******************************************************************************** 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_5_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_5_peaks/seqs-centered -oc /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_5_peaks/meme_out -mod zoops -nmotifs 10 -minw 5 -maxw 20 -bfile /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_5_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= 10056 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= 1005600 N= 10056 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.195 C 0.305 G 0.305 T 0.195 Background letter frequencies (from file /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_5_peaks/background): A 0.193 C 0.307 G 0.307 T 0.193 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF TMWAHWAAAAAWAMAAAAAW MEME-1 width = 20 sites = 1662 llr = 21414 E-value = 5.2e-428 ******************************************************************************** -------------------------------------------------------------------------------- Motif TMWAHWAAAAAWAMAAAAAW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 33364488977574977785 pos.-specific C :51231:21111:3::1111 probability G :1:111:1:111111111:: matrix T 7261241::21412:12124 bits 2.4 2.1 1.9 * 1.7 * * Relative 1.4 * * * * Entropy 1.2 * *** ** * (18.6 bits) 0.9 * ***** * *** * 0.7 * * ******* ****** 0.5 * *********** ****** 0.2 ******************** 0.0 -------------------- Multilevel TCTAAAAAAAAAAAAAAAAA consensus AAA CT T C T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TMWAHWAAAAAWAMAAAAAW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 814536 bayes= 11.0515 E= 5.2e-428 71 -583 -899 182 42 66 -221 -3 69 -202 -277 156 157 -66 -161 -53 108 5 -247 18 110 -164 -161 101 199 -271 -264 -47 200 -92 -220 -1734 224 -187 -799 -674 180 -157 -252 -19 190 -147 -231 -82 125 -208 -181 98 184 -424 -105 -39 96 2 -116 -13 220 -283 -220 -732 196 -519 -112 -93 182 -204 -189 -25 178 -137 -194 -46 200 -227 -641 -28 140 -224 -283 99 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TMWAHWAAAAAWAMAAAAAW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 1662 E= 5.2e-428 0.314681 0.005415 0.000602 0.679302 0.258724 0.486763 0.066185 0.188327 0.310469 0.075812 0.045126 0.568592 0.572202 0.193742 0.100481 0.133574 0.407341 0.318291 0.055355 0.219013 0.413357 0.098676 0.100481 0.387485 0.764741 0.046931 0.049338 0.138989 0.770758 0.162455 0.066787 0.000000 0.912756 0.084236 0.001203 0.001805 0.673285 0.103490 0.053550 0.169675 0.718412 0.110710 0.061974 0.108905 0.459085 0.072804 0.087846 0.380265 0.688327 0.016245 0.148616 0.146811 0.374850 0.311673 0.137184 0.176294 0.888688 0.043321 0.066787 0.001203 0.749097 0.008424 0.141396 0.101083 0.680505 0.074609 0.083032 0.161853 0.660650 0.119134 0.080024 0.140193 0.773767 0.063779 0.003610 0.158845 0.508424 0.064982 0.043321 0.383273 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TMWAHWAAAAAWAMAAAAAW MEME-1 regular expression -------------------------------------------------------------------------------- [TA][CA][TA]A[ACT][AT]AAAAA[AT]A[AC]AAAAA[AT] -------------------------------------------------------------------------------- Time 414.54 secs. ******************************************************************************** ******************************************************************************** MOTIF CTCCCAARKWGCTGGGATTA MEME-2 width = 20 sites = 554 llr = 11522 E-value = 6.0e-288 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTCCCAARKWGCTGGGATTA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::6a5:5:::1:1a::a pos.-specific C a:998::::::9:::::2:: probability G :::::3:55:9::999:::: matrix T :a::2:::55::a::::89: bits 2.4 * 2.1 * * * * * 1.9 * * * * ** 1.7 * * * * ** Relative 1.4 **** * ********** Entropy 1.2 **** * *********** (30.0 bits) 0.9 ******** *********** 0.7 ******************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel CTCCCAAATAGCTGGGATTA consensus G GGT C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCCAARKWGCTGGGATTA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 814536 bayes= 12.7626 E= 6.0e-288 -574 164 -1576 -222 -415 -383 -1576 233 -474 162 -641 -210 -674 163 -741 -204 -293 135 -409 -17 175 -360 4 -415 235 -1576 -424 -574 140 -509 63 -474 -249 -341 61 128 138 -541 -460 130 -257 -541 163 -393 -474 161 -509 -198 -574 -395 -1576 234 -149 -1576 159 -442 -210 -582 162 -474 -174 -509 160 -674 236 -741 -509 -1576 -674 -41 -541 198 -393 -295 -741 229 234 -482 -460 -674 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCCAARKWGCTGGGATTA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 554 E= 6.0e-288 0.003610 0.954874 0.000000 0.041516 0.010830 0.021661 0.000000 0.967509 0.007220 0.944043 0.003610 0.045126 0.001805 0.949458 0.001805 0.046931 0.025271 0.785199 0.018051 0.171480 0.648014 0.025271 0.315884 0.010830 0.980144 0.000000 0.016245 0.003610 0.509025 0.009025 0.474729 0.007220 0.034296 0.028881 0.467509 0.469314 0.503610 0.007220 0.012635 0.476534 0.032491 0.007220 0.947653 0.012635 0.007220 0.935018 0.009025 0.048736 0.003610 0.019856 0.000000 0.976534 0.068592 0.000000 0.922383 0.009025 0.045126 0.005415 0.942238 0.007220 0.057762 0.009025 0.931408 0.001805 0.989170 0.001805 0.009025 0.000000 0.001805 0.231047 0.007220 0.759928 0.012635 0.039711 0.001805 0.945848 0.974729 0.010830 0.012635 0.001805 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCCAARKWGCTGGGATTA MEME-2 regular expression -------------------------------------------------------------------------------- CTCCC[AG]A[AG][TG][AT]GCTGGGA[TC]TA -------------------------------------------------------------------------------- Time 757.87 secs. ******************************************************************************** ******************************************************************************** MOTIF TCRCYMTGTTGSCCAGGCTG MEME-3 width = 20 sites = 446 llr = 8316 E-value = 4.8e-180 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCRCYMTGTTGSCCAGGCTG MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::5::5::::2:::a::1:1 pos.-specific C 171953:::2:599:::9:: probability G ::3::1:9::84:::aa::9 matrix T 921141a:a7::1:::::a: bits 2.4 * 2.1 * * * * * 1.9 * * * * * 1.7 * * * ** * Relative 1.4 * *** **** * Entropy 1.2 * * **** ***** ** (26.9 bits) 0.9 * ** ***** ******** 0.7 ** ** ***** ******** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TCACCATGTTGCCCAGGCTG consensus TG TC C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCRCYMTGTTGSCCAGGCTG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 814536 bayes= 12.0533 E= 4.8e-180 -1544 -257 -1544 230 -284 122 -285 16 148 -181 -4 -134 -410 152 -1544 -81 -343 80 -1544 122 143 -2 -174 -118 -1544 -351 -709 233 -197 -477 161 -1544 -1544 -410 -709 234 -410 -44 -364 194 -5 -610 136 -326 -362 79 46 -273 -1544 154 -1544 -87 -543 162 -709 -197 235 -1544 -610 -410 -443 -1544 169 -1544 -484 -510 165 -343 -103 149 -477 -262 -1544 -610 -709 236 -130 -1544 157 -443 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCRCYMTGTTGSCCAGGCTG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 446 E= 4.8e-180 0.000000 0.051570 0.000000 0.948430 0.026906 0.715247 0.042601 0.215247 0.538117 0.087444 0.298206 0.076233 0.011211 0.878924 0.000000 0.109865 0.017937 0.533632 0.000000 0.448430 0.520179 0.302691 0.091928 0.085202 0.000000 0.026906 0.002242 0.970852 0.049327 0.011211 0.939462 0.000000 0.000000 0.017937 0.002242 0.979821 0.011211 0.226457 0.024664 0.737668 0.186099 0.004484 0.789238 0.020179 0.015695 0.531390 0.423767 0.029148 0.000000 0.894619 0.000000 0.105381 0.004484 0.943946 0.002242 0.049327 0.984305 0.000000 0.004484 0.011211 0.008969 0.000000 0.991031 0.000000 0.006726 0.008969 0.966368 0.017937 0.094170 0.863229 0.011211 0.031390 0.000000 0.004484 0.002242 0.993274 0.078475 0.000000 0.912556 0.008969 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCRCYMTGTTGSCCAGGCTG MEME-3 regular expression -------------------------------------------------------------------------------- T[CT][AG]C[CT][AC]TGT[TC]G[CG]CCAGGCTG -------------------------------------------------------------------------------- Time 1095.81 secs. ******************************************************************************** ******************************************************************************** MOTIF YTCAAGYGATYCTCCYGCCT MEME-4 width = 20 sites = 561 llr = 9642 E-value = 2.6e-138 ******************************************************************************** -------------------------------------------------------------------------------- Motif YTCAAGYGATYCTCCYGCCT MEME-4 Description -------------------------------------------------------------------------------- Simplified A 1::961:2a:::2:::2::: pos.-specific C 41a:1:41::68:994:99: probability G ::::29:7::::2:::8::: matrix T 49:1::6::a426116:11a bits 2.4 2.1 ** * 1.9 ** * 1.7 * * ** * Relative 1.4 *** ** * * Entropy 1.2 *** * ** ** *** (24.8 bits) 0.9 *** * **** ******* 0.7 ******************* 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel CTCAAGTGATCCTCCTGCCT consensus T CA T G CA sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTCAAGYGATYCTCCYGCCT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 814536 bayes= 12.5289 E= 2.6e-138 -51 51 -543 112 -1578 -120 -484 215 -444 164 -742 -267 216 -1578 -462 -59 167 -112 -62 -206 -100 -543 154 -517 -295 31 -318 154 14 -243 122 -359 232 -742 -326 -576 -444 -411 -484 232 -476 88 -1578 114 -330 141 -643 -28 6 -543 -51 158 -359 158 -643 -159 -344 157 -384 -190 -359 35 -584 160 18 -543 130 -330 -576 159 -742 -151 -576 159 -511 -163 -576 -426 -584 234 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTCAAGYGATYCTCCYGCCT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 561 E= 2.6e-138 0.135472 0.436720 0.007130 0.420677 0.000000 0.133690 0.010695 0.855615 0.008913 0.959002 0.001783 0.030303 0.859180 0.000000 0.012478 0.128342 0.613191 0.140820 0.199643 0.046346 0.096257 0.007130 0.891266 0.005348 0.024955 0.381462 0.033868 0.559715 0.212121 0.057041 0.714795 0.016043 0.962567 0.001783 0.032086 0.003565 0.008913 0.017825 0.010695 0.962567 0.007130 0.566845 0.000000 0.426025 0.019608 0.818182 0.003565 0.158645 0.201426 0.007130 0.215686 0.575758 0.016043 0.916221 0.003565 0.064171 0.017825 0.909091 0.021390 0.051693 0.016043 0.392157 0.005348 0.586453 0.219251 0.007130 0.754011 0.019608 0.003565 0.926916 0.001783 0.067736 0.003565 0.925134 0.008913 0.062389 0.003565 0.016043 0.005348 0.975045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTCAAGYGATYCTCCYGCCT MEME-4 regular expression -------------------------------------------------------------------------------- [CT]TCAAG[TC][GA]AT[CT]C[TGA]CC[TC][GA]CCT -------------------------------------------------------------------------------- Time 1431.57 secs. ******************************************************************************** ******************************************************************************** MOTIF ATCTYRGCTCACTGCAACCT MEME-5 width = 20 sites = 260 llr = 5494 E-value = 2.9e-111 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATCTYRGCTCACTGCAACCT MEME-5 Description -------------------------------------------------------------------------------- Simplified A 9::1:4::::a::1:a8::: pos.-specific C ::9:6::9:a:a1:a::89: probability G 1::::69::::::9::21:: matrix T :9184:::a:::9::::::a bits 2.4 2.1 * * * * 1.9 ** * * * * * 1.7 ** * * * * * Relative 1.4 **** * ***** *** ** Entropy 1.2 **** *********** ** (30.5 bits) 0.9 ***** ************** 0.7 ******************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel ATCTCGGCTCACTGCAACCT consensus TA G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCTYRGCTCACTGCAACCT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 814536 bayes= 13.8489 E= 2.9e-111 226 -532 -251 -406 -284 -351 -432 227 -465 161 -631 -184 -44 -400 -432 209 -565 104 -532 89 86 -351 96 -284 -219 -532 162 -565 -465 160 -400 -219 -1467 -432 -1467 235 -1467 166 -631 -284 232 -631 -332 -565 -465 164 -473 -284 -465 -232 -532 226 -165 -473 159 -565 -365 164 -631 -306 232 -532 -351 -1467 201 -473 -56 -565 -306 145 -162 -233 -565 162 -631 -206 -406 -400 -473 231 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCTYRGCTCACTGCAACCT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 260 E= 2.9e-111 0.926923 0.007692 0.053846 0.011538 0.026923 0.026923 0.015385 0.930769 0.007692 0.934615 0.003846 0.053846 0.142308 0.019231 0.015385 0.823077 0.003846 0.630769 0.007692 0.357692 0.350000 0.026923 0.596154 0.026923 0.042308 0.007692 0.946154 0.003846 0.007692 0.930769 0.019231 0.042308 0.000000 0.015385 0.000000 0.984615 0.000000 0.969231 0.003846 0.026923 0.961538 0.003846 0.030769 0.003846 0.007692 0.953846 0.011538 0.026923 0.007692 0.061538 0.007692 0.923077 0.061538 0.011538 0.923077 0.003846 0.015385 0.957692 0.003846 0.023077 0.965385 0.007692 0.026923 0.000000 0.776923 0.011538 0.207692 0.003846 0.023077 0.838462 0.100000 0.038462 0.003846 0.946154 0.003846 0.046154 0.011538 0.019231 0.011538 0.957692 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCTYRGCTCACTGCAACCT MEME-5 regular expression -------------------------------------------------------------------------------- ATCT[CT][GA]GCTCACTGCA[AG]CCT -------------------------------------------------------------------------------- Time 1762.25 secs. ******************************************************************************** ******************************************************************************** MOTIF CRTGMGCCACCAYGCCYGGC MEME-6 width = 20 sites = 454 llr = 6763 E-value = 3.0e-118 ******************************************************************************** -------------------------------------------------------------------------------- Motif CRTGMGCCACCAYGCCYGGC MEME-6 Description -------------------------------------------------------------------------------- Simplified A :4:142::a::7:3:::3:: pos.-specific C 7:323:9a:98:6:aa6::9 probability G :6:7:8:::::3:7:::79: matrix T 3:7:2:::::2:4:::4::: bits 2.4 2.1 * 1.9 * 1.7 * Relative 1.4 *** ** * Entropy 1.2 * **** * ** ** (21.5 bits) 0.9 * * ******* ** *** 0.7 *** *************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel CGTGAGCCACCACGCCCGGC consensus TAC C GTA TA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRTGMGCCACCAYGCCYGGC MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 814536 bayes= 9.83508 E= 3.0e-118 -345 123 -554 39 98 -354 88 -287 -487 -9 -480 185 -78 -84 119 -364 122 11 -512 13 -9 -380 136 -445 -345 163 -612 -275 -645 163 -712 -220 231 -612 -380 -328 -413 158 -332 -228 -328 135 -432 -9 177 -612 9 -413 -299 89 -480 103 38 -480 117 -199 -545 165 -554 -287 -487 164 -612 -255 -236 96 -1547 92 62 -612 115 -345 -236 -304 156 -345 -413 161 -512 -213 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRTGMGCCACCAYGCCYGGC MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 454 E= 3.0e-118 0.017621 0.722467 0.006608 0.253304 0.381057 0.026432 0.566079 0.026432 0.006608 0.288546 0.011013 0.693833 0.112335 0.171806 0.700441 0.015419 0.449339 0.330396 0.008811 0.211454 0.180617 0.022026 0.788546 0.008811 0.017621 0.949339 0.004405 0.028634 0.002203 0.953744 0.002203 0.041850 0.953744 0.004405 0.022026 0.019824 0.011013 0.918502 0.030837 0.039648 0.019824 0.784141 0.015419 0.180617 0.658590 0.004405 0.325991 0.011013 0.024229 0.570485 0.011013 0.394273 0.251101 0.011013 0.689427 0.048458 0.004405 0.962555 0.006608 0.026432 0.006608 0.955947 0.004405 0.033040 0.037445 0.596916 0.000000 0.365639 0.297357 0.004405 0.680617 0.017621 0.037445 0.037445 0.907489 0.017621 0.011013 0.936123 0.008811 0.044053 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRTGMGCCACCAYGCCYGGC MEME-6 regular expression -------------------------------------------------------------------------------- [CT][GA][TC]G[ACT]GCCACC[AG][CT][GA]CC[CT][GA]GC -------------------------------------------------------------------------------- Time 2092.06 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCGGSGGCGGCGGCG MEME-7 width = 16 sites = 1063 llr = 10350 E-value = 6.2e-074 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCGGSGGCGGCGGCG MEME-7 Description -------------------------------------------------------------------------------- Simplified A :111::1111::1::1 pos.-specific C 1:81161:81:7227: probability G 99179389:8a37728 matrix T :::::1::::::1::1 bits 2.4 2.1 1.9 1.7 * Relative 1.4 * * Entropy 1.2 ** * * * (14.0 bits) 0.9 ** * ** * * 0.7 ***** ****** * * 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel GGCGGCGGCGGCGGCG consensus G G CG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGSGGCGGCGGCG MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 854760 bayes= 11.6614 E= 6.2e-074 -292 -160 151 -1670 -143 -835 159 -1670 -65 134 -201 -298 -90 -113 126 -309 -768 -208 157 -359 -351 96 10 -173 -149 -171 141 -304 -108 -676 156 -1670 -89 142 -360 -201 -157 -108 132 -309 -1670 -735 170 -1670 -359 111 7 -1670 -143 -63 114 -182 -232 -55 125 -309 -268 117 -31 -277 -147 -396 142 -116 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGSGGCGGCGGCG MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 1063 E= 6.2e-074 0.025400 0.101599 0.873001 0.000000 0.071496 0.000941 0.927563 0.000000 0.123236 0.776105 0.076199 0.024459 0.103481 0.140169 0.733772 0.022578 0.000941 0.072437 0.910630 0.015992 0.016933 0.596425 0.328316 0.058325 0.068674 0.094073 0.813735 0.023518 0.091251 0.002822 0.905927 0.000000 0.104421 0.822201 0.025400 0.047977 0.064911 0.144873 0.767639 0.022578 0.000000 0.001881 0.998119 0.000000 0.015992 0.662277 0.321731 0.000000 0.071496 0.198495 0.675447 0.054563 0.038570 0.209784 0.729069 0.022578 0.030103 0.693321 0.248354 0.028222 0.069614 0.019755 0.824083 0.086548 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGSGGCGGCGGCG MEME-7 regular expression -------------------------------------------------------------------------------- GGCGG[CG]GGCGG[CG]G[GC][CG]G -------------------------------------------------------------------------------- Time 2419.31 secs. ******************************************************************************** ******************************************************************************** MOTIF YYCYCCTCCYYYCCYYCCYC MEME-8 width = 20 sites = 751 llr = 7292 E-value = 7.7e-041 ******************************************************************************** -------------------------------------------------------------------------------- Motif YYCYCCTCCYYYCCYYCCYC MEME-8 Description -------------------------------------------------------------------------------- Simplified A 1111::1:1:::::1::::: pos.-specific C 5575871676557a358739 probability G 21:1:1222:::1:12:11: matrix T 33242262:4553:54225: bits 2.4 2.1 1.9 1.7 Relative 1.4 * * Entropy 1.2 * * * (14.0 bits) 0.9 * *** * * * 0.7 * ** ***** ** * 0.5 * ********** ***** 0.2 ******************** 0.0 -------------------- Multilevel CCCCCCTCCCTCCCTCCCTC consensus TTTT GTCTT CTT C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYCYCCTCCYYYCCYYCCYC MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 814536 bayes= 12.1775 E= 7.7e-041 -109 68 -97 44 -148 72 -116 58 -103 117 -1620 15 -182 56 -119 89 -1620 134 -285 -8 -1620 124 -178 -5 -64 -129 -98 163 -265 100 -70 -21 -99 111 -36 -1620 -1620 88 -339 107 -1620 63 -1620 145 -1620 79 -468 124 -1620 113 -256 52 -1620 165 -304 -1620 -45 -21 -121 126 -1620 60 -77 88 -1620 135 -1620 18 -265 119 -199 -3 -218 8 -162 147 -209 160 -368 -1620 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYCYCCTCCYYYCCYYCCYC MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 751 E= 7.7e-041 0.090546 0.491345 0.157124 0.260985 0.069241 0.504660 0.137150 0.288948 0.094541 0.691079 0.000000 0.214381 0.054594 0.452730 0.134487 0.358189 0.000000 0.774967 0.042610 0.182423 0.000000 0.724368 0.089214 0.186418 0.123835 0.125166 0.155792 0.595206 0.030626 0.613848 0.189081 0.166445 0.097204 0.663116 0.239680 0.000000 0.000000 0.565912 0.029294 0.404794 0.000000 0.474035 0.000000 0.525965 0.000000 0.532623 0.011984 0.455393 0.000000 0.671105 0.051931 0.276964 0.000000 0.962716 0.037284 0.000000 0.141145 0.264980 0.133156 0.460719 0.000000 0.466045 0.179760 0.354194 0.000000 0.781625 0.000000 0.218375 0.030626 0.703063 0.077230 0.189081 0.042610 0.323569 0.099867 0.533955 0.045273 0.930759 0.023968 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYCYCCTCCYYYCCYYCCYC MEME-8 regular expression -------------------------------------------------------------------------------- [CT][CT][CT][CT]CCTC[CG][CT][TC][CT][CT]C[TC][CT][CT]C[TC]C -------------------------------------------------------------------------------- Time 2735.43 secs. ******************************************************************************** ******************************************************************************** MOTIF AGGAGTTCRAGA MEME-9 width = 12 sites = 265 llr = 3785 E-value = 3.9e-035 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGGAGTTCRAGA MEME-9 Description -------------------------------------------------------------------------------- Simplified A a:1a:2::3a:a pos.-specific C :::::::7:::: probability G :a9:a:::6:a: matrix T :::::8a3:::: bits 2.4 * * * 2.1 * * * * * 1.9 * * * * * 1.7 * * ** *** Relative 1.4 ******* *** Entropy 1.2 ******* *** (20.6 bits) 0.9 ******* **** 0.7 ************ 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel AGGAGTTCGAGA consensus TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGAGTTCRAGA MEME-9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 894984 bayes= 13.879 E= 3.9e-035 237 -1469 -1469 -1469 -235 -1469 165 -1469 -168 -1469 159 -368 232 -1469 -302 -1469 -251 -1469 165 -1469 0 -1469 -435 204 -1469 -435 -1469 235 -309 111 -289 49 78 -1469 108 -335 237 -1469 -634 -1469 -1469 -1469 170 -1469 237 -1469 -1469 -1469 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGAGTTCRAGA MEME-9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 265 E= 3.9e-035 1.000000 0.000000 0.000000 0.000000 0.037736 0.000000 0.962264 0.000000 0.060377 0.000000 0.924528 0.015094 0.962264 0.000000 0.037736 0.000000 0.033962 0.000000 0.966038 0.000000 0.192453 0.000000 0.015094 0.792453 0.000000 0.015094 0.000000 0.984906 0.022642 0.664151 0.041509 0.271698 0.332075 0.000000 0.649057 0.018868 0.996226 0.000000 0.003774 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGAGTTCRAGA MEME-9 regular expression -------------------------------------------------------------------------------- AGGAGTT[CT][GA]AGA -------------------------------------------------------------------------------- Time 3045.69 secs. ******************************************************************************** ******************************************************************************** MOTIF GCCACTGCACTC MEME-10 width = 12 sites = 220 llr = 2999 E-value = 9.8e-023 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCCACTGCACTC MEME-10 Description -------------------------------------------------------------------------------- Simplified A 3::a::::a::: pos.-specific C :aa:8::9:9:9 probability G 7:::::a::::: matrix T ::::2a:1:1a: bits 2.4 * 2.1 * * * * 1.9 * * * * 1.7 * * ** * * Relative 1.4 *** ******* Entropy 1.2 *********** (19.7 bits) 0.9 ************ 0.7 ************ 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel GCCACTGCACTC consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCACTGCACTC MEME-10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 894984 bayes= 13.9436 E= 9.8e-023 55 -1443 117 -282 -1443 168 -1443 -341 -1443 166 -1443 -260 233 -1443 -349 -1443 -1443 145 -1443 -28 -1443 -376 -1443 234 -382 -1443 168 -1443 -1443 160 -1443 -150 237 -1443 -1443 -1443 -1443 162 -607 -195 -382 -308 -1443 230 -1443 161 -327 -260 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCACTGCACTC MEME-10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 220 E= 9.8e-023 0.281818 0.000000 0.690909 0.027273 0.000000 0.981818 0.000000 0.018182 0.000000 0.968182 0.000000 0.031818 0.972727 0.000000 0.027273 0.000000 0.000000 0.840909 0.000000 0.159091 0.000000 0.022727 0.000000 0.977273 0.013636 0.000000 0.986364 0.000000 0.000000 0.931818 0.000000 0.068182 1.000000 0.000000 0.000000 0.000000 0.000000 0.945455 0.004545 0.050000 0.013636 0.036364 0.000000 0.950000 0.000000 0.936364 0.031818 0.031818 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCACTGCACTC MEME-10 regular expression -------------------------------------------------------------------------------- [GA]CCACTGCACTC -------------------------------------------------------------------------------- Time 3355.58 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (10) found. ******************************************************************************** CPU: cn45 ********************************************************************************