******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.5.1 (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= promoters.fa 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 promoters.fa -dna -mod zoops -nmotifs 5 -minw 4 -maxw 12 -oc meme_results model: mod= zoops nmotifs= 5 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 4 maxw= 12 nsites: minsites= 2 maxsites= 1462 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= 292400 N= 1462 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.373 C 0.14 G 0.161 T 0.327 Background letter frequencies (from file dataset with add-one prior applied): A 0.373 C 0.14 G 0.161 T 0.327 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CTCGSAATGACR MEME-1 width = 12 sites = 225 llr = 3048 E-value = 7.5e-174 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTCGSAATGACR MEME-1 Description -------------------------------------------------------------------------------- Simplified A :2:1:6a::a:5 pos.-specific C 9:9:6:::::a: probability G :1:942::a::5 matrix T 161::1:a:::: bits 2.8 2.6 * * 2.3 * ** * * 2.0 * ** * * Relative 1.7 * *** ** * Entropy 1.4 * *** **** (19.5 bits) 1.1 * *** ****** 0.9 * *** ****** 0.6 * *** ****** 0.3 ************ 0.0 ------------ Multilevel CTCGCAATGACG consensus A GG A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCGSAATGACR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 276318 bayes= 11.934 E= 7.5e-174 -481 273 -1446 -250 -64 -1446 -32 95 -439 269 -1446 -195 -258 -1446 255 -1446 -1446 211 128 -619 77 -297 41 -129 136 -1446 -201 -1446 -1446 -1446 -1446 161 -407 -1446 261 -1446 142 -1446 -1446 -619 -1446 280 -1446 -339 34 -1446 171 -619 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCGSAATGACR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 225 E= 7.5e-174 0.013333 0.928889 0.000000 0.057778 0.240000 0.000000 0.128889 0.631111 0.017778 0.897778 0.000000 0.084444 0.062222 0.000000 0.937778 0.000000 0.000000 0.604444 0.391111 0.004444 0.635556 0.017778 0.213333 0.133333 0.960000 0.000000 0.040000 0.000000 0.000000 0.000000 0.000000 1.000000 0.022222 0.000000 0.977778 0.000000 0.995556 0.000000 0.000000 0.004444 0.000000 0.968889 0.000000 0.031111 0.471111 0.000000 0.524444 0.004444 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCGSAATGACR MEME-1 regular expression -------------------------------------------------------------------------------- C[TA]CG[CG][AG]ATGAC[GA] -------------------------------------------------------------------------------- Time 129.59 secs. ******************************************************************************** ******************************************************************************** MOTIF YGTCATTSCGAG MEME-2 width = 12 sites = 182 llr = 2553 E-value = 2.9e-163 ******************************************************************************** -------------------------------------------------------------------------------- Motif YGTCATTSCGAG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :1::a:1::16: pos.-specific C 6::a::249:1: probability G :9:::::6:9:a matrix T 4:a::a7:1:2: bits 2.8 * 2.6 * * 2.3 * * * * 2.0 * * ** * Relative 1.7 *** *** * Entropy 1.4 ***** *** * (20.2 bits) 1.1 ****** *** * 0.9 ****** *** * 0.6 ********** * 0.3 ************ 0.0 ------------ Multilevel CGTCATTGCGAG consensus T CC T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGTCATTSCGAG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 276318 bayes= 12.4551 E= 2.9e-163 -1415 199 -387 41 -228 -1415 252 -1415 -1415 -1415 -1415 161 -1415 282 -1415 -431 142 -1415 -1415 -1415 -1415 -186 -1415 156 -169 69 -487 100 -1415 136 200 -1415 -1415 274 -1415 -231 -200 -1415 250 -1415 78 -2 -1415 -57 -408 -1415 261 -1415 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGTCATTSCGAG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 182 E= 2.9e-163 0.000000 0.554945 0.010989 0.434066 0.076923 0.000000 0.923077 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.983516 0.000000 0.016484 1.000000 0.000000 0.000000 0.000000 0.000000 0.038462 0.000000 0.961538 0.115385 0.225275 0.005495 0.653846 0.000000 0.357143 0.642857 0.000000 0.000000 0.934066 0.000000 0.065934 0.093407 0.000000 0.906593 0.000000 0.642857 0.137363 0.000000 0.219780 0.021978 0.000000 0.978022 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGTCATTSCGAG MEME-2 regular expression -------------------------------------------------------------------------------- [CT]GTCAT[TC][GC]CG[AT]G -------------------------------------------------------------------------------- Time 248.96 secs. ******************************************************************************** ******************************************************************************** MOTIF KRGATTGCYDCG MEME-3 width = 12 sites = 178 llr = 2138 E-value = 6.7e-103 ******************************************************************************** -------------------------------------------------------------------------------- Motif KRGATTGCYDCG MEME-3 Description -------------------------------------------------------------------------------- Simplified A 15:a:::::3:1 pos.-specific C ::2:::3a5:91 probability G 548:::7::3:8 matrix T 51::aa::5311 bits 2.8 2.6 * 2.3 * * 2.0 * * * Relative 1.7 * * ** * Entropy 1.4 ****** ** (17.3 bits) 1.1 ******* ** 0.9 * ******* ** 0.6 ********* ** 0.3 ************ 0.0 ------------ Multilevel GAGATTGCTTCG consensus TG C CG sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KRGATTGCYDCG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 276318 bayes= 11.6359 E= 6.7e-103 -259 -1412 157 50 34 -1412 129 -128 -1412 12 239 -586 142 -1412 -1412 -1412 -1412 -1412 -1412 161 -1412 -183 -1412 156 -605 101 215 -1412 -1412 277 -1412 -286 -1412 172 -484 71 -25 -1412 107 9 -1412 273 -1412 -216 -273 -105 229 -186 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KRGATTGCYDCG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 178 E= 6.7e-103 0.061798 0.000000 0.477528 0.460674 0.471910 0.000000 0.393258 0.134831 0.000000 0.151685 0.842697 0.005618 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.039326 0.000000 0.960674 0.005618 0.280899 0.713483 0.000000 0.000000 0.955056 0.000000 0.044944 0.000000 0.460674 0.005618 0.533708 0.314607 0.000000 0.337079 0.348315 0.000000 0.926966 0.000000 0.073034 0.056180 0.067416 0.786517 0.089888 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KRGATTGCYDCG MEME-3 regular expression -------------------------------------------------------------------------------- [GT][AG]GATT[GC]C[TC][TGA]CG -------------------------------------------------------------------------------- Time 370.06 secs. ******************************************************************************** ******************************************************************************** MOTIF CGYRGCAATCHM MEME-4 width = 12 sites = 185 llr = 2185 E-value = 1.5e-095 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGYRGCAATCHM MEME-4 Description -------------------------------------------------------------------------------- Simplified A 1:241:aa::33 pos.-specific C 7:4::7:::736 probability G :a:693:::3:: matrix T 1:4:::::9:4: bits 2.8 2.6 * 2.3 * * 2.0 * * * Relative 1.7 * ** * Entropy 1.4 ** **** * (17.0 bits) 1.1 ** ******* * 0.9 ** ******* * 0.6 ********** * 0.3 ************ 0.0 ------------ Multilevel CGCGGCAATCTC consensus TA G GCA sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGYRGCAATCHM MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 276318 bayes= 11.6128 E= 1.5e-095 -186 239 -231 -127 -1418 -1418 264 -1418 -102 160 -1418 27 16 -1418 186 -1418 -265 -1418 255 -1418 -1418 229 89 -392 141 -469 -489 -1418 138 -237 -1418 -1418 -411 -169 -1418 152 -1418 230 96 -1418 -47 119 -1418 33 -11 217 -1418 -359 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGYRGCAATCHM MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 185 E= 1.5e-095 0.102703 0.729730 0.032432 0.135135 0.000000 0.000000 1.000000 0.000000 0.183784 0.421622 0.000000 0.394595 0.416216 0.000000 0.583784 0.000000 0.059459 0.000000 0.940541 0.000000 0.000000 0.681081 0.297297 0.021622 0.989189 0.005405 0.005405 0.000000 0.972973 0.027027 0.000000 0.000000 0.021622 0.043243 0.000000 0.935135 0.000000 0.686486 0.313514 0.000000 0.270270 0.318919 0.000000 0.410811 0.345946 0.627027 0.000000 0.027027 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGYRGCAATCHM MEME-4 regular expression -------------------------------------------------------------------------------- CG[CT][GA]G[CG]AAT[CG][TCA][CA] -------------------------------------------------------------------------------- Time 489.46 secs. ******************************************************************************** ******************************************************************************** MOTIF GAYCVCGGGRTC MEME-5 width = 12 sites = 98 llr = 1290 E-value = 2.1e-034 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAYCVCGGGRTC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :9:14::::6:: pos.-specific C :1573a:::::9 probability G a::13:9784:: matrix T ::51:::32:a1 bits 2.8 * 2.6 * 2.3 * ** 2.0 * ** * Relative 1.7 * ** * * Entropy 1.4 * * ** * ** (19.0 bits) 1.1 **** **** ** 0.9 **** ******* 0.6 ************ 0.3 ************ 0.0 ------------ Multilevel GATCACGGGATC consensus C C TTG sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAYCVCGGGRTC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 276318 bayes= 12.5775 E= 2.1e-034 -519 -277 259 -1326 130 -145 -1326 -341 -1326 178 -1326 67 -139 242 -139 -268 13 123 72 -1326 -1326 284 -1326 -1326 -361 -1326 256 -400 -361 -1326 207 -14 -1326 -377 229 -68 61 -1326 142 -1326 -419 -277 -1326 155 -1326 265 -239 -183 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAYCVCGGGRTC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 98 E= 2.1e-034 0.010204 0.020408 0.969388 0.000000 0.918367 0.051020 0.000000 0.030612 0.000000 0.479592 0.000000 0.520408 0.142857 0.744898 0.061224 0.051020 0.408163 0.326531 0.265306 0.000000 0.000000 1.000000 0.000000 0.000000 0.030612 0.000000 0.948980 0.020408 0.030612 0.000000 0.673469 0.295918 0.000000 0.010204 0.785714 0.204082 0.571429 0.000000 0.428571 0.000000 0.020408 0.020408 0.000000 0.959184 0.000000 0.877551 0.030612 0.091837 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAYCVCGGGRTC MEME-5 regular expression -------------------------------------------------------------------------------- GA[TC]C[ACG]CG[GT][GT][AG]TC -------------------------------------------------------------------------------- Time 608.23 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: kodomo ********************************************************************************