**************************************************************************************************************************************************************************************************** MOTIFSIM - Motif Similarity Detection Tool Version 2.2 **************************************************************************************************************************************************************************************************** INPUT **************************************************************************************************************************************************************************************************** Input Parameters Number of files: 5 Number of top significant motifs: 5 Number of best matches: 5 Similarity cutoff: >= 0.75 Matching motif database: Jaspar Urochordates 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_DM230.txt 1 1 MEME_DM230.txt 20 2 PScanChIP_DM230.txt 14 3 RSAT_peak-motifs_DM230.txt 10 4 W-ChIPMotifs_DM230.txt 11 5 **************************************************************************************************************************************************************************************************** RESULTS **************************************************************************************************************************************************************************************************** ************************************************************ Combined Motifs for Top Global Significant Motif ID 24 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SP1 Motif 7 Original Motif Original Motif CCCCKCCCCC CSKCCCCGCCCCSY YCCCCGCCCCCCSK Direction: Backward Position #: 2 Overlap #: 10 Alignment: ---CCCCKCCCCC- CSKCCCCGCCCCSY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- csGCCCCGCCCCsc Combined Motif Reverse Complement Reverse Complement YSGGGGGGCGGGGM BBGGGGCGGGGCVD YSGGGGGGSGGSGGGGCVD Direction: Forward Position #: 6 Overlap #: 9 Alignment: YSGGGGGGCGGGGM----- -----BBGGGGCGGGGCVD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- cccGCCCCGCCCCsb Combined Motif Original Motif Reverse Complement YSGGGGGGSGGSGGGGCVD BBGGGGCGGGGCGGB YSGGGGGGSGGGGCGGSGCGGB Direction: Forward Position #: 8 Overlap #: 12 Alignment: YSGGGGGGSGGSGGGGCVD--- -------BBGGGGCGGGGCGGB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFF11 Combined Motif Original Motif Original Motif YSGGGGGGSGGGGCGGSGCGGB GGMGGRGGCGGVGC YSGGGGGGSGGVGSGGGSGGVGC Direction: Forward Position #: 10 Overlap #: 13 Alignment: YSGGGGGGSGGGGCGGSGCGGB- ---------GGMGGRGGCGGVGC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM12 Combined Motif Reverse Complement Original Motif GCVCCSCCCSCVCCSCCCCCCSK CYYCBBCYYYTCCHCCTYYY GCVCCSCCCCCBCCBCYYCBCCBCCTYYY Direction: Forward Position #: 10 Overlap #: 14 Alignment: GCVCCSCCCSCVCCSCCCCCCSK------ ---------CYYCBBCYYYTCCHCCTYYY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 45 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- wbgTAAATAww TFM11 Reverse Complement Reverse Complement DHTATTTACBD TWVHWWWYTTTYTTTTTHTTTVWBH TWVHWWWYTTTYTTTTTATTTAHBH Direction: Forward Position #: 15 Overlap #: 11 Alignment: --------------DHTATTTACBD TWVHWWWYTTTYTTTTTHTTTVWBH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 9 Combined Motif Original Motif Reverse Complement TWVHWWWYTTTYTTTTTATTTAHBH TTTDAWATATHATT TWVHWWWYTTTYTDAWWWWTTAHTH Direction: Forward Position #: 11 Overlap #: 14 Alignment: TWVHWWWYTTTYTTTTTATTTAHBH ----------TTTDAWATATHATT- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 6 Combined Motif Original Motif Reverse Complement TWVHWWWYTTTYTDAWWWWTTAHTH WWTAKTTCDKAATT TWVHWWWYTTTTTDDTTYWTWATTH Direction: Forward Position #: 11 Overlap #: 14 Alignment: TWVHWWWYTTTYTDAWWWWTTAHTH ----------WWTAKTTCDKAATT- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM1 Combined Motif Reverse Complement Reverse Complement HAATWAWKAADDAAAAAMWWWHBWA ABAAAAAAWHAAAAARAW HAATWAWKAAWDAAAAAAWDADAAARAW Direction: Forward Position #: 11 Overlap #: 15 Alignment: HAATWAWKAADDAAAAAMWWWHBWA--- ----------ABAAAAAAWHAAAAARAW ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM3 Combined Motif Reverse Complement Original Motif WTKTTTDTDWTTTTTTDWTTYWTWATTH WWHTTTTTCABAAWTTWA WTKTTTDTDWTTTWTTWTTTCWKAAWTWWA Direction: Forward Position #: 13 Overlap #: 16 Alignment: WTKTTTDTDWTTTTTTDWTTYWTWATTH-- ------------WWHTTTTTCABAAWTTWA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 27 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Klf4 Motif 7 Reverse Complement Original Motif GCCYCMCCCD CSKCCCCGCCCCSY CSGCCCCVCCCHSY Direction: Forward Position #: 3 Overlap #: 10 Alignment: --GCCYCMCCCD-- CSKCCCCGCCCCSY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- csGCCCCGCCCCsc Combined Motif Reverse Complement Reverse Complement MSDGGGVGGGGCSG BBGGGGCGGGGCVD MSDGGGVGGGGCGGGGCVD Direction: Forward Position #: 6 Overlap #: 9 Alignment: MSDGGGVGGGGCSG----- -----BBGGGGCGGGGCVD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- cccGCCCCGCCCCsb Combined Motif Original Motif Reverse Complement MSDGGGVGGGGCGGGGCVD BBGGGGCGGGGCGGB MSDGGGVGGGGSGSGGSGCGGB Direction: Forward Position #: 8 Overlap #: 12 Alignment: MSDGGGVGGGGCGGGGCVD--- -------BBGGGGCGGGGCGGB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFF11 Combined Motif Original Motif Original Motif MSDGGGVGGGGSGSGGSGCGGB GGMGGRGGCGGVGC MSDGGGVGGGGVGGGGGSGGVGC Direction: Forward Position #: 10 Overlap #: 13 Alignment: MSDGGGVGGGGSGSGGSGCGGB- ---------GGMGGRGGCGGVGC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM12 Combined Motif Reverse Complement Original Motif GCVCCSCCCCCVCCCCVCCCHSY CYYCBBCYYYTCCHCCTYYY GCVCCSCCCCCBCCBCBCCYCCYCCTYYY Direction: Forward Position #: 10 Overlap #: 14 Alignment: GCVCCSCCCCCVCCCCVCCCHSY------ ---------CYYCBBCYYYTCCHCCTYYY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ Combined Motifs for Top Global Significant Motif ID 44 and Its Best Matches *********************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- dhACATTCTkh TFM3 Original Motif Reverse Complement DHACATTCTGH TWAAWTTVTGAAAAAHWW AAAAHWWTWAMATTCTGW Direction: Backward Position #: 8 Overlap #: 11 Alignment: DHACATTCTGH------- TWAAWTTVTGAAAAAHWW ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 16 Reverse Complement Reverse Complement WCAGAATRTWAWWHTTTT TCAAAATKAWTTGT TCARAATKWWTTDTTTTT Direction: Forward Position #: 1 Overlap #: 14 Alignment: WCAGAATRTWAWWHTTTT TCAAAATKAWTTGT---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif TFM11 Reverse Complement Original Motif AAAAAHAAWWYATTKTGA HDWVAAAHAAAAAMAAAMWWWHBWA HDWVAAAHAAAAMAAAWMATTTTKA Direction: Forward Position #: 8 Overlap #: 18 Alignment: -------AAAAAHAAWWYATTKTGA HDWVAAAHAAAAAMAAAMWWWHBWA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFM13 Combined Motif Reverse Complement Reverse Complement TYAAAATRWTTTYTTTTHTTTVWBH WAHHTVTTYKAAAAWTTRAT TYAAAATRWTTWYTTWTTTTWVAWWTTRAT Direction: Forward Position #: 11 Overlap #: 15 Alignment: TYAAAATRWTTTYTTTTHTTTVWBH----- ----------WAHHTVTTYKAAAAWTTRAT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 6 Combined Motif Original Motif Reverse Complement TYAAAATRWTTWYTTWTTTTWVAWWTTRAT WWTAKTTCDKAATT TYAAAATRWTTWYWTTWTTTYDDAATTRAT Direction: Forward Position #: 14 Overlap #: 14 Alignment: TYAAAATRWTTWYTTWTTTTWVAWWTTRAT -------------WWTAKTTCDKAATT--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ************************************************************ 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 csGCCCCGCCCCsc Reverse Complement Original Motif GCCCCGCC HVGCCCCGCCCCBB HVGCCCCGCCCCBB Direction: Forward Position #: 3 Overlap #: 8 Alignment: --GCCCCGCC---- HVGCCCCGCCCCBB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif cccGCCCCGCCCCsb Reverse Complement Reverse Complement BBGGGGCGGGGCVD BBGGGGCGGGGCGGB BBGGGGCGGGGCGGGGCVD Direction: Forward Position #: 6 Overlap #: 10 Alignment: -----BBGGGGCGGGGCVD BBGGGGCGGGGCGGB---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 7 Combined Motif Reverse Complement Original Motif HVGCCCCGCCCCGCCCCBB CSKCCCCGCCCCSY HVGCCCCSCSCCSCSCCCCSY Direction: Forward Position #: 8 Overlap #: 12 Alignment: HVGCCCCGCCCCGCCCCBB-- -------CSKCCCCGCCCCSY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TFF11 Combined Motif Reverse Complement Original Motif MSGGGGSGSGGSGSGGGGCVD GGMGGRGGCGGVGC MSGGGGSGGGGGGVGGSGSVGC Direction: Forward Position #: 9 Overlap #: 13 Alignment: MSGGGGSGSGGSGSGGGGCVD- --------GGMGGRGGCGGVGC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Klf4 Reverse Complement Reverse Complement GCVSCSCCVCCCCCCSCCCCSY GCCYCMCCCD GCCBCVCCCHCCCCCSCCCCSY Direction: Forward Position #: 1 Overlap #: 10 Alignment: GCVSCSCCVCCCCCCSCCCCSY GCCYCMCCCD------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Zfx Combined Motif Original Motif Original Motif GCCBCVCCCHCCCCCSCCCCSY BBVGCCBVGGCCTV GCCBCVCCCVSVSCCSCSGCCTV Direction: Forward Position #: 10 Overlap #: 13 Alignment: GCCBCVCCCHCCCCCSCCCCSY- ---------BBVGCCBVGGCCTV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 11-21-2023 10:01:18 Runtime: 65.8356 seconds MOTIFSIM is written by Ngoc Tam L. 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