**************************************************************************************************************************************************************************************************** MOTIFSIM - Motif Similarity Detection Tool Version 2.2 **************************************************************************************************************************************************************************************************** INPUT **************************************************************************************************************************************************************************************************** Input Parameters Number of files: 2 Number of top significant motifs: 10 Number of best matches: 5 Similarity cutoff: >= 0.75 Matching motif database: UniProbe Mus Musculus Motif tree: Yes Combined similar motifs: Yes Output file type: All Output file format: All Input files and motif counts File name Count of motifs Dataset # W-ChIPMotifs_DM230.txt 11 1 RSAT_peak-motifs_DM230.txt 10 2 **************************************************************************************************************************************************************************************************** RESULTS **************************************************************************************************************************************************************************************************** ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 20 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- dhACATTCTkh TFM3 Reverse Complement Original Motif HCAGAATGTHD WWHTTTTTCABAAWTTWA WHAKWWTKYWDAAWTTWA Direction: Backward Position #: 8 Overlap #: 11 Alignment: HCAGAATGTHD------- WWHTTTTTCABAAWTTWA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 21 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- wbgTAAATAww tkAAATAATAtw Original Motif Original Motif DBGTAAATAHD HDAAATAATAHW HDHRWWAATAHD Direction: Backward Position #: 1 Overlap #: 11 Alignment: -DBGTAAATAHD HDAAATAATAHW ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- wwAAATAATAtw Combined Motif Original Motif Original Motif HDHRWWAATAHD HDAAATAATADD HDAAATAATAHD Direction: Forward Position #: 1 Overlap #: 12 Alignment: HDHRWWAATAHD HDAAATAATADD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFM11 Reverse Complement Reverse Complement DHTATTATTTDH TWVHWWWYTTTYTTTTTHTTTVWBH TWVHWWWYTTTYTTTTWTWTTHWTHDH Direction: Forward Position #: 16 Overlap #: 10 Alignment: ---------------DHTATTATTTDH TWVHWWWYTTTYTTTTTHTTTVWBH-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM1 Combined Motif Reverse Complement Reverse Complement HDHAWHAAWAWAAAAMAAAMWWWHBWA ABAAAAAAWHAAAAARAW HDHAWHAAWAWAAAAVAAAAAAWHVAAAARAW Direction: Forward Position #: 15 Overlap #: 13 Alignment: HDHAWHAAWAWAAAAMAAAMWWWHBWA----- --------------ABAAAAAAWHAAAAARAW ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM3 Combined Motif Reverse Complement Original Motif WTKTTTTBHWTTTTTTVTTTTWTWTTHWTHDH WWHTTTTTCABAAWTTWA WTKTTTTBHWTTTTTTVTWWWTTWTTHWBAAHTTWA Direction: Forward Position #: 19 Overlap #: 14 Alignment: WTKTTTTBHWTTTTTTVTTTTWTWTTHWTHDH---- ------------------WWHTTTTTCABAAWTTWA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 16 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- kcACCTGCAgc wsTACwGTAsw Original Motif Reverse Complement BCACCTGCABC DBTACWGTAVH DBWMCTGYAVH Direction: Backward Position #: 1 Overlap #: 11 Alignment: BCACCTGCABC DBTACWGTAVH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif dhACATTCTkh Reverse Complement Original Motif DVTKCAGYWBD DHACATTCTGH DHACATTCWGYWBD Direction: Forward Position #: 4 Overlap #: 8 Alignment: ---DVTKCAGYWBD DHACATTCTGH--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- wsTACwGTAsw kcACCTGCAgc Original Motif Reverse Complement HVTACWGTABD GBTGCAGGTGB DVTRCAGKWBH Direction: Backward Position #: 1 Overlap #: 11 Alignment: HVTACWGTABD GBTGCAGGTGB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wwAAATAATAtw Original Motif Reverse Complement DVTRCAGKWBH DDTATTATTTDH DVTAYWRTWDDH Direction: Forward Position #: 1 Overlap #: 11 Alignment: DVTRCAGKWBH- DDTATTATTTDH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- tkAAATAATAtw Combined Motif Original Motif Reverse Complement DVTAYWRTWDDH WHTATTATTTDH DHTATTATTTDH Direction: Forward Position #: 1 Overlap #: 12 Alignment: DVTAYWRTWDDH WHTATTATTTDH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wbgTAAATAww Original Motif Reverse Complement DHTATTATTTDH DHTATTTACBD DHTATTWWYDDH Direction: Forward Position #: 1 Overlap #: 11 Alignment: DHTATTATTTDH DHTATTTACBD- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFM3 Reverse Complement Reverse Complement HDDMWWAATAHD TWAAWTTVTGAAAAAHWW TWAAWTTVTGAADWAHWWAATAHD Direction: Forward Position #: 13 Overlap #: 6 Alignment: ------------HDDMWWAATAHD TWAAWTTVTGAAAAAHWW------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 15 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- kCAGCCAATmr tkAAATAATAtw Reverse Complement Reverse Complement MBATTGGCTGH WHTATTATTTDH WVTATTRKYTVH Direction: Forward Position #: 2 Overlap #: 11 Alignment: -MBATTGGCTGH WHTATTATTTDH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif dhACATTCTkh Reverse Complement Reverse Complement HVAKYMAATABW HCAGAATGTHD HCAGAAWRTMDW Direction: Forward Position #: 1 Overlap #: 11 Alignment: HVAKYMAATABW HCAGAATGTHD- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- wwAAATAATAtw Combined Motif Original Motif Original Motif HCAGAAWRTMDW HDAAATAATADD HHARAWAATADW Direction: Forward Position #: 1 Overlap #: 12 Alignment: HCAGAAWRTMDW HDAAATAATADD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- kcACCTGCAgc Combined Motif Reverse Complement Reverse Complement WDTATTWTMTDH GBTGCAGGTGB WDTATTWDHTGCAGGTGB Direction: Forward Position #: 8 Overlap #: 5 Alignment: WDTATTWTMTDH------ -------GBTGCAGGTGB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFF11 Reverse Complement Reverse Complement BCACCTGCADDWAATADW GCVCCGCCMCCYCC GCVCCGCCACCTSCADDWAATADW Direction: Forward Position #: 7 Overlap #: 8 Alignment: ------BCACCTGCADDWAATADW GCVCCGCCMCCYCC---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFF1 TFF11 Original Motif Original Motif CGGVGCCGCVGC GGMGGRGGCGGVGC GGVGGVGSCGSVGC Direction: Backward Position #: 1 Overlap #: 12 Alignment: --CGGVGCCGCVGC GGMGGRGGCGGVGC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- csGCCCCGCCCCsc Combined Motif Original Motif Reverse Complement GGVGGVGSCGSVGC BBGGGGCGGGGCVD GGVGGGSGSGGCGS Direction: Forward Position #: 1 Overlap #: 14 Alignment: GGVGGVGSCGSVGC BBGGGGCGGGGCVD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFM12 Reverse Complement Original Motif SCGCCSCSCCCVCC CYYCBBCYYYTCCHCCTYYY CYYCBBCYYYTCCHSCDCCCCSCCCVCC Direction: Forward Position #: 15 Overlap #: 6 Alignment: --------------SCGCCSCSCCCVCC CYYCBBCYYYTCCHCCTYYY-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- cccGCCCCGCCCCsb Combined Motif Original Motif Original Motif CYYCBBCYYYTCCHSCDCCCCSCCCVCC BCCGCCCCGCCCCBB CYYCBBCYYYTCCHSCBCCSCCCCSCCCCBB Direction: Forward Position #: 17 Overlap #: 12 Alignment: CYYCBBCYYYTCCHSCDCCCCSCCCVCC--- ----------------BCCGCCCCGCCCCBB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM2 Combined Motif Reverse Complement Original Motif BBGGGGSGGGGSGGBGSDGGAKKMGBBGKMG RGRGGAGRRGGHGGDG BBGGGGSGGGGSGGBGSDGGAGGAGVVGGHGGDG Direction: Forward Position #: 19 Overlap #: 13 Alignment: BBGGGGSGGGGSGGBGSDGGAKKMGBBGKMG--- ------------------RGRGGAGRRGGHGGDG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 17 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- wwAAATAATAtw tkAAATAATAtw Original Motif Original Motif HDAAATAATADD HDAAATAATAHW HDAAATAATAHW Direction: Forward Position #: 1 Overlap #: 12 Alignment: HDAAATAATADD HDAAATAATAHW ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFM1 Original Motif Reverse Complement HDAAATAATAHW ABAAAAAAWHAAAAARAW ABAAAAAAWHAAAAAAATAATAHW Direction: Forward Position #: 13 Overlap #: 6 Alignment: ------------HDAAATAATAHW ABAAAAAAWHAAAAARAW------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM11 Combined Motif Reverse Complement Reverse Complement WHTATTATTTTTTTHWTTTTTTBT TWVHWWWYTTTYTTTTTHTTTVWBH WHTATTATTTTWDHDWTTTTTTYTTTTHTTTVWBH Direction: Forward Position #: 11 Overlap #: 14 Alignment: WHTATTATTTTTTTHWTTTTTTBT----------- ----------TWVHWWWYTTTYTTTTTHTTTVWBH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM13 Combined Motif Original Motif Reverse Complement WHTATTATTTTWDHDWTTTTTTYTTTTHTTTVWBH WAHHTVTTYKAAAAWTTRAT WHTATTATTTTWDHDWTTTTTWHTTDTTTTWVAWWTTRAT Direction: Forward Position #: 21 Overlap #: 15 Alignment: WHTATTATTTTWDHDWTTTTTTYTTTTHTTTVWBH----- --------------------WAHHTVTTYKAAAAWTTRAT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM3 Combined Motif Original Motif Original Motif WHTATTATTTTWDHDWTTTTTWHTTDTTTTWVAWWTTRAT WWHTTTTTCABAAWTTWA WHTATTATTTTWDHDWTTTTTWHTTWTTTTWHMWHWWDWTWA Direction: Forward Position #: 25 Overlap #: 16 Alignment: WHTATTATTTTWDHDWTTTTTWHTTDTTTTWVAWWTTRAT-- ------------------------WWHTTTTTCABAAWTTWA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFW1 TFW3 Original Motif Original Motif GTCGCG CGGCYBCGCG CGGCGBCGCG Direction: Backward Position #: 1 Overlap #: 6 Alignment: ----GTCGCG CGGCYBCGCG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif sSGTCACGTGACSs Original Motif Reverse Complement CGGCGBCGCG SGGTCACGTGACCS CGGYSACGYGACCS Direction: Forward Position #: 1 Overlap #: 10 Alignment: CGGCGBCGCG---- SGGTCACGTGACCS ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFF11 Combined Motif Original Motif Reverse Complement CGGYSACGYGACCS GCVCCGCCMCCYCC CGGCVMCGCSACCBCC Direction: Forward Position #: 3 Overlap #: 12 Alignment: CGGYSACGYGACCS-- --GCVCCGCCMCCYCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFF1 Combined Motif Reverse Complement Original Motif GGBGGTSGCGRVGCCG CGGVGCCGCVGC GGBGGHGSCGVVGCCG Direction: Forward Position #: 3 Overlap #: 12 Alignment: GGBGGTSGCGRVGCCG --CGGVGCCGCVGC-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFW2 Combined Motif Reverse Complement Reverse Complement CGGCVVCGSCHCCBCC CCGCGCGS CGGCCGCGCSBCCBCC Direction: Forward Position #: 4 Overlap #: 8 Alignment: CGGCVVCGSCHCCBCC ---CCGCGCGS----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- csGCCCCGCCCCsc Combined Motif Original Motif Original Motif CGGCCGCGCSBCCBCC HVGCCCCGCCCCBB CSGSCSCSSCCCCBCC Direction: Forward Position #: 2 Overlap #: 14 Alignment: CGGCCGCGCSBCCBCC -HVGCCCCGCCCCBB- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 13 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- tkAAATAATAtw wwAAATAATAtw Original Motif Original Motif HDAAATAATAHW HDAAATAATADD HDAAATAATAHW Direction: Forward Position #: 1 Overlap #: 12 Alignment: HDAAATAATAHW HDAAATAATADD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFM11 Reverse Complement Reverse Complement WHTATTATTTDH TWVHWWWYTTTYTTTTTHTTTVWBH TWVHWWWYTTTYTTTTWTWTTATTWDH Direction: Forward Position #: 16 Overlap #: 10 Alignment: ---------------WHTATTATTTDH TWVHWWWYTTTYTTTTTHTTTVWBH-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM1 Combined Motif Reverse Complement Reverse Complement HDWAATAAWAWAAAAMAAAMWWWHBWA ABAAAAAAWHAAAAARAW HDWAATAAWAWAAAAVAAAAAAWHVAAAARAW Direction: Forward Position #: 15 Overlap #: 13 Alignment: HDWAATAAWAWAAAAMAAAMWWWHBWA----- --------------ABAAAAAAWHAAAAARAW ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM13 Combined Motif Reverse Complement Original Motif WTKTTTTBHWTTTTTTVTTTTWTWTTATTWDH ATKAAWTTTTRMAABAHHTW WTKTTTTBHWTTTTTTVTWTTWWWTTHTDHAABAHHTW Direction: Forward Position #: 19 Overlap #: 14 Alignment: WTKTTTTBHWTTTTTTVTTTTWTWTTATTWDH------ ------------------ATKAAWTTTTRMAABAHHTW ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM3 Combined Motif Reverse Complement Reverse Complement WAHHTVTTHDAHAAWWWAAWAVAAAAAAWHVAAAARAW TWAAWTTVTGAAAAAHWW WAHHTVTTHDAHAAWWWAAWAVAWAAAWTTVWRAARAAHWW Direction: Forward Position #: 24 Overlap #: 15 Alignment: WAHHTVTTHDAHAAWWWAAWAVAAAAAAWHVAAAARAW--- -----------------------TWAAWTTVTGAAAAAHWW ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 2 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFW2 csGCCCCGCCCCsc Original Motif Reverse Complement SCGCGCGG BBGGGGCGGGGCVD BBSGSGCGGGGCVD Direction: Forward Position #: 2 Overlap #: 8 Alignment: -SCGCGCGG----- BBGGGGCGGGGCVD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif cccGCCCCGCCCCsb Original Motif Reverse Complement BBSGSGCGGGGCVD BBGGGGCGGGGCGGB BBGGGGCGGGGCSSGSGCGGGGCVD Direction: Forward Position #: 12 Overlap #: 4 Alignment: -----------BBSGSGCGGGGCVD BBGGGGCGGGGCGGB---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFF11 Combined Motif Original Motif Original Motif BBGGGGCGGGGCSSGSGCGGGGCVD GGMGGRGGCGGVGC BBGGGGCGGGGCSSGGGSGGGGCGGVGC Direction: Forward Position #: 15 Overlap #: 11 Alignment: BBGGGGCGGGGCSSGSGCGGGGCVD--- --------------GGMGGRGGCGGVGC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFF1 Combined Motif Original Motif Original Motif BBGGGGCGGGGCSSGGGSGGGGCGGVGC CGGVGCCGCVGC BBGGGGCGGGGCSSGGGCGGGGCSGVGSC Direction: Forward Position #: 18 Overlap #: 11 Alignment: BBGGGGCGGGGCSSGGGSGGGGCGGVGC- -----------------CGGVGCCGCVGC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFW3 Combined Motif Original Motif Reverse Complement BBGGGGCGGGGCSSGGGCGGGGCSGVGSC CGCGBMGCCG BBGGGGCGGGGCSSGGGCSGSGCVGCSGC Direction: Forward Position #: 19 Overlap #: 10 Alignment: BBGGGGCGGGGCSSGGGCGGGGCSGVGSC ------------------CGCGBMGCCG- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 06-18-2018 21:47:01 Runtime: 633.592 seconds MOTIFSIM is written by Ngoc Tam L. 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