**************************************************************************************************************************************************************************************************** MOTIFSIM - Motif Similarity Detection Tool Version 2.1 **************************************************************************************************************************************************************************************************** INPUT **************************************************************************************************************************************************************************************************** Input Parameters Number of files: 5 Number of top significant motifs: 10 Number of best matches: 10 Similarity cutoff: >= 0.75 Matching motif database: UniProbe Mus Musculus Phylogenetic tree: Yes Combined similar motifs: Yes Output file type: All Output file format: All Input files and motif counts File name Count of motifs Dataset # MEME-ChIP_DM05.txt 4 1 MEME_DM05.txt 46 2 PScanChIP_DM05.txt 16 3 RSAT_peak-motifs_DM05.txt 17 4 W-ChIPMotifs_DM05.txt 11 5 **************************************************************************************************************************************************************************************************** RESULTS **************************************************************************************************************************************************************************************************** ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 55 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ZEB1 Motif 1 Original Motif Original Motif CACCTD YGCCACCTDSTGGY YGCCACCTDSTGGY Direction: Forward Position #: 4 Overlap #: 6 Alignment: ---CACCTD----- YGCCACCTDSTGGY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 9 Combined Motif Original Motif Reverse Complement YGCCACCTDSTGGY GAKAGKTGGCTCWG YGCCACCKAGWGGTGGCTCWG Direction: Forward Position #: 8 Overlap #: 7 Alignment: YGCCACCTDSTGGY------- -------GAKAGKTGGCTCWG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CTCF Reverse Complement Reverse Complement CWGAGCCACCWCTRGGTGGCK BMSMGCCYMCTKSTGGMHM CWGMGCCMCCTBBWGGYGGCK Direction: Forward Position #: 1 Overlap #: 19 Alignment: CWGAGCCACCWCTRGGTGGCK BMSMGCCYMCTKSTGGMHM-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RORA_1 Combined Motif Reverse Complement Reverse Complement YGCCMCCWBBAGGYGGCYCWG TGACCTDVWT YGYGACCTBBAKGYGGCYCWG Direction: Forward Position #: 3 Overlap #: 10 Alignment: YGCCMCCWBBAGGYGGCYCWG --TGACCTDVWT--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Original Motif CWGMGCCMCYTBVAGGTCMCK TTCAGCACCATGGACAGCKCC TTCAGMRCCHYSKACAGSTCMCK Direction: Forward Position #: 3 Overlap #: 19 Alignment: --CWGMGCCMCYTBVAGGTCMCK TTCAGCACCATGGACAGCKCC-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Esrrb Original Motif Original Motif TTCAGMRCCHYSKACAGSTCMCK VBBYCAAGGTCA VBBTCARGGYCAYSKACAGSTCMCK Direction: Forward Position #: 3 Overlap #: 10 Alignment: --TTCAGMRCCHYSKACAGSTCMCK VBBYCAAGGTCA------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR1H2RXRA Original Motif Original Motif VBBTCARGGYCAYSKACAGSTCMCK AAAGGTCAAAGGTCAAC AAAGGTCMAAGGTCAHSKACAGSTCMCK Direction: Forward Position #: 4 Overlap #: 14 Alignment: ---VBBTCARGGYCAYSKACAGSTCMCK AAAGGTCAAAGGTCAAC----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 84 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFW3 TgTGgTGTCACAGTGCTCC Reverse Complement Original Motif CAGTGC TGTGGTGTCACAGTGCTCC ACAGTGCTCCSRKKKCTGT Direction: Backward Position #: 11 Overlap #: 6 Alignment: ---CAGTGC---------- TGTGGTGTCACAGTGCTCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Original Motif Original Motif ACAGTGCTCCSRKKKCTGT CACTGTGRTRTCACAGTGSWSCACT CACWGTGVTVYCAYWGYKSTSCACT Direction: Forward Position #: 2 Overlap #: 19 Alignment: -ACAGTGCTCCSRKKKCTGT----- CACTGTGRTRTCACAGTGSWSCACT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TGGAGCACTGTGACAcCACAGTGg Original Motif Reverse Complement CACWGTGVTVYCAYWGYKSTSCACT CCACTGTGVTGTCACAGTGCTCCA CCACTGTGVTGTCACAGTGCTCCACT Direction: Forward Position #: 2 Overlap #: 23 Alignment: -CACWGTGVTVYCAYWGYKSTSCACT CCACTGTGVTGTCACAGTGCTCCA-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CAcCACAGTGGAGCAct Reverse Complement Reverse Complement AGTGGAGCACTGTGACAVCACAGTGG AGTGCTCCACTGTGDTG AGTGSWSCACTGTGVYRVCACAGTGG Direction: Forward Position #: 1 Overlap #: 17 Alignment: AGTGGAGCACTGTGACAVCACAGTGG AGTGCTCCACTGTGDTG--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CagTGCTCCACTGTGgT Original Motif Original Motif AGTGSWSCACTGTGVYRVCACAGTGG CAGTGCTCCACTGTGBT CAGTGCTCCACTGTGVTRVCACAGTGG Direction: Forward Position #: 2 Overlap #: 16 Alignment: -AGTGSWSCACTGTGVYRVCACAGTGG CAGTGCTCCACTGTGBT---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif AgTGCTCCACTGTGgTGTCACAgT Original Motif Reverse Complement CAGTGCTCCACTGTGVTRVCACAGTGG ACTGTGACACCACAGTGGAGCACT ACYRKKRCWCCACWGTGGWGCMMYAGTGG Direction: Forward Position #: 3 Overlap #: 22 Alignment: --CAGTGCTCCACTGTGVTRVCACAGTGG ACTGTGACACCACAGTGGAGCACT----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Reverse Complement CCACTKYYGCWCCACWGTGGWGKYRMMGT GGYGCTGTCCATGGTGCTGAA TGCTGAAGVHVCWSTSYRBKGCCACTKYYGCWCCAC Direction: Backward Position #: 8 Overlap #: 14 Alignment: CCACTKYYGCWCCACWGTGGWGKYRMMGT------- ---------------GGYGCTGTCCATGGTGCTGAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Tcfcp2l1 Reverse Complement Reverse Complement GTGGWGCMMYAGTGGCYBMKSASWGVHVCTTCAGCA CKGGDTBDMMCTGG STGGDKBVMHMKKGGCYBMKSASWGVHVCTTCAGCA Direction: Forward Position #: 1 Overlap #: 14 Alignment: GTGGWGCMMYAGTGGCYBMKSASWGVHVCTTCAGCA CKGGDTBDMMCTGG---------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 9 Combined Motif Reverse Complement Original Motif TGCTGAAGVHVCWSTSYRBKGCCRYRDYBBYDCCAS CWGAGCCAYCTYTC TGCTGAGSCABCTCTCYRBKGCCRYRDYBBYDCCAS Direction: Forward Position #: 3 Overlap #: 14 Alignment: TGCTGAAGVHVCWSTSYRBKGCCRYRDYBBYDCCAS --CWGAGCCAYCTYTC-------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- wwCCAmAGTCmt Combined Motif Reverse Complement Original Motif STGGDKBVMHMKKGGCYBMKGAGAGBTGSCTCAGCA DDCCAMAGTCHB STGGDDCCAMAGTSVCYBMKGAGAGBTGSCTCAGCA Direction: Forward Position #: 5 Overlap #: 12 Alignment: STGGDKBVMHMKKGGCYBMKGAGAGBTGSCTCAGCA ----DDCCAMAGTCHB-------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 85 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFW1 Motif 25 Original Motif Reverse Complement TTGCGCAA TTYGGAAAGCAG KWRMGCARTTYG Direction: Backward Position #: 1 Overlap #: 8 Alignment: ----TTGCGCAA TTYGGAAAGCAG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR2F1 Combined Motif Original Motif Original Motif KWRMGCARTTYG TGAMCTTTGMMCYT TTYGTDAMSYWDTGAMCT Direction: Backward Position #: 5 Overlap #: 8 Alignment: ------KWRMGCARTTYG ----TGAMCTTTGMMCYT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Reverse Complement Original Motif AGRTCADWKSYTHACKAA BTRGGDCARAGGKCA BTAGGTCARAGGYYAACKAA Direction: Forward Position #: 3 Overlap #: 13 Alignment: --AGRTCADWKSYTHACKAA BTRGGDCARAGGKCA----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 32 Original Motif Reverse Complement BTAGGTCARAGGYYAACKAA TTTACTAAAT ATKKTACWMDBTAGGTCARAGG Direction: Backward Position #: 3 Overlap #: 8 Alignment: BTAGGTCARAGGYYAACKAA-- ------------TTTACTAAAT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CAcCACAGTGGAGCAct Combined Motif Original Motif Original Motif ATKKTACWMDBTAGGTCARAGG CAHCACAGTGGAGCACT ATKYWHCACAGTRGRKCAVWGG Direction: Forward Position #: 4 Overlap #: 17 Alignment: ATKKTACWMDBTAGGTCARAGG ---CAHCACAGTGGAGCACT-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TGGAGCACTGTGACAcCACAGTGg Reverse Complement Reverse Complement CCWVTGYKCMACTGTGHWKRAT CCACTGTGVTGTCACAGTGCTCCA CCACYDTKGTKYCACWGTGCTBVAT Direction: Forward Position #: 4 Overlap #: 21 Alignment: ---CCWVTGYKCMACTGTGHWKRAT CCACTGTGVTGTCACAGTGCTCCA- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif AgTGCTCCACTGTGgTGTCACAgT Reverse Complement Original Motif ATVBAGCACWGTGMYACRAHMGTGG AGTGCTCCACTGTGGTGTCACAGT ARTGCWSCACTGTGVTRYVACAGTGG Direction: Forward Position #: 2 Overlap #: 23 Alignment: -ATVBAGCACWGTGMYACRAHMGTGG AGTGCTCCACTGTGGTGTCACAGT-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CagTGCTCCACTGTGgT Original Motif Original Motif ARTGCWSCACTGTGVTRYVACAGTGG CAGTGCTCCACTGTGBT CARTGCTCCACTGTGVTRYVACAGTGG Direction: Forward Position #: 2 Overlap #: 16 Alignment: -ARTGCWSCACTGTGVTRYVACAGTGG CAGTGCTCCACTGTGBT---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 83 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- srACyCCGAyr TFM11 Reverse Complement Reverse Complement KKTCGGKGTKS TGTGTGDKTGTGTGTGTRTG GTGTRTGKKTSGGTGTGBTG Direction: Backward Position #: 8 Overlap #: 11 Alignment: --KKTCGGKGTKS------- TGTGTGDKTGTGTGTGTRTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR1 Original Motif Reverse Complement GTGTRTGKKTSGGTGTGBTG MGGTCAGGGTGACCTRDBHV MGGTSWGKGTGWCBKDGTBBTG Direction: Forward Position #: 3 Overlap #: 18 Alignment: --GTGTRTGKKTSGGTGTGBTG MGGTCAGGGTGACCTRDBHV-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFM1 Original Motif Reverse Complement MGGTSWGKGTGWCBKDGTBBTG TGTGTGWGTGTGTGTGTG TVKGTSWGTGTGTSTGTGTBBTG Direction: Forward Position #: 2 Overlap #: 17 Alignment: -MGGTSWGKGTGWCBKDGTBBTG TGTGTGWGTGTGTGTGTG----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TGGAGCACTGTGACAcCACAGTGg Reverse Complement Original Motif CABBACACASACACACWSACRBA TGGAGCACTGTGACAVCACAGTGG TGGAGCACTGTGACAVCACAGTRSACASACACACWSACRBA Direction: Forward Position #: 19 Overlap #: 6 Alignment: ------------------CABBACACASACACACWSACRBA TGGAGCACTGTGACAVCACAGTGG----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR2 Reverse Complement Original Motif TVKGTSWGTGTGTSTGTSMACTGTGVTGTCACAGTGCTCCA VHRGGTCABDBTGMCCTB VTRKGTCABDGTGWCYBDSMACTGTGVTGTCACAGTGCTCCA Direction: Forward Position #: 2 Overlap #: 17 Alignment: -TVKGTSWGTGTGTSTGTSMACTGTGVTGTCACAGTGCTCCA VHRGGTCABDBTGMCCTB------------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TgTGgTGTCACAGTGCTCC Original Motif Original Motif VTRKGTCABDGTGWCYBDSMACTGTGVTGTCACAGTGCTCCA TGTGGTGTCACAGTGCTCC TGYKGTGTCACWGTGYYCBDSMACTGTGVTGTCACAGTGCTCCA Direction: Forward Position #: 3 Overlap #: 17 Alignment: --VTRKGTCABDGTGWCYBDSMACTGTGVTGTCACAGTGCTCCA TGTGGTGTCACAGTGCTCC------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 10 Reverse Complement Reverse Complement TGGAGCACTGTGACAVCACAGTRSDBGMKCACWGTGACACYMCA TGTGTSWGTBTSTG TGTGKADSWCTGTGACAVCACAGTRSDBGMKCACWGTGACACYMCA Direction: Forward Position #: 3 Overlap #: 12 Alignment: --TGGAGCACTGTGACAVCACAGTRSDBGMKCACWGTGACACYMCA TGTGTSWGTBTSTG-------------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CACTGTGrYrtCACAGTGswsCAcT Combined Motif Reverse Complement Original Motif TGYKGTGTCACWGTGYYCBDSMACTGTGVTGTCACAGWSHTRCACA CACTGTGRTRTCACAGTGSWSCACT TGYKGTGTCACASTGTKVYDBCACWGTGSTGYMMYAGWSHTRCACA Direction: Forward Position #: 11 Overlap #: 25 Alignment: TGYKGTGTCACWGTGYYCBDSMACTGTGVTGTCACAGWSHTRCACA ----------CACTGTGRTRTCACAGTGSWSCACT----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- REST Combined Motif Reverse Complement Original Motif TGTGKADSWCTMYYMCASCACWGTGVHMVYACASTGTGACACYMCA TTCAGCACCATGGACAGCKCC TGTGKADSWCTMYYHCAGCACHDTGGACAGMBMCTGTGACACYMCA Direction: Forward Position #: 14 Overlap #: 21 Alignment: TGTGKADSWCTMYYMCASCACWGTGVHMVYACASTGTGACACYMCA -------------TTCAGCACCATGGACAGCKCC------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 6 Combined Motif Reverse Complement Original Motif TGYKGTGTCACAGYBRCTGTCCAHDGTGCTGHMMYAGWSHTRCACA ACACACACACACAC TGYKGTGWCACACHBRCDSWCCAHDGTGCTGHMMYAGWSHTRCACA Direction: Forward Position #: 8 Overlap #: 14 Alignment: TGYKGTGTCACAGYBRCTGTCCAHDGTGCTGHMMYAGWSHTRCACA -------ACACACACACACAC------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 87 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFF1 HNF4A Reverse Complement Reverse Complement VVTCTTTGTCCT TGMYCTTTGBCCK TGVYCTTTGBCCT Direction: Forward Position #: 2 Overlap #: 12 Alignment: -VVTCTTTGTCCT TGMYCTTTGBCCK ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Original Motif Reverse Complement TGVYCTTTGBCCT TGRCCTKTGHCCKAB TKVHCYTTKBCCYKAB Direction: Forward Position #: 2 Overlap #: 12 Alignment: TGVYCTTTGBCCT--- -TGRCCTKTGHCCKAB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Reverse Complement Original Motif BTRKGGBRAAKGHVRA VHRGGTCABDBTGMCCTB BHDDGGTCAVDGTGVMCTB Direction: Forward Position #: 2 Overlap #: 15 Alignment: BTRKGGBRAAKGHVRA--- -VHRGGTCABDBTGMCCTB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Original Motif Reverse Complement BHDDGGTCAVDGTGVMCTB MGGTCAGGGTGACCTRDBHV BHDVGGTCAVGGTGACCTVDBHV Direction: Forward Position #: 4 Overlap #: 16 Alignment: BHDDGGTCAVDGTGVMCTB---- ---MGGTCAGGGTGACCTRDBHV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM12 Combined Motif Original Motif Reverse Complement BHDVGGTCAVGGTGACCTVDBHV VCTSTGKSCMKBCTRCYCTK VCWVKGBCMVKBYDRCCHDBBHV Direction: Forward Position #: 1 Overlap #: 20 Alignment: BHDVGGTCAVGGTGACCTVDBHV VCTSTGKSCMKBCTRCYCTK--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR2F1 Combined Motif Original Motif Reverse Complement VCWVKGBCMVKBYDRCCHDBBHV AKGYYCAAAGRTCA VCWVKGYBMADVGRDCMHDBBHV Direction: Forward Position #: 4 Overlap #: 14 Alignment: VCWVKGBCMVKBYDRCCHDBBHV ---AKGYYCAAAGRTCA------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR1H2RXRA Combined Motif Original Motif Original Motif VCWVKGYBMADVGRDCMHDBBHV AAAGGTCAAAGGTCAAC VCWARGGTCAAAGGTCAHBBBHV Direction: Forward Position #: 3 Overlap #: 17 Alignment: VCWVKGYBMADVGRDCMHDBBHV --AAAGGTCAAAGGTCAAC---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Original Motif Reverse Complement VCWARGGTCAAAGGTCAHBBBHV AGTGSWSCACTGTGAMAMCACAGTG AGTGSWSCACTGTGAMAVCAMAGKKCAAAGGTCAHBBBHV Direction: Forward Position #: 18 Overlap #: 8 Alignment: -----------------VCWARGGTCAAAGGTCAHBBBHV AGTGSWSCACTGTGAMAMCACAGTG--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TGGAGCACTGTGACAcCACAGTGg Combined Motif Original Motif Original Motif AGTGSWSCACTGTGAMAVCAMAGKKCAAAGGTCAHBBBHV TGGAGCACTGTGACAVCACAGTGG AGTGGAGCACTGTGACAVCACAGTGSAAAGGTCAHBBBHV Direction: Forward Position #: 3 Overlap #: 24 Alignment: AGTGSWSCACTGTGAMAVCAMAGKKCAAAGGTCAHBBBHV --TGGAGCACTGTGACAVCACAGTGG-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- REST Combined Motif Reverse Complement Reverse Complement VDBBBHTGACCTTTSCACTGTGVTGTCACAGTGCTCCACT GGYGCTGTCCATGGTGCTGAA VDBBBHKGHSCTKTCCAYKGTGCTGWMACAGTGCTCCACT Direction: Forward Position #: 7 Overlap #: 21 Alignment: VDBBBHTGACCTTTSCACTGTGVTGTCACAGTGCTCCACT ------GGYGCTGTCCATGGTGCTGAA------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 7 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 7 TFM12 Original Motif Original Motif HCAGRRVACASAG RAGKGMAGVRRGSRCASAGV RAGKGMWSARRRVRCASAGV Direction: Forward Position #: 7 Overlap #: 13 Alignment: ------HCAGRRVACASAG- RAGKGMAGVRRGSRCASAGV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Original Motif Reverse Complement RAGKGMWSARRRVRCASAGV MGGTCAGGGTGACCTRDBHV RAGGBCASDRKGRMCWSDGHV Direction: Forward Position #: 2 Overlap #: 19 Alignment: RAGKGMWSARRRVRCASAGV- -MGGTCAGGGTGACCTRDBHV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Reverse Complement Original Motif VDCDSWGRKCRMDSTGVCCTK CACTGTGRTRTCACAGTGSWSCACT CACTGTGRTVDCACWGTSCTBCACT Direction: Forward Position #: 1 Overlap #: 21 Alignment: VDCDSWGRKCRMDSTGVCCTK---- CACTGTGRTRTCACAGTGSWSCACT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFM2 Original Motif Original Motif CACTGTGRTVDCACWGTSCTBCACT CHHCHBTCCTSCYTCTGC CHHCHBTSVTSCCHCWGYSCTBCACT Direction: Forward Position #: 2 Overlap #: 17 Alignment: -CACTGTGRTVDCACWGTSCTBCACT CHHCHBTCCTSCYTCTGC-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CTCF Combined Motif Original Motif Reverse Complement CHHCHBTSVTSCCHCWGYSCTBCACT BMSMGCCYMCTKSTGGMHM CHHCHBHSMKCCCHCTGBBSKBCACT Direction: Forward Position #: 6 Overlap #: 19 Alignment: CHHCHBTSVTSCCHCWGYSCTBCACT -----BMSMGCCYMCTKSTGGMHM-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TGGAGCACTGTGACAcCACAGTGg Original Motif Reverse Complement CHHCHBHSMKCCCHCTGBBSKBCACT CCACTGTGVTGTCACAGTGCTCCA CCACTGTGVTSYCACWGTGSTCCACT Direction: Forward Position #: 1 Overlap #: 24 Alignment: CHHCHBHSMKCCCHCTGBBSKBCACT CCACTGTGVTGTCACAGTGCTCCA-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Reverse Complement Original Motif AGTGGASCACWGTGMSAVCACAGTGG BTRGGDCARAGGKCA VBDGGDSMAMDGTSASAVCACAGTGG Direction: Forward Position #: 1 Overlap #: 15 Alignment: AGTGGASCACWGTGMSAVCACAGTGG BTRGGDCARAGGKCA----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Tcfcp2l1 Combined Motif Reverse Complement Reverse Complement CCACTGTGVTSTSACHYTYSDCCDBB CKGGDTBDMMCTGG CCACTSTGGKBTBACCTKKSDCCDBB Direction: Forward Position #: 6 Overlap #: 14 Alignment: CCACTGTGVTSTSACHYTYSDCCDBB -----CKGGDTBDMMCTGG------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM13 Combined Motif Reverse Complement Reverse Complement VBDGGDSYYAGGTBABRCCASAGTGG WHAATTAAARAARAAAAAAA VBDGGDSYYAGGTBABRCCWBARTKRAARAARAAAAAAA Direction: Forward Position #: 20 Overlap #: 7 Alignment: VBDGGDSYYAGGTBABRCCASAGTGG------------- -------------------WHAATTAAARAARAAAAAAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFF11 Combined Motif Original Motif Original Motif VBDGGDSYYAGGTBABRCCWBARTKRAARAARAAAAAAA CTGCTGBDBBDGBD VBDGGDSYCWGSTGVBDCHDBDRTKRAARAARAAAAAAA Direction: Forward Position #: 9 Overlap #: 14 Alignment: VBDGGDSYYAGGTBABRCCWBARTKRAARAARAAAAAAA --------CTGCTGBDBBDGBD----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 61 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR4A2 NR1H2RXRA Original Motif Original Motif AAGGTCAC AAAGGTCAAAGGTCAAC AAAGGTCAMAGGTCAAC Direction: Forward Position #: 2 Overlap #: 8 Alignment: -AAGGTCAC-------- AAAGGTCAAAGGTCAAC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR1 Reverse Complement Reverse Complement GTTGACCTYTGACCTTT MGGTCAGGGTGACCTRDBHV MGGTCAGGKTGACCTBTGACCTTT Direction: Forward Position #: 8 Overlap #: 13 Alignment: -------GTTGACCTYTGACCTTT MGGTCAGGGTGACCTRDBHV---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR2 Reverse Complement Original Motif AAAGGTCAVAGGTCARCCTGACCY VHRGGTCABDBTGMCCTB MAAGGTCAVRGKKCMMYBTGACCY Direction: Forward Position #: 1 Overlap #: 18 Alignment: AAAGGTCAVAGGTCARCCTGACCY VHRGGTCABDBTGMCCTB------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 21 Reverse Complement Reverse Complement MGGTCABKRYGYYCKVTGACCTTY GAGGTCAGAAG GAGGTCAGAAGGYYCKVTGACCTTY Direction: Forward Position #: 2 Overlap #: 10 Alignment: -MGGTCABKRYGYYCKVTGACCTTY GAGGTCAGAAG-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 19 Reverse Complement Original Motif MAAGGTCAVRGKKCCTTCTGACCTC AAAGRTMAAACTA AAAGGTCAAASTACCTTCTGACCTC Direction: Forward Position #: 1 Overlap #: 13 Alignment: MAAGGTCAVRGKKCCTTCTGACCTC AAAGRTMAAACTA------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Original Motif Original Motif AAAGGTCAAASTACCTTCTGACCTC BTRGGDCARAGGKCA VWAGGTCAAAGKDCHTTCTGACCTC Direction: Forward Position #: 1 Overlap #: 15 Alignment: AAAGGTCAAASTACCTTCTGACCTC BTRGGDCARAGGKCA---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 28 Reverse Complement Original Motif GAGGTCAGAAHGDYCTTTGACCTWB AAAGWCATWAA RARGTCAKWAAGDYCTTTGACCTWB Direction: Forward Position #: 1 Overlap #: 11 Alignment: GAGGTCAGAAHGDYCTTTGACCTWB AAAGWCATWAA-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Original Motif Reverse Complement RARGTCAKWAAGDYCTTTGACCTWB AGTGSWSCACTGTGAMAMCACAGTG AGTGSWSCACTGTGAMRHCAYARWGDYCTTTGACCTWB Direction: Forward Position #: 14 Overlap #: 12 Alignment: -------------RARGTCAKWAAGDYCTTTGACCTWB AGTGSWSCACTGTGAMAMCACAGTG------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR2F1 Combined Motif Reverse Complement Reverse Complement VWAGGTCAAAGKDCWMTKTGHMYTCACAGTGSWSCACT AKGYYCAAAGRTCA VVRGBBCAAAGGTCAMTKTGHMYTCACAGTGSWSCACT Direction: Forward Position #: 2 Overlap #: 14 Alignment: VWAGGTCAAAGKDCWMTKTGHMYTCACAGTGSWSCACT -AKGYYCAAAGRTCA----------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 39 Combined Motif Reverse Complement Reverse Complement AGTGSWSCACTGTGAMRHCAYARTGACCTTTGVBCKBB CAAGAKCATCT TTGVBCKBBCAARAKSATCTAGTGSWSCACTGTGAMRH Direction: Backward Position #: 10 Overlap #: 11 Alignment: AGTGSWSCACTGTGAMRHCAYARTGACCTTTGVBCKBB ------------------CAAGAKCATCT--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 2 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 2 Motif 5 Original Motif Reverse Complement GCARRGGSAGS GCAGAGGSAKG GCAGAGGSAGS Direction: Backward Position #: 1 Overlap #: 11 Alignment: GCARRGGSAGS GCAGAGGSAKG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM2 Combined Motif Original Motif Reverse Complement GCAGAGGSAGS GCAGAKGSAGGABDGHDG GCAGAGGSAGGABDGHDG Direction: Forward Position #: 1 Overlap #: 11 Alignment: GCAGAGGSAGS------- GCAGAKGSAGGABDGHDG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CTCF Reverse Complement Reverse Complement CHHCHBTCCTSCCTCTGC BMSMGCCYMCTKSTGGMHM BHVMSCCYCCTGCYKSHBM Direction: Forward Position #: 2 Overlap #: 18 Alignment: -CHHCHBTCCTSCCTCTGC BMSMGCCYMCTKSTGGMHM ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFF11 Original Motif Reverse Complement BHVMSCCYCCTGCYKSHBM HVCDBBDBCAGCAG BHVHBCBBCMKCVBKSHBM Direction: Forward Position #: 1 Overlap #: 14 Alignment: BHVMSCCYCCTGCYKSHBM HVCDBBDBCAGCAG----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM12 Combined Motif Reverse Complement Original Motif RBHSYVBGYYGVBGBHVDV RAGKGMAGVRRGSRCASAGV RBHVHVDGCHGVVGVVVVASAGV Direction: Forward Position #: 4 Overlap #: 16 Alignment: RBHSYVBGYYGVBGBHVDV---- ---RAGKGMAGVRRGSRCASAGV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Tcfcp2l1 Combined Motif Original Motif Original Motif RBHVHVDGCHGVVGVVVVASAGV CCAGYYHVADCCRG RBHVCVDGYHBVRDCCRGASAGV Direction: Forward Position #: 5 Overlap #: 14 Alignment: RBHVHVDGCHGVVGVVVVASAGV ----CCAGYYHVADCCRG----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Reverse Complement VCTSTCKGGHKBBHKCDVGVHBM GGYGCTGTCCATGGTGCTGAA TGAAKSHSCTGTCCVHGSTGSVCTSTC Direction: Backward Position #: 5 Overlap #: 17 Alignment: VCTSTCKGGHKBBHKCDVGVHBM---- ------GGYGCTGTCCATGGTGCTGAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR1 Reverse Complement Reverse Complement GASAGVSCASCHVGGACAGSHSRTTCA MGGTCAGGGTGACCTRDBHV MGGTSASRGTGVMCYDDBBHCAGSHSRTTCA Direction: Forward Position #: 5 Overlap #: 16 Alignment: ----GASAGVSCASCHVGGACAGSHSRTTCA MGGTCAGGGTGACCTRDBHV----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 7 Combined Motif Original Motif Reverse Complement MGGTSASRGTGVMCYDDBBHCAGSHSRTTCA CTSTGTBKMCTGH MGGTCWSWGTBDMCTDVBBHCAGSHSRTTCA Direction: Forward Position #: 5 Overlap #: 13 Alignment: MGGTSASRGTGVMCYDDBBHCAGSHSRTTCA ----CTSTGTBKMCTGH-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Original Motif Original Motif MGGTCWSWGTBDMCTDVBBHCAGSHSRTTCA VHRGGTCABDBTGMCCTB MGGTCWSWRKGTCMBDDKGHCMBVHSRTTCA Direction: Forward Position #: 7 Overlap #: 18 Alignment: MGGTCWSWGTBDMCTDVBBHCAGSHSRTTCA ------VHRGGTCABDBTGMCCTB------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 78 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ssGCkTGCssk gCGCGCsCgsG Original Motif Original Motif SSGCKTGCSSK GCGCGCSCGCG SCGCGYGCSSG Direction: Backward Position #: 1 Overlap #: 11 Alignment: SSGCKTGCSSK GCGCGCSCGCG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ssCCCCGCSssk Original Motif Original Motif SCGCGYGCSSG SBCCCCGCCSBB SSSCSCGCSSBB Direction: Forward Position #: 1 Overlap #: 11 Alignment: SCGCGYGCSSG- SBCCCCGCCSBB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif sscCCCGCGcs Original Motif Original Motif SSSCSCGCSSBB BSCCCCGCGBS SSSCSCGCGSSB Direction: Forward Position #: 1 Overlap #: 11 Alignment: SSSCSCGCSSBB BSCCCCGCGBS- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif cCGCGGrCACG Reverse Complement Original Motif BSSCGCGSGSSS CCGCGGRCACG CCGCGSRSRSGS Direction: Forward Position #: 1 Overlap #: 11 Alignment: BSSCGCGSGSSS CCGCGGRCACG- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 79 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- cCGCGGrCACG gCGCGCsCgsG Original Motif Original Motif CCGCGGRCACG GCGCGCSCGCG SCGCGSRCRCG Direction: Backward Position #: 1 Overlap #: 11 Alignment: CCGCGGRCACG GCGCGCSCGCG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFF11 Original Motif Original Motif SCGCGSRCRCG CTGCTGBDBBDGBD SYGCKGVCDCDGBD Direction: Forward Position #: 1 Overlap #: 11 Alignment: SCGCGSRCRCG--- CTGCTGBDBBDGBD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Original Motif Reverse Complement SYGCKGVCDCDGBD GGYGCTGTCCATGGTGCTGAA GSYGCTGBCCVDGGTGCTGAA Direction: Forward Position #: 2 Overlap #: 14 Alignment: -SYGCKGVCDCDGBD------ GGYGCTGTCCATGGTGCTGAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Reverse Complement Reverse Complement TTCAGCACCDVGGVCAGCKSC MGGTCAGGGTGACCTRDBHV TTCARSRYCAVGGWSASCKVBBHV Direction: Forward Position #: 5 Overlap #: 17 Alignment: TTCAGCACCDVGGVCAGCKSC--- ----MGGTCAGGGTGACCTRDBHV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ssGCkTGCssk Combined Motif Reverse Complement Original Motif VDBBVRGSTSWCCVTGKMSMTGAA SSGCKTGCSSK VDBBSVGCKYGCSSKGKMSMTGAA Direction: Forward Position #: 5 Overlap #: 11 Alignment: VDBBVRGSTSWCCVTGKMSMTGAA ----SSGCKTGCSSK--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ssCCCCGCSssk Original Motif Reverse Complement VDBBSVGCKYGCSSKGKMSMTGAA BBSGGCGGGGBS BBSGGCGSKKVCSSKGKMSMTGAA Direction: Forward Position #: 1 Overlap #: 12 Alignment: VDBBSVGCKYGCSSKGKMSMTGAA BBSGGCGGGGBS------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CTCF Original Motif Reverse Complement BBSGGCGSKKVCSSKGKMSMTGAA BMSMGCCYMCTKSTGGMHM BVSVGCSCVCTBSBGGBCVMTGAA Direction: Forward Position #: 1 Overlap #: 19 Alignment: BBSGGCGSKKVCSSKGKMSMTGAA BMSMGCCYMCTKSTGGMHM----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 7 Combined Motif Reverse Complement Original Motif TTCARVGBCCVSBAGVGSGCVSBV HCAGRRVACASAG TTCARRRVMCASHRGVGSGCVSBV Direction: Forward Position #: 2 Overlap #: 13 Alignment: TTCARVGBCCVSBAGVGSGCVSBV -HCAGRRVACASAG---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 11-19-2016 20:57:29 Runtime: 853.531 seconds MOTIFSIM is written by Ngoc Tam L. 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