******************************************************************************** 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_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/MemeChipOutput/GRCh38-107_AZ_exp1_d6_LPS_TRIM1_8_peaks/seqs-centered -oc /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d6_LPS_TRIM1_8_peaks/meme_out -mod zoops -nmotifs 10 -minw 5 -maxw 20 -bfile /scratch/jngalang/MotifAnalysis/MemeChipOutput/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= 5 maxw= 20 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/MemeChipOutput/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 TTTTKTWTTTTTWKTWGAGA MEME-1 width = 20 sites = 1082 llr = 16119 E-value = 1.0e-347 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTKTWTTTTTWKTWGAGA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2112215111114:151828 pos.-specific C :11:11:11111::1:::1: probability G 111131:11:::15116:61 matrix T 87774758888755842222 bits 2.4 2.2 2.0 1.7 Relative 1.5 * * Entropy 1.2 * ** ******* * * * (21.5 bits) 1.0 **** *********** * * 0.7 **** *********** * * 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TTTTTTTTTTTTTTTAGAGA consensus G A AG TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTKTWTTTTTWKTWGAGA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 702837 bayes= 11.3583 E= 1.0e-347 1 -1672 -242 205 -64 -201 -200 198 -52 -200 -251 201 -9 -684 -178 200 -22 -217 8 126 -36 -188 -219 194 131 -417 -342 145 -93 -244 -198 206 -150 -195 -217 210 -105 -205 -281 211 -112 -212 -267 211 -55 -193 -275 202 111 -742 -256 159 -217 -742 52 145 -146 -240 -225 214 148 -342 -254 115 -43 -325 88 44 208 -378 -610 11 -12 -242 94 -16 204 -410 -219 -22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTKTWTTTTTWKTWGAGA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 1082 E= 1.0e-347 0.184843 0.000000 0.059150 0.756007 0.117375 0.078558 0.079482 0.724584 0.127542 0.079482 0.055453 0.737523 0.171904 0.002773 0.092421 0.732902 0.157116 0.070240 0.335490 0.437153 0.142329 0.085952 0.069316 0.702403 0.452865 0.017560 0.029575 0.500000 0.096118 0.058226 0.080407 0.765250 0.064695 0.082255 0.070240 0.782810 0.088725 0.076710 0.045287 0.789279 0.084104 0.073013 0.049908 0.792976 0.124769 0.083179 0.047135 0.744917 0.394640 0.001848 0.053604 0.549908 0.040665 0.001848 0.455638 0.501848 0.066543 0.060074 0.066543 0.806839 0.509242 0.029575 0.054529 0.406654 0.135860 0.033272 0.582255 0.248614 0.774492 0.023105 0.004621 0.197782 0.168207 0.059150 0.609057 0.163586 0.755083 0.018484 0.069316 0.157116 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTKTWTTTTTWKTWGAGA MEME-1 regular expression -------------------------------------------------------------------------------- TTTT[TG]T[TA]TTTTT[TA][TG]T[AT][GT]AGA -------------------------------------------------------------------------------- Time 412.95 secs. ******************************************************************************** ******************************************************************************** MOTIF CCTCRGCCTCCCRARKWGCT MEME-2 width = 20 sites = 412 llr = 8440 E-value = 6.5e-245 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCTCRGCCTCCCRARKWGCT MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::::7:::::::6a5:5::: pos.-specific C 9a:8::aa:a98::::::9: probability G ::::3a::::::3:55:a:: matrix T 1:a2::::a:12:::55:1a bits 2.4 * 2.2 * * * * 2.0 * * * * 1.7 * * * * * Relative 1.5 *** ***** * ** * Entropy 1.2 *** ******* * **** (29.6 bits) 1.0 ******************** 0.7 ******************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel CCTCAGCCTCCCAAGTAGCT consensus G G AGT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCRGCCTCCCRARKWGCT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 702837 bayes= 12.3608 E= 6.5e-245 -623 158 -702 -184 -623 161 -702 -265 -1533 -1533 -1533 245 -623 139 -544 -21 183 -603 10 -524 -292 -603 161 -623 -1533 161 -702 -254 -1533 160 -1533 -224 -391 -544 -1533 242 -1533 161 -702 -254 -391 156 -603 -184 -307 130 -422 -1 179 -471 10 -365 241 -1533 -371 -524 143 -1533 67 -623 -524 -386 60 143 148 -1533 -603 141 -623 -1533 165 -1533 -1533 155 -603 -143 -623 -403 -1533 242 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCRGCCTCCCRARKWGCT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 412 E= 6.5e-245 0.002427 0.944175 0.002427 0.050971 0.002427 0.966019 0.002427 0.029126 0.000000 0.000000 0.000000 1.000000 0.002427 0.832524 0.007282 0.157767 0.650485 0.004854 0.339806 0.004854 0.024272 0.004854 0.968447 0.002427 0.000000 0.966019 0.002427 0.031553 0.000000 0.961165 0.000000 0.038835 0.012136 0.007282 0.000000 0.980583 0.000000 0.966019 0.002427 0.031553 0.012136 0.932039 0.004854 0.050971 0.021845 0.779126 0.016990 0.182039 0.633495 0.012136 0.339806 0.014563 0.970874 0.000000 0.024272 0.004854 0.492718 0.000000 0.504854 0.002427 0.004854 0.021845 0.480583 0.492718 0.509709 0.000000 0.004854 0.485437 0.002427 0.000000 0.997573 0.000000 0.000000 0.927184 0.004854 0.067961 0.002427 0.019417 0.000000 0.978155 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCRGCCTCCCRARKWGCT MEME-2 regular expression -------------------------------------------------------------------------------- CCTC[AG]GCCTCCC[AG]A[GA][TG][AT]GCT -------------------------------------------------------------------------------- Time 756.21 secs. ******************************************************************************** ******************************************************************************** MOTIF GGATTACAGGCRTGMGCCAC MEME-3 width = 20 sites = 376 llr = 7866 E-value = 1.2e-183 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGATTACAGGCRTGMGCCAC MEME-3 Description -------------------------------------------------------------------------------- Simplified A 1:a::a:a:::4:152::a: pos.-specific C :::2::9:::7:323:aa:a probability G 9a::::::aa:6:7:8:::: matrix T :::8a:1:::3:7:2::::: bits 2.4 * * * 2.2 * ** * * 2.0 * ** * * 1.7 * ** * * Relative 1.5 ****** *** **** Entropy 1.2 ********** * **** (30.2 bits) 1.0 ************* ***** 0.7 ************* ****** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GGATTACAGGCGTGAGCCAC consensus C TAC C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGATTACAGGCRTGMGCCAC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 702837 bayes= 12.4407 E= 1.2e-183 -158 -689 156 -1520 -230 -1520 159 -452 245 -1520 -1520 -1520 -1520 -57 -1520 210 -1520 -409 -1520 242 242 -1520 -390 -1520 -1520 155 -589 -140 245 -1520 -1520 -1520 -230 -689 160 -1520 -610 -1520 163 -378 -352 117 -689 54 108 -457 90 -510 -1520 -10 -490 192 -94 -97 120 -352 152 -17 -1520 6 2 -689 136 -1520 -610 162 -1520 -278 -1520 161 -1520 -252 243 -457 -1520 -1520 -1520 159 -589 -220 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGATTACAGGCRTGMGCCAC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 376 E= 1.2e-183 0.061170 0.002660 0.936170 0.000000 0.037234 0.000000 0.954787 0.007979 1.000000 0.000000 0.000000 0.000000 0.000000 0.212766 0.000000 0.787234 0.000000 0.018617 0.000000 0.981383 0.978723 0.000000 0.021277 0.000000 0.000000 0.925532 0.005319 0.069149 1.000000 0.000000 0.000000 0.000000 0.037234 0.002660 0.960106 0.000000 0.002660 0.000000 0.984043 0.013298 0.015957 0.715426 0.002660 0.265957 0.388298 0.013298 0.593085 0.005319 0.000000 0.295213 0.010638 0.694149 0.095745 0.162234 0.726064 0.015957 0.526596 0.281915 0.000000 0.191489 0.186170 0.002660 0.811170 0.000000 0.002660 0.970745 0.000000 0.026596 0.000000 0.968085 0.000000 0.031915 0.986702 0.013298 0.000000 0.000000 0.000000 0.954787 0.005319 0.039894 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGATTACAGGCRTGMGCCAC MEME-3 regular expression -------------------------------------------------------------------------------- GGA[TC]TACAGG[CT][GA][TC]G[AC]GCCAC -------------------------------------------------------------------------------- Time 1097.75 secs. ******************************************************************************** ******************************************************************************** MOTIF WCCAGCCTGGSCAACA MEME-4 width = 16 sites = 404 llr = 6563 E-value = 1.9e-118 ******************************************************************************** -------------------------------------------------------------------------------- Motif WCCAGCCTGGSCAACA MEME-4 Description -------------------------------------------------------------------------------- Simplified A 6::a::::11::7a:a pos.-specific C :99::aa:::47::9: probability G ::::8:::995:3::: matrix T 4:1:1::a:::3::1: bits 2.4 * * 2.2 * * * * 2.0 * * * * 1.7 * * * * Relative 1.5 ** **** ** * Entropy 1.2 **** **** **** (23.4 bits) 1.0 ********** ***** 0.7 ********** ***** 0.5 ********** ***** 0.2 **************** 0.0 ---------------- Multilevel ACCAGCCTGGGCAACA consensus T CTG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCCAGCCTGGSCAACA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 737545 bayes= 12.4477 E= 1.9e-118 163 -1530 -400 117 -362 153 -383 -189 -1530 158 -700 -182 243 -700 -541 -1530 -262 -441 141 -69 -521 159 -500 -251 -1530 160 -1530 -221 -1530 -383 -600 241 -145 -1530 156 -1530 -59 -541 144 -421 -204 47 64 -304 -1530 122 -500 45 202 -1530 -30 -1530 245 -700 -1530 -1530 -340 155 -1530 -182 242 -1530 -400 -1530 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCCAGCCTGGSCAACA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 404 E= 1.9e-118 0.566832 0.000000 0.019802 0.413366 0.014851 0.913366 0.022277 0.049505 0.000000 0.945545 0.002475 0.051980 0.990099 0.002475 0.007426 0.000000 0.029703 0.014851 0.841584 0.113861 0.004950 0.952970 0.009901 0.032178 0.000000 0.960396 0.000000 0.039604 0.000000 0.022277 0.004950 0.972772 0.066832 0.000000 0.933168 0.000000 0.121287 0.007426 0.861386 0.009901 0.044554 0.438119 0.495050 0.022277 0.000000 0.740099 0.009901 0.250000 0.742574 0.000000 0.257426 0.000000 0.997525 0.002475 0.000000 0.000000 0.017327 0.930693 0.000000 0.051980 0.980198 0.000000 0.019802 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCCAGCCTGGSCAACA MEME-4 regular expression -------------------------------------------------------------------------------- [AT]CCAGCCTGG[GC][CT][AG]ACA -------------------------------------------------------------------------------- Time 1436.64 secs. ******************************************************************************** ******************************************************************************** MOTIF ATCRCTTGARSYCRGGAGKY MEME-5 width = 20 sites = 399 llr = 7247 E-value = 5.9e-152 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATCRCTTGARSYCRGGAGKY MEME-5 Description -------------------------------------------------------------------------------- Simplified A a::5::::a5:::6::9::: pos.-specific C ::7:92::::668::::::3 probability G ::14:::9:54::399:a4: matrix T :a2:17a::::32:::::56 bits 2.4 2.2 ** * * 2.0 ** * * * 1.7 ** * * * Relative 1.5 ** * * ** Entropy 1.2 ** ***** ***** * (26.2 bits) 1.0 ** ******* ******* * 0.7 ********** ********* 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel ATCACTTGAGCCCAGGAGTT consensus G C AGTTG GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCRCTTGARSYCRGGAGKY MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 702837 bayes= 12.7029 E= 5.9e-152 242 -498 -498 -619 -461 -328 -698 239 -338 118 -208 6 158 -340 38 -419 -619 157 -540 -187 -387 -51 -273 197 -519 -381 -440 239 -219 -598 156 -302 240 -440 -598 -361 130 -1528 77 -419 -302 83 27 -249 -461 100 -498 93 -461 128 -498 24 181 -540 9 -387 -194 -540 156 -461 -249 -366 156 -461 236 -1528 -308 -319 -249 -1528 161 -1528 -228 -466 49 146 -461 9 -598 183 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCRCTTGARSYCRGGAGKY MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 399 E= 5.9e-152 0.977444 0.010025 0.010025 0.002506 0.007519 0.032581 0.002506 0.957393 0.017544 0.716792 0.075188 0.190476 0.546366 0.030075 0.413534 0.010025 0.002506 0.939850 0.007519 0.050125 0.012531 0.223058 0.047619 0.716792 0.005013 0.022556 0.015038 0.957393 0.040100 0.005013 0.932331 0.022556 0.964912 0.015038 0.005013 0.015038 0.451128 0.000000 0.538847 0.010025 0.022556 0.563910 0.380952 0.032581 0.007519 0.634085 0.010025 0.348371 0.007519 0.766917 0.010025 0.215539 0.641604 0.007519 0.338346 0.012531 0.047619 0.007519 0.937343 0.007519 0.032581 0.025063 0.934837 0.007519 0.942356 0.000000 0.037594 0.020050 0.032581 0.000000 0.967419 0.000000 0.037594 0.012531 0.446115 0.503759 0.007519 0.338346 0.005013 0.649123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCRCTTGARSYCRGGAGKY MEME-5 regular expression -------------------------------------------------------------------------------- ATC[AG]C[TC]TGA[GA][CG][CT][CT][AG]GGAG[TG][TC] -------------------------------------------------------------------------------- Time 1771.80 secs. ******************************************************************************** ******************************************************************************** MOTIF CRCGATCTCGGCTCACTGCA MEME-6 width = 20 sites = 147 llr = 3141 E-value = 5.1e-083 ******************************************************************************** -------------------------------------------------------------------------------- Motif CRCGATCTCGGCTCACTGCA MEME-6 Description -------------------------------------------------------------------------------- Simplified A :4:2a::1:3::::a::::a pos.-specific C 7:7:::a:7::a:a:a1:a: probability G :6:8:::::7a::::::9:: matrix T 3:3::a:92:::a:::9::: bits 2.4 ** * * 2.2 ** * * * 2.0 ** * * * 1.7 **** * * * * Relative 1.5 **** ********** Entropy 1.2 **** ********** (30.8 bits) 1.0 *** **************** 0.7 ******************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel CGCGATCTCGGCTCACTGCA consensus TATA TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRCGATCTCGGCTCACTGCA MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 702837 bayes= 13.6414 E= 5.1e-083 -375 114 -1384 64 118 -454 83 -475 -475 113 -454 64 16 -396 125 -316 245 -1384 -1384 -1384 -1384 -1384 -554 244 -1384 165 -1384 -475 -84 -396 -1384 226 -475 120 -396 42 57 -1384 113 -243 -475 -1384 164 -475 -1384 159 -554 -217 -1384 -454 -1384 243 -1384 161 -1384 -243 243 -454 -1384 -1384 -475 164 -1384 -475 -375 -222 -396 229 -194 -1384 158 -475 -475 159 -1384 -217 240 -454 -396 -1384 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRCGATCTCGGCTCACTGCA MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 147 E= 5.1e-083 0.013605 0.700680 0.000000 0.285714 0.414966 0.013605 0.564626 0.006803 0.006803 0.693878 0.013605 0.285714 0.204082 0.020408 0.755102 0.020408 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.006803 0.993197 0.000000 0.993197 0.000000 0.006803 0.102041 0.020408 0.000000 0.877551 0.006803 0.727891 0.020408 0.244898 0.272109 0.000000 0.693878 0.034014 0.006803 0.000000 0.986395 0.006803 0.000000 0.952381 0.006803 0.040816 0.000000 0.013605 0.000000 0.986395 0.000000 0.965986 0.000000 0.034014 0.986395 0.013605 0.000000 0.000000 0.006803 0.986395 0.000000 0.006803 0.013605 0.068027 0.020408 0.897959 0.047619 0.000000 0.945578 0.006803 0.006803 0.952381 0.000000 0.040816 0.965986 0.013605 0.020408 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRCGATCTCGGCTCACTGCA MEME-6 regular expression -------------------------------------------------------------------------------- [CT][GA][CT][GA]ATCT[CT][GA]GCTCACTGCA -------------------------------------------------------------------------------- Time 2104.92 secs. ******************************************************************************** ******************************************************************************** MOTIF ADARAAAMWKAAANAA MEME-7 width = 16 sites = 783 llr = 7339 E-value = 8.1e-029 ******************************************************************************** -------------------------------------------------------------------------------- Motif ADARAAAMWKAAANAA MEME-7 Description -------------------------------------------------------------------------------- Simplified A 846575756:876358 pos.-specific C :1:1:11312:::21: probability G :233122:15:2322: matrix T 231122:233211322 bits 2.4 2.2 2.0 1.7 * * Relative 1.5 * * * Entropy 1.2 * * ** * (13.5 bits) 1.0 * * * * *** * 0.7 * * * *** *** * 0.5 * ******* *** ** 0.2 **************** 0.0 ---------------- Multilevel AAAAAAAAAGAAAAAA consensus TTGGTGGCTTT GTG sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ADARAAAMWKAAANAA MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 737545 bayes= 11.7929 E= 8.1e-029 206 -1626 -637 35 114 -155 -56 58 179 -1626 -33 -70 151 -220 -15 -58 187 -1626 -153 28 144 -195 -48 7 184 -231 -45 -199 148 -5 -1626 1 159 -253 -155 64 -195 -78 62 62 210 -1626 -1626 25 193 -1626 -77 -69 169 -1626 -20 -45 83 -69 -70 62 146 -158 -62 0 209 -1626 -331 5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ADARAAAMWKAAANAA MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 783 E= 8.1e-029 0.762452 0.000000 0.003831 0.233716 0.402299 0.108557 0.214559 0.274585 0.634738 0.000000 0.252874 0.112388 0.522350 0.068966 0.286079 0.122605 0.667944 0.000000 0.109834 0.222222 0.498084 0.081737 0.227331 0.192848 0.657727 0.063857 0.232439 0.045977 0.510856 0.305236 0.000000 0.183908 0.550447 0.054917 0.108557 0.286079 0.047254 0.185185 0.486590 0.280971 0.782886 0.000000 0.000000 0.217114 0.699872 0.000000 0.186462 0.113665 0.590038 0.000000 0.275862 0.134100 0.325670 0.196679 0.195402 0.282248 0.504470 0.106003 0.206897 0.182631 0.779055 0.000000 0.031928 0.189017 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ADARAAAMWKAAANAA MEME-7 regular expression -------------------------------------------------------------------------------- [AT][ATG][AG][AG][AT][AG][AG][AC][AT][GT][AT]A[AG][AT][AG]A -------------------------------------------------------------------------------- Time 2437.43 secs. ******************************************************************************** ******************************************************************************** MOTIF GATCACGAGGTCAGGAGATC MEME-8 width = 20 sites = 47 llr = 1171 E-value = 2.1e-024 ******************************************************************************** -------------------------------------------------------------------------------- Motif GATCACGAGGTCAGGAGATC MEME-8 Description -------------------------------------------------------------------------------- Simplified A :a::a:1a::::a1:a:7:: pos.-specific C :::a:a:::::a:::::::8 probability G a:::::9:aa:::9a:a::: matrix T ::a:::::::a::::::3a2 bits 2.4 * * * * * 2.2 ** * * * * * * 2.0 ** * * * * * * 1.7 **** * * * * ** Relative 1.5 ****** ****** ***** Entropy 1.2 ******************* (35.9 bits) 1.0 ******************* 0.7 ******************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GATCACGAGGTCAGGAGATC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATCACGAGGTCAGGAGATC MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 702837 bayes= 14.9503 E= 2.1e-024 -310 -1220 163 -1220 242 -1220 -1220 -310 -1220 -1220 -1220 245 -1220 166 -1220 -1220 239 -1220 -289 -1220 -1220 163 -389 -1220 -52 -1220 146 -1220 245 -1220 -1220 -1220 -1220 -389 163 -1220 -1220 -389 163 -1220 -1220 -1220 -1220 245 -1220 163 -1220 -310 245 -1220 -1220 -1220 -78 -1220 150 -1220 -210 -1220 159 -1220 239 -1220 -1220 -210 -310 -1220 163 -1220 198 -1220 -1220 60 -1220 -1220 -1220 245 -310 127 -289 -11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATCACGAGGTCAGGAGATC MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 47 E= 2.1e-024 0.021277 0.000000 0.978723 0.000000 0.978723 0.000000 0.000000 0.021277 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.957447 0.000000 0.042553 0.000000 0.000000 0.978723 0.021277 0.000000 0.127660 0.000000 0.872340 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.021277 0.978723 0.000000 0.000000 0.021277 0.978723 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.978723 0.000000 0.021277 1.000000 0.000000 0.000000 0.000000 0.106383 0.000000 0.893617 0.000000 0.042553 0.000000 0.957447 0.000000 0.957447 0.000000 0.000000 0.042553 0.021277 0.000000 0.978723 0.000000 0.723404 0.000000 0.000000 0.276596 0.000000 0.000000 0.000000 1.000000 0.021277 0.765957 0.042553 0.170213 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATCACGAGGTCAGGAGATC MEME-8 regular expression -------------------------------------------------------------------------------- GATCACGAGGTCAGGAG[AT]TC -------------------------------------------------------------------------------- Time 2761.51 secs. ******************************************************************************** ******************************************************************************** MOTIF SSCGCCSCCGCCGCCGCCSC MEME-9 width = 20 sites = 484 llr = 5260 E-value = 4.2e-032 ******************************************************************************** -------------------------------------------------------------------------------- Motif SSCGCCSCCGCCGCCGCCSC MEME-9 Description -------------------------------------------------------------------------------- Simplified A ::1:::1::1:::::1:::: pos.-specific C 4581993971883aa:9947 probability G 54:8:16:27:17::7:153 matrix T 1111::1111111::2::1: bits 2.4 2.2 2.0 1.7 Relative 1.5 ** Entropy 1.2 * ** * (15.7 bits) 1.0 * ** * * ** ** 0.7 * ** * ** ** ** * 0.5 **** *********** * 0.2 ******************** 0.0 -------------------- Multilevel GCCGCCGCCGCCGCCGCCGC consensus CG C G C CG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SSCGCCSCCGCCGCCGCCSC MEME-9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 702837 bayes= 12.4871 E= 4.2e-032 -230 33 67 -161 -547 73 17 -71 -147 141 -394 -143 -238 -113 125 -143 -201 149 -345 -247 -238 152 -256 -1556 -147 -15 82 -101 -201 145 -1556 -101 -330 117 -62 -156 -80 -240 114 -40 -1556 136 -294 -34 -277 129 -180 -74 -1556 -19 104 -134 -1556 162 -380 -1556 -330 163 -1556 -1556 -111 -287 112 1 -301 158 -1556 -247 -1556 144 -135 -347 -330 18 67 -64 -208 112 -24 -1556 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SSCGCCSCCGCCGCCGCCSC MEME-9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 484 E= 4.2e-032 0.037190 0.398760 0.504132 0.059917 0.004132 0.526860 0.357438 0.111570 0.066116 0.845041 0.020661 0.068182 0.035124 0.144628 0.752066 0.068182 0.045455 0.892562 0.028926 0.033058 0.035124 0.911157 0.053719 0.000000 0.066116 0.285124 0.557851 0.090909 0.045455 0.863636 0.000000 0.090909 0.018595 0.712810 0.206612 0.061983 0.105372 0.059917 0.696281 0.138430 0.000000 0.814050 0.041322 0.144628 0.026860 0.772727 0.090909 0.109504 0.000000 0.276860 0.650826 0.072314 0.000000 0.977273 0.022727 0.000000 0.018595 0.981405 0.000000 0.000000 0.084711 0.043388 0.688017 0.183884 0.022727 0.944215 0.000000 0.033058 0.000000 0.859504 0.123967 0.016529 0.018595 0.359504 0.504132 0.117769 0.043388 0.688017 0.268595 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SSCGCCSCCGCCGCCGCCSC MEME-9 regular expression -------------------------------------------------------------------------------- [GC][CG]CGCC[GC]C[CG]GCC[GC]CCGCC[GC][CG] -------------------------------------------------------------------------------- Time 3085.03 secs. ******************************************************************************** ******************************************************************************** MOTIF GGRGVHGGRGSCGGVG MEME-10 width = 16 sites = 859 llr = 7701 E-value = 7.1e-017 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGRGVHGGRGSCGGVG MEME-10 Description -------------------------------------------------------------------------------- Simplified A 1:4:24::41121:3: pos.-specific C 3:::43::1:34132: probability G 6a5a31a95952874a matrix T :::::2::1::2::1: bits 2.4 2.2 2.0 1.7 * Relative 1.5 * * * * Entropy 1.2 * * ** * * (12.9 bits) 1.0 *** ** * * 0.7 *** ** * ** * 0.5 **** **** ** * 0.2 *********** ** * 0.0 ---------------- Multilevel GGGGCAGGGGGCGGGG consensus C A GC A CA CA sequence AT C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGRGVHGGRGSCGGVG MEME-10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 737545 bayes= 11.691 E= 7.1e-017 -123 -5 96 -1639 -201 -1639 159 -1639 121 -1639 78 -254 -1639 -1639 166 -1639 27 47 9 -630 104 0 -166 18 -1639 -477 164 -1639 -384 -284 157 -1639 101 -233 53 -71 -64 -1639 148 -1639 -103 4 79 -230 20 45 -82 -4 -146 -157 135 -349 -1639 -12 116 -1639 59 -49 23 -52 -305 -709 162 -1639 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGRGVHGGRGSCGGVG MEME-10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 859 E= 7.1e-017 0.077998 0.306170 0.615832 0.000000 0.045402 0.000000 0.954598 0.000000 0.422584 0.000000 0.545984 0.031432 0.000000 0.000000 1.000000 0.000000 0.221187 0.440047 0.336438 0.002328 0.376019 0.316647 0.100116 0.207218 0.000000 0.011641 0.988359 0.000000 0.012806 0.044237 0.942957 0.000000 0.369034 0.062864 0.456345 0.111758 0.117579 0.000000 0.882421 0.000000 0.089639 0.325960 0.547148 0.037253 0.210710 0.431898 0.179278 0.178114 0.066356 0.107101 0.810244 0.016298 0.000000 0.292200 0.707800 0.000000 0.274738 0.225844 0.371362 0.128056 0.022119 0.002328 0.975553 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGRGVHGGRGSCGGVG MEME-10 regular expression -------------------------------------------------------------------------------- [GC]G[GA]G[CGA][ACT]GG[GA]G[GC][CA]G[GC][GAC]G -------------------------------------------------------------------------------- Time 3403.68 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (10) found. ******************************************************************************** CPU: cn45 ********************************************************************************