**************************************************************************************************************************************************************************************************** MOTIFSIM - Motif Similarity Detection Tool Version 2.2 **************************************************************************************************************************************************************************************************** INPUT **************************************************************************************************************************************************************************************************** Input Parameters Number of files: 1 Number of top significant motifs: 5 Number of best matches: 5 Similarity cutoff: >= 0.5 Matching motif database: None 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 # U20230328-stremeR.txt 365 1 **************************************************************************************************************************************************************************************************** RESULTS **************************************************************************************************************************************************************************************************** ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 318 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 318 Motif 88 Reverse Complement Original Motif CGGGGCTG ACCGGGGCTGCA CACGGGGCTGAC Direction: Backward Position #: 3 Overlap #: 8 Alignment: --CGGGGCTG-- ACCGGGGCTGCA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 183 Original Motif Reverse Complement CACGGGGCTGAC GGCCMGCAGGGCKGGC GGCCMSMMGGGSYKGMC Direction: Forward Position #: 6 Overlap #: 11 Alignment: -----CACGGGGCTGAC GGCCMGCAGGGCKGGC- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 78 Combined Motif Original Motif Original Motif GGCCMSMMGGGSYKGMC CGAGCCCTGCCCCGCGG GGCCMSCVRGSCCTGCCCCGCGG Direction: Forward Position #: 7 Overlap #: 11 Alignment: GGCCMSMMGGGSYKGMC------ ------CGAGCCCTGCCCCGCGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 92 Combined Motif Reverse Complement Original Motif CCGCGGGGCAGGSCKVGSYGGCC GGGGGCTGACCCCCCCACC CCGCGGGGCRGGGSYTGVCSSCCCCACC Direction: Forward Position #: 10 Overlap #: 14 Alignment: CCGCGGGGCAGGSCKVGSYGGCC----- ---------GGGGGCTGACCCCCCCACC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 122 Combined Motif Original Motif Original Motif CCGCGGGGCRGGGSYTGVCSSCCCCACC CCTTGGCCAGCCCAGAAAG CCGCGGGGCRGGSCTTGGCCMSCCCASMAAG Direction: Forward Position #: 13 Overlap #: 16 Alignment: CCGCGGGGCRGGGSYTGVCSSCCCCACC--- ------------CCTTGGCCAGCCCAGAAAG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 156 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 156 Motif 27 Original Motif Original Motif CACTTCCCAGAC CACTTCCCAGACGGGGCG GGGGCGCACTTCCCAGAC Direction: Backward Position #: 7 Overlap #: 12 Alignment: CACTTCCCAGAC------ CACTTCCCAGACGGGGCG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 95 Combined Motif Reverse Complement Reverse Complement GTCTGGGAAGTGCGCCCC CACCTCCCAGACMGGGT GTCTGGGMASYKCSCMSMCMGGGT Direction: Forward Position #: 8 Overlap #: 11 Alignment: GTCTGGGAAGTGCGCCCC------ -------CACCTCCCAGACMGGGT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 45 Combined Motif Original Motif Original Motif GTCTGGGMASYKCSCMSMCMGGGT TGCCCAGTCTGGAAAGTG GTCTGGGMASTGCCCAGTCTGGRWAGTG Direction: Forward Position #: 11 Overlap #: 14 Alignment: GTCTGGGMASYKCSCMSMCMGGGT---- ----------TGCCCAGTCTGGAAAGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 74 Combined Motif Original Motif Original Motif GTCTGGGMASTGCCCAGTCTGGRWAGTG CACTTCCTAGATGG GTCTGGGMASTGCMCWKCCTRGRTRGTG Direction: Forward Position #: 13 Overlap #: 14 Alignment: GTCTGGGMASTGCCCAGTCTGGRWAGTG ------------CACTTCCTAGATGG-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 72 Combined Motif Original Motif Original Motif GTCTGGGMASTGCMCWKCCTRGRTRGTG CGCACTCCTCAGCC GTCTGGGMASTGCGCAYTCYTSAKMSTG Direction: Forward Position #: 13 Overlap #: 14 Alignment: GTCTGGGMASTGCMCWKCCTRGRTRGTG ------------CGCACTCCTCAGCC-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 338 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 338 Motif 68 Reverse Complement Original Motif GGCTGCAG CATGGCGGGCTGCAGGTC CATGGCKGSMKGCAGGTC Direction: Forward Position #: 4 Overlap #: 8 Alignment: ---GGCTGCAG------- CATGGCGGGCTGCAGGTC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 219 Combined Motif Reverse Complement Original Motif GACCTGCRRSCRGCCATG CTGCAGCCTC GACCTGCMKGCAGCCWYG Direction: Forward Position #: 8 Overlap #: 10 Alignment: GACCTGCRRSCRGCCATG -------CTGCAGCCTC- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 149 Reverse Complement Reverse Complement CKWGGCTGCRRGCAGGTC GGGTGCAGGMGGGCTGAGT GGGTGCASGHGGSYKSAGKCAGGTC Direction: Forward Position #: 8 Overlap #: 12 Alignment: -------CKWGGCTGCRRGCAGGTC GGGTGCAGGMGGGCTGAGT------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 89 Combined Motif Original Motif Original Motif GGGTGCASGHGGSYKSAGKCAGGTC GGCTGCGGAGGGTGTA GGGTGCASGHGGCTGCRGDSRGKKYA Direction: Forward Position #: 11 Overlap #: 15 Alignment: GGGTGCASGHGGSYKSAGKCAGGTC- ----------GGCTGCGGAGGGTGTA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 220 Combined Motif Original Motif Reverse Complement GGGTGCASGHGGCTGCRGDSRGKKYA GTGGGTGCAGTGCA GGGTGCASGHGGYKGSTGMAGKGCHA Direction: Forward Position #: 12 Overlap #: 14 Alignment: GGGTGCASGHGGCTGCRGDSRGKKYA -----------GTGGGTGCAGTGCA- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 146 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 146 Motif 1 Reverse Complement Original Motif GGGGTGACAG GGGGTGACAGABGB KGRSWGACRGGGGG Direction: Backward Position #: 1 Overlap #: 10 Alignment: ----GGGGTGACAG GGGGTGACAGABGB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 209 Combined Motif Original Motif Reverse Complement KGRSWGACRGGGGG ATGGGCTGACAG KGRSWRWSRGSKGRCAG Direction: Forward Position #: 6 Overlap #: 9 Alignment: KGRSWGACRGGGGG--- -----ATGGGCTGACAG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 279 Combined Motif Original Motif Original Motif KGRSWRWSRGSKGRCAG GGGGGAGACATCACACR KGRSWRDGGGGAGACAKCACACR Direction: Forward Position #: 7 Overlap #: 11 Alignment: KGRSWRWSRGSKGRCAG------ ------GGGGGAGACATCACACR ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 193 Combined Motif Original Motif Reverse Complement KGRSWRDGGGGAGACAKCACACR GKCTGTACCCCCATTGTAT KGRSWRDGGGKHKRYABCMCMMKTGTAT Direction: Forward Position #: 10 Overlap #: 14 Alignment: KGRSWRDGGGGAGACAKCACACR----- ---------GKCTGTACCCCCATTGTAT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 205 Combined Motif Reverse Complement Reverse Complement ATACARYYGYGVTKMRDYCCCHKWSMCR TGGGCTGCCAGATG ATACARYYGYGVTGVGCTSCCAGATVCR Direction: Forward Position #: 13 Overlap #: 14 Alignment: ATACARYYGYGVTKMRDYCCCHKWSMCR ------------TGGGCTGCCAGATG-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 113 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 113 Motif 74 Reverse Complement Reverse Complement TAGGAAGTG CCATCTAGGAAGTG TAGGAAGTGCCATC Direction: Backward Position #: 1 Overlap #: 9 Alignment: -----TAGGAAGTG CCATCTAGGAAGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 153 Combined Motif Reverse Complement Original Motif GATGGCACTTCCTA CACTAGGGAGTGCC GATGGCACTWSSKAGTGCC Direction: Forward Position #: 6 Overlap #: 9 Alignment: GATGGCACTTCCTA----- -----CACTAGGGAGTGCC ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 156 Combined Motif Reverse Complement Reverse Complement GGCACTRSSWAGTGCCATC GTCTGGGAAGTG GGCACTRGYYWGKGMMRTS Direction: Forward Position #: 8 Overlap #: 12 Alignment: GGCACTRSSWAGTGCCATC -------GTCTGGGAAGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 27 Combined Motif Reverse Complement Original Motif SAMYYCYCWKMCKAGTGCC CACTTCCCAGACGGGGCG SAMYYCYCASHYCMSWGMCGGGGCG Direction: Forward Position #: 8 Overlap #: 12 Alignment: SAMYYCYCWKMCKAGTGCC------ -------CACTTCCCAGACGGGGCG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 339 Combined Motif Original Motif Original Motif SAMYYCYCASHYCMSWGMCGGGGCG CTCACCTCCTGC SAMYYCYCASCTCACHKCCKGSGCG Direction: Forward Position #: 11 Overlap #: 12 Alignment: SAMYYCYCASHYCMSWGMCGGGGCG ----------CTCACCTCCTGC--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 03-28-2023 08:14:22 Runtime: 573.345 seconds MOTIFSIM is written by Ngoc Tam L. 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