**************************************************************************************************************************************************************************************************** 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_DM05.txt 46 1 MEME-ChIP_DM05.txt 4 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 47 Original Motif Original Motif CACCTD YGCCACCTDSTGGY YGCCACCTDSTGGY Direction: Backward Position #: 6 Overlap #: 6 Alignment: ---CACCTD----- YGCCACCTDSTGGY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 5 Original Motif Original Motif YGCCACCTDSTGGY CWGAGCCAYCTYTC CWGHGCCACCTBBYGGY Direction: Forward Position #: 4 Overlap #: 11 Alignment: ---YGCCACCTDSTGGY CWGAGCCAYCTYTC--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CTCF Original Motif Reverse Complement CWGHGCCACCTBBYGGY BMSMGCCYMCTKSTGGMHM CWGMGCCMCCTBSTGGHHM Direction: Forward Position #: 1 Overlap #: 17 Alignment: CWGHGCCACCTBBYGGY-- BMSMGCCYMCTKSTGGMHM ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RORA_1 Reverse Complement Reverse Complement YDDCCASVAGGYGGCRCWG TGACCTDVWT TGACCWBVAKGYGGCRCWG Direction: Forward Position #: 1 Overlap #: 10 Alignment: YDDCCASVAGGYGGCRCWG TGACCTDVWT--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Original Motif Reverse Complement TGACCWBVAKGYGGCRCWG GGYGCTGTCCATGGTGCTGAA KGHSCTGTMSRTGGYGCTGAA Direction: Forward Position #: 1 Overlap #: 19 Alignment: TGACCWBVAKGYGGCRCWG-- GGYGCTGTCCATGGTGCTGAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Esrrb Original Motif Reverse Complement KGHSCTGTMSRTGGYGCTGAA TGACCTTGMBBB TGACCTKBMBVHGGYGCTGAA Direction: Forward Position #: 1 Overlap #: 12 Alignment: KGHSCTGTMSRTGGYGCTGAA TGACCTTGMBBB--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR1H2RXRA Original Motif Reverse Complement TGACCTKBMBVHGGYGCTGAA GTTGACCTTTGACCTTT GTTGACCTTTGACCTTBMBVHGGYGCTGAA Direction: Forward Position #: 10 Overlap #: 8 Alignment: ---------TGACCTKBMBVHGGYGCTGAA GTTGACCTTTGACCTTT------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 46 Original Motif Reverse Complement GTTGACCTTTGACCTTBMBVHGGYGCTGAA TATKCTAAACCTAT TATKCTWRACCTWTGACCTTBMBVHGGYGCTGAA Direction: Forward Position #: 5 Overlap #: 10 Alignment: ----GTTGACCTTTGACCTTBMBVHGGYGCTGAA TATKCTAAACCTAT-------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Original Motif Reverse Complement TATKCTWRACCTWTGACCTTBMBVHGGYGCTGAA TGRCCTKTGHCCKAB TATKCTTGACCTWTGMCCTDBMBVHGGYGCTGAA Direction: Forward Position #: 7 Overlap #: 15 Alignment: TATKCTWRACCTWTGACCTTBMBVHGGYGCTGAA ------TGRCCTKTGHCCKAB------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR4A2 Original Motif Reverse Complement TATKCTTGACCTWTGMCCTDBMBVHGGYGCTGAA GTGACCTT GTRWBCTTGACCTWTGMCCTDBMBVHGGYGCTGAA Direction: Forward Position #: 2 Overlap #: 7 Alignment: -TATKCTTGACCTWTGMCCTDBMBVHGGYGCTGAA GTGACCTT--------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* 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 Original Motif Reverse Complement GCACTG GGAGCACTGTGACACCACA GGAGCACTGTGMMMYSACA Direction: Forward Position #: 11 Overlap #: 6 Alignment: ----------GCACTG--- GGAGCACTGTGACACCACA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Original Motif Reverse Complement GGAGCACTGTGMMMYSACA AGTGSWSCACTGTGAMAMCACAGTG AGTGGAGCACTGTGMMMHCACAGTG Direction: Forward Position #: 4 Overlap #: 19 Alignment: ---GGAGCACTGTGMMMYSACA--- AGTGSWSCACTGTGAMAMCACAGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TGGAGCACTGTGACAcCACAGTGg Original Motif Original Motif AGTGGAGCACTGTGMMMHCACAGTG TGGAGCACTGTGACAVCACAGTGG TGGAGCACTGTGACAVCACAGTGGAGCACTGTGMMMHCACAGTG Direction: Forward Position #: 20 Overlap #: 5 Alignment: -------------------AGTGGAGCACTGTGMMMHCACAGTG TGGAGCACTGTGACAVCACAGTGG-------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CAcCACAGTGGAGCAct Combined Motif Reverse Complement Reverse Complement CACTGTGDYRYCACAGTGCTCCACTGTGVTGTCACAGTGCTCCA AGTGCTCCACTGTGDTG CACTGTGDYRYCACAGTGCTCCACTGTGVTGTCACAGTGCTCCA Direction: Forward Position #: 15 Overlap #: 17 Alignment: CACTGTGDYRYCACAGTGCTCCACTGTGVTGTCACAGTGCTCCA --------------AGTGCTCCACTGTGDTG------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CagTGCTCCACTGTGgT Combined Motif Original Motif Original Motif CACTGTGDYRYCACAGTGCTCCACTGTGVTGTCACAGTGCTCCA CAGTGCTCCACTGTGBT CACTGTGDYRYCACAGTGCTCCACTGTGBTGTCACAGTGCTCCA Direction: Forward Position #: 14 Overlap #: 17 Alignment: CACTGTGDYRYCACAGTGCTCCACTGTGVTGTCACAGTGCTCCA -------------CAGTGCTCCACTGTGBT-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- AgTGCTCCACTGTGgTGTCACAgT Combined Motif Reverse Complement Reverse Complement TGGAGCACTGTGACABCACAGTGGAGCACTGTGMMMHCACAGTG ACTGTGACACCACAGTGGAGCACT TGGAGCACTGTGACACCACAGTGGAGCACTGTGMMMHCACAGTG Direction: Forward Position #: 7 Overlap #: 24 Alignment: TGGAGCACTGTGACABCACAGTGGAGCACTGTGMMMHCACAGTG ------ACTGTGACACCACAGTGGAGCACT-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Reverse Complement CACTGTGDYRYCACAGTGCTCCACTGTGGTGTCACAGTGCTCCA GGYGCTGTCCATGGTGCTGAA GGYGCTGTCCAYKGTGCTGHMACAGTGCTCCACTGTGGTGTCACAGTGCTCCA Direction: Forward Position #: 10 Overlap #: 12 Alignment: ---------CACTGTGDYRYCACAGTGCTCCACTGTGGTGTCACAGTGCTCCA GGYGCTGTCCATGGTGCTGAA-------------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Tcfcp2l1 Original Motif Original Motif GGYGCTGTCCAYKGTGCTGHMACAGTGCTCCACTGTGGTGTCACAGTGCTCCA CCAGYYHVADCCRG CCRGYBCTRTCCAGKGTGCTGHMACAGTGCTCCACTGTGGTGTCACAGTGCTCCA Direction: Forward Position #: 3 Overlap #: 12 Alignment: --GGYGCTGTCCAYKGTGCTGHMACAGTGCTCCACTGTGGTGTCACAGTGCTCCA CCAGYYHVADCCRG----------------------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 5 Original Motif Original Motif CCRGYBCTRTCCAGKGTGCTGHMACAGTGCTCCACTGTGGTGTCACAGTGCTCCA CWGAGCCAYCTYTC CWGAGCCASCTCTBTCCAGKGTGCTGHMACAGTGCTCCACTGTGGTGTCACAGTGCTCCA Direction: Forward Position #: 6 Overlap #: 9 Alignment: -----CCRGYBCTRTCCAGKGTGCTGHMACAGTGCTCCACTGTGGTGTCACAGTGCTCCA CWGAGCCAYCTYTC---------------------------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- wwCCAmAGTCmt Combined Motif Original Motif Original Motif CWGAGCCASCTCTBTCCAGKGTGCTGHMACAGTGCTCCACTGTGGTGTCACAGTGCTCCA DDCCAMAGTCHB CWGAGCCASCTCTBTCCAGKGTGCTDCCACAGTSCTCCACTGTGGTGTCACAGTGCTCCA Direction: Forward Position #: 25 Overlap #: 12 Alignment: CWGAGCCASCTCTBTCCAGKGTGCTGHMACAGTGCTCCACTGTGGTGTCACAGTGCTCCA ------------------------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 21 Original Motif Reverse Complement TTGCGCAA TTYGGAAAGCAG TTYGKWRMGCAR Direction: Backward Position #: 1 Overlap #: 8 Alignment: ----TTGCGCAA TTYGGAAAGCAG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Original Motif Original Motif TTYGKWRMGCAR TGAMCTTTGMMCYT TGAMCTTTGDWVMKCAR Direction: Forward Position #: 6 Overlap #: 9 Alignment: -----TTYGKWRMGCAR TGAMCTTTGMMCYT--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Original Motif Reverse Complement TGAMCTTTGDWVMKCAR TGRCCTKTGHCCKAB TGACCTTTGBMCDDCAR Direction: Forward Position #: 1 Overlap #: 15 Alignment: TGAMCTTTGDWVMKCAR TGRCCTKTGHCCKAB-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* 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 TGKKTSGGTGTGBGTGTRTG Direction: Backward Position #: 8 Overlap #: 11 Alignment: --KKTCGGKGTKS------- TGTGTGDKTGTGTGTGTRTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR1 Reverse Complement Original Motif CAMACACVCACACCSAYRCA VDBHMAGGTCACCCTGACCY VDBHMHRSWCACVCWSACCBAYRCA Direction: Forward Position #: 6 Overlap #: 15 Alignment: -----CAMACACVCACACCSAYRCA VDBHMAGGTCACCCTGACCY----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM1 Combined Motif Original Motif Original Motif VDBHMHRSWCACVCWSACCBAYRCA CACACACACACWCACACA VDBHMHRSWCACACACACMCAYACACACA Direction: Forward Position #: 12 Overlap #: 14 Alignment: VDBHMHRSWCACVCWSACCBAYRCA---- -----------CACACACACACWCACACA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TGGAGCACTGTGACAcCACAGTGg Reverse Complement Original Motif TGTGTGTKTGYGTGTGTGTGWSMDRDBHV TGGAGCACTGTGACAVCACAGTGG TGGAGCACTGTGACAVCWSWGTGKKTGYGTGTGTGTGWSMDRDBHV Direction: Forward Position #: 18 Overlap #: 7 Alignment: -----------------TGTGTGTKTGYGTGTGTGTGWSMDRDBHV TGGAGCACTGTGACAVCACAGTGG---------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Original Motif Original Motif TGGAGCACTGTGACAVCWSWGTGKKTGYGTGTGTGTGWSMDRDBHV VHRGGTCABDBTGMCCTB TGGAGCACTGTGACAVCWSWGTGKKTGYGTGTVHRKGTCAVDDBVHCCTB Direction: Forward Position #: 33 Overlap #: 14 Alignment: TGGAGCACTGTGACAVCWSWGTGKKTGYGTGTGTGTGWSMDRDBHV---- --------------------------------VHRGGTCABDBTGMCCTB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TgTGgTGTCACAGTGCTCC Combined Motif Original Motif Original Motif TGGAGCACTGTGACAVCWSWGTGKKTGYGTGTVHRKGTCAVDDBVHCCTB TGTGGTGTCACAGTGCTCC TGGAGCACTGTGACAVCWSWGTKGKKGTGTSWCWGTGYYMCDDBVHCCTB Direction: Forward Position #: 23 Overlap #: 19 Alignment: TGGAGCACTGTGACAVCWSWGTGKKTGYGTGTVHRKGTCAVDDBVHCCTB ----------------------TGTGGTGTCACAGTGCTCC--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 6 Combined Motif Reverse Complement Original Motif BAGGHVVHHGRMKCACWGWSACACRRCYACWSWGVTGTCACAGTGCTCCA CASABACWSACACA BAGGHVVHHGRMKCACWSASACWSAVACACWSWGVTGTCACAGTGCTCCA Direction: Forward Position #: 16 Overlap #: 14 Alignment: BAGGHVVHHGRMKCACWGWSACACRRCYACWSWGVTGTCACAGTGCTCCA ---------------CASABACWSACACA--------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Reverse Complement Reverse Complement TGGAGCACTGTGACAVCWSWGTGTVTSWGTSTSWGTGYYMCDDBVHCCTB AGTGSWSCACTGTGAMAMCACAGTG AGTGGAGCACTGTGACAVCACAGTGTVTSWGTSTSWGTGYYMCDDBVHCCTB Direction: Forward Position #: 3 Overlap #: 23 Alignment: --TGGAGCACTGTGACAVCWSWGTGTVTSWGTSTSWGTGYYMCDDBVHCCTB AGTGSWSCACTGTGAMAMCACAGTG--------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Original Motif BAGGHVVHHGRMKCACWSASACWSAVACACTGTGVTGTCACAGTGCTCCACT TTCAGCACCATGGACAGCKCC TTCAGCACCHHGGACAGCDVMKCACWSASACWSAVACACTGTGVTGTCACAGTGCTCCACT Direction: Forward Position #: 10 Overlap #: 12 Alignment: ---------BAGGHVVHHGRMKCACWSASACWSAVACACTGTGVTGTCACAGTGCTCCACT TTCAGCACCATGGACAGCKCC---------------------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 2 Combined Motif Reverse Complement Reverse Complement AGTGGAGCACTGTGACAVCACAGTGTVTSWGTSTSWGTGYRVHGCTGTCCHHGGTGCTGAA GTGTGTGTGTGTGT AGTGGAGCACTGTGACAVCACAGTGTGTGTGTGTGTGTGYRVHGCTGTCCHHGGTGCTGAA Direction: Forward Position #: 25 Overlap #: 14 Alignment: AGTGGAGCACTGTGACAVCACAGTGTVTSWGTSTSWGTGYRVHGCTGTCCHHGGTGCTGAA ------------------------GTGTGTGTGTGTGT----------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Original Motif Reverse Complement TGVYCTTTGBCCT TGRCCTKTGHCCKAB TGRCCTKTGHCYKVBCTTTGBCCT Direction: Forward Position #: 12 Overlap #: 4 Alignment: -----------TGVYCTTTGBCCT TGRCCTKTGHCCKAB--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Original Motif Original Motif TGRCCTKTGHCYKVBCTTTGBCCT VHRGGTCABDBTGMCCTB HDRSSTYWSBBTGMCCTBTGBCCT Direction: Forward Position #: 1 Overlap #: 18 Alignment: TGRCCTKTGHCYKVBCTTTGBCCT VHRGGTCABDBTGMCCTB------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Original Motif Original Motif HDRSSTYWSBBTGMCCTBTGBCCT VDBHMAGGTCACCCTGACCY HDRVVBCHVGGTSACCYTKRCCCT Direction: Forward Position #: 4 Overlap #: 20 Alignment: HDRSSTYWSBBTGMCCTBTGBCCT ---VDBHMAGGTCACCCTGACCY- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM12 Combined Motif Reverse Complement Reverse Complement AGGGMYAMGGTSACCBHGVVVKHH VCTSTGKSCMKBCTRCYCTK AGGGMYAMGGTSVCHBTGDSVHBHCTRCYCTK Direction: Forward Position #: 13 Overlap #: 12 Alignment: AGGGMYAMGGTSACCBHGVVVKHH-------- ------------VCTSTGKSCMKBCTRCYCTK ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Original Motif Reverse Complement AGGGMYAMGGTSVCHBTGDSVHBHCTRCYCTK AKGYYCAAAGRTCA ARGBBCWAAGRTCACHBTGDSVHBHCTRCYCTK Direction: Forward Position #: 2 Overlap #: 13 Alignment: -AGGGMYAMGGTSVCHBTGDSVHBHCTRCYCTK AKGYYCAAAGRTCA------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR1H2RXRA Original Motif Original Motif ARGBBCWAAGRTCACHBTGDSVHBHCTRCYCTK AAAGGTCAAAGGTCAAC AAAGGTCAAAGGTCAMYBTGDSVHBHCTRCYCTK Direction: Forward Position #: 2 Overlap #: 16 Alignment: -ARGBBCWAAGRTCACHBTGDSVHBHCTRCYCTK AAAGGTCAAAGGTCAAC----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Reverse Complement Reverse Complement RAGKGMAGHVHVSHCABKYTGACCTTTGACCTTT AGTGSWSCACTGTGAMAMCACAGTG AGTGVAGBRCWGTGHVVHCACAGTGACCTTTGACCTTT Direction: Forward Position #: 5 Overlap #: 21 Alignment: ----RAGKGMAGHVHVSHCABKYTGACCTTTGACCTTT AGTGSWSCACTGTGAMAMCACAGTG------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TGGAGCACTGTGACAcCACAGTGg Original Motif Reverse Complement AGTGVAGBRCWGTGHVVHCACAGTGACCTTTGACCTTT CCACTGTGVTGTCACAGTGCTCCA CCACTGTRGTGBMRCASTGYKMCAHCACAGTGACCTTTGACCTTT Direction: Forward Position #: 8 Overlap #: 17 Alignment: -------AGTGVAGBRCWGTGHVVHCACAGTGACCTTTGACCTTT CCACTGTGVTGTCACAGTGCTCCA--------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Original Motif AAAGGTCAAAGGTCACTGTGDTGRRKCASTGKRVCACKACAGTGG TTCAGCACCATGGACAGCKCC TWMAGSWCMAWGGWCAGBGYSDTGRRKCASTGKRVCACKACAGTGG Direction: Forward Position #: 2 Overlap #: 20 Alignment: -AAAGGTCAAAGGTCACTGTGDTGRRKCASTGKRVCACKACAGTGG TTCAGCACCATGGACAGCKCC------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 3 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 3 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CACTGTGrYrtCACAGTGswsCAcT Combined Motif Reverse Complement Original Motif VDCDSWGRKCRMDSTGVCCTK CACTGTGRTRTCACAGTGSWSCACT CACTGTGRTVDCACWGTSCTBCACT Direction: Forward Position #: 1 Overlap #: 21 Alignment: VDCDSWGRKCRMDSTGVCCTK---- CACTGTGRTRTCACAGTGSWSCACT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM2 Combined Motif Reverse Complement Original Motif AGTGBAGSACWGTGDVAMCACAGTG CHHCHBTCCTSCYTCTGC AGTGBABBHCHBTSHDVCCWCWGYG Direction: Forward Position #: 7 Overlap #: 18 Alignment: AGTGBAGSACWGTGDVAMCACAGTG ------CHHCHBTCCTSCYTCTGC- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CTCF Combined Motif Original Motif Reverse Complement AGTGBABBHCHBTSHDVCCWCWGYG BMSMGCCYMCTKSTGGMHM AGTGSMGCCCMCTBVTGSCHVWGYG Direction: Forward Position #: 3 Overlap #: 19 Alignment: AGTGBABBHCHBTSHDVCCWCWGYG --BMSMGCCYMCTKSTGGMHM---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TGGAGCACTGTGACAcCACAGTGg Combined Motif Original Motif Original Motif AGTGSMGCCCMCTBVTGSCHVWGYG TGGAGCACTGTGACAVCACAGTGG AGTGGAGCMCTSTGAYRSCACAGTGG Direction: Forward Position #: 3 Overlap #: 23 Alignment: AGTGSMGCCCMCTBVTGSCHVWGYG- --TGGAGCACTGTGACAVCACAGTGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Original Motif Reverse Complement AGTGGAGCMCTSTGAYRSCACAGTGG TGRCCTKTGHCCKAB AGTGGWGVMCTKTGVCMBMVCAGTGG Direction: Forward Position #: 6 Overlap #: 15 Alignment: AGTGGAGCMCTSTGAYRSCACAGTGG -----TGRCCTKTGHCCKAB------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Tcfcp2l1 Combined Motif Reverse Complement Reverse Complement CCACTGBRBRGBCAYAGRVCWCCACT CKGGDTBDMMCTGG CCACYKGGBDDBMACWGGVCWCCACT Direction: Forward Position #: 5 Overlap #: 14 Alignment: CCACTGBRBRGBCAYAGRVCWCCACT ----CKGGDTBDMMCTGG-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFM13 Reverse Complement Original Motif AGTGGWGVCCWGTRVHDVCCYKGTGG TTTTTTTKTTKTTTAATTHW TTTTTTTKTTKTTTARTKVWGVCCWGTRVHDVCCYKGTGG Direction: Forward Position #: 15 Overlap #: 6 Alignment: --------------AGTGGWGVCCWGTRVHDVCCYKGTGG TTTTTTTKTTKTTTAATTHW-------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFF11 Combined Motif Original Motif Original Motif TTTTTTTKTTKTTTARTKVWGVCCWGTRVHDVCCYKGTGG CTGCTGBDBBDGBD TTTTTTTKTTKTTTARTKVWGVCCWSTGCTGVVBHDGHGG Direction: Forward Position #: 26 Overlap #: 14 Alignment: TTTTTTTKTTKTTTARTKVWGVCCWGTRVHDVCCYKGTGG -------------------------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: Backward Position #: 9 Overlap #: 8 Alignment: -AAGGTCAC-------- AAAGGTCAAAGGTCAAC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR1 Reverse Complement Reverse Complement GTTGACCTYTGACCTTT MGGTCAGGGTGACCTRDBHV MGGTCAGGKTGACCTBTGACCTTT Direction: Forward Position #: 8 Overlap #: 13 Alignment: -------GTTGACCTYTGACCTTT MGGTCAGGGTGACCTRDBHV---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Original Motif Original Motif MGGTCAGGKTGACCTBTGACCTTT VHRGGTCABDBTGMCCTB MGGTCADRKKKMMCTBTGACCTBT Direction: Forward Position #: 6 Overlap #: 18 Alignment: MGGTCAGGKTGACCTBTGACCTTT -----VHRGGTCABDBTGMCCTB- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 17 Original Motif Reverse Complement MGGTCADRKKKMMCTBTGACCTBT GAGGTCAGAAG GAGGTCAGAAGKMMCTBTGACCTBT Direction: Forward Position #: 2 Overlap #: 10 Alignment: -MGGTCADRKKKMMCTBTGACCTBT GAGGTCAGAAG-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 15 Reverse Complement Original Motif AVAGGTCABAGYRYCTTCTGACCTC AAAGRTMAAACTA AAAGRTMAAASTAYCTTCTGACCTC Direction: Forward Position #: 1 Overlap #: 13 Alignment: AVAGGTCABAGYRYCTTCTGACCTC AAAGRTMAAACTA------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Original Motif Original Motif AAAGRTMAAASTAYCTTCTGACCTC BTRGGDCARAGGKCA VDAGGBCAAAGKDCMTTCTGACCTC Direction: Forward Position #: 1 Overlap #: 15 Alignment: AAAGRTMAAASTAYCTTCTGACCTC BTRGGDCARAGGKCA---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 48 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 48 Motif 1 Original Motif Reverse Complement GCARRGGSAGS GCAGAGGSAKG GCAGAGGSAGS Direction: Forward Position #: 1 Overlap #: 11 Alignment: GCARRGGSAGS GCAGAGGSAKG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFM2 Reverse Complement Original Motif SCTSCCTCTGC CHHCHBTCCTSCYTCTGC CHHCHBTCCTSCYYCTSCCTCTGC Direction: Forward Position #: 14 Overlap #: 5 Alignment: -------------SCTSCCTCTGC CHHCHBTCCTSCYTCTGC------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CTCF Combined Motif Original Motif Reverse Complement CHHCHBTCCTSCYYCTSCCTCTGC BMSMGCCYMCTKSTGGMHM CHHMVHKCCYSCTBSTGSCBMTGC Direction: Forward Position #: 3 Overlap #: 19 Alignment: CHHCHBTCCTSCYYCTSCCTCTGC --BMSMGCCYMCTKSTGGMHM--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFF11 Combined Motif Original Motif Original Motif CHHMVHKCCYSCTBSTGSCBMTGC CTGCTGBDBBDGBD CHHMVCDSCTGCHBSTGBVBMTGC Direction: Forward Position #: 6 Overlap #: 14 Alignment: CHHMVHKCCYSCTBSTGSCBMTGC -----CTGCTGBDBBDGBD----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM12 Combined Motif Reverse Complement Original Motif GCARVVBCASBHGCAGSDGVRHDG RAGKGMAGVRRGSRCASAGV GCARVVBCASBHGMRGSVDGVVRGSRCASAGV Direction: Forward Position #: 13 Overlap #: 12 Alignment: GCARVVBCASBHGCAGSDGVRHDG-------- ------------RAGKGMAGVRRGSRCASAGV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Tcfcp2l1 Combined Motif Original Motif Reverse Complement GCARVVBCASBHGMRGSVDGVVRGSRCASAGV CKGGDTBDMMCTGG GCARVVBCASBHGMRGSCDGGDDBVVMMBRGV Direction: Forward Position #: 18 Overlap #: 14 Alignment: GCARVVBCASBHGMRGSVDGVVRGSRCASAGV -----------------CKGGDTBDMMCTGG- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Original Motif Original Motif GCARVVBCASBHGMRGSCDGGDDBVVMMBRGV TTCAGCACCATGGACAGCKCC TKCAGVACCABGGACAGSVBSGDDBVVMMBRGV Direction: Forward Position #: 2 Overlap #: 20 Alignment: -GCARVVBCASBHGMRGSCDGGDDBVVMMBRGV TTCAGCACCATGGACAGCKCC------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Reverse Complement Original Motif VCMBRRBVBDDCSBVSCTGTCCVTGGTVCTGYA VDBHMAGGTCACCCTGACCY VCMBRRBVBDDCSBVSCTVBVCVWGGTSMYSBWGACCY Direction: Forward Position #: 19 Overlap #: 15 Alignment: VCMBRRBVBDDCSBVSCTGTCCVTGGTVCTGYA----- ------------------VDBHMAGGTCACCCTGACCY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 3 Combined Motif Reverse Complement Reverse Complement MGGTCWBSMYSACCWVGVVVAGSVBSGDDBVVMMBRGV CTSTGTBKMCTGH MGGTCWBSMYSACCWVGVVVAGSCHSKRKBKMMHGDGV Direction: Forward Position #: 24 Overlap #: 13 Alignment: MGGTCWBSMYSACCWVGVVVAGSVBSGDDBVVMMBRGV -----------------------CTSTGTBKMCTGH-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Original Motif Original Motif MGGTCWBSMYSACCWVGVVVAGSCHSKRKBKMMHGDGV VHRGGTCABDBTGMCCTB MGGTCWBSMYSACCWVGVVVAGSCHVDGGTCAVDBDGHCCTB Direction: Forward Position #: 25 Overlap #: 14 Alignment: MGGTCWBSMYSACCWVGVVVAGSCHSKRKBKMMHGDGV---- ------------------------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 Reverse Complement Original Motif CSSGCKCGCGS SBCCCCGCCSBB SBCCCCGCCSSGCKCGCGS Direction: Forward Position #: 9 Overlap #: 4 Alignment: --------CSSGCKCGCGS SBCCCCGCCSBB------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- sscCCCGCGcs Combined Motif Original Motif Reverse Complement SBCCCCGCCSSGCKCGCGS SBCGCGGGGSB SBCCSCGCSGSGSKCGCGS Direction: Forward Position #: 4 Overlap #: 11 Alignment: SBCCCCGCCSSGCKCGCGS ---SBCGCGGGGSB----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- cCGCGGrCACG Combined Motif Original Motif Original Motif SBCCSCGCSGSGSKCGCGS CCGCGGRCACG SBCCCCGCGGRSVSSGCGS Direction: Forward Position #: 5 Overlap #: 11 Alignment: SBCCSCGCSGSGSKCGCGS ----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 Reverse Complement Original Motif HVCHGHGVCYGCMS TTCAGCACCATGGACAGCKCC TTCAGCACCATGGACAGCDCCGHGVCYGCMS Direction: Forward Position #: 18 Overlap #: 4 Alignment: -----------------HVCHGHGVCYGCMS TTCAGCACCATGGACAGCKCC---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Reverse Complement Reverse Complement SYGCKGVCDCGGHGCTGTCCATGGTGCTGAA MGGTCAGGGTGACCTRDBHV SYGCKGVBGYSRVGCTGWCCHDGGTVCTGAA Direction: Forward Position #: 7 Overlap #: 20 Alignment: SYGCKGVCDCGGHGCTGTCCATGGTGCTGAA ------MGGTCAGGGTGACCTRDBHV----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ssGCkTGCssk Original Motif Original Motif SYGCKGVBGYSRVGCTGWCCHDGGTVCTGAA SSGCKTGCSSK SBGCKKGCGSBRVGCTGWCCHDGGTVCTGAA Direction: Forward Position #: 1 Overlap #: 11 Alignment: SYGCKGVBGYSRVGCTGWCCHDGGTVCTGAA SSGCKTGCSSK-------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ssCCCCGCSssk Combined Motif Reverse Complement Reverse Complement TTCAGVACCDHGGWCAGCVKBSCGCRYGCBS BBSGGCGGGGBS TTCAGVACCBDGGRCRGSGBBSCGCRYGCBS Direction: Forward Position #: 10 Overlap #: 12 Alignment: TTCAGVACCDHGGWCAGCVKBSCGCRYGCBS ---------BBSGGCGGGGBS---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CTCF Combined Motif Reverse Complement Original Motif SBGCKKGCGSBBCSCMGMCCDVGGTVCTGAA YDRCCASYAGRKGGCRSYV SBGCKKGYGBCCMSCAGVSSGCGSYVCTGAA Direction: Forward Position #: 8 Overlap #: 19 Alignment: SBGCKKGCGSBBCSCMGMCCDVGGTVCTGAA -------YDRCCASYAGRKGGCRSYV----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 3 Combined Motif Reverse Complement Reverse Complement TTCAGVMSCGCSSVCTGSYGGBCKCRYGCBS CTSTGTBKMCTGH TTCAGVMSCVHSTVYTKSHKGHCKCRYGCBS Direction: Forward Position #: 10 Overlap #: 13 Alignment: TTCAGVMSCGCSSVCTGSYGGBCKCRYGCBS ---------CTSTGTBKMCTGH--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 11-20-2016 22:58:31 Runtime: 1057.23 seconds MOTIFSIM is written by Ngoc Tam L. 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