******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.1 (Release date: Sat Aug 21 19:23:23 2021 -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= /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_4_peaks/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 /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_4_peaks/seqs-centered -oc /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_4_peaks/meme_out -mod zoops -nmotifs 10 -minw 5 -maxw 20 -bfile /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_4_peaks/background -dna -revcomp -nostatus model: mod= zoops nmotifs= 10 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + - width: minw= 5 maxw= 20 nsites: minsites= 2 maxsites= 10218 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= 1021800 N= 10218 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.189 C 0.311 G 0.311 T 0.189 Background letter frequencies (from file /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_4_peaks/background): A 0.188 C 0.312 G 0.312 T 0.188 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF TTTTDTWTTTTTWKTWKAGA MEME-1 width = 20 sites = 1947 llr = 21802 E-value = 9.8e-226 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTDTWTTTTTWKTWKAGA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 22223241111141251627 pos.-specific C 1:11111121:1:11:112: probability G :1123:111:11141:514: matrix T 77664747687754653323 bits 2.4 2.2 1.9 1.7 Relative 1.4 * Entropy 1.2 ** * * (16.2 bits) 1.0 ** * * **** * * 0.7 **** * ****** ** * * 0.5 **** *********** * * 0.2 ****************** * 0.0 -------------------- Multilevel TTTTTTATTTTTTTTAGAGA consensus AAAAG T AGATTTAT sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTDTWTTTTTWKTWKAGA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 827658 bayes= 10.7159 E= 9.8e-226 26 -225 -285 182 21 -1757 -137 181 21 -254 -162 174 24 -228 -95 155 44 -187 -21 105 0 -131 -314 179 107 -181 -125 103 -80 -240 -109 187 -100 -95 -168 178 -98 -123 -724 203 -33 -308 -182 194 -39 -143 -210 183 107 -924 -210 149 -127 -180 41 115 37 -165 -262 169 141 -624 -287 126 -59 -219 74 61 168 -226 -199 42 22 -83 52 -27 190 -444 -1757 57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTDTWTTTTTWKTWKAGA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 1947 E= 9.8e-226 0.225475 0.065742 0.043143 0.665639 0.217257 0.000000 0.120699 0.662044 0.217771 0.053416 0.101695 0.627119 0.222393 0.064201 0.161274 0.552131 0.255265 0.085259 0.270159 0.389317 0.188495 0.125835 0.035439 0.650231 0.394967 0.088855 0.130971 0.385208 0.107858 0.059065 0.146893 0.686184 0.093991 0.161787 0.097586 0.646636 0.095532 0.133025 0.002054 0.769389 0.149974 0.036980 0.088341 0.724705 0.143297 0.116076 0.072933 0.667694 0.396507 0.000514 0.072933 0.530046 0.078069 0.089368 0.414997 0.417565 0.242938 0.099640 0.050847 0.606574 0.501284 0.004109 0.042630 0.451977 0.124807 0.068310 0.519774 0.287108 0.605033 0.065229 0.078582 0.251156 0.219825 0.175655 0.448382 0.156138 0.705187 0.014381 0.000000 0.280431 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTDTWTTTTTWKTWKAGA MEME-1 regular expression -------------------------------------------------------------------------------- [TA][TA][TA][TA][TGA]T[AT]TTTTT[TA][TG][TA][AT][GT][AT][GA][AT] -------------------------------------------------------------------------------- Time 412.14 secs. ******************************************************************************** ******************************************************************************** MOTIF GTAATCCCAGCWMYTTGG MEME-2 width = 18 sites = 497 llr = 9273 E-value = 2.8e-178 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTAATCCCAGCWMYTTGG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1:a8::::a1:55:::11 pos.-specific C :::::999::9:54:3:: probability G 9::2:::::9::::::89 matrix T :a::a::1:::5:6a7:: bits 2.4 2.2 ** * * * 1.9 ** * * * 1.7 ** * * * Relative 1.4 ***** ** * * * Entropy 1.2 ************ * * (26.9 bits) 1.0 ************ ***** 0.7 ****************** 0.5 ****************** 0.2 ****************** 0.0 ------------------ Multilevel GTAATCCCAGCACTTTGG consensus G TAC C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTAATCCCAGCWMYTTGG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 848094 bayes= 12.8837 E= 2.8e-178 -126 -495 154 -555 -655 -395 -1560 238 234 -495 -311 -655 208 -1560 -62 -1560 -1560 -410 -1560 238 -455 160 -1560 -196 -374 158 -569 -202 -1560 160 -1560 -169 237 -1560 -447 -396 -169 -627 158 -455 -374 160 -569 -246 145 -727 -469 132 128 68 -447 -274 -655 49 -627 156 -655 -328 -627 235 -338 -7 -347 180 -48 -727 144 -338 -185 -1560 159 -455 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTAATCCCAGCWMYTTGG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 497 E= 2.8e-178 0.078471 0.010060 0.907445 0.004024 0.002012 0.020121 0.000000 0.977867 0.951710 0.010060 0.036217 0.002012 0.796781 0.000000 0.203219 0.000000 0.000000 0.018109 0.000000 0.981891 0.008048 0.943662 0.000000 0.048290 0.014085 0.933602 0.006036 0.046278 0.000000 0.941650 0.000000 0.058350 0.973843 0.000000 0.014085 0.012072 0.058350 0.004024 0.929577 0.008048 0.014085 0.945674 0.006036 0.034205 0.515091 0.002012 0.012072 0.470825 0.456740 0.501006 0.014085 0.028169 0.002012 0.438632 0.004024 0.555332 0.002012 0.032193 0.004024 0.961771 0.018109 0.297787 0.028169 0.655936 0.134809 0.002012 0.845070 0.018109 0.052314 0.000000 0.939638 0.008048 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTAATCCCAGCWMYTTGG MEME-2 regular expression -------------------------------------------------------------------------------- GTA[AG]TCCCAGC[AT][CA][TC]T[TC]GG -------------------------------------------------------------------------------- Time 751.92 secs. ******************************************************************************** ******************************************************************************** MOTIF ATCRCTTGARSYCAGGAGKT MEME-3 width = 20 sites = 330 llr = 6470 E-value = 9.0e-149 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATCRCTTGARSYCAGGAGKT MEME-3 Description -------------------------------------------------------------------------------- Simplified A a::5::::a4:::7::a::: pos.-specific C ::8:a3::::668::::::3 probability G ::14:1:a:64::3aa:a5: matrix T :a2::7a::::42:::::57 bits 2.4 * * * 2.2 ** * * * 1.9 ** * * * 1.7 ** * * * Relative 1.4 ** * *** **** Entropy 1.2 ** * *** ***** * (28.3 bits) 1.0 ** ******* ******* * 0.7 ********** ********* 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel ATCACTTGAGCCCAGGAGTT consensus G C AGT G GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCRCTTGARSYCAGGAGKT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 827658 bayes= 13.5459 E= 9.0e-149 237 -1501 -410 -496 -595 -388 -1501 237 -437 130 -236 -20 151 -668 51 -337 -1501 163 -1501 -237 -595 -31 -251 188 -1501 -668 -510 239 -279 -568 163 -1501 239 -668 -568 -595 123 -668 83 -1501 -595 89 27 -205 -1501 98 -1501 103 -315 139 -1501 -20 188 -668 -10 -363 -237 -1501 162 -595 -496 -668 166 -437 240 -668 -668 -1501 -250 -1501 162 -437 -215 -668 53 142 -1501 -6 -468 187 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCRCTTGARSYCAGGAGKT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 330 E= 9.0e-149 0.975758 0.000000 0.018182 0.006061 0.003030 0.021212 0.000000 0.975758 0.009091 0.766667 0.060606 0.163636 0.536364 0.003030 0.442424 0.018182 0.000000 0.963636 0.000000 0.036364 0.003030 0.251515 0.054545 0.690909 0.000000 0.003030 0.009091 0.987879 0.027273 0.006061 0.966667 0.000000 0.987879 0.003030 0.006061 0.003030 0.442424 0.003030 0.554545 0.000000 0.003030 0.575758 0.375758 0.045455 0.000000 0.615152 0.000000 0.384848 0.021212 0.815152 0.000000 0.163636 0.690909 0.003030 0.290909 0.015152 0.036364 0.000000 0.960606 0.003030 0.006061 0.003030 0.981818 0.009091 0.993939 0.003030 0.003030 0.000000 0.033333 0.000000 0.957576 0.009091 0.042424 0.003030 0.451515 0.503030 0.000000 0.300000 0.012121 0.687879 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCRCTTGARSYCAGGAGKT MEME-3 regular expression -------------------------------------------------------------------------------- ATC[AG]C[TC]TGA[GA][CG][CT]C[AG]GGAG[TG][TC] -------------------------------------------------------------------------------- Time 1087.66 secs. ******************************************************************************** ******************************************************************************** MOTIF WCCAGCCTGGSCAACA MEME-4 width = 16 sites = 529 llr = 7874 E-value = 8.6e-089 ******************************************************************************** -------------------------------------------------------------------------------- Motif WCCAGCCTGGSCAACA MEME-4 Description -------------------------------------------------------------------------------- Simplified A 6::a:::::1::7a:9 pos.-specific C :99::99:::47::9: probability G ::::8:::995:2::1 matrix T 411:111a:::2::1: bits 2.4 2.2 * * * 1.9 * * * 1.7 * * * * Relative 1.4 * ** * * Entropy 1.2 **** ***** ** * (21.5 bits) 1.0 ********** **** 0.7 ********** ***** 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel ACCAGCCTGGGCAACA consensus T CTG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCCAGCCTGGSCAACA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 868530 bayes= 12.6902 E= 8.6e-089 165 -337 -504 97 -464 157 -504 -168 -364 156 -504 -168 239 -736 -536 -564 -247 -337 139 -68 -364 157 -578 -188 -464 159 -736 -188 -364 -578 -736 238 -218 -436 159 -564 -53 -578 146 -564 -225 51 66 -294 -283 120 -404 34 197 -578 -37 -347 234 -1569 -356 -318 -405 147 -337 -99 227 -346 -237 -564 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCCAGCCTGGSCAACA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 529 E= 8.6e-089 0.591682 0.030246 0.009452 0.368620 0.007561 0.924386 0.009452 0.058601 0.015123 0.916824 0.009452 0.058601 0.986767 0.001890 0.007561 0.003781 0.034026 0.030246 0.818526 0.117202 0.015123 0.928166 0.005671 0.051040 0.007561 0.939509 0.001890 0.051040 0.015123 0.005671 0.001890 0.977316 0.041588 0.015123 0.939509 0.003781 0.130435 0.005671 0.860113 0.003781 0.039698 0.442344 0.493384 0.024575 0.026465 0.716446 0.018904 0.238185 0.735350 0.005671 0.241966 0.017013 0.952741 0.000000 0.026465 0.020794 0.011342 0.863894 0.030246 0.094518 0.907372 0.028355 0.060491 0.003781 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCCAGCCTGGSCAACA MEME-4 regular expression -------------------------------------------------------------------------------- [AT]CCAGCCTGG[GC][CT][AG]ACA -------------------------------------------------------------------------------- Time 1418.97 secs. ******************************************************************************** ******************************************************************************** MOTIF ATCTCRGCTCACTGCAACCT MEME-5 width = 20 sites = 150 llr = 3482 E-value = 5.5e-093 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATCTCRGCTCACTGCAACCT MEME-5 Description -------------------------------------------------------------------------------- Simplified A a::1:3::::a::1:a8::: pos.-specific C ::a:7::a:a:a1:9::9a: probability G :::::6a::::::9::21:: matrix T :a:931::a:::9:1::::a bits 2.4 * * * 2.2 ** * * * * 1.9 ** * * * * * * 1.7 ** * *** * ** * Relative 1.4 **** *********** ** Entropy 1.2 **** *********** ** (33.5 bits) 1.0 ***** ************** 0.7 ******************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel ATCTCGGCTCACTGCAACCT consensus TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCTCRGCTCACTGCAACCT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 827658 bayes= 13.8616 E= 5.5e-093 235 -1387 -296 -1387 -1387 -322 -1387 236 -1387 165 -1387 -323 -57 -1387 -1387 221 -382 111 -1387 73 82 -454 94 -182 -250 -1387 163 -1387 -482 162 -1387 -250 -1387 -554 -1387 240 -1387 168 -1387 -1387 239 -1387 -1387 -382 -1387 163 -1387 -250 -482 -196 -1387 228 -165 -1387 159 -1387 -1387 160 -1387 -182 240 -1387 -554 -1387 212 -1387 -79 -1387 -323 145 -130 -1387 -1387 165 -1387 -323 -282 -1387 -554 236 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCTCRGCTCACTGCAACCT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 150 E= 5.5e-093 0.960000 0.000000 0.040000 0.000000 0.000000 0.033333 0.000000 0.966667 0.000000 0.980000 0.000000 0.020000 0.126667 0.000000 0.000000 0.873333 0.013333 0.673333 0.000000 0.313333 0.333333 0.013333 0.600000 0.053333 0.033333 0.000000 0.966667 0.000000 0.006667 0.960000 0.000000 0.033333 0.000000 0.006667 0.000000 0.993333 0.000000 1.000000 0.000000 0.000000 0.986667 0.000000 0.000000 0.013333 0.000000 0.966667 0.000000 0.033333 0.006667 0.080000 0.000000 0.913333 0.060000 0.000000 0.940000 0.000000 0.000000 0.946667 0.000000 0.053333 0.993333 0.000000 0.006667 0.000000 0.820000 0.000000 0.180000 0.000000 0.020000 0.853333 0.126667 0.000000 0.000000 0.980000 0.000000 0.020000 0.026667 0.000000 0.006667 0.966667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCTCRGCTCACTGCAACCT MEME-5 regular expression -------------------------------------------------------------------------------- ATCT[CT][GA]GCTCACTGCAACCT -------------------------------------------------------------------------------- Time 1748.46 secs. ******************************************************************************** ******************************************************************************** MOTIF GVGGCBGVGGCVGGRG MEME-6 width = 16 sites = 2816 llr = 22910 E-value = 4.5e-069 ******************************************************************************** -------------------------------------------------------------------------------- Motif GVGGCBGVGGCVGGRG MEME-6 Description -------------------------------------------------------------------------------- Simplified A :41111:4:1:31131 pos.-specific C 13::83:3:1621321 probability G 9399149498248648 matrix T ::::13::::2:::1: bits 2.4 2.2 1.9 1.7 Relative 1.4 * Entropy 1.2 * ** * * (11.7 bits) 1.0 * ** * * * * 0.7 * *** * ** * * 0.5 * *** ***** ** * 0.2 **************** 0.0 ---------------- Multilevel GAGGCGGAGGCGGGGG consensus G T G A CA sequence C C C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVGGCBGVGGCVGGRG MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 868530 bayes= 10.142 E= 4.5e-069 -1810 -241 159 -535 106 -18 4 -392 -93 -392 150 -1810 -178 -1810 159 -473 -141 139 -237 -188 -162 -32 36 62 -241 -301 157 -1810 100 -26 22 -1810 -198 -311 156 -1810 -129 -137 131 -275 -213 105 -103 -22 54 -37 51 -211 -186 -162 144 -1810 -149 -2 101 -1810 52 -76 53 -97 -129 -168 141 -1810 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVGGCBGVGGCVGGRG MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 2816 E= 4.5e-069 0.000000 0.058594 0.936790 0.004616 0.392401 0.275568 0.319602 0.012429 0.098722 0.020597 0.880682 0.000000 0.054688 0.000000 0.938210 0.007102 0.071023 0.817472 0.060369 0.051136 0.061435 0.250000 0.398793 0.289773 0.035511 0.038707 0.925781 0.000000 0.376420 0.261009 0.362571 0.000000 0.047585 0.036222 0.916193 0.000000 0.077060 0.120384 0.774503 0.028054 0.042969 0.643466 0.152344 0.161222 0.273082 0.240412 0.442827 0.043679 0.051847 0.101207 0.846946 0.000000 0.067116 0.306818 0.626065 0.000000 0.270241 0.184659 0.449219 0.095881 0.077060 0.096946 0.825994 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVGGCBGVGGCVGGRG MEME-6 regular expression -------------------------------------------------------------------------------- G[AGC]GGC[GTC]G[AGC]GGC[GAC]G[GC][GA]G -------------------------------------------------------------------------------- Time 2077.01 secs. ******************************************************************************** ******************************************************************************** MOTIF AGGCRTGAGCCACCRY MEME-7 width = 16 sites = 362 llr = 5301 E-value = 2.6e-053 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGGCRTGAGCCACCRY MEME-7 Description -------------------------------------------------------------------------------- Simplified A a:::4:161::a::6: pos.-specific C :::7:222:aa:a8:6 probability G :aa:6:8:9:::::4: matrix T :::3:8:2:::::2:4 bits 2.4 * * 2.2 * * 1.9 * * 1.7 * * Relative 1.4 *** * **** Entropy 1.2 *** * ***** * (21.1 bits) 1.0 **** * ******** 0.7 **************** 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel AGGCGTGAGCCACCAC consensus TA C TGT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGCRTGAGCCACCRY MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 868530 bayes= 13.1133 E= 2.6e-053 239 -1514 -482 -1514 -263 -582 162 -509 -277 -1514 164 -1514 -1514 118 -1514 65 101 -382 90 -351 -1514 -67 -365 205 -151 -99 132 -1514 162 -46 -1514 6 -51 -1514 148 -1514 -1514 165 -523 -351 -1514 162 -1514 -209 240 -1514 -1514 -451 -1514 162 -681 -218 -1514 130 -582 27 166 -1514 38 -1514 -1514 105 -1514 92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGCRTGAGCCACCRY MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 362 E= 2.6e-053 0.988950 0.000000 0.011050 0.000000 0.030387 0.005525 0.958564 0.005525 0.027624 0.000000 0.972376 0.000000 0.000000 0.704420 0.000000 0.295580 0.378453 0.022099 0.582873 0.016575 0.000000 0.196133 0.024862 0.779006 0.066298 0.157459 0.776243 0.000000 0.577348 0.226519 0.000000 0.196133 0.132597 0.000000 0.867403 0.000000 0.000000 0.975138 0.008287 0.016575 0.000000 0.955801 0.000000 0.044199 0.991713 0.000000 0.000000 0.008287 0.000000 0.955801 0.002762 0.041436 0.000000 0.767956 0.005525 0.226519 0.593923 0.000000 0.406077 0.000000 0.000000 0.643646 0.000000 0.356354 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGCRTGAGCCACCRY MEME-7 regular expression -------------------------------------------------------------------------------- AGG[CT][GA]TG[AC]GCCAC[CT][AG][CT] -------------------------------------------------------------------------------- Time 2385.86 secs. ******************************************************************************** ******************************************************************************** MOTIF AGGTCAGGAGTTCGAG MEME-8 width = 16 sites = 96 llr = 1660 E-value = 6.0e-013 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGGTCAGGAGTTCGAG MEME-8 Description -------------------------------------------------------------------------------- Simplified A 91:::a::913::2a: pos.-specific C :::29::::::18::: probability G 19a:::a9:9:::8:a matrix T :1:8::::::792::: bits 2.4 * * 2.2 * * 1.9 * * * * * 1.7 * * ** * * ** Relative 1.4 * ** **** ** ** Entropy 1.2 * ********** ** (24.9 bits) 1.0 ************ *** 0.7 **************** 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel AGGTCAGGAGTTCGAG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGTCAGGAGTTCGAG MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 868530 bayes= 14.7282 E= 6.0e-013 227 -1323 -210 -317 -137 -490 147 -185 -317 -490 164 -1323 -1323 -100 -1323 216 -218 159 -390 -1323 239 -1323 -490 -1323 -417 -1323 167 -1323 -259 -490 160 -417 232 -1323 -390 -218 -118 -490 152 -417 78 -1323 -1323 185 -1323 -258 -490 232 -259 131 -390 -9 -1 -1323 133 -259 239 -1323 -490 -1323 -417 -1323 167 -1323 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGTCAGGAGTTCGAG MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 96 E= 6.0e-013 0.906250 0.000000 0.072917 0.020833 0.072917 0.010417 0.864583 0.052083 0.020833 0.010417 0.968750 0.000000 0.000000 0.156250 0.000000 0.843750 0.041667 0.937500 0.020833 0.000000 0.989583 0.000000 0.010417 0.000000 0.010417 0.000000 0.989583 0.000000 0.031250 0.010417 0.947917 0.010417 0.937500 0.000000 0.020833 0.041667 0.083333 0.010417 0.895833 0.010417 0.322917 0.000000 0.000000 0.677083 0.000000 0.052083 0.010417 0.937500 0.031250 0.770833 0.020833 0.177083 0.187500 0.000000 0.781250 0.031250 0.989583 0.000000 0.010417 0.000000 0.010417 0.000000 0.989583 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGTCAGGAGTTCGAG MEME-8 regular expression -------------------------------------------------------------------------------- AGGTCAGGAG[TA]TCGAG -------------------------------------------------------------------------------- Time 2694.37 secs. ******************************************************************************** ******************************************************************************** MOTIF AGMTWWWWTTWKTWTT MEME-9 width = 16 sites = 69 llr = 946 E-value = 8.4e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGMTWWWWTTWKTWTT MEME-9 Description -------------------------------------------------------------------------------- Simplified A 724:6343233:3712 pos.-specific C ::42:::1:::::::: probability G 36::::::2::4:::1 matrix T :228476667767397 bits 2.4 2.2 1.9 * 1.7 * * Relative 1.4 * **** * *** Entropy 1.2 * **** ******* (19.8 bits) 1.0 * ***** ******* 0.7 * ************* 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel AGCTATTTTTTTTATT consensus GAACTAAAAAAGAT sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGMTWWWWTTWKTWTT MEME-9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 868530 bayes= 15.6407 E= 8.4e-010 191 -1275 -10 -1275 21 -1275 90 11 100 48 -1275 0 -1275 -43 -1275 203 155 -1275 -1275 125 82 -1275 -1275 182 94 -1275 -442 173 62 -126 -442 159 21 -1275 -52 159 76 -442 -442 179 82 -442 -1275 179 -1275 -1275 38 166 47 -1275 -1275 197 179 -1275 -1275 89 -70 -1275 -1275 223 0 -442 -184 191 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGMTWWWWTTWKTWTT MEME-9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 69 E= 8.4e-010 0.710145 0.000000 0.289855 0.000000 0.217391 0.000000 0.579710 0.202899 0.376812 0.434783 0.000000 0.188406 0.000000 0.231884 0.000000 0.768116 0.550725 0.000000 0.000000 0.449275 0.333333 0.000000 0.000000 0.666667 0.362319 0.000000 0.014493 0.623188 0.289855 0.130435 0.014493 0.565217 0.217391 0.000000 0.217391 0.565217 0.318841 0.014493 0.014493 0.652174 0.333333 0.014493 0.000000 0.652174 0.000000 0.000000 0.405797 0.594203 0.260870 0.000000 0.000000 0.739130 0.652174 0.000000 0.000000 0.347826 0.115942 0.000000 0.000000 0.884058 0.188406 0.014493 0.086957 0.710145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGMTWWWWTTWKTWTT MEME-9 regular expression -------------------------------------------------------------------------------- [AG][GAT][CA][TC][AT][TA][TA][TA][TAG][TA][TA][TG][TA][AT]TT -------------------------------------------------------------------------------- Time 3002.53 secs. ******************************************************************************** ******************************************************************************** MOTIF RGGARGRRGGRRRRRGVMRG MEME-10 width = 20 sites = 522 llr = 5209 E-value = 1.3e-015 ******************************************************************************** -------------------------------------------------------------------------------- Motif RGGARGRRGGRRRRRGVMRG MEME-10 Description -------------------------------------------------------------------------------- Simplified A 411841542235453:4531 pos.-specific C :::::12:11::21::23:1 probability G 48925735855544584177 matrix T 21:::1:1:12:::11:2:: bits 2.4 2.2 1.9 1.7 * Relative 1.4 * Entropy 1.2 * (14.4 bits) 1.0 *** * * * * 0.7 **** *** * *** ** 0.5 ********* ********** 0.2 ******************** 0.0 -------------------- Multilevel GGGAGGAGGGGGAAGGGAGG consensus A A GA AAAGGA ACA sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGGARGRRGGRRRRRGVMRG MEME-10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 827658 bayes= 12.3767 E= 1.3e-015 100 -476 51 -16 -47 -476 134 -162 -110 -326 149 -503 214 -1567 -89 -1567 112 -265 80 -1567 -45 -185 117 -137 153 -102 -3 -1567 107 -535 68 -95 -32 -235 134 -1567 16 -142 76 -39 88 -1567 56 4 128 -418 76 -1567 124 -95 34 -1567 139 -162 38 -1567 84 -1567 77 -53 -362 -454 140 -33 92 -33 35 -1567 140 -29 -179 -24 87 -1567 107 -1567 -47 -202 125 -198 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGGARGRRGGRRRRRGVMRG MEME-10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 522 E= 1.3e-015 0.375479 0.011494 0.444444 0.168582 0.136015 0.011494 0.791188 0.061303 0.088123 0.032567 0.873563 0.005747 0.831418 0.000000 0.168582 0.000000 0.408046 0.049808 0.542146 0.000000 0.137931 0.086207 0.703065 0.072797 0.542146 0.153257 0.304598 0.000000 0.396552 0.007663 0.498084 0.097701 0.151341 0.061303 0.787356 0.000000 0.210728 0.116858 0.528736 0.143678 0.346743 0.000000 0.459770 0.193487 0.455939 0.017241 0.526820 0.000000 0.444444 0.160920 0.394636 0.000000 0.492337 0.101533 0.406130 0.000000 0.337165 0.000000 0.532567 0.130268 0.015326 0.013410 0.821839 0.149425 0.356322 0.247126 0.396552 0.000000 0.496169 0.254789 0.090038 0.159004 0.344828 0.000000 0.655172 0.000000 0.136015 0.076628 0.739464 0.047893 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGGARGRRGGRRRRRGVMRG MEME-10 regular expression -------------------------------------------------------------------------------- [GA]GGA[GA]G[AG][GA]G[GA][GA][GA][AG][AG][GA]G[GAC][AC][GA]G -------------------------------------------------------------------------------- Time 3308.28 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (10) found. ******************************************************************************** CPU: cn45 ********************************************************************************