******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.5.2 (Release date: Sun Jan 29 10:33:12 2023 -0800) 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= GSM4160247-ETO--BTZ_WO_meme-chip/seqs-centered CONTROL SEQUENCES= --none-- ALPHABET= ACGT ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme GSM4160247-ETO--BTZ_WO_meme-chip/seqs-centered -oc GSM4160247-ETO--BTZ_WO_meme-chip/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 15 -bfile GSM4160247-ETO--BTZ_WO_meme-chip/background -dna -searchsize 100000 -revcomp -nostatus -mpi 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= 6 maxw= 15 nsites: minsites= 2 maxsites= 2000 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= 200000 N= 2000 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.252 C 0.248 G 0.248 T 0.252 Background letter frequencies (from file GSM4160247-ETO--BTZ_WO_meme-chip/background): A 0.261 C 0.239 G 0.239 T 0.261 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF ACRDACGGWGGRWNG MEME-1 width = 15 sites = 414 llr = 3493 E-value = 3.3e-037 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACRDACGGWGGRWNG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 52547:124::3321 pos.-specific C 2711:9:112::131 probability G 21421197:8a5:38 matrix T 11:21:::5::2521 bits 2.1 * 1.9 * 1.7 ** * 1.4 ** * Relative 1.2 ** ** Entropy 1.0 ** ** * (12.2 bits) 0.8 **** ** * 0.6 * **** ** * 0.4 ** ********* * 0.2 ************* * 0.0 --------------- Multilevel ACAAACGGTGGGTGG consensus G GG AC AAC sequence T A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACRDACGGWGGRWNG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 172000 bayes= 9.85755 E= 3.3e-037 94 -65 -15 -100 -55 149 -150 -200 92 -167 69 -251 72 -172 6 -7 151 -246 -95 -155 -517 196 -182 -1534 -180 -1534 196 -1534 -57 -123 157 -444 44 -79 -662 95 -1534 -23 171 -417 -1534 -1534 207 -1534 22 -272 100 -53 39 -163 -293 107 -17 14 33 -35 -167 -210 176 -223 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACRDACGGWGGRWNG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 414 E= 3.3e-037 0.502415 0.152174 0.214976 0.130435 0.178744 0.671498 0.084541 0.065217 0.495169 0.074879 0.384058 0.045894 0.429952 0.072464 0.248792 0.248792 0.743961 0.043478 0.123188 0.089372 0.007246 0.925121 0.067633 0.000000 0.074879 0.000000 0.925121 0.000000 0.176329 0.101449 0.710145 0.012077 0.355072 0.137681 0.002415 0.504831 0.000000 0.202899 0.782609 0.014493 0.000000 0.000000 1.000000 0.000000 0.304348 0.036232 0.478261 0.181159 0.342995 0.077295 0.031401 0.548309 0.231884 0.263285 0.299517 0.205314 0.082126 0.055556 0.806763 0.055556 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACRDACGGWGGRWNG MEME-1 regular expression -------------------------------------------------------------------------------- [AG]C[AG][AGT]ACGG[TA][GC]G[GA][TA][GCAT]G -------------------------------------------------------------------------------- Time 32.80 secs. ******************************************************************************** ******************************************************************************** MOTIF AAARAAAAAAAWAAA MEME-2 width = 15 sites = 107 llr = 1209 E-value = 1.4e-030 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAARAAAAAAAWAAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 9885a8887984979 pos.-specific C 1::1::1:2:111:1 probability G ::13:::2::12:2: matrix T :21::2::11:3:1: bits 2.1 1.9 * 1.7 * 1.4 * * * * Relative 1.2 * * * * * * Entropy 1.0 ** **** ** * * (16.3 bits) 0.8 *** **** ** *** 0.6 *********** *** 0.4 *********** *** 0.2 *************** 0.0 --------------- Multilevel AAAAAAAAAAAAAAA consensus G T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAARAAAAAAAWAAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 172000 bayes= 11.8371 E= 1.4e-030 172 -135 -1339 -248 159 -1339 -367 -41 157 -267 -150 -135 105 -135 54 -380 194 -1339 -1339 -1339 155 -467 -1339 -22 164 -135 -235 -248 162 -1339 -28 -1339 138 -35 -367 -122 181 -1339 -1339 -164 165 -97 -209 -1339 69 -209 -43 40 176 -109 -1339 -1339 150 -1339 -43 -164 179 -187 -1339 -322 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAARAAAAAAAWAAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 107 E= 1.4e-030 0.859813 0.093458 0.000000 0.046729 0.785047 0.000000 0.018692 0.196262 0.775701 0.037383 0.084112 0.102804 0.542056 0.093458 0.345794 0.018692 1.000000 0.000000 0.000000 0.000000 0.766355 0.009346 0.000000 0.224299 0.813084 0.093458 0.046729 0.046729 0.803738 0.000000 0.196262 0.000000 0.682243 0.186916 0.018692 0.112150 0.915888 0.000000 0.000000 0.084112 0.822430 0.121495 0.056075 0.000000 0.420561 0.056075 0.177570 0.345794 0.887850 0.112150 0.000000 0.000000 0.738318 0.000000 0.177570 0.084112 0.906542 0.065421 0.000000 0.028037 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAARAAAAAAAWAAA MEME-2 regular expression -------------------------------------------------------------------------------- AAA[AG]A[AT]AAAAA[AT]AAA -------------------------------------------------------------------------------- Time 55.60 secs. ******************************************************************************** ******************************************************************************** MOTIF TRYGTGYGTRTGTGT MEME-3 width = 15 sites = 57 llr = 733 E-value = 2.9e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif TRYGTGYGTRTGTGT MEME-3 Description -------------------------------------------------------------------------------- Simplified A :4:::3:::4:112: pos.-specific C 1:6:215:3:31::3 probability G :6:a:6:a:6:9:8: matrix T 9:4:8:5:7:7:9:7 bits 2.1 * * 1.9 * * 1.7 * * 1.4 * * * * Relative 1.2 * * * *** Entropy 1.0 * *** *** **** (18.6 bits) 0.8 *************** 0.6 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel TGCGTGTGTGTGTGT consensus AT AC CAC AC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TRYGTGYGTRTGTGT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 172000 bayes= 13.524 E= 2.9e-014 -1248 -118 -1248 178 63 -1248 128 -389 -1248 140 -1248 50 -1248 -1248 207 -1248 -1248 -44 -276 159 1 -118 140 -1248 -1248 99 -276 91 -1248 -1248 207 -1248 -1248 23 -1248 146 69 -1248 128 -1248 -1248 23 -276 139 -157 -218 185 -1248 -231 -1248 -376 183 -20 -1248 169 -1248 -1248 23 -1248 146 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TRYGTGYGTRTGTGT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 57 E= 2.9e-014 0.000000 0.105263 0.000000 0.894737 0.403509 0.000000 0.578947 0.017544 0.000000 0.631579 0.000000 0.368421 0.000000 0.000000 1.000000 0.000000 0.000000 0.175439 0.035088 0.789474 0.263158 0.105263 0.631579 0.000000 0.000000 0.473684 0.035088 0.491228 0.000000 0.000000 1.000000 0.000000 0.000000 0.280702 0.000000 0.719298 0.421053 0.000000 0.578947 0.000000 0.000000 0.280702 0.035088 0.684211 0.087719 0.052632 0.859649 0.000000 0.052632 0.000000 0.017544 0.929825 0.228070 0.000000 0.771930 0.000000 0.000000 0.280702 0.000000 0.719298 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TRYGTGYGTRTGTGT MEME-3 regular expression -------------------------------------------------------------------------------- T[GA][CT]GT[GA][TC]G[TC][GA][TC]GT[GA][TC] -------------------------------------------------------------------------------- Time 79.39 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: snode023.sibcb.ac.cn ********************************************************************************