******************************************************************************** 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/NewMemeChip/GRCh38-107_AZ_exp1_d6_LPS_TRIM1_8_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/NewMemeChip/GRCh38-107_AZ_exp1_d6_LPS_TRIM1_8_peaks/seqs-centered -oc /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d6_LPS_TRIM1_8_peaks/meme_out -mod zoops -nmotifs 10 -minw 6 -maxw 15 -bfile /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d6_LPS_TRIM1_8_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= 6 maxw= 15 nsites: minsites= 2 maxsites= 8677 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= 867700 N= 8677 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.185 C 0.315 G 0.315 T 0.185 Background letter frequencies (from file /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d6_LPS_TRIM1_8_peaks/background): A 0.183 C 0.317 G 0.317 T 0.183 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF AMWAAAAAWAHAAAA MEME-1 width = 15 sites = 1265 llr = 16091 E-value = 5.1e-285 ******************************************************************************** -------------------------------------------------------------------------------- Motif AMWAAAAAWAHAAAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 754788785848988 pos.-specific C :4111:111:3111: probability G :1:11:11:1::::: matrix T 2:51:1215221112 bits 2.4 2.2 2.0 1.7 * * Relative 1.5 * ** * *** Entropy 1.2 * ** * * **** (18.4 bits) 1.0 * ******** **** 0.7 * ******** **** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel AATAAAAAAAAAAAA consensus TCA T C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMWAAAAAWAHAAAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 746222 bayes= 11.0353 E= 5.1e-285 203 -389 -465 25 130 43 -212 -188 124 -209 -1695 143 201 -212 -165 -102 213 -258 -127 -386 216 -348 -279 -76 193 -240 -189 -20 210 -209 -227 -132 133 -197 -1695 132 210 -1695 -254 -18 105 10 -316 42 209 -197 -274 -101 225 -238 -1695 -138 220 -252 -303 -150 215 -1695 -1695 1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMWAAAAAWAHAAAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1265 E= 5.1e-285 0.747826 0.021344 0.012648 0.218182 0.450593 0.426877 0.072727 0.049802 0.431621 0.074308 0.000000 0.494071 0.735968 0.072727 0.101186 0.090119 0.803162 0.052964 0.131225 0.012648 0.817391 0.028458 0.045850 0.108300 0.695652 0.060079 0.085375 0.158893 0.786561 0.074308 0.065613 0.073518 0.460870 0.080632 0.000000 0.458498 0.783399 0.000000 0.054545 0.162055 0.378656 0.340711 0.035573 0.245059 0.781028 0.080632 0.047431 0.090909 0.868775 0.060870 0.000000 0.070356 0.841107 0.055336 0.038735 0.064822 0.815020 0.000000 0.000000 0.184980 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMWAAAAAWAHAAAA MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AC][TA]AAAAA[AT]A[ACT]AAAA -------------------------------------------------------------------------------- Time 302.82 secs. ******************************************************************************** ******************************************************************************** MOTIF CCTGTAATCCCAGCW MEME-2 width = 15 sites = 408 llr = 7378 E-value = 2.5e-166 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCTGTAATCCCAGCW MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::1:a8::::a1:5 pos.-specific C aa::::::aa9::a: probability G :::9::2:::::9:: matrix T ::a:a::a::1:::5 bits 2.4 * * 2.2 * ** * * 2.0 * ** * * 1.7 * ** * * * Relative 1.5 *** ****** * ** Entropy 1.2 *************** (26.1 bits) 1.0 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel CCTGTAATCCCAGCA consensus G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGTAATCCCAGCW MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 746222 bayes= 12.7649 E= 2.5e-166 -364 164 -1532 -1532 -1532 161 -1532 -252 -1532 -1532 -1532 245 -158 -501 155 -1532 -1532 -384 -1532 242 242 -1532 -384 -1532 206 -1532 -43 -1532 -1532 -1532 -1532 245 -464 160 -1532 -242 -1532 159 -1532 -190 -390 154 -1532 -152 242 -1532 -421 -1532 -147 -543 155 -1532 -1532 166 -1532 -1532 148 -1532 -1532 142 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGTAATCCCAGCW MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 408 E= 2.5e-166 0.014706 0.985294 0.000000 0.000000 0.000000 0.968137 0.000000 0.031863 0.000000 0.000000 0.000000 1.000000 0.061275 0.009804 0.928922 0.000000 0.000000 0.022059 0.000000 0.977941 0.977941 0.000000 0.022059 0.000000 0.764706 0.000000 0.235294 0.000000 0.000000 0.000000 0.000000 1.000000 0.007353 0.958333 0.000000 0.034314 0.000000 0.950980 0.000000 0.049020 0.012255 0.924020 0.000000 0.063725 0.982843 0.000000 0.017157 0.000000 0.066176 0.007353 0.926471 0.000000 0.000000 1.000000 0.000000 0.000000 0.509804 0.000000 0.000000 0.490196 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGTAATCCCAGCW MEME-2 regular expression -------------------------------------------------------------------------------- CCTGTA[AG]TCCCAGC[AT] -------------------------------------------------------------------------------- Time 540.25 secs. ******************************************************************************** ******************************************************************************** MOTIF CCTCRGCCTCCCRAR MEME-3 width = 15 sites = 596 llr = 8432 E-value = 1.4e-152 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCTCRGCCTCCCRAR MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::51::::::685 pos.-specific C 9a:81:aa:a98::: probability G ::::39::::::425 matrix T ::a21:::a::2::: bits 2.4 * 2.2 * * 2.0 * * 1.7 * * Relative 1.5 *** ***** * Entropy 1.2 *** ****** * (20.4 bits) 1.0 **** ********** 0.7 **** ********** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel CCTCAGCCTCCCAAG consensus G G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCRGCCTCCCRAR MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 746222 bayes= 12.0961 E= 1.4e-152 -577 158 -756 -191 -396 160 -1586 -277 -360 -1586 -1586 243 -677 138 -424 -22 152 -195 10 -177 -156 -1586 157 -1586 -577 161 -756 -286 -677 163 -756 -360 -377 -475 -656 241 -1586 161 -656 -252 -360 155 -475 -207 -296 132 -424 -11 176 -756 16 -286 217 -456 -96 -1586 137 -475 69 -577 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCRGCCTCCCRAR MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 596 E= 1.4e-152 0.003356 0.946309 0.001678 0.048658 0.011745 0.961409 0.000000 0.026846 0.015101 0.000000 0.000000 0.984899 0.001678 0.823826 0.016779 0.157718 0.523490 0.082215 0.340604 0.053691 0.062081 0.000000 0.937919 0.000000 0.003356 0.969799 0.001678 0.025168 0.001678 0.981544 0.001678 0.015101 0.013423 0.011745 0.003356 0.971477 0.000000 0.964765 0.003356 0.031879 0.015101 0.929530 0.011745 0.043624 0.023490 0.790268 0.016779 0.169463 0.619128 0.001678 0.354027 0.025168 0.823826 0.013423 0.162752 0.000000 0.474832 0.011745 0.510067 0.003356 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCRGCCTCCCRAR MEME-3 regular expression -------------------------------------------------------------------------------- CCTC[AG]GCCTCCC[AG]A[GA] -------------------------------------------------------------------------------- Time 776.73 secs. ******************************************************************************** ******************************************************************************** MOTIF CCAGCCTGGSCAACA MEME-4 width = 15 sites = 435 llr = 6539 E-value = 7.7e-103 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCAGCCTGGSCAACA MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::a::::11::7a:a pos.-specific C 99::aa:::47::9: probability G :::8:::995:3::: matrix T :1:1::a:::2::1: bits 2.4 * 2.2 * * * * 2.0 * * * * 1.7 * * * * Relative 1.5 * *** ** * Entropy 1.2 *** **** **** (21.7 bits) 1.0 ********* ***** 0.7 ********* ***** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel CCAGCCTGGGCAACA consensus CTG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAGCCTGGSCAACA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 746222 bayes= 12.3984 E= 7.7e-103 -399 154 -394 -192 -431 155 -552 -173 242 -710 -430 -1541 -273 -430 141 -70 -1541 159 -411 -261 -531 159 -710 -215 -1541 -411 -610 242 -151 -1541 156 -631 -56 -511 143 -373 -315 45 73 -299 -431 121 -430 40 202 -1541 -33 -631 244 -552 -1541 -1541 -332 154 -610 -173 241 -710 -365 -1541 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAGCCTGGSCAACA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 435 E= 7.7e-103 0.011494 0.919540 0.020690 0.048276 0.009195 0.928736 0.006897 0.055172 0.981609 0.002299 0.016092 0.000000 0.027586 0.016092 0.843678 0.112644 0.000000 0.951724 0.018391 0.029885 0.004598 0.951724 0.002299 0.041379 0.000000 0.018391 0.004598 0.977011 0.064368 0.000000 0.933333 0.002299 0.124138 0.009195 0.852874 0.013793 0.020690 0.432184 0.524138 0.022989 0.009195 0.733333 0.016092 0.241379 0.744828 0.000000 0.252874 0.002299 0.993103 0.006897 0.000000 0.000000 0.018391 0.921839 0.004598 0.055172 0.972414 0.002299 0.025287 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAGCCTGGSCAACA MEME-4 regular expression -------------------------------------------------------------------------------- CCAGCCTGG[GC][CT][AG]ACA -------------------------------------------------------------------------------- Time 1010.17 secs. ******************************************************************************** ******************************************************************************** MOTIF AGGTCAGGAGTTCGA MEME-5 width = 15 sites = 280 llr = 4484 E-value = 3.3e-081 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGGTCAGGAGTTCGA MEME-5 Description -------------------------------------------------------------------------------- Simplified A a1:::a119:2::3a pos.-specific C ::22a:::::::7:: probability G :98:::99:a:::7: matrix T :::8::::::8a3:: bits 2.4 * 2.2 * * * * 2.0 * * * * * 1.7 * * * ** * Relative 1.5 * *** **** * Entropy 1.2 ** ********* * (23.1 bits) 1.0 ** ********* ** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel AGGTCAGGAGTTCGA consensus C A TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGTCAGGAGTTCGA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 746222 bayes= 13.1586 E= 3.3e-081 241 -447 -647 -409 -168 -488 155 -568 -251 -101 132 -336 -568 -45 -1477 206 -368 162 -547 -468 238 -1477 -277 -568 -159 -547 155 -568 -187 -389 153 -409 234 -488 -289 -336 -268 -547 161 -1477 25 -547 -1477 208 -1477 -647 -1477 244 -568 113 -366 61 64 -415 114 -1477 241 -647 -389 -1477 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGTCAGGAGTTCGA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 280 E= 3.3e-081 0.971429 0.014286 0.003571 0.010714 0.057143 0.010714 0.928571 0.003571 0.032143 0.157143 0.792857 0.017857 0.003571 0.232143 0.000000 0.764286 0.014286 0.971429 0.007143 0.007143 0.950000 0.000000 0.046429 0.003571 0.060714 0.007143 0.928571 0.003571 0.050000 0.021429 0.917857 0.010714 0.928571 0.010714 0.042857 0.017857 0.028571 0.007143 0.964286 0.000000 0.217857 0.007143 0.000000 0.775000 0.000000 0.003571 0.000000 0.996429 0.003571 0.692857 0.025000 0.278571 0.285714 0.017857 0.696429 0.000000 0.975000 0.003571 0.021429 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGTCAGGAGTTCGA MEME-5 regular expression -------------------------------------------------------------------------------- AGG[TC]CAGGAG[TA]T[CT][GA]A -------------------------------------------------------------------------------- Time 1242.25 secs. ******************************************************************************** ******************************************************************************** MOTIF GYGARACCCYGTCTC MEME-6 width = 15 sites = 431 llr = 5748 E-value = 1.6e-069 ******************************************************************************** -------------------------------------------------------------------------------- Motif GYGARACCCYGTCTC MEME-6 Description -------------------------------------------------------------------------------- Simplified A :1275a::::3:::: pos.-specific C :4:2::7876::a:a probability G a:8:5:::::72::: matrix T :6:1::3234:7:a: bits 2.4 * * 2.2 * * 2.0 * * 1.7 * * Relative 1.5 * * *** Entropy 1.2 * * * **** (19.2 bits) 1.0 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GTGAAACCCCGTCTC consensus CA G TTTTAG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGARACCCYGTCTC MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 746222 bayes= 12.7043 E= 1.6e-069 -313 -429 160 -1540 -126 14 -1540 165 44 -1540 125 -1540 203 -75 -551 -172 157 -1540 52 -1540 243 -1540 -477 -1540 -349 120 -1540 48 -398 126 -1540 33 -272 116 -1540 53 -398 99 -551 95 77 -609 109 -430 -372 -509 -44 202 -1540 164 -1540 -398 -1540 -509 -1540 244 -330 159 -1540 -260 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGARACCCYGTCTC MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 431 E= 1.6e-069 0.020882 0.016241 0.962877 0.000000 0.076566 0.350348 0.000000 0.573086 0.248260 0.000000 0.751740 0.000000 0.749420 0.187935 0.006961 0.055684 0.545244 0.000000 0.454756 0.000000 0.988399 0.000000 0.011601 0.000000 0.016241 0.728538 0.000000 0.255220 0.011601 0.758701 0.000000 0.229698 0.027842 0.707657 0.000000 0.264501 0.011601 0.628770 0.006961 0.352668 0.313225 0.004640 0.672854 0.009281 0.013921 0.009281 0.234339 0.742459 0.000000 0.988399 0.000000 0.011601 0.000000 0.009281 0.000000 0.990719 0.018561 0.951276 0.000000 0.030162 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGARACCCYGTCTC MEME-6 regular expression -------------------------------------------------------------------------------- G[TC][GA]A[AG]A[CT][CT][CT][CT][GA][TG]CTC -------------------------------------------------------------------------------- Time 1471.94 secs. ******************************************************************************** ******************************************************************************** MOTIF TRGCYRGGCRTGGTG MEME-7 width = 15 sites = 355 llr = 4853 E-value = 5.1e-062 ******************************************************************************** -------------------------------------------------------------------------------- Motif TRGCYRGGCRTGGTG MEME-7 Description -------------------------------------------------------------------------------- Simplified A 26:::3:::3:1::: pos.-specific C 1::a7:::7:3:::: probability G :4a::6a9:6:9a:a matrix T 7:::3:::3:7::a: bits 2.4 * 2.2 * 2.0 * 1.7 * Relative 1.5 ** * * *** Entropy 1.2 **** ** ***** (19.7 bits) 1.0 ***** ********* 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel TAGCCGGGCGTGGTG consensus G TA TAC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TRGCYRGGCRTGGTG MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 746222 bayes= 12.9151 E= 5.1e-062 7 -257 -281 195 182 -1512 16 -1512 -321 -1512 163 -1512 -402 160 -481 -344 -1512 107 -1512 87 84 -523 99 -244 -244 -1512 160 -502 -202 -523 156 -402 -1512 123 -1512 50 90 -1512 102 -344 -1512 -18 -1512 198 -56 -1512 147 -1512 -232 -1512 160 -1512 -1512 -1512 -1512 245 -302 -1512 162 -1512 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TRGCYRGGCRTGGTG MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 355 E= 5.1e-062 0.191549 0.053521 0.045070 0.709859 0.645070 0.000000 0.354930 0.000000 0.019718 0.000000 0.980282 0.000000 0.011268 0.960563 0.011268 0.016901 0.000000 0.664789 0.000000 0.335211 0.326761 0.008451 0.630986 0.033803 0.033803 0.000000 0.960563 0.005634 0.045070 0.008451 0.935211 0.011268 0.000000 0.740845 0.000000 0.259155 0.340845 0.000000 0.642254 0.016901 0.000000 0.278873 0.000000 0.721127 0.123944 0.000000 0.876056 0.000000 0.036620 0.000000 0.963380 0.000000 0.000000 0.000000 0.000000 1.000000 0.022535 0.000000 0.977465 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TRGCYRGGCRTGGTG MEME-7 regular expression -------------------------------------------------------------------------------- T[AG]GC[CT][GA]GG[CT][GA][TC]GGTG -------------------------------------------------------------------------------- Time 1699.94 secs. ******************************************************************************** ******************************************************************************** MOTIF CRGGAGRATCRCTTG MEME-8 width = 15 sites = 448 llr = 5726 E-value = 3.7e-053 ******************************************************************************** -------------------------------------------------------------------------------- Motif CRGGAGRATCRCTTG MEME-8 Description -------------------------------------------------------------------------------- Simplified A :611624a::6:::: pos.-specific C 7:1:2:::18:93:: probability G :499:86:::4:::9 matrix T 2:::2:::92::7a: bits 2.4 2.2 * * 2.0 ** * 1.7 ** * Relative 1.5 ** * Entropy 1.2 ** **** (18.4 bits) 1.0 *** **** ***** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel CAGGAGGATCACTTG consensus TG C A G C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRGGAGRATCRCTTG MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 746222 bayes= 12.661 E= 3.7e-053 -204 119 -515 29 171 -415 16 -277 -183 -256 148 -377 -93 -290 144 -636 168 -55 -515 5 -4 -515 134 -436 120 -615 84 -477 240 -456 -456 -536 -477 -263 -515 235 -336 125 -345 12 171 -515 26 -404 -536 156 -483 -197 -436 -29 -615 199 -1545 -345 -556 240 -204 -556 152 -219 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRGGAGRATCRCTTG MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 448 E= 3.7e-053 0.044643 0.723214 0.008929 0.223214 0.600446 0.017857 0.354911 0.026786 0.051339 0.053571 0.881696 0.013393 0.095982 0.042411 0.859375 0.002232 0.584821 0.216518 0.008929 0.189732 0.178571 0.008929 0.803571 0.008929 0.419643 0.004464 0.569196 0.006696 0.968750 0.013393 0.013393 0.004464 0.006696 0.051339 0.008929 0.933036 0.017857 0.754464 0.029018 0.198661 0.600446 0.008929 0.379464 0.011161 0.004464 0.937500 0.011161 0.046875 0.008929 0.258929 0.004464 0.727679 0.000000 0.029018 0.006696 0.964286 0.044643 0.006696 0.908482 0.040179 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRGGAGRATCRCTTG MEME-8 regular expression -------------------------------------------------------------------------------- [CT][AG]GG[AC]G[GA]ATC[AG]C[TC]TG -------------------------------------------------------------------------------- Time 1926.87 secs. ******************************************************************************** ******************************************************************************** MOTIF ACTGCAACCTCCRCC MEME-9 width = 15 sites = 99 llr = 1691 E-value = 7.0e-018 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACTGCAACCTCCRCC MEME-9 Description -------------------------------------------------------------------------------- Simplified A a::::a8:::::3:: pos.-specific C :a::a::89:a7:99 probability G :::a::22::::7:: matrix T ::a:::::1a:3:11 bits 2.4 * * * 2.2 * * * * 2.0 * * * * 1.7 *** *** ** Relative 1.5 ******* ** * Entropy 1.2 ******* *** ** (24.6 bits) 1.0 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel ACTGCAACCTCCGCC consensus TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTGCAACCTCCRCC MEME-9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 746222 bayes= 14.7977 E= 7.0e-018 245 -1327 -1327 -1327 -1327 166 -1327 -1327 -1327 -339 -1327 240 -1327 -397 163 -1327 -1327 166 -1327 -1327 245 -1327 -1327 -1327 221 -1327 -106 -1327 -1327 140 -97 -1327 -418 155 -1327 -159 -1327 -1327 -1327 245 -1327 166 -1327 -1327 -1327 114 -497 68 91 -1327 105 -1327 -1327 157 -1327 -159 -418 150 -1327 -101 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTGCAACCTCCRCC MEME-9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 99 E= 7.0e-018 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.969697 0.000000 0.020202 0.979798 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.848485 0.000000 0.151515 0.000000 0.000000 0.838384 0.161616 0.000000 0.010101 0.929293 0.000000 0.060606 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.696970 0.010101 0.292929 0.343434 0.000000 0.656566 0.000000 0.000000 0.939394 0.000000 0.060606 0.010101 0.898990 0.000000 0.090909 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTGCAACCTCCRCC MEME-9 regular expression -------------------------------------------------------------------------------- ACTGCAACCTC[CT][GA]CC -------------------------------------------------------------------------------- Time 2154.14 secs. ******************************************************************************** ******************************************************************************** MOTIF GTGCAGTGGCRCGA MEME-10 width = 14 sites = 75 llr = 1151 E-value = 4.2e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGCAGTGGCRCGA MEME-10 Description -------------------------------------------------------------------------------- Simplified A ::::a1::::4:2a pos.-specific C :::a:::::8:71: probability G a:a::9:aa:6:6: matrix T :a::::a::2:31: bits 2.4 * * * * 2.2 * * * * 2.0 * * * * 1.7 **** * * * Relative 1.5 ***** *** * Entropy 1.2 ********** * (22.1 bits) 1.0 ********** * 0.7 ************ * 0.5 ************** 0.2 ************** 0.0 -------------- Multilevel GTGCAGTGGCGCGA consensus ATA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCAGTGGCRCGA MEME-10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 754899 bayes= 14.7289 E= 4.2e-011 -1287 -1287 164 -378 -1287 -1287 -457 243 -1287 -1287 166 -1287 -1287 166 -1287 -1287 245 -1287 -1287 -1287 -61 -1287 147 -1287 -1287 -1287 -1287 245 -1287 -1287 164 -378 -1287 -1287 166 -1287 -1287 136 -1287 3 103 -357 92 -1287 -1287 104 -298 74 13 -157 98 -146 245 -1287 -1287 -1287 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCAGTGGCRCGA MEME-10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 75 E= 4.2e-011 0.000000 0.000000 0.986667 0.013333 0.000000 0.000000 0.013333 0.986667 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.120000 0.000000 0.880000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.986667 0.013333 0.000000 0.000000 1.000000 0.000000 0.000000 0.813333 0.000000 0.186667 0.373333 0.026667 0.600000 0.000000 0.000000 0.653333 0.040000 0.306667 0.200000 0.106667 0.626667 0.066667 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCAGTGGCRCGA MEME-10 regular expression -------------------------------------------------------------------------------- GTGCAGTGGC[GA][CT][GA]A -------------------------------------------------------------------------------- Time 2380.73 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (10) found. ******************************************************************************** CPU: cn45 ********************************************************************************