**************************************************************************************************************************************************************************************************** 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 **************************************************************************************************************************************************************************************************** ********************************************************************** Best Matches in Database 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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0528.1 ZNF263 Original Motif Original Motif Forward 3 14 0.00563526 Taxon: Vertebrates Consensus sequence (original motif): GGAGGAGGRRGRGGRGGRRGR Consensus sequence (reverse complement motif): KCMKCCKCCMCMKCCTCCTCC Alignment: GGAGGAGGRRGRGGRGGRRGR --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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0555.1 SVP Reverse Complement Reverse Complement Backward 7 14 0.024813 Taxon: Plants Consensus sequence (original motif): VWWHCCAAAAADGGAAARAH Consensus sequence (reverse complement motif): HTMTTTCCDTTTTTGGHWWB Alignment: HTMTTTCCDTTTTTGGHWWB 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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0390.1 STB3 Reverse Complement Original Motif Forward 2 11 0.0463699 Taxon: Fungi Consensus sequence (original motif): GBYHAAAWTTTTTCACTBHDD Consensus sequence (reverse complement motif): HHHBAGTGAAAAAWTTTDKVC Alignment: GBYHAAAWTTTTTCACTBHDD -AWGKAAWTTTT--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0869.1 Sox11 Reverse Complement Reverse Complement Forward 2 14 0.0734794 Taxon: Vertebrates Consensus sequence (original motif): AACAATTKCAGTGTT Consensus sequence (reverse complement motif): AACACTGRAATTGTT Alignment: AACACTGRAATTGTT -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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0400.1 SUT2 Reverse Complement Reverse Complement Backward 7 14 0.0872945 Taxon: Fungi Consensus sequence (original motif): HDDHHRAACTCCGAAHHDBD Consensus sequence (reverse complement motif): DVDHHTTCGGAGTTKHHHDH Alignment: DVDHHTTCGGAGTTKHHHDH 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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0685.1 SP4 Original Motif Original Motif Backward 3 14 0.0325695 Taxon: Vertebrates Consensus sequence (original motif): BWRGCCACGCCCMCTYH Consensus sequence (reverse complement motif): HMAGRGGGCGTGGCKWV Alignment: BWRGCCACGCCCMCTYH -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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0729.1 RARA Reverse Complement Reverse Complement Backward 2 14 0.078646 Taxon: Vertebrates Consensus sequence (original motif): GAGGTCAAAAGGTCAAKK Consensus sequence (reverse complement motif): YRTTGACCTTTTGACCTC Alignment: YRTTGACCTTTTGACCTC ---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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0345.1 NHP6A Reverse Complement Reverse Complement Forward 5 14 0.045914 Taxon: Fungi Consensus sequence (original motif): VHDHHYWHTATATAADDDHDH Consensus sequence (reverse complement motif): HHHDDDTTATATAHWKDHHHB Alignment: HHHDDDTTATATAHWKDHHHB ----TTTDAWATATHATT--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0683.1 POU4F2 Reverse Complement Reverse Complement Forward 7 10 0.0571343 Taxon: Vertebrates Consensus sequence (original motif): DTGCATAATTAATGAG Consensus sequence (reverse complement motif): CTCATTAATTATGCAD Alignment: CTCATTAATTATGCAD ------AWTTATGAAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0906.1 HOXC12 Original Motif Reverse Complement Backward 1 11 0.0786043 Taxon: Vertebrates Consensus sequence (original motif): RGTCGTAAAAH Consensus sequence (reverse complement motif): HTTTTACGACM Alignment: HTTTTACGACM ATTTWATGAAA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0481.1 FOXP1 Original Motif Original Motif Forward 7 8 0.0249742 Taxon: Vertebrates Consensus sequence (original motif): HHDADGTAAACAAAV Consensus sequence (reverse complement motif): VTTTGTTTACDTDHD Alignment: HHDADGTAAACAAAV ------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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0435.1 YPR015C Original Motif Reverse Complement Backward 10 8 0.0240145 Taxon: Fungi Consensus sequence (original motif): TBDHDACGTAAATCMTDDHH Consensus sequence (reverse complement motif): HDDDARGATTTACGTHHDBA Alignment: HDDDARGATTTACGTHHDBA ---AAAGATTT--------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0052.3 MEF2A Original Motif Original Motif Backward 2 8 0 Taxon: Vertebrates Consensus sequence (original motif): KCTAWAAATAGM Consensus sequence (reverse complement motif): YCTATTTWTAGR Alignment: KCTAWAAATAGM ---AWAAATAA- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0050.2 IRF1 Reverse Complement Original Motif Forward 7 12 0.101031 Taxon: Vertebrates Consensus sequence (original motif): HBBYASTTTCACTTTCDBTTT Consensus sequence (reverse complement motif): AAABDGAAAGTGAAASTMVHH Alignment: HBBYASTTTCACTTTCDBTTT ------TTTTATTGTYAT--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0868.1 SOX8 Reverse Complement Original Motif Backward 2 14 0.0986809 Taxon: Vertebrates Consensus sequence (original motif): AACAATRTGCAGTGTT Consensus sequence (reverse complement motif): AACACTGCAMATTGTT Alignment: AACAATRTGCAGTGTT -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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0757.1 ONECUT3 Reverse Complement Reverse Complement Backward 2 10 0.0366805 Taxon: Vertebrates Consensus sequence (original motif): VAAAAATCRATAAH Consensus sequence (reverse complement motif): HTTATKGATTTTTB Alignment: HTTATKGATTTTTB ---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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0683.1 POU4F2 Reverse Complement Reverse Complement Forward 2 11 0.0672954 Taxon: Vertebrates Consensus sequence (original motif): DTGCATAATTAATGAG Consensus sequence (reverse complement motif): CTCATTAATTATGCAD Alignment: CTCATTAATTATGCAD -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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0731.1 BCL6B Reverse Complement Original Motif Backward 5 13 0.0706727 Taxon: Vertebrates Consensus sequence (original motif): TGCTTTCTAGGAATTCM Consensus sequence (reverse complement motif): YGAATTCCTAGAAAGCA Alignment: TGCTTTCTAGGAATTCM TWTAATCTAWGAA---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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) ************************************************************************ Motif ID Motif name Matching format of first motif Matching format of second motif Direction Position # # of overlap Similarity score MA0731.1 BCL6B Original Motif Original Motif Forward 5 11 0.0492255 Taxon: Vertebrates Consensus sequence (original motif): TGCTTTCTAGGAATTCM Consensus sequence (reverse complement motif): YGAATTCCTAGAAAGCA Alignment: TGCTTTCTAGGAATTCM ----TTMAAAGATTT-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 11-20-2023 13:26:32 Runtime: 48.2818 seconds MOTIFSIM is written by Ngoc Tam L. 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