**************************************************************************************************************************************************************************************************** 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: 5 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_DM01.txt 51 1 MEME-CHIP_DM01.txt 9 2 PScanChIP_DM01.txt 27 3 RSAT_peak-motifs_DM01.txt 40 4 **************************************************************************************************************************************************************************************************** RESULTS **************************************************************************************************************************************************************************************************** ************************************************************ Combined Motifs for Top Global Significant Motif ID 69 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NKX3-1 ymTACATAyw Reverse Complement Reverse Complement TAAGTAT DBTATGTAHH HTAWGTADDB Direction: Backward Position #: 2 Overlap #: 7 Alignment: --TAAGTAT- DBTATGTAHH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 10 Original Motif Original Motif HTAWGTADDB HTACATA HTAYRTADDB Direction: Forward Position #: 1 Overlap #: 7 Alignment: HTAWGTADDB HTACATA--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 34 Original Motif Original Motif HTAYRTADDB ATATTTA ATATDTADDB Direction: Forward Position #: 1 Overlap #: 7 Alignment: HTAYRTADDB ATATTTA--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wtAATTAAtw Reverse Complement Reverse Complement BDDTADATAT HATTAATTAD HHTTAAWTAT Direction: Forward Position #: 1 Overlap #: 10 Alignment: BDDTADATAT HATTAATTAD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wwTAATAAww Original Motif Reverse Complement HHTTAAWTAT DDTTATTAHD HHTTAWTWAD Direction: Forward Position #: 1 Overlap #: 10 Alignment: HHTTAAWTAT DDTTATTAHD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 53 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 53 Motif 7 Reverse Complement Original Motif MACASA CACASASA CACASACA Direction: Backward Position #: 1 Overlap #: 6 Alignment: --MACASA CACASASA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif awAACAcAAwa Original Motif Original Motif CACASACA DDAACACAADV MAMACACAADV Direction: Forward Position #: 1 Overlap #: 8 Alignment: CACASACA--- DDAACACAADV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 23 Original Motif Reverse Complement MAMACACAADV TACASAR TACASAVAADV Direction: Forward Position #: 1 Overlap #: 7 Alignment: MAMACACAADV TACASAR---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 2 Reverse Complement Reverse Complement BDTTVTSTGTA GTGTGTGT GTKTGTGTGTA Direction: Forward Position #: 1 Overlap #: 8 Alignment: BDTTVTSTGTA GTGTGTGT--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 12 Original Motif Reverse Complement GTKTGTGTGTA MTGTGTGC VTGTGTGYGTA Direction: Forward Position #: 1 Overlap #: 8 Alignment: GTKTGTGTGTA MTGTGTGC--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 25 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 25 wtATTTTAww Reverse Complement Reverse Complement WWTAAA HWTAAAATHD WWTAAAATHD Direction: Forward Position #: 1 Overlap #: 6 Alignment: WWTAAA---- HWTAAAATHD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wwATkTTTAww Reverse Complement Original Motif DHATTTTAWW DHATKTTTAHH DHATTTTWAHH Direction: Forward Position #: 1 Overlap #: 10 Alignment: DHATTTTAWW- DHATKTTTAHH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Foxq1 Original Motif Original Motif DHATTTTWAHH HATTGTTTATW HDATKTTTATW Direction: Forward Position #: 1 Overlap #: 11 Alignment: DHATTTTWAHH HATTGTTTATW ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 55 Reverse Complement Original Motif WATAAAYATDH TTTAAAA TTTAAAMATDH Direction: Forward Position #: 1 Overlap #: 7 Alignment: WATAAAYATDH TTTAAAA---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif FOXI1 Reverse Complement Original Motif HDATYTTTAAA KBDTRTTTRTTT DDWTDTTTAWWT Direction: Forward Position #: 1 Overlap #: 11 Alignment: HDATYTTTAAA- KBDTRTTTRTTT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 24 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 24 Motif 56 Reverse Complement Reverse Complement BCGTG TCCGTG TCCGTG Direction: Forward Position #: 2 Overlap #: 5 Alignment: -BCGTG TCCGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ysCmAGCACwy Reverse Complement Original Motif CACGGA HVCMAGCACHH HVCAMGSACHH Direction: Forward Position #: 3 Overlap #: 6 Alignment: --CACGGA--- HVCMAGCACHH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif crCGyGCRcg Original Motif Original Motif HVCAMGSACHH CGCGTGCACG HVCRYGCACDH Direction: Forward Position #: 1 Overlap #: 10 Alignment: HVCAMGSACHH CGCGTGCACG- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 58 Original Motif Original Motif HVCRYGCACDH CACACACACACACA CACAYRCACACACA Direction: Forward Position #: 1 Overlap #: 11 Alignment: HVCRYGCACDH--- CACACACACACACA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- cmCARCACTwr Combined Motif Original Motif Original Motif CACAYRCACACACA BHCAGCACTHV CVCMMRCACWHACA Direction: Forward Position #: 2 Overlap #: 11 Alignment: CACAYRCACACACA -BHCAGCACTHV-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 54 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 54 Motif 26 Original Motif Original Motif RGAAA RGARGAAA RGARGAAA Direction: Forward Position #: 4 Overlap #: 5 Alignment: ---RGAAA RGARGAAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 28 Reverse Complement Reverse Complement TTTCKTCK TTTCTVT TTTCTBYK Direction: Forward Position #: 1 Overlap #: 7 Alignment: TTTCKTCK TTTCTVT- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 33 Combined Motif Reverse Complement Reverse Complement RKVAGAAA GGAAARG RKVRGAAARG Direction: Forward Position #: 4 Overlap #: 5 Alignment: RKVAGAAA-- ---GGAAARG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 46 Reverse Complement Reverse Complement CMTTTCMBYK TSTTTCC YVTTTCCBYK Direction: Forward Position #: 1 Overlap #: 7 Alignment: CMTTTCMBYK TSTTTCC--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 44 Original Motif Reverse Complement YVTTTCCBYK CATTTCT CATTTCYBYK Direction: Forward Position #: 1 Overlap #: 7 Alignment: YVTTTCCBYK CATTTCT--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 64 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ARID3A wtAATTAAtw Original Motif Original Motif ATYAAA DTAATTAATH DTAATTAAWH Direction: Forward Position #: 4 Overlap #: 6 Alignment: ---ATYAAA- DTAATTAATH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 20 Reverse Complement Reverse Complement HWTTAATTAD CCTYTAAT CCTTTAATTAD Direction: Forward Position #: 2 Overlap #: 7 Alignment: -HWTTAATTAD CCTYTAAT--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 49 Combined Motif Original Motif Reverse Complement CCTTTAATTAD KTTTATCT CBTTTAWYTAD Direction: Forward Position #: 2 Overlap #: 8 Alignment: CCTTTAATTAD -KTTTATCT-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 25 Combined Motif Original Motif Original Motif CBTTTAWYTAD TTTAWW CTTTWAWYTAD Direction: Forward Position #: 2 Overlap #: 6 Alignment: CBTTTAWYTAD -TTTAWW---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wwTAATAAww Reverse Complement Reverse Complement DTAKWTWAAAG DDTTATTAHD DTWTATTAADG Direction: Forward Position #: 1 Overlap #: 10 Alignment: DTAKWTWAAAG DDTTATTAHD- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 6 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 6 ysCmAGCACwy Reverse Complement Reverse Complement GYGSTGGG DHGTGCTRGVH DHGTGCTGGGH Direction: Forward Position #: 3 Overlap #: 8 Alignment: --GYGSTGGG- DHGTGCTRGVH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ccCCmCaCCCCcc Original Motif Reverse Complement DHGTGCTGGGH DBGGGGTGGGGBD DVGKGSTGGGGBD Direction: Forward Position #: 1 Overlap #: 11 Alignment: DHGTGCTGGGH-- DBGGGGTGGGGBD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif cmCARCACTwr Reverse Complement Original Motif HBCCCCASCYCBH BHCAGCACTHV BHCMSCACYHCBH Direction: Forward Position #: 1 Overlap #: 11 Alignment: HBCCCCASCYCBH BHCAGCACTHV-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif cbCCAGCTCmyk Original Motif Original Motif BHCMSCACYHCBH BBCCAGCTCMBD BBCCASMYCMBDH Direction: Forward Position #: 1 Overlap #: 12 Alignment: BHCMSCACYHCBH BBCCAGCTCMBD- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif csCACCCCgg Original Motif Original Motif BBCCASMYCMBDH HVCACCCCBB HBCMCCCCBHBDH Direction: Forward Position #: 1 Overlap #: 10 Alignment: BBCCASMYCMBDH HVCACCCCBB--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 94 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- yrTCWCAAyr Sox2 Reverse Complement Original Motif HKTTGTGABH CCWTTGTYATGCAAA ATGTTRTGMDVCCWT Direction: Backward Position #: 2 Overlap #: 10 Alignment: ----HKTTGTGABH- CCWTTGTYATGCAAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Pou5f1 Reverse Complement Reverse Complement AWGGBDYCAMAACAT ATTTGCATHACAAWG AWTKGCATCACAAHDT Direction: Forward Position #: 2 Overlap #: 14 Alignment: -AWGGBDYCAMAACAT ATTTGCATHACAAWG- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pax4 Combined Motif Original Motif Reverse Complement AWTKGCATCACAAHDT GRKGRGDRHVHDDVBBHHBRGDWAWTWTTM AWTKGBDDVAVAAHDDVBBHHBRGDWAWTWTTM Direction: Forward Position #: 4 Overlap #: 13 Alignment: AWTKGCATCACAAHDT----------------- ---GRKGRGDRHVHDDVBBHHBRGDWAWTWTTM ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TBP Combined Motif Reverse Complement Original Motif RAAWAWTWDCMBHHVBBDHHTTVTVDDBCYAWT STATAAAWRVVVVBV VWATAAAWDVVBVHVBBDHHTTVTVDDBCYAWT Direction: Forward Position #: 1 Overlap #: 15 Alignment: RAAWAWTWDCMBHHVBBDHHTTVTVDDBCYAWT STATAAAWRVVVVBV------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NR2F1 Combined Motif Reverse Complement Original Motif AWTKGBDDVAVAAHDDVBBHVBVVHWTTTATWV TGAMCTTTGMMCYT AWTGRVCTTWGAACHBVBBHVBVVHWTTTATWV Direction: Forward Position #: 3 Overlap #: 14 Alignment: AWTKGBDDVAVAAHDDVBBHVBVVHWTTTATWV --TGAMCTTTGMMCYT----------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 55 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 55 wtTTTwAAAaw Original Motif Original Motif TTTAAAA HHTTTWAAADD HHTTTAAAADD Direction: Forward Position #: 3 Overlap #: 7 Alignment: --TTTAAAA-- HHTTTWAAADD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 9 Original Motif Original Motif HHTTTAAAADD TTTWWAAA TTTTTAAAADD Direction: Forward Position #: 1 Overlap #: 8 Alignment: HHTTTAAAADD TTTWWAAA--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wtATTTTAww Reverse Complement Original Motif DDTTTTAAAAA DHATTTTAWH DHWTTTWAAHA Direction: Forward Position #: 1 Overlap #: 10 Alignment: DDTTTTAAAAA DHATTTTAWH- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wwATkTTTAww Reverse Complement Reverse Complement THTTWAAAWHD HHTAAARATHD THTWAAAATHD Direction: Forward Position #: 1 Overlap #: 11 Alignment: THTTWAAAWHD HHTAAARATHD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TBP Combined Motif Original Motif Original Motif THTWAAAATHD STATAAAWRVVVVBV TBTAWAAAWDVVVVBV Direction: Forward Position #: 2 Overlap #: 10 Alignment: THTWAAAATHD----- -STATAAAWRVVVVBV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 96 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- mdAAcCAACG Motif 60 Reverse Complement Reverse Complement CGTTGGTTDB YTTTTTRTTTTDTT TTYKTTGKTTTBYT Direction: Backward Position #: 3 Overlap #: 10 Alignment: --CGTTGGTTDB-- YTTTTTRTTTTDTT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Foxq1 Reverse Complement Reverse Complement AMVAAARCAARKAA WATAAACAATH AATAAACMAWVKAA Direction: Forward Position #: 1 Overlap #: 11 Alignment: AMVAAARCAARKAA WATAAACAATH--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif FOXI1 Original Motif Reverse Complement AATAAACMAWVKAA AAAMAAAMADBY AAWAAAAMADVBAA Direction: Forward Position #: 1 Overlap #: 12 Alignment: AATAAACMAWVKAA AAAMAAAMADBY-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif NR2F1 Reverse Complement Original Motif TTVBDTRTTTTWTT TGAMCTTTGMMCYT TGAMCTTTGVHYVTTTTWTT Direction: Forward Position #: 7 Overlap #: 8 Alignment: ------TTVBDTRTTTTWTT TGAMCTTTGMMCYT------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Sox2 Reverse Complement Original Motif AAWAAAABMHBCAAAGRTCA CCWTTGTYATGCAAA HHWWWRWBMTBCAAAGRTCA Direction: Forward Position #: 1 Overlap #: 15 Alignment: AAWAAAABMHBCAAAGRTCA CCWTTGTYATGCAAA----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 11-19-2016 22:23:05 Runtime: 867.303 seconds MOTIFSIM is written by Ngoc Tam L. 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