******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.1 (Release date: Sat Aug 21 19:23:23 2021 -0700) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** PRIMARY SEQUENCES= promotors-test.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 21promotor 1.0000 150 85promotor 1.0000 150 114promotor 1.0000 150 119promotor 1.0000 150 142promotor 1.0000 150 143promotor 1.0000 150 151promotor 1.0000 150 170promotor 1.0000 150 185promotor 1.0000 150 194promotor 1.0000 150 240promotor 1.0000 150 242promotor 1.0000 150 277promotor 1.0000 150 287promotor 1.0000 150 308promotor 1.0000 150 309promotor 1.0000 150 331promotor 1.0000 150 352promotor 1.0000 150 353promotor 1.0000 150 421promotor 1.0000 150 440promotor 1.0000 150 448promotor 1.0000 150 458promotor 1.0000 150 459promotor 1.0000 150 462promotor 1.0000 150 496promotor 1.0000 150 504promotor 1.0000 150 526promotor 1.0000 150 530promotor 1.0000 150 540promotor 1.0000 150 544promotor 1.0000 150 549promotor 1.0000 150 551promotor 1.0000 150 560promotor 1.0000 150 597promotor 1.0000 150 598promotor 1.0000 150 599promotor 1.0000 150 611promotor 1.0000 150 671promotor 1.0000 150 729promotor 1.0000 150 752promotor 1.0000 150 769promotor 1.0000 150 795promotor 1.0000 150 797promotor 1.0000 150 799promotor 1.0000 150 821promotor 1.0000 150 831promotor 1.0000 150 837promotor 1.0000 150 843promotor 1.0000 150 854promotor 1.0000 150 867promotor 1.0000 150 875promotor 1.0000 150 900promotor 1.0000 150 904promotor 1.0000 150 926promotor 1.0000 150 959promotor 1.0000 150 985promotor 1.0000 150 1038promotor 1.0000 150 1048promotor 1.0000 150 1074promotor 1.0000 150 1099promotor 1.0000 150 1103promotor 1.0000 150 1109promotor 1.0000 150 1139promotor 1.0000 150 1205promotor 1.0000 150 1254promotor 1.0000 150 1265promotor 1.0000 150 1273promotor 1.0000 150 1404promotor 1.0000 150 1416promotor 1.0000 150 1508promotor 1.0000 150 1512promotor 1.0000 150 1531promotor 1.0000 150 1547promotor 1.0000 150 1631promotor 1.0000 150 1636promotor 1.0000 150 1648promotor 1.0000 150 1658promotor 1.0000 150 1670promotor 1.0000 150 1695promotor 1.0000 150 1712promotor 1.0000 150 1719promotor 1.0000 150 1723promotor 1.0000 150 1769promotor 1.0000 150 1779promotor 1.0000 150 1790promotor 1.0000 150 1796promotor 1.0000 150 1813promotor 1.0000 150 1827promotor 1.0000 150 1844promotor 1.0000 150 1850promotor 1.0000 150 1851promotor 1.0000 150 1880promotor 1.0000 150 1883promotor 1.0000 150 1932promotor 1.0000 150 1988promotor 1.0000 150 1991promotor 1.0000 150 2025promotor 1.0000 150 2033promotor 1.0000 150 2035promotor 1.0000 150 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme promotors-test.fasta -dna -oc . -nostatus -time 14400 -mod zoops -nmotifs 3 -minw 25 -maxw 60 -objfun classic -markov_order 0 model: mod= zoops nmotifs= 3 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 25 maxw= 60 nsites: minsites= 2 maxsites= 100 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 15000 N= 100 sample: seed= 0 hsfrac= 0 searchsize= 15000 norand= no csites= 1000 Letter frequencies in dataset: A 0.281 C 0.226 G 0.245 T 0.249 Background letter frequencies (from file dataset with add-one prior applied): A 0.281 C 0.226 G 0.245 T 0.249 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GCCGGATGCGGCGTGAACGCCTTATCCGGCCTAC MEME-1 width = 34 sites = 9 llr = 322 E-value = 6.3e-053 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCCGGATGCGGCGTGAACGCCTTATCCGGCCTAC MEME-1 Description -------------------------------------------------------------------------------- Simplified A 1::1:a:22:::::189::::::9:::1212:81 pos.-specific C :8a:::::7::a:1:1:a:8a12::aa:1882:7 probability G 8::9a::81aa:a:7:1:a::1:::::97::121 matrix T 12::::a::::::921:::2:881a::::1:7:1 bits 2.1 * * * * ** 1.9 * *** **** ** * *** 1.7 * *** **** ** * *** 1.5 ***** ***** ** * **** Relative 1.3 ******* ***** ***** ****** * Entropy 1.1 ******** ***** ************ ** * (51.7 bits) 0.9 ********************************* 0.6 ********************************** 0.4 ********************************** 0.2 ********************************** 0.0 ---------------------------------- Multilevel GCCGGATGCGGCGTGAACGCCTTATCCGGCCTAC consensus T AA T T C A ACG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCGGATGCGGCGTGAACGCCTTATCCGGCCTAC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------------------------- 421promotor 1 3.31e-20 . GCCGGATGCGGCGTAAACGCCTTATCCGGCCTAC AAAAGCATGC 540promotor 59 6.20e-20 TGGCGCAGTT GCCGGATGCGGCGTGAACGTCTTATCCGGCCCAC AGGAACTGTA 1404promotor 59 9.36e-20 GGCAACGGCT GTCGGATGCGGCGTGAACGCCTTATCCGACCTAC GGTTCTGTTC 1636promotor 90 1.55e-19 GTGCACGATT GCCGGATGCGGCGTGAACGCCTTATCCGGCCTGG ATGGCTTGCT 530promotor 48 9.53e-19 ACTGAAAGTG GCCGGATGCGGCGTGAACGCCTTTTCCGGTCTAC GCATTAGACA 597promotor 61 2.64e-17 CGTGTATTAT TCCGGATGGGGCGCGAACGCCTTATCCGGCCCAC AAAACCCGCA 1988promotor 77 2.49e-16 GGCAAAGATT ACCGGATGCGGCGTGAACGTCTTATCCACCCGAC AGGTCAGGCG 598promotor 92 2.38e-14 GGTTTTGTGG GCCGGATAAGGCGTTCGCGCCCCATCCGGAATAA TACACGCGCA 1723promotor 106 6.86e-14 CAAACCGTAG GTCAGATAAGGCGTTTACGCCGCATCCGACATGT TTTCCCTCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCGGATGCGGCGTGAACGCCTTATCCGGCCTAC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 421promotor 3.3e-20 [+1]_116 540promotor 6.2e-20 58_[+1]_58 1404promotor 9.4e-20 58_[+1]_58 1636promotor 1.5e-19 89_[+1]_27 530promotor 9.5e-19 47_[+1]_69 597promotor 2.6e-17 60_[+1]_56 1988promotor 2.5e-16 76_[+1]_40 598promotor 2.4e-14 91_[+1]_25 1723promotor 6.9e-14 105_[+1]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCGGATGCGGCGTGAACGCCTTATCCGGCCTAC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCCGGATGCGGCGTGAACGCCTTATCCGGCCTAC width=34 seqs=9 421promotor ( 1) GCCGGATGCGGCGTAAACGCCTTATCCGGCCTAC 1 540promotor ( 59) GCCGGATGCGGCGTGAACGTCTTATCCGGCCCAC 1 1404promotor ( 59) GTCGGATGCGGCGTGAACGCCTTATCCGACCTAC 1 1636promotor ( 90) GCCGGATGCGGCGTGAACGCCTTATCCGGCCTGG 1 530promotor ( 48) GCCGGATGCGGCGTGAACGCCTTTTCCGGTCTAC 1 597promotor ( 61) TCCGGATGGGGCGCGAACGCCTTATCCGGCCCAC 1 1988promotor ( 77) ACCGGATGCGGCGTGAACGTCTTATCCACCCGAC 1 598promotor ( 92) GCCGGATAAGGCGTTCGCGCCCCATCCGGAATAA 1 1723promotor ( 106) GTCAGATAAGGCGTTTACGCCGCATCCGACATGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCGGATGCGGCGTGAACGCCTTATCCGGCCTAC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 34 n= 11700 bayes= 11.1917 E= 6.3e-053 -134 -982 167 -116 -982 178 -982 -16 -982 215 -982 -982 -134 -982 186 -982 -982 -982 203 -982 183 -982 -982 -982 -982 -982 -982 201 -34 -982 167 -982 -34 156 -114 -982 -982 -982 203 -982 -982 -982 203 -982 -982 215 -982 -982 -982 -982 203 -982 -982 -102 -982 184 -134 -982 145 -16 147 -102 -982 -116 166 -982 -114 -982 -982 215 -982 -982 -982 -982 203 -982 -982 178 -982 -16 -982 215 -982 -982 -982 -102 -114 164 -982 -2 -982 164 166 -982 -982 -116 -982 -982 -982 201 -982 215 -982 -982 -982 215 -982 -982 -134 -982 186 -982 -34 -102 145 -982 -134 178 -982 -116 -34 178 -982 -982 -982 -2 -114 142 147 -982 -14 -982 -134 156 -114 -116 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCGGATGCGGCGTGAACGCCTTATCCGGCCTAC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 34 nsites= 9 E= 6.3e-053 0.111111 0.000000 0.777778 0.111111 0.000000 0.777778 0.000000 0.222222 0.000000 1.000000 0.000000 0.000000 0.111111 0.000000 0.888889 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.222222 0.000000 0.777778 0.000000 0.222222 0.666667 0.111111 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.111111 0.000000 0.888889 0.111111 0.000000 0.666667 0.222222 0.777778 0.111111 0.000000 0.111111 0.888889 0.000000 0.111111 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.777778 0.000000 0.222222 0.000000 1.000000 0.000000 0.000000 0.000000 0.111111 0.111111 0.777778 0.000000 0.222222 0.000000 0.777778 0.888889 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.111111 0.000000 0.888889 0.000000 0.222222 0.111111 0.666667 0.000000 0.111111 0.777778 0.000000 0.111111 0.222222 0.777778 0.000000 0.000000 0.000000 0.222222 0.111111 0.666667 0.777778 0.000000 0.222222 0.000000 0.111111 0.666667 0.111111 0.111111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCGGATGCGGCGTGAACGCCTTATCCGGCCTAC MEME-1 regular expression -------------------------------------------------------------------------------- G[CT]CGGAT[GA][CA]GGCGT[GT]AACG[CT]CT[TC]ATCCG[GA]C[CA][TC][AG]C -------------------------------------------------------------------------------- Time 5.79 secs. ******************************************************************************** ******************************************************************************** MOTIF TTCAATATATTGCAGNNHYBTSGWAGGCCTGATAAGCVTVGCGCATCAGSCDATBTTGC MEME-2 width = 59 sites = 5 llr = 243 E-value = 1.7e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTCAATATATTGCAGNNHYBTSGWAGGCCTGATAAGCVTVGCGCATCAGSCDATBTTGC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::a8282a22::82222::2::4a::::::a288:22:4::::8::8:::46::2222 pos.-specific C ::8:::::::::82224464:6:::2:a8:::::2:64:4:8:82:8::46:2:4:::8 probability G :::::::2:::a::622::2248::6a:::a::2:824228:a2:2228622222:26: matrix T aa2:2826:88:2::424446:26:2::2a::8::2::8:22:::8::2:24:84862: bits 2.1 * 1.9 ** * * * * ** *** * 1.7 ** * * * * ** *** * 1.5 **** * ** * ****** *** * Relative 1.3 **** * ***** * * ******* * * **** ** * * * * Entropy 1.1 ******* ****** * ** * ********** * ********** * * * (70.1 bits) 0.9 ******* ****** * **** ********** * ********** * * * 0.6 *************** ******************* * *********** ******* 0.4 *************** ****************************************** 0.2 *************** ******************************************* 0.0 ----------------------------------------------------------- Multilevel TTCAATATATTGCAGTCCCCTCGTAGGCCTGATAAGCCTAGCGCATCAGGCAATCTTGC consensus T TATA AA TCAAATTTAGTA C T AGCTAGGCTT GCGGGTCGTCGTAAAA sequence G CCGA GG T GA G TGG G GT GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAATATATTGCAGNNHYBTSGWAGGCCTGATAAGCVTVGCGCATCAGSCDATBTTGC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------------------------------------- 440promotor 40 7.84e-30 GTCCTGCAGA TTCAATATATTGCAGGTACTGCGTAGGCCTGATAAGCGTAGCGCATCAGGCTATTTTGC ATTTGTCATC 421promotor 48 6.60e-29 AGCATGCAAA TTCAATATATTGCAGAGTTCACGTAGGCCTGATAAGCGTAGCGCATCAGGCAGTTTTGC GTTTGTTCAT 544promotor 1 6.27e-28 . TTCAATATATTGCAATCTTCTGGTAGGCCTGATAAGCATCGCGCATCAGGCAAGCTTAC ATTTGTCATC 1723promotor 26 1.08e-18 GGCGTTTACG TTTATTAAATAGCAGCCCCTTGTAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGC CTACAACGAT 448promotor 5 4.12e-18 CACA TTCAAATGAATGTCCTACCGTCGAACGCTTGAAAATGCTGGCGGATGAGCGGCTGTATA AGAGTAAGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAATATATTGCAGNNHYBTSGWAGGCCTGATAAGCVTVGCGCATCAGSCDATBTTGC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 440promotor 7.8e-30 39_[+2]_52 421promotor 6.6e-29 47_[+2]_44 544promotor 6.3e-28 [+2]_91 1723promotor 1.1e-18 25_[+2]_66 448promotor 4.1e-18 4_[+2]_87 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAATATATTGCAGNNHYBTSGWAGGCCTGATAAGCVTVGCGCATCAGSCDATBTTGC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTCAATATATTGCAGNNHYBTSGWAGGCCTGATAAGCVTVGCGCATCAGSCDATBTTGC width=59 seqs=5 440promotor ( 40) TTCAATATATTGCAGGTACTGCGTAGGCCTGATAAGCGTAGCGCATCAGGCTATTTTGC 1 421promotor ( 48) TTCAATATATTGCAGAGTTCACGTAGGCCTGATAAGCGTAGCGCATCAGGCAGTTTTGC 1 544promotor ( 1) TTCAATATATTGCAATCTTCTGGTAGGCCTGATAAGCATCGCGCATCAGGCAAGCTTAC 1 1723promotor ( 26) TTTATTAAATAGCAGCCCCTTGTAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGC 1 448promotor ( 5) TTCAAATGAATGTCCTACCGTCGAACGCTTGAAAATGCTGGCGGATGAGCGGCTGTATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAATATATTGCAGNNHYBTSGWAGGCCTGATAAGCVTVGCGCATCAGSCDATBTTGC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 59 n= 9200 bayes= 11.0964 E= 1.7e-011 -897 -897 -897 201 -897 -897 -897 201 -897 182 -897 -31 183 -897 -897 -897 151 -897 -897 -31 -49 -897 -897 168 151 -897 -897 -31 -49 -897 -29 127 183 -897 -897 -897 -49 -897 -897 168 -49 -897 -897 168 -897 -897 203 -897 -897 182 -897 -31 151 -17 -897 -897 -49 -17 129 -897 -49 -17 -29 69 -49 82 -29 -31 -49 82 -897 69 -897 141 -897 69 -897 82 -29 69 -49 -897 -29 127 -897 141 71 -897 -897 -897 171 -31 51 -897 -897 127 183 -897 -897 -897 -897 -17 129 -31 -897 -897 203 -897 -897 215 -897 -897 -897 182 -897 -31 -897 -897 -897 201 -897 -897 203 -897 183 -897 -897 -897 -49 -897 -897 168 151 -897 -29 -897 151 -17 -897 -897 -897 -897 171 -31 -49 141 -29 -897 -49 82 71 -897 -897 -897 -29 168 51 82 -29 -897 -897 -897 171 -31 -897 182 -897 -31 -897 -897 203 -897 -897 182 -29 -897 151 -17 -897 -897 -897 -897 -29 168 -897 182 -29 -897 151 -897 -29 -897 -897 -897 171 -31 -897 82 129 -897 -897 141 -29 -31 51 -897 -29 69 109 -17 -29 -897 -897 -897 -29 168 -897 82 -29 69 -49 -897 -897 168 -49 -897 -29 127 -49 -897 129 -31 -49 182 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAATATATTGCAGNNHYBTSGWAGGCCTGATAAGCVTVGCGCATCAGSCDATBTTGC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 59 nsites= 5 E= 1.7e-011 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 1.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.200000 0.000000 0.000000 0.800000 0.800000 0.000000 0.000000 0.200000 0.200000 0.000000 0.200000 0.600000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.800000 0.200000 0.000000 0.000000 0.200000 0.200000 0.600000 0.000000 0.200000 0.200000 0.200000 0.400000 0.200000 0.400000 0.200000 0.200000 0.200000 0.400000 0.000000 0.400000 0.000000 0.600000 0.000000 0.400000 0.000000 0.400000 0.200000 0.400000 0.200000 0.000000 0.200000 0.600000 0.000000 0.600000 0.400000 0.000000 0.000000 0.000000 0.800000 0.200000 0.400000 0.000000 0.000000 0.600000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.600000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.800000 0.800000 0.000000 0.200000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.200000 0.600000 0.200000 0.000000 0.200000 0.400000 0.400000 0.000000 0.000000 0.000000 0.200000 0.800000 0.400000 0.400000 0.200000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.800000 0.200000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.400000 0.600000 0.000000 0.000000 0.600000 0.200000 0.200000 0.400000 0.000000 0.200000 0.400000 0.600000 0.200000 0.200000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.400000 0.200000 0.400000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.200000 0.600000 0.200000 0.000000 0.600000 0.200000 0.200000 0.800000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAATATATTGCAGNNHYBTSGWAGGCCTGATAAGCVTVGCGCATCAGSCDATBTTGC MEME-2 regular expression -------------------------------------------------------------------------------- TT[CT]A[AT][TA][AT][TAG]A[TA][TA]G[CT][AC][GAC][TACG][CAGT][CTA][CT][CTG][TAG][CG][GT][TA]A[GCT]GC[CT]TGA[TA][AG][AC][GT][CAG][CGA][TG][ACG][GT][CT]G[CG][AC][TG][CG][AG][GT][GC][CGT][ATG][ACG][TG][CTG][TA][TAG][GAT][CA] -------------------------------------------------------------------------------- Time 11.67 secs. ******************************************************************************** ******************************************************************************** MOTIF VSGNKHWAVSYCGCATYCGGCATBA MEME-3 width = 25 sites = 10 llr = 174 E-value = 2.6e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif VSGNKHWAVSYCGCATYCGGCATBA MEME-3 Description -------------------------------------------------------------------------------- Simplified A 41:313674:::::8::2:::a2:7 pos.-specific C 2323:31:355a17::65::9::4: probability G 358261:235::91::11a9:::32 matrix T 11:23331::5::22a32:11:831 bits 2.1 * 1.9 * * * * 1.7 * * * ** 1.5 ** * **** Relative 1.3 * ** * ***** Entropy 1.1 * **** ** ***** (25.1 bits) 0.9 * ******** ***** 0.6 * * ** ******** ***** * 0.4 ** * *********** ******* 0.2 *** * ******************* 0.0 ------------------------- Multilevel AGGAGAAAACCCGCATCCGGCATCA consensus GCCCTCTGCGT TT TA AGG sequence C G T G T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VSGNKHWAVSYCGCATYCGGCATBA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------- 799promotor 120 4.40e-13 CTGCCGGGTA AGGCGTTACGCCGCATCCGGCATCA AATGAC 287promotor 120 3.11e-10 CGATAACCGG ATGCGAAAACTCGCATCCGGCAATA GCGCAA 540promotor 24 1.00e-09 CTGAAAAGAC GCGTTTAGCGTCGCATCAGGCATTA TGGCGCAGTT 1636promotor 56 4.81e-09 CCTGATAAGA CGCGGCAGCGTCGCATCAGGCATTG TGCACGATTG 1254promotor 116 1.02e-08 ATTCAAACAA GGGAGATAGCTCCCTTTTGGCATGA AGAAGTAAAA 599promotor 106 1.11e-08 AGGGTAAGTT TGGATTTAAGCCGGATGCGGCATCA CATGCCGCAT 21promotor 126 1.20e-08 CATCTTATCC AGCAACCAGGTCGCATCCGGCAAGA 1531promotor 19 1.74e-08 TTTAATCGTT CAGGGGAAGCCCGCATCGGGCATCT GGATGAGGTA 729promotor 18 1.74e-08 CGGGCTTCGC ACGTTCAAACCCGTTTTCGGTATCA TAATCAGCAT 185promotor 63 7.80e-08 GTTGTTATCG GCGCGAATACCCGTATTTGTCATGG TGCCGTTATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VSGNKHWAVSYCGCATYCGGCATBA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 799promotor 4.4e-13 119_[+3]_6 287promotor 3.1e-10 119_[+3]_6 540promotor 1e-09 23_[+3]_102 1636promotor 4.8e-09 55_[+3]_70 1254promotor 1e-08 115_[+3]_10 599promotor 1.1e-08 105_[+3]_20 21promotor 1.2e-08 125_[+3] 1531promotor 1.7e-08 18_[+3]_107 729promotor 1.7e-08 17_[+3]_108 185promotor 7.8e-08 62_[+3]_63 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VSGNKHWAVSYCGCATYCGGCATBA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF VSGNKHWAVSYCGCATYCGGCATBA width=25 seqs=10 799promotor ( 120) AGGCGTTACGCCGCATCCGGCATCA 1 287promotor ( 120) ATGCGAAAACTCGCATCCGGCAATA 1 540promotor ( 24) GCGTTTAGCGTCGCATCAGGCATTA 1 1636promotor ( 56) CGCGGCAGCGTCGCATCAGGCATTG 1 1254promotor ( 116) GGGAGATAGCTCCCTTTTGGCATGA 1 599promotor ( 106) TGGATTTAAGCCGGATGCGGCATCA 1 21promotor ( 126) AGCAACCAGGTCGCATCCGGCAAGA 1 1531promotor ( 19) CAGGGGAAGCCCGCATCGGGCATCT 1 729promotor ( 18) ACGTTCAAACCCGTTTTCGGTATCA 1 185promotor ( 63) GCGCGAATACCCGTATTTGTCATGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VSGNKHWAVSYCGCATYCGGCATBA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 25 n= 12600 bayes= 8.83138 E= 2.6e-003 51 -17 29 -131 -149 41 103 -131 -997 -17 171 -997 9 41 -29 -31 -149 -997 129 27 9 41 -129 27 109 -117 -997 27 132 -997 -29 -131 51 41 29 -997 -997 115 103 -997 -997 115 -997 101 -997 215 -997 -997 -997 -117 188 -997 -997 163 -129 -31 151 -997 -997 -31 -997 -997 -997 201 -997 141 -129 27 -49 115 -129 -31 -997 -997 203 -997 -997 -997 188 -131 -997 199 -997 -131 183 -997 -997 -997 -49 -997 -997 169 -997 82 29 27 132 -997 -29 -131 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VSGNKHWAVSYCGCATYCGGCATBA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 25 nsites= 10 E= 2.6e-003 0.400000 0.200000 0.300000 0.100000 0.100000 0.300000 0.500000 0.100000 0.000000 0.200000 0.800000 0.000000 0.300000 0.300000 0.200000 0.200000 0.100000 0.000000 0.600000 0.300000 0.300000 0.300000 0.100000 0.300000 0.600000 0.100000 0.000000 0.300000 0.700000 0.000000 0.200000 0.100000 0.400000 0.300000 0.300000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.100000 0.900000 0.000000 0.000000 0.700000 0.100000 0.200000 0.800000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.100000 0.300000 0.200000 0.500000 0.100000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.900000 0.100000 0.000000 0.900000 0.000000 0.100000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.400000 0.300000 0.300000 0.700000 0.000000 0.200000 0.100000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VSGNKHWAVSYCGCATYCGGCATBA MEME-3 regular expression -------------------------------------------------------------------------------- [AGC][GC][GC][ACGT][GT][ACT][AT][AG][ACG][CG][CT]CG[CT][AT]T[CT][CAT]GGCA[TA][CGT][AG] -------------------------------------------------------------------------------- Time 17.40 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21promotor 2.53e-06 125_[+3(1.20e-08)] 85promotor 1.40e-01 150 114promotor 5.16e-01 150 119promotor 1.01e-02 150 142promotor 2.42e-01 150 143promotor 8.88e-01 150 151promotor 9.91e-01 150 170promotor 1.02e-01 150 185promotor 3.36e-04 62_[+3(7.80e-08)]_63 194promotor 5.94e-01 150 240promotor 5.12e-01 150 242promotor 6.57e-02 150 277promotor 9.69e-01 150 287promotor 3.16e-06 119_[+3(3.11e-10)]_6 308promotor 4.31e-01 150 309promotor 3.16e-01 150 331promotor 4.16e-03 63_[+2(3.26e-05)]_28 352promotor 9.21e-01 150 353promotor 6.50e-03 91_[+3(2.21e-05)]_34 421promotor 1.39e-41 [+1(3.31e-20)]_13_[+2(6.60e-29)]_44 440promotor 4.96e-26 39_[+2(7.84e-30)]_52 448promotor 4.92e-14 4_[+2(4.12e-18)]_87 458promotor 8.94e-01 150 459promotor 9.85e-01 150 462promotor 2.64e-01 150 496promotor 8.72e-01 150 504promotor 1.22e-01 150 526promotor 4.34e-01 150 530promotor 4.46e-17 47_[+1(9.53e-19)]_69 540promotor 2.69e-22 23_[+3(1.00e-09)]_10_[+1(6.20e-20)]_\ 58 544promotor 1.64e-24 [+2(6.27e-28)]_91 549promotor 4.29e-01 150 551promotor 7.49e-02 21_[+1(6.18e-05)]_95 560promotor 4.49e-01 150 597promotor 1.44e-13 60_[+1(2.64e-17)]_56 598promotor 2.17e-14 91_[+1(2.38e-14)]_25 599promotor 6.91e-05 105_[+3(1.11e-08)]_20 611promotor 4.47e-01 150 671promotor 1.28e-01 150 729promotor 1.59e-04 17_[+3(1.74e-08)]_108 752promotor 4.52e-01 150 769promotor 5.49e-01 150 795promotor 3.06e-01 150 797promotor 2.10e-01 150 799promotor 2.49e-10 119_[+3(4.40e-13)]_6 821promotor 3.76e-01 150 831promotor 5.56e-01 150 837promotor 2.48e-01 150 843promotor 9.16e-01 150 854promotor 5.84e-02 150 867promotor 7.19e-01 150 875promotor 4.79e-01 150 900promotor 3.46e-01 150 904promotor 7.15e-01 150 926promotor 2.91e-02 150 959promotor 8.89e-01 150 985promotor 8.39e-01 150 1038promotor 9.66e-01 150 1048promotor 8.96e-01 150 1074promotor 9.13e-01 150 1099promotor 1.43e-02 150 1103promotor 5.09e-01 150 1109promotor 5.67e-01 150 1139promotor 3.07e-01 150 1205promotor 5.80e-01 150 1254promotor 9.89e-06 115_[+3(1.02e-08)]_10 1265promotor 4.75e-01 150 1273promotor 1.22e-01 150 1404promotor 2.85e-19 30_[+3(2.09e-06)]_3_[+1(9.36e-20)]_\ 29_[+3(2.09e-06)]_4 1416promotor 2.24e-02 120_[+3(4.98e-05)]_5 1508promotor 7.27e-01 150 1512promotor 3.48e-01 150 1531promotor 1.40e-05 18_[+3(1.74e-08)]_107 1547promotor 6.58e-01 150 1631promotor 3.99e-01 150 1636promotor 6.14e-21 55_[+3(4.81e-09)]_9_[+1(1.55e-19)]_\ 27 1648promotor 4.79e-01 150 1658promotor 7.51e-01 150 1670promotor 2.34e-01 150 1695promotor 9.31e-02 150 1712promotor 4.47e-01 150 1719promotor 4.81e-01 150 1723promotor 1.71e-28 25_[+2(1.08e-18)]_21_[+1(6.86e-14)]_\ 11 1769promotor 3.11e-01 150 1779promotor 4.78e-01 150 1790promotor 1.68e-01 150 1796promotor 2.46e-01 150 1813promotor 2.46e-01 150 1827promotor 3.85e-01 150 1844promotor 5.44e-01 150 1850promotor 2.14e-01 150 1851promotor 9.12e-01 150 1880promotor 4.43e-01 150 1883promotor 1.41e-01 150 1932promotor 2.20e-01 150 1988promotor 2.73e-12 76_[+1(2.49e-16)]_40 1991promotor 1.40e-02 150 2025promotor 7.26e-01 150 2033promotor 3.14e-01 150 2035promotor 4.01e-01 150 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************