**************************************************************************************************************************************************************************************************** MOTIFSIM - Motif Similarity Detection Tool Version 2.2 **************************************************************************************************************************************************************************************************** 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 Motif 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 STGGYCACCTDYGC Direction: Backward Position #: 6 Overlap #: 6 Alignment: ---CACCTD----- YGCCACCTDSTGGY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 5 Original Motif Original Motif STGGYCACCTDYGC CWGAGCCAYCTYTC CBKGGCCACCTBTSC Direction: Forward Position #: 2 Overlap #: 13 Alignment: -STGGYCACCTDYGC CWGAGCCAYCTYTC- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CTCF Original Motif Reverse Complement CBKGGCCACCTBTSC BMSMGCCYMCTKSTGGMHM CHBVGCCMCCTBBKSGMHM Direction: Forward Position #: 1 Overlap #: 15 Alignment: CBKGGCCACCTBTSC---- BMSMGCCYMCTKSTGGMHM ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RORA_1 Reverse Complement Reverse Complement YDRCSRBVAGGYGGCBBHG TGACCTDVWT TGACCDBVAKGYGGCBBHG Direction: Forward Position #: 1 Overlap #: 10 Alignment: YDRCSRBVAGGYGGCBBHG TGACCTDVWT--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Original Motif CHBVGCCMCYTVVDGGTCA TTCAGCACCATGGACAGCKCC TTCAGVRCCAYSKACAGSKCM Direction: Forward Position #: 3 Overlap #: 19 Alignment: --CHBVGCCMCYTVVDGGTCA TTCAGCACCATGGACAGCKCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Esrrb Reverse Complement Reverse Complement YGRSCTGTYSKTGGKVCTGAA TGACCTTGMBBB TGACCTKBHBBHGGKVCTGAA Direction: Forward Position #: 1 Overlap #: 12 Alignment: YGRSCTGTYSKTGGKVCTGAA TGACCTTGMBBB--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR1H2RXRA Combined Motif Reverse Complement Original Motif TTCAGVRCCHBBDBRAGGTCA AAAGGTCAAAGGTCAAC TTCAGVRCCHBBDHAAGGTCAAAGGTCAAC Direction: Forward Position #: 14 Overlap #: 8 Alignment: TTCAGVRCCHBBDBRAGGTCA--------- -------------AAAGGTCAAAGGTCAAC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 46 Combined Motif Original Motif Original Motif TTCAGVRCCHBBDHAAGGTCAAAGGTCAAC ATAGGTTTAGYATA TTCAGVRCCHBBDHAAGGTCAWAGGTYWAGYATA Direction: Forward Position #: 21 Overlap #: 10 Alignment: TTCAGVRCCHBBDHAAGGTCAAAGGTCAAC---- --------------------ATAGGTTTAGYATA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Original Motif Original Motif TTCAGVRCCHBBDHAAGGTCAWAGGTYWAGYATA BTRGGDCARAGGKCA BTVRGVVMMAGGKHAAGGTCAWAGGTYWAGYATA Direction: Forward Position #: 1 Overlap #: 15 Alignment: TTCAGVRCCHBBDHAAGGTCAWAGGTYWAGYATA BTRGGDCARAGGKCA------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR4A2 Combined Motif Original Motif Original Motif BTVRGVVMMAGGKHAAGGTCAWAGGTYWAGYATA AAGGTCAC BDAGGBCACAGGKHAAGGTCAWAGGTYWAGYATA Direction: Forward Position #: 2 Overlap #: 8 Alignment: BTVRGVVMMAGGKHAAGGTCAWAGGTYWAGYATA -AAGGTCAC------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* 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 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----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- REST Combined Motif Reverse Complement Reverse Complement CCACTKYYGCWCCACWGTGGWGKYRMMGT GGYGCTGTCCATGGTGCTGAA CCACTKYYGCWCCACDGTGSTGTCMMHGKTGCTGAA Direction: Forward Position #: 16 Overlap #: 14 Alignment: CCACTKYYGCWCCACWGTGGWGKYRMMGT------- ---------------GGYGCTGTCCATGGTGCTGAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Tcfcp2l1 Combined Motif Reverse Complement Original Motif TTCAGCAYCHYRGACASCACHGTGGWGCMMYAGTGG CCAGYYHVADCCRG TTCASCASYHHVRACMVSACHGTGGWGCMMYAGTGG Direction: Forward Position #: 5 Overlap #: 14 Alignment: TTCAGCAYCHYRGACASCACHGTGGWGCMMYAGTGG ----CCAGYYHVADCCRG------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 5 Combined Motif Reverse Complement Original Motif CCACTKYYGCWCCACDGTSVYGTMVDHKSTGSTGAA CWGAGCCAYCTYTC CCACTKYTGMKCCACBKYBCYGTMVDHKSTGSTGAA Direction: Forward Position #: 7 Overlap #: 14 Alignment: CCACTKYYGCWCCACDGTSVYGTMVDHKSTGSTGAA ------CWGAGCCAYCTYTC---------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wwCCAmAGTCmt Reverse Complement Original Motif TTCASCASYHHVRACMGVMRBGTGGYYCAKYAGTGG DDCCAMAGTCHB DTCMACAGTCHDRACMGVMRBGTGGYYCAKYAGTGG Direction: Forward Position #: 1 Overlap #: 12 Alignment: TTCASCASYHHVRACMGVMRBGTGGYYCAKYAGTGG 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 KWRMGCARTTYG Direction: Backward Position #: 1 Overlap #: 8 Alignment: ----TTGCGCAA TTYGGAAAGCAG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Original Motif Original Motif KWRMGCARTTYG TGAMCTTTGMMCYT TGAMCTTTRMVCADTTYG Direction: Forward Position #: 7 Overlap #: 8 Alignment: ------KWRMGCARTTYG TGAMCTTTGMMCYT---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Original Motif Reverse Complement TGAMCTTTRMVCADTTYG TGRCCTKTGHCCKAB TGACCTTTGVVCDDTTYG Direction: Forward Position #: 1 Overlap #: 15 Alignment: TGAMCTTTRMVCADTTYG TGRCCTKTGHCCKAB--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 28 Original Motif Original Motif TGACCTTTGVVCDDTTYG ATTTAGTAAA TAAARTTYAGTGACCTTTGVVC Direction: Backward Position #: 5 Overlap #: 6 Alignment: TGACCTTTGVVCDDTTYG---- ------------ATTTAGTAAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CAcCACAGTGGAGCAct Combined Motif Reverse Complement Original Motif GVVCAAAGGTCACTMAAKTTTA CAHCACAGTGGAGCACT GVVCAAAGGTCACYACAKTKKAGCACT Direction: Forward Position #: 11 Overlap #: 12 Alignment: GVVCAAAGGTCACTMAAKTTTA----- ----------CAHCACAGTGGAGCACT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TGGAGCACTGTGACAcCACAGTGg Original Motif Original Motif GVVCAAAGGTCACYACAKTKKAGCACT TGGAGCACTGTGACAVCACAGTGG TGGRGVMMWRKGWCACCACAGTGKAGCACT Direction: Forward Position #: 4 Overlap #: 21 Alignment: ---GVVCAAAGGTCACYACAKTKKAGCACT TGGAGCACTGTGACAVCACAGTGG------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif AgTGCTCCACTGTGgTGTCACAgT Reverse Complement Original Motif AGTGCTYCACTGTGGTGWCYMWYYVCKCCA AGTGCTCCACTGTGGTGTCACAGT AGTGCTCCACTGTGGTGTCMCABTVCKCCA Direction: Forward Position #: 1 Overlap #: 24 Alignment: AGTGCTYCACTGTGGTGWCYMWYYVCKCCA AGTGCTCCACTGTGGTGTCACAGT------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CagTGCTCCACTGTGgT Original Motif Original Motif AGTGCTCCACTGTGGTGTCMCABTVCKCCA CAGTGCTCCACTGTGBT CAGTGCTCCACTGTGGTGTCMCABTVCKCCA Direction: Forward Position #: 2 Overlap #: 16 Alignment: -AGTGCTCCACTGTGGTGTCMCABTVCKCCA CAGTGCTCCACTGTGBT-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM3 Combined Motif Original Motif Reverse Complement CAGTGCTCCACTGTGGTGTCMCABTVCKCCA BTTHAAAAAAYAAAAAAR CAGTGCTCCACTGTGGTGTCMCABTVCTYCAAAAAAYAAAAAAR Direction: Forward Position #: 27 Overlap #: 5 Alignment: CAGTGCTCCACTGTGGTGTCMCABTVCKCCA------------- --------------------------BTTHAAAAAAYAAAAAAR ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CACTGTGrYrtCACAGTGswsCAcT Combined Motif Original Motif Reverse Complement CAGTGCTCCACTGTGGTGTCMCABTVCTYCAAAAAAYAAAAAAR AGTGSWSCACTGTGAMAMCACAGTG CAGTGCTSCACTGTGVYRHCACAGTGCTYCAAAAAAYAAAAAAR Direction: Forward Position #: 2 Overlap #: 25 Alignment: CAGTGCTCCACTGTGGTGTCMCABTVCTYCAAAAAAYAAAAAAR -AGTGSWSCACTGTGAMAMCACAGTG------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 83 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- srACyCCGAyr TFM11 Reverse Complement Reverse Complement KKTCGGKGTKS TGTGTGDKTGTGTGTGTRTG GTGTRTGKKTSGGTGTGBTG Direction: Backward Position #: 8 Overlap #: 11 Alignment: --KKTCGGKGTKS------- TGTGTGDKTGTGTGTGTRTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR1 Original Motif Reverse Complement GTGTRTGKKTSGGTGTGBTG MGGTCAGGGTGACCTRDBHV MGGTSWGKGTGWCBKDGTBBTG Direction: Forward Position #: 3 Overlap #: 18 Alignment: --GTGTRTGKKTSGGTGTGBTG MGGTCAGGGTGACCTRDBHV-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFM1 Original Motif Reverse Complement MGGTSWGKGTGWCBKDGTBBTG TGTGTGWGTGTGTGTGTG TVKGTSWGTGTGTSTGTGTBBTG Direction: Forward Position #: 2 Overlap #: 17 Alignment: -MGGTSWGKGTGWCBKDGTBBTG TGTGTGWGTGTGTGTGTG----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TGGAGCACTGTGACAcCACAGTGg Reverse Complement Original Motif CABBACACASACACACWSACRBA TGGAGCACTGTGACAVCACAGTGG TGGAGCACTGTGACABCACABWGRCACACWSACRBA Direction: Forward Position #: 14 Overlap #: 11 Alignment: -------------CABBACACASACACACWSACRBA TGGAGCACTGTGACAVCACAGTGG------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR2 Reverse Complement Reverse Complement TVKGTSWGTGTGKCWBTGTGBTGTCACAGTGCTCCA BAGGYCABHBTGACCKHV TAGGTSABBGTGDCHBTGTGBTGTCACAGTGCTCCA Direction: Forward Position #: 1 Overlap #: 18 Alignment: TVKGTSWGTGTGKCWBTGTGBTGTCACAGTGCTCCA BAGGYCABHBTGACCKHV------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TgTGgTGTCACAGTGCTCC Original Motif Original Motif TAGGTSABBGTGDCHBTGTGBTGTCACAGTGCTCCA TGTGGTGTCACAGTGCTCC TGTKVKGTCACWGTGHYCCTGTGBTGTCACAGTGCTCCA Direction: Forward Position #: 4 Overlap #: 16 Alignment: ---TAGGTSABBGTGDCHBTGTGBTGTCACAGTGCTCCA TGTGGTGTCACAGTGCTCC-------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 6 Reverse Complement Reverse Complement TGGAGCACTGTGACABCACAGGMDCACWGTGACRVYACA TGTGTSWGTBTSTG TGTGKADSWCTGTGACABCACAGGMDCACWGTGACRVYACA Direction: Forward Position #: 3 Overlap #: 12 Alignment: --TGGAGCACTGTGACABCACAGGMDCACWGTGACRVYACA TGTGTSWGTBTSTG--------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Original Motif Reverse Complement TGTGKADSWCTGTGACABCACAGGMDCACWGTGACRVYACA AGTGSWSCACTGTGAMAMCACAGTG WGTGBAGCACTGTGACAVCACAGKVDCACWGTGACRVYACA Direction: Forward Position #: 1 Overlap #: 25 Alignment: TGTGKADSWCTGTGACABCACAGGMDCACWGTGACRVYACA AGTGSWSCACTGTGAMAMCACAGTG---------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- REST Combined Motif Reverse Complement Original Motif TGTKVKGTCACWGTGHVRCTGTGVTGTCACAGTGCTBCACW TTCAGCACCATGGACAGCKCC TGTKVKGTCACWGTGHVRCTGTGVTKTCASMRYSHTGSACAGCKCC Direction: Forward Position #: 26 Overlap #: 16 Alignment: TGTKVKGTCACWGTGHVRCTGTGVTGTCACAGTGCTBCACW----- -------------------------TTCAGCACCATGGACAGCKCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 2 Combined Motif Original Motif Reverse Complement TGTKVKGTCACWGTGHVRCTGTGVTKTCASMRYSHTGSACAGCKCC GTGTGTGTGTGTGT TGKKGTGTSWSTGTGTVRCTGTGVTKTCASMRYSHTGSACAGCKCC Direction: Forward Position #: 3 Overlap #: 14 Alignment: TGTKVKGTCACWGTGHVRCTGTGVTKTCASMRYSHTGSACAGCKCC --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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Original Motif Reverse Complement TGVYCTTTGBCCT TGRCCTKTGHCCKAB TKVHCYTTKBCCYKAB Direction: Forward Position #: 2 Overlap #: 12 Alignment: TGVYCTTTGBCCT--- -TGRCCTKTGHCCKAB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Reverse Complement Reverse Complement BTRKGGBRAAKGHVRA BAGGYCABHBTGACCKHV BTRBRGBDMABBBTGACCKHV Direction: Forward Position #: 4 Overlap #: 13 Alignment: BTRKGGBRAAKGHVRA----- ---BAGGYCABHBTGACCKHV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Original Motif Reverse Complement BTRBRGBDMABBBTGACCKHV MGGTCAGGGTGACCTRDBHV BTRBVGGHCABGBTGACCKDDBHV Direction: Forward Position #: 5 Overlap #: 17 Alignment: BTRBRGBDMABBBTGACCKHV--- ----MGGTCAGGGTGACCTRDBHV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM12 Combined Motif Original Motif Reverse Complement BTRBVGGHCABGBTGACCKDDBHV VCTSTGKSCMKBCTRCYCTK BTRBVGSTCWGBVHVDCCTDVBHBK Direction: Forward Position #: 6 Overlap #: 19 Alignment: BTRBVGGHCABGBTGACCKDDBHV- -----VCTSTGKSCMKBCTRCYCTK ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR2F1 Combined Motif Original Motif Original Motif BTRBVGSTCWGBVHVDCCTDVBHBK TGAMCTTTGMMCYT BTKGAVCTYTGVVCHDCCTDVBHBK Direction: Forward Position #: 3 Overlap #: 14 Alignment: BTRBVGSTCWGBVHVDCCTDVBHBK --TGAMCTTTGMMCYT--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR1H2RXRA Original Motif Reverse Complement BTKGAVCTYTGVVCHDCCTDVBHBK GTTGACCTTTGACCTTT STTGACCTTTGACCBTYCTDVBHBK Direction: Forward Position #: 1 Overlap #: 17 Alignment: BTKGAVCTYTGVVCHDCCTDVBHBK GTTGACCTTTGACCTTT-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Original Motif Reverse Complement STTGACCTTTGACCBTYCTDVBHBK AGTGSWSCACTGTGAMAMCACAGTG AGTGBWGMMCTKTGACMHYACWGTBHBK Direction: Forward Position #: 4 Overlap #: 22 Alignment: ---STTGACCTTTGACCBTYCTDVBHBK AGTGSWSCACTGTGAMAMCACAGTG--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TGGAGCACTGTGACAcCACAGTGg Reverse Complement Original Motif RVDBACWGTKDRGTCAYAGYRCWVCACT TGGAGCACTGTGACAVCACAGTGG TGGAGCACTGTGAVRBCACAGTGSWVCACT Direction: Forward Position #: 3 Overlap #: 22 Alignment: --RVDBACWGTKDRGTCAYAGYRCWVCACT TGGAGCACTGTGACAVCACAGTGG------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Reverse Complement AGTGBWSCACTGTGVKVTCACAGTGCTCCA GGYGCTGTCCATGGTGCTGAA GGAGYKGTCCAYKGTGCTGDHACAGTGCTCCA Direction: Forward Position #: 3 Overlap #: 19 Alignment: --AGTGBWSCACTGTGVKVTCACAGTGCTCCA GGYGCTGTCCATGGTGCTGAA----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Reverse Complement Original Motif VDCDSWGRKCRMDSTGVCCTK CACTGTGRTRTCACAGTGSWSCACT CACTGTGRTVDCACWGTSCTBCACT Direction: Forward Position #: 1 Overlap #: 21 Alignment: VDCDSWGRKCRMDSTGVCCTK---- CACTGTGRTRTCACAGTGSWSCACT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFM2 Original Motif Original Motif CACTGTGRTVDCACWGTSCTBCACT CHHCHBTCCTSCYTCTGC CHHCHBTSVTSCCHCWGYSCTBCACT Direction: Forward Position #: 2 Overlap #: 17 Alignment: -CACTGTGRTVDCACWGTSCTBCACT CHHCHBTCCTSCYTCTGC-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CTCF Reverse Complement Reverse Complement AGTGBAGSMCWGHGGSAVSABHGHDG BMSMGCCYMCTKSTGGMHM BAGYGCMBCCYDGTGGVHVSABHGHDG Direction: Forward Position #: 2 Overlap #: 18 Alignment: -AGTGBAGSMCWGHGGSAVSABHGHDG BMSMGCCYMCTKSTGGMHM-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TGGAGCACTGTGACAcCACAGTGg Combined Motif Original Motif Original Motif BAGYGCMBCCYDGTGGVHVSABHGHDG TGGAGCACTGTGACAVCACAGTGG BAGTGSAGCMCTGTGRCAVCACAGTGG Direction: Forward Position #: 4 Overlap #: 24 Alignment: BAGYGCMBCCYDGTGGVHVSABHGHDG ---TGGAGCACTGTGACAVCACAGTGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Reverse Complement Original Motif CCACTGTGVTGKCACAGYGCTSCACTV BTRGGDCARAGGKCA CCACTSTGGKGBMAMRGTSVTSCACTV Direction: Forward Position #: 6 Overlap #: 15 Alignment: CCACTGTGVTGKCACAGYGCTSCACTV -----BTRGGDCARAGGKCA------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Tcfcp2l1 Original Motif Original Motif CCACTSTGGKGBMAMRGTSVTSCACTV CCAGYYHVADCCRG CCASTBHVRDSCARMRGTSVTSCACTV Direction: Forward Position #: 1 Overlap #: 14 Alignment: CCACTSTGGKGBMAMRGTSVTSCACTV CCAGYYHVADCCRG------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFM13 Reverse Complement Reverse Complement BAGTGSABSACMYMTGSHKVHVASTGG WHAATTAAARAARAAAAAAA ARAARAAAAAAAHBAHHTADBAGTGSABSACMYMTGSHK Direction: Backward Position #: 13 Overlap #: 8 Alignment: BAGTGSABSACMYMTGSHKVHVASTGG------------ -------------------WHAATTAAARAARAAAAAAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFF11 Combined Motif Reverse Complement Original Motif RDSCARMRGTSVTSCACTVDTAHDTBHTTTTTTTKTTKT CTGCTGBDBBDGBD RDSCARMRSTGCTGCHBYDDHVHDTBHTTTTTTTKTTKT Direction: Forward Position #: 9 Overlap #: 14 Alignment: RDSCARMRGTSVTSCACTVDTAHDTBHTTTTTTTKTTKT --------CTGCTGBDBBDGBD----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 61 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR4A2 NR1H2RXRA Original Motif Original Motif AAGGTCAC AAAGGTCAAAGGTCAAC AAAGGTCAMAGGTCAAC Direction: Forward Position #: 2 Overlap #: 8 Alignment: -AAGGTCAC-------- AAAGGTCAAAGGTCAAC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR1 Reverse Complement Original Motif GTTGACCTYTGACCTTT VDBHMAGGTCACCCTGACCY VDBHMAGGTCACSYTGACCTYTGACCTTT Direction: Forward Position #: 13 Overlap #: 8 Alignment: ------------GTTGACCTYTGACCTTT VDBHMAGGTCACCCTGACCY--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Original Motif Reverse Complement VDBHMAGGTCACSYTGACCTYTGACCTTT BAGGYCABHBTGACCKHV VDBHVAGGTCABBBTGACCTTTGACCTTT Direction: Forward Position #: 5 Overlap #: 18 Alignment: VDBHMAGGTCACSYTGACCTYTGACCTTT ----BAGGYCABHBTGACCKHV------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 17 Combined Motif Reverse Complement Reverse Complement AAAGGTCAAAGGTCAVBBTGACCTVDBHV GAGGTCAGAAG ARAGGTCAGARGTCAVBBTGACCTVDBHV Direction: Forward Position #: 2 Overlap #: 11 Alignment: AAAGGTCAAAGGTCAVBBTGACCTVDBHV -GAGGTCAGAAG----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 15 Original Motif Original Motif ARAGGTCAGARGTCAVBBTGACCTVDBHV AAAGRTMAAACTA AAAGGTCAAAMKWCAVBBTGACCTVDBHV Direction: Forward Position #: 1 Overlap #: 13 Alignment: ARAGGTCAGARGTCAVBBTGACCTVDBHV AAAGRTMAAACTA---------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Reverse Complement Original Motif VDBHVAGGTCABBBTGWRRTTTGACCTTT BTRGGDCARAGGKCA VDBBHAGGBCAVVGKGHARTTTGACCTTT Direction: Forward Position #: 4 Overlap #: 15 Alignment: VDBHVAGGTCABBBTGWRRTTTGACCTTT ---BTRGGDCARAGGKCA----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 24 Reverse Complement Original Motif AAAGGTCAAAMTDCRCBBTGVCCTHBBHV AAAGWCATWAA AAAGDYMWAAATDCRCBBTGVCCTHBBHV Direction: Forward Position #: 1 Overlap #: 11 Alignment: AAAGGTCAAAMTDCRCBBTGVCCTHBBHV AAAGWCATWAA------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Original Motif Original Motif AAAGDYMWAAATDCRCBBTGVCCTHBBHV CACTGTGRTRTCACAGTGSWSCACT CACTVHMTRWRDTVDCACWGTSCTVAAAGDYMW Direction: Backward Position #: 5 Overlap #: 21 Alignment: AAAGDYMWAAATDCRCBBTGVCCTHBBHV---- --------CACTGTGRTRTCACAGTGSWSCACT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Reverse Complement Original Motif WYKDCTTTVAGSACWGTGDVADMWMARHVAGTG TGAMCTTTGMMCYT TKRHCTTTGAVCHYWGTGDVADMWMARHVAGTG Direction: Forward Position #: 1 Overlap #: 14 Alignment: WYKDCTTTVAGSACWGTGDVADMWMARHVAGTG TGAMCTTTGMMCYT------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 35 Reverse Complement Reverse Complement CACTVHMTRWRDTVDCACWKHGVTCAAAGHKYA CAAGAKCATCT TCTCAMRADSACACTVHMTRWRDTVDCACWKHGVTC Direction: Backward Position #: 4 Overlap #: 8 Alignment: CACTVHMTRWRDTVDCACWKHGVTCAAAGHKYA--- -------------------------CAAGAKCATCT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM2 Combined Motif Original Motif Reverse Complement GCAGAGGSAGS GCAGAKGSAGGABDGHDG GCAGAGGSAGGABDGHDG Direction: Forward Position #: 1 Overlap #: 11 Alignment: GCAGAGGSAGS------- GCAGAKGSAGGABDGHDG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CTCF Reverse Complement Reverse Complement CHHCHBTCCTSCCTCTGC BMSMGCCYMCTKSTGGMHM BHVMSCCYCCTGCYKSHBM Direction: Forward Position #: 2 Overlap #: 18 Alignment: -CHHCHBTCCTSCCTCTGC BMSMGCCYMCTKSTGGMHM ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFF11 Original Motif Reverse Complement BHVMSCCYCCTGCYKSHBM HVCDBBDBCAGCAG BHVHBCBBCMKCVBKSHBM Direction: Forward Position #: 1 Overlap #: 14 Alignment: BHVMSCCYCCTGCYKSHBM HVCDBBDBCAGCAG----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM12 Combined Motif Reverse Complement Original Motif RBHSYVBGYYGVBGBHVDV RAGKGMAGVRRGSRCASAGV RBHVHVDGCHGVVGVVVVASAGV Direction: Forward Position #: 4 Overlap #: 16 Alignment: RBHSYVBGYYGVBGBHVDV---- ---RAGKGMAGVRRGSRCASAGV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Tcfcp2l1 Original Motif Original Motif RBHVHVDGCHGVVGVVVVASAGV CCAGYYHVADCCRG SCAGHBBVHDSCRGVVVVASAGV Direction: Forward Position #: 1 Overlap #: 14 Alignment: RBHVHVDGCHGVVGVVVVASAGV CCAGYYHVADCCRG--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Reverse Complement VCTSTVVVVCKGSDHVVVHCTGS GGYGCTGTCCATGGTGCTGAA GGYVCTSTCCVBSGTSCTGAVHCTGS Direction: Forward Position #: 4 Overlap #: 18 Alignment: ---VCTSTVVVVCKGSDHVVVHCTGS GGYGCTGTCCATGGTGCTGAA----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR1 Original Motif Original Motif GGYVCTSTCCVBSGTSCTGAVHCTGS VDBHMAGGTCACCCTGACCY GVHVCWGKBCABSBTGMYSHVHCTGS Direction: Forward Position #: 1 Overlap #: 20 Alignment: GGYVCTSTCCVBSGTSCTGAVHCTGS VDBHMAGGTCACCCTGACCY------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 3 Reverse Complement Original Motif SCAGHBHSKYCABSBTGBYCWGVDVC HCAGRRVACASAG HCAGDDHVBWCAGSBTGBYCWGVDVC Direction: Forward Position #: 1 Overlap #: 13 Alignment: SCAGHBHSKYCABSBTGBYCWGVDVC HCAGRRVACASAG------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR2 Original Motif Original Motif HCAGDDHVBWCAGSBTGBYCWGVDVC VHRGGTCABDBTGMCCTB HHAGGTCABDSWGVBYBBYCWGVDVC Direction: Forward Position #: 1 Overlap #: 18 Alignment: HCAGDDHVBWCAGSBTGBYCWGVDVC 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ssCCCCGCSssk Combined Motif Reverse Complement Original Motif CSSGCKCGCGS SBCCCCGCCSBB CSSSCBCGCSSBB Direction: Forward Position #: 2 Overlap #: 10 Alignment: CSSGCKCGCGS-- -SBCCCCGCCSBB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif sscCCCGCGcs Reverse Complement Original Motif BBSSGCGBGSSSG BSCCCCGCGBS BBSCSCGCGSSSG Direction: Forward Position #: 1 Overlap #: 11 Alignment: BBSSGCGBGSSSG BSCCCCGCGBS-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif cCGCGGrCACG Reverse Complement Reverse Complement CSSSCGCGSGSBB CGTGKCCGCGG CGBGYSCGCGSBB Direction: Forward Position #: 1 Overlap #: 11 Alignment: CSSSCGCGSGSBB CGTGKCCGCGG-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 79 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- cCGCGGrCACG gCGCGCsCgsG Original Motif Original Motif CCGCGGRCACG GCGCGCSCGCG SCGCGSRCRCG Direction: Backward Position #: 1 Overlap #: 11 Alignment: CCGCGGRCACG GCGCGCSCGCG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFF11 Original Motif Original Motif SCGCGSRCRCG CTGCTGBDBBDGBD SYGCKGVCDCDGBD Direction: Forward Position #: 1 Overlap #: 11 Alignment: SCGCGSRCRCG--- CTGCTGBDBBDGBD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Original Motif Reverse Complement SYGCKGVCDCDGBD GGYGCTGTCCATGGTGCTGAA GSYGCTGBCCVDGGTGCTGAA Direction: Forward Position #: 2 Overlap #: 14 Alignment: -SYGCKGVCDCDGBD------ GGYGCTGTCCATGGTGCTGAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR1 Original Motif Original Motif GSYGCTGBCCVDGGTGCTGAA VDBHMAGGTCACCCTGACCY VGBHVMKGTCMVBSKKVCYKAA Direction: Forward Position #: 2 Overlap #: 19 Alignment: -GSYGCTGBCCVDGGTGCTGAA VDBHMAGGTCACCCTGACCY-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ssGCkTGCssk Combined Motif Original Motif Original Motif VGBHVMKGTCMVBSKKVCYKAA SSGCKTGCSSK VGSSGCKKGCVSBSKKVCYKAA Direction: Forward Position #: 3 Overlap #: 11 Alignment: VGBHVMKGTCMVBSKKVCYKAA --SSGCKTGCSSK--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ssCCCCGCSssk Combined Motif Original Motif Reverse Complement VGSSGCKKGCVSBSKKVCYKAA BBSGGCGGGGBS VGSSBCKGGCGSGGBBVCYKAA Direction: Forward Position #: 5 Overlap #: 12 Alignment: VGSSGCKKGCVSBSKKVCYKAA ----BBSGGCGGGGBS------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CTCF Combined Motif Reverse Complement Reverse Complement TTYMGBBBCCSCGCCYGBSSCV BMSMGCCYMCTKSTGGMHM TTBMGHGCCYCCKBSTGGVBMV Direction: Forward Position #: 3 Overlap #: 19 Alignment: TTYMGBBBCCSCGCCYGBSSCV --BMSMGCCYMCTKSTGGMHM- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 3 Original Motif Reverse Complement TTBMGHGCCYCCKBSTGGVBMV CTSTGTBKMCTGH CTBTVKBKCCYSCKBSTGGVBMV Direction: Forward Position #: 2 Overlap #: 12 Alignment: -TTBMGHGCCYCCKBSTGGVBMV CTSTGTBKMCTGH---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 06-18-2018 15:05:43 Runtime: 848.838 seconds MOTIFSIM is written by Ngoc Tam L. 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