GENES 2867:::H37Ra..Sauton.s.media.replicate.1 2885:::Strain.1254...replicate.4 2885:::Strain.9700665..replicate.4 4062:::CDC1551.Ctrl.vs.0.05.mM.DETA.NO.40.min.rep.5 4062:::H37Rv.ctrl.vs.Rv3132.34.KO..complemented...0.05.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.3 4062:::MTB.strain.1254.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.7 4062:::MTB.strain.1254.Ctrl.vs.high.aeration...0.001.mM.DETA.NO.rep.3 4062:::MTB.strain.1254.Ctrl.vs.high.aeration...0.005.mM.DETA.NO.rep.2 4062:::MTB.strain.1254.Ctrl.vs.high.aeration...0.01.mM.DETA.NO.rep.2 4062:::MTB.strain.1254.Ctrl.vs.high.aeration.rep3 4062:::MTB.strain.1254.Ctrl.vs.low.aeration..0.2..oxygen..2hr.rep.1 4062:::MTB.strain.1254.Ctrl.vs.low.aeration..0.2..oxygen..2hr.rep.2 4089:::MTB1254.control.vs..0.5.ug.ml.Streptomycin.for.15.min.rep.4 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.15.min.rep.2 4089:::MTB1254.control.vs..1.0.ug.ml.Streptomycin.for.15.min.rep.3 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.1 4089:::MTB1254.control.vs..100.ug.ml.Streptomycin.for.15.min.rep.2 4089:::MTB1254.control.vs..100.ug.ml.Streptomycin.for.15.min.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.2 4089:::MTB1254.control.vs..5.0.ug.ml.Streptomycin.for.15.min.rep.2 4089:::MTB1254.control.vs..5.0.ug.ml.Streptomycin.for.15.min.rep.3 4089:::MTB1254.control.vs..5.0.ug.ml.Streptomycin.for.15.min.rep.4 4089:::MTB1254.ethanol.vs..100.ug.ml.Erythromycin.for.15.min.rep.3 4089:::MTB1254.vs..MTB1254.rep5 4107:::EMB.10ug.mL.vs.DMSO.12h.1 4107:::Palmitate.Glucose..2 4107:::pH4.8vspH6.8..6h. 4107:::X0.1mMGSNO.5ug.mLKCNvsDMSO.6h 4107:::X0.2mM.NaN3.DMSO 4107:::X0.5ug.mL..121940vsDMSO.6h 4107:::X0.5ug.mL..124196vsDMSO..6h 4107:::X1.ug.mL..111891vsDMSO..6h 4107:::X10mM.succinatevs10mM.glucose 4107:::X10ug.mL.Amikacin.EtOH..6h 4107:::X10ug.mL.capreomycinvsEtOH..6h 4107:::X10ug.mL.RoxvsEtOH..6h 4107:::X10ug.mL.RoxvsEtOH..6hA 4107:::X10ug.mL.TetvsEtOH..6h 4107:::X20ug.mL.Procept.6776vsDMSO..6h 4107:::X20ug.mLProcept6778vsDMSO.6hA 4107:::X2ug.mL..121940vsDMSO..6hA 4107:::X2ug.mL.SMvsEtOH..6h 4107:::X30ug.mL.RoxvsEtOH..6h 4107:::X30ug.mL.RoxvsEtOH..6hA 4107:::X50ug.mL.Thioridazine.DMSO..6h 4107:::X5ug.mL.AmivsEtOH..6h 4107:::X5ug.mL.AmivsEtOH..6hA 4107:::X5ug.mL.CapvsEtOH..6h 4107:::X5ug.mL.CapvsEtOH..6hA 4107:::X5ug.mLProcept.6778vsDMSO.6hA 4107:::X5ug.mLStreptomycinvsEtOH.6h 4363:::H37Rv.hypoxia.4hr.rep.7 4396:::Strain.27.cDNA.Cy3.vs.H37Rv.gDNA.Cy5..DS..rep.1 4523:::H37Rv.sigB.null.mutant.control.vs.5mM.Diamide.for.60.min.rep.1 4523:::H37Rv.sigB.null.mutant.control.vs.5mM.Diamide.for.60.min.rep.5 4523:::H37Rv.wild.type.control.vs.0.05..SDS.for.60.min.rep.4 4523:::H37Rv.wild.type.control.vs.5mM.Diamide.for.60.min.rep.6 4523:::H37Rv.wild.type.vs.H37Rv.sigB.null.mutant.rep.4 4575:::Extracted.Lung.Surfactant.30min.rep.3 4575:::Extracted.Lung.Surfactant.30min.rep.4 4575:::Purified.Human.SP.A.Uncoated.2hrs.rep4 4575:::Purified.Surfactant.Lipids.2hrs.rep.2 4583:::X5ug.ml.KCN.vs.DMSO.6hrs.rep.1 4615:::AA_30uM_10.min_06 4615:::AA_30uM_10.min_07 4615:::AA_30uM_24h_02 4615:::AA_30uM_24h_03 4615:::AA_30uM_24h_T0_01 4615:::AA_30uM_4h_06 4615:::AA_30uM_4h_07 4615:::Acetate.3mM.30m.04 4615:::Acetate.3mM.30m.07 4615:::CA_50uM_10min_01 4615:::CHP.AA.2h.1 4615:::CK_AA_NA.2h 4615:::CK_LA_2h 4615:::CK_LA_2h.3 4615:::CK_OA_NA_0.05_2h 4615:::CK_OA_NA_2h.02 4615:::CK.for.AA.NA.2h.2 4615:::CK.for.MDG.OA.4h 4615:::CK.for.OA.PA.Na.4h 4615:::CK.OA_NA_2H 4615:::CK.PA.NA.2h.3..101801 4615:::ETYA_30uM_10min.03 4615:::Glucose_5mM_10min_01 4615:::Glycerol_1. 4615:::Glycerol_1._30M_01 4615:::L2A_30uM_10min_06 4615:::L2A_30uM_1h_03 4615:::L2A_30uM_4h_03 4615:::L2A_30uM_4h_07 4615:::MTB1248_PA50_1h_01 4615:::MTB1248_PA50_1h_02 4615:::MTB1254_Bottom_21D_02 4615:::MTB1254_INH_20MIN 4615:::MTB1254_Pellicle_42D_02 4615:::MTB1254.0485.1._PA_12h_02 4615:::MTB1254.0485.1._PA_4h_01 4615:::MTB1254.0485.1._PA_4h_03 4615:::MTB1254.0485.1._PA_4h_04 4615:::MTB1254.0494.4._OA_30MIN_01 4615:::MTB1254.3219.3._01 4615:::MTB1254.3524.1._OA_10min_02 4615:::MTB1254.3524.1._PA_12h_01 4615:::MTB1254.3524.1._PA_12h_02 4615:::MTB1254.3524.1._PA_12h_03 4615:::MTB1254.3524.1._PA_12h_04 4615:::MTB1254.3524.1._PA_12h_05 4615:::MTB1254.3524.1._PA_12h_06 4615:::MTB1254.3524.2._INH_20MIN 4615:::MTB1254.B4.1._PA_30MIN_01 4615:::MTB1254.B4.1._PA_4h_01 4615:::MTB1254.B4.1._PA_4h_02 4615:::MTB1254.B4.1._PA_4h_03 4615:::MTB1254.B4.1._PA_4h_04 4615:::MTB1254.B4.1.Compl._PA_30MIN_02 4615:::MTB1254.B4.1.Compl._PA_30MIN_03 4615:::MTB1254.B4.1.Compl._PA_30MIN_04 4615:::MTB1254.B4.1.Compl._PA_4h_01 4615:::MTB1254.B4.1.Compl._PA_4h_02 4615:::MTB1254.B4.1.Compl._PA_4h_03 4615:::MTB1254.B4.1.Compl._PA_4h_04 4615:::MTB1254.B4.1.Compl._PA_4h_05 4615:::MTB1254.B4.1.Compl._PA_4h_06 4615:::MTB1254TA1_OA.30min_04 4615:::MTB1370_PA50_1h_01 4615:::MTB1370_PA50_1h_03 4615:::MTB6548_PA50_1h_01 4615:::MTB6548_PA50_1h_02 4615:::MTB889_PA50_1h_01 4615:::MTB889_PA50_1h_02 4615:::MTB889_PA50_1h_03 4615:::OA_50uM_1h_06 4615:::OA_50uM_24h_02 4615:::OA_50uM_2h..1.0..BSA.10mMGlu._30.min._01 4615:::OA_50uM_2h..1.5.BSA.10mMGlu._30.min_01 4615:::OA_50uM_30min_05 4615:::PA_100uM_24h_01 4615:::PA_100uM_2h_T0_02 4615:::PA_50uM_10min_05 4615:::PA_50uM_10min_T0_01 4615:::PA_50uM_12h_01 4615:::PA_50uM_12h_02 4615:::PA_50uM_12h_03 4615:::PA_50uM_12h_04 4615:::PA_50uM_12h_05 4615:::PA_50uM_12h_06 4615:::PA_50uM_1h_01 4615:::PA_50uM_1h_02 4615:::PA_50uM_1h_03 4615:::PA_50uM_1h_08 4615:::PA_50uM_1h_09 4615:::PA_50uM_1h_12 4615:::PA_50uM_24h_04 4615:::PA_50uM_24h_10 4615:::PA_50uM_2h_03 4615:::PA_50uM_2h_05 4615:::PA_50uM_2h_06 4615:::PA_50uM_2h_07 4615:::PA_50uM_30.min_05 4615:::PA_50uM_30min_01 4615:::PA_50uM_30min_02 4615:::PA_50uM_3d_01 4615:::PA_50uM_3d_02 4615:::PA_50uM_3d_04 4615:::PA_50uM_3d_05 4615:::PA_50uM_4h 4615:::PA_50uM_4h_02 4615:::PA_50uM_4h_04 4615:::PA_50uM_4h_06 4615:::PA_50uM_4h_T0_01 4615:::PA_50uM_8h_01 4615:::PA_50uM_8h_03 4615:::PA_50uM_8h_05 4615:::PA_50uM_8h_06 4615:::PA_50uM.AA_30uM_30min_01 4615:::PA_50uM.MAPP_30m_01 4615:::PA_50uM.OA_10uM_12h_02 4615:::PA_50uM.OA_10uM_24h_02 4615:::PA_50uM.OA_10uM_2h_01 4615:::PA_50uM.OA_10uM_30min_01 4615:::PA_50uM.OA_10uM_30min_04 4615:::Rv_TA_OA30_30mim_03 4615:::Rv.MT71_100503_02 4615:::Rv.MT90_100603_01 4615:::Spe_100uM_30M_01 4615:::Starvation_1254_PA50_6h_01 4615:::Starvation_1254_PA50_6h_02 4615:::Starvation_1254_PA50_6h_04 4615:::Starvation_OA50_6h_02 4615:::Starvation_OA50_6h_03 4615:::Starvation_OA50_6h_04 4615:::Starvation_T0 4615:::TBD040 4615:::TBD044 4615:::TBD1113 4615:::TBD1114 4615:::TBD1115 4615:::TBD625 4615:::TBD816 4615:::TBD817 4615:::TBD818 4615:::TBD819 4615:::TBE059 4615:::TBE735 4615:::TBF466 4615:::Test.4 4615:::Tet_20uM_30M_01 4615:::WT_65.4_SDS_01 4615:::X7H9_MTB1254_OA100_10M_01 4615:::X7H9_MTB1254.3524.1._OA100_10M_01 4615:::X7H9_MTB1254.3524.1._OA50_10M_01 4630:::H37Rv.wild.type.Cy5.vs.Rv0485.Tn.mutant.Cy3..DS..rep.1 4696:::H37Rv.wt.vs.dosT.null.anaerobic.Gaspak24hr.rep.2 4699:::CDC1551.Ctrl.vs.clinical.isolate.10514.01_Afri2.rep.3 4699:::CDC1551.Ctrl.vs.clinical.isolate.10517.01_Afri2.rep.1 4699:::CDC1551.Ctrl.vs.clinical.isolate.1797.03_EAI.rep.2 4699:::CDC1551.Ctrl.vs.clinical.isolate.2336.02_Haarlem.rep.2 4699:::CDC1551.Ctrl.vs.H37Rv.rep.2 4703:::CDC1551.extra.vs.intracellular.in.resting.macrophages.rep.2 4703:::Clinical.isolate.10514.01_Afri2.extra.vs.intracellular.in.resting.macrophages.rep.2 4703:::Clinical.isolate.2333.99_Uganda.extra.vs.intracellular.in.resting.macrophages.rep.1 4703:::Clinical.isolate.4130.02_Haarlem.extra.vs.intracellular.in.resting.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.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.1 4704:::Clinical.isolate.4130.02_Haarlem.extra.vs.intracellular.in.activated.macrophages.rep.2 4731:::X0.2mg.ml.Ampicillin.vs.Ethanol.6hrs 4731:::X5ug.ml.Capreomycin.vs.Ethanol.6hrs.A 4731:::X5ug.ml.Rifampicin.vs.DMSO.2.5hrs 4731:::X5ug.ml.Streptomycin.vs.Ethanol.6hrs 4802:::H37Rv.ctrl.vs.relE1.overexpression.72.hr.rep.4 4802:::H37Rv.ctrl.vs.relE2.overexpression.72.hr.rep.5 4815:::H37Rv.reaeration.for.12hrs.rep.6 Provvedi_Microbiology2009:::H37Rv.Control.vs.subinhibitory.conc..5.ug.ml..vancomycin.DS.rep.2 Raghavan_Nature2008:::espR.mutant.complemented.with.N.terminal.Flag.espR..RFL..rep2 RV0332 0.216800601260334 0.909778233712617 -1.4430965086476 -0.177497568283315 0.0709990273133258 -0.319495622909966 0.958486868729898 0.0709990273133258 0.390494650223292 0.390494650223292 0.0354995136566629 -0.354995136566629 0.0354995136566629 -0.106498540969989 0.153293354426499 0.459880063279497 0.521197405050096 -1.99281360754449 0.521197405050096 -0.766466772132494 0.183952025311799 -0.306586708852998 -0.122634683541199 0.674490759476595 0.122634683541199 0.398562721508897 -0.183952025311799 -0.735808101247195 -0.0306586708852996 0.582514746820696 -0.269796303790638 0.847931240484862 -0.32760979746006 -1.40679501262261 0.0192711645564741 0.192711645564741 0.134898151895319 0.385423291129483 0.0192711645564741 -0.211982810121216 0.0192711645564741 2.11982810121216 1.92711645564741 -0.520321443024802 0.32760979746006 0.539592607581276 1.6380489873003 0.346880962016535 -0.0963558227823708 0.23125397467769 -1.1948122025014 0.192711645564741 -0.250525139234164 0.655219594920121 0.674490759476595 0.809388911371914 1.1948122025014 -1.9569731894673 0.8 1.34898151895319 1.10646798745599 -0.515341254431556 2.47060660212775 -0.742697690210184 0.663433533911405 -0.199030060173422 -0.685547985041785 1.43743932347471 -0.738389884058589 1.47161620249439 2.17676563285628 0.214610696197098 0.306586708852998 -1.16502949364139 -1.50227487337969 -0.183952025311799 -1.71688556957679 -1.44095753160909 -0.0613173417705996 -1.87017892400329 0.153293354426499 -0.551856075935396 0.674490759476595 0.153293354426499 -0.245269367082398 -1.93149626577389 0.797125443017794 -3.09652575941528 -1.71688556957679 -0.367904050623597 -0.459880063279497 -0.153293354426499 -1.44095753160909 -0.705149430361895 2.05413094931508 NA -0.0613173417705996 -1.68622689869149 2.39137632905338 2.97389107587408 -0.674490759476595 -0.214610696197098 -2.23808297462688 0.459880063279497 0.398562721508897 -0.735808101247195 0.521197405050096 -0.122634683541199 -0.551856075935396 -0.183952025311799 -0.367904050623597 -0.858442784788394 -0.521197405050096 0.521197405050096 0.858442784788394 1.99281360754449 -0.459880063279497 1.07305348098549 0.245269367082398 0.490538734164796 0.981077468329593 1.28766417718259 1.25700550629729 0.337245379738298 0.153293354426499 1.22634683541199 0.367904050623597 1.19568816452669 0.919760126558993 1.25700550629729 1.16502949364139 0.306586708852998 0.981077468329593 1.65556822780619 3.06586708852998 3.58706449358007 1.59425088603559 1.31832284806789 1.90083759488859 0.889101455673693 -0.735808101247195 -0.214610696197098 -0.367904050623597 1.68622689869149 3.89365120243307 -0.0613173417705996 0.490538734164796 -1.22634683541199 -0.367904050623597 -1.47161620249439 -0.183952025311799 -1.41029886072379 -0.429221392394197 -1.47161620249439 0.797125443017794 -0.153293354426499 0.214610696197098 1.59425088603559 NA 1.87017892400329 2.05413094931508 -0.306586708852998 0.613173417705996 2.82059772144758 2.29940031639748 1.04239481010019 0.245269367082398 0.735808101247195 0.459880063279497 0.337245379738298 0.183952025311799 -0.337245379738298 NA 1.53293354426499 0.521197405050096 1.83952025311799 1.13437082275609 NA -0.214610696197098 -1.25700550629729 -0.797125443017794 -1.56359221515029 0.981077468329593 1.90083759488859 0.0306586708852997 0.981077468329593 1.41029886072379 1.47161620249439 0.122634683541199 0.490538734164796 -0.889101455673693 0.551856075935396 0.674490759476595 0.459880063279497 1.34898151895319 0 0.183952025311799 -0.337245379738298 -0.858442784788394 -1.44095753160909 -0.919760126558993 -0.950418797444293 1.28766417718259 0 1.77820291134739 3.03520841764468 0.275928037967698 -0.429221392394197 0 0.613173417705996 -0.459880063279497 -0.613173417705996 0.827784113903094 -0.429221392394197 0.245269367082398 -0.735808101247195 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POSITION A C G T 1 0 0 0 1 2 0 0.75 0.25 0 3 0 0 0 1 4 0 0.5 0 0.5 5 0 1 0 0 6 0 0 0 1 7 0 0.75 0.25 0 8 0 0.75 0.25 0 9 0 0.25 0 0.75 10 0 0 1 0 11 1 0 0 0 12 0.25 0.75 0 0 13 1 0 0 0 14 0 0.25 0.75 0 15 0.5 0 0 0.5 16 0 0.75 0 0.25 17 0 0.25 0.5 0.25 18 0.75 0.25 0 0 19 0 0.75 0.25 0 20 0 1 0 0 21 0 0 1 0 22 0.75 0 0 0.25

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