**************************************************************************************************************************************************************************************************** MOTIFSIM - Motif Similarity Detection Tool Version 2.2 **************************************************************************************************************************************************************************************************** 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 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 # DREME_DM254.txt 45 1 MEME-CHIP_DM254.txt 24 2 PScanChIP_DM254.txt 63 3 RSAT_peak-motifs_DM254.txt 39 4 **************************************************************************************************************************************************************************************************** RESULTS **************************************************************************************************************************************************************************************************** ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 71 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Arnt Motif 20 Original Motif Reverse Complement CACGTG MACGTG CACGTG Direction: Forward Position #: 1 Overlap #: 6 Alignment: CACGTG MACGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MAX Reverse Complement Reverse Complement CACGTG BCACGTGDTD BCACGTGDTD Direction: Forward Position #: 2 Overlap #: 6 Alignment: -CACGTG--- BCACGTGDTD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif USF1 Original Motif Reverse Complement BCACGTGDTD MCACGTG HCACGTGDTD Direction: Forward Position #: 1 Overlap #: 7 Alignment: BCACGTGDTD MCACGTG--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MYCMAX Reverse Complement Original Motif HAHCACGTGD RASCACGTGGT DAVCACGTGGT Direction: Forward Position #: 1 Overlap #: 10 Alignment: HAHCACGTGD- RASCACGTGGT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Myc Reverse Complement Reverse Complement ACCACGTGVTD DCCACGTGCV DCCACGTGVDD Direction: Forward Position #: 1 Overlap #: 10 Alignment: ACCACGTGVTD DCCACGTGCV- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 46 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 46 Motif 1 Original Motif Original Motif AGRKGGCR AGRKGGCR AGRKGGCR Direction: Forward Position #: 1 Overlap #: 8 Alignment: AGRKGGCR AGRKGGCR ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif asCAGrkGGCrsy Reverse Complement Reverse Complement KGCCYKCT BSKGCCCMCTGST BSKGCCYBCTGST Direction: Forward Position #: 3 Overlap #: 8 Alignment: --KGCCYKCT--- BSKGCCCMCTGST ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wgGCCAshAGrGGGCrsy Original Motif Reverse Complement BSKGCCYBCTGST KBKGCCCKCTHGTGGCHH BSKGCCCBCTBSTGGCHH Direction: Forward Position #: 1 Overlap #: 13 Alignment: BSKGCCYBCTGST----- KBKGCCCKCTHGTGGCHH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CasCAGrGGGCrsy Original Motif Reverse Complement BSKGCCCBCTBSTGGCHH BSKGCCCKCTGGTG BSKGCCCKCTGSTGGCHH Direction: Forward Position #: 1 Overlap #: 14 Alignment: BSKGCCCBCTBSTGGCHH BSKGCCCKCTGGTG---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif gwGGCCAGmAGAGGGCrby Original Motif Reverse Complement BSKGCCCKCTGSTGGCHH KBKGCCCTCTYCTGGCCHV KBKGCCCTCTBSTGGCCHV Direction: Forward Position #: 1 Overlap #: 18 Alignment: BSKGCCCKCTGSTGGCHH- KBKGCCCTCTYCTGGCCHV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 133 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- shAGrGGGCAgy wgGCCAshAGrGGGCrsy Original Motif Original Motif SHAGRGGGCABH HDGCCACHAGRGGGCRBY HDGCCASHAGRGGGCABH Direction: Forward Position #: 7 Overlap #: 12 Alignment: ------SHAGRGGGCABH HDGCCACHAGRGGGCRBY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- AgmAGAGGGCrscAGak Combined Motif Original Motif Original Motif HDGCCASHAGRGGGCABH AGMAGAGGGCASCAGAK HDGCCASMAGAGGGCASYAGAK Direction: Forward Position #: 6 Overlap #: 13 Alignment: HDGCCASHAGRGGGCABH---- -----AGMAGAGGGCASCAGAK ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif gwGGCCAGmAGAGGGCrby Original Motif Original Motif HDGCCASMAGAGGGCASYAGAK VHGGCCAGMAGAGGGCRBY VHGGCCAGMAGAGGGCRBYAGAK Direction: Forward Position #: 2 Overlap #: 18 Alignment: -HDGCCASMAGAGGGCASYAGAK VHGGCCAGMAGAGGGCRBY---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CasCAGrGGGCrsy Original Motif Reverse Complement VHGGCCAGMAGAGGGCRBYAGAK BSKGCCCKCTGGTG DVKGCCMKCWGRKGGCRBYAGAK Direction: Forward Position #: 1 Overlap #: 14 Alignment: VHGGCCAGMAGAGGGCRBYAGAK BSKGCCCKCTGGTG--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif asCAGrkGGCrsy Original Motif Reverse Complement DVKGCCMKCWGRKGGCRBYAGAK BSKGCCCMCTGST BVKGCCCVCTGVKGGCRBYAGAK Direction: Forward Position #: 1 Overlap #: 13 Alignment: DVKGCCMKCWGRKGGCRBYAGAK BSKGCCCMCTGST---------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 8 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 8 waATwAAAATAww Original Motif Original Motif AAATAH DHATWAAAATAHD DAAATAHDHATWA Direction: Backward Position #: 2 Overlap #: 6 Alignment: ------AAATAH- DHATWAAAATAHD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- wtATTTTTAww Combined Motif Original Motif Reverse Complement DAAATAHDHATWA WWTAAAAATAD DAAATAAAAATWA Direction: Forward Position #: 3 Overlap #: 11 Alignment: DAAATAHDHATWA --WWTAAAAATAD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 68 Combined Motif Reverse Complement Reverse Complement TWATTTTTATTTD TTWWWTWTTTWTTW TWWTTTTTATTTWTTW Direction: Forward Position #: 3 Overlap #: 11 Alignment: TWATTTTTATTTD--- --TTWWWTWTTTWTTW ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 52 Reverse Complement Original Motif WAAWAAATAAAAAWWA AAATAAAW WAATAAAWAAAAAWWA Direction: Forward Position #: 1 Overlap #: 8 Alignment: WAAWAAATAAAAAWWA AAATAAAW-------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SRF Combined Motif Reverse Complement Reverse Complement TWWTTTTTWTTTATTW CCATATATGGGC TWWTTTTTMYWTATWTGGGC Direction: Forward Position #: 9 Overlap #: 8 Alignment: TWWTTTTTWTTTATTW---- --------CCATATATGGGC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 153 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- scAGrkGGCGcy rgCGCCmyCTgs Reverse Complement Original Motif VGCGCCCMCTDS VGCGCCCYCTDS VGCGCCCCCTDS Direction: Forward Position #: 1 Overlap #: 12 Alignment: VGCGCCCMCTDS VGCGCCCYCTDS ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif asCAGrkGGCrsy Original Motif Reverse Complement VGCGCCCCCTDS BSKGCCCMCTGST DSYGCCCMCTGST Direction: Forward Position #: 1 Overlap #: 12 Alignment: VGCGCCCCCTDS- BSKGCCCMCTGST ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CTCF Original Motif Reverse Complement DSYGCCCMCTGST BMSMGCCYMCTKSTGGMHM BVSCGCCYMCTGSTGGMHM Direction: Forward Position #: 2 Overlap #: 13 Alignment: -DSYGCCCMCTGST----- BMSMGCCYMCTKSTGGMHM ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wgGCCAshAGrGGGCrsy Reverse Complement Original Motif YDRCCASCAGRKGGCGSBV HDGCCACHAGRGGGCRBY HDGCCASHAGRGGGCRSHV Direction: Forward Position #: 1 Overlap #: 18 Alignment: YDRCCASCAGRKGGCGSBV HDGCCACHAGRGGGCRBY- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CasCAGrGGGCrsy Original Motif Reverse Complement HDGCCASHAGRGGGCRSHV BSKGCCCKCTGGTG BBKGCCMBCWGRKGGCRSHV Direction: Forward Position #: 2 Overlap #: 13 Alignment: -HDGCCASHAGRGGGCRSHV BSKGCCCKCTGGTG------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 20 Arnt Original Motif Reverse Complement CACGTR CACGTG CACGTG Direction: Forward Position #: 1 Overlap #: 6 Alignment: CACGTR CACGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MYCMAX Original Motif Reverse Complement CACGTG ACCACGTGSTM ACCACGTGSTM Direction: Forward Position #: 3 Overlap #: 6 Alignment: --CACGTG--- ACCACGTGSTM ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif MAX Reverse Complement Original Motif RASCACGTGGT DAHCACGTGD DAVCACGTGGT Direction: Forward Position #: 1 Overlap #: 10 Alignment: RASCACGTGGT DAHCACGTGD- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- USF1 Combined Motif Reverse Complement Reverse Complement ACCACGTGVTH MCACGTG ACCACGTGVTH Direction: Forward Position #: 2 Overlap #: 7 Alignment: ACCACGTGVTH -MCACGTG--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Myc Original Motif Reverse Complement ACCACGTGVTH DCCACGTGCV DCCACGTGVDH Direction: Forward Position #: 1 Overlap #: 10 Alignment: ACCACGTGVTH DCCACGTGCV- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 Motif 46 Original Motif Original Motif AGRKGGCR AGRKGGCR AGRKGGCR Direction: Forward Position #: 1 Overlap #: 8 Alignment: AGRKGGCR AGRKGGCR ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif asCAGrkGGCrsy Reverse Complement Reverse Complement KGCCYKCT BSKGCCCMCTGST BSKGCCYBCTGST Direction: Forward Position #: 3 Overlap #: 8 Alignment: --KGCCYKCT--- BSKGCCCMCTGST ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wgGCCAshAGrGGGCrsy Original Motif Reverse Complement BSKGCCYBCTGST KBKGCCCKCTHGTGGCHH BSKGCCCBCTBSTGGCHH Direction: Forward Position #: 1 Overlap #: 13 Alignment: BSKGCCYBCTGST----- KBKGCCCKCTHGTGGCHH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CasCAGrGGGCrsy Original Motif Reverse Complement BSKGCCCBCTBSTGGCHH BSKGCCCKCTGGTG BSKGCCCKCTGSTGGCHH Direction: Forward Position #: 1 Overlap #: 14 Alignment: BSKGCCCBCTBSTGGCHH BSKGCCCKCTGGTG---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif gwGGCCAGmAGAGGGCrby Original Motif Reverse Complement BSKGCCCKCTGSTGGCHH KBKGCCCTCTYCTGGCCHV KBKGCCCTCTBSTGGCCHV Direction: Forward Position #: 1 Overlap #: 18 Alignment: BSKGCCCKCTGSTGGCHH- KBKGCCCTCTYCTGGCCHV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif asyAGrkGGCRGCAga Original Motif Reverse Complement KBKGCCCTCTBSTGGCCHV HBTGCTGCCYMCTKST BBTGCYSYCTVCTGGYCHV Direction: Forward Position #: 1 Overlap #: 16 Alignment: KBKGCCCTCTBSTGGCCHV HBTGCTGCCYMCTKST--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 136 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- dwCAGAAGwh agrCCAGmAGrg Original Motif Original Motif DHCAGAAGDH HVGCCAGMAGRG HVRCCAGAAGDB Direction: Forward Position #: 3 Overlap #: 10 Alignment: --DHCAGAAGDH HVGCCAGMAGRG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif raCAAAACam Reverse Complement Reverse Complement BDCTTCTGGMVH HTGTTTTGTD HTSTTYTGDHVH Direction: Forward Position #: 1 Overlap #: 10 Alignment: BDCTTCTGGMVH HTGTTTTGTD-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif grCCACwAGrk Original Motif Reverse Complement HTSTTYTGDHVH YMCTWGTGGHH HHCTTGTGGHHH Direction: Forward Position #: 1 Overlap #: 11 Alignment: HTSTTYTGDHVH YMCTWGTGGHH- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif mkCTyTTCsg Original Motif Original Motif HHCTTGTGGHHH HBCTTTTCBD HBCTTTTSGBHH Direction: Forward Position #: 1 Overlap #: 10 Alignment: HHCTTGTGGHHH HBCTTTTCBD-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif gwGGCCAGmAGAGGGCrby Reverse Complement Original Motif HDBCSAAAAGVD VHGGCCAGMAGAGGGCRBY VHGGCCARAAGAGGGCRBY Direction: Forward Position #: 2 Overlap #: 12 Alignment: -HDBCSAAAAGVD------ VHGGCCAGMAGAGGGCRBY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 127 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- YY1 Motif 61 Original Motif Reverse Complement RCCATB KCCATCT KCCMWYT Direction: Forward Position #: 2 Overlap #: 6 Alignment: -RCCATB KCCATCT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 12 Original Motif Reverse Complement KCCMWYT GAGCCATC GAGCCATCT Direction: Forward Position #: 3 Overlap #: 6 Alignment: --KCCMWYT GAGCCATC- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- grCCACyAGAkG Combined Motif Original Motif Original Motif GAGCCATCT DDCCACYAGAKG GAGCCAYYWGAKG Direction: Forward Position #: 2 Overlap #: 8 Alignment: GAGCCATCT---- -DDCCACYAGAKG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CTCF Original Motif Original Motif GAGCCAYYWGAKG YDRCCASYAGRKGGCRSYV KDGCCACYAGAKGGCRSYV Direction: Forward Position #: 1 Overlap #: 13 Alignment: GAGCCAYYWGAKG------ YDRCCASYAGRKGGCRSYV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- grCCACyAGAkG Combined Motif Original Motif Original Motif KDGCCACYAGAKGGCRSYV DDCCACYAGAKG KDDCCACYAGAKGGCRSYV Direction: Forward Position #: 2 Overlap #: 12 Alignment: KDGCCACYAGAKGGCRSYV -DDCCACYAGAKG------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 72 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ArntAhr HIF1AARNT Original Motif Original Motif YGCGTG VBACGTGV VBRCGTGV Direction: Backward Position #: 2 Overlap #: 6 Alignment: -YGCGTG- VBACGTGV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ssCGwGCGss Original Motif Original Motif VBRCGTGV BSCGWGCGBV BVCGCGYGVV Direction: Forward Position #: 2 Overlap #: 8 Alignment: -VBRCGTGV- BSCGWGCGBV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Arnt Original Motif Original Motif BVCGCGYGVV CACGTG CACGTGYGVV Direction: Forward Position #: 1 Overlap #: 6 Alignment: BVCGCGYGVV CACGTG---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 20 Original Motif Reverse Complement CACGTGYGVV MACGTG CACGTGYGVV Direction: Forward Position #: 1 Overlap #: 6 Alignment: CACGTGYGVV MACGTG---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif USF1 Original Motif Original Motif CACGTGYGVV CACGTGR CACGTGBGVV Direction: Forward Position #: 1 Overlap #: 7 Alignment: CACGTGYGVV CACGTGR--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 06-18-2018 16:50:38 Runtime: 1017.73 seconds MOTIFSIM is written by Ngoc Tam L. 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