**************************************************************************************************************************************************************************************************** MOTIFSIM - Motif Similarity Detection Tool Version 2.1 **************************************************************************************************************************************************************************************************** INPUT **************************************************************************************************************************************************************************************************** Input Parameters Number of files: 2 Number of top significant motifs: 10 Number of best matches: 10 Similarity cutoff: >= 0.75 Matching motif database: UniProbe Mus Musculus Phylogenetic tree: Yes Combined similar motifs: Yes Output file type: All Output file format: All Input files and motif counts File name Count of motifs Dataset # MEME-ChIP_DM721.txt 11 1 PScanChIP_DM721.txt 37 2 **************************************************************************************************************************************************************************************************** RESULTS **************************************************************************************************************************************************************************************************** ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 14 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ZEB1 RORA_1 Original Motif Reverse Complement CACCTD TGACCTDVWT VWTSACCTDT Direction: Backward Position #: 4 Overlap #: 6 Alignment: -CACCTD--- TGACCTDVWT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Original Motif Original Motif VWTSACCTDT TTCAGCACCATGGACAGCKCC TTSAKSACCWDKGACAGCKCC Direction: Forward Position #: 3 Overlap #: 10 Alignment: --VWTSACCTDT--------- TTCAGCACCATGGACAGCKCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Arnt Combined Motif Reverse Complement Original Motif GGYGCTGTCRDWGGTSYTSAA CACGTG GGYGCTGTCRMASGTGYTSAA Direction: Forward Position #: 11 Overlap #: 6 Alignment: GGYGCTGTCRDWGGTSYTSAA ----------CACGTG----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Esrrb Combined Motif Original Motif Original Motif GGYGCTGTCRMASGTGYTSAA CACGTG GGYGCTGTCRCACGTGYTSAA Direction: Forward Position #: 11 Overlap #: 6 Alignment: GGYGCTGTCRMASGTGYTSAA ----------CACGTG----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR1H2RXRA Combined Motif Original Motif Original Motif GGYGCTGTCRCACGTGYTSAA AAAGGTCAAAGGTCAAC GGMRMKGTCAMASGTSAWSAA Direction: Forward Position #: 3 Overlap #: 17 Alignment: GGYGCTGTCRCACGTGYTSAA --AAAGGTCAAAGGTCAAC-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HIF1AARNT Combined Motif Reverse Complement Reverse Complement TTSWTSACSTYTGACYRMYCC VCACGTBV TTSWBCACGTYBGACYRMYCC Direction: Forward Position #: 5 Overlap #: 8 Alignment: TTSWTSACSTYTGACYRMYCC ----VCACGTBV--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif INSM1 Reverse Complement Original Motif GGMRMKGTCVMACGTGVWSAA TGYCAGGGGGCR TGKVAGGGGKCRMACGTGVWSAA Direction: Forward Position #: 3 Overlap #: 10 Alignment: --GGMRMKGTCVMACGTGVWSAA TGYCAGGGGGCR----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Original Motif Reverse Complement TGKVAGGGGKCRMACGTGVWSAA TGRCCTKTGHCCKAB TGDCMKBKGBCVDASGTGVWSAA Direction: Forward Position #: 1 Overlap #: 15 Alignment: TGKVAGGGGKCRMACGTGVWSAA TGRCCTKTGHCCKAB-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MYCMAX Combined Motif Reverse Complement Original Motif TTSWBCACSTHVGVCRBRRGHCA RASCACGTGGT TTVABCACGTGGDVCRBRRGHCA Direction: Forward Position #: 3 Overlap #: 11 Alignment: TTSWBCACSTHVGVCRBRRGHCA --RASCACGTGGT---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR4A2 Original Motif Original Motif TTVABCACGTGGDVCRBRRGHCA AAGGTCAC DWGRBCACGTGGDVCRBRRGHCA Direction: Forward Position #: 1 Overlap #: 8 Alignment: TTVABCACGTGGDVCRBRRGHCA AAGGTCAC--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 4 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 4 NR1H2RXRA Reverse Complement Original Motif KCAGAG AAAGGTCAAAGGTCAAC AAAGGTCARAGGTCAAC Direction: Forward Position #: 6 Overlap #: 6 Alignment: -----KCAGAG------ AAAGGTCAAAGGTCAAC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Original Motif Original Motif AAAGGTCARAGGTCAAC BTRGGDCARAGGKCA VDRGGKCARAGGTCAAC Direction: Forward Position #: 1 Overlap #: 15 Alignment: AAAGGTCARAGGTCAAC BTRGGDCARAGGKCA-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR2F1 Combined Motif Original Motif Reverse Complement VDRGGKCARAGGTCAAC AKGYYCAAAGRTCA VVRGBKCAAAGGTCAAC Direction: Forward Position #: 2 Overlap #: 14 Alignment: VDRGGKCARAGGTCAAC -AKGYYCAAAGRTCA-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HNF4A Combined Motif Original Motif Original Motif VVRGBKCAAAGGTCAAC RGGBCAAAGKYCA VVGGBYMAARGBYMAAC Direction: Forward Position #: 2 Overlap #: 13 Alignment: VVRGBKCAAAGGTCAAC -RGGBCAAAGKYCA--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MIZF Combined Motif Original Motif Reverse Complement VVGGBYMAARGBYMAAC GCGGACGTTV VVGGBYMAARGGCSRACGTTV Direction: Forward Position #: 12 Overlap #: 6 Alignment: VVGGBYMAARGBYMAAC---- -----------GCGGACGTTV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- INSM1 Combined Motif Original Motif Original Motif VVGGBYMAARGGCSRACGTTV TGYCAGGGGGCR VVKGBCARRGGGCRRACGTTV Direction: Forward Position #: 3 Overlap #: 12 Alignment: VVGGBYMAARGGCSRACGTTV --TGYCAGGGGGCR------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif SP1 Original Motif Reverse Complement VVKGBCARRGGGCRRACGTTV GGGGGYGGGG VRKGKYDGGGGGCRRACGTTV Direction: Forward Position #: 1 Overlap #: 10 Alignment: VVKGBCARRGGGCRRACGTTV GGGGGYGGGG----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- REST Combined Motif Reverse Complement Original Motif BAACGTMMGCCCCCHKYCYMV TTCAGCACCATGGACAGCKCC BAACKTCAGCMCCMHGGMCAGCKCC Direction: Forward Position #: 5 Overlap #: 17 Alignment: BAACGTMMGCCCCCHKYCYMV---- ----TTCAGCACCATGGACAGCKCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 8 Combined Motif Original Motif Reverse Complement BAACKTCAGCMCCMHGGMCAGCKCC TCCCAG CKCCKCCCAGBAACKTCAGCMCCMH Direction: Backward Position #: 5 Overlap #: 6 Alignment: BAACKTCAGCMCCMHGGMCAGCKCC ---------------TCCCAG---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Zfx Reverse Complement Reverse Complement HRGGYGCTGAYGTTVCTGGGRGGYG VAGGCCBBGGCVBB HAGGCSCYGVCGTHVCTGGGRGGYG Direction: Forward Position #: 1 Overlap #: 14 Alignment: HRGGYGCTGAYGTTVCTGGGRGGYG VAGGCCBBGGCVBB----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 5 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 5 RREB1 Reverse Complement Reverse Complement RARAT BGRRRGRGGRTGRTTYGGGG GRTTYGGGGRRGATBGRRRG Direction: Backward Position #: 10 Overlap #: 5 Alignment: ------RARAT--------- BGRRRGRGGRTGRTTYGGGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 10 Combined Motif Reverse Complement Reverse Complement CMMMCBATCKMCCCCMAAMC AAAAAAACAAARRA CMMMCBATCKMCCCCAAAAMAACAAARRA Direction: Forward Position #: 16 Overlap #: 5 Alignment: CMMMCBATCKMCCCCMAAMC--------- ---------------AAAAAAACAAARRA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR4A2 Combined Motif Original Motif Original Motif CMMMCBATCKMCCCCAAAAMAACAAARRA AAGGTCAC CMMMCDAKVTCMCCCAAAAMAACAAARRA Direction: Forward Position #: 6 Overlap #: 8 Alignment: CMMMCBATCKMCCCCAAAAMAACAAARRA -----AAGGTCAC---------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Original Motif Reverse Complement CMMMCDAKVTCMCCCAAAAMAACAAARRA AKGYYCAAAGRTCA AKSHHCMAAGRTCACCCAAAAMAACAAARRA Direction: Forward Position #: 3 Overlap #: 12 Alignment: --CMMMCDAKVTCMCCCAAAAMAACAAARRA AKGYYCAAAGRTCA----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MIZF Combined Motif Original Motif Original Motif AKSHHCMAAGRTCACCCAAAAMAACAAARRA BAACGTCCGC AKSHHCHAASGTCMSCCAAAAMAACAAARRA Direction: Forward Position #: 7 Overlap #: 10 Alignment: AKSHHCMAAGRTCACCCAAAAMAACAAARRA ------BAACGTCCGC--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR1H2RXRA Original Motif Original Motif AKSHHCHAASGTCMSCCAAAAMAACAAARRA AAAGGTCAAAGGTCAAC AARGBTCAAAGGTCAVCCAAAAMAACAAARRA Direction: Forward Position #: 2 Overlap #: 16 Alignment: -AKSHHCHAASGTCMSCCAAAAMAACAAARRA AAAGGTCAAAGGTCAAC--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Original Motif Original Motif AARGBTCAAAGGTCAVCCAAAAMAACAAARRA BTRGGDCARAGGKCA VDRGGBCAAAGGTCAVCCAAAAMAACAAARRA Direction: Forward Position #: 1 Overlap #: 15 Alignment: AARGBTCAAAGGTCAVCCAAAAMAACAAARRA BTRGGDCARAGGKCA----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Original Motif Original Motif VDRGGBCAAAGGTCAVCCAAAAMAACAAARRA TTCAGCACCATGGACAGCKCC THCAGSACMAWGGWCAGCCMMAAMAACAAARRA Direction: Forward Position #: 2 Overlap #: 20 Alignment: -VDRGGBCAAAGGTCAVCCAAAAMAACAAARRA TTCAGCACCATGGACAGCKCC------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RXRRAR_DR5 Original Motif Original Motif THCAGSACMAWGGWCAGCCMMAAMAACAAARRA RGKTCABVVRGAGGTCA RGKTVRBVSMRAGGTCAGCCMMAAMAACAAARRA Direction: Forward Position #: 2 Overlap #: 16 Alignment: -THCAGSACMAWGGWCAGCCMMAAMAACAAARRA RGKTCABVVRGAGGTCA----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RORA_1 Combined Motif Original Motif Original Motif RGKTVRBVSMRAGGTCAGCCMMAAMAACAAARRA AWVDAGGTCA RGKTVRBDHVDAGGTCAGCCMMAAMAACAAARRA Direction: Forward Position #: 8 Overlap #: 10 Alignment: RGKTVRBVSMRAGGTCAGCCMMAAMAACAAARRA -------AWVDAGGTCA----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 26 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ArntAhr Egr1 Reverse Complement Reverse Complement CACGCM YCGCCCACGCH CACGCMYCGCC Direction: Backward Position #: 1 Overlap #: 6 Alignment: -----CACGCM YCGCCCACGCH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif HIF1AARNT Original Motif Reverse Complement CACGCMYCGCC VCACGTBV VCACGYHHCGCC Direction: Forward Position #: 2 Overlap #: 7 Alignment: -CACGCMYCGCC VCACGTBV---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 11 Original Motif Original Motif VCACGYHHCGCC CAYACACACACACA CAYACACACACACRYHHCGCC Direction: Forward Position #: 10 Overlap #: 5 Alignment: ---------VCACGYHHCGCC CAYACACACACACA------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Esrrb Original Motif Reverse Complement CAYACACACACACRYHHCGCC CACGTG CACRYRCACACACRYHHCGCC Direction: Forward Position #: 1 Overlap #: 6 Alignment: CAYACACACACACRYHHCGCC CACGTG--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Arnt Original Motif Reverse Complement CACRYRCACACACRYHHCGCC CACGTG CACGTRCACACACRYHHCGCC Direction: Forward Position #: 1 Overlap #: 6 Alignment: CACRYRCACACACRYHHCGCC CACGTG--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 9 Combined Motif Original Motif Original Motif CACGTRCACACACRYHHCGCC CACACAVRCACACA CACGYACACACACACACMGCC Direction: Forward Position #: 5 Overlap #: 14 Alignment: CACGTRCACACACRYHHCGCC ----CACACAVRCACACA--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MYCMAX Combined Motif Original Motif Reverse Complement CACGYACACACACACACMGCC ACCACGTGSTM CACGYACACACACACACCRCSTGSTM Direction: Forward Position #: 16 Overlap #: 6 Alignment: CACGYACACACACACACMGCC----- ---------------ACCACGTGSTM ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Mycn Combined Motif Reverse Complement Original Motif RASCASGKGGTGTGTGTGTGTKCGTG HSCACGTGGC RASCACGTGGYGTGTGTGTGTKCGTG Direction: Forward Position #: 2 Overlap #: 10 Alignment: RASCASGKGGTGTGTGTGTGTKCGTG -HSCACGTGGC--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Myc Combined Motif Original Motif Original Motif RASCACGTGGYGTGTGTGTGTKCGTG VGCACGTGGH RVSCACGTGGHGTGTGTGTGTKCGTG Direction: Forward Position #: 2 Overlap #: 10 Alignment: RASCACGTGGYGTGTGTGTGTKCGTG -VGCACGTGGH--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RREB1 Reverse Complement Original Motif CACGYACACACACACDCCACGTGSBM CCCCMAAMCAMCCMCMMMCV CMCSMAMACACMCMCHCCMCGTGSBM Direction: Forward Position #: 1 Overlap #: 20 Alignment: CACGYACACACACACDCCACGTGSBM CCCCMAAMCAMCCMCMMMCV------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 6 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 6 REST Original Motif Original Motif CMGCRGC TTCAGCACCATGGACAGCKCC ATGGACAGCKCCCAGCASCTT Direction: Backward Position #: 13 Overlap #: 7 Alignment: --CMGCRGC------------ TTCAGCACCATGGACAGCKCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MIZF Original Motif Reverse Complement ATGGACAGCKCCCAGCASCTT GCGGACGTTV DYGGACRKHDCCCAGCASCTT Direction: Forward Position #: 1 Overlap #: 10 Alignment: ATGGACAGCKCCCAGCASCTT GCGGACGTTV----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Zfx Original Motif Reverse Complement DYGGACRKHDCCCAGCASCTT VAGGCCBBGGCVBB VMGGMCDKBVCCCVGCASCTT Direction: Forward Position #: 1 Overlap #: 14 Alignment: DYGGACRKHDCCCAGCASCTT VAGGCCBBGGCVBB------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFAP2A Combined Motif Original Motif Original Motif VMGGMCDKBVCCCVGCASCTT GCCBBVRGS VMGSCCBBDGSCCVGCASCTT Direction: Forward Position #: 3 Overlap #: 9 Alignment: VMGGMCDKBVCCCVGCASCTT --GCCBBVRGS---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 7 Combined Motif Reverse Complement Reverse Complement AAGSTGCBGGSCHBBGGSCYV GGGGMGGG AAGGKGCGGGSCHBBGGSCYV Direction: Forward Position #: 3 Overlap #: 8 Alignment: AAGSTGCBGGSCHBBGGSCYV --GGGGMGGG----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Pax5 Original Motif Reverse Complement AAGGKGCGGGSCHBBGGSCYV MSGKKRCGCWDCABTGBBCD MVGGKGCGSKBCVBHGBBCHV Direction: Forward Position #: 1 Overlap #: 20 Alignment: AAGGKGCGGGSCHBBGGSCYV MSGKKRCGCWDCABTGBBCD- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Egr1 Original Motif Original Motif MVGGKGCGSKBCVBHGBBCHV HGCGTGGGCGK HGSGKGSGCGKCVBHGBBCHV Direction: Forward Position #: 1 Overlap #: 11 Alignment: MVGGKGCGSKBCVBHGBBCHV HGCGTGGGCGK---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Klf4 Original Motif Original Motif HGSGKGSGCGKCVBHGBBCHV DGGGYGKGGC HGGGTGBGSBKCVBHGBBCHV Direction: Forward Position #: 1 Overlap #: 10 Alignment: HGSGKGSGCGKCVBHGBBCHV DGGGYGKGGC----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif SP1 Original Motif Reverse Complement HGGGTGBGSBKCVBHGBBCHV GGGGGYGGGG DGGGKBGGGGKCVBHGBBCHV Direction: Forward Position #: 1 Overlap #: 10 Alignment: HGGGTGBGSBKCVBHGBBCHV GGGGGYGGGG----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RREB1 Original Motif Reverse Complement DGGGKBGGGGKCVBHGBBCHV BGRRRGRGGRTGRTTYGGGG BGRRDGGGGGKGGKTYGGGGBBCHV Direction: Forward Position #: 5 Overlap #: 16 Alignment: ----DGGGKBGGGGKCVBHGBBCHV BGRRRGRGGRTGRTTYGGGG----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 2 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 2 Motif 11 Reverse Complement Reverse Complement TGTRT TGTGTGTGTGTKTG TGTGTGTGTGTKTG Direction: Forward Position #: 5 Overlap #: 5 Alignment: ----TGTRT----- TGTGTGTGTGTKTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 9 Reverse Complement Original Motif CAYACACACACACA CACACAVRCACACA CACACACACACACA Direction: Forward Position #: 1 Overlap #: 14 Alignment: CAYACACACACACA CACACAVRCACACA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RREB1 Combined Motif Reverse Complement Reverse Complement TGTGTGTGTGTGTG BGRRRGRGGRTGRTTYGGGG TGTGKGKGDGKGTGRTTYGGGG Direction: Forward Position #: 3 Overlap #: 12 Alignment: TGTGTGTGTGTGTG-------- --BGRRRGRGGRTGRTTYGGGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 10 Combined Motif Reverse Complement Reverse Complement CCCCMAAMCACYCDCRCRCACA AAAAAAACAAARRA CCCCAAAAMAMYMAMRVACACA Direction: Forward Position #: 5 Overlap #: 14 Alignment: CCCCMAAMCACYCDCRCRCACA ----AAAAAAACAAARRA---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Ar Combined Motif Original Motif Original Motif CCCCAAAAMAMYMAMRVACACA HWDAGHACRHHVTGTHCCHVMV CCCCAAAAVAACAHMVHRYACMHVMV Direction: Forward Position #: 5 Overlap #: 18 Alignment: CCCCAAAAMAMYMAMRVACACA---- ----HWDAGHACRHHVTGTHCCHVMV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Reverse Complement Reverse Complement VRVDYGTMMHBRHTGTTVTTTTGGGG TGRCCTKTGHCCKAB TGRCCTKTVCCBDHBGTTVTTTTGGGG Direction: Forward Position #: 2 Overlap #: 14 Alignment: -VRVDYGTMMHBRHTGTTVTTTTGGGG TGRCCTKTGHCCKAB------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ArntAhr Combined Motif Reverse Complement Reverse Complement CCCCAAAAVAACVHHBGGVAYAGGKCA CACGCM CCMCRMAAVAACVHHBGGVAYAGGKCA Direction: Forward Position #: 2 Overlap #: 6 Alignment: CCCCAAAAVAACVHHBGGVAYAGGKCA -CACGCM-------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pax5 Combined Motif Reverse Complement Original Motif TGRCCTKTVCCBDHBGTTVTTRMGYGG DGVBCABTGDWGCGKRRCSR TGVBCHBTGVHGBRKGDYSDTRMGYGG Direction: Forward Position #: 1 Overlap #: 20 Alignment: TGRCCTKTVCCBDHBGTTVTTRMGYGG DGVBCABTGDWGCGKRRCSR------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Original Motif Original Motif TGVBCHBTGVHGBRKGDYSDTRMGYGG TGAMCTTTGMMCYT TGAVCTTTGVHSHBKGDYSDTRMGYGG Direction: Forward Position #: 1 Overlap #: 14 Alignment: TGVBCHBTGVHGBRKGDYSDTRMGYGG TGAMCTTTGMMCYT------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif INSM1 Original Motif Reverse Complement TGAVCTTTGVHSHBKGDYSDTRMGYGG MGCCCCCTGMCA HGHCCYCTGMCVHBKGDYSDTRMGYGG Direction: Forward Position #: 1 Overlap #: 12 Alignment: TGAVCTTTGVHSHBKGDYSDTRMGYGG MGCCCCCTGMCA--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 23 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MZF1_1-4 INSM1 Reverse Complement Reverse Complement TCCCCV MGCCCCCTGMCA GMCAYCCCCWMG Direction: Backward Position #: 5 Overlap #: 6 Alignment: --TCCCCV---- MGCCCCCTGMCA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MZF1_5-13 Reverse Complement Original Motif CRWGGGGMTGYC BKAGGGGDAD BDAGGGGVWGYC Direction: Forward Position #: 1 Overlap #: 10 Alignment: CRWGGGGMTGYC BKAGGGGDAD-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Klf4 Reverse Complement Reverse Complement GMCWBCCCCTHB GCCYCMCCCD GCCHCCCCCWHB Direction: Forward Position #: 1 Overlap #: 10 Alignment: GMCWBCCCCTHB GCCYCMCCCD-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PLAG1 Combined Motif Reverse Complement Original Motif BDWGGGGGHGGC GGGGCCCAAGGGGG BDGGGGSSHRRBGGGG Direction: Forward Position #: 3 Overlap #: 10 Alignment: BDWGGGGGHGGC---- --GGGGCCCAAGGGGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 8 Reverse Complement Reverse Complement CCCCBKKDSSCCCCHB TCCCAG YCCCMGKDSSCCCCHB Direction: Forward Position #: 1 Overlap #: 6 Alignment: CCCCBKKDSSCCCCHB TCCCAG---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SP1 Combined Motif Reverse Complement Reverse Complement BDGGGGSSHRCYGGGM GGGGGYGGGG BDGGGGGGHGSKGGGM Direction: Forward Position #: 4 Overlap #: 10 Alignment: BDGGGGSSHRCYGGGM ---GGGGGYGGGG--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RREB1 Combined Motif Original Motif Reverse Complement BDGGGGGGHGSKGGGM BGRRRGRGGRTGRTTYGGGG BDGBGGGGVRGGGKGVTTYGGGG Direction: Forward Position #: 4 Overlap #: 13 Alignment: BDGGGGGGHGSKGGGM------- ---BGRRRGRGGRTGRTTYGGGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NFKB1 Combined Motif Original Motif Original Motif BDGBGGGGVRGGGKGVTTYGGGG GGGGRTTCCCC GGGGGRTTYSSSBDGBGGGGVRG Direction: Backward Position #: 2 Overlap #: 11 Alignment: BDGBGGGGVRGGGKGVTTYGGGG -----------GGGGRTTCCCC- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- REST Combined Motif Original Motif Reverse Complement GGGGGRTTYSSSBDGBGGGGVRG GGYGCTGTCCATGGTGCTGAA GGGGGRTTYSSSBDGBGGVGCKGTCCATGGTGCTGAA Direction: Forward Position #: 17 Overlap #: 7 Alignment: GGGGGRTTYSSSBDGBGGGGVRG-------------- ----------------GGYGCTGTCCATGGTGCTGAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Ar Reverse Complement Original Motif TTCAGCACCATGGACRGCVCCBCHBSSSKAAKCCCCC HWDAGHACRHHVTGTHCCHVMV HTHAGHACMHHGKRYDSCVVCBCHBSSSKAAKCCCCC Direction: Forward Position #: 1 Overlap #: 22 Alignment: TTCAGCACCATGGACRGCVCCBCHBSSSKAAKCCCCC HWDAGHACRHHVTGTHCCHVMV--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 44 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--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR2 Reverse Complement Original Motif AAAGGTCAMAGGTCAMSGTGACCTRDBHV VHRGGTCABDBTGMCCTB MAAGGTCAVVGKKCMMBBTGACCTRDBHV Direction: Forward Position #: 1 Overlap #: 18 Alignment: AAAGGTCAMAGGTCAMSGTGACCTRDBHV VHRGGTCABDBTGMCCTB----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Ar Combined Motif Original Motif Original Motif MAAGGTCAVVGKKCMMBBTGACCTRDBHV HWDAGHACRHHVTGTHCCHVMV MAAGGTCAHAGDDCAHBVTGWCCYVDVVV Direction: Forward Position #: 7 Overlap #: 22 Alignment: MAAGGTCAVVGKKCMMBBTGACCTRDBHV ------HWDAGHACRHHVTGTHCCHVMV- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Original Motif Original Motif MAAGGTCAHAGDDCAHBVTGWCCYVDVVV BTRGGDCARAGGKCA MAAGGTCWDRGDVMAAGGTSACCYVDVVV Direction: Forward Position #: 7 Overlap #: 15 Alignment: MAAGGTCAHAGDDCAHBVTGWCCYVDVVV ------BTRGGDCARAGGKCA-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR2F1 Combined Motif Original Motif Reverse Complement MAAGGTCWDRGDVMAAGGTSACCYVDVVV AKGYYCAAAGRTCA MARGBTCAAAGRTCAAGGTSACCYVDVVV Direction: Forward Position #: 2 Overlap #: 14 Alignment: MAAGGTCWDRGDVMAAGGTSACCYVDVVV -AKGYYCAAAGRTCA-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Original Motif Original Motif MARGBTCAAAGRTCAAGGTSACCYVDVVV TTCAGCACCATGGACAGCKCC THMAGBWCMAHGGWCARBGBSACCYVDVVV Direction: Forward Position #: 2 Overlap #: 20 Alignment: -MARGBTCAAAGRTCAAGGTSACCYVDVVV TTCAGCACCATGGACAGCKCC--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Zfx Combined Motif Reverse Complement Original Motif VVVHVMGGTSVCBMTGWCCHTRGWBCTRHA BBVGCCBVGGCCTV VVVVVCGVKGCCTVTGWCCHTRGWBCTRHA Direction: Forward Position #: 1 Overlap #: 14 Alignment: VVVHVMGGTSVCBMTGWCCHTRGWBCTRHA BBVGCCBVGGCCTV---------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RREB1 Combined Motif Reverse Complement Original Motif THMAGBWCMAHGGWCAVAGGCYVCGVVVVV CCCCMAAMCAMCCMCMMMCV THMAGBMCMMMRRMCAMMSVCHMCSVVVVV Direction: Forward Position #: 7 Overlap #: 20 Alignment: THMAGBWCMAHGGWCAVAGGCYVCGVVVVV ------CCCCMAAMCAMCCMCMMMCV---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Tcfcp2l1 Combined Motif Original Motif Original Motif THMAGBMCMMMRRMCAMMSVCHMCSVVVVV CCAGYYHVADCCRG TCCAGBHCVMDSVVSAMMSVCHMCSVVVVV Direction: Forward Position #: 2 Overlap #: 14 Alignment: THMAGBMCMMMRRMCAMMSVCHMCSVVVVV -CCAGYYHVADCCRG--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 15 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFAP2A Zfx Reverse Complement Original Motif SCMVBBGGC BBVGCCBVGGCCTV TVSCCBVGGSCBBV Direction: Backward Position #: 3 Overlap #: 9 Alignment: ---SCMVBBGGC-- BBVGCCBVGGCCTV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PLAG1 Combined Motif Reverse Complement Reverse Complement VBBGSCCVBGGSVA CCCCCTTGGGCCCC VBCSCCCBDGGSCMCC Direction: Forward Position #: 3 Overlap #: 12 Alignment: VBBGSCCVBGGSVA-- --CCCCCTTGGGCCCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Zfp423 Reverse Complement Original Motif GGRGSCCDVGGGSGBV GSMMCCYARGGKKKC GGVVCCYAVGGGKGCV Direction: Forward Position #: 1 Overlap #: 15 Alignment: GGRGSCCDVGGGSGBV GSMMCCYARGGKKKC- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Original Motif Original Motif GGVVCCYAVGGGKGCV VDBHMAGGTCACCCTGACCY GGVVBCCHRGGKSRCVCTGACCY Direction: Forward Position #: 4 Overlap #: 13 Alignment: GGVVCCYAVGGGKGCV------- ---VDBHMAGGTCACCCTGACCY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR2 Original Motif Original Motif GGVVBCCHRGGKSRCVCTGACCY VHRGGTCABDBTGMCCTB SVRGGYCAVGGTSVCCYTGACCY Direction: Forward Position #: 1 Overlap #: 18 Alignment: GGVVBCCHRGGKSRCVCTGACCY VHRGGTCABDBTGMCCTB----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Mycn Reverse Complement Original Motif MGGTCAKGGBSACCBTGMCCKVS HSCACGTGGC MGSWCRTGGHSACCBTGMCCKVS Direction: Forward Position #: 1 Overlap #: 10 Alignment: MGGTCAKGGBSACCBTGMCCKVS HSCACGTGGC------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pax5 Combined Motif Original Motif Original Motif MGSWCRTGGHSACCBTGMCCKVS DGVBCABTGDWGCGKRRCSR VGVDCRBKGHVGCVKDGMSVKVS Direction: Forward Position #: 1 Overlap #: 20 Alignment: MGSWCRTGGHSACCBTGMCCKVS DGVBCABTGDWGCGKRRCSR--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RXRRAR_DR5 Original Motif Original Motif VGVDCRBKGHVGCVKDGMSVKVS RGKTCABVVRGAGGTCA RGBTCABBGDVRSGTBRMSVKVS Direction: Forward Position #: 1 Overlap #: 17 Alignment: VGVDCRBKGHVGCVKDGMSVKVS RGKTCABVVRGAGGTCA------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Myc Reverse Complement Original Motif SVRVSRKBACSKVDCBVTGABCK VGCACGTGGH VVCACGTGRCSKVDCBVTGABCK Direction: Forward Position #: 1 Overlap #: 10 Alignment: SVRVSRKBACSKVDCBVTGABCK VGCACGTGGH------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Tcfcp2l1 Combined Motif Reverse Complement Reverse Complement RGBTCABBGDVRSGMCACGTGVV CKGGDTBDMMCTGG CKGKBDBBVHCDGGMCACGTGVV Direction: Forward Position #: 1 Overlap #: 14 Alignment: RGBTCABBGDVRSGMCACGTGVV CKGGDTBDMMCTGG--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 25 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Arnt Esrrb Original Motif Original Motif CACGTG CACGTG CACGTG Direction: Backward Position #: 1 Overlap #: 6 Alignment: CACGTG CACGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MYCMAX Reverse Complement Reverse Complement CACGTG ACCACGTGSTM ACCACGTGSTM Direction: Forward Position #: 3 Overlap #: 6 Alignment: --CACGTG--- ACCACGTGSTM ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Myc Original Motif Reverse Complement ACCACGTGSTM DCCACGTGCV DCCACGTGSDM Direction: Forward Position #: 1 Overlap #: 10 Alignment: ACCACGTGSTM DCCACGTGCV- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Mycn Original Motif Reverse Complement DCCACGTGSDM GCCACGTGSD DCCACGTGSDM Direction: Forward Position #: 1 Overlap #: 10 Alignment: DCCACGTGSDM GCCACGTGSD- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif HIF1AARNT Reverse Complement Original Motif RHSCACGTGGH VBACGTGV VBRCRYGYGGH Direction: Forward Position #: 1 Overlap #: 8 Alignment: RHSCACGTGGH VBACGTGV--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ArntAhr Reverse Complement Reverse Complement DCCMCMMGKBV CACGCM CMCGCMMGKBV Direction: Forward Position #: 1 Overlap #: 6 Alignment: DCCMCMMGKBV CACGCM----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ZEB1 Combined Motif Reverse Complement Reverse Complement VBRCRYGCGYG HAGGTG VHASGTGCGYG Direction: Forward Position #: 2 Overlap #: 6 Alignment: VBRCRYGCGYG -HAGGTG---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Egr1 Original Motif Original Motif VHASGTGCGYG HGCGTGGGCGK HGCRBGKGCGBG Direction: Forward Position #: 2 Overlap #: 10 Alignment: -VHASGTGCGYG HGCGTGGGCGK- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MIZF Reverse Complement Original Motif CVCGCYCVMGCH BAACGTCCGC BHACGYCCGCGCH Direction: Forward Position #: 2 Overlap #: 9 Alignment: -CVCGCYCVMGCH BAACGTCCGC--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PLAG1 Reverse Complement Original Motif HGCGCGGKCGTHV GGGGCCCAAGGGGG GGGGCCHRMGSGGGCGTHV Direction: Forward Position #: 7 Overlap #: 8 Alignment: ------HGCGCGGKCGTHV GGGGCCCAAGGGGG----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 11-20-2016 13:44:02 Runtime: 673.485 seconds MOTIFSIM is written by Ngoc Tam L. 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