**************************************************************************************************************************************************************************************************** MOTIFSIM - Motif Similarity Detection Tool Version 2.2 **************************************************************************************************************************************************************************************************** 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 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-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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Esrrb Combined Motif Original Motif Reverse Complement TTSAKSACCWDKGACAGCKCC CACGTG TTSAKCACSTDKGACAGCKCC Direction: Forward Position #: 6 Overlap #: 6 Alignment: TTSAKSACCWDKGACAGCKCC -----CACGTG---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Arnt Combined Motif Original Motif Reverse Complement TTSAKCACSTDKGACAGCKCC CACGTG TTSAKCACGTGKGACAGCKCC Direction: Forward Position #: 6 Overlap #: 6 Alignment: TTSAKCACSTDKGACAGCKCC -----CACGTG---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR1H2RXRA Combined Motif Original Motif Reverse Complement TTSAKCACGTGKGACAGCKCC GTTGACCTTTGACCTTT TTSWTSACSTKTGACMKBDCC Direction: Forward Position #: 3 Overlap #: 17 Alignment: TTSAKCACGTGKGACAGCKCC --GTTGACCTTTGACCTTT-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HIF1AARNT Combined Motif Original Motif Reverse Complement TTSWTSACSTKTGACMKBDCC VCACGTBV TTSWKCACGTBBGACMKBDCC Direction: Forward Position #: 5 Overlap #: 8 Alignment: TTSWTSACSTKTGACMKBDCC ----VCACGTBV--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- INSM1 Combined Motif Reverse Complement Original Motif GGDVYRGTCVVACGTGRWSAA TGYCAGGGGGCR AATSBVASGKGGHVGGDVYRG Direction: Backward Position #: 3 Overlap #: 12 Alignment: GGDVYRGTCVVACGTGRWSAA -------TGYCAGGGGGCR-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Original Motif Original Motif AATSBVASGKGGHVGGDVYRG BTRGGDCARAGGKCA BHRKGBCARRGGKHAGGDVYRG Direction: Forward Position #: 2 Overlap #: 14 Alignment: -AATSBVASGKGGHVGGDVYRG BTRGGDCARAGGKCA------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MYCMAX Combined Motif Original Motif Original Motif BHRKGBCARRGGKHAGGDVYRG RASCACGTGGT BHRKRBCACGKGGYAGGDVYRG Direction: Forward Position #: 4 Overlap #: 11 Alignment: BHRKGBCARRGGKHAGGDVYRG ---RASCACGTGGT-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR4A2 Combined Motif Original Motif Original Motif BHRKRBCACGKGGYAGGDVYRG AAGGTCAC BAAGRBCACGKGGYAGGDVYRG Direction: Forward Position #: 2 Overlap #: 8 Alignment: BHRKRBCACGKGGYAGGDVYRG -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----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR1H2RXRA Original Motif Original Motif AKSHHCMAAGRTCACCCAAAAMAACAAARRA AAAGGTCAAAGGTCAAC AARGBTCAAAGGTCAMCCAAAAMAACAAARRA Direction: Forward Position #: 2 Overlap #: 16 Alignment: -AKSHHCMAAGRTCACCCAAAAMAACAAARRA AAAGGTCAAAGGTCAAC--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MIZF Combined Motif Original Motif Reverse Complement AARGBTCAAAGGTCAMCCAAAAMAACAAARRA GCGGACGTTV AARGBKCRRASGTYAMCCAAAAMAACAAARRA Direction: Forward Position #: 6 Overlap #: 10 Alignment: AARGBTCAAAGGTCAMCCAAAAMAACAAARRA -----GCGGACGTTV----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Original Motif Original Motif AARGBKCRRASGTYAMCCAAAAMAACAAARRA BTRGGDCARAGGKCA VDRGGBCARAGGTCAMCCAAAAMAACAAARRA Direction: Forward Position #: 1 Overlap #: 15 Alignment: AARGBKCRRASGTYAMCCAAAAMAACAAARRA BTRGGDCARAGGKCA----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Reverse Complement TKKTTTGTTRTTTTGGYTGACCTKTGBCCKDB GGYGCTGTCCATGGTGCTGAA AKBYGSTKKMCMTGKKBCYGHTKKTTTGTTRTT Direction: Backward Position #: 2 Overlap #: 20 Alignment: TKKTTTGTTRTTTTGGYTGACCTKTGBCCKDB- ------------GGYGCTGTCCATGGTGCTGAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RXRRAR_DR5 Combined Motif Original Motif Reverse Complement AKBYGSTKKMCMTGKKBCYGHTKKTTTGTTRTT TGACCTCKVVBTGAYCK AKBYGSTTKMCCTBKBVCTGATCKTTTGTTRTT Direction: Forward Position #: 8 Overlap #: 17 Alignment: AKBYGSTKKMCMTGKKBCYGHTKKTTTGTTRTT -------TGACCTCKVVBTGAYCK--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RORA_1 Combined Motif Original Motif Reverse Complement AKBYGSTTKMCCTBKBVCTGATCKTTTGTTRTT TGACCTDVWT AKBYGSTTGACCTDKHDCTGATCKTTTGTTRTT Direction: Forward Position #: 8 Overlap #: 10 Alignment: AKBYGSTTKMCCTBKBVCTGATCKTTTGTTRTT -------TGACCTDVWT---------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* 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--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 9 Original Motif Original Motif CACGTRCACACACRYHHCGCC CACACAVRCACACA CACRYRCACACACAYHHCGCC Direction: Forward Position #: 1 Overlap #: 14 Alignment: CACGTRCACACACRYHHCGCC CACACAVRCACACA------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MYCMAX Combined Motif Original Motif Reverse Complement CACRYRCACACACAYHHCGCC ACCACGTGSTM CGCCMMCACRYRBBHCACRYR Direction: Backward Position #: 5 Overlap #: 11 Alignment: CACRYRCACACACAYHHCGCC ------ACCACGTGSTM---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Mycn Combined Motif Original Motif Original Motif CGCCMMCACRYRBBHCACRYR HSCACGTGGC CGCCMVCACGYGSHHCACRYR Direction: Forward Position #: 5 Overlap #: 10 Alignment: CGCCMMCACRYRBBHCACRYR ----HSCACGTGGC------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Myc Combined Motif Original Motif Original Motif CGCCMVCACGYGSHHCACRYR VGCACGTGGH CGCCVVCACGTGGHHCACRYR Direction: Forward Position #: 5 Overlap #: 10 Alignment: CGCCMVCACGYGSHHCACRYR ----VGCACGTGGH------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RREB1 Combined Motif Original Motif Original Motif CGCCVVCACGTGGHHCACRYR CCCCMAAMCAMCCMCMMMCV CGCCVVCACGTGGHCCMCAMAMCAMCCMCMMMCV Direction: Forward Position #: 15 Overlap #: 7 Alignment: CGCCVVCACGTGGHHCACRYR------------- --------------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 Reverse Complement Reverse Complement GCKGCYG GGYGCTGTCCATGGTGCTGAA GGYGCTGTCCATGSTGCTGAA Direction: Forward Position #: 13 Overlap #: 7 Alignment: ------------GCKGCYG-- GGYGCTGTCCATGGTGCTGAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MIZF Combined Motif Original Motif Original Motif GGYGCTGTCCATGSTGCTGAA BAACGTCCGC GGHDMYGTCCRYGSTGCTGAA Direction: Forward Position #: 3 Overlap #: 10 Alignment: GGYGCTGTCCATGSTGCTGAA --BAACGTCCGC--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Zfx Original Motif Original Motif GGHDMYGTCCRYGSTGCTGAA BBVGCCBVGGCCTV BBGGBHVHGKCCTBGSTGCTGAA Direction: Forward Position #: 3 Overlap #: 12 Alignment: --GGHDMYGTCCRYGSTGCTGAA BBVGCCBVGGCCTV--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFAP2A Original Motif Reverse Complement BBGGBHVHGKCCTBGSTGCTGAA SCMVBBGGC SCVVBBGGSKCCTBGSTGCTGAA Direction: Forward Position #: 1 Overlap #: 9 Alignment: BBGGBHVHGKCCTBGSTGCTGAA SCMVBBGGC-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 7 Combined Motif Reverse Complement Original Motif TTCAGCASCBAGGYSCCBBVVGS CCCRCCCC TYCMGCMCCBAGGYSCCBBVVGS Direction: Forward Position #: 2 Overlap #: 8 Alignment: TTCAGCASCBAGGYSCCBBVVGS -CCCRCCCC-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pax5 Combined Motif Reverse Complement Reverse Complement SCVVBBGGSKCCTBGGRGCRGKA MSGKKRCGCWDCABTGBBCD VSGBBVSGCKCCDBKGVGCRGKA Direction: Forward Position #: 1 Overlap #: 20 Alignment: SCVVBBGGSKCCTBGGRGCRGKA MSGKKRCGCWDCABTGBBCD--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Egr1 Combined Motif Original Motif Original Motif VSGBBVSGCKCCDBKGVGCRGKA HGCGTGGGCGK KAYSCGKGGGCGGVSGBBVSGCK Direction: Backward Position #: 3 Overlap #: 11 Alignment: VSGBBVSGCKCCDBKGVGCRGKA ----------HGCGTGGGCGK-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Klf4 Original Motif Original Motif KAYSCGKGGGCGGVSGBBVSGCK DGGGYGKGGC KGGGYGKGGSCGGVSGBBVSGCK Direction: Forward Position #: 1 Overlap #: 10 Alignment: KAYSCGKGGGCGGVSGBBVSGCK DGGGYGKGGC------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SP1 Combined Motif Original Motif Reverse Complement KGGGYGKGGSCGGVSGBBVSGCK GGGGGYGGGG KGGGBGKGGBVGGGSGBBVSGCK Direction: Forward Position #: 5 Overlap #: 10 Alignment: KGGGYGKGGSCGGVSGBBVSGCK ----GGGGGYGGGG--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RREB1 Original Motif Reverse Complement KGGGBGKGGBVGGGSGBBVSGCK BGRRRGRGGRTGRTTYGGGG BGRDRGGGGGKGVBKKGGGGBVSGCK Direction: Forward Position #: 4 Overlap #: 17 Alignment: ---KGGGBGKGGBVGGGSGBBVSGCK 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 Original Motif Original Motif AMACA CAYACACACACACA CAYACACACACACA Direction: Forward Position #: 6 Overlap #: 5 Alignment: -----AMACA---- CAYACACACACACA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 9 Original Motif 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 Original Motif Reverse Complement CCMCRMAAVAACVHHBGGVAYAGGKCA MSGKKRCGCWDCABTGBBCD CCMCRMVRBDACVCHDVRVWBHBVKCA Direction: Forward Position #: 6 Overlap #: 20 Alignment: CCMCRMAAVAACVHHBGGVAYAGGKCA -----MSGKKRCGCWDCABTGBBCD-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR2F1 Combined Motif Reverse Complement Original Motif TGRVBHBWVKVDHGVGTDBMBRMGYGG TGAMCTTTGMMCYT TGAMCTTTGVVVHKVGTDBMBRMGYGG Direction: Forward Position #: 1 Overlap #: 14 Alignment: TGRVBHBWVKVDHGVGTDBMBRMGYGG TGAMCTTTGMMCYT------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif INSM1 Original Motif Reverse Complement TGAMCTTTGVVVHKVGTDBMBRMGYGG MGCCCCCTGMCA HGHCCCCTGVCAHKVGTDBMBRMGYGG Direction: Forward Position #: 1 Overlap #: 12 Alignment: TGAMCTTTGVVVHKVGTDBMBRMGYGG 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--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RREB1 Reverse Complement Original Motif YCCCYSCDCCCCCCHB CCCCMAAMCAMCCMCMMMCV CCCCCMMMCMCCCCCMVMCV Direction: Forward Position #: 2 Overlap #: 16 Alignment: -YCCCYSCDCCCCCCHB--- CCCCMAAMCAMCCMCMMMCV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NFKB1 Combined Motif Reverse Complement Original Motif BGRVRGGGGGYGRRYGGGGG GGGGRTTCCCC GGGGGGGGRTBBCCSBGRVR Direction: Backward Position #: 5 Overlap #: 11 Alignment: BGRVRGGGGGYGRRYGGGGG -----GGGGRTTCCCC---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- REST Combined Motif Original Motif Reverse Complement GGGGGGGGRTBBCCSBGRVR GGYGCTGTCCATGGTGCTGAA GGGGGGBGCTGTCCVHGGTGCTGAA Direction: Forward Position #: 5 Overlap #: 16 Alignment: GGGGGGGGRTBBCCSBGRVR----- ----GGYGCTGTCCATGGTGCTGAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Ar Reverse Complement Original Motif TTCAGCACCHBGGACAGCBCCCCCC HWDAGHACRHHVTGTHCCHVMV HTHAGHACVHBGBGYACCBVCCCCC Direction: Forward Position #: 1 Overlap #: 22 Alignment: TTCAGCACCHBGGACAGCBCCCCCC 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 Reverse Complement GTTGACCTYTGACCTTT MGGTCAGGGTGACCTRDBHV MGGTCAGGKTGACCTBTGACCTTT Direction: Forward Position #: 8 Overlap #: 13 Alignment: -------GTTGACCTYTGACCTTT MGGTCAGGGTGACCTRDBHV---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Original Motif Original Motif MGGTCAGGKTGACCTBTGACCTTT VHRGGTCABDBTGMCCTB MGGTCADRKKKMMCTBTGACCTBT Direction: Forward Position #: 6 Overlap #: 18 Alignment: MGGTCAGGKTGACCTBTGACCTTT -----VHRGGTCABDBTGMCCTB- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Ar Combined Motif Reverse Complement Reverse Complement AVAGGTCABAGYRYYYMHTGACCY VRVDGGHACAVDDKGTHCTDWH VRAGGKHACASBDTGYHCTGACCY Direction: Forward Position #: 1 Overlap #: 22 Alignment: AVAGGTCABAGYRYYYMHTGACCY VRVDGGHACAVDDKGTHCTDWH-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Original Motif Reverse Complement VRAGGKHACASBDTGYHCTGACCY TGRCCTKTGHCCKAB VRAGGKBACMKKTBBYCBDBACCY Direction: Forward Position #: 6 Overlap #: 15 Alignment: VRAGGKHACASBDTGYHCTGACCY -----TGRCCTKTGHCCKAB---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Original Motif Original Motif VRAGGKBACMKKTBBYCBDBACCY TGAMCTTTGMMCYT TGAVCKKTGACCBTTBBYCBDBACCY Direction: Forward Position #: 3 Overlap #: 12 Alignment: --VRAGGKBACMKKTBBYCBDBACCY TGAMCTTTGMMCYT------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Original Motif Original Motif TGAVCKKTGACCBTTBBYCBDBACCY TTCAGCACCATGGACAGCKCC TTCWGVACCDTGGMCAGBDBCCBDBACCY Direction: Forward Position #: 4 Overlap #: 18 Alignment: ---TGAVCKKTGACCBTTBBYCBDBACCY TTCAGCACCATGGACAGCKCC-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Zfx Combined Motif Original Motif Original Motif TTCWGVACCDTGGMCAGBDBCCBDBACCY BBVGCCBVGGCCTV TTCDGVRCCDHGGCCTGBDBCCBDBACCY Direction: Forward Position #: 4 Overlap #: 14 Alignment: TTCWGVACCDTGGMCAGBDBCCBDBACCY ---BBVGCCBVGGCCTV------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RREB1 Combined Motif Original Motif Original Motif TTCDGVRCCDHGGCCTGBDBCCBDBACCY CCCCMAAMCAMCCMCMMMCV TTCDGVMCCCHRRMCAVCVCCMHHSHCCY Direction: Forward Position #: 7 Overlap #: 20 Alignment: TTCDGVRCCDHGGCCTGBDBCCBDBACCY ------CCCCMAAMCAMCCMCMMMCV--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Tcfcp2l1 Combined Motif Reverse Complement Reverse Complement MGGHSDDRGGVGVTGRKMHGGGRVCDGAA CKGGDTBDMMCTGG MGGHCDGGGDBGVWSKGGHGGGRVCDGAA Direction: Forward Position #: 5 Overlap #: 14 Alignment: MGGHSDDRGGVGVTGRKMHGGGRVCDGAA ----CKGGDTBDMMCTGG----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PLAG1 Reverse Complement Original Motif VBBGSCCVBGGSVA GGGGCCCAAGGGGG GGGGSCCDVGGGGR Direction: Forward Position #: 1 Overlap #: 14 Alignment: VBBGSCCVBGGSVA GGGGCCCAAGGGGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Zfp423 Original Motif Original Motif GGGGSCCDVGGGGR GSMMCCYARGGKKKC GSVVCCYAVGGGKDC Direction: Forward Position #: 1 Overlap #: 14 Alignment: GGGGSCCDVGGGGR- GSMMCCYARGGKKKC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Reverse Complement Original Motif GHYCCCBTKGGVVSC VDBHMAGGTCACCCTGACCY GHBBCCBWGGKCASCCTGACCY Direction: Forward Position #: 3 Overlap #: 13 Alignment: GHYCCCBTKGGVVSC------- --VDBHMAGGTCACCCTGACCY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR2 Original Motif Reverse Complement GHBBCCBWGGKCASCCTGACCY BAGGYCABHBTGACCKHV VMGBYCHHBGTSACCBTGACCY Direction: Forward Position #: 1 Overlap #: 18 Alignment: GHBBCCBWGGKCASCCTGACCY BAGGYCABHBTGACCKHV---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Mycn Combined Motif Original Motif Original Motif VMGBYCHHBGTSACCBTGACCY HSCACGTGGC VMSCACRTGGBSACCBTGACCY Direction: Forward Position #: 2 Overlap #: 10 Alignment: VMGBYCHHBGTSACCBTGACCY -HSCACGTGGC----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pax5 Combined Motif Reverse Complement Reverse Complement MGGTCAVGGTSVCCAMGTGSYV MSGKKRCGCWDCABTGBBCD MGGTCVGGGDCVCHDCRBBVYBCD Direction: Forward Position #: 5 Overlap #: 18 Alignment: MGGTCAVGGTSVCCAMGTGSYV-- ----MSGKKRCGCWDCABTGBBCD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RXRRAR_DR5 Combined Motif Original Motif Original Motif MGGTCVGGGDCVCHDCRBBVYBCD RGKTCABVVRGAGGTCA MGGTCRGKTBMVCBDSRGKBCACD Direction: Forward Position #: 6 Overlap #: 17 Alignment: MGGTCVGGGDCVCHDCRBBVYBCD -----RGKTCABVVRGAGGTCA-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Myc Combined Motif Original Motif Reverse Complement MGGTCRGKTBMVCBDSRGKBCACD DCCACGTGCV MGGYCASGTGMVCBDSRGKBCACD Direction: Forward Position #: 3 Overlap #: 10 Alignment: MGGTCRGKTBMVCBDSRGKBCACD --DCCACGTGCV------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Tcfcp2l1 Combined Motif Reverse Complement Original Motif HGTGVYCKSDBGVRCACSTGKCCY CCAGYYHVADCCRG HGTGVCCDGHBBVRVMCVKGKCCY Direction: Forward Position #: 6 Overlap #: 14 Alignment: HGTGVYCKSDBGVRCACSTGKCCY -----CCAGYYHVADCCRG----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* 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 GGGGCSCRMGGGSGTHV Direction: Forward Position #: 5 Overlap #: 10 Alignment: ----HGCGCGGKCGTHV GGGGCCCAAGGGGG--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 06-18-2018 13:28:24 Runtime: 667.125 seconds MOTIFSIM is written by Ngoc Tam L. 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