**************************************************************************************************************************************************************************************************** MOTIFSIM - Motif Similarity Detection Tool Version 2.1 **************************************************************************************************************************************************************************************************** INPUT **************************************************************************************************************************************************************************************************** Input Parameters Number of files: 4 Number of top significant motifs: 10 Number of best matches: 5 Similarity cutoff: >= 0.75 Matching motif database: UniProbe Mus Musculus Phylogenetic 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_DM01.txt 51 1 MEME-CHIP_DM01.txt 9 2 PScanChIP_DM01.txt 27 3 RSAT_peak-motifs_DM01.txt 40 4 **************************************************************************************************************************************************************************************************** RESULTS **************************************************************************************************************************************************************************************************** ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 69 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- NKX3-1 ymTACATAyw Original Motif Original Motif ATACTTA HHTACATABD HDTACWTABD Direction: Forward Position #: 2 Overlap #: 7 Alignment: -ATACTTA-- HHTACATABD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Lhx3 Original Motif Reverse Complement HDTACWTABD BMWTAATTAATTW BHWTAMTTAATTW Direction: Forward Position #: 2 Overlap #: 10 Alignment: -HDTACWTABD-- BMWTAATTAATTW ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 10 Reverse Complement Reverse Complement WAATTAARTAWHB TATGTAD TATKTAWRTAWHB Direction: Forward Position #: 1 Overlap #: 7 Alignment: WAATTAARTAWHB TATGTAD------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 34 Original Motif Reverse Complement TATKTAWRTAWHB TAAATAT TAWRTATRTAWHB Direction: Forward Position #: 1 Overlap #: 7 Alignment: TATKTAWRTAWHB TAAATAT------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wtAATTAAtw Reverse Complement Reverse Complement BHWTAMATAKWTA HATTAATTAD DHTTAAWTADWTA Direction: Forward Position #: 1 Overlap #: 10 Alignment: BHWTAMATAKWTA HATTAATTAD--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 94 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- yrTCWCAAyr awAACAcAAwa Reverse Complement Reverse Complement HKTTGTGABH BDTTGTGTTDD HDTTGTGWTHD Direction: Forward Position #: 1 Overlap #: 10 Alignment: HKTTGTGABH- BDTTGTGTTDD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Sox2 Reverse Complement Reverse Complement DHAWCACAADD TTTGCATMACAAWGG DDWDCAYAAVAAWGG Direction: Forward Position #: 1 Overlap #: 11 Alignment: DHAWCACAADD---- TTTGCATMACAAWGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- wwTAATAAww Combined Motif Original Motif Original Motif DDWDCAYAAVAAWGG DHTAATAADD DDDTMATAAHAAWGG Direction: Forward Position #: 2 Overlap #: 10 Alignment: DDWDCAYAAVAAWGG -DHTAATAADD---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pou5f1 Combined Motif Reverse Complement Reverse Complement CCWTTDTTATYADDD ATTTGCATHACAAWG CCWTTDKYATHAHAAWG Direction: Forward Position #: 3 Overlap #: 13 Alignment: CCWTTDTTATYADDD-- --ATTTGCATHACAAWG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- aaACAAAACaa Combined Motif Original Motif Reverse Complement CCWTTDKYATHAHAAWG BHGTTTTGTTT CYWKTTTTRTHWHAAWG Direction: Forward Position #: 2 Overlap #: 11 Alignment: CCWTTDKYATHAHAAWG -BHGTTTTGTTT----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 77 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sox5 SOX9 Reverse Complement Reverse Complement ATTGTTH CMATTGTTH ATTGTTHCM Direction: Backward Position #: 1 Overlap #: 7 Alignment: --ATTGTTH CMATTGTTH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif SRY Reverse Complement Original Motif RGHAACAAT BDWAACAAT DDHAACAAT Direction: Forward Position #: 1 Overlap #: 9 Alignment: RGHAACAAT BDWAACAAT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Sox2 Reverse Complement Reverse Complement ATTGTTHHH TTTGCATMACAAWGG WTTGYWTHACAAWGG Direction: Forward Position #: 1 Overlap #: 9 Alignment: ATTGTTHHH------ TTTGCATMACAAWGG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Foxq1 Original Motif Original Motif WTTGYWTHACAAWGG HATTGTTTATW HATTGTTTADHAAWGG Direction: Forward Position #: 2 Overlap #: 10 Alignment: -WTTGYWTHACAAWGG HATTGTTTATW----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif aaACAAAACaa Original Motif Reverse Complement HATTGTTTADHAAWGG BHGTTTTGTTT HWKTKTTKWDHAAWGG Direction: Forward Position #: 1 Overlap #: 11 Alignment: HATTGTTTADHAAWGG BHGTTTTGTTT----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 53 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 53 Motif 7 Original Motif Reverse Complement TSTGTR TSTSTGTG TSTGTGTG Direction: Forward Position #: 1 Overlap #: 6 Alignment: TSTGTR-- TSTSTGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif awAACAcAAwa Reverse Complement Original Motif CACACASA DDAACACAADV CAMACASAADV Direction: Forward Position #: 1 Overlap #: 8 Alignment: CACACASA--- DDAACACAADV ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 23 Original Motif Reverse Complement CAMACASAADV TACASAR YACASAVAADV Direction: Forward Position #: 1 Overlap #: 7 Alignment: CAMACASAADV TACASAR---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 2 Reverse Complement Reverse Complement BDTTVTSTGTM GTGTGTGT GTKTGTGTGTM Direction: Forward Position #: 1 Overlap #: 8 Alignment: BDTTVTSTGTM GTGTGTGT--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 58 Combined Motif Original Motif Reverse Complement GTKTGTGTGTM TGTGTGTGTGTGTG GTGTGTGTGTVTGTG Direction: Forward Position #: 2 Overlap #: 10 Alignment: GTKTGTGTGTM---- -TGTGTGTGTGTGTG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 102 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ssCkGGYCCCsg csCCaGCTCCCgs Reverse Complement Reverse Complement VVGGGGCCRGBB BVGGGAGCTGGBB BVGGGRGCYGGBB Direction: Forward Position #: 2 Overlap #: 12 Alignment: -VVGGGGCCRGBB BVGGGAGCTGGBB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif cswGGGCCCwsg Reverse Complement Reverse Complement BBCCKGCMCCCVB BBWGGGCCCWVV BBHSGGCCCHVVB Direction: Forward Position #: 1 Overlap #: 12 Alignment: BBCCKGCMCCCVB BBWGGGCCCWVV- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ccCCmCaCCCCcc Combined Motif Reverse Complement Reverse Complement BVVDGGGCCSDBB DBGGGGTGGGGBD BVVDGGGSYGRGGBD Direction: Forward Position #: 3 Overlap #: 11 Alignment: BVVDGGGCCSDBB-- --DBGGGGTGGGGBD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif hsCCAGGCCTGGsr Original Motif Reverse Complement BVVDGGGSYGRGGBD HBCCAGGCCTGGVD BVVCRGGCCKGGBDD Direction: Forward Position #: 1 Overlap #: 14 Alignment: BVVDGGGSYGRGGBD HBCCAGGCCTGGVD- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif cbCCAGCTCmyk Reverse Complement Original Motif HHBCCRGGCCKGVVB BBCCAGCTCMBD HBCCMGSKCCBBVVB Direction: Forward Position #: 1 Overlap #: 12 Alignment: HHBCCRGGCCKGVVB BBCCAGCTCMBD--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 95 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- rmATGCTAww wtATTTTAww Original Motif Original Motif DHATGCTADH DHATTTTAWH DHATKYTAHH Direction: Backward Position #: 1 Overlap #: 10 Alignment: DHATGCTADH DHATTTTAWH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ysCmAGCACwy Original Motif Reverse Complement DHATKYTAHH DHGTGCTRGVH DHRTGCTAGBH Direction: Forward Position #: 1 Overlap #: 10 Alignment: DHATKYTAHH- DHGTGCTRGVH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Pou5f1 Original Motif Reverse Complement DHRTGCTAGBH ATTTGCATHACAAWG DTDTGCWWVDVAAWG Direction: Forward Position #: 1 Overlap #: 11 Alignment: DHRTGCTAGBH---- ATTTGCATHACAAWG ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif asMAAGCTTKst Original Motif Reverse Complement DTDTGCWWVDVAAWG DVCAAGCTTGBH DDYAWGCTTRHVAAWG Direction: Forward Position #: 2 Overlap #: 11 Alignment: -DTDTGCWWVDVAAWG DVCAAGCTTGBH---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif cmCARCACTwr Original Motif Reverse Complement DDYAWGCTTRHVAAWG VHAGTGCTGHB HHARTGCTKDDVAAWG Direction: Forward Position #: 1 Overlap #: 11 Alignment: DDYAWGCTTRHVAAWG VHAGTGCTGHB----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 105 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ccGCAGCCss yvTGCAGsCAcg Reverse Complement Reverse Complement BBGGCTGCGV VBTGSCTGCAVB BBTGGCTGCRVV Direction: Backward Position #: 2 Overlap #: 10 Alignment: -BBGGCTGCGV- VBTGSCTGCAVB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif csCCaGCTCCCgs Reverse Complement Reverse Complement VVKGCAGCCABB BVGGGAGCTGGBB BVGGSAGCCRSBB Direction: Forward Position #: 1 Overlap #: 12 Alignment: VVKGCAGCCABB- BVGGGAGCTGGBB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ssCkGGYCCCsg Original Motif Original Motif BVGGSAGCCRSBB BBCKGGCCCCVV BBCKGGMSCCVVBB Direction: Forward Position #: 2 Overlap #: 11 Alignment: -BVGGSAGCCRSBB BBCKGGCCCCVV-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif cbCCAGCTCmyk Reverse Complement Original Motif BBVVGGSRCCYGBB BBCCAGCTCMBD BBCCRGCTCCBVBB Direction: Forward Position #: 1 Overlap #: 12 Alignment: BBVVGGSRCCYGBB BBCCAGCTCMBD-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif dyCTGCyTCyc Original Motif Original Motif BBCCRGCTCCBVBB DHCTGCYTCHB BBCYGSCTCHBVBB Direction: Forward Position #: 1 Overlap #: 11 Alignment: BBCCRGCTCCBVBB DHCTGCYTCHB--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 24 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 24 Motif 56 Original Motif Original Motif CACGB CACGGA ACACGG Direction: Backward Position #: 2 Overlap #: 5 Alignment: CACGB- CACGGA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif ysCmAGCACwy Reverse Complement Reverse Complement CCGTGT DHGTGCTRGVH BCGTGYTRGVH Direction: Forward Position #: 1 Overlap #: 6 Alignment: CCGTGT----- DHGTGCTRGVH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif crCGyGCRcg Reverse Complement Original Motif HVCMAMCACGB CGCGTGCACG HVCVWRCACGB Direction: Forward Position #: 1 Overlap #: 10 Alignment: HVCMAMCACGB CGCGTGCACG- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 12 Combined Motif Original Motif Original Motif HVCVWRCACGB GCACACAY HGCACACAYGB Direction: Forward Position #: 2 Overlap #: 8 Alignment: HVCVWRCACGB -GCACACAY-- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 7 Original Motif Original Motif HGCACACAYGB CACASASA CRCASACAYGB Direction: Forward Position #: 1 Overlap #: 8 Alignment: HGCACACAYGB CACASASA--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 25 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 25 wtATTTTAww Reverse Complement Reverse Complement WWTAAA HWTAAAATHD WWTAAAATHD Direction: Forward Position #: 1 Overlap #: 6 Alignment: WWTAAA---- HWTAAAATHD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wwATkTTTAww Reverse Complement Original Motif DHATTTTAWW DHATKTTTAHH DHATTTTWAHH Direction: Forward Position #: 1 Overlap #: 10 Alignment: DHATTTTAWW- DHATKTTTAHH ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Foxq1 Original Motif Original Motif DHATTTTWAHH HATTGTTTATW HDATKTTTATW Direction: Forward Position #: 1 Overlap #: 11 Alignment: DHATTTTWAHH HATTGTTTATW ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 3 Combined Motif Reverse Complement Original Motif WATAAAYATDH AWATAMA WAWAWAYATDH Direction: Forward Position #: 2 Overlap #: 7 Alignment: WATAAAYATDH -AWATAMA--- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif Motif 55 Original Motif Original Motif WAWAWAYATDH TTTAAAA TWTAAAAATDH Direction: Forward Position #: 1 Overlap #: 7 Alignment: WAWAWAYATDH TTTAAAA---- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ******************************************************* Combined Motifs for Top Global and Local Significant Motif ID 109 and Its Best Matches ****************************************************** ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1st motif name 2nd motif name 1st format 2nd format 1st motif 2nd motif Combined motif ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- aaCAAAAACaa aaACAAAACaa Reverse Complement Reverse Complement HHGTTTTTGHH BHGTTTTGTTT HHGTTTTKKTT Direction: Backward Position #: 1 Overlap #: 11 Alignment: HHGTTTTTGHH BHGTTTTGTTT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif yaCATAYACay Original Motif Reverse Complement HHGTTTTKKTT DTGTGTATGBD DTGTKTWTGDD Direction: Forward Position #: 1 Overlap #: 11 Alignment: HHGTTTTKKTT DTGTGTATGBD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif wwATkTTTAww Reverse Complement Reverse Complement DDCAWARACAD HHTAAARATHD DHYAAARAYHD Direction: Forward Position #: 1 Overlap #: 11 Alignment: DDCAWARACAD HHTAAARATHD ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Combined Motif FOXF2 Reverse Complement Reverse Complement DHMTKTTTMHD DTTGTTTACSBTBB DTWKTTTWMVDTBB Direction: Forward Position #: 1 Overlap #: 11 Alignment: DHMTKTTTMHD--- DTTGTTTACSBTBB ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- FOXI1 Combined Motif Reverse Complement Reverse Complement BHADVRWAAARWAD AAAMAAAMADBY BHADVVAAAAAHHH Direction: Forward Position #: 3 Overlap #: 12 Alignment: BHADVRWAAARWAD --AAAMAAAMADBY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Results created by MOTIFSIM on 11-19-2016 22:23:05 Runtime: 867.303 seconds MOTIFSIM is written by Ngoc Tam L. 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