669 -0.190240983442117 -0.709080029193344 0.933910282352209 0.933910282352209 0.32859806230911 -0.985794186927331 -0.536133680609601 -1.05497272636083 -1.40086542352831 -0.743669298910092 -0.639901489759847 -0.224830253158865 -0.968499552068957 -1.48733859782018 -0.44966050631773 0.276714157733988 -0.0172946348583742 0.190240983442117 0.190240983442117 -0.553428315467976 1.24521370980294 0.951204917210583 2.2137132618719 0.864731742918712 0.864731742918712 2.36936497559727 2.16182935729678 2.52501668932264 2.59419522875614 -0.103767809150245 -0.674490759476595 -2.04076691328816 -2.49042741960589 -3.40704306709972 -1.1414459006527 -1.62569567668718 -3.45892697167485 -3.73564112940883 -1.85052592984604 -2.12724008758003 -1.57381177211206 -1.10685663093595 -4.25448017516006 -3.47622160653322 -2.16182935729678 -1.47004396296181 -0.985794186927331 -1.12415126579433 -1.19332980522782 -1.41816005838669 -1.97158837385466 -2.57690059389776 -2.23100789673028 -1.59110640697043 -2.09265081786328 0.207535618300491 0.172946348583742 0.380481966884233 -0.415071236600982 -0.242124888017239 1.02038345664408 -0.311303427450736 -0.501544410892853 -0.57072295032635 1.6084010418288 -1.17603517036945 -1.93699910413791 -0.0864731742918712 1.01173613921489 -0.0141998054626652 1.15018424247588 -0.854354962003687 -3.64225010117361 0.44966050631773 0.044966050631773 0.649038277986912 -0.776300685435327 0.954468055863106 -0.552861278259504 0.552861278259504 -1.25 0.688841626699502 -0.650572647438418 0.382689792610834 0.924302151875334 0.224830253158865 -0.674490759476595 -0.330362820968128 -0.867202405041337 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POSITION A C G T 1 0.5 0 0 0.5 2 0.5 0 0 0.5 3 0.75 0.25 0 0 4 0 0.5 0.5 0 5 0.5 0.5 0 0 6 0.25 0 0.75 0 7 1 0 0 0 8 0.75 0.25 0 0 9 0.75 0 0 0.25 10 0.25 0.5 0 0.25 11 0 1 0 0 12 0.25 0 0 0.75 13 1 0 0 0 14 1 0 0 0 15 0 0 1 0 16 1 0 0 0 17 0 0.5 0.5 0 18 0.5 0.25 0.25 0 19 1 0 0 0 20 0 0 0.75 0.25 21 0 0 0.75 0.25 22 0 0 0.25 0.75 23 0 0 0.25 0.75

POSITION A C G T 1 0.909352 0.035092 0.035092 0.020463 2 1 0 0 0 3 0 0.222222 0 0.777778 4 0 0.222222 0 0.777778 5 0.222222 0 0.777778 0 6 0 1 0 0 7 0 0.111111 0.666667 0.222222 8 0.333333 0 0 0.666667