******************************************************************************** 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= GSM4160260-co-BTZ--ETO_WO_2h_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 GSM4160260-co-BTZ--ETO_WO_2h_meme-chip/seqs-centered -oc GSM4160260-co-BTZ--ETO_WO_2h_meme-chip/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 15 -bfile GSM4160260-co-BTZ--ETO_WO_2h_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 0.29 C 0.21 G 0.21 T 0.29 Background letter frequencies (from file GSM4160260-co-BTZ--ETO_WO_2h_meme-chip/background): A 0.292 C 0.208 G 0.208 T 0.292 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF CBCTCTTCCKMTCTN MEME-1 width = 15 sites = 363 llr = 4129 E-value = 2.1e-245 ******************************************************************************** -------------------------------------------------------------------------------- Motif CBCTCTTCCKMTCTN MEME-1 Description -------------------------------------------------------------------------------- Simplified A 11:1:::::15:::2 pos.-specific C 6382a:199131a:3 probability G 14:::::::41:::2 matrix T 2327:9811419:a3 bits 2.3 * * 2.0 * * 1.8 * ** 1.6 * ** ** Relative 1.4 ** ** *** Entropy 1.1 * ** ** *** (16.4 bits) 0.9 * ***** *** 0.7 ******* *** 0.5 * ******** *** 0.2 ************** 0.0 --------------- Multilevel CGCTCTTCCGATCTT consensus TC C TC C sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CBCTCTTCCKMTCTN MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 172000 bayes= 11.1781 E= 2.1e-245 -156 150 -107 -44 -182 46 81 -13 -373 188 -243 -73 -227 -3 -278 127 -1515 225 -524 -672 -573 -207 -623 169 -441 -51 -324 149 -1515 207 -1515 -121 -292 208 -1515 -182 -177 -124 106 43 86 36 -111 -148 -1515 -178 -291 164 -1515 225 -1515 -473 -1515 -1515 -1515 177 -82 46 22 7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CBCTCTTCCKMTCTN MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 363 E= 2.1e-245 0.099174 0.586777 0.099174 0.214876 0.082645 0.286501 0.363636 0.267218 0.022039 0.763085 0.038567 0.176309 0.060606 0.203857 0.030303 0.705234 0.000000 0.991736 0.005510 0.002755 0.005510 0.049587 0.002755 0.942149 0.013774 0.146006 0.022039 0.818182 0.000000 0.873278 0.000000 0.126722 0.038567 0.878788 0.000000 0.082645 0.085399 0.088154 0.432507 0.393939 0.531680 0.267218 0.096419 0.104683 0.000000 0.060606 0.027548 0.911846 0.000000 0.988981 0.000000 0.011019 0.000000 0.000000 0.000000 1.000000 0.165289 0.286501 0.242424 0.305785 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CBCTCTTCCKMTCTN MEME-1 regular expression -------------------------------------------------------------------------------- [CT][GCT]C[TC]CTTCC[GT][AC]TCT[TCG] -------------------------------------------------------------------------------- Time 22.73 secs. ******************************************************************************** ******************************************************************************** MOTIF CCTBCCYCYSYCYCY MEME-2 width = 15 sites = 258 llr = 2430 E-value = 1.7e-050 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCTBCCYCYSYCYCY MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::1:::::2:1:::: pos.-specific C 692499463546477 probability G 1114:111141:12: matrix T 2:721:535143513 bits 2.3 2.0 1.8 * 1.6 * ** Relative 1.4 * ** Entropy 1.1 * ** * (13.6 bits) 0.9 ** ** * * ** 0.7 ** ***** * **** 0.5 ******** ****** 0.2 *************** 0.0 --------------- Multilevel CCTCCCTCTCCCTCC consensus T G CTCGTTC T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTBCCYCYSYCYCY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 172000 bayes= 10.7075 E= 1.7e-050 -1466 163 -84 -28 -1466 209 -110 -391 -171 -10 -204 119 -1466 94 83 -33 -1466 204 -1466 -103 -1466 211 -99 -1466 -424 84 -135 86 -278 151 -104 -15 -81 43 -194 77 -424 140 83 -207 -224 109 -157 55 -307 163 -228 -7 -1466 101 -142 79 -1466 175 -32 -111 -1466 166 -1466 24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTBCCYCYSYCYCY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 258 E= 1.7e-050 0.000000 0.643411 0.116279 0.240310 0.000000 0.883721 0.096899 0.019380 0.089147 0.193798 0.050388 0.666667 0.000000 0.399225 0.368217 0.232558 0.000000 0.856589 0.000000 0.143411 0.000000 0.895349 0.104651 0.000000 0.015504 0.372093 0.081395 0.531008 0.042636 0.593023 0.100775 0.263566 0.166667 0.279070 0.054264 0.500000 0.015504 0.546512 0.368217 0.069767 0.062016 0.441860 0.069767 0.426357 0.034884 0.643411 0.042636 0.279070 0.000000 0.418605 0.077519 0.503876 0.000000 0.697674 0.166667 0.135659 0.000000 0.655039 0.000000 0.344961 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTBCCYCYSYCYCY MEME-2 regular expression -------------------------------------------------------------------------------- [CT]CT[CGT]CC[TC][CT][TC][CG][CT][CT][TC]C[CT] -------------------------------------------------------------------------------- Time 40.66 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCTGBCCTGGAACT MEME-3 width = 15 sites = 43 llr = 685 E-value = 2.7e-044 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCTGBCCTGGAACT MEME-3 Description -------------------------------------------------------------------------------- Simplified A 1:2::::::1199:: pos.-specific C ::7:12aa:1:::9: probability G 9a::83:::791::: matrix T :::a14::a1::::a bits 2.3 * * 2.0 * ** 1.8 * *** ** 1.6 ** * *** * ** Relative 1.4 ** ** *** ***** Entropy 1.1 ***** *** ***** (23.0 bits) 0.9 ***** *** ***** 0.7 ***** ********* 0.5 ***** ********* 0.2 *************** 0.0 --------------- Multilevel GGCTGTCCTGGAACT consensus G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTGBCCTGGAACT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 172000 bayes= 12.2958 E= 2.7e-044 -133 -1207 209 -1207 -1207 -1207 227 -1207 -65 184 -216 -365 -1207 -316 -1207 174 -1207 -116 197 -165 -265 1 65 52 -265 220 -1207 -1207 -1207 227 -1207 -1207 -1207 -1207 -1207 177 -133 -57 165 -165 -207 -216 209 -1207 167 -1207 -157 -1207 167 -316 -1207 -265 -1207 216 -316 -265 -1207 -1207 -1207 177 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTGBCCTGGAACT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 43 E= 2.7e-044 0.116279 0.000000 0.883721 0.000000 0.000000 0.000000 1.000000 0.000000 0.186047 0.744186 0.046512 0.023256 0.000000 0.023256 0.000000 0.976744 0.000000 0.093023 0.813953 0.093023 0.046512 0.209302 0.325581 0.418605 0.046512 0.953488 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.116279 0.139535 0.651163 0.093023 0.069767 0.046512 0.883721 0.000000 0.930233 0.000000 0.069767 0.000000 0.930233 0.023256 0.000000 0.046512 0.000000 0.930233 0.023256 0.046512 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTGBCCTGGAACT MEME-3 regular expression -------------------------------------------------------------------------------- GGCTG[TGC]CCTGGAACT -------------------------------------------------------------------------------- Time 58.83 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: snode048.sibcb.ac.cn ********************************************************************************