**************************************************************************************************************************************************************************************************** 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_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 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 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wtATTTTTAww Reverse Complement Original Motif TWATHDHTATTTD DTATTTTTAWW TWATTTTTATTTD Direction: Forward Position #: 1 Overlap #: 11 Alignment: TWATHDHTATTTD DTATTTTTAWW-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 68 Combined Motif Original Motif 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 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: Backward 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 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 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 Reverse Complement Original Motif BATGGM AGATGGY YARWKGG Direction: Backward Position #: 2 Overlap #: 6 Alignment: BATGGM- AGATGGY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 12 Original Motif Original Motif YARWKGG GATGGCTC CTCSADDGYA Direction: Backward Position #: 4 Overlap #: 5 Alignment: YARWKGG--- --GATGGCTC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif grCCACyAGAkG Original Motif Original Motif CTCSADDGYA DDCCACYAGAKG DDCCACTMGAKGGYA Direction: Forward Position #: 6 Overlap #: 7 Alignment: -----CTCSADDGYA DDCCACYAGAKG--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif grCCACyAGAkG Original Motif Original Motif DDCCACTMGAKGGYA DDCCACYAGAKG DDCCACTAGAKGGYA Direction: Forward Position #: 1 Overlap #: 12 Alignment: DDCCACTMGAKGGYA DDCCACYAGAKG--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif rgyGCCMyCTksTGGccd Reverse Complement Reverse Complement TKCCYTCTAGTGGHH DDGCCASYAGMGGGCKVM DKBCCWCYAGWGGGCKVM Direction: Forward Position #: 1 Overlap #: 15 Alignment: TKCCYTCTAGTGGHH--- DDGCCASYAGMGGGCKVM ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 48 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 48 Motif 21 Original Motif Original Motif CCACYAGR CCACYAGG CCACYAGG Direction: Backward Position #: 1 Overlap #: 8 Alignment: CCACYAGR CCACYAGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif grCCACyAGAkG Original Motif Original Motif CCACYAGG DDCCACYAGAKG DDCCACYAGRKG Direction: Forward Position #: 3 Overlap #: 8 Alignment: --CCACYAGG-- DDCCACYAGAKG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif grCCACwAGrk Original Motif Original Motif DDCCACYAGRKG DDCCACWAGRK DDCCACYAGRKG Direction: Forward Position #: 1 Overlap #: 11 Alignment: DDCCACYAGRKG DDCCACWAGRK- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif grCCACyAGAkG Original Motif Original Motif DDCCACYAGRKG DDCCACYAGAKG DDCCACYAGAKG Direction: Forward Position #: 1 Overlap #: 12 Alignment: DDCCACYAGRKG DDCCACYAGAKG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif CTCF Original Motif Original Motif DDCCACYAGAKG YDRCCASYAGRKGGCRSYV YDDCCACYAGRKGGCRSYV Direction: Forward Position #: 2 Overlap #: 12 Alignment: -DDCCACYAGAKG------ YDRCCASYAGRKGGCRSYV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 65 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 65 raCAAAACam Original Motif Original Motif ARAACA DACAAAACAH DACAAAACAH Direction: Forward Position #: 4 Overlap #: 6 Alignment: ---ARAACA- DACAAAACAH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 44 Original Motif Original Motif DACAAAACAH GDAAACA GDMAAMACAH Direction: Forward Position #: 1 Overlap #: 7 Alignment: DACAAAACAH GDAAACA--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif kkAAGAGCAsy Original Motif Original Motif GDMAAMACAH DBAAGAGCAVH GDAARARCAVH Direction: Forward Position #: 1 Overlap #: 10 Alignment: GDMAAMACAH- DBAAGAGCAVH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TAL1TCF3 Reverse Complement Original Motif HBTGKTMTTDC HVAMCATCTGKT HVAMCABCTGKTMTTDC Direction: Forward Position #: 7 Overlap #: 6 Alignment: ------HBTGKTMTTDC HVAMCATCTGKT----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 2 Reverse Complement Original Motif GDAARARCAGVTGRTVD AAAAHAAA DAAAVAAMAGVTGRTVD Direction: Forward Position #: 1 Overlap #: 8 Alignment: GDAARARCAGVTGRTVD AAAAHAAA--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 5 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 5 Motif 59 Original Motif Original Motif CCCCDCCC CCCCRCCC CCCCRCCC Direction: Forward Position #: 1 Overlap #: 8 Alignment: CCCCDCCC CCCCRCCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif csCSCCdCCCcs Reverse Complement Reverse Complement GGGKGGGG VDGGGDGGGGBV GGGGGGGGGGBV Direction: Forward Position #: 1 Overlap #: 8 Alignment: GGGKGGGG---- VDGGGDGGGGBV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Klf4 Reverse Complement Reverse Complement VBCCCCCCCCCC GCCYCMCCCD BCCCCCCCCCCC Direction: Forward Position #: 1 Overlap #: 10 Alignment: VBCCCCCCCCCC GCCYCMCCCD-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif csCsCCTCCcc Original Motif Original Motif BCCCCCCCCCCC VBCCCCTCCHB BBCCCCYCCHCC Direction: Forward Position #: 1 Overlap #: 11 Alignment: BCCCCCCCCCCC VBCCCCTCCHB- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif SP1 Reverse Complement Reverse Complement GGDGGMGGGGBB GGGGGYGGGG GGGGGHGGGGBB Direction: Forward Position #: 1 Overlap #: 10 Alignment: GGDGGMGGGGBB GGGGGYGGGG-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global 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 ssCGwGCGss Original Motif Original Motif YGCGTG BSCGWGCGBV CGBVBGCGTG Direction: Backward Position #: 5 Overlap #: 6 Alignment: YGCGTG---- BSCGWGCGBV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 20 Reverse Complement Original Motif CACGCBVBCG CACGTR CACGYDVBCG Direction: Forward Position #: 1 Overlap #: 6 Alignment: CACGCBVBCG CACGTR---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 42 Original Motif Original Motif CACGYDVBCG CGCGCSG CRCGCSGBCG Direction: Forward Position #: 1 Overlap #: 7 Alignment: CACGYDVBCG CGCGCSG--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif yrCATGCAyr Reverse Complement Reverse Complement CGBCSGCGMG HVTGCATGKV HVTGCAYGBVSGCGMG Direction: Forward Position #: 7 Overlap #: 4 Alignment: ------CGBCSGCGMG HVTGCATGKV------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 57 Original Motif Original Motif HVTGCAYGBVSGCGMG ACACACAY ACAYRCAYGBVSGCGMG Direction: Forward Position #: 2 Overlap #: 7 Alignment: -HVTGCAYGBVSGCGMG ACACACAY--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 101 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NFIC wgGCCAshAGrGGGCrsy Reverse Complement Original Motif DGCCAA HDGCCACHAGRGGGCRBY HAGRGGGCRBYDGCCAMH Direction: Backward Position #: 12 Overlap #: 6 Alignment: -DGCCAA----------- HDGCCACHAGRGGGCRBY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif rgyGCCMyCTksTGGccd Reverse Complement Reverse Complement HRTGGCDKBKGCCCKCTH DDGCCASYAGMGGGCKVM DDGCCASYAGMKGGCKBVKGCCCKCTH Direction: Forward Position #: 10 Overlap #: 9 Alignment: ---------HRTGGCDKBKGCCCKCTH DDGCCASYAGMGGGCKVM--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif agrCCAGmAGrg Original Motif Original Motif DDGCCASYAGMKGGCKBVKGCCCKCTH HVGCCAGMAGRG DDGCCAGMAGVKGGCKBVKGCCCKCTH Direction: Forward Position #: 1 Overlap #: 12 Alignment: DDGCCASYAGMKGGCKBVKGCCCKCTH HVGCCAGMAGRG--------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 9 Original Motif Reverse Complement DDGCCAGMAGVKGGCKBVKGCCCKCTH SWGCCACC VDGCCASCAGVKGGCKBVKGCCCKCTH Direction: Forward Position #: 1 Overlap #: 8 Alignment: DDGCCAGMAGVKGGCKBVKGCCCKCTH SWGCCACC------------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif gwGGCCAGmAGAGGGCrby Original Motif Original Motif VDGCCASCAGVKGGCKBVKGCCCKCTH VHGGCCAGMAGAGGGCRBY VVGGCCASMAGAGGGCRBBKGCCCKCTH Direction: Forward Position #: 2 Overlap #: 18 Alignment: -VDGCCASCAGVKGGCKBVKGCCCKCTH VHGGCCAGMAGAGGGCRBY--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 11-19-2016 22:45:25 Runtime: 1028.98 seconds MOTIFSIM is written by Ngoc Tam L. 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