**************************************************************************************************************************************************************************************************** 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 # PScanChIP_DM05.txt 16 1 RSAT_peak-motifs_DM05.txt 17 2 **************************************************************************************************************************************************************************************************** RESULTS **************************************************************************************************************************************************************************************************** ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 5 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ZEB1 CTCF Reverse Complement Original Motif HAGGTG YDRCCASYAGRKGGCRSYV YDRCCASYAGGTGGCRSYV Direction: Forward Position #: 8 Overlap #: 6 Alignment: -------HAGGTG------ YDRCCASYAGRKGGCRSYV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RORA_1 Reverse Complement Reverse Complement BMSMGCCACCTKSTGGMHM TGACCTDVWT TGACCTHGMKCCACCTKSTGGMHM Direction: Forward Position #: 6 Overlap #: 5 Alignment: -----BMSMGCCACCTKSTGGMHM TGACCTDVWT-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Original Motif YDRCCASYAGGTGGYYCHAGGTCA TTCAGCACCATGGACAGCKCC TTCAGCACCAYGGMCAGCASSTGGYYCHAGGTCA Direction: Forward Position #: 11 Overlap #: 11 Alignment: ----------YDRCCASYAGGTGGYYCHAGGTCA TTCAGCACCATGGACAGCKCC------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Esrrb Combined Motif Original Motif Reverse Complement TTCAGCACCAYGGMCAGCASSTGGYYCHAGGTCA TGACCTTGMBBB TTCAGCACCATGRCCWKSASVKGGYYCHAGGTCA Direction: Forward Position #: 11 Overlap #: 12 Alignment: TTCAGCACCAYGGMCAGCASSTGGYYCHAGGTCA ----------TGACCTTGMBBB------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR1H2RXRA Reverse Complement Reverse Complement TGACCTHGMKCCRVSTSRWGGKCATGGTGCTGAA GTTGACCTTTGACCTTT GTTGACCTTTRACCDBBTSRWGGKCATGGTGCTGAA Direction: Forward Position #: 3 Overlap #: 15 Alignment: --TGACCTHGMKCCRVSTSRWGGKCATGGTGCTGAA GTTGACCTTTGACCTTT------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Reverse Complement Original Motif TTCAGCACCATGRCCWKSAVVDGGTMAAAGGTCAAC BTRGGDCARAGGKCA TTCAGCACCATGVHVDGBVARAGGTCAAAGGTCAAC Direction: Forward Position #: 13 Overlap #: 15 Alignment: TTCAGCACCATGRCCWKSAVVDGGTMAAAGGTCAAC ------------BTRGGDCARAGGKCA--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR4A2 Reverse Complement Original Motif GTTGACCTTTGACCTKTVBCHVDVCATGGTGCTGAA AAGGTCAC AAGKTSACCTTTGACCTKTVBCHVDVCATGGTGCTGAA Direction: Forward Position #: 3 Overlap #: 6 Alignment: --GTTGACCTTTGACCTKTVBCHVDVCATGGTGCTGAA AAGGTCAC------------------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Original Motif Original Motif AAGKTSACCTTTGACCTKTVBCHVDVCATGGTGCTGAA VDBHMAGGTCACCCTGACCY AAGKTSACCBDBVVMSKTYABCHDGMCMTGGTGCTGAA Direction: Forward Position #: 10 Overlap #: 20 Alignment: AAGKTSACCTTTGACCTKTVBCHVDVCATGGTGCTGAA ---------VDBHMAGGTCACCCTGACCY--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Mycn Combined Motif Reverse Complement Original Motif TTCAGCACCARGYCDDGBTKAYSRBVVDVGGTSAYCTT HSCACGTGGC TTCAGCACSHGGYCDDGBTKAYSRBVVDVGGTSAYCTT Direction: Forward Position #: 4 Overlap #: 10 Alignment: TTCAGCACCARGYCDDGBTKAYSRBVVDVGGTSAYCTT ---HSCACGTGGC------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Myc Original Motif Reverse Complement TTCAGCACSHGGYCDDGBTKAYSRBVVDVGGTSAYCTT DCCACGTGCV DCCACGTKCVGCACSHGGYCDDGBTKAYSRBVVDVGGTSAYCTT Direction: Forward Position #: 7 Overlap #: 4 Alignment: ------TTCAGCACSHGGYCDDGBTKAYSRBVVDVGGTSAYCTT DCCACGTGCV---------------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 28 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ssGCkTGCssk gCGCGCsCgsG Original Motif Original Motif SSGCKTGCSSK GCGCGCSCGCG SCGCGYGCSSG Direction: Backward Position #: 1 Overlap #: 11 Alignment: SSGCKTGCSSK GCGCGCSCGCG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ssCCCCGCSssk Reverse Complement Original Motif CSSGCKCGCGS SBCCCCGCCSBB SBCCCCGCCSSGCKCGCGS Direction: Forward Position #: 9 Overlap #: 4 Alignment: --------CSSGCKCGCGS SBCCCCGCCSBB------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- sscCCCGCGcs Combined Motif Original Motif Reverse Complement SBCCCCGCCSSGCKCGCGS SBCGCGGGGSB SBCCSCGCSGSGSKCGCGS Direction: Forward Position #: 4 Overlap #: 11 Alignment: SBCCCCGCCSSGCKCGCGS ---SBCGCGGGGSB----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- cCGCGGrCACG Combined Motif Original Motif Original Motif SBCCSCGCSGSGSKCGCGS CCGCGGRCACG SBCCCCGCGGRSVSSGCGS Direction: Forward Position #: 5 Overlap #: 11 Alignment: SBCCSCGCSGSGSKCGCGS ----CCGCGGRCACG---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CTCF Combined Motif Reverse Complement Reverse Complement SCGCSSBSMCCGCGGGGBS BMSMGCCYMCTKSTGGMHM BVGCGCCBMCYGCKGGVBV Direction: Forward Position #: 1 Overlap #: 19 Alignment: SCGCSSBSMCCGCGGGGBS BMSMGCCYMCTKSTGGMHM ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Esrrb Reverse Complement Reverse Complement VBVCCYGCMGRBGGCGCVB TGACCTTGMBBB TGACCTKSMGVBGGCGCVB Direction: Forward Position #: 1 Overlap #: 12 Alignment: VBVCCYGCMGRBGGCGCVB TGACCTTGMBBB------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Reverse Complement Reverse Complement BVGCGCCBVCYSRAGGTCA BAGGYCABHBTGACCKHV BMGSBCMBVBTGAMSGHVA Direction: Forward Position #: 1 Overlap #: 18 Alignment: BVGCGCCBVCYSRAGGTCA BAGGYCABHBTGACCKHV- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- REST Combined Motif Original Motif Reverse Complement BMGSBCMBVBTGAMSGHVA GGYGCTGTCCATGGTGCTGAA BMGSBSVHVCTGWCCDTGGTGCTGAA Direction: Forward Position #: 6 Overlap #: 14 Alignment: BMGSBCMBVBTGAMSGHVA------- -----GGYGCTGTCCATGGTGCTGAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Original Motif Reverse Complement BMGSBSVHVCTGWCCDTGGTGCTGAA TGRCCTKTGHCCKAB BMGSTGVCCYTKDCCVKVVTGCTGAA Direction: Forward Position #: 5 Overlap #: 15 Alignment: BMGSBSVHVCTGWCCDTGGTGCTGAA ----TGRCCTKTGHCCKAB------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HNF4A Combined Motif Reverse Complement Original Motif TTCAGCAVVRVGGHRAMGGBCASCYB RGGBCAAAGKYCA TTCAGCAVVRGGBCAAAGKBCASCYB Direction: Forward Position #: 10 Overlap #: 13 Alignment: TTCAGCAVVRVGGHRAMGGBCASCYB ---------RGGBCAAAGKYCA---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 25 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- wwCCAmAGTCmt CACTGTGrYrtCACAGTGswsCAcT Original Motif Original Motif DDCCAMAGTCHB CACTGTGRTRTCACAGTGSWSCACT CACTGTGRHDYCACAGTSBWSCACT Direction: Backward Position #: 6 Overlap #: 12 Alignment: --------DDCCAMAGTCHB----- CACTGTGRTRTCACAGTGSWSCACT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CagTGCTCCACTGTGgT Combined Motif Reverse Complement Reverse Complement AGTGSWBSACTGTGKHHMCACAGTG ABCACAGTGGAGCACTG AGTGSABCACWGTGGAGCMMYRGTG Direction: Forward Position #: 6 Overlap #: 17 Alignment: AGTGSWBSACTGTGKHHMCACAGTG -----ABCACAGTGGAGCACTG--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CAcCACAGTGGAGCAct Combined Motif Original Motif Original Motif AGTGSABCACWGTGGAGCMMYRGTG CAHCACAGTGGAGCACT AGTGCABCACWGTGGAGCAMYRGTG Direction: Forward Position #: 5 Overlap #: 17 Alignment: AGTGSABCACWGTGGAGCMMYRGTG ----CAHCACAGTGGAGCACT---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- AgTGCTCCACTGTGgTGTCACAgT Combined Motif Original Motif Original Motif AGTGCABCACWGTGGAGCAMYRGTG AGTGCTCCACTGTGGTGTCACAGT AGTGCWCCACWGTGGWGYMAYAGTG Direction: Forward Position #: 1 Overlap #: 24 Alignment: AGTGCABCACWGTGGAGCAMYRGTG AGTGCTCCACTGTGGTGTCACAGT- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HNF4A Combined Motif Original Motif Reverse Complement AGTGCWCCACWGTGGWGYMAYAGTG TGMYCTTTGBCCK AGTGCTSCACTKTGGHSBMAYAGTG Direction: Forward Position #: 6 Overlap #: 13 Alignment: AGTGCWCCACWGTGGWGYMAYAGTG -----TGMYCTTTGBCCK------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TGGAGCACTGTGACAcCACAGTGg Combined Motif Original Motif Original Motif AGTGCTSCACTKTGGHSBMAYAGTG TGGAGCACTGTGACAVCACAGTGG AGTGSWGCACTGTGRCABCACAGTGG Direction: Forward Position #: 3 Overlap #: 23 Alignment: AGTGCTSCACTKTGGHSBMAYAGTG- --TGGAGCACTGTGACAVCACAGTGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Reverse Complement CCACTGTGBTGKCACAGTGCWSCACT GGYGCTGTCCATGGTGCTGAA GGYGCTGTCCAYKGTGCTGDMACAGTGCWSCACT Direction: Forward Position #: 9 Overlap #: 13 Alignment: --------CCACTGTGBTGKCACAGTGCWSCACT GGYGCTGTCCATGGTGCTGAA------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TgTGgTGTCACAGTGCTCC Reverse Complement Original Motif AGTGSWGCACTGTRDCAGCACYKTGGACAGCKCC TGTGGTGTCACAGTGCTCC TGTRGTGBMRCASTGYKBCAGCACYKTGGACAGCKCC Direction: Forward Position #: 4 Overlap #: 16 Alignment: ---AGTGSWGCACTGTRDCAGCACYKTGGACAGCKCC TGTGGTGTCACAGTGCTCC------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Original Motif Original Motif TGTRGTGBMRCASTGYKBCAGCACYKTGGACAGCKCC VDBHMAGGTCACCCTGACCY TGTRGTGBHVCAGKKCWBCMKSACCBTGGACAGCKCC Direction: Forward Position #: 7 Overlap #: 20 Alignment: TGTRGTGBMRCASTGYKBCAGCACYKTGGACAGCKCC ------VDBHMAGGTCACCCTGACCY----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR1H2RXRA Combined Motif Reverse Complement Original Motif GGYGCTGTCCAVGGTSRYGBWGYYCTGBDVCACMACA AAAGGTCAAAGGTCAAC GGMRMKGTCMAAGGTCAHSBWGYYCTGBDVCACMACA Direction: Forward Position #: 3 Overlap #: 17 Alignment: GGYGCTGTCCAVGGTSRYGBWGYYCTGBDVCACMACA --AAAGGTCAAAGGTCAAC------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 19 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- atactttggc wwCCAmAGTCmt Reverse Complement Original Motif GCCAAAGTAT DDCCAMAGTCHB DGCCAAAGTMTB Direction: Forward Position #: 2 Overlap #: 10 Alignment: -GCCAAAGTAT- DDCCAMAGTCHB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif taaacgatgcc Original Motif Original Motif DGCCAAAGTMTB TAAACGATGCC TAAACGATGCCAAAGTMTB Direction: Forward Position #: 8 Overlap #: 4 Alignment: -------DGCCAAAGTMTB TAAACGATGCC-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR1H2RXRA Original Motif Reverse Complement TAAACGATGCCAAAGTMTB GTTGACCTTTGACCTTT GTTGACCTTTRAMCKWTGCCAAAGTMTB Direction: Forward Position #: 10 Overlap #: 8 Alignment: ---------TAAACGATGCCAAAGTMTB GTTGACCTTTGACCTTT----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TgTGgTGTCACAGTGCTCC Reverse Complement Reverse Complement VAYACTTTGGCAWYGYTKAAAGGTCAAC GGAGCACTGTGACACCACA GGARCACTKTGRCAHCRYWKAAAGGTCAAC Direction: Forward Position #: 3 Overlap #: 17 Alignment: --VAYACTTTGGCAWYGYTKAAAGGTCAAC GGAGCACTGTGACACCACA----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Original Motif Reverse Complement GGARCACTKTGRCAHCRYWKAAAGGTCAAC AGTGSWSCACTGTGAMAMCACAGTG AGTGGAGCACTGTGACAHCACAGWRAGGTCAAC Direction: Forward Position #: 4 Overlap #: 22 Alignment: ---GGARCACTKTGRCAHCRYWKAAAGGTCAAC AGTGSWSCACTGTGAMAMCACAGTG-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif HNF4A Reverse Complement Reverse Complement GTTGACCTKWCTGTGDTGTCACAGTGCTCCACT TGMYCTTTGBCCK TGMYCKTTGACCTKWCTGTGDTGTCACAGTGCTCCACT Direction: Forward Position #: 6 Overlap #: 8 Alignment: -----GTTGACCTKWCTGTGDTGTCACAGTGCTCCACT TGMYCTTTGBCCK------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Original Motif Original Motif TGMYCKTTGACCTKWCTGTGDTGTCACAGTGCTCCACT TGAMCTTTGMMCYT TGAMCTTTGVCCYKWCTGTGDTGTCACAGTGCTCCACT Direction: Forward Position #: 1 Overlap #: 14 Alignment: TGMYCKTTGACCTKWCTGTGDTGTCACAGTGCTCCACT TGAMCTTTGMMCYT------------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TGGAGCACTGTGACAcCACAGTGg Combined Motif Original Motif Original Motif TGAMCTTTGVCCYKWCTGTGDTGTCACAGTGCTCCACT TGGAGCACTGTGACAVCACAGTGG TGAMCTTTKRSMBYACTGTGAYRBCACAGTGSTCCACT Direction: Forward Position #: 9 Overlap #: 24 Alignment: TGAMCTTTGVCCYKWCTGTGDTGTCACAGTGCTCCACT --------TGGAGCACTGTGACAVCACAGTGG------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif AgTGCTCCACTGTGgTGTCACAgT Reverse Complement Original Motif AGTGGASCACTGTGVKKTCACAGTKBYSMYAAAGRTCA AGTGCTCCACTGTGGTGTCACAGT AGTGSTCCACTGTGVTGTCACAGTKBYSMYAAAGRTCA Direction: Forward Position #: 1 Overlap #: 24 Alignment: AGTGGASCACTGTGVKKTCACAGTKBYSMYAAAGRTCA AGTGCTCCACTGTGGTGTCACAGT-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CAcCACAGTGGAGCAct Combined Motif Reverse Complement Original Motif TGAMCTTTKRSMBYACTGTGACAVCACAGTGGASCACT CAHCACAGTGGAGCACT TGAMCTTTKRCABCACWGTGRMRCMMYAGTGGASCACT Direction: Forward Position #: 11 Overlap #: 17 Alignment: TGAMCTTTKRSMBYACTGTGACAVCACAGTGGASCACT ----------CAHCACAGTGGAGCACT----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 11 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR4A2 NR1H2RXRA Original Motif Original Motif AAGGTCAC AAAGGTCAAAGGTCAAC AAAGGTCAMAGGTCAAC Direction: Backward Position #: 9 Overlap #: 8 Alignment: -AAGGTCAC-------- AAAGGTCAAAGGTCAAC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR1 Reverse Complement Reverse Complement GTTGACCTYTGACCTTT MGGTCAGGGTGACCTRDBHV MGGTCAGGKTGACCTBTGACCTTT Direction: Forward Position #: 8 Overlap #: 13 Alignment: -------GTTGACCTYTGACCTTT MGGTCAGGGTGACCTRDBHV---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Original Motif Original Motif MGGTCAGGKTGACCTBTGACCTTT VHRGGTCABDBTGMCCTB MGGTCADRKKKMMCTBTGACCTBT Direction: Forward Position #: 6 Overlap #: 18 Alignment: MGGTCAGGKTGACCTBTGACCTTT -----VHRGGTCABDBTGMCCTB- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Reverse Complement Reverse Complement AVAGGTCABAGYRYYYMHTGACCY TGRCCTKTGHCCKAB AVWGRYCWBWGYVCBHVHTGACCY Direction: Forward Position #: 3 Overlap #: 15 Alignment: AVAGGTCABAGYRYYYMHTGACCY --TGRCCTKTGHCCKAB------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Original Motif Reverse Complement AVWGRYCWBWGYVCBHVHTGACCY AGTGSWSCACTGTGAMAMCACAGTG AGTGSWSCACTGTGAMAVVACAGTGYVCBHVHTGACCY Direction: Forward Position #: 15 Overlap #: 11 Alignment: --------------AVWGRYCWBWGYVCBHVHTGACCY AGTGSWSCACTGTGAMAMCACAGTG------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Reverse Complement Reverse Complement MGGTCADVDVGVKCACTGTVVTRTCACAGTGSWSCACT AKGYYCAAAGRTCA ADGBTCAAVGRKCRCACTGTVVTRTCACAGTGSWSCACT Direction: Forward Position #: 2 Overlap #: 13 Alignment: -MGGTCADVDVGVKCACTGTVVTRTCACAGTGSWSCACT AKGYYCAAAGRTCA------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Original Motif Original Motif ADGBTCAAVGRKCRCACTGTVVTRTCACAGTGSWSCACT TTCAGCACCATGGACAGCKCC TTCAGCACCAHGGHCARVGVBCRCACTGTVVTRTCACAGTGSWSCACT Direction: Forward Position #: 10 Overlap #: 12 Alignment: ---------ADGBTCAAVGRKCRCACTGTVVTRTCACAGTGSWSCACT TTCAGCACCATGGACAGCKCC--------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TGGAGCACTGTGACAcCACAGTGg Combined Motif Reverse Complement Original Motif AGTGSWSCACTGTGAMAVVACAGTGKGVVCVMTGHCCHTGGTGCTGAA TGGAGCACTGTGACAVCACAGTGG AGTGSWSCACTGTKRVAGCACWGTGASAVCACWGTSSHTGGTGCTGAA Direction: Forward Position #: 14 Overlap #: 24 Alignment: AGTGSWSCACTGTGAMAVVACAGTGKGVVCVMTGHCCHTGGTGCTGAA -------------TGGAGCACTGTGACAVCACAGTGG----------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif AmTGTGACACCACAGT Original Motif Original Motif AGTGSWSCACTGTKRVAGCACWGTGASAVCACWGTSSHTGGTGCTGAA AMTGTGACACCACAGT AMTRKKRCASCACWGTKRVAGCACWGTGASAVCACWGTSSHTGGTGCTGAA Direction: Forward Position #: 4 Overlap #: 13 Alignment: ---AGTGSWSCACTGTKRVAGCACWGTGASAVCACWGTSSHTGGTGCTGAA AMTGTGACACCACAGT----------------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TgTGgTGTCACAGTGCTCC Combined Motif Reverse Complement Reverse Complement TTCAGCACCAHSSACWGTGVTSTCACWGTGCTVMYACWGTGSTGKRRMART GGAGCACTGTGACACCACA TTCAGCACCAHSSACWGTGGKRKCACWGTGMYACCACWGTGSTGKRRMART Direction: Forward Position #: 20 Overlap #: 19 Alignment: TTCAGCACCAHSSACWGTGVTSTCACWGTGCTVMYACWGTGSTGKRRMART -------------------GGAGCACTGTGACACCACA------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 4 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Esrrb NR2F1 Reverse Complement Original Motif TGACCTTGMBBB TGAMCTTTGMMCYT TGWSMYYTKRMCHB Direction: Backward Position #: 1 Overlap #: 12 Alignment: --TGACCTTGMBBB TGAMCTTTGMMCYT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Reverse Complement Reverse Complement VDGYMYAKKRSWCA TGRCCTKTGHCCKAB TGRCCTKTGHCMKVBMYAKKRSWCA Direction: Forward Position #: 12 Overlap #: 4 Alignment: -----------VDGYMYAKKRSWCA TGRCCTKTGHCCKAB---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HNF4A Combined Motif Original Motif Reverse Complement TGRCCTKTGHCMKVBMYAKKRSWCA TGMYCTTTGBCCK TGRCCTTKVYCHTTBVYMKKRSWCA Direction: Forward Position #: 7 Overlap #: 13 Alignment: TGRCCTKTGHCMKVBMYAKKRSWCA ------TGMYCTTTGBCCK------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR1H2RXRA Original Motif Reverse Complement TGRCCTTKVYCHTTBVYMKKRSWCA GTTGACCTTTGACCTTT GTTGACCTTTGACCTTBVYMKKRSWCA Direction: Forward Position #: 3 Overlap #: 15 Alignment: --TGRCCTTKVYCHTTBVYMKKRSWCA GTTGACCTTTGACCTTT---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Original Motif Reverse Complement GTTGACCTTTGACCTTBVYMKKRSWCA MGGTCAGGGTGACCTRDBHV VKKKMMCKKTGACCTDBBHVKKRSWCA Direction: Forward Position #: 1 Overlap #: 20 Alignment: GTTGACCTTTGACCTTBVYMKKRSWCA MGGTCAGGGTGACCTRDBHV------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Reverse Complement Reverse Complement TGWSMYYBDBBDAGGTCARRGRRYYRV BAGGYCABHBTGACCKHV TGWVMBBYVVBVVKGWCMDDGRRYYRV Direction: Forward Position #: 4 Overlap #: 18 Alignment: TGWSMYYBDBBDAGGTCARRGRRYYRV ---BAGGYCABHBTGACCKHV------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Original Motif VKKKMMCDHYGWCRBBBBVMBBYVWCA TTCAGCACCATGGACAGCKCC TTCAGBACCDHGGACAGBDBBMBBYVWCA Direction: Forward Position #: 3 Overlap #: 19 Alignment: --VKKKMMCDHYGWCRBBBBVMBBYVWCA TTCAGCACCATGGACAGCKCC-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TgTGgTGTCACAGTGCTCC Reverse Complement Original Motif TGWVMBBYBBHBCTGTCCHDGGTBCTGAA TGTGGTGTCACAGTGCTCC TGTGGTGTCACDBTGCTCYGTCCHDGGTBCTGAA Direction: Forward Position #: 6 Overlap #: 14 Alignment: -----TGWVMBBYBBHBCTGTCCHDGGTBCTGAA TGTGGTGTCACAGTGCTCC--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TGGAGCACTGTGACAcCACAGTGg Combined Motif Original Motif Reverse Complement TGTGGTGTCACDBTGCTCYGTCCHDGGTBCTGAA CCACTGTGVTGTCACAGTGCTCCA TGTGGTGHCACTGTGBTSTSWCHVTGSTCCWGAA Direction: Forward Position #: 8 Overlap #: 24 Alignment: TGTGGTGTCACDBTGCTCYGTCCHDGGTBCTGAA -------CCACTGTGVTGTCACAGTGCTCCA--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Reverse Complement Reverse Complement TTCWGGASCAVHGWSASABCACAGTGHCACCACA AGTGSWSCACTGTGAMAMCACAGTG AKTSBDSMACWGTGWCAVMACASWGTGHCACCACA Direction: Forward Position #: 2 Overlap #: 24 Alignment: -TTCWGGASCAVHGWSASABCACAGTGHCACCACA AGTGSWSCACTGTGAMAMCACAGTG---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 1 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HNF4A PPARGRXRA Reverse Complement Reverse Complement TGMYCTTTGBCCK TGRCCTKTGHCCKAB TGACCTTTGBCCKAB Direction: Backward Position #: 3 Overlap #: 13 Alignment: TGMYCTTTGBCCK-- TGRCCTKTGHCCKAB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Original Motif Original Motif TGACCTTTGBCCKAB TGAMCTTTGMMCYT TGACCTTTGVMCBHB Direction: Forward Position #: 1 Overlap #: 14 Alignment: TGACCTTTGBCCKAB TGAMCTTTGMMCYT- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR1H2RXRA Reverse Complement Original Motif BHVGRVCAAAGGTCA AAAGGTCAAAGGTCAAC VAAGGTCAAAGGTCAAC Direction: Forward Position #: 1 Overlap #: 15 Alignment: BHVGRVCAAAGGTCA-- AAAGGTCAAAGGTCAAC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Reverse Complement Reverse Complement GTTGACCTTTGACCTTB AGTGSWSCACTGTGAMAMCACAGTG AGTGBTGMMCTKTGACMHYACAGTG Direction: Forward Position #: 4 Overlap #: 17 Alignment: ---GTTGACCTTTGACCTTB----- AGTGSWSCACTGTGAMAMCACAGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TGGAGCACTGTGACAcCACAGTGg Combined Motif Original Motif Original Motif AGTGBTGMMCTKTGACMHYACAGTG TGGAGCACTGTGACAVCACAGTGG AGTGGWGCACTGTGACAHCACAGTGG Direction: Forward Position #: 3 Overlap #: 23 Alignment: AGTGBTGMMCTKTGACMHYACAGTG- --TGGAGCACTGTGACAVCACAGTGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Original Motif Reverse Complement AGTGGWGCACTGTGACAHCACAGTGG BAGGYCABHBTGACCKHV AGTRGDBCACTGTGACMBHDCAGTGG Direction: Forward Position #: 3 Overlap #: 18 Alignment: AGTGGWGCACTGTGACAHCACAGTGG --BAGGYCABHBTGACCKHV------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TgTGgTGTCACAGTGCTCC Combined Motif Original Motif Reverse Complement AGTRGDBCACTGTGACMBHDCAGTGG GGAGCACTGTGACACCACA AGTGGAGCACTGTGACABCACAGTGG Direction: Forward Position #: 4 Overlap #: 19 Alignment: AGTRGDBCACTGTGACMBHDCAGTGG ---GGAGCACTGTGACACCACA---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Original Motif Original Motif AGTGGAGCACTGTGACABCACAGTGG VDBHMAGGTCACCCTGACCY AGTGGDBCMVKGTSACMBYRMMSTGG Direction: Forward Position #: 5 Overlap #: 20 Alignment: AGTGGAGCACTGTGACABCACAGTGG ----VDBHMAGGTCACCCTGACCY-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Original Motif CCASRRMMBRGTSACYVYGBDCCACT TTCAGCACCATGGACAGCKCC TTCMRSACCABGGWCASCDYBBDCCACT Direction: Forward Position #: 3 Overlap #: 19 Alignment: --CCASRRMMBRGTSACYVYGBDCCACT TTCAGCACCATGGACAGCKCC------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif AgTGCTCCACTGTGgTGTCACAgT Reverse Complement Reverse Complement AGTGGDBBKHGSTGWCCVTGGTSMYGAA ACTGTGACACCACAGTGGAGCACT ACTGTGACACCACAGTGGAGCACKSTGWCCVTGGTSMYGAA Direction: Forward Position #: 14 Overlap #: 11 Alignment: -------------AGTGGDBBKHGSTGWCCVTGGTSMYGAA ACTGTGACACCACAGTGGAGCACT----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CTCF Combined Motif Original Motif Original Motif ACTGTGACACCACAGTGGAGCACKSTGWCCVTGGTSMYGAA YDRCCASYAGRKGGCRSYV ACTGTGACABVMCASYRGRGGRCDSTVWCCVTGGTSMYGAA Direction: Forward Position #: 9 Overlap #: 19 Alignment: ACTGTGACACCACAGTGGAGCACKSTGWCCVTGGTSMYGAA --------YDRCCASYAGRKGGCRSYV-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 12 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RORA_1 Esrrb Original Motif Original Motif AWVDAGGTCA VBBYCAAGGTCA VBDTCAAGGTCA Direction: Backward Position #: 1 Overlap #: 10 Alignment: --AWVDAGGTCA VBBYCAAGGTCA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ESR1 Original Motif Reverse Complement VBDTCAAGGTCA MGGTCAGGGTGACCTRDBHV VGGTCARGGTSACCTRDBHV Direction: Forward Position #: 1 Overlap #: 12 Alignment: VBDTCAAGGTCA-------- MGGTCAGGGTGACCTRDBHV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR1H2RXRA Original Motif Original Motif VGGTCARGGTSACCTRDBHV AAAGGTCAAAGGTCAAC AAAGGTCMAAGGTCAMCTRDBHV Direction: Forward Position #: 4 Overlap #: 14 Alignment: ---VGGTCARGGTSACCTRDBHV AAAGGTCAAAGGTCAAC------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR2F1 Combined Motif Original Motif Reverse Complement AAAGGTCMAAGGTCAMCTRDBHV AKGYYCAAAGRTCA AAAGGTYMAARGKYMACTRDBHV Direction: Forward Position #: 3 Overlap #: 14 Alignment: AAAGGTCMAAGGTCAMCTRDBHV --AKGYYCAAAGRTCA------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Original Motif Reverse Complement AAAGGTYMAARGKYMACTRDBHV TGRCCTKTGHCCKAB AAAGGTBMMMDGTBMMCKVBBHV Direction: Forward Position #: 6 Overlap #: 15 Alignment: AAAGGTYMAARGKYMACTRDBHV -----TGRCCTKTGHCCKAB--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif REST Reverse Complement Original Motif VDBBBRGRRBACDRYYBACCTTT TTCAGCACCATGGACAGCKCC TTCAGVACCDDGGACASVRYYBACCTTT Direction: Forward Position #: 6 Overlap #: 16 Alignment: -----VDBBBRGRRBACDRYYBACCTTT TTCAGCACCATGGACAGCKCC------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HNF4A Combined Motif Reverse Complement Reverse Complement AAAGGTBKKMVSTGTCCDDGGTVCTGAA TGMYCTTTGBCCK AAAGGTBGVYCYTKKCCHDGGTVCTGAA Direction: Forward Position #: 7 Overlap #: 13 Alignment: AAAGGTBKKMVSTGTCCDDGGTVCTGAA ------TGMYCTTTGBCCK--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TgTGgTGTCACAGTGCTCC Original Motif Original Motif AAAGGTBGVYCYTKKCCHDGGTVCTGAA TGTGGTGTCACAGTGCTCC TGTGGTGTMAMRGTGSTCCYTKKCCHDGGTVCTGAA Direction: Forward Position #: 9 Overlap #: 11 Alignment: --------AAAGGTBGVYCYTKKCCHDGGTVCTGAA TGTGGTGTCACAGTGCTCC----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wwCCAmAGTCmt Reverse Complement Original Motif TTCAGVACCDDGGYRAMGGASCACKRTRACACCACA DDCCAMAGTCHB DDYCASARYCVDGGYRAMGGASCACKRTRACACCACA Direction: Forward Position #: 2 Overlap #: 11 Alignment: -TTCAGVACCDDGGYRAMGGASCACKRTRACACCACA DDCCAMAGTCHB------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Original Motif Reverse Complement DDYCASARYCVDGGYRAMGGASCACKRTRACACCACA BAGGYCABHBTGACCKHV DDYCASARYCVBVGBHMABBVTSACBDTRACACCACA Direction: Forward Position #: 12 Overlap #: 18 Alignment: DDYCASARYCVDGGYRAMGGASCACKRTRACACCACA -----------BAGGYCABHBTGACCKHV-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 6 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Mycn Myc Reverse Complement Reverse Complement GCCACGTGSD DCCACGTGCV GCCACGTGSV Direction: Forward Position #: 1 Overlap #: 10 Alignment: GCCACGTGSD DCCACGTGCV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif sscCCCGCGcs Reverse Complement Reverse Complement VSCACGTGGC SBCGCGGGGSB VSCRCGKGGVB Direction: Forward Position #: 1 Overlap #: 10 Alignment: VSCACGTGGC- SBCGCGGGGSB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CTCF Reverse Complement Original Motif BVCCYCGMGSV YDRCCASYAGRKGGCRSYV YBVCCHCGAGVKGGCRSYV Direction: Forward Position #: 2 Overlap #: 11 Alignment: -BVCCYCGMGSV------- YDRCCASYAGRKGGCRSYV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ssCCCCGCSssk Combined Motif Original Motif Reverse Complement YBVCCHCGAGVKGGCRSYV BBSGGCGGGGBS YBVCCVSGMGGGGGCRSYV Direction: Forward Position #: 4 Overlap #: 12 Alignment: YBVCCHCGAGVKGGCRSYV ---BBSGGCGGGGBS---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Reverse Complement Original Motif BMSMGCCCCCRCSVGGVBM CACTGTGRTRTCACAGTGSWSCACT CACTGTGRTRTCACAGTGBWSCRCYCCCRCSVGGVBM Direction: Forward Position #: 19 Overlap #: 7 Alignment: ------------------BMSMGCCCCCRCSVGGVBM CACTGTGRTRTCACAGTGSWSCACT------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Original Motif Original Motif CACTGTGRTRTCACAGTGBWSCRCYCCCRCSVGGVBM VDBHMAGGTCACCCTGACCY CACTGTGRTRTCACAGTGBWSCRCBBSCVVGGKSABMCTGACCY Direction: Forward Position #: 25 Overlap #: 13 Alignment: CACTGTGRTRTCACAGTGBWSCRCYCCCRCSVGGVBM------- ------------------------VDBHMAGGTCACCCTGACCY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CagTGCTCCACTGTGgT Original Motif Reverse Complement CACTGTGRTRTCACAGTGBWSCRCBBSCVVGGKSABMCTGACCY ABCACAGTGGAGCACTG ABCACWGTGGWGYMMYRGTGBWSCRCBBSCVVGGKSABMCTGACCY Direction: Forward Position #: 3 Overlap #: 15 Alignment: --CACTGTGRTRTCACAGTGBWSCRCBBSCVVGGKSABMCTGACCY ABCACAGTGGAGCACTG----------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HNF4A Combined Motif Original Motif Reverse Complement ABCACWGTGGWGYMMYRGTGBWSCRCBBSCVVGGKSABMCTGACCY TGMYCTTTGBCCK ABCACWGTGGWGYMMYRGTGBWSCRCBBSMHCKKTGVHCBTGACCY Direction: Forward Position #: 28 Overlap #: 13 Alignment: ABCACWGTGGWGYMMYRGTGBWSCRCBBSCVVGGKSABMCTGACCY ---------------------------TGMYCTTTGBCCK------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif AgTGCTCCACTGTGgTGTCACAgT Original Motif Original Motif ABCACWGTGGWGYMMYRGTGBWSCRCBBSMHCKKTGVHCBTGACCY AGTGCTCCACTGTGGTGTCACAGT AGTGCWCCACTGTGGTGTCACAGTGBWSCRCBBSMHCKKTGVHCBTGACCY Direction: Forward Position #: 6 Overlap #: 19 Alignment: -----ABCACWGTGGWGYMMYRGTGBWSCRCBBSMHCKKTGVHCBTGACCY AGTGCTCCACTGTGGTGTCACAGT--------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PPARGRXRA Combined Motif Original Motif Original Motif AGTGCWCCACTGTGGTGTCACAGTGBWSCRCBBSMHCKKTGVHCBTGACCY BTRGGDCARAGGKCA AGTGCWCCACTGTGGTGTCACAGTGBWSCVYVBGVCMDDKGBCMBTGACCY Direction: Forward Position #: 30 Overlap #: 15 Alignment: AGTGCWCCACTGTGGTGTCACAGTGBWSCRCBBSMHCKKTGVHCBTGACCY -----------------------------BTRGGDCARAGGKCA------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 8 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Myc Mycn Original Motif Original Motif VGCACGTGGH HSCACGTGGC VSCACGTGGC Direction: Backward Position #: 1 Overlap #: 10 Alignment: VGCACGTGGH HSCACGTGGC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif sscCCCGCGcs Original Motif Reverse Complement VSCACGTGGC SBCGCGGGGSB VSCRCGKGGVB Direction: Forward Position #: 1 Overlap #: 10 Alignment: VSCACGTGGC- SBCGCGGGGSB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ssCCCCGCSssk Reverse Complement Original Motif BVCCYCGMGSV SBCCCCGCCSBB SBCCCCGCSSBB Direction: Forward Position #: 1 Overlap #: 11 Alignment: BVCCYCGMGSV- SBCCCCGCCSBB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CTCF Reverse Complement Original Motif BBSSGCGGGGBS YDRCCASYAGRKGGCRSYV YDRCCASYAGRBGGCRCGVGGBS Direction: Forward Position #: 12 Overlap #: 8 Alignment: -----------BBSSGCGGGGBS YDRCCASYAGRKGGCRSYV---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACTGTGrYrtCACAGTGswsCAcT Original Motif Original Motif YDRCCASYAGRBGGCRCGVGGBS CACTGTGRTRTCACAGTGSWSCACT CACTGTGDBRYCACARKGSDSCRCKVGGBS Direction: Forward Position #: 8 Overlap #: 18 Alignment: -------YDRCCASYAGRBGGCRCGVGGBS CACTGTGRTRTCACAGTGSWSCACT----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HNF4A Combined Motif Reverse Complement Reverse Complement SBCCVRGKGSDSCYKTGTGKMVDCACAGTG TGMYCTTTGBCCK SBCCVRGKKSVBCTTTGTSBBVDCACAGTG Direction: Forward Position #: 9 Overlap #: 13 Alignment: SBCCVRGKGSDSCYKTGTGKMVDCACAGTG --------TGMYCTTTGBCCK--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR1 Combined Motif Reverse Complement Original Motif CACTGTGDBBBSACAAAGBBSYRCKVGGBS VDBHMAGGTCACCCTGACCY CACTGTGDBBBSACAAAGBBCHASGDSRBBCTGACCY Direction: Forward Position #: 18 Overlap #: 13 Alignment: CACTGTGDBBBSACAAAGBBSYRCKVGGBS------- -----------------VDBHMAGGTCACCCTGACCY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CagTGCTCCACTGTGgT Original Motif Reverse Complement CACTGTGDBBBSACAAAGBBCHASGDSRBBCTGACCY ABCACAGTGGAGCACTG ABCACWGTGGAGCVMYRAAGBBCHASGDSRBBCTGACCY Direction: Forward Position #: 3 Overlap #: 15 Alignment: --CACTGTGDBBBSACAAAGBBCHASGDSRBBCTGACCY ABCACAGTGGAGCACTG---------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ESR2 Combined Motif Original Motif Reverse Complement ABCACWGTGGAGCVMYRAAGBBCHASGDSRBBCTGACCY BAGGYCABHBTGACCKHV ABCACWGTGGAGCVMYRAAGBBCBAGGBCABBBTGACCTHV Direction: Forward Position #: 24 Overlap #: 16 Alignment: ABCACWGTGGAGCVMYRAAGBBCHASGDSRBBCTGACCY-- -----------------------BAGGYCABHBTGACCKHV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TGGAGCACTGTGACAcCACAGTGg Combined Motif Reverse Complement Original Motif VHAGGTCABBBTGVCCTBGBBCTTKKRBGCTCCACWGTGBT TGGAGCACTGTGACAVCACAGTGG VHAGGTCABBBTGVCCTGGAGCWBTGTGRCACCACAGTGGT Direction: Forward Position #: 17 Overlap #: 24 Alignment: VHAGGTCABBBTGVCCTBGBBCTTKKRBGCTCCACWGTGBT ----------------TGGAGCACTGTGACAVCACAGTGG- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 11-20-2016 21:11:03 Runtime: 725.149 seconds MOTIFSIM is written by Ngoc Tam L. 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