**************************************************************************************************************************************************************************************************** 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 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 GTCAACTCARAGAAAGG Direction: Backward Position #: 7 Overlap #: 6 Alignment: -----KCAGAG------ AAAGGTCAAAGGTCAAC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Original Motif Original Motif GTCAACTCARAGAAAGG BTRGGDCARAGGKCA GTCAACTCARAGHRRGGCARAGGKCA Direction: Forward Position #: 12 Overlap #: 6 Alignment: GTCAACTCARAGAAAGG--------- -----------BTRGGDCARAGGKCA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Reverse Complement Original Motif TGRCCTKTGCCMKHCTMTGAGTTGAC TGAMCTTTGMMCYT TGACCTTTGMCCHHCTMTGAGTTGAC Direction: Forward Position #: 1 Overlap #: 14 Alignment: TGRCCTKTGCCMKHCTMTGAGTTGAC TGAMCTTTGMMCYT------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif HNF4A Original Motif Reverse Complement TGACCTTTGMCCHHCTMTGAGTTGAC TGMYCTTTGBCCK TGACCTTTGBCCBHCTMTGAGTTGAC Direction: Forward Position #: 1 Overlap #: 13 Alignment: TGACCTTTGMCCHHCTMTGAGTTGAC TGMYCTTTGBCCK------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MIZF Reverse Complement Original Motif GTCAACTCARAGHVGGBCAAAGGTCA BAACGTCCGC CBMAMRKSYSGTCAACTCARAGHVGGB Direction: Backward Position #: 2 Overlap #: 9 Alignment: GTCAACTCARAGHVGGBCAAAGGTCA- -----------------BAACGTCCGC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- INSM1 Combined Motif Reverse Complement Original Motif BCCBHCTMTGAGTTGACSKSRMRTRBG TGYCAGGGGGCR BCCBHCTMTGAGTTGACSKSRMRTGBVAGGGGGCR Direction: Forward Position #: 24 Overlap #: 4 Alignment: BCCBHCTMTGAGTTGACSKSRMRTRBG-------- -----------------------TGYCAGGGGGCR ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SP1 Combined Motif Reverse Complement Original Motif MGCCCCCTVVCAMRKSYSGTCAACTCARAGHVGGB CCCCKCCCCC MGCCCCCTCCCMCRKSYSGTCAACTCARAGHVGGB Direction: Forward Position #: 4 Overlap #: 10 Alignment: MGCCCCCTVVCAMRKSYSGTCAACTCARAGHVGGB ---CCCCKCCCCC---------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- REST Combined Motif Original Motif Reverse Complement MGCCCCCTCCCMCRKSYSGTCAACTCARAGHVGGB GGYGCTGTCCATGGTGCTGAA MGCCCCCTCCCMCRKSYSGTCAACTCARAGVHGSTGTCCATGGTGCTGAA Direction: Forward Position #: 30 Overlap #: 6 Alignment: MGCCCCCTCCCMCRKSYSGTCAACTCARAGHVGGB--------------- -----------------------------GGYGCTGTCCATGGTGCTGAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Zfx Combined Motif Original Motif Original Motif MGCCCCCTCCCMCRKSYSGTCAACTCARAGVHGSTGTCCATGGTGCTGAA BBVGCCBVGGCCTV MGCCCCCTCCCVVGBCBVGKCMWSTCARAGVHGSTGTCCATGGTGCTGAA Direction: Forward Position #: 11 Overlap #: 14 Alignment: MGCCCCCTCCCMCRKSYSGTCAACTCARAGVHGSTGTCCATGGTGCTGAA ----------BBVGCCBVGGCCTV-------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Reverse Complement Reverse Complement TTCAGCACCATGGACASCHVCTMTGASWYGRCVBGBCVVGGGAGGGGGCR MGGTCAGGGTGACCTRDBHV TTCAGCACCAHGGWCAGBBHSWCYKRBDYGRCVBGBCVVGGGAGGGGGCR Direction: Forward Position #: 11 Overlap #: 20 Alignment: TTCAGCACCATGGACASCHVCTMTGASWYGRCVBGBCVVGGGAGGGGGCR ----------MGGTCAGGGTGACCTRDBHV-------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ 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 GRTTYGGGGRRGATBGRRRG Direction: Backward Position #: 10 Overlap #: 5 Alignment: ------RARAT--------- BGRRRGRGGRTGRTTYGGGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR4A2 Combined Motif Original Motif Original Motif GRTTYGGGGRRGATBGRRRG AAGGTCAC RRGRAGRTCRVGRTTYGGGG Direction: Backward Position #: 4 Overlap #: 8 Alignment: GRTTYGGGGRRGATBGRRRG ---------AAGGTCAC--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR2F1 Combined Motif Reverse Complement Original Motif CCCCMAAMCVKGAMCTKCMM TGAMCTTTGMMCYT CCCYRAMCYBTGAMCTKCMM Direction: Forward Position #: 4 Overlap #: 14 Alignment: CCCCMAAMCVKGAMCTKCMM ---TGAMCTTTGMMCYT--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MIZF Reverse Complement Reverse Complement RRGRAGRTCAVKGYTMKGGG GCGGACGTTV GCGGACGTTCAVKGYTMKGGG Direction: Forward Position #: 2 Overlap #: 9 Alignment: -RRGRAGRTCAVKGYTMKGGG GCGGACGTTV----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR1H2RXRA Combined Motif Original Motif Original Motif GCGGACGTTCAVKGYTMKGGG AAAGGTCAAAGGTCAAC GCGGACGTTCAVKGYTMDRGGTCAAAGGTCAAC Direction: Forward Position #: 17 Overlap #: 5 Alignment: GCGGACGTTCAVKGYTMKGGG------------ ----------------AAAGGTCAAAGGTCAAC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Reverse Complement Reverse Complement GTTGACCTTTGACCKHYAMCYBTGAACGTCCGC TGRCCTKTGHCCKAB GTTGACCTTTGACCKHBAMCYBTGAACGTCCGC Direction: Forward Position #: 3 Overlap #: 15 Alignment: GTTGACCTTTGACCKHYAMCYBTGAACGTCCGC --TGRCCTKTGHCCKAB---------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Reverse Complement GCGGACGTTCAVKGYTBHRGGTCAAAGGTCAAC GGYGCTGTCCATGGTGCTGAA GSVGMYGTYCAHGGTKCTGRRTCAAAGGTCAAC Direction: Forward Position #: 1 Overlap #: 21 Alignment: GCGGACGTTCAVKGYTBHRGGTCAAAGGTCAAC GGYGCTGTCCATGGTGCTGAA------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RXRRAR_DR5 Original Motif Reverse Complement GSVGMYGTYCAHGGTKCTGRRTCAAAGGTCAAC TGACCTCKVVBTGAYCK KGDSCTSTCCDTGRYCBTGRRTCAAAGGTCAAC Direction: Forward Position #: 1 Overlap #: 17 Alignment: GSVGMYGTYCAHGGTKCTGRRTCAAAGGTCAAC TGACCTCKVVBTGAYCK---------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RORA_1 Original Motif Reverse Complement KGDSCTSTCCDTGRYCBTGRRTCAAAGGTCAAC TGACCTDVWT TGACCTDDHHDTGRYCBTGRRTCAAAGGTCAAC Direction: Forward Position #: 1 Overlap #: 10 Alignment: KGDSCTSTCCDTGRYCBTGRRTCAAAGGTCAAC TGACCTDVWT----------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HNF4A Combined Motif Original Motif Reverse Complement TGACCTDDHHDTGRYCBTGRRTCAAAGGTCAAC TGMYCTTTGBCCK TGACCTDGHYCTKDBBBYGRRTCAAAGGTCAAC Direction: Forward Position #: 7 Overlap #: 13 Alignment: TGACCTDDHHDTGRYCBTGRRTCAAAGGTCAAC ------TGMYCTTTGBCCK-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ 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 ATGGACAGCKCCCAGCASCTT Direction: Backward Position #: 13 Overlap #: 7 Alignment: --CMGCRGC------------ TTCAGCACCATGGACAGCKCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MIZF Original Motif Reverse Complement ATGGACAGCKCCCAGCASCTT GCGGACGTTV DYGGACRKHDCCCAGCASCTT Direction: Forward Position #: 1 Overlap #: 10 Alignment: ATGGACAGCKCCCAGCASCTT GCGGACGTTV----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Zfx Original Motif Reverse Complement DYGGACRKHDCCCAGCASCTT VAGGCCBBGGCVBB VMGGMCDKBVCCCVGCASCTT Direction: Forward Position #: 1 Overlap #: 14 Alignment: DYGGACRKHDCCCAGCASCTT VAGGCCBBGGCVBB------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFAP2A Combined Motif Original Motif Original Motif VMGGMCDKBVCCCVGCASCTT GCCBBVRGS VMGSCCBBDGSCCVGCASCTT Direction: Forward Position #: 3 Overlap #: 9 Alignment: VMGGMCDKBVCCCVGCASCTT --GCCBBVRGS---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pax5 Combined Motif Reverse Complement Reverse Complement AAGSTGCBGGSCHBBGGSCYV MSGKKRCGCWDCABTGBBCD MVGBTRCBSDBCVBHGBBCHV Direction: Forward Position #: 1 Overlap #: 20 Alignment: AAGSTGCBGGSCHBBGGSCYV MSGKKRCGCWDCABTGBBCD- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Egr1 Combined Motif Original Motif Original Motif MVGBTRCBSDBCVBHGBBCHV HGCGTGGGCGK MVGBTGCGBGGSMGKGBBCHV Direction: Forward Position #: 5 Overlap #: 11 Alignment: MVGBTRCBSDBCVBHGBBCHV ----HGCGTGGGCGK------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Klf4 Original Motif Original Motif MVGBTGCGBGGSMGKGBBCHV DGGGYGKGGC HGGGYGBGGBGSMGKGBBCHV Direction: Forward Position #: 1 Overlap #: 10 Alignment: MVGBTGCGBGGSMGKGBBCHV DGGGYGKGGC----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SP1 Combined Motif Reverse Complement Original Motif VHGBBCRCRSCBCCBCMCCCH CCCCKCCCCC VHGBCCCCDCCCCCBCMCCCH Direction: Forward Position #: 5 Overlap #: 10 Alignment: VHGBBCRCRSCBCCBCMCCCH ----CCCCKCCCCC------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RREB1 Original Motif Original Motif VHGBCCCCDCCCCCBCMCCCH CCCCMAAMCAMCCMCMMMCV CCMSVMMMCACCCCCBCMCCCH Direction: Forward Position #: 2 Overlap #: 19 Alignment: -VHGBCCCCDCCCCCBCMCCCH CCCCMAAMCAMCCMCMMMCV-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif INSM1 Reverse Complement Original Motif HGGGYGBGGGGGTGRRYVSRGG TGYCAGGGGGCR TGBSWGGGGGSRTGRRYVSRGG Direction: Forward Position #: 1 Overlap #: 12 Alignment: HGGGYGBGGGGGTGRRYVSRGG 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 GTGCTGAATCCCHGGGYGCTG Direction: Backward Position #: 9 Overlap #: 6 Alignment: -------TCCCAG-------- GGYGCTGTCCATGGTGCTGAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MZF1_1-4 Combined Motif Reverse Complement Reverse Complement CAGCKCCCHGGGATTCAGCAC TCCCCV CAGYCCCCHGGGATTCAGCAC Direction: Forward Position #: 4 Overlap #: 6 Alignment: CAGCKCCCHGGGATTCAGCAC ---TCCCCV------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RREB1 Combined Motif Original Motif Original Motif CAGYCCCCHGGGATTCAGCAC CCCCMAAMCAMCCMCMMMCV CHGGGATTCAGCACCMVHCCCCAGYCCCCHGGGAT Direction: Backward Position #: 15 Overlap #: 7 Alignment: -------------CAGYCCCCHGGGATTCAGCAC --------------CCCCMAAMCAMCCMCMMMCV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif INSM1 Reverse Complement Reverse Complement ATCCCHGGGGMCTGGGGDVYGGTGCTGAATCCCHG MGCCCCCTGMCA MRYCCCCKGRCACTGGGGDVYGGTGCTGAATCCCHG Direction: Forward Position #: 2 Overlap #: 11 Alignment: -ATCCCHGGGGMCTGGGGDVYGGTGCTGAATCCCHG MGCCCCCTGMCA------------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Zfp423 Original Motif Reverse Complement MRYCCCCKGRCACTGGGGDVYGGTGCTGAATCCCHG GYRYCCMTKGGYRSC GHRYCCCYKGGYRCYGGGGDVYGGTGCTGAATCCCHG Direction: Forward Position #: 2 Overlap #: 14 Alignment: -MRYCCCCKGRCACTGGGGDVYGGTGCTGAATCCCHG GYRYCCMTKGGYRSC---------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR1H2RXRA Combined Motif Original Motif Original Motif GHRYCCCYKGGYRCYGGGGDVYGGTGCTGAATCCCHG AAAGGTCAAAGGTCAAC GHRYCCCYKGGYRCYGGGGDVYGGTGCTGAATCMMAGGTCAAAGGTCAAC Direction: Forward Position #: 34 Overlap #: 4 Alignment: GHRYCCCYKGGYRCYGGGGDVYGGTGCTGAATCCCHG------------- ---------------------------------AAAGGTCAAAGGTCAAC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Tcfcp2l1 Combined Motif Original Motif Original Motif GHRYCCCYKGGYRCYGGGGDVYGGTGCTGAATCMMAGGTCAAAGGTCAAC CCAGYYHVADCCRG GHRYCCCYKGSCRSYBVVRDCYRGTGCTGAATCMMAGGTCAAAGGTCAAC Direction: Forward Position #: 11 Overlap #: 14 Alignment: GHRYCCCYKGGYRCYGGGGDVYGGTGCTGAATCMMAGGTCAAAGGTCAAC ----------CCAGYYHVADCCRG-------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Egr1 Combined Motif Original Motif Reverse Complement GHRYCCCYKGSCRSYBVVRDCYRGTGCTGAATCMMAGGTCAAAGGTCAAC YCGCCCACGCH GYCBCCCACGCHRSYBVVRDCYRGTGCTGAATCMMAGGTCAAAGGTCAAC Direction: Forward Position #: 2 Overlap #: 11 Alignment: GHRYCCCYKGSCRSYBVVRDCYRGTGCTGAATCMMAGGTCAAAGGTCAAC -YCGCCCACGCH-------------------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Ar Original Motif Original Motif GYCBCCCACGCHRSYBVVRDCYRGTGCTGAATCMMAGGTCAAAGGTCAAC HWDAGHACRHHVTGTHCCHVMV HDHVGCMCABBSYGBHCBVVHCYRGTGCTGAATCMMAGGTCAAAGGTCAAC Direction: Forward Position #: 2 Overlap #: 21 Alignment: -GYCBCCCACGCHRSYBVVRDCYRGTGCTGAATCMMAGGTCAAAGGTCAAC HWDAGHACRHHVTGTHCCHVMV----------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Zfx Combined Motif Original Motif Reverse Complement HDHVGCMCABBSYGBHCBVVHCYRGTGCTGAATCMMAGGTCAAAGGTCAAC VAGGCCBBGGCVBB HDHVGCMCABBSAGGCCBBGVCCVGTGCTGAATCMMAGGTCAAAGGTCAAC Direction: Forward Position #: 12 Overlap #: 14 Alignment: HDHVGCMCABBSYGBHCBVVHCYRGTGCTGAATCMMAGGTCAAAGGTCAAC -----------VAGGCCBBGGCVBB-------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ 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 MCCMCMMMCVAMACACCCCM Direction: Backward Position #: 11 Overlap #: 5 Alignment: -----AMACA---------- CCCCMAAMCAMCCMCMMMCV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Ar Original Motif Original Motif MCCMCMMMCVAMACACCCCM HWDAGHACRHHVTGTHCCHVMV HWDAGHACRHHVTGTMCCVCMVMCVAMACACCCCM Direction: Forward Position #: 16 Overlap #: 7 Alignment: ---------------MCCMCMMMCVAMACACCCCM HWDAGHACRHHVTGTHCCHVMV------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Original Motif Reverse Complement HWDAGHACRHHVTGTMCCVCMVMCVAMACACCCCM TGRCCTKTGHCCKAB HWDAGHAYRHCCTGTVCCCBMVMCVAMACACCCCM Direction: Forward Position #: 8 Overlap #: 15 Alignment: HWDAGHACRHHVTGTMCCVCMVMCVAMACACCCCM -------TGRCCTKTGHCCKAB------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ArntAhr Combined Motif Reverse Complement Original Motif YGGGGTGTYTBGRVYBGGGVACAGGHMKTHCTDWH YGCGTG YGGSGTGTYTBGRVYBGGGVACAGGHMKTHCTDWH Direction: Forward Position #: 2 Overlap #: 6 Alignment: YGGGGTGTYTBGRVYBGGGVACAGGHMKTHCTDWH -YGCGTG---------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Pax5 Reverse Complement Reverse Complement HWDAGHAYRHCCTGTVCCCBMVMCBAMACACSCCM MSGKKRCGCWDCABTGBBCD MVDDDGMRCDDCMBKKBBCHBMVMCBAMACACSCCM Direction: Forward Position #: 2 Overlap #: 19 Alignment: -HWDAGHAYRHCCTGTVCCCBMVMCBAMACACSCCM MSGKKRCGCWDCABTGBBCD---------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR2F1 Combined Motif Reverse Complement Original Motif YGGSGTGTYTBGRVYBDGBBRRVRGDDGKRCHDHVR TGAMCTTTGMMCYT YGGBGWSYTTTGRVCHBGBBRRVRGDDGKRCHDHVR Direction: Forward Position #: 4 Overlap #: 14 Alignment: YGGSGTGTYTBGRVYBDGBBRRVRGDDGKRCHDHVR ---TGAMCTTTGMMCYT------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif INSM1 Reverse Complement Original Motif MVDDDGMRCDDCMBKKBBCVDGBKCAAAKSWCVCCM TGYCAGGGGGCR TGHHDGGGGRCRDCMBKKBBCVDGBKCAAAKSWCVCCM Direction: Forward Position #: 3 Overlap #: 10 Alignment: --MVDDDGMRCDDCMBKKBBCVDGBKCAAAKSWCVCCM TGYCAGGGGGCR-------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif HIF1AARNT Reverse Complement Original Motif YGGBGWSYTTTGRVCHBGBBRRVRGDMGMCCCCDDDCA VBACGTGV BBRCGTGCTTTGRVCHBGBBRRVRGDMGMCCCCDDDCA Direction: Forward Position #: 1 Overlap #: 8 Alignment: YGGBGWSYTTTGRVCHBGBBRRVRGDMGMCCCCDDDCA VBACGTGV------------------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Myc Original Motif Reverse Complement BBRCGTGCTTTGRVCHBGBBRRVRGDMGMCCCCDDDCA DCCACGTGCV DCCACGTGCBTTGRVCHBGBBRRVRGDMGMCCCCDDDCA Direction: Forward Position #: 2 Overlap #: 9 Alignment: -BBRCGTGCTTTGRVCHBGBBRRVRGDMGMCCCCDDDCA DCCACGTGCV----------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif HNF4A Reverse Complement Reverse Complement TGHHDGGGGRCRDCMBKKBBCVDGBKCAAVGCACGTGGH TGMYCTTTGBCCK TGHHVKKKGBCVDCMBKKBBCVDGBKCAAVGCACGTGGH Direction: Forward Position #: 1 Overlap #: 13 Alignment: TGHHDGGGGRCRDCMBKKBBCVDGBKCAAVGCACGTGGH TGMYCTTTGBCCK-------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ 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 Original Motif CCVSYYCCWRCCWKCCTTCC TTCAGCACCATGGACAGCKCC TTCAGCACCATGGACMGSBYCCWRCCWKCCTTCC Direction: Forward Position #: 15 Overlap #: 7 Alignment: --------------CCVSYYCCWRCCWKCCTTCC TTCAGCACCATGGACAGCKCC------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SP1 Combined Motif Reverse Complement Reverse Complement GGAAGGRWGGMWGGKVSCYGTCCATGGTGCTGAA GGGGGYGGGG GGAAGGRDGGVKBGGGGCYGTCCATGGTGCTGAA Direction: Forward Position #: 8 Overlap #: 10 Alignment: GGAAGGRWGGMWGGKVSCYGTCCATGGTGCTGAA -------GGGGGYGGGG----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Zfx Original Motif Reverse Complement GGAAGGRDGGVKBGGGGCYGTCCATGGTGCTGAA VAGGCCBBGGCVBB VAGGMMGGGGSSVBBGGGGCYGTCCATGGTGCTGAA Direction: Forward Position #: 3 Overlap #: 12 Alignment: --GGAAGGRDGGVKBGGGGCYGTCCATGGTGCTGAA VAGGCCBBGGCVBB---------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR1 Original Motif Reverse Complement VAGGMMGGGGSSVBBGGGGCYGTCCATGGTGCTGAA MGGTCAGGGTGACCTRDBHV MGGTCAGGVHGRSSBGVBBVGGGCYGTCCATGGTGCTGAA Direction: Forward Position #: 5 Overlap #: 16 Alignment: ----VAGGMMGGGGSSVBBGGGGCYGTCCATGGTGCTGAA MGGTCAGGGTGACCTRDBHV-------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RORA_1 Combined Motif Reverse Complement Reverse Complement TTCAGCACCATGGACMGCCCVBBVCVSSMCHVCCTGACCY TGACCTDVWT TTCAKSACCWHGRWCMGCCCVBBVCVSSMCHVCCTGACCY Direction: Forward Position #: 5 Overlap #: 10 Alignment: TTCAGCACCATGGACMGCCCVBBVCVSSMCHVCCTGACCY ----TGACCTDVWT-------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Klf4 Reverse Complement Original Motif MGGTCAGGVHGRSSBGVBBVGGGCYGWMCHWGGTSRTGAA DGGGYGKGGC DRGGYSDGGCHGRSSBGVBBVGGGCYGWMCHWGGTSRTGAA Direction: Forward Position #: 2 Overlap #: 9 Alignment: -MGGTCAGGVHGRSSBGVBBVGGGCYGWMCHWGGTSRTGAA DGGGYGKGGC------------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MYCMAX Combined Motif Reverse Complement Original Motif TTCAKSACCWHGRWCMGCCCVBBVCVSSMCHGCCDSMCCMD RASCACGTGGT TTVABCACSTGGDWCMGCCCVBBVCVSSMCHGCCDSMCCMD Direction: Forward Position #: 3 Overlap #: 11 Alignment: TTCAKSACCWHGRWCMGCCCVBBVCVSSMCHGCCDSMCCMD --RASCACGTGGT---------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MIZF Combined Motif Original Motif Original Motif GGAAGGAAGGAAGGAAGG BAACGTCCGC GGAAGGAAGGAAGGAASGTCCGC Direction: Forward Position #: 14 Overlap #: 5 Alignment: GGAAGGAAGGAAGGAAGG----- -------------BAACGTCCGC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MZF1_5-13 Combined Motif Original Motif Reverse Complement GGAAGGAAGGAAGGAASGTCCGC BTHCCCCTYB GGAAGGAAGGAAGGAABKTCCSCTYB Direction: Forward Position #: 17 Overlap #: 7 Alignment: GGAAGGAAGGAAGGAASGTCCGC--- ----------------BTHCCCCTYB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NFKB1 Combined Motif Reverse Complement Original Motif BKAGSGGAYBTTCCTTCCTTCCTTCC GGGGRTTCCCC BKAGGGGAYBYYCCTTCCTTCCTTCC Direction: Forward Position #: 4 Overlap #: 11 Alignment: BKAGSGGAYBTTCCTTCCTTCCTTCC ---GGGGRTTCCCC------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Reverse Complement Reverse Complement GGAAGGAAGGAAGGKMVMTCCCCTYB TGRCCTKTGHCCKAB GGAAGGAAGGAAGGKMVMTSMCCTTTGHCCKAB Direction: Forward Position #: 19 Overlap #: 8 Alignment: GGAAGGAAGGAAGGKMVMTCCCCTYB------- ------------------TGRCCTKTGHCCKAB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Original Motif BTRGGDCAAAGGRSAYBYYCCTTCCTTCCTTCC TTCAGCACCATGGACAGCKCC TBYAGSACMAWGGASAGBBCCCTTCCTTCCTTCC Direction: Forward Position #: 2 Overlap #: 20 Alignment: -BTRGGDCAAAGGRSAYBYYCCTTCCTTCCTTCC TTCAGCACCATGGACAGCKCC------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif INSM1 Original Motif Original Motif TBYAGSACMAWGGASAGBBCCCTTCCTTCCTTCC TGYCAGGGGGCR TKYCAGGGSVMRGGASAGBBCCCTTCCTTCCTTCC Direction: Forward Position #: 2 Overlap #: 11 Alignment: -TBYAGSACMAWGGASAGBBCCCTTCCTTCCTTCC TGYCAGGGGGCR----------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RREB1 Combined Motif Reverse Complement Original Motif GGAAGGAAGGAAGGGVBCTSTCCKRVSCCCTGMYA CCCCMAAMCAMCCMCMMMCV GGAAGGAAGGAAGGGVBCTSTCCKRCCCCMWVMCAMCCMCMMMCV Direction: Forward Position #: 26 Overlap #: 10 Alignment: GGAAGGAAGGAAGGGVBCTSTCCKRVSCCCTGMYA---------- -------------------------CCCCMAAMCAMCCMCMMMCV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Ar Reverse Complement Reverse Complement BGRRRGRGGRTGYBWRGGGGMRGGASAGBBCCCTTCCTTCCTTCC VRVDGGHACAVDDKGTHCTDWH VRVBGGDASRGGRTGTBYKDDBGMRGGASAGBBCCCTTCCTTCCTTCC Direction: Forward Position #: 4 Overlap #: 19 Alignment: ---BGRRRGRGGRTGYBWRGGGGMRGGASAGBBCCCTTCCTTCCTTCC VRVDGGHACAVDDKGTHCTDWH-------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- E2F1 Combined Motif Original Motif Original Motif VRVBGGDASRGGRTGTBYKDDBGMRGGASAGBBCCCTTCCTTCCTTCC TTTSGCGC VRVBGGDASRGGRTGTBYKDDBGMRGGASAGBBCCCTTCCTTCYTTCSCGC Direction: Forward Position #: 44 Overlap #: 5 Alignment: VRVBGGDASRGGRTGTBYKDDBGMRGGASAGBBCCCTTCCTTCCTTCC--- -------------------------------------------TTTSGCGC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Zfp423 Combined Motif Reverse Complement Original Motif GCGSGAAMGAAGGAAGGGVBCTSTCCKRCBHHYKVACAMCCKSTDCCVVMV GSMMCCYARGGKKKC VVMVVSMMCMYMVGGKKBCGCGSGAAMGAAGGAAGGGVBCTSTCCKRCBHH Direction: Backward Position #: 5 Overlap #: 15 Alignment: GCGSGAAMGAAGGAAGGGVBCTSTCCKRCBHHYKVACAMCCKSTDCCVVMV --------------------------------GSMMCCYARGGKKKC---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ 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 Original Motif Reverse Complement DGSGKGGGSGK BGRRRGRGGRTGRTTYGGGG BGGGKGGGGGTGRTTYGGGG Direction: Forward Position #: 1 Overlap #: 11 Alignment: DGSGKGGGSGK--------- BGRRRGRGGRTGRTTYGGGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NFKB1 Combined Motif Original Motif Original Motif BGGGKGGGGGTGRTTYGGGG GGGGRTTCCCC GGGGGGGGRTKBYYYBGGGK Direction: Backward Position #: 5 Overlap #: 11 Alignment: BGGGKGGGGGTGRTTYGGGG -----GGGGRTTCCCC---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif INSM1 Original Motif Original Motif GGGGGGGGRTKBYYYBGGGK TGYCAGGGGGCR TGBSRGGGGGYGBYYYBGGGK Direction: Forward Position #: 2 Overlap #: 11 Alignment: -GGGGGGGGRTKBYYYBGGGK TGYCAGGGGGCR--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- EWSR1-FLI1 Combined Motif Reverse Complement Reverse Complement YCCCVKKKBCMCCCCCKSBCA CCTTCCTTCCTTCCTTCC YCCCVKKKBCMCCCCCTTCCWTCCTTCCTTCC Direction: Forward Position #: 15 Overlap #: 7 Alignment: YCCCVKKKBCMCCCCCKSBCA----------- --------------CCTTCCTTCCTTCCTTCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PLAG1 Combined Motif Original Motif Reverse Complement YCCCVKKKBCMCCCCCTTCCWTCCTTCCTTCC CCCCCTTGGGCCCC YCCCCSBKDVVSCCCCTTCCWTCCTTCCTTCC Direction: Forward Position #: 3 Overlap #: 14 Alignment: YCCCVKKKBCMCCCCCTTCCWTCCTTCCTTCC --CCCCCTTGGGCCCC---------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Zfx Combined Motif Original Motif Original Motif YCCCCSBKDVVSCCCCTTCCWTCCTTCCTTCC BBVGCCBVGGCCTV YCCCCSBBDSBBCSSCYTSCWTCCTTCCTTCC Direction: Forward Position #: 6 Overlap #: 14 Alignment: YCCCCSBKDVVSCCCCTTCCWTCCTTCCTTCC -----BBVGCCBVGGCCTV------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Pax5 Original Motif Original Motif YCCCCSBBDSBBCSSCYTSCWTCCTTCCTTCC DGVBCABTGDWGCGKRRCSR DGHBCMCBSDDGCGBVVCBDSCWTCCTTCCTTCC Direction: Forward Position #: 3 Overlap #: 18 Alignment: --YCCCCSBBDSBBCSSCYTSCWTCCTTCCTTCC DGVBCABTGDWGCGKRRCSR-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ 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------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 3 Reverse Complement Original Motif TGTGTGRGRGTGYG AGSCWGG GRGGYDBTGTGTGRG Direction: Backward Position #: 2 Overlap #: 6 Alignment: TGTGTGRGRGTGYG- --------AGSCWGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 2 Combined Motif Reverse Complement Original Motif CMCACACABHKCCKC AMACA CACACACABHKCCKC Direction: Forward Position #: 2 Overlap #: 5 Alignment: CMCACACABHKCCKC -AMACA--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 6 Combined Motif Reverse Complement Reverse Complement GRGGYDBTGTGTGTG GCKGCYG GRGSBGCTGTGTGTG Direction: Forward Position #: 3 Overlap #: 7 Alignment: GRGGYDBTGTGTGTG --GCKGCYG------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 8 Combined Motif Reverse Complement Reverse Complement CACACACAGCVSCKC TCCCAG ACAGCVSCKCCMCASCACACACAGC Direction: Backward Position #: 11 Overlap #: 5 Alignment: -CACACACAGCVSCKC ----------TCCCAG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 4 Reverse Complement Reverse Complement GCTGTGTGTGSTGRGGRGSBGCTGT KCAGAG GCWGWGTGTGSTGRGGRGSBGCTGT Direction: Forward Position #: 1 Overlap #: 6 Alignment: GCTGTGTGTGSTGRGGRGSBGCTGT KCAGAG------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ 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 ARCACRYACCACAC Direction: Backward Position #: 2 Overlap #: 8 Alignment: -----VCACGTBV- CACACAVRCACACA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 11 Original Motif Original Motif ARCACRYACCACAC CAYACACACACACA CAYACAMACACACACCACAC Direction: Forward Position #: 7 Overlap #: 8 Alignment: ------ARCACRYACCACAC CAYACACACACACA------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 7 Combined Motif Reverse Complement Reverse Complement GTGTGGTGTGTGTYTGTKTG GGGGMGGG GTGKGGHGKGTGTYTGTKTG Direction: Forward Position #: 3 Overlap #: 8 Alignment: GTGTGGTGTGTGTYTGTKTG --GGGGMGGG---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 3 Combined Motif Original Motif Original Motif GTGKGGHGKGTGTYTGTKTG AGSCWGG GTGDGGCDGGTGTYTGTKTG Direction: Forward Position #: 4 Overlap #: 7 Alignment: GTGKGGHGKGTGTYTGTKTG ---AGSCWGG---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 2 Combined Motif Reverse Complement Original Motif CAYACAMACACCHGCCDCAC AMACA CACACAMACACCHGCCDCAC Direction: Forward Position #: 2 Overlap #: 5 Alignment: CAYACAMACACCHGCCDCAC -AMACA-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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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