**************************************************************************************************************************************************************************************************** MOTIFSIM - Motif Similarity Detection Tool Version 2.1 **************************************************************************************************************************************************************************************************** INPUT **************************************************************************************************************************************************************************************************** Input Parameters Number of files: 4 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 # DREME_DM721.txt 16 1 MEME-ChIP_DM721.txt 11 2 PScanChIP_DM721.txt 37 3 RSAT_peak-motifs_DM721.txt 40 4 **************************************************************************************************************************************************************************************************** RESULTS **************************************************************************************************************************************************************************************************** ************************************************************ Combined Motifs for Top Global Significant Motif ID 18 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 18 Motif 2 Reverse Complement Reverse Complement TGTRT TGTGTGTG GTGTGTRT Direction: Backward Position #: 4 Overlap #: 5 Alignment: TGTRT--- TGTGTGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACACACACACA Reverse Complement Original Motif AMACACAC CACACACACACA CACACACACACA Direction: Forward Position #: 2 Overlap #: 8 Alignment: -AMACACAC--- CACACACACACA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACACACACACA Reverse Complement Reverse Complement TGTGTGTGTGTG TGTGTGTGTGTG TGTGTGTGTGTG Direction: Forward Position #: 1 Overlap #: 12 Alignment: TGTGTGTGTGTG TGTGTGTGTGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif aaACAAAACaa Original Motif Reverse Complement TGTGTGTGTGTG TTGTTTTGTTT TBKKTKTGTKTG Direction: Forward Position #: 1 Overlap #: 11 Alignment: TGTGTGTGTGTG TTGTTTTGTTT- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif aaCAAAAACaa Original Motif Reverse Complement TBKKTKTGTKTG HTGTTTTTGHH TBGTTTTKKDTG Direction: Forward Position #: 1 Overlap #: 11 Alignment: TBKKTKTGTKTG HTGTTTTTGHH- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ryayAyAyrtGTRTrTry Combined Motif Reverse Complement Reverse Complement CADYRAAAACVA HDAMACACAKKTKTKTHD CAVBAAAMACADKTKTKTHD Direction: Forward Position #: 3 Overlap #: 10 Alignment: CADYRAAAACVA-------- --HDAMACACAKKTKTKTHD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wrTGTATACAyw Reverse Complement Original Motif DHAYAYAYDTGTYTTTVBTG HDTGTATACAHD HDTRTAYACAHDTYTTTVBTG Direction: Forward Position #: 2 Overlap #: 11 Alignment: -DHAYAYAYDTGTYTTTVBTG HDTGTATACAHD--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 5 Reverse Complement Original Motif CAVBAAAMAHHTGTMTAMADH AAAASAAA AMAABAAAMAHHTGTMTAMADH Direction: Forward Position #: 2 Overlap #: 7 Alignment: -CAVBAAAMAHHTGTMTAMADH AAAASAAA-------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif tyTCTkTkTCyy Original Motif Reverse Complement AMAABAAAMAHHTGTMTAMADH VHGARAYAGAVV VHRAAAYARAMAHHTGTMTAMADH Direction: Forward Position #: 3 Overlap #: 10 Alignment: --AMAABAAAMAHHTGTMTAMADH VHGARAYAGAVV------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 14 Combined Motif Reverse Complement Original Motif HDTRTAYACAHDTYTMTKTTTKHB GCRCACRC HDTGYACACACDTYTMTKTTTKHB Direction: Forward Position #: 4 Overlap #: 8 Alignment: HDTRTAYACAHDTYTMTKTTTKHB ---GCRCACRC------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 30 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ZEB1 ccCCmCACCcc Original Motif Original Motif CACCTD HBCCMCACCHH CACCTBHBCCM Direction: Backward Position #: 1 Overlap #: 6 Alignment: -----CACCTD HBCCMCACCHH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif rrAGGGGGArr Original Motif Reverse Complement CACCTBHBCCM VVTCCCCCTVV VVTCCMCCTVVBCCM Direction: Forward Position #: 5 Overlap #: 7 Alignment: ----CACCTBHBCCM VVTCCCCCTVV---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif yayAyAyACATrya Original Motif Original Motif VVTCCMCCTVVBCCM HACAYAYACATRHD HACATMCACMTVHVCCM Direction: Forward Position #: 3 Overlap #: 12 Alignment: --VVTCCMCCTVVBCCM HACAYAYACATRHD--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ryayAyAyrtGTRTrTry Reverse Complement Original Motif RGGBDBARGTGRATGTD DHAYAYAYRTGTGTRTDH RGRYAYABGTGDRTGTDH Direction: Forward Position #: 1 Overlap #: 17 Alignment: RGGBDBARGTGRATGTD- DHAYAYAYRTGTGTRTDH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif yrTGTGCACAyr Original Motif Original Motif RGRYAYABGTGDRTGTDH BVTGTGCACABV BRTGTRCACRYGDRTGTDH Direction: Forward Position #: 2 Overlap #: 11 Alignment: -RGRYAYABGTGDRTGTDH BVTGTGCACABV------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ssCGCCsCCrCCCss Combined Motif Reverse Complement Original Motif HHACAKDCMKGTGMACAMV SSCGCCSCCGCCCSS MKGTGMACAMVMCRCMBVVHHACAKDCMKG Direction: Backward Position #: 12 Overlap #: 8 Alignment: -------HHACAKDCMKGTGMACAMV -----------SSCGCCSCCGCCCSS ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 4 Combined Motif Reverse Complement Reverse Complement CRYGDRTGTDHVBBRGKGRBRTGTRCACRY GGAGGVMG CRYGDRTGTDHVBBGGAGGHMGGTRCACRY Direction: Forward Position #: 15 Overlap #: 8 Alignment: CRYGDRTGTDHVBBRGKGRBRTGTRCACRY --------------GGAGGVMG-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- wsAGCTACwy Combined Motif Original Motif Reverse Complement CRYGDRTGTDHVBBGGAGGHMGGTRCACRY VHGTAGCTVD CVHGTAKSTDHVBBGGAGGHMGGTRCACRY Direction: Forward Position #: 2 Overlap #: 10 Alignment: CRYGDRTGTDHVBBGGAGGHMGGTRCACRY -VHGTAGCTVD------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ssCrCYyYCGss Original Motif Reverse Complement CVHGTAKSTDHVBBGGAGGHMGGTRCACRY BBCGGKGGMGBB BVCGKRKGYGBVBBGGAGGHMGGTRCACRY Direction: Forward Position #: 1 Overlap #: 12 Alignment: CVHGTAKSTDHVBBGGAGGHMGGTRCACRY BBCGGKGGMGBB------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ssCGsCwsCss Combined Motif Reverse Complement Original Motif MKGTGMACCYDCCTCCBVVBCMCYKRCGVB BBCGSCWSCBB MKGTGMVCCGSCHBCCBVVBCMCYKRCGVB Direction: Forward Position #: 7 Overlap #: 11 Alignment: MKGTGMACCYDCCTCCBVVBCMCYKRCGVB ------BBCGSCWSCBB------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ 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 tyTCTkTkTCyy Reverse Complement Original Motif TTCTSTST BBTCTKTKTCHB CHBTTCTSTBTB Direction: Backward Position #: 4 Overlap #: 8 Alignment: -TTCTSTST--- BBTCTKTKTCHB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif aaACAAAACaa Original Motif Reverse Complement CHBTTCTSTBTB TTGTTTTGTTT CYGTTYTGTBTB Direction: Forward Position #: 1 Overlap #: 11 Alignment: CHBTTCTSTBTB TTGTTTTGTTT- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif rmACAGCAGsr Original Motif Reverse Complement CYGTTYTGTBTB DVCTGCTGTVB BHSTKCTGTBTB Direction: Forward Position #: 1 Overlap #: 11 Alignment: CYGTTYTGTBTB DVCTGCTGTVB- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACACACACACA Original Motif Reverse Complement BHSTKCTGTBTB TGTGTGTGTGTG TBYKTSTGTGTB Direction: Forward Position #: 1 Overlap #: 12 Alignment: BHSTKCTGTBTB TGTGTGTGTGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACACACACACA Original Motif Reverse Complement TBYKTSTGTGTB TGTGTGTGTGTG TGTGTGTGTGTG Direction: Forward Position #: 1 Overlap #: 12 Alignment: TBYKTSTGTGTB TGTGTGTGTGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif AAAAAAAAAAA Original Motif Reverse Complement TGTGTGTGTGTG TTTTTTTTTTT TKTKTKTKTKTG Direction: Forward Position #: 1 Overlap #: 11 Alignment: TGTGTGTGTGTG TTTTTTTTTTT- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 26 Original Motif Original Motif TKTKTKTKTKTG TKKTTTGTTTTTTT TKTTTTTTTTTKTT Direction: Forward Position #: 1 Overlap #: 12 Alignment: TKTKTKTKTKTG-- TKKTTTGTTTTTTT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 27 Original Motif Reverse Complement TKTTTTTTTTTKTT TGTGTGTGTGTKTG TGTKTKTKTKTKTK Direction: Forward Position #: 1 Overlap #: 14 Alignment: TKTTTTTTTTTKTT TGTGTGTGTGTKTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 25 Reverse Complement Original Motif YAYAYAYAYAYACA CACACAVRCACACA CACACABACACACA Direction: Forward Position #: 1 Overlap #: 14 Alignment: YAYAYAYAYAYACA CACACAVRCACACA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 21 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 21 Motif 15 Original Motif Reverse Complement ATKTM CATTTKC CATTTBC Direction: Forward Position #: 2 Overlap #: 5 Alignment: -ATKTM- CATTTKC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 10 Original Motif Reverse Complement CATTTBC TATRTA YATDTAC Direction: Forward Position #: 1 Overlap #: 6 Alignment: CATTTBC TATRTA- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wtATTTTTAww Original Motif Original Motif YATDTAC DHATTTTTADD DHATTTWYADD Direction: Forward Position #: 2 Overlap #: 7 Alignment: -YATDTAC--- DHATTTTTADD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wyATTTTAww Original Motif Original Motif DHATTTWYADD DHATTTTADD DHATTTTHADD Direction: Forward Position #: 1 Overlap #: 10 Alignment: DHATTTWYADD DHATTTTADD- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif tyTCTkTkTCyy Reverse Complement Reverse Complement DDTHAAAATHD VHGARAYAGAVV HHKAAAHAKAHV Direction: Forward Position #: 1 Overlap #: 11 Alignment: DDTHAAAATHD- VHGARAYAGAVV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif twTACATAvw Reverse Complement Reverse Complement BHTRTHTTTYHH DBTATGTAHH HBTATGTWHHHH Direction: Forward Position #: 1 Overlap #: 10 Alignment: BHTRTHTTTYHH DBTATGTAHH-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wwTAAAwAww Original Motif Reverse Complement HBTATGTWHHHH HHTWTTTADD HHTATTTAHHHH Direction: Forward Position #: 1 Overlap #: 10 Alignment: HBTATGTWHHHH HHTWTTTADD-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wwWAAAAAwa Original Motif Reverse Complement HHTATTTAHHHH HWTTTTTTWW HHTWTTTWWHHH Direction: Forward Position #: 1 Overlap #: 10 Alignment: HHTATTTAHHHH HWTTTTTTWW-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif AAAAAAAAAAA Reverse Complement Original Motif HHHWWAAAWAHH HVCATGCATGCABD HVCATGCATGCAHDWAAAWAHH Direction: Forward Position #: 11 Overlap #: 4 Alignment: ----------HHHWWAAAWAHH HVCATGCATGCABD-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wrTGTATACAyw Reverse Complement Original Motif HHTWTTTWDHTGCATGCATGBH HDTGTATACAHD HDTKTWTAHATDCATGCATGBH Direction: Forward Position #: 1 Overlap #: 12 Alignment: HHTWTTTWDHTGCATGCATGBH HDTGTATACAHD---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ 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 EWSR1-FLI1 Reverse Complement Original Motif GGAGGVMG GGAAGGAAGGAAGGAAGG GAAGGGRAGGAAGGGAAG Direction: Backward Position #: 6 Overlap #: 8 Alignment: -----GGAGGVMG----- GGAAGGAAGGAAGGAAGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif SP1 Original Motif Reverse Complement GAAGGGRAGGAAGGGAAG GGGGGYGGGG GRRGGGGRGGAAGGGAAG Direction: Forward Position #: 1 Overlap #: 10 Alignment: GAAGGGRAGGAAGGGAAG GGGGGYGGGG-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif rrAGGGGGArr Original Motif Original Motif GRRGGGGRGGAAGGGAAG VVAGGGGGAVV GRAGGGGGRGVAGGGAAG Direction: Forward Position #: 1 Overlap #: 11 Alignment: GRRGGGGRGGAAGGGAAG VVAGGGGGAVV------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ssCGCCsCCrCCCss Combined Motif Reverse Complement Original Motif CTTCCCTBCKCCCCCTKC SSCGCCSCCGCCCSS CTTCCCBBCBCCBCCYBC Direction: Forward Position #: 4 Overlap #: 15 Alignment: CTTCCCTBCKCCCCCTKC ---SSCGCCSCCGCCCSS ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Klf4 Reverse Complement Original Motif GBKGGBGGBGBVGGGAAG DGGGYGKGGC DGGGBGKGGCGBVGGGAAG Direction: Forward Position #: 2 Overlap #: 9 Alignment: -GBKGGBGGBGBVGGGAAG DGGGYGKGGC--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ssCrCYyYCGss Original Motif Reverse Complement DGGGBGKGGCGBVGGGAAG BBCGGKGGMGBB DGSGGGGGVGGBVGGGAAG Direction: Forward Position #: 1 Overlap #: 12 Alignment: DGGGBGKGGCGBVGGGAAG BBCGGKGGMGBB------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ssCGsCTCss Original Motif Reverse Complement DGSGGGGGVGGBVGGGAAG BBGAGSCGVV BSGRGGSGVSGBVGGGAAG Direction: Forward Position #: 1 Overlap #: 10 Alignment: DGSGGGGGVGGBVGGGAAG BBGAGSCGVV--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MZF1_5-13 Reverse Complement Reverse Complement CTTCCCBBCSVCSCCKCSB BTHCCCCTYB CTTCCCYTYBVCSCCKCSB Direction: Forward Position #: 1 Overlap #: 10 Alignment: CTTCCCBBCSVCSCCKCSB BTHCCCCTYB--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- RREB1 Combined Motif Original Motif Original Motif CTTCCCYTYBVCSCCKCSB CCCCMAAMCAMCCMCMMMCV CTTCCCCHMMVCRCCBCCHMMCV Direction: Forward Position #: 4 Overlap #: 16 Alignment: CTTCCCYTYBVCSCCKCSB---- ---CCCCMAAMCAMCCMCMMMCV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ccCCmCACCcc Combined Motif Reverse Complement Reverse Complement BGRRDGGBGGKGVYYHGGGGAAG DDGGTGRGGBD BGRDDGGTGGGGVBYHGGGGAAG Direction: Forward Position #: 4 Overlap #: 11 Alignment: BGRRDGGBGGKGVYYHGGGGAAG ---DDGGTGRGGBD--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ 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 CACACACACACA Original Motif Original Motif CACACACA CACACACACACA CACACACACACA Direction: Forward Position #: 3 Overlap #: 8 Alignment: --CACACACA-- CACACACACACA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACACACACACA Reverse Complement Reverse Complement TGTGTGTGTGTG TGTGTGTGTGTG TGTGTGTGTGTG Direction: Forward Position #: 1 Overlap #: 12 Alignment: TGTGTGTGTGTG TGTGTGTGTGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 27 Original Motif Reverse Complement TGTGTGTGTGTG TGTGTGTGTGTKTG TGTGTGTGTGTGTG Direction: Forward Position #: 1 Overlap #: 12 Alignment: TGTGTGTGTGTG-- TGTGTGTGTGTKTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 25 Reverse Complement Original Motif CACACACACACACA CACACAVRCACACA CACACACACACACA Direction: Forward Position #: 1 Overlap #: 14 Alignment: CACACACACACACA CACACAVRCACACA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ryayAyAyrtGTRTrTry Reverse Complement Original Motif TGTGTGTGTGTGTG DHAYAYAYRTGTGTRTDH DTRTRYRTRTGTGTGTDH Direction: Forward Position #: 2 Overlap #: 14 Alignment: -TGTGTGTGTGTGTG--- DHAYAYAYRTGTGTRTDH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif yayAyAyACATrya Reverse Complement Original Motif HDACACACAMAKMMAMAD HACAYAYACATRHD HVBACACACAYRBAMAMAD Direction: Forward Position #: 2 Overlap #: 13 Alignment: -HDACACACAMAKMMAMAD HACAYAYACATRHD----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif aaCAAAAACaa Original Motif Original Motif HVBACACACAYRBAMAMAD HHCAAAAACAH HHCAMAMACAHRBAMAMAD Direction: Forward Position #: 1 Overlap #: 11 Alignment: HVBACACACAYRBAMAMAD HHCAAAAACAH-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif twTACATAvw Original Motif Original Motif HHCAMAMACAHRBAMAMAD HHTACATAVD HHYACATACAHRBAMAMAD Direction: Forward Position #: 1 Overlap #: 10 Alignment: HHCAMAMACAHRBAMAMAD HHTACATAVD--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif RREB1 Original Motif Original Motif HHYACATACAHRBAMAMAD CCCCMAAMCAMCCMCMMMCV MCYMMAWACAMMHMCMMMBV Direction: Forward Position #: 1 Overlap #: 19 Alignment: HHYACATACAHRBAMAMAD- CCCCMAAMCAMCCMCMMMCV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif AAAAAAAAAAA Reverse Complement Reverse Complement BBYRYGYDRRTGTWTRRKGR DVTGCATGCATGBH BVTGCRTGSATGTHTRRKGR Direction: Forward Position #: 1 Overlap #: 14 Alignment: BBYRYGYDRRTGTWTRRKGR DVTGCATGCATGBH------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 20 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 20 ssGCTswGCCms Original Motif Original Motif CTCTGY VBGCTSAGCCHB VBGCTCWGCCHB Direction: Forward Position #: 4 Overlap #: 6 Alignment: ---CTCTGY--- VBGCTSAGCCHB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 7 Combined Motif Original Motif Reverse Complement VBGCTCWGCCHB TTCTSTST VTKCTCTGYCHB Direction: Forward Position #: 2 Overlap #: 8 Alignment: VBGCTCWGCCHB -TTCTSTST--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR1H2RXRA Reverse Complement Original Motif BDGMCAGAGRAV AAAGGTCAAAGGTCAAC AAAGGTCAACHDRRSWSBDGMC Direction: Backward Position #: 11 Overlap #: 7 Alignment: BDGMCAGAGRAV---------- -----AAAGGTCAAAGGTCAAC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif PPARGRXRA Reverse Complement Reverse Complement GYCHBSWSMMDHGTTGACCTTT TGRCCTKTGHCCKAB TGHCCTKTSVCHDVBTGACCTTT Direction: Forward Position #: 2 Overlap #: 14 Alignment: -GYCHBSWSMMDHGTTGACCTTT TGRCCTKTGHCCKAB-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 11 Combined Motif Original Motif Original Motif TGHCCTKTSVCHDVBTGACCTTT CCGCCGCC CTKTSVCHDVBTGACCTTTYGCCTGHCCTKTSVCHDVBTGAC Direction: Backward Position #: 20 Overlap #: 4 Alignment: ----TGHCCTKTSVCHDVBTGACCTTT -------------------CCGCCGCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ssCKCwsCGss Original Motif Reverse Complement CTKTSVCHDVBTGACCTTTYGCCTGHCCTKTSVCHDVBTGAC VBCGSWGCGVB VBCDSHSCGVBTGACCTTTYGCCTGHCCTKTSVCHDVBTGAC Direction: Forward Position #: 1 Overlap #: 11 Alignment: CTKTSVCHDVBTGACCTTTYGCCTGHCCTKTSVCHDVBTGAC VBCGSWGCGVB------------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR2F1 Combined Motif Reverse Complement Reverse Complement GTCAVVDDGVSAYAGGHCAGGCMAAAGGTCAVVCGSHSHGVV AKGYYCAAAGRTCA GTCAVVDGBBCAHAGGTCAGGCMAAAGGTCAVVCGSHSHGVV Direction: Forward Position #: 6 Overlap #: 14 Alignment: GTCAVVDDGVSAYAGGHCAGGCMAAAGGTCAVVCGSHSHGVV -----AKGYYCAAAGRTCA----------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif tyTCTkTkTCyy Reverse Complement Original Motif VBCDSHSCGVBTGACCTTTYGCCTGACCTHTGBBCHBBTGAC BBTCTKTKTCHB HBTBTCYBTKTSVBCDSHSCGVBTGACCTTTYGCCTGACCTHTG Direction: Backward Position #: 3 Overlap #: 10 Alignment: VBCDSHSCGVBTGACCTTTYGCCTGACCTHTGBBCHBBTGAC-- --------------------------------BBTCTKTKTCHB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HNF4A Combined Motif Original Motif Reverse Complement HBTBTCYBTKTSVBCDSHSCGVBTGACCTTTYGCCTGACCTHTG TGMYCTTTGBCCK HBTBTCYBTKTGVBCTKTGBBCBTGACCTTTYGCCTGACCTHTG Direction: Forward Position #: 11 Overlap #: 13 Alignment: HBTBTCYBTKTSVBCDSHSCGVBTGACCTTTYGCCTGACCTHTG ----------TGMYCTTTGBCCK--------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MIZF Combined Motif Reverse Complement Original Motif CAHAGGTCAGGCMAAAGGTCAVGBBCARAGVVCARAVMGABAVH BAACGTCCGC CHAASGTCMGBCMAAAGGTCAVGBBCARAGVVCARAVMGABAVH Direction: Forward Position #: 2 Overlap #: 10 Alignment: CAHAGGTCAGGCMAAAGGTCAVGBBCARAGVVCARAVMGABAVH -BAACGTCCGC--------------------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 42 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ArntAhr Motif 27 Original Motif Reverse Complement YGCGTG TGTGTGTGTGTKTG TGTGTGTGYGTGTG Direction: Forward Position #: 7 Overlap #: 6 Alignment: ------YGCGTG-- TGTGTGTGTGTKTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACACACACACA Original Motif Reverse Complement TGTGTGTGYGTGTG TGTGTGTGTGTG TGTGTGTGTGTGTG Direction: Forward Position #: 1 Overlap #: 12 Alignment: TGTGTGTGYGTGTG TGTGTGTGTGTG-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 25 Original Motif Reverse Complement TGTGTGTGTGTGTG TGTGTGKVTGTGTG TGTGTGTGTGTGTG Direction: Forward Position #: 1 Overlap #: 14 Alignment: TGTGTGTGTGTGTG TGTGTGKVTGTGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif AAAAAAAAAAA Reverse Complement Original Motif CACACACACACACA HVCATGCATGCABD CACAYRCAYRCACA Direction: Forward Position #: 1 Overlap #: 14 Alignment: CACACACACACACA HVCATGCATGCABD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACACACACACA Original Motif Original Motif CACAYRCAYRCACA CACACACACACA CACACACACACACA Direction: Forward Position #: 1 Overlap #: 12 Alignment: CACAYRCAYRCACA CACACACACACA-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif yrTGTGCACAyr Original Motif Original Motif CACACACACACACA BVTGTGCACABV YAYRYRCACACACA Direction: Forward Position #: 1 Overlap #: 12 Alignment: CACACACACACACA BVTGTGCACABV-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ccCCmCACCcc Reverse Complement Reverse Complement TGTGTGTGMMMMTK DDGGTGRGGBD DGGGTGKGSVVMTK Direction: Forward Position #: 1 Overlap #: 11 Alignment: TGTGTGTGMMMMTK DDGGTGRGGBD--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ssCGrGCGss Original Motif Original Motif DGGGTGKGSVVMTK VSCGRGCGBV BGSGKGCGSVVMTK Direction: Forward Position #: 1 Overlap #: 10 Alignment: DGGGTGKGSVVMTK VSCGRGCGBV---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 2 Combined Motif Original Motif Reverse Complement BGSGKGCGSVVMTK TGTGTGTG BGTGTGTGTVVMTK Direction: Forward Position #: 3 Overlap #: 8 Alignment: BGSGKGCGSVVMTK --TGTGTGTG---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ssGMsGRGCGss Original Motif Original Motif BGTGTGTGTVVMTK VVGCSGGGCGBB BVGSKGDGYGVVTK Direction: Forward Position #: 1 Overlap #: 12 Alignment: BGTGTGTGTVVMTK VVGCSGGGCGBB-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 13 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 13 tyTCTkTkTCyy Original Motif Reverse Complement GAGRCAGR VHGARAYAGAVV VHGAGACAGAVV Direction: Forward Position #: 3 Overlap #: 8 Alignment: --GAGRCAGR-- VHGARAYAGAVV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ssCGsCTCss Original Motif Reverse Complement VHGAGACAGAVV BBGAGSCGVV VVGAGRCRGRVV Direction: Forward Position #: 1 Overlap #: 10 Alignment: VHGAGACAGAVV BBGAGSCGVV-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 14 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 14 Motif 27 Original Motif Original Motif GCRCACRC CAYACACACACACA CAYRCACACACACA Direction: Forward Position #: 4 Overlap #: 8 Alignment: ---GCRCACRC--- CAYACACACACACA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACACACACACA Reverse Complement Reverse Complement TGTGTGTGTGMKTG TGTGTGTGTGTG TGTGTGTGTGHGTG Direction: Forward Position #: 1 Overlap #: 12 Alignment: TGTGTGTGTGMKTG TGTGTGTGTGTG-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CACACACACACA Original Motif Reverse Complement TGTGTGTGTGHGTG TGTGTGTGTGTG TGTGTGTGTGTGTG Direction: Forward Position #: 1 Overlap #: 12 Alignment: TGTGTGTGTGHGTG TGTGTGTGTGTG-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Klf4 Original Motif Original Motif TGTGTGTGTGTGTG DGGGYGKGGC TGKGTGTGKSTGTG Direction: Forward Position #: 1 Overlap #: 10 Alignment: TGTGTGTGTGTGTG DGGGYGKGGC---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 25 Original Motif Reverse Complement TGKGTGTGKSTGTG TGTGTGKVTGTGTG TGTGTGTGTGTGTG Direction: Forward Position #: 1 Overlap #: 14 Alignment: TGKGTGTGKSTGTG TGTGTGKVTGTGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Egr1 Combined Motif Original Motif Original Motif TGTGTGTGTGTGTG HGCGTGGGCGK TGTGYGTGKGYGTG Direction: Forward Position #: 3 Overlap #: 11 Alignment: TGTGTGTGTGTGTG --HGCGTGGGCGK- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ccCCmCACCcc Original Motif Reverse Complement TGTGYGTGKGYGTG DDGGTGRGGBD DGKGTGKGGGHGTG Direction: Forward Position #: 1 Overlap #: 11 Alignment: TGTGYGTGKGYGTG DDGGTGRGGBD--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif yrTGTGCACAyr Original Motif Original Motif DGKGTGKGGGHGTG BVTGTGCACABV BGTGTGBRSRBGTG Direction: Forward Position #: 1 Overlap #: 12 Alignment: DGKGTGKGGGHGTG BVTGTGCACABV-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ssCGrGCGss Original Motif Original Motif BGTGTGBRSRBGTG VSCGRGCGBV BGYGTGCGSVBGTG Direction: Forward Position #: 1 Overlap #: 10 Alignment: BGTGTGBRSRBGTG VSCGRGCGBV---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ssCGCCsCCrCCCss Combined Motif Reverse Complement Original Motif CACVVSCGCACKCB SSCGCCSCCGCCCSS CACVCGCSCVCGCCCSS Direction: Forward Position #: 3 Overlap #: 12 Alignment: CACVVSCGCACKCB--- --SSCGCCSCCGCCCSS ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 11-20-2016 14:49:39 Runtime: 837.987 seconds MOTIFSIM is written by Ngoc Tam L. Tran