**************************************************************************************************************************************************************************************************** MOTIFSIM - Motif Similarity Detection Tool Version 2.2 **************************************************************************************************************************************************************************************************** INPUT **************************************************************************************************************************************************************************************************** Input Parameters Number of files: 2 Number of top significant motifs: 1 Number of best matches: 1 Similarity cutoff: >= 0.75 Matching motif database: Jaspar Core Motif tree: No Combined similar motifs: No Output file type: All Output file format: Text Input files and motif counts File name Count of motifs Dataset # U20231120-testA.txt 19 1 U20231120-testB.txt 0 2 **************************************************************************************************************************************************************************************************** RESULTS **************************************************************************************************************************************************************************************************** ****************************************************************** Top 1 Significant Motifs - Global Matching (Highest to Lowest) ****************************************************************** **************************************************************************************************************************************************************************************************** **************************************************************** Significant Motifs - Global and Local Matching (Highest to Lowest) **************************************************************** Dataset #: 1 Motif ID: 12 Motif name: Motif 12 Consensus sequence (original motif): AAAGATTT Consensus sequence (reverse complement motif): AAATCTTT ************************************************************** Best Matches for Significant Motif ID 12 (Highest to Lowest) ************************************************************** Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 19 Motif 19 Reverse Complement Reverse Complement Backward 4 8 0 Consensus sequence (original motif): TTMAAAGATTT Consensus sequence (reverse complement motif): AAATCTTTYAA Alignment: AAATCTTTYAA AAATCTTT--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- **************************************************************************************************************************************************************************************************** ********************************************************************** Best Matches for Each Motif (Highest to Lowest) ***************************************************************************** Dataset #: 1 Motif ID: 1 Motif name: Motif 1 Consensus sequence (original motif): RGRAGARRGARRAR Consensus sequence (reverse complement motif): MTMMTCMMTCTKCK ************************************************************************ Best Matches for Motif ID 1 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 2 Motif 2 Original Motif Original Motif Forward 2 13 0.0388225 Consensus sequence (original motif): AWAAAWTWAAASWA Consensus sequence (reverse complement motif): TWSTTTWAWTTTWT Alignment: AWAAAWTWAAASWA- -RGRAGARRGARRAR ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 6 Motif 6 Original Motif Reverse Complement Backward 4 11 1.03508 Consensus sequence (original motif): CSKCCCCGCCCCSY Consensus sequence (reverse complement motif): MSGGGGCGGGGYSG Alignment: ---MSGGGGCGGGGYSG RGRAGARRGARRAR--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 2 Motif name: Motif 2 Consensus sequence (original motif): AWAAAWTWAAASWA Consensus sequence (reverse complement motif): TWSTTTWAWTTTWT ************************************************************************ Best Matches for Motif ID 2 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 7 Motif 7 Reverse Complement Reverse Complement Backward 1 14 0.0394231 Consensus sequence (original motif): AAATRWTAAAATCA Consensus sequence (reverse complement motif): TGATTTTAWKATTT Alignment: TGATTTTAWKATTT TWSTTTWAWTTTWT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 3 Motif name: Motif 3 Consensus sequence (original motif): AAAAWTTRCWT Consensus sequence (reverse complement motif): AWGKAAWTTTT ************************************************************************ Best Matches for Motif ID 3 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 4 Motif 4 Original Motif Reverse Complement Forward 1 11 0.0786484 Consensus sequence (original motif): AWTAAATAYAATTT Consensus sequence (reverse complement motif): AAATTKTATTTAWT Alignment: AAATTKTATTTAWT AAAAWTTRCWT--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 4 Motif name: Motif 4 Consensus sequence (original motif): AWTAAATAYAATTT Consensus sequence (reverse complement motif): AAATTKTATTTAWT ************************************************************************ Best Matches for Motif ID 4 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 2 Motif 2 Reverse Complement Reverse Complement Backward 1 14 0.101648 Consensus sequence (original motif): AWAAAWTWAAASWA Consensus sequence (reverse complement motif): TWSTTTWAWTTTWT Alignment: TWSTTTWAWTTTWT AAATTKTATTTAWT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 5 Motif name: Motif 5 Consensus sequence (original motif): AATTYDGAARTAWW Consensus sequence (reverse complement motif): WWTAKTTCDKAATT ************************************************************************ Best Matches for Motif ID 5 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 4 Motif 4 Reverse Complement Original Motif Forward 1 14 0.0741071 Consensus sequence (original motif): AWTAAATAYAATTT Consensus sequence (reverse complement motif): AAATTKTATTTAWT Alignment: AWTAAATAYAATTT WWTAKTTCDKAATT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 6 Motif name: Motif 6 Consensus sequence (original motif): CSKCCCCGCCCCSY Consensus sequence (reverse complement motif): MSGGGGCGGGGYSG ************************************************************************ Best Matches for Motif ID 6 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 1 Motif 1 Original Motif Reverse Complement Forward 4 11 0.0157992 Consensus sequence (original motif): RGRAGARRGARRAR Consensus sequence (reverse complement motif): MTMMTCMMTCTKCK Alignment: MTMMTCMMTCTKCK--- ---CSKCCCCGCCCCSY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 7 Motif name: Motif 7 Consensus sequence (original motif): AAATRWTAAAATCA Consensus sequence (reverse complement motif): TGATTTTAWKATTT ************************************************************************ Best Matches for Motif ID 7 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 2 Motif 2 Reverse Complement Reverse Complement Backward 1 14 0.0961539 Consensus sequence (original motif): AWAAAWTWAAASWA Consensus sequence (reverse complement motif): TWSTTTWAWTTTWT Alignment: TWSTTTWAWTTTWT TGATTTTAWKATTT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 8 Motif name: Motif 8 Consensus sequence (original motif): AATHATATWTHAAA Consensus sequence (reverse complement motif): TTTDAWATATHATT ************************************************************************ Best Matches for Motif ID 8 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 2 Motif 2 Original Motif Reverse Complement Backward 1 14 0.0675748 Consensus sequence (original motif): AWAAAWTWAAASWA Consensus sequence (reverse complement motif): TWSTTTWAWTTTWT Alignment: TWSTTTWAWTTTWT AATHATATWTHAAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 9 Motif name: Motif 9 Consensus sequence (original motif): TTTCATAAWT Consensus sequence (reverse complement motif): AWTTATGAAA ************************************************************************ Best Matches for Motif ID 9 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 10 Motif 10 Original Motif Reverse Complement Backward 2 10 0.01875 Consensus sequence (original motif): ATTTWATGAAA Consensus sequence (reverse complement motif): TTTCATWAAAT Alignment: TTTCATWAAAT TTTCATAAWT- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 10 Motif name: Motif 10 Consensus sequence (original motif): ATTTWATGAAA Consensus sequence (reverse complement motif): TTTCATWAAAT ************************************************************************ Best Matches for Motif ID 10 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 7 Motif 7 Reverse Complement Original Motif Backward 2 11 0.0795455 Consensus sequence (original motif): AAATRWTAAAATCA Consensus sequence (reverse complement motif): TGATTTTAWKATTT Alignment: AAATRWTAAAATCA --TTTCATWAAAT- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 4 Motif 4 Reverse Complement Original Motif Forward 3 11 0.0795455 Consensus sequence (original motif): AWTAAATAYAATTT Consensus sequence (reverse complement motif): AAATTKTATTTAWT Alignment: AWTAAATAYAATTT --TTTCATWAAAT- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 11 Motif name: Motif 11 Consensus sequence (original motif): AAAACAAA Consensus sequence (reverse complement motif): TTTGTTTT ************************************************************************ Best Matches for Motif ID 11 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 14 Motif 14 Original Motif Original Motif Forward 4 8 0.0625 Consensus sequence (original motif): ATMACAATAAAA Consensus sequence (reverse complement motif): TTTTATTGTYAT Alignment: ATMACAATAAAA ---AAAACAAA- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 12 Motif name: Motif 12 Consensus sequence (original motif): AAAGATTT Consensus sequence (reverse complement motif): AAATCTTT ************************************************************************ Best Matches for Motif ID 12 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 19 Motif 19 Reverse Complement Reverse Complement Backward 4 8 0 Consensus sequence (original motif): TTMAAAGATTT Consensus sequence (reverse complement motif): AAATCTTTYAA Alignment: AAATCTTTYAA AAATCTTT--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 13 Motif name: Motif 13 Consensus sequence (original motif): AWAAATAA Consensus sequence (reverse complement motif): TTATTTWT ************************************************************************ Best Matches for Motif ID 13 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 4 Motif 4 Reverse Complement Reverse Complement Forward 6 8 0.021875 Consensus sequence (original motif): AWTAAATAYAATTT Consensus sequence (reverse complement motif): AAATTKTATTTAWT Alignment: AAATTKTATTTAWT -----TTATTTWT- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 14 Motif name: Motif 14 Consensus sequence (original motif): ATMACAATAAAA Consensus sequence (reverse complement motif): TTTTATTGTYAT ************************************************************************ Best Matches for Motif ID 14 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 7 Motif 7 Original Motif Original Motif Forward 3 12 0.104167 Consensus sequence (original motif): AAATRWTAAAATCA Consensus sequence (reverse complement motif): TGATTTTAWKATTT Alignment: AAATRWTAAAATCA --ATMACAATAAAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 15 Motif name: Motif 15 Consensus sequence (original motif): ACAAWTRATTTTGA Consensus sequence (reverse complement motif): TCAAAATKAWTTGT ************************************************************************ Best Matches for Motif ID 15 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 4 Motif 4 Reverse Complement Original Motif Backward 1 14 0.1 Consensus sequence (original motif): AWTAAATAYAATTT Consensus sequence (reverse complement motif): AAATTKTATTTAWT Alignment: AWTAAATAYAATTT TCAAAATKAWTTGT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 16 Motif name: Motif 16 Consensus sequence (original motif): AAAAATGAAT Consensus sequence (reverse complement motif): ATTCATTTTT ************************************************************************ Best Matches for Motif ID 16 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 15 Motif 15 Reverse Complement Original Motif Backward 4 10 0.05 Consensus sequence (original motif): ACAAWTRATTTTGA Consensus sequence (reverse complement motif): TCAAAATKAWTTGT Alignment: ACAAWTRATTTTGA -ATTCATTTTT--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 17 Motif name: Motif 17 Consensus sequence (original motif): TTAGWTWATAA Consensus sequence (reverse complement motif): TTATWAWCTAA ************************************************************************ Best Matches for Motif ID 17 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 5 Motif 5 Reverse Complement Original Motif Forward 2 11 0.0625 Consensus sequence (original motif): AATTYDGAARTAWW Consensus sequence (reverse complement motif): WWTAKTTCDKAATT Alignment: AATTYDGAARTAWW -TTATWAWCTAA-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 18 Motif name: Motif 18 Consensus sequence (original motif): TTCWTAGATTAWA Consensus sequence (reverse complement motif): TWTAATCTAWGAA ************************************************************************ Best Matches for Motif ID 18 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 8 Motif 8 Original Motif Original Motif Forward 2 13 0.0641025 Consensus sequence (original motif): AATHATATWTHAAA Consensus sequence (reverse complement motif): TTTDAWATATHATT Alignment: AATHATATWTHAAA -TTCWTAGATTAWA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset #: 1 Motif ID: 19 Motif name: Motif 19 Consensus sequence (original motif): TTMAAAGATTT Consensus sequence (reverse complement motif): AAATCTTTYAA ************************************************************************ Best Matches for Motif ID 19 (Highest to Lowest) ************************************************************************ Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 7 Motif 7 Reverse Complement Original Motif Backward 1 11 0.0681818 Consensus sequence (original motif): AAATRWTAAAATCA Consensus sequence (reverse complement motif): TGATTTTAWKATTT Alignment: AAATRWTAAAATCA ---AAATCTTTYAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dataset # Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score 1 18 Motif 18 Original Motif Original Motif Backward 3 11 0.0681818 Consensus sequence (original motif): TTCWTAGATTAWA Consensus sequence (reverse complement motif): TWTAATCTAWGAA Alignment: TTCWTAGATTAWA TTMAAAGATTT-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 11-20-2023 13:26:32 Runtime: 48.2818 seconds MOTIFSIM is written by Ngoc Tam L. Tran