******************************************************************************** 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= GSM4160267-RNF4_ETO_ExoT_only_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 GSM4160267-RNF4_ETO_ExoT_only_meme-chip/seqs-centered -oc GSM4160267-RNF4_ETO_ExoT_only_meme-chip/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 15 -bfile GSM4160267-RNF4_ETO_ExoT_only_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 0.249 C 0.251 G 0.251 T 0.249 Background letter frequencies (from file GSM4160267-RNF4_ETO_ExoT_only_meme-chip/background): A 0.263 C 0.237 G 0.237 T 0.263 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF CNWYCCTCCGSYYKB MEME-1 width = 15 sites = 1227 llr = 10178 E-value = 1.1e-513 ******************************************************************************** -------------------------------------------------------------------------------- Motif CNWYCCTCCGSYYKB MEME-1 Description -------------------------------------------------------------------------------- Simplified A 1241:::::::1:12 pos.-specific C 7314aa:87144423 probability G 1311:::::85:142 matrix T 1244::923114534 bits 2.1 * 1.9 ** 1.7 ** 1.5 **** Relative 1.2 **** * Entropy 1.0 ****** (12.0 bits) 0.8 ****** 0.6 * ******* 0.4 * ********* 0.2 * ************ 0.0 --------------- Multilevel CCACCCTCCGGTTGT consensus GTT T CCCTC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CNWYCCTCCGSYYKB MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 172000 bayes= 8.03119 E= 1.1e-513 -150 152 -142 -96 -56 41 23 -20 60 -123 -100 54 -128 80 -160 61 -433 204 -438 -1690 -1690 206 -1690 -501 -733 -226 -428 183 -633 182 -586 -77 -1690 155 -394 14 -1690 -176 179 -128 -338 77 96 -127 -154 85 -246 74 -242 67 -171 93 -133 -51 73 35 -75 22 -27 50 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CNWYCCTCCGSYYKB MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1227 E= 1.1e-513 0.092910 0.682967 0.088835 0.135289 0.178484 0.314588 0.278729 0.228199 0.398533 0.101059 0.118989 0.381418 0.108394 0.414018 0.078240 0.399348 0.013040 0.975550 0.011410 0.000000 0.000000 0.991850 0.000000 0.008150 0.001630 0.049715 0.012225 0.936430 0.003260 0.838631 0.004075 0.154034 0.000000 0.695192 0.015485 0.289324 0.000000 0.070090 0.821516 0.108394 0.025265 0.404238 0.461288 0.109209 0.090465 0.428688 0.043195 0.437653 0.048900 0.378973 0.072535 0.499593 0.104319 0.166259 0.395273 0.334148 0.155664 0.277099 0.197229 0.370008 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CNWYCCTCCGSYYKB MEME-1 regular expression -------------------------------------------------------------------------------- C[CGT][AT][CT]CCTC[CT]G[GC][TC][TC][GT][TC] -------------------------------------------------------------------------------- Time 39.76 secs. ******************************************************************************** ******************************************************************************** MOTIF CCCTAACCCTAACCC MEME-2 width = 15 sites = 134 llr = 2352 E-value = 1.2e-250 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCCTAACCCTAACCC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 23::aa::3:7a::: pos.-specific C 87a:::aa7:::aaa probability G :::::::::3::::: matrix T :::a:::::73:::: bits 2.1 * ** * 1.9 ****** * ** 1.7 ****** **** 1.5 ****** **** Relative 1.2 ********* **** Entropy 1.0 *************** (25.3 bits) 0.8 *************** 0.6 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel CCCTAACCCTAACCC consensus AA AGT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTAACCCTAACCC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 172000 bayes= 11.106 E= 1.2e-250 -9 167 -1371 -1371 7 161 -1371 -1371 -1371 206 -499 -1371 -513 -1371 -1371 192 193 -1371 -1371 -1371 193 -1371 -1371 -1371 -1371 207 -1371 -1371 -1371 207 -1371 -1371 3 162 -1371 -1371 -355 -1371 10 146 149 -1371 -1371 -1 193 -1371 -1371 -1371 -1371 201 -341 -355 -1371 205 -1371 -413 -1371 207 -1371 -1371 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTAACCCTAACCC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 134 E= 1.2e-250 0.246269 0.753731 0.000000 0.000000 0.276119 0.723881 0.000000 0.000000 0.000000 0.992537 0.007463 0.000000 0.007463 0.000000 0.000000 0.992537 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.268657 0.731343 0.000000 0.000000 0.022388 0.000000 0.253731 0.723881 0.738806 0.000000 0.000000 0.261194 1.000000 0.000000 0.000000 0.000000 0.000000 0.955224 0.022388 0.022388 0.000000 0.985075 0.000000 0.014925 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTAACCCTAACCC MEME-2 regular expression -------------------------------------------------------------------------------- [CA][CA]CTAACC[CA][TG][AT]ACCC -------------------------------------------------------------------------------- Time 72.90 secs. ******************************************************************************** ******************************************************************************** MOTIF CCCTAACCCTAACCC MEME-3 width = 15 sites = 96 llr = 1996 E-value = 2.0e-240 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCCTAACCCTAACCC MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::aa::::aa::: pos.-specific C aaa:::aaa:::aaa probability G ::::::::::::::: matrix T :::a:::::a::::: bits 2.1 *** *** *** 1.9 *************** 1.7 *************** 1.5 *************** Relative 1.2 *************** Entropy 1.0 *************** (30.0 bits) 0.8 *************** 0.6 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel CCCTAACCCTAACCC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTAACCCTAACCC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 172000 bayes= 12.3918 E= 2.0e-240 -1323 207 -1323 -1323 -1323 207 -1323 -1323 -1323 207 -1323 -1323 -465 -1323 -1323 191 193 -1323 -1323 -1323 193 -1323 -1323 -1323 -1323 207 -1323 -1323 -1323 206 -451 -1323 -1323 207 -1323 -1323 -465 -1323 -1323 191 193 -1323 -1323 -1323 193 -1323 -1323 -1323 -1323 207 -1323 -1323 -1323 207 -1323 -1323 -1323 207 -1323 -1323 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTAACCCTAACCC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 96 E= 2.0e-240 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.010417 0.000000 0.000000 0.989583 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.989583 0.010417 0.000000 0.000000 1.000000 0.000000 0.000000 0.010417 0.000000 0.000000 0.989583 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTAACCCTAACCC MEME-3 regular expression -------------------------------------------------------------------------------- CCCTAACCCTAACCC -------------------------------------------------------------------------------- Time 96.46 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: snode035.sibcb.ac.cn ********************************************************************************