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share/homer/config.txt
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share/homer/cpp/analyzeHiC
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share/homer/data/knownTFs/motifs/cre.motif
share/homer/data/knownTFs/motifs/creb5.motif
share/homer/data/knownTFs/motifs/crx.motif
share/homer/data/knownTFs/motifs/ctcf-mys.motif
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share/homer/data/knownTFs/motifs/cux1.motif
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share/homer/data/knownTFs/motifs/dmc1.motif
share/homer/data/knownTFs/motifs/dmrt1.motif
share/homer/data/knownTFs/motifs/dmrt6.motif
share/homer/data/knownTFs/motifs/dr0.motif
share/homer/data/knownTFs/motifs/dr5.motif
share/homer/data/knownTFs/motifs/dux.motif
share/homer/data/knownTFs/motifs/dux4.motif
share/homer/data/knownTFs/motifs/duxbl.motif
share/homer/data/knownTFs/motifs/e2a.motif
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share/homer/data/knownTFs/motifs/e2f3.motif
share/homer/data/knownTFs/motifs/e2f4.motif
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share/homer/data/knownTFs/motifs/e2f7.motif
share/homer/data/knownTFs/motifs/e47.motif
share/homer/data/knownTFs/motifs/ebf-old.motif
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share/homer/data/knownTFs/motifs/ebf2.motif
share/homer/data/knownTFs/motifs/ebna1.motif
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share/homer/data/knownTFs/motifs/egr1.motif
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share/homer/data/knownTFs/motifs/elk1.motif
share/homer/data/knownTFs/motifs/elk4.motif
share/homer/data/knownTFs/motifs/emx2.motif
share/homer/data/knownTFs/motifs/en1.motif
share/homer/data/knownTFs/motifs/eomes.motif
share/homer/data/knownTFs/motifs/erb.motif
share/homer/data/knownTFs/motifs/ere.motif
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share/homer/data/knownTFs/motifs/es.motif
share/homer/data/knownTFs/motifs/esrrb.motif
share/homer/data/knownTFs/motifs/ets-distal.motif
share/homer/data/knownTFs/motifs/ets-ebox.motif
share/homer/data/knownTFs/motifs/ets-runx.motif
share/homer/data/knownTFs/motifs/ets.motif
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share/homer/data/knownTFs/motifs/etv1.motif
share/homer/data/knownTFs/motifs/etv2.motif
share/homer/data/knownTFs/motifs/etv4.motif
share/homer/data/knownTFs/motifs/ews-erg.motif
share/homer/data/knownTFs/motifs/ews-fli1.motif
share/homer/data/knownTFs/motifs/extras/createMotifTable.pl
share/homer/data/knownTFs/motifs/extras/motifTable.txt
share/homer/data/knownTFs/motifs/extras/motifs2symbol.txt
share/homer/data/knownTFs/motifs/extras/notes.txt
share/homer/data/knownTFs/motifs/extras/symbol2motifFile.txt
share/homer/data/knownTFs/motifs/extras/table.txt
share/homer/data/knownTFs/motifs/fli.motif
share/homer/data/knownTFs/motifs/fos.motif
share/homer/data/knownTFs/motifs/fosl2.motif
share/homer/data/knownTFs/motifs/fox-ebox.motif
share/homer/data/knownTFs/motifs/foxa1.lncap.motif
share/homer/data/knownTFs/motifs/foxa1.mcf7.motif
share/homer/data/knownTFs/motifs/foxa2.motif
share/homer/data/knownTFs/motifs/foxa3.motif
share/homer/data/knownTFs/motifs/foxd3.motif
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share/homer/data/knownTFs/motifs/foxh1.motif
share/homer/data/knownTFs/motifs/foxk1.motif
share/homer/data/knownTFs/motifs/foxk2.motif
share/homer/data/knownTFs/motifs/foxl2.motif
share/homer/data/knownTFs/motifs/foxm1.motif
share/homer/data/knownTFs/motifs/foxo1.motif
share/homer/data/knownTFs/motifs/foxo3.motif
share/homer/data/knownTFs/motifs/foxp1.motif
share/homer/data/knownTFs/motifs/fra1.motif
share/homer/data/knownTFs/motifs/fra2.motif
share/homer/data/knownTFs/motifs/fxr.er2.motif
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share/homer/data/knownTFs/motifs/gabp.motif
share/homer/data/knownTFs/motifs/gata-scl.motif
share/homer/data/knownTFs/motifs/gata.motif
share/homer/data/knownTFs/motifs/gata2.motif
share/homer/data/knownTFs/motifs/gata3.dr4.motif
share/homer/data/knownTFs/motifs/gata3.dr8.motif
share/homer/data/knownTFs/motifs/gata3.ir3.motif
share/homer/data/knownTFs/motifs/gata3.ir4.motif
share/homer/data/knownTFs/motifs/gata3.motif
share/homer/data/knownTFs/motifs/gata4.motif
share/homer/data/knownTFs/motifs/gata6.motif
share/homer/data/knownTFs/motifs/gfi1b.motif
share/homer/data/knownTFs/motifs/gfx.motif
share/homer/data/knownTFs/motifs/gfy-staf.motif
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share/homer/data/knownTFs/motifs/gli.motif
share/homer/data/knownTFs/motifs/gli2.motif
share/homer/data/knownTFs/motifs/gli3.motif
share/homer/data/knownTFs/motifs/glis3.motif
share/homer/data/knownTFs/motifs/gre-raw.motif
share/homer/data/knownTFs/motifs/gre.motif
share/homer/data/knownTFs/motifs/grhl2.motif
share/homer/data/knownTFs/motifs/groups/Tal1.motif
share/homer/data/knownTFs/motifs/groups/all.motifs
share/homer/data/knownTFs/motifs/groups/amy.motifs
share/homer/data/knownTFs/motifs/groups/cd4.motifs
share/homer/data/knownTFs/motifs/groups/dnase.motifs
share/homer/data/knownTFs/motifs/groups/enhancer.motifs
share/homer/data/knownTFs/motifs/groups/es.motifs
share/homer/data/knownTFs/motifs/groups/id2.motifs
share/homer/data/knownTFs/motifs/groups/ik1.motif
share/homer/data/knownTFs/motifs/groups/inflammatory.motifs
share/homer/data/knownTFs/motifs/groups/ivan.motifs
share/homer/data/knownTFs/motifs/groups/ivan2.motifs
share/homer/data/knownTFs/motifs/groups/liver.motifs
share/homer/data/knownTFs/motifs/groups/pol2-cd4.motifs
share/homer/data/knownTFs/motifs/groups/promoter.motifs
share/homer/data/knownTFs/motifs/groups/sven.motifs
share/homer/data/knownTFs/motifs/groups/yin.motifs
share/homer/data/knownTFs/motifs/gsc.motif
share/homer/data/knownTFs/motifs/gsx2.motif
share/homer/data/knownTFs/motifs/hand2.motif
share/homer/data/knownTFs/motifs/heb.motif
share/homer/data/knownTFs/motifs/hic1.motif
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share/homer/data/knownTFs/motifs/hif1b.motif
share/homer/data/knownTFs/motifs/hif2a.motif
share/homer/data/knownTFs/motifs/hinfp.motif
share/homer/data/knownTFs/motifs/hlf.motif
share/homer/data/knownTFs/motifs/hnf1.motif
share/homer/data/knownTFs/motifs/hnf1b.motif
share/homer/data/knownTFs/motifs/hnf4.motif
share/homer/data/knownTFs/motifs/hnf6.motif
share/homer/data/knownTFs/motifs/hnf6b.motif
share/homer/data/knownTFs/motifs/hoxa1.motif
share/homer/data/knownTFs/motifs/hoxa10.motif
share/homer/data/knownTFs/motifs/hoxa11.motif
share/homer/data/knownTFs/motifs/hoxa13.motif
share/homer/data/knownTFs/motifs/hoxa2.motif
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share/homer/data/knownTFs/motifs/hoxa9.motif
share/homer/data/knownTFs/motifs/hoxb13.motif
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share/homer/data/knownTFs/motifs/hoxc10.motif
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share/homer/data/knownTFs/motifs/hoxc6.motif
share/homer/data/knownTFs/motifs/hoxc9.motif
share/homer/data/knownTFs/motifs/hoxd10.motif
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share/homer/data/knownTFs/motifs/hoxd12.motif
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share/homer/data/knownTFs/motifs/hsf.motif
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share/homer/data/knownTFs/motifs/in
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share/homer/data/knownTFs/motifs/insects/caudal.motif
share/homer/data/knownTFs/motifs/insects/dHnf4.motif
share/homer/data/knownTFs/motifs/insects/dctcf.motif
share/homer/data/knownTFs/motifs/insects/dl.motif
share/homer/data/knownTFs/motifs/insects/dref.motif
share/homer/data/knownTFs/motifs/insects/ebox.motif
share/homer/data/knownTFs/motifs/insects/gaf.motif
share/homer/data/knownTFs/motifs/insects/ini-nr.motif
share/homer/data/knownTFs/motifs/insects/ini.motif
share/homer/data/knownTFs/motifs/insects/lolai.motif
share/homer/data/knownTFs/motifs/insects/m1bp.motif
share/homer/data/knownTFs/motifs/insects/tata.motif
share/homer/data/knownTFs/motifs/insects/unkprm2.motif
share/homer/data/knownTFs/motifs/insects/unkprm3.motif
share/homer/data/knownTFs/motifs/insects/unkprm4.motif
share/homer/data/knownTFs/motifs/insects/unkprm5.motif
share/homer/data/knownTFs/motifs/insects/unkprm6.motif
share/homer/data/knownTFs/motifs/insects/zelda.motif
share/homer/data/knownTFs/motifs/irf1.motif
share/homer/data/knownTFs/motifs/irf2.motif
share/homer/data/knownTFs/motifs/irf3.motif
share/homer/data/knownTFs/motifs/irf4.motif
share/homer/data/knownTFs/motifs/irf8.motif
share/homer/data/knownTFs/motifs/isl1.motif
share/homer/data/knownTFs/motifs/isre.motif
share/homer/data/knownTFs/motifs/jun-ap1.motif
share/homer/data/knownTFs/motifs/jun-cre.motif
share/homer/data/knownTFs/motifs/junb.motif
share/homer/data/knownTFs/motifs/jund.motif
share/homer/data/knownTFs/motifs/klf1.motif
share/homer/data/knownTFs/motifs/klf10.motif
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share/homer/data/knownTFs/motifs/klf15.motif
share/homer/data/knownTFs/motifs/klf17.motif
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share/homer/data/knownTFs/motifs/klf5.motif
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share/homer/data/knownTFs/motifs/klf9.motif
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share/homer/data/knownTFs/motifs/lhx1.motif
share/homer/data/knownTFs/motifs/lhx2.motif
share/homer/data/knownTFs/motifs/lhx3.motif
share/homer/data/knownTFs/motifs/lhx6.motif
share/homer/data/knownTFs/motifs/lhx9.motif
share/homer/data/knownTFs/motifs/limb.motif
share/homer/data/knownTFs/motifs/lrf.motif
share/homer/data/knownTFs/motifs/lrh1.motif
share/homer/data/knownTFs/motifs/lxre.motif
share/homer/data/knownTFs/motifs/m
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share/homer/data/knownTFs/motifs/mafb.motif
share/homer/data/knownTFs/motifs/mafk.motif
share/homer/data/knownTFs/motifs/max.motif
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share/homer/data/knownTFs/motifs/mef2b.motif
share/homer/data/knownTFs/motifs/mef2c.motif
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share/homer/data/knownTFs/motifs/meirlop/allHomer.jaspar
share/homer/data/knownTFs/motifs/meirlop/allHomer.motifs
share/homer/data/knownTFs/motifs/meirlop/fly.motifs.jaspar
share/homer/data/knownTFs/motifs/meirlop/m
share/homer/data/knownTFs/motifs/meirlop/mm
share/homer/data/knownTFs/motifs/meirlop/motifs.txt
share/homer/data/knownTFs/motifs/meirlop/nonredundant.homer.motifs
share/homer/data/knownTFs/motifs/meirlop/nonredundant.homer.motifs.jaspar
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share/homer/data/knownTFs/motifs/mesp1.motif
share/homer/data/knownTFs/motifs/mitf.motif
share/homer/data/knownTFs/motifs/mixl1.motif
share/homer/data/knownTFs/motifs/mnt.motif
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share/homer/data/knownTFs/motifs/myb.motif
share/homer/data/knownTFs/motifs/myba.motif
share/homer/data/knownTFs/motifs/myf5.motif
share/homer/data/knownTFs/motifs/mynn.motif
share/homer/data/knownTFs/motifs/myod.motif
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share/homer/data/knownTFs/motifs/nanog.motif
share/homer/data/knownTFs/motifs/neurod1.motif
share/homer/data/knownTFs/motifs/neurog2.motif
share/homer/data/knownTFs/motifs/nf1-fox.motif
share/homer/data/knownTFs/motifs/nf1-half.motif
share/homer/data/knownTFs/motifs/nf1.motif
share/homer/data/knownTFs/motifs/nfat-ap1.motif
share/homer/data/knownTFs/motifs/nfatc1.motif
share/homer/data/knownTFs/motifs/nfatc2.motif
share/homer/data/knownTFs/motifs/nfe2.motif
share/homer/data/knownTFs/motifs/nfe2l2.motif
share/homer/data/knownTFs/motifs/nfil3.motif
share/homer/data/knownTFs/motifs/nfkb.motif
share/homer/data/knownTFs/motifs/nfy.motif
share/homer/data/knownTFs/motifs/nkx2.1.motif
share/homer/data/knownTFs/motifs/nkx2.2.motif
share/homer/data/knownTFs/motifs/nkx2.5.motif
share/homer/data/knownTFs/motifs/nkx3.1.motif
share/homer/data/knownTFs/motifs/nkx6.1.motif
share/homer/data/knownTFs/motifs/nmyc.motif
share/homer/data/knownTFs/motifs/npas.motif
share/homer/data/knownTFs/motifs/npas2.motif
share/homer/data/knownTFs/motifs/npas4.motif
share/homer/data/knownTFs/motifs/nr2f6.motif
share/homer/data/knownTFs/motifs/nr5a2.motif
share/homer/data/knownTFs/motifs/nrf.motif
share/homer/data/knownTFs/motifs/nrf1.motif
share/homer/data/knownTFs/motifs/nrf2.motif
share/homer/data/knownTFs/motifs/nur77.motif
share/homer/data/knownTFs/motifs/o
share/homer/data/knownTFs/motifs/oct-oct.motif
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share/homer/data/knownTFs/motifs/oct.ir.motif
share/homer/data/knownTFs/motifs/oct.ir1.motif
share/homer/data/knownTFs/motifs/oct11.motif
share/homer/data/knownTFs/motifs/oct2.motif
share/homer/data/knownTFs/motifs/oct4-sox17.motif
share/homer/data/knownTFs/motifs/oct4-sox2.motif
share/homer/data/knownTFs/motifs/oct4.motif
share/homer/data/knownTFs/motifs/oct6.motif
share/homer/data/knownTFs/motifs/old/hoxa9.motif
share/homer/data/knownTFs/motifs/old/hoxd13.motif
share/homer/data/knownTFs/motifs/old/tcf4.motif
share/homer/data/knownTFs/motifs/olig2.motif
share/homer/data/knownTFs/motifs/otx2.motif
share/homer/data/knownTFs/motifs/p50.motif
share/homer/data/knownTFs/motifs/p52.motif
share/homer/data/knownTFs/motifs/p53-myc.motif
share/homer/data/knownTFs/motifs/p53.motif
share/homer/data/knownTFs/motifs/p53.saos.motif
share/homer/data/knownTFs/motifs/p63.motif
share/homer/data/knownTFs/motifs/p65.motif
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share/homer/data/knownTFs/motifs/pax3-fkhr.motif
share/homer/data/knownTFs/motifs/pax5-short.motif
share/homer/data/knownTFs/motifs/pax5.motif
share/homer/data/knownTFs/motifs/pax6.motif
share/homer/data/knownTFs/motifs/pax7-long.motif
share/homer/data/knownTFs/motifs/pax7-longest.motif
share/homer/data/knownTFs/motifs/pax7.motif
share/homer/data/knownTFs/motifs/pax8.motif
share/homer/data/knownTFs/motifs/pbx1.motif
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share/homer/data/knownTFs/motifs/pdx1.motif
share/homer/data/knownTFs/motifs/pgr.motif
share/homer/data/knownTFs/motifs/phox2a.motif
share/homer/data/knownTFs/motifs/phox2b.motif
share/homer/data/knownTFs/motifs/pit1-long.motif
share/homer/data/knownTFs/motifs/pit1.motif
share/homer/data/knownTFs/motifs/pitx1-ebox.motif
share/homer/data/knownTFs/motifs/pitx1.motif
share/homer/data/knownTFs/motifs/pknox1.motif
share/homer/data/knownTFs/motifs/plants/ABF2.motif
share/homer/data/knownTFs/motifs/plants/ABI5.motif
share/homer/data/knownTFs/motifs/plants/ABR1.motif
share/homer/data/knownTFs/motifs/plants/AGL13.motif
share/homer/data/knownTFs/motifs/plants/AGL15.motif
share/homer/data/knownTFs/motifs/plants/AGL16.motif
share/homer/data/knownTFs/motifs/plants/AGL25.motif
share/homer/data/knownTFs/motifs/plants/AGL6.motif
share/homer/data/knownTFs/motifs/plants/AGL63.motif
share/homer/data/knownTFs/motifs/plants/AGL95.motif
share/homer/data/knownTFs/motifs/plants/AIL7.motif
share/homer/data/knownTFs/motifs/plants/ANAC004.motif
share/homer/data/knownTFs/motifs/plants/ANAC005.motif
share/homer/data/knownTFs/motifs/plants/ANAC011.motif
share/homer/data/knownTFs/motifs/plants/ANAC013.motif
share/homer/data/knownTFs/motifs/plants/ANAC016.motif
share/homer/data/knownTFs/motifs/plants/ANAC017.motif
share/homer/data/knownTFs/motifs/plants/ANAC020.motif
share/homer/data/knownTFs/motifs/plants/ANAC028.motif
share/homer/data/knownTFs/motifs/plants/ANAC038.motif
share/homer/data/knownTFs/motifs/plants/ANAC042.motif
share/homer/data/knownTFs/motifs/plants/ANAC045.motif
share/homer/data/knownTFs/motifs/plants/ANAC046.motif
share/homer/data/knownTFs/motifs/plants/ANAC047.motif
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share/homer/motifs/are.motif
share/homer/motifs/arnt.motif
share/homer/motifs/ascl1.motif
share/homer/motifs/ascl2.motif
share/homer/motifs/atf1.motif
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share/homer/motifs/atf7.motif
share/homer/motifs/atoh1.motif
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share/homer/motifs/bach1.motif
share/homer/motifs/bach2.motif
share/homer/motifs/banp.motif
share/homer/motifs/bapx1.motif
share/homer/motifs/barx1.motif
share/homer/motifs/batf.motif
share/homer/motifs/batf3-irf8.motif
share/homer/motifs/bcl11a.motif
share/homer/motifs/bcl6.motif
share/homer/motifs/bhlha15.motif
share/homer/motifs/bhlhe40.motif
share/homer/motifs/bhlhe41.motif
share/homer/motifs/bmal.motif
share/homer/motifs/bmyb.motif
share/homer/motifs/boris.motif
share/homer/motifs/brachyury.motif
share/homer/motifs/brn1.motif
share/homer/motifs/brn2.motif
share/homer/motifs/bzip-irf.motif
share/homer/motifs/cMyc.lncap.motif
share/homer/motifs/cdx2.motif
share/homer/motifs/cdx4.motif
share/homer/motifs/cebp-ap1.motif
share/homer/motifs/cebp-cebp.motif
share/homer/motifs/cebp.motif
share/homer/motifs/chop.motif
share/homer/motifs/chr.motif
share/homer/motifs/clock.motif
share/homer/motifs/cmyc.motif
share/homer/motifs/core/cTATA.motif
share/homer/motifs/core/dpr.motif
share/homer/motifs/core/hInr.motif
share/homer/motifs/core/hTCT.motif
share/homer/motifs/core/inr.motif
share/homer/motifs/core/tata.motif
share/homer/motifs/couptf1.motif
share/homer/motifs/couptf2.motif
share/homer/motifs/crap/a.repeat.motif
share/homer/motifs/crap/aare.motif
share/homer/motifs/crap/c.repeat.motif
share/homer/motifs/crap/ca.bias.motif
share/homer/motifs/crap/ca.repeat.motif
share/homer/motifs/crap/cg.bias.motif
share/homer/motifs/crap/cg.repeat.motif
share/homer/motifs/crap/ga.bias.motif
share/homer/motifs/crap/ga.repeat.motif
share/homer/motifs/crap/gca.repeat.motif
share/homer/motifs/crap/ta.bias.motif
share/homer/motifs/crap/ta.repeat.motif
share/homer/motifs/cre.motif
share/homer/motifs/creb5.motif
share/homer/motifs/crx.motif
share/homer/motifs/ctcf-mys.motif
share/homer/motifs/ctcf.motif
share/homer/motifs/cux1.motif
share/homer/motifs/cux2.motif
share/homer/motifs/dlx1.motif
share/homer/motifs/dlx2.motif
share/homer/motifs/dlx3.motif
share/homer/motifs/dlx5.motif
share/homer/motifs/dmc1.motif
share/homer/motifs/dmrt1.motif
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share/homer/motifs/dr0.motif
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share/homer/motifs/dux.motif
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share/homer/motifs/duxbl.motif
share/homer/motifs/e2a.motif
share/homer/motifs/e2f.motif
share/homer/motifs/e2f1.motif
share/homer/motifs/e2f3.motif
share/homer/motifs/e2f4.motif
share/homer/motifs/e2f6.motif
share/homer/motifs/e2f7.motif
share/homer/motifs/e47.motif
share/homer/motifs/ebf-old.motif
share/homer/motifs/ebf.motif
share/homer/motifs/ebf2.motif
share/homer/motifs/ebna1.motif
share/homer/motifs/ebox.motif
share/homer/motifs/egr1.motif
share/homer/motifs/egr2.motif
share/homer/motifs/ehf.motif
share/homer/motifs/eklf.motif
share/homer/motifs/elf1.motif
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share/homer/motifs/elf4.motif
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share/homer/motifs/elk1.motif
share/homer/motifs/elk4.motif
share/homer/motifs/emx2.motif
share/homer/motifs/en1.motif
share/homer/motifs/eomes.motif
share/homer/motifs/erb.motif
share/homer/motifs/ere.motif
share/homer/motifs/erg.motif
share/homer/motifs/erra.motif
share/homer/motifs/errg.motif
share/homer/motifs/esrrb.motif
share/homer/motifs/ets-distal.motif
share/homer/motifs/ets-ebox.motif
share/homer/motifs/ets-runx.motif
share/homer/motifs/ets.motif
share/homer/motifs/ets1.motif
share/homer/motifs/etv1.motif
share/homer/motifs/etv2.motif
share/homer/motifs/etv4.motif
share/homer/motifs/ews-erg.motif
share/homer/motifs/ews-fli1.motif
share/homer/motifs/extras/createMotifTable.pl
share/homer/motifs/extras/motifTable.txt
share/homer/motifs/extras/motifs2symbol.txt
share/homer/motifs/extras/notes.txt
share/homer/motifs/extras/symbol2motifFile.txt
share/homer/motifs/fli.motif
share/homer/motifs/fos.motif
share/homer/motifs/fosl2.motif
share/homer/motifs/fox-ebox.motif
share/homer/motifs/foxa1.lncap.motif
share/homer/motifs/foxa1.mcf7.motif
share/homer/motifs/foxa2.motif
share/homer/motifs/foxa3.motif
share/homer/motifs/foxd3.motif
share/homer/motifs/foxf1.motif
share/homer/motifs/foxh1.motif
share/homer/motifs/foxk1.motif
share/homer/motifs/foxk2.motif
share/homer/motifs/foxl2.motif
share/homer/motifs/foxm1.motif
share/homer/motifs/foxo1.motif
share/homer/motifs/foxo3.motif
share/homer/motifs/foxp1.motif
share/homer/motifs/fra1.motif
share/homer/motifs/fra2.motif
share/homer/motifs/fxr.er2.motif
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share/homer/motifs/gabp.motif
share/homer/motifs/gata-scl.motif
share/homer/motifs/gata.motif
share/homer/motifs/gata2.motif
share/homer/motifs/gata3.dr4.motif
share/homer/motifs/gata3.dr8.motif
share/homer/motifs/gata3.ir3.motif
share/homer/motifs/gata3.ir4.motif
share/homer/motifs/gata3.motif
share/homer/motifs/gata4.motif
share/homer/motifs/gata6.motif
share/homer/motifs/gfi1b.motif
share/homer/motifs/gfx.motif
share/homer/motifs/gfy-staf.motif
share/homer/motifs/gfy.motif
share/homer/motifs/gli.motif
share/homer/motifs/gli2.motif
share/homer/motifs/gli3.motif
share/homer/motifs/glis3.motif
share/homer/motifs/gre-raw.motif
share/homer/motifs/gre.motif
share/homer/motifs/grhl2.motif
share/homer/motifs/groups/Tal1.motif
share/homer/motifs/groups/all.motifs
share/homer/motifs/groups/amy.motifs
share/homer/motifs/groups/cd4.motifs
share/homer/motifs/groups/dnase.motifs
share/homer/motifs/groups/enhancer.motifs
share/homer/motifs/groups/es.motifs
share/homer/motifs/groups/id2.motifs
share/homer/motifs/groups/ik1.motif
share/homer/motifs/groups/inflammatory.motifs
share/homer/motifs/groups/ivan.motifs
share/homer/motifs/groups/ivan2.motifs
share/homer/motifs/groups/liver.motifs
share/homer/motifs/groups/pol2-cd4.motifs
share/homer/motifs/groups/promoter.motifs
share/homer/motifs/groups/sven.motifs
share/homer/motifs/groups/yin.motifs
share/homer/motifs/gsc.motif
share/homer/motifs/gsx2.motif
share/homer/motifs/hand2.motif
share/homer/motifs/heb.motif
share/homer/motifs/hic1.motif
share/homer/motifs/hif1a.motif
share/homer/motifs/hif1b.motif
share/homer/motifs/hif2a.motif
share/homer/motifs/hinfp.motif
share/homer/motifs/hlf.motif
share/homer/motifs/hnf1.motif
share/homer/motifs/hnf1b.motif
share/homer/motifs/hnf4.motif
share/homer/motifs/hnf6.motif
share/homer/motifs/hnf6b.motif
share/homer/motifs/hoxa1.motif
share/homer/motifs/hoxa10.motif
share/homer/motifs/hoxa11.motif
share/homer/motifs/hoxa13.motif
share/homer/motifs/hoxa2.motif
share/homer/motifs/hoxa3.motif
share/homer/motifs/hoxa9.motif
share/homer/motifs/hoxb13.motif
share/homer/motifs/hoxb4.motif
share/homer/motifs/hoxc10.motif
share/homer/motifs/hoxc13.motif
share/homer/motifs/hoxc6.motif
share/homer/motifs/hoxc9.motif
share/homer/motifs/hoxd10.motif
share/homer/motifs/hoxd11.motif
share/homer/motifs/hoxd12.motif
share/homer/motifs/hoxd13.motif
share/homer/motifs/hoxd9.motif
share/homer/motifs/hsf.motif
share/homer/motifs/hsf1.motif
share/homer/motifs/insects/bcd.motif
share/homer/motifs/insects/caudal.motif
share/homer/motifs/insects/dHnf4.motif
share/homer/motifs/insects/dctcf.motif
share/homer/motifs/insects/dl.motif
share/homer/motifs/insects/dref.motif
share/homer/motifs/insects/ebox.motif
share/homer/motifs/insects/gaf.motif
share/homer/motifs/insects/ini-nr.motif
share/homer/motifs/insects/ini.motif
share/homer/motifs/insects/lolai.motif
share/homer/motifs/insects/m1bp.motif
share/homer/motifs/insects/tata.motif
share/homer/motifs/insects/unkprm2.motif
share/homer/motifs/insects/unkprm3.motif
share/homer/motifs/insects/unkprm4.motif
share/homer/motifs/insects/unkprm5.motif
share/homer/motifs/insects/unkprm6.motif
share/homer/motifs/insects/zelda.motif
share/homer/motifs/irf1.motif
share/homer/motifs/irf2.motif
share/homer/motifs/irf3.motif
share/homer/motifs/irf4.motif
share/homer/motifs/irf8.motif
share/homer/motifs/isl1.motif
share/homer/motifs/isre.motif
share/homer/motifs/jun-ap1.motif
share/homer/motifs/jun-cre.motif
share/homer/motifs/junb.motif
share/homer/motifs/jund.motif
share/homer/motifs/klf1.motif
share/homer/motifs/klf10.motif
share/homer/motifs/klf14.motif
share/homer/motifs/klf15.motif
share/homer/motifs/klf17.motif
share/homer/motifs/klf3.motif
share/homer/motifs/klf4.motif
share/homer/motifs/klf5.motif
share/homer/motifs/klf6.motif
share/homer/motifs/klf9.motif
share/homer/motifs/lef1.motif
share/homer/motifs/lhx1.motif
share/homer/motifs/lhx2.motif
share/homer/motifs/lhx3.motif
share/homer/motifs/lhx6.motif
share/homer/motifs/lhx9.motif
share/homer/motifs/limb.motif
share/homer/motifs/lrf.motif
share/homer/motifs/lrh1.motif
share/homer/motifs/lxre.motif
share/homer/motifs/m
share/homer/motifs/mafF.motif
share/homer/motifs/mafa.motif
share/homer/motifs/mafb.motif
share/homer/motifs/mafk.motif
share/homer/motifs/max.motif
share/homer/motifs/maz.motif
share/homer/motifs/mef2a.motif
share/homer/motifs/mef2b.motif
share/homer/motifs/mef2c.motif
share/homer/motifs/mef2d.motif
share/homer/motifs/meirlop/allHomer.jaspar
share/homer/motifs/meirlop/allHomer.motifs
share/homer/motifs/meirlop/fly.motifs.jaspar
share/homer/motifs/meirlop/m
share/homer/motifs/meirlop/mm
share/homer/motifs/meirlop/motifs.txt
share/homer/motifs/meirlop/nonredundant.homer.motifs
share/homer/motifs/meirlop/nonredundant.homer.motifs.jaspar
share/homer/motifs/meirlop/nonredundant.homer.motifs.v2.jaspar
share/homer/motifs/meis1.motif
share/homer/motifs/mesp1.motif
share/homer/motifs/mitf.motif
share/homer/motifs/mixl1.motif
share/homer/motifs/mnt.motif
share/homer/motifs/mre.motif
share/homer/motifs/myb.motif
share/homer/motifs/myba.motif
share/homer/motifs/myf5.motif
share/homer/motifs/mynn.motif
share/homer/motifs/myod.motif
share/homer/motifs/myog.motif
share/homer/motifs/myrf.motif
share/homer/motifs/nanog.motif
share/homer/motifs/neurod1.motif
share/homer/motifs/neurog2.motif
share/homer/motifs/nf1-fox.motif
share/homer/motifs/nf1-half.motif
share/homer/motifs/nf1.motif
share/homer/motifs/nfat-ap1.motif
share/homer/motifs/nfatc1.motif
share/homer/motifs/nfatc2.motif
share/homer/motifs/nfe2.motif
share/homer/motifs/nfe2l2.motif
share/homer/motifs/nfil3.motif
share/homer/motifs/nfkb.motif
share/homer/motifs/nfy.motif
share/homer/motifs/nkx2.1.motif
share/homer/motifs/nkx2.2.motif
share/homer/motifs/nkx2.5.motif
share/homer/motifs/nkx3.1.motif
share/homer/motifs/nkx6.1.motif
share/homer/motifs/nmyc.motif
share/homer/motifs/npas.motif
share/homer/motifs/npas2.motif
share/homer/motifs/npas4.motif
share/homer/motifs/nr2f6.motif
share/homer/motifs/nr5a2.motif
share/homer/motifs/nrf.motif
share/homer/motifs/nrf1.motif
share/homer/motifs/nrf2.motif
share/homer/motifs/nur77.motif
share/homer/motifs/oct-oct.motif
share/homer/motifs/oct-oct.short.motif
share/homer/motifs/oct.ir.motif
share/homer/motifs/oct.ir1.motif
share/homer/motifs/oct11.motif
share/homer/motifs/oct2.motif
share/homer/motifs/oct4-sox17.motif
share/homer/motifs/oct4-sox2.motif
share/homer/motifs/oct4.motif
share/homer/motifs/oct6.motif
share/homer/motifs/old/hoxa9.motif
share/homer/motifs/old/hoxd13.motif
share/homer/motifs/old/tcf4.motif
share/homer/motifs/olig2.motif
share/homer/motifs/otx2.motif
share/homer/motifs/p50.motif
share/homer/motifs/p52.motif
share/homer/motifs/p53-myc.motif
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share/homer/motifs/p63.motif
share/homer/motifs/p65.motif
share/homer/motifs/p73.motif
share/homer/motifs/pax3-fkhr.motif
share/homer/motifs/pax5-short.motif
share/homer/motifs/pax5.motif
share/homer/motifs/pax6.motif
share/homer/motifs/pax7-long.motif
share/homer/motifs/pax7-longest.motif
share/homer/motifs/pax7.motif
share/homer/motifs/pax8.motif
share/homer/motifs/pbx1.motif
share/homer/motifs/pbx2.motif
share/homer/motifs/pbx3.motif
share/homer/motifs/pdx1.motif
share/homer/motifs/pgr.motif
share/homer/motifs/phox2a.motif
share/homer/motifs/phox2b.motif
share/homer/motifs/pit1-long.motif
share/homer/motifs/pit1.motif
share/homer/motifs/pitx1-ebox.motif
share/homer/motifs/pitx1.motif
share/homer/motifs/pknox1.motif
share/homer/motifs/plants/ABF2.motif
share/homer/motifs/plants/ABI5.motif
share/homer/motifs/plants/ABR1.motif
share/homer/motifs/plants/AGL13.motif
share/homer/motifs/plants/AGL15.motif
share/homer/motifs/plants/AGL16.motif
share/homer/motifs/plants/AGL25.motif
share/homer/motifs/plants/AGL6.motif
share/homer/motifs/plants/AGL63.motif
share/homer/motifs/plants/AGL95.motif
share/homer/motifs/plants/AIL7.motif
share/homer/motifs/plants/ANAC004.motif
share/homer/motifs/plants/ANAC005.motif
share/homer/motifs/plants/ANAC011.motif
share/homer/motifs/plants/ANAC013.motif
share/homer/motifs/plants/ANAC016.motif
share/homer/motifs/plants/ANAC017.motif
share/homer/motifs/plants/ANAC020.motif
share/homer/motifs/plants/ANAC028.motif
share/homer/motifs/plants/ANAC038.motif
share/homer/motifs/plants/ANAC042.motif
share/homer/motifs/plants/ANAC045.motif
share/homer/motifs/plants/ANAC046.motif
share/homer/motifs/plants/ANAC047.motif
share/homer/motifs/plants/ANAC050.motif
share/homer/motifs/plants/ANAC053.motif
share/homer/motifs/plants/ANAC057.motif
share/homer/motifs/plants/ANAC058.motif
share/homer/motifs/plants/ANAC062.motif
share/homer/motifs/plants/ANAC070.motif
share/homer/motifs/plants/ANAC071.motif
share/homer/motifs/plants/ANAC075.motif
share/homer/motifs/plants/ANAC079.motif
share/homer/motifs/plants/ANAC083.motif
share/homer/motifs/plants/ANAC087.motif
share/homer/motifs/plants/ANAC092.motif
share/homer/motifs/plants/ANAC094.motif
share/homer/motifs/plants/ANAC096.motif
share/homer/motifs/plants/ANAC103.motif
share/homer/motifs/plants/ANL2.motif
share/homer/motifs/plants/AREB3.motif
share/homer/motifs/plants/ARF16.motif
share/homer/motifs/plants/ARF2.motif
share/homer/motifs/plants/AS2.motif
share/homer/motifs/plants/ASHR1.motif
share/homer/motifs/plants/ASL18.motif
share/homer/motifs/plants/AT1G01250.motif
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share/homer/motifs/plants/AT1G19040.motif
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share/homer/motifs/plants/AT1G24250.motif
share/homer/motifs/plants/AT1G28160.motif
share/homer/motifs/plants/AT1G44830.motif
share/homer/motifs/plants/AT1G47655.motif
share/homer/motifs/plants/AT1G49560.motif
share/homer/motifs/plants/AT1G69570.motif
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share/homer/motifs/plants/AT1G76870.motif
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share/homer/motifs/plants/AT1G77200.motif
share/homer/motifs/plants/AT2G01818.motif
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share/homer/motifs/plants/AT3G09735.motif
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share/homer/motifs/plants/AT3G25990.motif
share/homer/motifs/plants/AT3G42860.motif
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share/homer/motifs/plants/AT3G52440.motif
share/homer/motifs/plants/AT3G57600.motif
share/homer/motifs/plants/AT3G58630.motif
share/homer/motifs/plants/AT3G60490.motif
share/homer/motifs/plants/AT4G00250.motif
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share/homer/motifs/plants/AT4G18450.motif
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share/homer/motifs/plants/AT5G02460.motif
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share/homer/update/motifs/oRNAment/PWMs/conv.sh
share/homer/update/motifs/oRNAment/RBP_id_encoding.csv
share/homer/update/motifs/oRNAment/notes.txt
share/homer/update/motifs/oRNAment/ornament.motif
share/homer/update/motifs/oRNAment/parse_oRNAment.pl
share/homer/update/motifs/parseAthaMap.pl
share/homer/update/motifs/parseJasparMatrix.pl
share/homer/update/motifs/parseStromoMotifs.pl
share/homer/update/motifs/plants/athaMap.motifs
share/homer/update/motifs/plants/athamap.table.txt
share/homer/update/motifs/plants/jaspar.motifs
share/homer/update/motifs/ready2Homer.pl
share/homer/update/motifs/rna-hughes/parseHughesRNA.pl
share/homer/update/motifs/rna-hughes/rna.motifs
share/homer/update/motifs/rna-hughes/table.txt
share/homer/update/motifs/transfac2homer.pl
share/homer/update/motifs/vertebrates/jaspar.motifs
share/homer/update/motifs/vertebrates/vert.extra.jaspar.motifs
share/homer/update/motifs/worms/hlh.jaspar.motifs
share/homer/update/motifs/worms/jaspar.motifs
share/homer/update/motifs/worms/jaspar.worms.motifs
share/homer/update/motifs/worms/matrix_only.txt
share/homer/update/motifs/yeast/harbison.yeast.motifs
share/homer/update/motifs/yeast/jaspar.motifs
share/homer/update/motifs/yeast/macIssac.yeast.motifs
share/homer/update/promoters/fasta2tabMrna.pl
share/homer/update/promoters/getRedunMrna.pl
share/homer/update/promoters/parseUTRs.pl
share/homer/update/taxids.tsv
share/homer/update/ucsc.txt
share/homer/update/updateGeneIdentifiers.pl
share/homer/update/updateMotifFiles.pl
share/homer/update/updateMotifScanningTracks.pl
share/homer/update/updatePromoters.pl
share/homer/update/updateUCSCGenomeAnnotations.pl
share/homer/update/utils/cons2fasta.pl
share/homer/update/utils/downloadConservation.pl
share/homer/update/utils/downloadRepeats.pl
share/homer/update/utils/getSpliceJunc.pl
share/homer/update/utils/parseExons.pl
share/homer/update/utils/refGene2pos.pl
share/homer/update/utils/refseq2pos.pl
share/homer/update/utils/removeChrNameSpaces.pl
