**************************************************************************************************************************************************************************************************** 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 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 Original Motif Reverse Complement GCACTG GGAGCACTGTGACACCACA ACAGMMMYSGGAGCACTGT Direction: Backward Position #: 4 Overlap #: 6 Alignment: ----------GCACTG--- GGAGCACTGTGACACCACA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Reverse Complement Original Motif ACAGTGCTCCSMRRYCTGT CACTGTGRTRTCACAGTGSWSCACT CACWGTGVTVYCAVABYKSTSCACT Direction: Forward Position #: 2 Overlap #: 19 Alignment: -ACAGTGCTCCSMRRYCTGT----- CACTGTGRTRTCACAGTGSWSCACT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TGGAGCACTGTGACAcCACAGTGg Original Motif Reverse Complement CACWGTGVTVYCAVABYKSTSCACT CCACTGTGVTGTCACAGTGCTCCA CCACTGTGVTGTCACAGTGCTCCACT Direction: Forward Position #: 2 Overlap #: 23 Alignment: -CACWGTGVTVYCAVABYKSTSCACT 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 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---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CACTGTGrYrtCACAGTGswsCAcT Combined Motif Reverse Complement Reverse Complement CCACTGTVMMAVCACAGTGGAGCAMTG AGTGSWSCACTGTGAMAMCACAGTG CCACTRKDRSASCACWGTGVMRCMAYRGTG Direction: Forward Position #: 6 Overlap #: 22 Alignment: CCACTGTVMMAVCACAGTGGAGCAMTG--- -----AGTGSWSCACTGTGAMAMCACAGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 20 Combined Motif Original Motif Original Motif CCACTRKDRSASCACWGTGVMRCMAYRGTG TCTKTGTCAAWA YRGTGWCTGTGTCAAWACCACTRKDRSASC Direction: Backward Position #: 6 Overlap #: 12 Alignment: CCACTRKDRSASCACWGTGVMRCMAYRGTG -------------TCTKTGTCAAWA----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global 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 STGGYCACCTDYGC Direction: Backward Position #: 6 Overlap #: 6 Alignment: ---CACCTD----- YGCCACCTDSTGGY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 9 Original Motif Original Motif STGGYCACCTDYGC CWGAGCCAYCTYTC CBKGGCCACCTBTSC Direction: Forward Position #: 2 Overlap #: 13 Alignment: -STGGYCACCTDYGC CWGAGCCAYCTYTC- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 50 Combined Motif Original Motif Reverse Complement CBKGGCCACCTBTSC TATKCTAAACCTAT CBKGGCCACCTATKCTAAACCTAT Direction: Forward Position #: 11 Overlap #: 5 Alignment: CBKGGCCACCTBTSC--------- ----------TATKCTAAACCTAT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 24 Combined Motif Original Motif Original Motif CBKGGCCACCTATKCTAAACCTAT TCCTCCTGGAA CBKGGCCACCTATKCTAAWCCTMYTGGAA Direction: Forward Position #: 19 Overlap #: 6 Alignment: CBKGGCCACCTATKCTAAACCTAT----- ------------------TCCTCCTGGAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 16 Combined Motif Reverse Complement Original Motif TTCCAKYAGGWTTAGYATAGGTGGCCYVG ACAACACATTT TTMCADCASRTTTAGYATAGGTGGCCYVG Direction: Forward Position #: 3 Overlap #: 11 Alignment: TTCCAKYAGGWTTAGYATAGGTGGCCYVG --ACAACACATTT---------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 38 Combined Motif Reverse Complement Reverse Complement CBKGGCCACCTATKCTAAAKSTGDTGYAA TCATCTTT CBKGGYCAYCTTTKCTAAAKSTGDTGYAA Direction: Forward Position #: 6 Overlap #: 8 Alignment: CBKGGCCACCTATKCTAAAKSTGDTGYAA -----TCATCTTT---------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 26 Combined Motif Original Motif Original Motif CBKGGYCAYCTTTKCTAAAKSTGDTGYAA TTTATGGTGAGCAT CBKGGYCAYCTTTKCTAAAKSTGDTKTAWGGTGAGCAT Direction: Forward Position #: 25 Overlap #: 5 Alignment: CBKGGYCAYCTTTKCTAAAKSTGDTGYAA--------- ------------------------TTTATGGTGAGCAT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 21 Reverse Complement Original Motif ATGCTCACCWTAYADCASYTTTAGYAAAGMTGMCCYVG CTTCTGACCTC MTKCTSACCTYAYADCASYTTTAGYAAAGMTGMCCYVG Direction: Forward Position #: 1 Overlap #: 11 Alignment: ATGCTCACCWTAYADCASYTTTAGYAAAGMTGMCCYVG CTTCTGACCTC--------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFM11 Reverse Complement Reverse Complement CBKGGYCAYCTTTKCTAAAKSTGDTKTKAGGTSAGYAY TGTGTGDKTGTGTGTGTRTG GWGBKKGTKTGWGKKBRKBWCBKGGYCAYCTTTKCTAAA Direction: Backward Position #: 2 Overlap #: 19 Alignment: CBKGGYCAYCTTTKCTAAAKSTGDTKTKAGGTSAGYAY- -------------------TGTGTGDKTGTGTGTGTRTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM1 Combined Motif Original Motif Reverse Complement GWGBKKGTKTGWGKKBRKBWCBKGGYCAYCTTTKCTAAA TGTGTGWGTGTGTGTGTG GWGBKTGTGTGWGTGTRTGTSTKGGYCAYCTTTKCTAAA Direction: Forward Position #: 6 Overlap #: 18 Alignment: GWGBKKGTKTGWGKKBRKBWCBKGGYCAYCTTTKCTAAA -----TGTGTGWGTGTGTGTGTG---------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global 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 Reverse Complement Reverse Complement VCTSTGKVMMMTSWRCYCTK MGGTCAGGGTGACCTRDBHV VCTSWGGHCAVDSTGVCCTDDBHV Direction: Forward Position #: 5 Overlap #: 16 Alignment: VCTSTGKVMMMTSWRCYCTK---- ----MGGTCAGGGTGACCTRDBHV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CACTGTGrYrtCACAGTGswsCAcT Combined Motif Reverse Complement Reverse Complement VDBHHAGGBCASDVTGHCCWSAGV AGTGSWSCACTGTGAMAMCACAGTG VDVBTRGDBCACTGTGACMHCASAGTG Direction: Forward Position #: 3 Overlap #: 22 Alignment: VDBHHAGGBCASDVTGHCCWSAGV--- --AGTGSWSCACTGTGAMAMCACAGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM2 Combined Motif Reverse Complement Original Motif CACTSTGHRGTCACAGTGBDCMABBHV CHHCHBTCCTSCYTCTGC CMCTSTBHVBTCMCHSTGBDCMABBHV Direction: Forward Position #: 2 Overlap #: 18 Alignment: CACTSTGHRGTCACAGTGBDCMABBHV -CHHCHBTCCTSCYTCTGC-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CTCF Combined Motif Reverse Complement Original Motif VDVBTRGDBCASHGRGABVHBASAGYG YDRCCASYAGRKGGCRSYV VDVBTDGDCCASHRGGDGGMVVBVGYG Direction: Forward Position #: 6 Overlap #: 19 Alignment: VDVBTRGDBCASHGRGABVHBASAGYG -----YDRCCASYAGRKGGCRSYV--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TGGAGCACTGTGACAcCACAGTGg Reverse Complement Reverse Complement CMCBBVVRCCDCCKHSTGGHCHABBHV CCACTGTGVTGTCACAGTGCTCCA CCACTGTGGYSTCMBAGTGSTCCABBHV Direction: Forward Position #: 2 Overlap #: 23 Alignment: -CMCBBVVRCCDCCKHSTGGHCHABBHV CCACTGTGVTGTCACAGTGCTCCA---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Original Motif Reverse Complement CCACTGTGGYSTCMBAGTGSTCCABBHV TGRCCTKTGHCCKAB CCWSDSYKKTGBCMBASTGSTCCABBHV Direction: Forward Position #: 3 Overlap #: 15 Alignment: CCACTGTGGYSTCMBAGTGSTCCABBHV --TGRCCTKTGHCCKAB----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Tcfcp2l1 Combined Motif Original Motif Original Motif CCWSDSYKKTGBCMBASTGSTCCABBHV CCAGYYHVADCCRG CCCCDGYTBHVDCCDRSTGSTCCABBHV Direction: Forward Position #: 3 Overlap #: 14 Alignment: CCWSDSYKKTGBCMBASTGSTCCABBHV --CCAGYYHVADCCRG------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM13 Combined Motif Original Motif Reverse Complement CCCCDGYTBHVDCCDRSTGSTCCABBHV WHAATTAAARAARAAAAAAA CCCCDGYTBHVDCCDRSTGSWHVATTAAARAARAAAAAAA Direction: Forward Position #: 21 Overlap #: 8 Alignment: CCCCDGYTBHVDCCDRSTGSTCCABBHV------------ --------------------WHAATTAAARAARAAAAAAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFF11 Combined Motif Original Motif Original Motif CCCCDGYTBHVDCCDRSTGSWHVATTAAARAARAAAAAAA CTGCTGBDBBDGBD CYSCTGHBBBDDCVDRSTGSWHVATTAAARAARAAAAAAA Direction: Forward Position #: 1 Overlap #: 14 Alignment: CCCCDGYTBHVDCCDRSTGSWHVATTAAARAARAAAAAAA CTGCTGBDBBDGBD-------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global 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 Reverse Complement Original Motif SCTSCCKMTGC CYTSCCTCTGC SCTSCCTCTGC Direction: Forward Position #: 1 Overlap #: 11 Alignment: SCTSCCKMTGC CYTSCCTCTGC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFM2 Reverse Complement Reverse Complement GCAGAGGSAGS GCAGAKGSAGGABDGHDG GCAGAGGSAGGABDGHDG Direction: Forward Position #: 1 Overlap #: 11 Alignment: GCAGAGGSAGS------- GCAGAKGSAGGABDGHDG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CTCF Original Motif Original Motif GCAGAGGSAGGABDGHDG YDRCCASYAGRKGGCRSYV YDRSCASHRGSDGGMDVBHDG Direction: Forward Position #: 4 Overlap #: 16 Alignment: ---GCAGAGGSAGGABDGHDG YDRCCASYAGRKGGCRSYV-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFF11 Reverse Complement Reverse Complement CHHBVHRCCDSCKHSTGSMHM HVCDBBDBCAGCAG HHHHBHDSCAGCWBSTGSMHM Direction: Forward Position #: 1 Overlap #: 14 Alignment: CHHBVHRCCDSCKHSTGSMHM HVCDBBDBCAGCAG------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM12 Combined Motif Reverse Complement Original Motif YDRSCASBWGCTGSHDBHDDD RAGKGMAGVRRGSRCASAGV YDRSCAGDDGVKGVVGVVBDVAGV Direction: Forward Position #: 5 Overlap #: 17 Alignment: YDRSCASBWGCTGSHDBHDDD--- ----RAGKGMAGVRRGSRCASAGV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Tcfcp2l1 Combined Motif Original Motif Original Motif YDRSCAGDDGVKGVVGVVBDVAGV CCAGYYHVADCCRG YDRCCAGBDVVDDCVRGVBDVAGV Direction: Forward Position #: 4 Overlap #: 14 Alignment: YDRSCAGDDGVKGVVGVVBDVAGV ---CCAGYYHVADCCRG------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Original Motif Original Motif YDRCCAGBDVVDDCVRGVBDVAGV TTCAGCACCATGGACAGCKCC KCCBYMRGBACVDBGGRVAGVYDRCCA Direction: Backward Position #: 4 Overlap #: 18 Alignment: YDRCCAGBDVVDDCVRGVBDVAGV--- ------TTCAGCACCATGGACAGCKCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Reverse Complement Reverse Complement TGGMHMVCTVKCCBDVGTBCKRKBGGY MGGTCAGGGTGACCTRDBHV HGGYCAVVBKGMCBTVGBBVKRKBGGY Direction: Forward Position #: 1 Overlap #: 20 Alignment: TGGMHMVCTVKCCBDVGTBCKRKBGGY MGGTCAGGGTGACCTRDBHV------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 7 Combined Motif Original Motif Reverse Complement HGGYCAVVBKGMCBTVGBBVKRKBGGY CTSTGTBKMCTGH HGGYCWSBDTKDCCTGVBBVKRKBGGY Direction: Forward Position #: 5 Overlap #: 13 Alignment: HGGYCAVVBKGMCBTVGBBVKRKBGGY ----CTSTGTBKMCTGH---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Reverse Complement Original Motif KCCBYMRVBVVCAGGDYAHVSWGMCCH VHRGGTCABDBTGMCCTB KCCBYVDRGGTCAVGDTRHMCTGMCCH Direction: Forward Position #: 6 Overlap #: 18 Alignment: KCCBYMRVBVVCAGGDYAHVSWGMCCH -----VHRGGTCABDBTGMCCTB---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Original Motif Reverse Complement TGVYCTTTGBCCT TGRCCTKTGHCCKAB TGVYCTTTGBCCKAB Direction: Forward Position #: 1 Overlap #: 13 Alignment: TGVYCTTTGBCCT-- TGRCCTKTGHCCKAB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Reverse Complement Reverse Complement BTRGGBCAAAGKBCA BAGGYCABHBTGACCKHV BTVRGGYMAVGBTSACCKHV Direction: Forward Position #: 3 Overlap #: 13 Alignment: BTRGGBCAAAGKBCA----- --BAGGYCABHBTGACCKHV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Original Motif Original Motif BTVRGGYMAVGBTSACCKHV VDBHMAGGTCACCCTGACCY BTVRGDBMMAGGTSACCBTGACCY Direction: Forward Position #: 5 Overlap #: 16 Alignment: BTVRGGYMAVGBTSACCKHV---- ----VDBHMAGGTCACCCTGACCY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Reverse Complement Reverse Complement MGGTCAVGGTSACCTYRBHCMBAB AKGYYCAAAGRTCA AKVBGYMAAGGTCACCTYRBHCMBAB Direction: Forward Position #: 3 Overlap #: 12 Alignment: --MGGTCAVGGTSACCTYRBHCMBAB AKGYYCAAAGRTCA------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR1H2RXRA Reverse Complement Original Motif BTVRGDBMMAGGTGACCTTYKCBVYT AAAGGTCAAAGGTCAAC VDAGGTCAAAGGTCAMCTTYKCBVYT Direction: Forward Position #: 1 Overlap #: 17 Alignment: BTVRGDBMMAGGTGACCTTYKCBVYT AAAGGTCAAAGGTCAAC--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Original Motif Original Motif VDAGGTCAAAGGTCAMCTTYKCBVYT CACTGTGRTRTCACAGTGSWSCACT CACTGTGRBGTCAMAGKKSAVCWYTKCBVYT Direction: Forward Position #: 6 Overlap #: 20 Alignment: -----VDAGGTCAAAGGTCAMCTTYKCBVYT CACTGTGRTRTCACAGTGSWSCACT------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TGGAGCACTGTGACAcCACAGTGg Original Motif Reverse Complement CACTGTGRBGTCAMAGKKSAVCWYTKCBVYT CCACTGTGVTGTCACAGTGCTCCA CCACTGTGVTGTCACAGTGCWCCAYTKCBVYT Direction: Forward Position #: 2 Overlap #: 23 Alignment: -CACTGTGRBGTCAMAGKKSAVCWYTKCBVYT CCACTGTGVTGTCACAGTGCTCCA-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Original Motif AKVBGYAMTGGWGCACTGTGACAVCACAGTGG TTCAGCACCATGGACAGCKCC ACAGCKCCWKCASYRYSAYRGAKVBGYAMTGGWGCACTGT Direction: Backward Position #: 9 Overlap #: 13 Alignment: AKVBGYAMTGGWGCACTGTGACAVCACAGTGG-------- -------------------TTCAGCACCATGGACAGCKCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- AgTGCTCCACTGTGgTGTCACAgT Combined Motif Reverse Complement Original Motif ACAGTGCWCCAYTKCBVYTCMKTSKKMSTGYWGGYGCTGT AGTGCTCCACTGTGGTGTCACAGT ACAGTGCTCCACTGTGVTKYCAYVKTMSTGYWGGYGCTGT Direction: Forward Position #: 3 Overlap #: 24 Alignment: ACAGTGCWCCAYTKCBVYTCMKTSKKMSTGYWGGYGCTGT --AGTGCTCCACTGTGGTGTCACAGT-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 41 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 41 atactttggc Reverse Complement Reverse Complement CCAAAGT GCCAAAGTAT GCCAAAGTAT Direction: Forward Position #: 2 Overlap #: 7 Alignment: -CCAAAGT-- GCCAAAGTAT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wwCCAmAGTCmt Original Motif Original Motif GCCAAAGTAT DDCCAMAGTCHB DGCCAAAGTMTB Direction: Forward Position #: 2 Overlap #: 10 Alignment: -GCCAAAGTAT- DDCCAMAGTCHB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif AgTGCTCCACTGTGgTGTCACAgT Original Motif Original Motif DGCCAAAGTMTB AGTGCTCCACTGTGGTGTCACAGT AGTGHTCCAMWGTVBTGTCACAGT Direction: Forward Position #: 5 Overlap #: 12 Alignment: ----DGCCAAAGTMTB-------- AGTGCTCCACTGTGGTGTCACAGT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif AmTGTGACACCACAGT Reverse Complement Original Motif ACTGTGACAVVACWRTGGADCACT AMTGTGACACCACAGT ACTGTGACAVCACAGTGGADCACT Direction: Forward Position #: 1 Overlap #: 16 Alignment: ACTGTGACAVVACWRTGGADCACT AMTGTGACACCACAGT-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CAcCACAGTGGAGCAct Reverse Complement Reverse Complement AGTGHTCCACTGTGVTGTCACAGT AGTGCTCCACTGTGDTG AGTGCTCCACTGTGVTGTCACAGT Direction: Forward Position #: 1 Overlap #: 17 Alignment: AGTGHTCCACTGTGVTGTCACAGT AGTGCTCCACTGTGDTG------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CagTGCTCCACTGTGgT Original Motif Original Motif AGTGCTCCACTGTGVTGTCACAGT CAGTGCTCCACTGTGBT CAGTGCTCCACTGTGBTGTCACAGT Direction: Forward Position #: 2 Overlap #: 16 Alignment: -AGTGCTCCACTGTGVTGTCACAGT CAGTGCTCCACTGTGBT-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Original Motif Reverse Complement CAGTGCTCCACTGTGBTGTCACAGT AKGYYCAAAGRTCA TCAWGKBBYRWMRVCAGTGCTCCACTGT Direction: Backward Position #: 4 Overlap #: 11 Alignment: CAGTGCTCCACTGTGBTGTCACAGT--- --------------AKGYYCAAAGRTCA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CACTGTGrYrtCACAGTGswsCAcT Combined Motif Original Motif Original Motif TCAWGKBBYRWMRVCAGTGCTCCACTGT CACTGTGRTRTCACAGTGSWSCACT TCAHKGTGHDDHVACAGTGCTCCACTGT Direction: Forward Position #: 2 Overlap #: 25 Alignment: TCAWGKBBYRWMRVCAGTGCTCCACTGT -CACTGTGRTRTCACAGTGSWSCACT-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TGGAGCACTGTGACAcCACAGTGg Original Motif Reverse Complement TCAHKGTGHDDHVACAGTGCTCCACTGT CCACTGTGVTGTCACAGTGCTCCA YCACTGTGVTGTCACAGTGCTCCACTGT Direction: Forward Position #: 1 Overlap #: 24 Alignment: TCAHKGTGHDDHVACAGTGCTCCACTGT CCACTGTGVTGTCACAGTGCTCCA---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR1H2RXRA Original Motif Original Motif YCACTGTGVTGTCACAGTGCTCCACTGT AAAGGTCAAAGGTCAAC CAACWMASRKYRMWSSWYCACTGTGVTGTCAC Direction: Backward Position #: 5 Overlap #: 13 Alignment: YCACTGTGVTGTCACAGTGCTCCACTGT---- ---------------AAAGGTCAAAGGTCAAC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 4 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 4 Motif 25 Reverse Complement Original Motif YTTCC CTGCTTTCCMAA CTGCTTTCCMAA Direction: Forward Position #: 5 Overlap #: 5 Alignment: ----YTTCC--- CTGCTTTCCMAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 45 Reverse Complement Original Motif TTYGGAAAGCAG TGGAGGAAA TKKHGGAAAGCAG Direction: Forward Position #: 2 Overlap #: 8 Alignment: -TTYGGAAAGCAG TGGAGGAAA---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 47 Reverse Complement Reverse Complement CTGCTTTCCHYYA TGCCTTTCYTT YKSCTTTCCTTYA Direction: Forward Position #: 1 Overlap #: 11 Alignment: CTGCTTTCCHYYA TGCCTTTCYTT-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 48 Combined Motif Original Motif Reverse Complement YKSCTTTCCTTYA TTCTTYCATT YTBCTTTCMTTYA Direction: Forward Position #: 2 Overlap #: 10 Alignment: YKSCTTTCCTTYA -TTCTTYCATT-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 32 Reverse Complement Reverse Complement TKAAYGAAAGVAK TTTACTAAAT TTWACKAAAKVAK Direction: Forward Position #: 1 Overlap #: 10 Alignment: TKAAYGAAAGVAK TTTACTAAAT--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 12 Combined Motif Reverse Complement Original Motif YTBYTTTYGTWAA TGAAAATSCTT YTBYTTTYKKAAAATSCTT Direction: Forward Position #: 9 Overlap #: 5 Alignment: YTBYTTTYGTWAA------ --------TGAAAATSCTT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 13 Reverse Complement Original Motif AAGSATTTTYRKAAAKVAK AACATATTTTCA AAMRBATTTTCAKAAAKVAK Direction: Forward Position #: 2 Overlap #: 11 Alignment: -AAGSATTTTYRKAAAKVAK AACATATTTTCA-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 23 Reverse Complement Reverse Complement YTBYTTTYTGAAAATVKYTT CTTTCTCT CTTTCTYTYTGAAAATVKYTT Direction: Forward Position #: 2 Overlap #: 7 Alignment: -YTBYTTTYTGAAAATVKYTT CTTTCTCT------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Original Motif Reverse Complement CTTTCTYTYTGAAAATVKYTT GGYGCTGTCCATGGTGCTGAA GGYGCTGTCYWTSKTKCTGAAAATVKYTT Direction: Forward Position #: 9 Overlap #: 13 Alignment: --------CTTTCTYTYTGAAAATVKYTT GGYGCTGTCCATGGTGCTGAA-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 27 Combined Motif Original Motif Original Motif GGYGCTGTCYWTSKTKCTGAAAATVKYTT ATGTWTTCATTMAT GGYGCTGTCYWTSKTKCTGAAAATGTHTTCATTMAT Direction: Forward Position #: 23 Overlap #: 7 Alignment: GGYGCTGTCYWTSKTKCTGAAAATVKYTT------- ----------------------ATGTWTTCATTMAT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global 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 Motif 21 Reverse Complement Original Motif GTGACCTT CTTCTGACCTC STKMYSWYCTC Direction: Forward Position #: 1 Overlap #: 8 Alignment: GTGACCTT--- CTTCTGACCTC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 19 Original Motif Reverse Complement STKMYSWYCTC TAGTTTYAKCTTT TAGTTTYAKCTTYYSWYCTC Direction: Forward Position #: 10 Overlap #: 4 Alignment: ---------STKMYSWYCTC TAGTTTYAKCTTT------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 28 Combined Motif Original Motif Reverse Complement TAGTTTYAKCTTYYSWYCTC TTWATGWCTTT TAKTTWTRDCTTTYSWYCTC Direction: Forward Position #: 3 Overlap #: 11 Alignment: TAGTTTYAKCTTYYSWYCTC --TTWATGWCTTT------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Reverse Complement Reverse Complement GAGKWSMAAAGDKAWAAYTA AGTGSWSCACTGTGAMAMCACAGTG AGWGSWSCAMWGTGAHAACWMAGTG Direction: Forward Position #: 2 Overlap #: 20 Alignment: -GAGKWSMAAAGDKAWAAYTA---- AGTGSWSCACTGTGAMAMCACAGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global 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 TFF11 Reverse Complement Reverse Complement CGTGKCCGCGG HVCDBBDBCAGCAG MGTGKCMGCRGHVC Direction: Backward Position #: 1 Overlap #: 11 Alignment: ---CGTGKCCGCGG HVCDBBDBCAGCAG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- REST Combined Motif Reverse Complement Reverse Complement GBDCMGCRGYCACR GGYGCTGTCCATGGTGCTGAA GBGSHGCDGTCCVDGGTGCTGAA Direction: Forward Position #: 3 Overlap #: 12 Alignment: GBDCMGCRGYCACR--------- --GGYGCTGTCCATGGTGCTGAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR1 Original Motif Original Motif GBGSHGCDGTCCVDGGTGCTGAA VDBHMAGGTCACCCTGACCY VBBBHRSGKYMCCBKGWSCTGAA Direction: Forward Position #: 1 Overlap #: 20 Alignment: GBGSHGCDGTCCVDGGTGCTGAA VDBHMAGGTCACCCTGACCY--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CTCF Combined Motif Original Motif Reverse Complement VBBBHRSGKYMCCBKGWSCTGAA BMSMGCCYMCTKSTGGMHM VBVSMGCSBCCYBSTGDCCHGAA Direction: Forward Position #: 2 Overlap #: 19 Alignment: VBBBHRSGKYMCCBKGWSCTGAA -BMSMGCCYMCTKSTGGMHM--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 7 Reverse Complement Original Motif TTCHGGHCASBMGGVSGCRSBVV HCAGRRVACASAG HYMDGRHMMVSAGGVSGCRSBVV Direction: Forward Position #: 1 Overlap #: 13 Alignment: TTCHGGHCASBMGGVSGCRSBVV 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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