**************************************************************************************************************************************************************************************************** MOTIFSIM - Motif Similarity Detection Tool Version 2.2 **************************************************************************************************************************************************************************************************** INPUT **************************************************************************************************************************************************************************************************** Input Parameters Number of files: 1 Number of top significant motifs: 4 Number of best matches: 4 Similarity cutoff: >= 0.5 Matching motif database: Jaspar Core Motif tree: Yes Combined similar motifs: No Output file type: All Output file format: All Input files and motif counts File name Count of motifs Dataset # U20240419_R_04-19-24_1712_InsertFile1.txt 3 1 **************************************************************************************************************************************************************************************************** RESULTS **************************************************************************************************************************************************************************************************** ********************************************************************** Best Matches in Database for Each Motif (Highest to Lowest) ***************************************************************** Dataset #: 1 Motif ID: 1 Motif name: Motif 1 Consensus sequence (original motif): AGATGGCGCTATWHM Consensus sequence (reverse complement motif): RDWATAGCGCCATCT ************************************************************************ Best Matches for Motif ID 1 (Highest to Lowest) ************************************************************************* Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0469.2 E2F3 Reverse Complement Reverse Complement Backward 3 15 0.038099 Taxon: Vertebrates Consensus sequence (original motif): AAAAAKGGCGCCAWTTTT Consensus sequence (reverse complement motif): AAAAWTGGCGCCRTTTTT Alignment: AAAAWTGGCGCCRTTTTT -RDWATAGCGCCATCT-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0864.1 E2F2 Reverse Complement Reverse Complement Forward 1 15 0.0458125 Taxon: Vertebrates Consensus sequence (original motif): AAAATGGCGCCATTTT Consensus sequence (reverse complement motif): AAAATGGCGCCATTTT Alignment: AAAATGGCGCCATTTT RDWATAGCGCCATCT- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0395.1 STP2 Reverse Complement Original Motif Backward 6 15 0.0557025 Taxon: Fungi Consensus sequence (original motif): HVVHBGGCGCCGYRYVHHBH Consensus sequence (reverse complement motif): HBDHVKKKCGGCGCCBHBVH Alignment: HVVHBGGCGCCGYRYVHHBH RDWATAGCGCCATCT----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0269.1 AFT1 Original Motif Reverse Complement Forward 4 15 0.0580634 Taxon: Fungi Consensus sequence (original motif): BBDBHTAKTGCACCCSVDWBV Consensus sequence (reverse complement motif): VBWDBSGGGTGCARTAHBDVV Alignment: VBWDBSGGGTGCARTAHBDVV ---AGATGGCGCTATWHM--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 2 Motif name: Motif 2 Consensus sequence (original motif): AGCGCCVCCTR Consensus sequence (reverse complement motif): KAGGVGGCGCT ************************************************************************ Best Matches for Motif ID 2 (Highest to Lowest) ************************************************************************* Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0139.1 CTCF Original Motif Reverse Complement Forward 2 11 0.0371543 Taxon: Vertebrates Consensus sequence (original motif): YDRCCASYAGRKGGCRSYV Consensus sequence (reverse complement motif): BMSMGCCYMCTKSTGGMHM Alignment: BMSMGCCYMCTKSTGGMHM -AGCGCCVCCTR------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0685.1 SP4 Reverse Complement Reverse Complement Backward 6 11 0.0623319 Taxon: Vertebrates Consensus sequence (original motif): BWRGCCACGCCCMCTYH Consensus sequence (reverse complement motif): HMAGRGGGCGTGGCKWV Alignment: HMAGRGGGCGTGGCKWV -KAGGVGGCGCT----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0516.1 SP2 Reverse Complement Reverse Complement Forward 3 11 0.0637624 Taxon: Vertebrates Consensus sequence (original motif): GYCCCGCCYCYBBBB Consensus sequence (reverse complement motif): BBBVKGKGGCGGGKC Alignment: BBBVKGKGGCGGGKC --KAGGVGGCGCT-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0740.1 KLF14 Reverse Complement Reverse Complement Forward 1 11 0.0647375 Taxon: Vertebrates Consensus sequence (original motif): DRCCACGCCCMCYH Consensus sequence (reverse complement motif): HMGRGGGCGTGGMH Alignment: HMGRGGGCGTGGMH KAGGVGGCGCT--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 3 Motif name: Motif 3 Consensus sequence (original motif): AGCGCCVCCTR Consensus sequence (reverse complement motif): KAGGVGGCGCT ************************************************************************ Best Matches for Motif ID 3 (Highest to Lowest) ************************************************************************* Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0139.1 CTCF Original Motif Reverse Complement Forward 2 11 0.0371543 Taxon: Vertebrates Consensus sequence (original motif): YDRCCASYAGRKGGCRSYV Consensus sequence (reverse complement motif): BMSMGCCYMCTKSTGGMHM Alignment: BMSMGCCYMCTKSTGGMHM -AGCGCCVCCTR------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0685.1 SP4 Reverse Complement Reverse Complement Backward 6 11 0.0623319 Taxon: Vertebrates Consensus sequence (original motif): BWRGCCACGCCCMCTYH Consensus sequence (reverse complement motif): HMAGRGGGCGTGGCKWV Alignment: HMAGRGGGCGTGGCKWV -KAGGVGGCGCT----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0516.1 SP2 Reverse Complement Reverse Complement Forward 3 11 0.0637624 Taxon: Vertebrates Consensus sequence (original motif): GYCCCGCCYCYBBBB Consensus sequence (reverse complement motif): BBBVKGKGGCGGGKC Alignment: BBBVKGKGGCGGGKC --KAGGVGGCGCT-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0740.1 KLF14 Reverse Complement Reverse Complement Forward 1 11 0.0647375 Taxon: Vertebrates Consensus sequence (original motif): DRCCACGCCCMCYH Consensus sequence (reverse complement motif): HMGRGGGCGTGGMH Alignment: HMGRGGGCGTGGMH KAGGVGGCGCT--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 04-19-2024 14:13:07 Runtime: 532.394 seconds MOTIFSIM is written by Ngoc Tam L. 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