**************************************************************************************************************************************************************************************************** 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 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: Backward Position #: 7 Overlap #: 6 Alignment: -----KCAGAG------ AAAGGTCAAAGGTCAAC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Original Motif Original Motif AAAGGTCARAGGTCAAC BTRGGDCARAGGKCA VDRGGKCARAGGTCAAC Direction: Forward Position #: 1 Overlap #: 15 Alignment: AAAGGTCARAGGTCAAC BTRGGDCARAGGKCA-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Reverse Complement Original Motif GTTGACCTKTGRCCKDB TGAMCTTTGMMCYT TGAMCKTTGACCTKTGRCCKDB Direction: Forward Position #: 6 Overlap #: 9 Alignment: -----GTTGACCTKTGRCCKDB TGAMCTTTGMMCYT-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif HNF4A Original Motif Reverse Complement TGAMCKTTGACCTKTGRCCKDB TGMYCTTTGBCCK TGAMCTTTGVCCTKTGRCCKDB Direction: Forward Position #: 1 Overlap #: 13 Alignment: TGAMCKTTGACCTKTGRCCKDB TGMYCTTTGBCCK--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MIZF Reverse Complement Original Motif VDRGGKCARAGGBCAAAGRTCA BAACGTCCGC HWASGTCMGHGGBCAAAGRTCA Direction: Forward Position #: 1 Overlap #: 10 Alignment: VDRGGKCARAGGBCAAAGRTCA BAACGTCCGC------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif INSM1 Reverse Complement Reverse Complement TGAMCTTTGVCCDCRGACSTWD MGCCCCCTGMCA HGMCCYYTGVCMDCRGACSTWD Direction: Forward Position #: 1 Overlap #: 12 Alignment: TGAMCTTTGVCCDCRGACSTWD MGCCCCCTGMCA---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SP1 Combined Motif Reverse Complement Reverse Complement HWASGTCMGHRGBCAKKGGRCH GGGGGYGGGG HWASGTCVGBGGYSRGGGGRCH Direction: Forward Position #: 8 Overlap #: 10 Alignment: HWASGTCMGHRGBCAKKGGRCH -------GGGGGYGGGG----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Original Motif Reverse Complement HWASGTCVGBGGYSRGGGGRCH GGYGCTGTCCATGGTGCTGAA GGHDMTGTCCRBGGTSVKGRRRCH Direction: Forward Position #: 3 Overlap #: 19 Alignment: --HWASGTCVGBGGYSRGGGGRCH GGYGCTGTCCATGGTGCTGAA--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Zfx Combined Motif Reverse Complement Reverse Complement HGMMMCRVSACCVKGGACARHDCC VAGGCCBBGGCVBB HGMMMCAGGMCCBKGSVCVRHDCC Direction: Forward Position #: 6 Overlap #: 14 Alignment: HGMMMCRVSACCVKGGACARHDCC -----VAGGCCBBGGCVBB----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Original Motif Original Motif HGMMMCAGGMCCBKGSVCVRHDCC VDBHMAGGTCACCCTGACCY HGMMMCAGGMCCVDSBMVGGHBMCCCTGACCY Direction: Forward Position #: 13 Overlap #: 12 Alignment: HGMMMCAGGMCCBKGSVCVRHDCC-------- ------------VDBHMAGGTCACCCTGACCY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global 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 BGRRRGRRGATGRTTYGGGG Direction: Backward Position #: 10 Overlap #: 5 Alignment: ------RARAT--------- BGRRRGRGGRTGRTTYGGGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR4A2 Reverse Complement Original Motif CCCCMAAMCATCKMCMMMCB AAGGTCAC AAGGYCMCMAAMCATCKMCMMMCB Direction: Forward Position #: 5 Overlap #: 4 Alignment: ----CCCCMAAMCATCKMCMMMCB AAGGTCAC---------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Original Motif Reverse Complement AAGGYCMCMAAMCATCKMCMMMCB AKGYYCAAAGRTCA AAGBYCAMARAYCATCKMCMMMCB Direction: Forward Position #: 1 Overlap #: 14 Alignment: AAGGYCMCMAAMCATCKMCMMMCB AKGYYCAAAGRTCA---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MIZF Combined Motif Reverse Complement Reverse Complement BGRRRGRRGATGMTMTYTGMBCTT GCGGACGTTV BGRRRGSRGAYGTTMTYTGMBCTT Direction: Forward Position #: 6 Overlap #: 10 Alignment: BGRRRGRRGATGMTMTYTGMBCTT -----GCGGACGTTV--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR1H2RXRA Reverse Complement Original Motif AAGBYCAKARAACMTCMSCMMMCB AAAGGTCAAAGGTCAAC AAAGGTCADAGRTCAWCMSCMMMCB Direction: Forward Position #: 2 Overlap #: 16 Alignment: -AAGBYCAKARAACMTCMSCMMMCB AAAGGTCAAAGGTCAAC-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Original Motif Original Motif AAAGGTCADAGRTCAWCMSCMMMCB BTRGGDCARAGGKCA VDRGGBCARAGGTCAWCMSCMMMCB Direction: Forward Position #: 1 Overlap #: 15 Alignment: AAAGGTCADAGRTCAWCMSCMMMCB BTRGGDCARAGGKCA---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Original Motif Original Motif VDRGGBCARAGGTCAWCMSCMMMCB TTCAGCACCATGGACAGCKCC THCAGSACMAWGGWCAGCVSCMMMCB Direction: Forward Position #: 2 Overlap #: 20 Alignment: -VDRGGBCARAGGTCAWCMSCMMMCB TTCAGCACCATGGACAGCKCC----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RXRRAR_DR5 Combined Motif Original Motif Original Motif THCAGSACMAWGGWCAGCVSCMMMCB RGKTCABVVRGAGGTCA THCRGGTCADVGRVMRGYCACMMMCB Direction: Forward Position #: 4 Overlap #: 17 Alignment: THCAGSACMAWGGWCAGCVSCMMMCB ---RGKTCABVVRGAGGTCA------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RORA_1 Original Motif Original Motif THCRGGTCADVGRVMRGYCACMMMCB AWVDAGGTCA ATHHAGGTCADVGRVMRGYCACMMMCB Direction: Forward Position #: 2 Overlap #: 9 Alignment: -THCRGGTCADVGRVMRGYCACMMMCB AWVDAGGTCA----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HNF4A Combined Motif Original Motif Original Motif ATHHAGGTCADVGRVMRGYCACMMMCB RGGBCAAAGKYCA ATHHAGGTCRDBSRAAGKYCACMMMCB Direction: Forward Position #: 9 Overlap #: 13 Alignment: ATHHAGGTCADVGRVMRGYCACMMMCB --------RGGBCAAAGKYCA------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global 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 TTCAGCASCATGGACAGCKCC Direction: Backward Position #: 13 Overlap #: 7 Alignment: --CMGCRGC------------ TTCAGCACCATGGACAGCKCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MIZF Original Motif Original Motif TTCAGCASCATGGACAGCKCC BAACGTCCGC BAACGTCMGCASCATGGACAGCKCC Direction: Forward Position #: 5 Overlap #: 6 Alignment: ----TTCAGCASCATGGACAGCKCC BAACGTCCGC--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Zfx Reverse Complement Original Motif GGYGCTGTCCATGSTGCRGACGTTV BBVGCCBVGGCCTV BBGGCSCTGKCCTDGSTGCRGACGTTV Direction: Forward Position #: 3 Overlap #: 12 Alignment: --GGYGCTGTCCATGSTGCRGACGTTV BBVGCCBVGGCCTV------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFAP2A Combined Motif Reverse Complement Original Motif BAACGTCMGCASCDAGGYCAGSGCCBB GCCBBVRGS BAACGTCMGCMSCVDGGYCAGSGCCBB Direction: Forward Position #: 9 Overlap #: 9 Alignment: BAACGTCMGCASCDAGGYCAGSGCCBB --------GCCBBVRGS---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pax5 Combined Motif Original Motif Original Motif BAACGTCMGCMSCVDGGYCAGSGCCBB DGVBCABTGDWGCGKRRCSR BAACGTCMGCMSCVDGGHCHVBBSVDGCGKRRCSR Direction: Forward Position #: 16 Overlap #: 12 Alignment: BAACGTCMGCMSCVDGGYCAGSGCCBB-------- ---------------DGVBCABTGDWGCGKRRCSR ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Egr1 Reverse Complement Reverse Complement MSGKKRCGCDBSVBVDGDCCDVGSRGCRGACGTTV YCGCCCACGCH YCGSCBACGCHBSVBVDGDCCDVGSRGCRGACGTTV Direction: Forward Position #: 2 Overlap #: 10 Alignment: -MSGKKRCGCDBSVBVDGDCCDVGSRGCRGACGTTV YCGCCCACGCH------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Klf4 Combined Motif Original Motif Original Motif YCGSCBACGCHBSVBVDGDCCDVGSRGCRGACGTTV DGGGYGKGGC YCGSCBACGCHDGGGHGKGSCDVGSRGCRGACGTTV Direction: Forward Position #: 12 Overlap #: 10 Alignment: YCGSCBACGCHBSVBVDGDCCDVGSRGCRGACGTTV -----------DGGGYGKGGC--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SP1 Combined Motif Original Motif Reverse Complement YCGSCBACGCHDGGGHGKGSCDVGSRGCRGACGTTV GGGGGYGGGG YCGSCBACGCHDGGGHGKGSCDVGGGGSVGRSGTTV Direction: Forward Position #: 24 Overlap #: 10 Alignment: YCGSCBACGCHDGGGHGKGSCDVGSRGCRGACGTTV -----------------------GGGGGYGGGG--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RREB1 Combined Motif Original Motif Reverse Complement YCGSCBACGCHDGGGHGKGSCDVGGGGSVGRSGTTV BGRRRGRGGRTGRTTYGGGG YCGSCBACGCHDGGGHGKGSCDHGGRGGVGGGKKDHTYGGGG Direction: Forward Position #: 23 Overlap #: 14 Alignment: YCGSCBACGCHDGGGHGKGSCDVGGGGSVGRSGTTV------ ----------------------BGRRRGRGGRTGRTTYGGGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- INSM1 Combined Motif Original Motif Original Motif YCGSCBACGCHDGGGHGKGSCDHGGRGGVGGGKKDHTYGGGG TGYCAGGGGGCR YCGSCBACGCHDGGGHGKGBCWGGGGGSRGGGKKDHTYGGGG Direction: Forward Position #: 18 Overlap #: 12 Alignment: YCGSCBACGCHDGGGHGKGSCDHGGRGGVGGGKKDHTYGGGG -----------------TGYCAGGGGGCR------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 8 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 8 REST Reverse Complement Reverse Complement TCCCAG GGYGCTGTCCATGGTGCTGAA GGYGCTGTCCCHGGTGCTGAA Direction: Backward Position #: 9 Overlap #: 6 Alignment: -------TCCCAG-------- GGYGCTGTCCATGGTGCTGAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MZF1_1-4 Combined Motif Reverse Complement Reverse Complement TTCAGCACCHGGGACAGCKCC TCCCCV TTCAKCMCCHGGGACAGCKCC Direction: Forward Position #: 5 Overlap #: 6 Alignment: TTCAGCACCHGGGACAGCKCC ----TCCCCV----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RREB1 Original Motif Original Motif TTCAKCMCCHGGGACAGCKCC CCCCMAAMCAMCCMCMMMCV CCCCMAHYCABCMCCHVSSACAGCKCC Direction: Forward Position #: 7 Overlap #: 14 Alignment: ------TTCAKCMCCHGGGACAGCKCC CCCCMAAMCAMCCMCMMMCV------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif INSM1 Original Motif Reverse Complement CCCCMAHYCABCMCCHVSSACAGCKCC MGCCCCCTGMCA MGCCCCCWDHCABCMCCHVSSACAGCKCC Direction: Forward Position #: 3 Overlap #: 10 Alignment: --CCCCMAHYCABCMCCHVSSACAGCKCC MGCCCCCTGMCA----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Zfp423 Original Motif Original Motif MGCCCCCWDHCABCMCCHVSSACAGCKCC GSMMCCYARGGKKKC VGMCCCCARGSDBCMCCHVSSACAGCKCC Direction: Forward Position #: 1 Overlap #: 15 Alignment: MGCCCCCWDHCABCMCCHVSSACAGCKCC GSMMCCYARGGKKKC-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR1H2RXRA Reverse Complement Reverse Complement GGYGCTGTSSVHGGRGBDSCMTGGGGRCV GTTGACCTTTGACCTTT GTTGACCTTKGASCTKTSSVHGGRGBDSCMTGGGGRCV Direction: Forward Position #: 10 Overlap #: 8 Alignment: ---------GGYGCTGTSSVHGGRGBDSCMTGGGGRCV GTTGACCTTTGACCTTT--------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Tcfcp2l1 Combined Motif Reverse Complement Original Motif VGMCCCCARGSDBCMCCHVSSAYAGSTCRAAGGTCAAC CCAGYYHVADCCRG VGMCCCCARGSDBCMCCCRGBHYARVYCRRAGGTCAAC Direction: Forward Position #: 17 Overlap #: 14 Alignment: VGMCCCCARGSDBCMCCHVSSAYAGSTCRAAGGTCAAC ----------------CCAGYYHVADCCRG-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Egr1 Original Motif Reverse Complement VGMCCCCARGSDBCMCCCRGBHYARVYCRRAGGTCAAC YCGCCCACGCH YCGCSCMCSCARGSDBCMCCCRGBHYARVYCRRAGGTCAAC Direction: Forward Position #: 4 Overlap #: 8 Alignment: ---VGMCCCCARGSDBCMCCCRGBHYARVYCRRAGGTCAAC YCGCCCACGCH------------------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Ar Combined Motif Original Motif Original Motif YCGCSCMCSCARGSDBCMCCCRGBHYARVYCRRAGGTCAAC HWDAGHACRHHVTGTHCCHVMV YCGCSCMCSMWDRGDDCMCCVDGTHCMVVCCRRAGGTCAAC Direction: Forward Position #: 10 Overlap #: 22 Alignment: YCGCSCMCSCARGSDBCMCCCRGBHYARVYCRRAGGTCAAC ---------HWDAGHACRHHVTGTHCCHVMV---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Zfx Combined Motif Reverse Complement Original Motif GTTGACCTKKGGVVRGHACDVGGYGDDCKDWRSGYGSGCGK BBVGCCBVGGCCTV GTTGACCTKKGGVVRGHACDVGGYGDDSBDDVCGHGGSCKK Direction: Forward Position #: 28 Overlap #: 14 Alignment: GTTGACCTKKGGVVRGHACDVGGYGDDCKDWRSGYGSGCGK ---------------------------BBVGCCBVGGCCTV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 2 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 2 RREB1 Original Motif Original Motif AMACA CCCCMAAMCAMCCMCMMMCV CCCCMAMACAMCCMCMMMCV Direction: Backward Position #: 11 Overlap #: 5 Alignment: -----AMACA---------- CCCCMAAMCAMCCMCMMMCV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Ar Reverse Complement Reverse Complement BGRRRGRGGRTGTYTYGGGG VRVDGGHACAVDDKGTHCTDWH VRVBGGDASRGGRTGTYYTGRDG Direction: Forward Position #: 4 Overlap #: 19 Alignment: ---BGRRRGRGGRTGTYTYGGGG VRVDGGHACAVDDKGTHCTDWH- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Original Motif Original Motif VRVBGGDASRGGRTGTYYTGRDG BTRGGDCARAGGKCA VRVBBRGRSVARRKGTYHTGRDG Direction: Forward Position #: 4 Overlap #: 15 Alignment: VRVBGGDASRGGRTGTYYTGRDG ---BTRGGDCARAGGKCA----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ArntAhr Reverse Complement Reverse Complement CHMCAHKACYKMTVSMCMBBVMV CACGCM CACGCHAHKACYKMTVSMCMBBVMV Direction: Forward Position #: 3 Overlap #: 4 Alignment: --CHMCAHKACYKMTVSMCMBBVMV CACGCM------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pax5 Combined Motif Original Motif Original Motif CACGCHAHKACYKMTVSMCMBBVMV DGVBCABTGDWGCGKRRCSR CACGCHAHKACYDVBBCMHHBDDVCGKRRCSR Direction: Forward Position #: 13 Overlap #: 13 Alignment: CACGCHAHKACYKMTVSMCMBBVMV------- ------------DGVBCABTGDWGCGKRRCSR ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Reverse Complement Original Motif MSGKKRCGVDDBDDYGBVVDKGTYHTDGCGTG TGAMCTTTGMMCYT TGAMCKTTRMVCHBBDDYGBVVDKGTYHTDGCGTG Direction: Forward Position #: 4 Overlap #: 11 Alignment: ---MSGKKRCGVDDBDDYGBVVDKGTYHTDGCGTG TGAMCTTTGMMCYT--------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif INSM1 Reverse Complement Reverse Complement CACGCHAHKACYDVBBCMHHBVHGBRMAAYGRTCA MGCCCCCTGMCA CRCCCCMWGACHDVBBCMHHBVHGBRMAAYGRTCA Direction: Forward Position #: 1 Overlap #: 12 Alignment: CACGCHAHKACYDVBBCMHHBVHGBRMAAYGRTCA MGCCCCCTGMCA----------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif HIF1AARNT Original Motif Reverse Complement CRCCCCMWGACHDVBBCMHHBVHGBRMAAYGRTCA VCACGTBV VCACGYCMWGACHDVBBCMHHBVHGBRMAAYGRTCA Direction: Forward Position #: 2 Overlap #: 7 Alignment: -CRCCCCMWGACHDVBBCMHHBVHGBRMAAYGRTCA VCACGTBV---------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Myc Reverse Complement Original Motif TGAMCKTTRMVCHBBDDYGBVVDHGTCWRGKCGTGV VGCACGTGGH BGMACGTKGMVCHBBDDYGBVVDHGTCWRGKCGTGV Direction: Forward Position #: 1 Overlap #: 10 Alignment: TGAMCKTTRMVCHBBDDYGBVVDHGTCWRGKCGTGV VGCACGTGGH-------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HNF4A Combined Motif Reverse Complement Original Motif VCACGYCMWGACHDVBBCMHHBVHGBRCYACGTRCV RGGBCAAAGKYCA VCACGYCMWGACHDVBBCMHHBRDGBVMHASGYVMV Direction: Forward Position #: 23 Overlap #: 13 Alignment: VCACGYCMWGACHDVBBCMHHBVHGBRCYACGTRCV ----------------------RGGBCAAAGKYCA- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 3 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 3 EWSR1-FLI1 Original Motif Original Motif AGSCWGG GGAAGGAAGGAAGGAAGG GGAAGGAAGGMAGGAAGG Direction: Forward Position #: 8 Overlap #: 7 Alignment: -------AGSCWGG---- GGAAGGAAGGAAGGAAGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif INSM1 Reverse Complement Reverse Complement CCTTCCTRCCTTCCTTCC MGCCCCCTGMCA MSCYYCCTRCCWTCCTTCC Direction: Forward Position #: 2 Overlap #: 11 Alignment: -CCTTCCTRCCTTCCTTCC MGCCCCCTGMCA------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Tcfcp2l1 Original Motif Original Motif MSCYYCCTRCCWTCCTTCC CCAGYYHVADCCRG CCVSYYCCWRCCWKCCTTCC Direction: Forward Position #: 2 Overlap #: 13 Alignment: -MSCYYCCTRCCWTCCTTCC CCAGYYHVADCCRG------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Original Motif Reverse Complement CCVSYYCCWRCCWKCCTTCC GGYGCTGTCCATGGTGCTGAA GGYGCTGTCCMDGGTSCTGMMWKCCTTCC Direction: Forward Position #: 10 Overlap #: 12 Alignment: ---------CCVSYYCCWRCCWKCCTTCC GGYGCTGTCCATGGTGCTGAA-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif SP1 Reverse Complement Reverse Complement GGAAGGRWRRCAGSACCDRGGACAGCKCC GGGGGYGGGG GGGGRAGGGGRRCAGSACCDRGGACAGCKCC Direction: Forward Position #: 3 Overlap #: 8 Alignment: --GGAAGGRWRRCAGSACCDRGGACAGCKCC GGGGGYGGGG--------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Zfx Combined Motif Reverse Complement Reverse Complement GGYGCTGTCCMDGGTSCTGMMCCCCTKCCCC VAGGCCBBGGCVBB GGYGCTGTCCVAGGYCCBGVCHCCCTKCCCC Direction: Forward Position #: 11 Overlap #: 14 Alignment: GGYGCTGTCCMDGGTSCTGMMCCCCTKCCCC ----------VAGGCCBBGGCVBB------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Original Motif Original Motif GGYGCTGTCCVAGGYCCBGVCHCCCTKCCCC VDBHMAGGTCACCCTGACCY GGYGCTGTCCVAGGYCBDGVCVSSYYDCCCYGACCY Direction: Forward Position #: 17 Overlap #: 15 Alignment: GGYGCTGTCCVAGGYCCBGVCHCCCTKCCCC----- ----------------VDBHMAGGTCACCCTGACCY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RORA_1 Reverse Complement Original Motif MGGTCMGGGDKKSSBGVCDBGKCCTVGGACAGCKCC AWVDAGGTCA AWVDAGGTCAGGGDKKSSBGVCDBGKCCTVGGACAGCKCC Direction: Forward Position #: 5 Overlap #: 6 Alignment: ----MGGTCMGGGDKKSSBGVCDBGKCCTVGGACAGCKCC AWVDAGGTCA------------------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Klf4 Combined Motif Original Motif Original Motif AWVDAGGTCAGGGDKKSSBGVCDBGKCCTVGGACAGCKCC DGGGYGKGGC AWVDAGGTCAGGGDKKSBGGGYGKGGCCTVGGACAGCKCC Direction: Forward Position #: 18 Overlap #: 10 Alignment: AWVDAGGTCAGGGDKKSSBGVCDBGKCCTVGGACAGCKCC -----------------DGGGYGKGGC------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MYCMAX Reverse Complement Reverse Complement GGYGCTGTCCVAGGCCYCKCCCBSYYDCCCTGACCTDVWT ACCACGTGSTM ACCACGTGSTVCTGTCCVAGGCCYCKCCCBSYYDCCCTGACCTDVWT Direction: Forward Position #: 8 Overlap #: 4 Alignment: -------GGYGCTGTCCVAGGCCYCKCCCBSYYDCCCTGACCTDVWT ACCACGTGSTM------------------------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 1 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 EWSR1-FLI1 Original Motif Original Motif RGGAAR GGAAGGAAGGAAGGAAGG GGAAGGAAGGAAGGAAGG Direction: Forward Position #: 12 Overlap #: 6 Alignment: -----------RGGAAR- GGAAGGAAGGAAGGAAGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MIZF Original Motif Reverse Complement GGAAGGAAGGAAGGAAGG GCGGACGTTV GCGGAMGKWAGGAAGGAAGG Direction: Forward Position #: 3 Overlap #: 8 Alignment: --GGAAGGAAGGAAGGAAGG GCGGACGTTV---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MZF1_5-13 Original Motif Original Motif GCGGAMGKWAGGAAGGAAGG BKAGGGGDAD BKAGSGGAAGKWAGGAAGGAAGG Direction: Forward Position #: 4 Overlap #: 7 Alignment: ---GCGGAMGKWAGGAAGGAAGG BKAGGGGDAD------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NFKB1 Combined Motif Reverse Complement Reverse Complement CCTTCCTTCCTWRCTTCCSCTYB GGGGAAKCCCC CCTTCCTTCSKKGMWTCCCCTYB Direction: Forward Position #: 10 Overlap #: 11 Alignment: CCTTCCTTCCTWRCTTCCSCTYB ---------GGGGAAKCCCC--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Reverse Complement Original Motif BKAGGGGAWYCYYSGAAGGAAGG BTRGGDCARAGGKCA BKAGGGSAAHVBYSRAAGGAAGG Direction: Forward Position #: 1 Overlap #: 15 Alignment: BKAGGGGAWYCYYSGAAGGAAGG BTRGGDCARAGGKCA-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Original Motif Original Motif BKAGGGSAAHVBYSRAAGGAAGG TTCAGCACCATGGACAGCKCC TTCAGCACCDDGGRSAGHDBYSRAAGGAAGG Direction: Forward Position #: 9 Overlap #: 13 Alignment: --------BKAGGGSAAHVBYSRAAGGAAGG TTCAGCACCATGGACAGCKCC---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif INSM1 Reverse Complement Reverse Complement CCTTCCTTMSKBHDCTSKCCDDGGTGCTGAA MGCCCCCTGMCA MGCCCCCTKCCWTMSKBHDCTSKCCDDGGTGCTGAA Direction: Forward Position #: 6 Overlap #: 7 Alignment: -----CCTTCCTTMSKBHDCTSKCCDDGGTGCTGAA MGCCCCCTGMCA------------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RREB1 Combined Motif Reverse Complement Reverse Complement TTCAGCACCDDGGRSAGHDBYSRAWGGRAGGGGGCR BGRRRGRGGRTGRTTYGGGG TTCAGCACCDDGGVSRRVGVVGRWGGBDWGGGGGCR Direction: Forward Position #: 14 Overlap #: 20 Alignment: TTCAGCACCDDGGRSAGHDBYSRAWGGRAGGGGGCR -------------BGRRRGRGGRTGRTTYGGGG--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Ar Combined Motif Original Motif Reverse Complement TTCAGCACCDDGGVSRRVGVVGRWGGBDWGGGGGCR VRVDGGHACAVDDKGTHCTDWH TTCAGCACSDHGGGBACVGVBKGTDSKDWGGGGGCR Direction: Forward Position #: 9 Overlap #: 22 Alignment: TTCAGCACCDDGGVSRRVGVVGRWGGBDWGGGGGCR --------VRVDGGHACAVDDKGTHCTDWH------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif E2F1 Reverse Complement Original Motif MGCCCCCWDRSDACYBVCBGTBCCCHDSGTGCTGAA TTTSGCGC TTTVGCSCCCWDRSDACYBVCBGTBCCCHDSGTGCTGAA Direction: Forward Position #: 4 Overlap #: 5 Alignment: ---MGCCCCCWDRSDACYBVCBGTBCCCHDSGTGCTGAA TTTSGCGC------------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Zfp423 Original Motif Reverse Complement TTTVGCSCCCWDRSDACYBVCBGTBCCCHDSGTGCTGAA GYRYCCMTKGGYRSC GYRYCCTTTGGCRCCCWDRSDACYBVCBGTBCCCHDSGTGCTGAA Direction: Forward Position #: 7 Overlap #: 9 Alignment: ------TTTVGCSCCCWDRSDACYBVCBGTBCCCHDSGTGCTGAA GYRYCCMTKGGYRSC------------------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 7 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 7 SP1 Original Motif Original Motif CCCRCCCC CCCCKCCCCC CCCCDCCCCC Direction: Backward Position #: 2 Overlap #: 8 Alignment: -CCCRCCCC- CCCCKCCCCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Klf4 Original Motif Reverse Complement CCCCDCCCCC GCCYCMCCCD SCCCCCCCCH Direction: Forward Position #: 1 Overlap #: 10 Alignment: CCCCDCCCCC GCCYCMCCCD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Egr1 Reverse Complement Original Motif DGGGGGGGGS HGCGTGGGCGK DGSGKGGGSGK Direction: Forward Position #: 1 Overlap #: 10 Alignment: DGGGGGGGGS- HGCGTGGGCGK ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RREB1 Reverse Complement Original Motif YCSCCCRCSCD CCCCMAAMCAMCCMCMMMCV CCCCMAAMCAMCCCCVCCCVCSCD Direction: Forward Position #: 14 Overlap #: 7 Alignment: -------------YCSCCCRCSCD CCCCMAAMCAMCCMCMMMCV---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NFKB1 Original Motif Original Motif CCCCMAAMCAMCCCCVCCCVCSCD GGGGRTTCCCC GGGGRTYCCCMAAMCAMCCCCVCCCVCSCD Direction: Forward Position #: 7 Overlap #: 5 Alignment: ------CCCCMAAMCAMCCCCVCCCVCSCD GGGGRTTCCCC------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- INSM1 Combined Motif Original Motif Reverse Complement GGGGRTYCCCMAAMCAMCCCCVCCCVCSCD MGCCCCCTGMCA GGGGRTYCCCMAAMSMCCCCHVMCMVCSCD Direction: Forward Position #: 14 Overlap #: 12 Alignment: GGGGRTYCCCMAAMCAMCCCCVCCCVCSCD -------------MGCCCCCTGMCA----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global 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 Motif 11 Original Motif Reverse Complement YGCGTG TGTGTGTGTGTKTG TGTGTGTGYGTGTG Direction: Forward Position #: 7 Overlap #: 6 Alignment: ------YGCGTG-- TGTGTGTGTGTKTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 9 Original Motif Reverse Complement TGTGTGTGYGTGTG TGTGTGKVTGTGTG TGTGTGTGTGTGTG Direction: Forward Position #: 1 Overlap #: 14 Alignment: TGTGTGTGYGTGTG TGTGTGKVTGTGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 7 Reverse Complement Original Motif CACACACACACACA CCCRCCCC CMCACMCMCACACA Direction: Forward Position #: 1 Overlap #: 8 Alignment: CACACACACACACA CCCRCCCC------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 3 Combined Motif Reverse Complement Original Motif TGTGTGRGRGTGYG AGSCWGG TGTGTGRGAGBSTGG Direction: Forward Position #: 9 Overlap #: 6 Alignment: TGTGTGRGRGTGYG- --------AGSCWGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 2 Original Motif Reverse Complement TGTGTGRGAGBSTGG TGTRT TGTGTGRGAGBSTGG Direction: Forward Position #: 1 Overlap #: 5 Alignment: TGTGTGRGAGBSTGG TGTRT---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 6 Reverse Complement Reverse Complement CCASBCTCMCACACA GCKGCYG GCKSCHGBCTCMCACACA Direction: Forward Position #: 4 Overlap #: 4 Alignment: ---CCASBCTCMCACACA GCKGCYG----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 8 Combined Motif Reverse Complement Original Motif TGTGTGRGAGBCHGSRGC CTGGGA TGTSTGGGAGBCHGSRGC Direction: Forward Position #: 4 Overlap #: 6 Alignment: TGTGTGRGAGBCHGSRGC ---CTGGGA--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 4 Reverse Complement Original Motif GCKSCHGBCTCCCASACA CTCTGY CKCTGCHGBCTCCCASACA Direction: Forward Position #: 2 Overlap #: 5 Alignment: -GCKSCHGBCTCCCASACA CTCTGY------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 33 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HIF1AARNT Motif 9 Reverse Complement Original Motif VCACGTBV CACACAVRCACACA CACACRCACRYACA Direction: Backward Position #: 2 Overlap #: 8 Alignment: -----VCACGTBV- CACACAVRCACACA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 11 Original Motif Original Motif CACACRCACRYACA CAYACACACACACA CACACACACACACA Direction: Forward Position #: 1 Overlap #: 14 Alignment: CACACRCACRYACA CAYACACACACACA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 7 Original Motif Original Motif CACACACACACACA CCCRCCCC CMCRCMCMCACACA Direction: Forward Position #: 1 Overlap #: 8 Alignment: CACACACACACACA CCCRCCCC------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 3 Combined Motif Reverse Complement Original Motif TGTGTGRGRGKGYG AGSCWGG TGTGTGRGAGBSTGG Direction: Forward Position #: 9 Overlap #: 6 Alignment: TGTGTGRGRGKGYG- --------AGSCWGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 2 Original Motif Reverse Complement TGTGTGRGAGBSTGG TGTRT TGTGTGRGAGBSTGG Direction: Forward Position #: 1 Overlap #: 5 Alignment: TGTGTGRGAGBSTGG TGTRT---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 11-20-2016 21:31:13 Runtime: 756.479 seconds MOTIFSIM is written by Ngoc Tam L. Tran