******************************************************************************** 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_d0_TRIM1_0_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_d0_TRIM1_0_peaks/seqs-centered -oc /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d0_TRIM1_0_peaks/meme_out -mod zoops -nmotifs 10 -minw 5 -maxw 20 -bfile /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d0_TRIM1_0_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= 15721 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= 1572100 N= 15721 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.198 C 0.302 G 0.302 T 0.198 Background letter frequencies (from file /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d0_TRIM1_0_peaks/background): A 0.196 C 0.304 G 0.304 T 0.196 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF WAMWAAAAAWAMAAAAAHWW MEME-1 width = 20 sites = 2847 llr = 30940 E-value = 4.3e-247 ******************************************************************************** -------------------------------------------------------------------------------- Motif WAMWAAAAAWAMAAAAAHWW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 36356777746477776455 pos.-specific C 1:511:1:1114111112:: probability G :11:11121:111:111:11 matrix T 53141211152111:12454 bits 2.3 2.1 1.9 1.6 Relative 1.4 Entropy 1.2 * (15.7 bits) 0.9 ** * * * **** ** 0.7 ** ******** ***** ** 0.5 ** ******** ******** 0.2 ******************** 0.0 -------------------- Multilevel TACAAAAAATAAAAAAAAAA consensus ATAT A C TTT sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAMWAAAAAWAMAAAAAHWW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1273401 bayes= 10.8876 E= 4.3e-247 74 -128 -1812 148 171 -875 -189 49 46 63 -103 -84 126 -123 -390 96 172 -153 -110 -87 178 -285 -129 -30 177 -222 -119 -57 187 -476 -89 -84 174 -192 -133 -46 116 -254 -284 125 166 -237 -119 -6 105 31 -171 -65 184 -241 -160 -50 181 -130 -290 -43 193 -112 -206 -240 184 -157 -192 -75 158 -169 -111 -15 105 -57 -363 90 126 -585 -220 122 142 -975 -132 85 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAMWAAAAAWAMAAAAAHWW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 2847 E= 4.3e-247 0.326660 0.124693 0.000000 0.548648 0.642079 0.000702 0.081841 0.275378 0.269758 0.471725 0.149280 0.109238 0.468563 0.129610 0.020372 0.381454 0.645592 0.105374 0.141553 0.107482 0.674043 0.042150 0.123990 0.159817 0.669477 0.065332 0.132771 0.132420 0.714787 0.011240 0.164384 0.109589 0.656481 0.080084 0.121180 0.142255 0.439059 0.052336 0.042501 0.466105 0.620302 0.058658 0.133123 0.187917 0.404988 0.376888 0.093080 0.125044 0.703899 0.057253 0.100457 0.138391 0.690200 0.123288 0.040745 0.145767 0.749912 0.140148 0.072708 0.037232 0.701089 0.102564 0.080084 0.116263 0.587987 0.094134 0.141201 0.176677 0.404988 0.205128 0.024587 0.365297 0.471022 0.005269 0.066034 0.457675 0.525114 0.000351 0.121531 0.353003 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAMWAAAAAWAMAAAAAHWW MEME-1 regular expression -------------------------------------------------------------------------------- [TA][AT][CA][AT]AAAAA[TA]A[AC]AAAAA[ATC][AT][AT] -------------------------------------------------------------------------------- Time 420.04 secs. ******************************************************************************** ******************************************************************************** MOTIF GTAATCCCAGCWMYTYGGGA MEME-2 width = 20 sites = 741 llr = 14237 E-value = 7.9e-186 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTAATCCCAGCWMYTYGGGA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1:97::::91:55:::21:9 pos.-specific C :::::999::9:55:3:::: probability G 9:13:::::9::::::8991 matrix T :9::a111:::5:596:::: bits 2.3 2.1 * 1.9 ** * * * * 1.6 ** * * * * Relative 1.4 ** ****** * * Entropy 1.2 ************ * *** (27.7 bits) 0.9 ******************** 0.7 ******************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GTAATCCCAGCACTTTGGGA consensus G TAC C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTAATCCCAGCWMYTYGGGA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1273401 bayes= 12.9492 E= 7.9e-186 -123 -357 154 -438 -460 -373 -381 227 221 -435 -206 -618 188 -581 -19 -460 -486 -423 -581 231 -486 162 -623 -186 -560 160 -549 -148 -486 159 -1618 -138 227 -681 -349 -301 -194 -464 162 -718 -401 159 -329 -233 131 -373 -464 129 128 69 -481 -318 -560 67 -481 136 -438 -296 -449 226 -318 9 -329 167 -15 -449 138 -338 -183 -449 160 -401 -201 -464 161 -386 224 -581 -253 -372 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTAATCCCAGCWMYTYGGGA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 741 E= 7.9e-186 0.083671 0.025641 0.881242 0.009447 0.008097 0.022942 0.021592 0.947368 0.909582 0.014845 0.072874 0.002699 0.720648 0.005398 0.265857 0.008097 0.006748 0.016194 0.005398 0.971660 0.006748 0.935223 0.004049 0.053981 0.004049 0.919028 0.006748 0.070175 0.006748 0.917679 0.000000 0.075574 0.946019 0.002699 0.026991 0.024291 0.051282 0.012146 0.935223 0.001350 0.012146 0.917679 0.031039 0.039136 0.485830 0.022942 0.012146 0.479082 0.476383 0.491228 0.010796 0.021592 0.004049 0.481781 0.010796 0.503374 0.009447 0.039136 0.013495 0.937922 0.021592 0.323887 0.031039 0.623482 0.176788 0.013495 0.790823 0.018893 0.055331 0.013495 0.919028 0.012146 0.048583 0.012146 0.925776 0.013495 0.927126 0.005398 0.052632 0.014845 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTAATCCCAGCWMYTYGGGA MEME-2 regular expression -------------------------------------------------------------------------------- GTA[AG]TCCCAGC[AT][CA][TC]T[TC]GGGA -------------------------------------------------------------------------------- Time 765.92 secs. ******************************************************************************** ******************************************************************************** MOTIF CTCGAMCTCCTGRSCTCAAG MEME-3 width = 20 sites = 575 llr = 9971 E-value = 2.6e-141 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTCGAMCTCCTGRSCTCAAG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::286:::::151:::961 pos.-specific C 9:82:3a:992::57:9::: probability G :::52::::::954:::129 matrix T 1a21:1:a:18:::3a::1: bits 2.3 * 2.1 * * * 1.9 * * * 1.6 * * * * Relative 1.4 * * ***** *** Entropy 1.2 ** * ****** *** * (25.0 bits) 0.9 *** * ******* **** * 0.7 *** ********* ****** 0.5 *** **************** 0.2 ******************** 0.0 -------------------- Multilevel CTCGAACTCCTGACCTCAAG consensus A C C GGT G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCGAMCTCCTGRSCTCAAG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1273401 bayes= 12.9033 E= 2.6e-141 -450 158 -386 -173 -582 -364 -586 230 -523 135 -345 -2 18 -58 62 -86 201 -486 -68 -450 159 -3 -386 -112 -523 166 -744 -265 -401 -375 -1581 230 -1581 164 -586 -201 -423 162 -744 -186 -682 -57 -464 199 -67 -645 152 -682 137 -545 65 -482 -191 69 53 -350 -401 121 -464 47 -682 -545 -1581 234 -1581 164 -645 -201 216 -645 -140 -523 167 -345 -46 -63 -161 -513 159 -401 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCGAMCTCCTGRSCTCAAG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 575 E= 2.6e-141 0.008696 0.911304 0.020870 0.059130 0.003478 0.024348 0.005217 0.966957 0.005217 0.773913 0.027826 0.193043 0.222609 0.203478 0.466087 0.107826 0.791304 0.010435 0.189565 0.008696 0.591304 0.297391 0.020870 0.090435 0.005217 0.961739 0.001739 0.031304 0.012174 0.022609 0.000000 0.965217 0.000000 0.946087 0.005217 0.048696 0.010435 0.933913 0.001739 0.053913 0.001739 0.205217 0.012174 0.780870 0.123478 0.003478 0.871304 0.001739 0.507826 0.006957 0.478261 0.006957 0.052174 0.490435 0.440000 0.017391 0.012174 0.704348 0.012174 0.271304 0.001739 0.006957 0.000000 0.991304 0.000000 0.947826 0.003478 0.048696 0.876522 0.003478 0.114783 0.005217 0.624348 0.027826 0.220870 0.126957 0.064348 0.008696 0.914783 0.012174 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCGAMCTCCTGRSCTCAAG MEME-3 regular expression -------------------------------------------------------------------------------- CTC[GAC]A[AC]CTCC[TC]G[AG][CG][CT]TCA[AG]G -------------------------------------------------------------------------------- Time 1110.16 secs. ******************************************************************************** ******************************************************************************** MOTIF AACATGGTGAAACCCCRTCT MEME-4 width = 20 sites = 355 llr = 7437 E-value = 2.4e-115 ******************************************************************************** -------------------------------------------------------------------------------- Motif AACATGGTGAAACCCCRTCT MEME-4 Description -------------------------------------------------------------------------------- Simplified A 9a:a:3:12a8a::::4::: pos.-specific C ::9:1::3::::a897::a: probability G 1:::279:8:2:::::6::: matrix T ::1:7::7:::::213:a:a bits 2.3 * * * * 2.1 * * * * * * 1.9 * * * * * * 1.6 ** * * * *** Relative 1.4 ** * * **** * *** Entropy 1.2 **** * ***** * *** (30.2 bits) 0.9 **** *************** 0.7 ******************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel AACATGGTGAAACCCCGTCT consensus A C G TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACATGGTGAAACCCCRTCT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1273401 bayes= 14.0668 E= 2.4e-115 214 -475 -126 -1512 232 -443 -575 -1512 -266 158 -575 -180 231 -443 -475 -1512 -231 -133 -75 175 63 -675 119 -1512 -222 -575 164 -612 -180 -9 -675 174 -10 -1512 142 -612 234 -575 -675 -1512 195 -1512 -34 -1512 234 -675 -675 -1512 -412 167 -675 -354 -454 140 -443 -17 -512 160 -675 -148 -331 115 -1512 63 93 -1512 104 -612 -1512 -443 -1512 233 -1512 170 -675 -454 -612 -1512 -517 233 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACATGGTGAAACCCCRTCT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 355 E= 2.4e-115 0.861972 0.011268 0.126761 0.000000 0.980282 0.014085 0.005634 0.000000 0.030986 0.907042 0.005634 0.056338 0.974648 0.014085 0.011268 0.000000 0.039437 0.121127 0.180282 0.659155 0.304225 0.002817 0.692958 0.000000 0.042254 0.005634 0.949296 0.002817 0.056338 0.284507 0.002817 0.656338 0.183099 0.000000 0.814085 0.002817 0.991549 0.005634 0.002817 0.000000 0.760563 0.000000 0.239437 0.000000 0.994366 0.002817 0.002817 0.000000 0.011268 0.969014 0.002817 0.016901 0.008451 0.802817 0.014085 0.174648 0.005634 0.921127 0.002817 0.070423 0.019718 0.676056 0.000000 0.304225 0.374648 0.000000 0.622535 0.002817 0.000000 0.014085 0.000000 0.985915 0.000000 0.988732 0.002817 0.008451 0.002817 0.000000 0.008451 0.988732 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACATGGTGAAACCCCRTCT MEME-4 regular expression -------------------------------------------------------------------------------- AACAT[GA]G[TC]GA[AG]ACCC[CT][GA]TCT -------------------------------------------------------------------------------- Time 1450.15 secs. ******************************************************************************** ******************************************************************************** MOTIF AGGCRTGMGCCACCRYGCCC MEME-5 width = 20 sites = 640 llr = 10294 E-value = 1.0e-108 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGGCRTGMGCCACCRYGCCC MEME-5 Description -------------------------------------------------------------------------------- Simplified A a:1:4:152::a::6:3::: pos.-specific C :::7:323:aa:a8:6:996 probability G :a9:6:7:8:::::3:7::: matrix T :::3:7:2:::::2:4:1:3 bits 2.3 2.1 * * 1.9 * * 1.6 * ** Relative 1.4 ** **** * Entropy 1.2 *** ***** * ** (23.2 bits) 0.9 *** ** ******* *** 0.7 ****** ************ 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel AGGCGTGAGCCACCACGCCC consensus TAC CA GTA T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGCRTGMGCCACCRYGCCC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1273401 bayes= 13.017 E= 1.0e-108 231 -380 -528 -1597 -222 -760 165 -697 -197 -502 160 -339 -288 112 -414 60 91 -528 102 -497 -465 8 -414 174 -71 -100 122 -339 124 2 -502 17 3 -660 139 -1597 -439 164 -1597 -227 -697 170 -1597 -380 230 -760 -414 -397 -1597 165 -460 -245 -272 135 -402 -14 171 -502 19 -597 -297 95 -390 90 58 -560 116 -316 -339 157 -390 -172 -439 163 -602 -211 -272 108 -480 70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGCRTGMGCCACCRYGCCC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 640 E= 1.0e-108 0.970313 0.021875 0.007812 0.000000 0.042188 0.001563 0.954688 0.001563 0.050000 0.009375 0.921875 0.018750 0.026562 0.659375 0.017188 0.296875 0.368750 0.007812 0.617188 0.006250 0.007812 0.320312 0.017188 0.654687 0.120313 0.151562 0.709375 0.018750 0.462500 0.307812 0.009375 0.220312 0.200000 0.003125 0.796875 0.000000 0.009375 0.950000 0.000000 0.040625 0.001563 0.984375 0.000000 0.014063 0.968750 0.001563 0.017188 0.012500 0.000000 0.951562 0.012500 0.035937 0.029687 0.773438 0.018750 0.178125 0.640625 0.009375 0.346875 0.003125 0.025000 0.587500 0.020313 0.367188 0.293750 0.006250 0.678125 0.021875 0.018750 0.901563 0.020313 0.059375 0.009375 0.940625 0.004687 0.045312 0.029687 0.640625 0.010937 0.318750 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGCRTGMGCCACCRYGCCC MEME-5 regular expression -------------------------------------------------------------------------------- AGG[CT][GA][TC]G[ACT][GA]CCACC[AG][CT][GA]CC[CT] -------------------------------------------------------------------------------- Time 1788.29 secs. ******************************************************************************** ******************************************************************************** MOTIF ATYCTCCYGCCTCRGC MEME-6 width = 16 sites = 600 llr = 9188 E-value = 1.5e-092 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATYCTCCYGCCTCRGC MEME-6 Description -------------------------------------------------------------------------------- Simplified A a:::2:::3::::6:: pos.-specific C ::68:994:a9:8::9 probability G ::::2:::7::::4a: matrix T :a4161:6::1a2::: bits 2.3 * 2.1 ** * 1.9 ** * 1.6 ** * Relative 1.4 ** ** *** ** Entropy 1.2 ** ** ******* (22.1 bits) 0.9 **** *********** 0.7 **************** 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel ATCCTCCTGCCTCAGC consensus T G CA TG sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATYCTCCYGCCTCRGC MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 1336285 bayes= 13.2965 E= 1.5e-092 228 -1587 -305 -456 -688 -405 -1587 232 -1587 106 -1587 90 -356 145 -470 -45 11 -551 -45 151 -1587 162 -1587 -156 -1587 163 -405 -218 -1587 42 -419 156 36 -1587 125 -297 -488 165 -1587 -229 -1587 164 -1587 -188 -1587 -1587 -1587 235 -1587 140 -1587 3 168 -1587 28 -1587 -271 -551 166 -1587 -388 164 -1587 -229 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATYCTCCYGCCTCRGC MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 600 E= 1.5e-092 0.955000 0.000000 0.036667 0.008333 0.001667 0.018333 0.000000 0.980000 0.000000 0.633333 0.000000 0.366667 0.016667 0.828333 0.011667 0.143333 0.211667 0.006667 0.221667 0.560000 0.000000 0.933333 0.000000 0.066667 0.000000 0.938333 0.018333 0.043333 0.000000 0.406667 0.016667 0.576667 0.251667 0.000000 0.723333 0.025000 0.006667 0.953333 0.000000 0.040000 0.000000 0.946667 0.000000 0.053333 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.630000 0.000000 0.370000 0.000000 0.030000 0.006667 0.963333 0.000000 0.013333 0.946667 0.000000 0.040000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATYCTCCYGCCTCRGC MEME-6 regular expression -------------------------------------------------------------------------------- AT[CT]C[TGA]CC[TC][GA]CCT[CT][AG]GC -------------------------------------------------------------------------------- Time 2124.20 secs. ******************************************************************************** ******************************************************************************** MOTIF TTGCAGTGAGCCGAGATCRY MEME-7 width = 20 sites = 160 llr = 3478 E-value = 3.0e-050 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTGCAGTGAGCCGAGATCRY MEME-7 Description -------------------------------------------------------------------------------- Simplified A ::1:9:::a:::39:a::3: pos.-specific C 2::a::::::a7:::::7:6 probability G ::9:1a:a:a::7:a::17: matrix T 8a::::a::::3:1::a2:4 bits 2.3 * * * 2.1 * * * ** 1.9 * * * * ** 1.6 ** * ***** **** Relative 1.4 *********** **** Entropy 1.2 *********** **** (31.4 bits) 0.9 ***************** ** 0.7 ******************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TTGCAGTGAGCCGAGATCGC consensus TA TAT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGCAGTGAGCCGAGATCRY MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1273401 bayes= 15.0172 E= 3.0e-050 -497 -85 -1397 207 -1397 -1397 -1397 235 -180 -1397 163 -497 -1397 166 -1397 -239 226 -560 -260 -497 -265 -460 165 -1397 -497 -460 -460 230 -397 -1397 168 -397 235 -1397 -1397 -1397 -497 -1397 170 -497 -1397 169 -560 -397 -265 120 -560 42 73 -1397 114 -497 215 -1397 -560 -65 -497 -1397 169 -397 230 -1397 -360 -497 -1397 -1397 -460 233 -339 122 -202 3 76 -560 112 -1397 -1397 101 -560 96 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGCAGTGAGCCGAGATCRY MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 160 E= 3.0e-050 0.006250 0.168750 0.000000 0.825000 0.000000 0.000000 0.000000 1.000000 0.056250 0.000000 0.937500 0.006250 0.000000 0.962500 0.000000 0.037500 0.937500 0.006250 0.050000 0.006250 0.031250 0.012500 0.956250 0.000000 0.006250 0.012500 0.012500 0.968750 0.012500 0.000000 0.975000 0.012500 1.000000 0.000000 0.000000 0.000000 0.006250 0.000000 0.987500 0.006250 0.000000 0.981250 0.006250 0.012500 0.031250 0.700000 0.006250 0.262500 0.325000 0.000000 0.668750 0.006250 0.868750 0.000000 0.006250 0.125000 0.006250 0.000000 0.981250 0.012500 0.968750 0.000000 0.025000 0.006250 0.000000 0.000000 0.012500 0.987500 0.018750 0.706250 0.075000 0.200000 0.331250 0.006250 0.662500 0.000000 0.000000 0.612500 0.006250 0.381250 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGCAGTGAGCCGAGATCRY MEME-7 regular expression -------------------------------------------------------------------------------- TTGCAGTGAGC[CT][GA]AGAT[CT][GA][CT] -------------------------------------------------------------------------------- Time 2457.79 secs. ******************************************************************************** ******************************************************************************** MOTIF CSCCGCCGCCGCCGCC MEME-8 width = 16 sites = 1421 llr = 13752 E-value = 9.4e-045 ******************************************************************************** -------------------------------------------------------------------------------- Motif CSCCGCCGCCGCCGCC MEME-8 Description -------------------------------------------------------------------------------- Simplified A :1:1:::1::::1::: pos.-specific C 8487297199397:a8 probability G 15227128:16119:1 matrix T 1::1111:::1:11:: bits 2.3 2.1 1.9 1.6 Relative 1.4 * * * Entropy 1.2 * ** * ** (14.0 bits) 0.9 * * * ** * *** 0.7 * * * *** * *** 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel CGCCGCCGCCGCCGCC consensus CG G C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSCCGCCGCCGCCGCC MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 1336285 bayes= 12.0743 E= 9.4e-045 -1712 142 -225 -67 -189 39 85 -1712 -1712 135 -44 -1712 -175 117 -88 -107 -204 -86 115 -86 -1712 153 -247 -152 -260 115 -48 -141 -157 -148 139 -273 -242 158 -367 -254 -1712 163 -240 -1712 -280 -10 101 -140 -1712 161 -228 -442 -87 113 -105 -130 -317 -1712 153 -99 -380 168 -443 -1712 -422 147 -157 -201 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSCCGCCGCCGCCGCC MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 1421 E= 9.4e-045 0.000000 0.812808 0.064039 0.123153 0.052780 0.398311 0.548909 0.000000 0.000000 0.775510 0.224490 0.000000 0.058410 0.683322 0.164673 0.093596 0.047854 0.167488 0.676284 0.108374 0.000000 0.876847 0.054891 0.068262 0.032372 0.675581 0.218156 0.073892 0.066151 0.109078 0.795215 0.029557 0.036594 0.905700 0.023927 0.033779 0.000000 0.942294 0.057706 0.000000 0.028149 0.283603 0.613652 0.074595 0.000000 0.928220 0.062632 0.009148 0.107671 0.665728 0.147080 0.079521 0.021816 0.000000 0.879662 0.098522 0.014075 0.971851 0.014075 0.000000 0.010556 0.838846 0.102041 0.048557 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSCCGCCGCCGCCGCC MEME-8 regular expression -------------------------------------------------------------------------------- C[GC][CG]CGC[CG]GCC[GC]CCGCC -------------------------------------------------------------------------------- Time 2788.92 secs. ******************************************************************************** ******************************************************************************** MOTIF GCCACTGCACTCCAGCCTGG MEME-9 width = 20 sites = 168 llr = 3794 E-value = 1.7e-043 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCCACTGCACTCCAGCCTGG MEME-9 Description -------------------------------------------------------------------------------- Simplified A 2::a::1:a::::a:::::: pos.-specific C :aa:9::9:a:aa::aa::: probability G 7:::::9:::::::a:::a9 matrix T ::::19:1::a::::::a:: bits 2.3 * 2.1 * * * * * 1.9 * * * * * * 1.6 *** * * ** ***** Relative 1.4 *** ** ************ Entropy 1.2 ******************* (32.6 bits) 0.9 ******************** 0.7 ******************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GCCACTGCACTCCAGCCTGG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCACTGCACTCCAGCCTGG MEME-9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1273401 bayes= 15.0786 E= 1.7e-043 28 -467 128 -404 -504 169 -567 -504 -504 168 -567 -404 233 -1404 -467 -1404 -1404 151 -467 -65 -304 -267 -1404 224 -172 -1404 161 -404 -304 158 -1404 -158 228 -567 -287 -1404 -504 167 -1404 -272 -504 -1404 -467 232 -346 168 -567 -1404 -504 166 -567 -272 231 -567 -567 -404 -272 -1404 168 -1404 -1404 168 -567 -346 -504 170 -1404 -504 -346 -1404 -1404 232 -224 -1404 166 -1404 -204 -1404 163 -404 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCACTGCACTCCAGCCTGG MEME-9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 168 E= 1.7e-043 0.238095 0.011905 0.738095 0.011905 0.005952 0.982143 0.005952 0.005952 0.005952 0.976190 0.005952 0.011905 0.988095 0.000000 0.011905 0.000000 0.000000 0.863095 0.011905 0.125000 0.023810 0.047619 0.000000 0.928571 0.059524 0.000000 0.928571 0.011905 0.023810 0.910714 0.000000 0.065476 0.952381 0.005952 0.041667 0.000000 0.005952 0.964286 0.000000 0.029762 0.005952 0.000000 0.011905 0.982143 0.017857 0.976190 0.005952 0.000000 0.005952 0.958333 0.005952 0.029762 0.976190 0.005952 0.005952 0.011905 0.029762 0.000000 0.970238 0.000000 0.000000 0.976190 0.005952 0.017857 0.005952 0.988095 0.000000 0.005952 0.017857 0.000000 0.000000 0.982143 0.041667 0.000000 0.958333 0.000000 0.047619 0.000000 0.940476 0.011905 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCACTGCACTCCAGCCTGG MEME-9 regular expression -------------------------------------------------------------------------------- [GA]CCACTGCACTCCAGCCTGG -------------------------------------------------------------------------------- Time 3110.86 secs. ******************************************************************************** ******************************************************************************** MOTIF CCSBSCBCSBCCYCCBCCCC MEME-10 width = 20 sites = 1028 llr = 9758 E-value = 6.1e-028 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCSBSCBCSBCCYCCBCCCC MEME-10 Description -------------------------------------------------------------------------------- Simplified A ::::1:1:::::::21:::1 pos.-specific C 8853693854a859528878 probability G 2134312154:12:23::11 matrix T :123::42:2:13114222: bits 2.3 2.1 1.9 1.6 * Relative 1.4 * Entropy 1.2 * * * ** (13.7 bits) 0.9 * * * * * ** * 0.7 ** * * ** * **** 0.5 ** ** ** ** * **** 0.2 ******************** 0.0 -------------------- Multilevel CCCGCCTCGGCCCCCTCCCC consensus GCG C CC T GGTTT sequence T G T G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCSBSCBCSBCCYCCBCCCC MEME-10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1273401 bayes= 12.427 E= 6.1e-028 -285 135 -98 -210 -1665 139 -173 -84 -433 73 -7 1 -1665 5 51 37 -120 93 15 -1665 -1665 156 -157 -1665 -94 11 -59 90 -1665 137 -238 -35 -220 60 71 -1665 -333 25 34 25 -1665 169 -438 -533 -1665 132 -113 -94 -375 65 -37 48 -253 158 -1665 -175 -27 77 -51 -91 -182 -32 -11 109 -1665 138 -1665 10 -1665 132 -1665 29 -433 115 -200 28 -159 140 -117 -1665 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCSBSCBCSBCCYCCBCCCC MEME-10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 1028 E= 6.1e-028 0.027237 0.773346 0.153696 0.045720 0.000000 0.798638 0.091440 0.109922 0.009728 0.502918 0.289883 0.197471 0.000000 0.314202 0.432879 0.252918 0.085603 0.576848 0.337549 0.000000 0.000000 0.897860 0.102140 0.000000 0.102140 0.328794 0.202335 0.366732 0.000000 0.787938 0.058366 0.153696 0.042802 0.461089 0.496109 0.000000 0.019455 0.361868 0.385214 0.233463 0.000000 0.980545 0.014591 0.004864 0.000000 0.758755 0.139105 0.102140 0.014591 0.475681 0.235409 0.274319 0.034047 0.907588 0.000000 0.058366 0.162451 0.519455 0.214008 0.104086 0.055447 0.244163 0.282101 0.418288 0.000000 0.789883 0.000000 0.210117 0.000000 0.760700 0.000000 0.239300 0.009728 0.676070 0.075875 0.238327 0.065175 0.799611 0.135214 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCSBSCBCSBCCYCCBCCCC MEME-10 regular expression -------------------------------------------------------------------------------- CC[CG][GCT][CG]C[TCG]C[GC][GCT]CC[CTG]C[CG][TGC][CT][CT][CT]C -------------------------------------------------------------------------------- Time 3433.22 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (10) found. ******************************************************************************** CPU: cn45 ********************************************************************************