******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.5.4 (Release date: Fri Jun 16 12:19:08 2023 -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= SRR20755928_megahit_contigs.fasta 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 -oc SRR20755928_megahit_xstreme/meme_out -mod zoops -minw 6 -maxw 15 -bfile SRR20755928_megahit_xstreme/background -markov_order 2 -seed 0 -dna -revcomp -evt 0.05 -p 6 -nostatus -searchsize 200000 SRR20755928_megahit_contigs.fasta model: mod= zoops nmotifs= 1000 evt= 0.05 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= 139566 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= 104021758 N= 139566 sample: seed= 0 hsfrac= 0 searchsize= 200000 norand= no csites= 1000 Letter frequencies in dataset: A 0.288 C 0.212 G 0.212 T 0.288 Background letter frequencies (from file SRR20755928_megahit_xstreme/background): A 0.288 C 0.212 G 0.212 T 0.288 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF CACACCACACAYACA MEME-1 width = 15 sites = 47428 llr = 765379 E-value = 4.7e-213 ******************************************************************************** -------------------------------------------------------------------------------- Motif CACACCACACAYACA MEME-1 Description -------------------------------------------------------------------------------- Simplified A :a:8:19:a:9:a:7 pos.-specific C 9:a2a917:9:4:93 probability G ::::::::::1:::: matrix T 1::::::3:1:6:1: bits 2.2 * 2.0 * * 1.8 *** * * * 1.6 *** *** ** ** Relative 1.3 *** *** *** ** Entropy 1.1 *************** (23.3 bits) 0.9 *************** 0.7 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel CACACCACACATACA consensus C T C C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACCACACAYACA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 102067834 bayes= 13.3931 E= 4.7e-213 -1215 215 -1130 -236 180 -1171 -1329 -1041 -399 221 -1171 -893 142 11 -630 -790 -751 223 -921 -765 -179 204 -1171 -274 171 -191 -1171 -1093 -353 170 -2218 -2 179 -1097 -707 -1115 -324 207 -374 -215 156 -1171 -52 -898 -1057 78 -1230 114 180 -1097 -997 -1141 -367 209 -2218 -198 137 26 -1071 -1004 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACCACACAYACA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 47428 E= 4.7e-213 0.000063 0.943831 0.000084 0.056022 0.999705 0.000063 0.000021 0.000211 0.018133 0.981214 0.000063 0.000590 0.767458 0.228641 0.002699 0.001202 0.001581 0.996626 0.000358 0.001434 0.082968 0.873956 0.000063 0.043013 0.943219 0.056570 0.000063 0.000148 0.024838 0.691047 0.000000 0.284115 0.998187 0.000105 0.001581 0.000127 0.030530 0.888905 0.015877 0.064688 0.851101 0.000063 0.148267 0.000569 0.000190 0.363709 0.000042 0.636059 0.999578 0.000105 0.000211 0.000105 0.022624 0.904339 0.000000 0.073037 0.744898 0.254702 0.000127 0.000274 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACCACACAYACA MEME-1 regular expression -------------------------------------------------------------------------------- CAC[AC]CCA[CT]ACA[TC]AC[AC] -------------------------------------------------------------------------------- Time 184.96 secs. ******************************************************************************** ******************************************************************************** MOTIF CACACACACCA MEME-2 width = 11 sites = 48152 llr = 660253 E-value = 3.7e-136 ******************************************************************************** -------------------------------------------------------------------------------- Motif CACACACACCA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :a:a:a:91:a pos.-specific C a:7:a:a19a: probability G ::::::::::: matrix T ::3:::::::: bits 2.2 * * 2.0 * * * * 1.8 ** **** ** 1.6 ** ******** Relative 1.3 *********** Entropy 1.1 *********** (19.8 bits) 0.9 *********** 0.7 *********** 0.4 *********** 0.2 *********** 0.0 ----------- Multilevel CACACACACCA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACACACCA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 102626098 bayes= 13.3717 E= 3.7e-136 -2220 217 -380 -326 180 -2220 -2220 -2220 -2220 176 -2220 -2 180 -2220 -2220 -2220 -2220 217 -2220 -266 179 -511 -2220 -2220 -2220 224 -2220 -2220 170 -167 -2220 -2220 -129 206 -2220 -2220 -2220 224 -2220 -2220 178 -2220 -2220 -490 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACACACCA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 48152 E= 3.7e-136 0.000000 0.954685 0.015285 0.030030 1.000000 0.000000 0.000000 0.000000 0.000000 0.716606 0.000000 0.283394 1.000000 0.000000 0.000000 0.000000 0.000000 0.954540 0.000000 0.045460 0.993853 0.006147 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.933398 0.066602 0.000000 0.000000 0.117939 0.882061 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.990364 0.000000 0.000000 0.009636 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACACACCA MEME-2 regular expression -------------------------------------------------------------------------------- CA[CT]ACACACCA -------------------------------------------------------------------------------- Time 363.84 secs. ******************************************************************************** ******************************************************************************** MOTIF TGTGTGGTRTG MEME-3 width = 11 sites = 45432 llr = 604993 E-value = 7.9e-129 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGTGTGGTRTG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :1:1:1::4:: pos.-specific C ::::::::::: probability G :9:9:8a:6:a matrix T a:a:a1:a:a: bits 2.2 * * 2.0 * * * 1.8 **** * ** 1.6 ***** ** ** Relative 1.3 ******** ** Entropy 1.1 *********** (19.2 bits) 0.9 *********** 0.7 *********** 0.4 *********** 0.2 *********** 0.0 ----------- Multilevel TGTGTGGTGTG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGGTRTG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 102626098 bayes= 13.4551 E= 7.9e-129 -2212 -2212 -2212 180 -243 -2212 216 -2212 -2212 -2212 -2212 180 -200 -2212 213 -2212 -2212 -2212 -354 177 -153 -2212 198 -224 -497 -2212 222 -2212 -2212 -2212 -224 173 51 -2212 148 -2212 -2212 -2212 -2212 180 -2212 -2212 224 -2212 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGGTRTG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 45432 E= 7.9e-129 0.000000 0.000000 0.000000 1.000000 0.053420 0.000000 0.946580 0.000000 0.000000 0.000000 0.000000 1.000000 0.072086 0.000000 0.927914 0.000000 0.000000 0.000000 0.018203 0.981797 0.099555 0.000000 0.839628 0.060816 0.009157 0.000000 0.990843 0.000000 0.000000 0.000000 0.044792 0.955208 0.409579 0.000000 0.590421 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGGTRTG MEME-3 regular expression -------------------------------------------------------------------------------- TGTGTGGT[GA]TG -------------------------------------------------------------------------------- Time 546.91 secs. ******************************************************************************** ******************************************************************************** MOTIF GTGTGGTGTGTGTG MEME-4 width = 14 sites = 44782 llr = 690322 E-value = 9.8e-184 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGTGGTGTGTGTG MEME-4 Description -------------------------------------------------------------------------------- Simplified A 1:::12:1:::1:3 pos.-specific C :::::1:::::::: probability G 9:a287:9:9:9:7 matrix T :a:82:a:a:a:a: bits 2.2 2.0 * 1.8 ** * ***** 1.6 *** ******* Relative 1.3 *** ******* Entropy 1.1 ***** ******** (22.2 bits) 0.9 ************** 0.7 ************** 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel GTGTGGTGTGTGTG consensus A A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGTGGTGTGTGTG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 102207400 bayes= 13.476 E= 9.8e-184 -161 -2209 208 -480 -2209 -2209 -2209 180 -352 -2209 220 -2209 -2209 -2209 -35 153 -224 -2209 186 -79 -23 -164 169 -685 -466 -2209 -2209 178 -126 -2209 205 -1165 -444 -2209 -2209 178 -257 -421 215 -2209 -2209 -508 -2209 179 -197 -446 211 -2209 -2209 -2209 -2209 180 20 -2209 165 -2209 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGTGGTGTGTGTG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 44782 E= 9.8e-184 0.094435 0.000000 0.895248 0.010317 0.000000 0.000000 0.000000 1.000000 0.025122 0.000000 0.974878 0.000000 0.000000 0.000000 0.166875 0.833125 0.061074 0.000000 0.772342 0.166585 0.245076 0.067862 0.684561 0.002501 0.011366 0.000000 0.000000 0.988634 0.120182 0.000000 0.879728 0.000089 0.013220 0.000000 0.000000 0.986780 0.048345 0.011478 0.940177 0.000000 0.000000 0.006253 0.000000 0.993747 0.073266 0.009624 0.917110 0.000000 0.000000 0.000000 0.000000 1.000000 0.331740 0.000000 0.668260 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGTGGTGTGTGTG MEME-4 regular expression -------------------------------------------------------------------------------- GTGTG[GA]TGTGTGT[GA] -------------------------------------------------------------------------------- Time 731.99 secs. ******************************************************************************** ******************************************************************************** MOTIF ACACACMTACACACA MEME-5 width = 15 sites = 49833 llr = 738749 E-value = 2.1e-179 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACACACMTACACACA MEME-5 Description -------------------------------------------------------------------------------- Simplified A 7:a:a:6:a:a:a:9 pos.-specific C 39:8:931:9:9:71 probability G ::::::1:::::::: matrix T 11:1:1:8:1:1:3: bits 2.2 2.0 1.8 * **** 1.6 **** ***** Relative 1.3 ***** ***** * Entropy 1.1 ***** ******* (21.4 bits) 0.9 ***** ******** 0.7 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel ACACACATACACACA consensus C C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACACMTACACACA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 102067834 bayes= 13.3145 E= 2.1e-179 118 27 -346 -200 -258 202 -431 -182 173 -223 -744 -1281 -1222 200 -424 -105 179 -1237 -2225 -770 -363 202 -1237 -131 109 63 -188 -1222 -276 -125 -301 155 176 -2225 -324 -2225 -2225 211 -407 -205 180 -1178 -2225 -2225 -1081 210 -2225 -168 180 -1337 -1337 -1100 -1281 171 -2225 8 159 -67 -1237 -1181 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACACMTACACACA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 49833 E= 2.1e-179 0.653362 0.255614 0.019284 0.071740 0.048040 0.859651 0.010696 0.081613 0.953605 0.045131 0.001224 0.000040 0.000060 0.849899 0.011217 0.138824 0.998575 0.000040 0.000000 0.001385 0.023258 0.860514 0.000040 0.116188 0.612967 0.329139 0.057833 0.000060 0.042502 0.089258 0.026268 0.841972 0.977525 0.000000 0.022475 0.000000 0.000000 0.917966 0.012662 0.069372 0.999940 0.000060 0.000000 0.000000 0.000161 0.909718 0.000000 0.090121 0.999819 0.000020 0.000020 0.000140 0.000040 0.696386 0.000000 0.303574 0.866454 0.133426 0.000040 0.000080 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACACMTACACACA MEME-5 regular expression -------------------------------------------------------------------------------- [AC]CACAC[AC]TACACA[CT]A -------------------------------------------------------------------------------- Time 914.51 secs. ******************************************************************************** ******************************************************************************** MOTIF GTRTGTGGTRTGTGT MEME-6 width = 15 sites = 41185 llr = 583191 E-value = 8.8e-134 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTRTGTGGTRTGTGT MEME-6 Description -------------------------------------------------------------------------------- Simplified A 1:4:3:21:5:1:2: pos.-specific C :1::::::2:::::: probability G 8:5:7:79:5:9:8: matrix T :9:a:a1:8:a:a:a bits 2.2 2.0 1.8 * * 1.6 * * * * * * Relative 1.3 ** *** * ***** Entropy 1.1 ** ************ (20.4 bits) 0.9 *************** 0.7 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel GTGTGTGGTGTGTGT consensus A A A A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTRTGTGGTRTGTGT MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 102067834 bayes= 13.588 E= 8.8e-134 -105 -220 194 -2197 -1195 -75 -1209 160 57 -291 136 -1095 -1253 -1209 -232 173 -16 -566 180 -1253 -494 -1009 -290 174 -64 -2197 178 -172 -218 -2197 214 -2197 -738 -31 -268 146 78 -1109 126 -914 -1021 -326 -308 173 -153 -337 201 -348 -1195 -1309 -2197 180 -41 -1109 188 -1353 -2197 -729 -220 173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTRTGTGGTRTGTGT MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 41185 E= 8.8e-134 0.138910 0.046230 0.814860 0.000000 0.000073 0.125920 0.000049 0.873959 0.428044 0.028166 0.543645 0.000146 0.000049 0.000049 0.042491 0.957412 0.257715 0.004201 0.738036 0.000049 0.009348 0.000194 0.028360 0.962098 0.185165 0.000000 0.727546 0.087289 0.063640 0.000000 0.936360 0.000000 0.001724 0.170766 0.033143 0.794367 0.492752 0.000097 0.506641 0.000510 0.000243 0.022144 0.025082 0.952531 0.099866 0.020469 0.853927 0.025738 0.000073 0.000024 0.000000 0.999903 0.216608 0.000097 0.783271 0.000024 0.000000 0.001360 0.046060 0.952580 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTRTGTGGTRTGTGT MEME-6 regular expression -------------------------------------------------------------------------------- GT[GA]T[GA]TGGT[GA]TGT[GA]T -------------------------------------------------------------------------------- Time 1099.42 secs. ******************************************************************************** ******************************************************************************** MOTIF CMCATACACWAMCMC MEME-7 width = 15 sites = 47262 llr = 606367 E-value = 7.1e-094 ******************************************************************************** -------------------------------------------------------------------------------- Motif CMCATACACWAMCMC MEME-7 Description -------------------------------------------------------------------------------- Simplified A 25:9:a19:55514: pos.-specific C 75a12:81912595a probability G ::::::::::::::: matrix T ::::8:1:142::1: bits 2.2 2.0 * 1.8 * * * * * 1.6 * * * * * Relative 1.3 ** **** * * Entropy 1.1 * ** **** ** * (18.5 bits) 0.9 ********* ** * 0.7 ********* **** 0.4 ********** **** 0.2 *************** 0.0 --------------- Multilevel CACATACACAAACCC consensus AC TCC A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CMCATACACWAMCMC MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 102067834 bayes= 13.3906 E= 7.1e-094 -43 178 -332 -296 92 110 -2217 -1141 -2217 218 -248 -1273 166 -166 -1329 -371 -257 -10 -2217 139 180 -2217 -2217 -2217 -159 197 -462 -219 157 -55 -948 -1056 -2217 215 -2217 -236 71 -81 -2217 51 86 15 -272 -45 83 121 -1329 -2217 -220 211 -2217 -384 40 131 -309 -203 -388 217 -1329 -338 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CMCATACACWAMCMC MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 47262 E= 7.1e-094 0.213872 0.727836 0.021307 0.036985 0.543460 0.456434 0.000000 0.000106 0.000000 0.961957 0.038001 0.000042 0.910689 0.067242 0.000021 0.022047 0.048453 0.197452 0.000000 0.754094 1.000000 0.000000 0.000000 0.000000 0.095404 0.832974 0.008654 0.062968 0.855000 0.144514 0.000296 0.000190 0.000000 0.943866 0.000000 0.056134 0.469828 0.120668 0.000000 0.409504 0.522830 0.234776 0.032098 0.210296 0.510727 0.489251 0.000021 0.000000 0.062439 0.917502 0.000000 0.020058 0.378846 0.525750 0.024988 0.070416 0.019614 0.952626 0.000021 0.027739 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CMCATACACWAMCMC MEME-7 regular expression -------------------------------------------------------------------------------- [CA][AC]CATACAC[AT][ACT][AC]C[CA]C -------------------------------------------------------------------------------- Time 1286.18 secs. ******************************************************************************** ******************************************************************************** MOTIF CACATACACYACMYM MEME-8 width = 15 sites = 48901 llr = 570985 E-value = 1.7e-056 ******************************************************************************** -------------------------------------------------------------------------------- Motif CACATACACYACMYM MEME-8 Description -------------------------------------------------------------------------------- Simplified A 17:a:a18:18:4:5 pos.-specific C 637:3:61851a554 probability G ::::::::::1:::: matrix T 3:3:7:2124::151 bits 2.2 * 2.0 * 1.8 * * 1.6 * * * Relative 1.3 ** * * * Entropy 1.1 ***** ** * * (16.8 bits) 0.9 ******** **** 0.7 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel CACATACACCACCCA consensus TCT C T T ATC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACATACACYACMYM MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 102067834 bayes= 13.3416 E= 1.7e-056 -138 148 -1334 4 123 62 -1176 -1278 -1120 181 -2222 -16 179 -1234 -685 -2222 -1097 31 -1334 136 175 -736 -271 -1178 -118 160 -2222 -31 153 -109 -613 -216 -300 192 -743 -83 -147 111 -1102 60 147 -96 -115 -1378 -1219 224 -2222 -1146 48 136 -576 -251 -1061 134 -848 68 79 100 -328 -240 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACATACACYACMYM MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 48901 E= 1.7e-056 0.110345 0.593096 0.000020 0.296538 0.674301 0.325597 0.000061 0.000041 0.000123 0.742459 0.000000 0.257418 0.998119 0.000041 0.001840 0.000000 0.000143 0.263205 0.000020 0.736631 0.966299 0.001288 0.032331 0.000082 0.126787 0.641337 0.000000 0.231877 0.832928 0.099569 0.003027 0.064477 0.035868 0.801456 0.001227 0.161449 0.104231 0.458518 0.000102 0.437149 0.795280 0.109282 0.095417 0.000020 0.000061 0.999836 0.000000 0.000102 0.400810 0.544713 0.003926 0.050551 0.000184 0.538946 0.000593 0.460277 0.498374 0.425186 0.021779 0.054661 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACATACACYACMYM MEME-8 regular expression -------------------------------------------------------------------------------- [CT][AC][CT]A[TC]A[CT]AC[CT]AC[CA][CT][AC] -------------------------------------------------------------------------------- Time 1476.75 secs. ******************************************************************************** ******************************************************************************** MOTIF CMACMYVCACACACC MEME-9 width = 15 sites = 43399 llr = 494322 E-value = 5.5e-025 ******************************************************************************** -------------------------------------------------------------------------------- Motif CMACMYVCACACACC MEME-9 Description -------------------------------------------------------------------------------- Simplified A 34715:42a:a:9:2 pos.-specific C 65395547:9:8:87 probability G ::::::2::::::1: matrix T :1:::4:1:::2::1 bits 2.2 2.0 1.8 * 1.6 * *** Relative 1.3 * ***** Entropy 1.1 * ******* (16.4 bits) 0.9 * *** ******** 0.7 ****** ******** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel CCACACCCACACACC consensus AAC CTAA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CMACMYVCACACACC MEME-9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 102067834 bayes= 13.5209 E= 5.5e-025 9 155 -269 -294 39 137 -444 -216 123 44 -306 -441 -229 207 -417 -291 86 110 -446 -459 -304 131 -423 57 31 84 21 -405 -36 175 -486 -235 173 -356 -431 -403 -292 213 -420 -378 173 -340 -397 -441 -318 191 -478 -83 169 -222 -407 -426 -274 192 -103 -254 -64 181 -394 -236 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CMACMYVCACACACC MEME-9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 43399 E= 5.5e-025 0.306482 0.623102 0.032904 0.037512 0.375930 0.549828 0.009770 0.064472 0.674025 0.286919 0.025508 0.013549 0.059011 0.891011 0.011774 0.038204 0.521948 0.456416 0.009655 0.011982 0.035093 0.527201 0.011291 0.426415 0.356828 0.381138 0.244614 0.017420 0.224890 0.711330 0.007327 0.056453 0.953663 0.017996 0.010691 0.017650 0.037950 0.929515 0.011567 0.020968 0.952879 0.020047 0.013572 0.013503 0.031660 0.798889 0.007742 0.161709 0.926680 0.045646 0.012673 0.015000 0.043135 0.803429 0.103827 0.049609 0.185073 0.745248 0.013802 0.055877 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CMACMYVCACACACC MEME-9 regular expression -------------------------------------------------------------------------------- [CA][CA][AC]C[AC][CT][CAG][CA]ACACACC -------------------------------------------------------------------------------- Time 1661.85 secs. ******************************************************************************** ******************************************************************************** MOTIF ACACACATACA MEME-10 width = 11 sites = 44457 llr = 500220 E-value = 8.7e-037 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACACACATACA MEME-10 Description -------------------------------------------------------------------------------- Simplified A 8:a:9:7:a:8 pos.-specific C 29:9:933:a1 probability G :1::::1:::: matrix T :::111:7::1 bits 2.2 * 2.0 * 1.8 * * * ** 1.6 ***** ** Relative 1.3 ***** ** Entropy 1.1 ****** *** (16.2 bits) 0.9 ****** **** 0.7 *********** 0.4 *********** 0.2 *********** 0.0 ----------- Multilevel ACACACATACA consensus CC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACACATACA MEME-10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 102626098 bayes= 13.4862 E= 8.7e-037 151 -27 -491 -2208 -2208 213 -161 -2208 176 -304 -2208 -2208 -2208 210 -2208 -168 171 -2208 -2208 -230 -2208 208 -2208 -150 120 28 -138 -2208 -2208 34 -2208 135 180 -2208 -2208 -2208 -2208 222 -457 -2208 141 -64 -2208 -151 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACACATACA MEME-10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 44457 E= 8.7e-037 0.816947 0.176013 0.007041 0.000000 0.000000 0.930337 0.069663 0.000000 0.974245 0.025755 0.000000 0.000000 0.000000 0.910430 0.000000 0.089570 0.941719 0.000000 0.000000 0.058281 0.000000 0.898599 0.000000 0.101401 0.661133 0.257507 0.081360 0.000000 0.000000 0.268462 0.000000 0.731538 1.000000 0.000000 0.000000 0.000000 0.000000 0.991048 0.008952 0.000000 0.762805 0.136401 0.000000 0.100794 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACACATACA MEME-10 regular expression -------------------------------------------------------------------------------- ACACAC[AC][TC]ACA -------------------------------------------------------------------------------- Time 1842.48 secs. ******************************************************************************** ******************************************************************************** MOTIF GTRTGGKGTGT MEME-11 width = 11 sites = 34292 llr = 403670 E-value = 7.2e-036 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTRTGGKGTGT MEME-11 Description -------------------------------------------------------------------------------- Simplified A ::5::1:::2: pos.-specific C 1:::::::::: probability G 9:5:993a:82 matrix T :a:a1:7:a:8 bits 2.2 * 2.0 * 1.8 ** ** ** 1.6 ** ** *** Relative 1.3 ** *** *** Entropy 1.1 ********** (17.0 bits) 0.9 *********** 0.7 *********** 0.4 *********** 0.2 *********** 0.0 ----------- Multilevel GTGTGGTGTGT consensus A G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTRTGGKGTGT MEME-11 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 102626098 bayes= 13.8637 E= 7.2e-036 -2171 -88 206 -2171 -2171 -2171 -2171 180 76 -2171 127 -2171 -2171 -423 -2171 178 -2171 -2171 212 -191 -153 -2171 201 -263 -2171 -2171 69 119 -2171 -595 223 -2171 -2171 -2171 -2171 180 -66 -2171 195 -2171 -2171 -210 -41 146 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTRTGGKGTGT MEME-11 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 34292 E= 7.2e-036 0.000000 0.115012 0.884988 0.000000 0.000000 0.000000 0.000000 1.000000 0.488627 0.000000 0.511373 0.000000 0.000000 0.011315 0.000000 0.988685 0.000000 0.000000 0.923656 0.076344 0.099848 0.000000 0.853523 0.046629 0.000000 0.000000 0.343170 0.656830 0.000000 0.003441 0.996559 0.000000 0.000000 0.000000 0.000000 1.000000 0.181821 0.000000 0.818179 0.000000 0.000000 0.049545 0.159308 0.791147 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTRTGGKGTGT MEME-11 regular expression -------------------------------------------------------------------------------- GT[GA]TGG[TG]GTGT -------------------------------------------------------------------------------- Time 2027.14 secs. ******************************************************************************** ******************************************************************************** MOTIF TGTRTGTGTGGKGTR MEME-12 width = 15 sites = 29650 llr = 362912 E-value = 1.6e-024 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGTRTGTGTGGKGTR MEME-12 Description -------------------------------------------------------------------------------- Simplified A :2:4:2:3::21214 pos.-specific C 1:::12::::2:::: probability G 28:6:5:718638:6 matrix T 7:a:91a:82:6:9: bits 2.2 2.0 1.8 * 1.6 ** * ** Relative 1.3 ** * ** * ** Entropy 1.1 **** **** *** (17.7 bits) 0.9 **** **** *** 0.7 ***** ********* 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel TGTGTGTGTGGTGTG consensus G A A A CG A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTRTGTGTGGKGTR MEME-12 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 102067834 bayes= 14.0586 E= 1.6e-024 -387 -188 12 127 -83 -2150 198 -2150 -490 -2150 -2150 178 48 -2150 150 -2150 -718 -164 -2150 169 -30 -46 135 -204 -2150 -440 -261 173 -11 -2150 179 -789 -357 -2150 -69 155 -543 -2150 192 -60 -55 -6 141 -297 -204 -2150 70 102 -85 -2150 199 -2150 -237 -2150 -2150 171 40 -2150 155 -2150 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTRTGTGTGGKGTR MEME-12 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 29650 E= 1.6e-024 0.019663 0.057572 0.230759 0.692007 0.162395 0.000000 0.837605 0.000000 0.009612 0.000000 0.000000 0.990388 0.400944 0.000000 0.599056 0.000000 0.001990 0.068061 0.000000 0.929949 0.233895 0.154098 0.542057 0.069949 0.000000 0.010017 0.034739 0.955245 0.265801 0.000000 0.732985 0.001214 0.024216 0.000000 0.131636 0.844148 0.006678 0.000000 0.803676 0.189646 0.196627 0.203845 0.562698 0.036830 0.069815 0.000000 0.344654 0.585531 0.159325 0.000000 0.840675 0.000000 0.055582 0.000000 0.000000 0.944418 0.380202 0.000000 0.619798 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTRTGTGTGGKGTR MEME-12 regular expression -------------------------------------------------------------------------------- [TG]GT[GA]T[GA]T[GA]TG[GC][TG]GT[GA] -------------------------------------------------------------------------------- Time 2213.70 secs. ******************************************************************************** ******************************************************************************** Stopped because the next motif E-value > 5.00e-02. ******************************************************************************** CPU: alainadev ********************************************************************************