******************************************************************************** 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_d1_LPS_TRIM1_4_peaks/seqs-centered CONTROL SEQUENCES= --none-- ALPHABET= ACGT ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_4_peaks/seqs-centered -oc /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_4_peaks/meme_out -mod zoops -nmotifs 10 -minw 6 -maxw 15 -bfile /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_4_peaks/background -dna -revcomp -nostatus model: mod= zoops nmotifs= 10 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + - width: minw= 6 maxw= 15 nsites: minsites= 2 maxsites= 10218 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 1021800 N= 10218 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.189 C 0.311 G 0.311 T 0.189 Background letter frequencies (from file /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_4_peaks/background): A 0.188 C 0.312 G 0.312 T 0.188 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF TTTTKTWTTTTTWKT MEME-1 width = 15 sites = 1241 llr = 15651 E-value = 2.2e-163 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTKTWTTTTTWKT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 22111:41:112422 pos.-specific C :::1:11:1:111:: probability G :::14::111::141 matrix T 889758588887447 bits 2.4 2.2 1.9 1.7 ** Relative 1.4 *** * ** * Entropy 1.2 *** * ***** * (18.2 bits) 1.0 **** ******* * 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel TTTTTTTTTTTTTTT consensus G A AGA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTKTWTTTTTWKT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 878748 bayes= 11.7168 E= 2.2e-163 -30 -701 -276 208 6 -759 -659 209 -57 -701 -627 220 -136 -210 -146 198 -51 -759 32 134 -787 -119 -379 216 117 -166 -759 134 -97 -627 -142 206 -1692 -154 -171 208 -34 -659 -168 199 -95 -169 -859 210 0 -194 -627 195 104 -253 -138 122 -5 -859 29 121 28 -701 -204 188 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTKTWTTTTTWKT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1241 E= 2.2e-163 0.153102 0.002417 0.045931 0.798550 0.195810 0.001612 0.003223 0.799355 0.126511 0.002417 0.004029 0.867043 0.073328 0.072522 0.113618 0.740532 0.132151 0.001612 0.389202 0.477035 0.000806 0.136180 0.022562 0.840451 0.424658 0.098308 0.001612 0.475423 0.095890 0.004029 0.116841 0.783239 0.000000 0.107172 0.095085 0.797744 0.149073 0.003223 0.097502 0.750201 0.097502 0.096696 0.000806 0.804996 0.188558 0.081386 0.004029 0.726027 0.388396 0.053989 0.120064 0.437550 0.181305 0.000806 0.381950 0.435939 0.228042 0.002417 0.075745 0.693795 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTKTWTTTTTWKT MEME-1 regular expression -------------------------------------------------------------------------------- TTTT[TG]T[TA]TTTTT[TA][TG][TA] -------------------------------------------------------------------------------- Time 301.03 secs. ******************************************************************************** ******************************************************************************** MOTIF TAATCCCAGCWMYTT MEME-2 width = 15 sites = 538 llr = 8519 E-value = 5.9e-138 ******************************************************************************** -------------------------------------------------------------------------------- Motif TAATCCCAGCWMYTT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :a8::::a1:54::: pos.-specific C ::::999::9:54:3 probability G ::2:::::9:::::: matrix T a::a111:::5:696 bits 2.4 * 2.2 * * * 1.9 ** * * * 1.7 ** * * * Relative 1.4 **** ** * Entropy 1.2 *********** * (22.8 bits) 1.0 *********** *** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel TAATCCCAGCACTTT consensus G TAC C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAATCCCAGCWMYTT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 878748 bayes= 12.8332 E= 5.9e-138 -1572 -539 -1572 240 234 -480 -322 -566 207 -1572 -57 -666 -1572 -393 -1572 238 -508 156 -739 -141 -466 158 -539 -176 -1572 158 -739 -153 236 -1572 -439 -334 -162 -507 156 -408 -349 159 -507 -234 147 -739 -480 130 125 69 -407 -257 -466 47 -639 156 -385 -330 -580 233 -334 -4 -330 178 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAATCCCAGCWMYTT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 538 E= 5.9e-138 0.000000 0.007435 0.000000 0.992565 0.951673 0.011152 0.033457 0.003717 0.788104 0.000000 0.210037 0.001859 0.000000 0.020446 0.000000 0.979554 0.005576 0.921933 0.001859 0.070632 0.007435 0.929368 0.007435 0.055762 0.000000 0.933086 0.001859 0.065056 0.966543 0.000000 0.014870 0.018587 0.061338 0.009294 0.918216 0.011152 0.016729 0.936803 0.009294 0.037175 0.522305 0.001859 0.011152 0.464684 0.447955 0.501859 0.018587 0.031599 0.007435 0.433086 0.003717 0.555762 0.013011 0.031599 0.005576 0.949814 0.018587 0.302974 0.031599 0.646840 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAATCCCAGCWMYTT MEME-2 regular expression -------------------------------------------------------------------------------- TA[AG]TCCCAGC[AT][CA][TC]T[TC] -------------------------------------------------------------------------------- Time 541.19 secs. ******************************************************************************** ******************************************************************************** MOTIF GGAGGCKGMGGCGGS MEME-3 width = 15 sites = 1540 llr = 15346 E-value = 1.1e-110 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGAGGCKGMGGCGGS MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::6111116:::31: pos.-specific C 1:3::82:4::7::4 probability G 99:99:49:9a:695 matrix T :::::13::::22:: bits 2.4 2.2 1.9 1.7 Relative 1.4 * * Entropy 1.2 * ** * ** * (14.4 bits) 1.0 ****** **** * 0.7 ****** ***** * 0.5 ****** ******** 0.2 ****** ******** 0.0 --------------- Multilevel GGAGGCGGAGGCGGG consensus C T C TA C sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGCKGMGGCGGS MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 878748 bayes= 11.2559 E= 1.1e-110 -232 -240 151 -359 -199 -1723 159 -354 173 -3 -272 -309 -92 -1723 152 -518 -180 -466 156 -354 -158 139 -351 -102 -74 -57 44 43 -100 -421 151 -1723 161 30 -286 -1723 -237 -466 160 -437 -275 -1723 164 -1723 -257 122 -395 23 43 -410 82 -10 -131 -315 151 -1723 -263 51 67 -259 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGCKGMGGCGGS MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1540 E= 1.1e-110 0.037662 0.059091 0.887662 0.015584 0.047403 0.000000 0.936364 0.016234 0.624675 0.305844 0.047403 0.022078 0.099351 0.000000 0.895455 0.005195 0.053896 0.012338 0.917532 0.016234 0.062987 0.816883 0.027273 0.092857 0.112987 0.210390 0.422078 0.254545 0.094156 0.016883 0.888961 0.000000 0.574026 0.383117 0.042857 0.000000 0.036364 0.012338 0.942208 0.009091 0.027922 0.000000 0.972078 0.000000 0.031818 0.727273 0.020130 0.220779 0.253896 0.018182 0.551948 0.175974 0.075974 0.035065 0.888961 0.000000 0.030519 0.442857 0.495455 0.031169 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGCKGMGGCGGS MEME-3 regular expression -------------------------------------------------------------------------------- GG[AC]GGC[GTC]G[AC]GG[CT][GA]G[GC] -------------------------------------------------------------------------------- Time 778.49 secs. ******************************************************************************** ******************************************************************************** MOTIF CCAGGCTGGWSTSSA MEME-4 width = 15 sites = 455 llr = 6455 E-value = 2.0e-076 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCAGGCTGGWSTSSA MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::a::1:::4:::2a pos.-specific C 9a:::9::::6:44: probability G :::a9::99:4:45: matrix T 1:::::a::6:a2:: bits 2.4 * * 2.2 * * * * 1.9 * * * * 1.7 * * * * Relative 1.4 *** * * * * Entropy 1.2 ***** **** * * (20.5 bits) 1.0 ********** * * 0.7 ********** * * 0.5 ************ * 0.2 *************** 0.0 --------------- Multilevel CCAGGCTGGTCTCGA consensus AG GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAGGCTGGWSTSSA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 878748 bayes= 12.5931 E= 2.0e-076 -1547 149 -1547 -61 -1547 162 -1547 -225 237 -1547 -1547 -296 -242 -1547 163 -1547 -210 -415 156 -342 -90 145 -415 -261 -361 -1547 -1547 239 -196 -556 158 -361 -196 -434 159 -1547 101 -1547 -515 170 -284 92 24 -342 -384 -1547 -1547 239 -296 47 21 -3 -21 30 54 -1547 237 -1547 -369 -1547 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAGGCTGGWSTSSA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 455 E= 2.0e-076 0.000000 0.876923 0.000000 0.123077 0.000000 0.960440 0.000000 0.039560 0.975824 0.000000 0.000000 0.024176 0.035165 0.000000 0.964835 0.000000 0.043956 0.017582 0.920879 0.017582 0.101099 0.850549 0.017582 0.030769 0.015385 0.000000 0.000000 0.984615 0.048352 0.006593 0.929670 0.015385 0.048352 0.015385 0.936264 0.000000 0.378022 0.000000 0.008791 0.613187 0.026374 0.589011 0.367033 0.017582 0.013187 0.000000 0.000000 0.986813 0.024176 0.430769 0.360440 0.184615 0.162637 0.384615 0.452747 0.000000 0.975824 0.000000 0.024176 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAGGCTGGWSTSSA MEME-4 regular expression -------------------------------------------------------------------------------- CCAGGCTGG[TA][CG]T[CG][GC]A -------------------------------------------------------------------------------- Time 1008.39 secs. ******************************************************************************** ******************************************************************************** MOTIF RSYTCAAGYGATYCT MEME-5 width = 15 sites = 369 llr = 5320 E-value = 4.3e-065 ******************************************************************************** -------------------------------------------------------------------------------- Motif RSYTCAAGYGATYCT MEME-5 Description -------------------------------------------------------------------------------- Simplified A 41:::a8::2a:::2 pos.-specific C :35:a:::4:::58: probability G 66::::2a:8::::2 matrix T ::5a::::5::a526 bits 2.4 * 2.2 * * ** 1.9 * * ** 1.7 * * ** Relative 1.4 ***** ** Entropy 1.2 ***** ** (20.8 bits) 1.0 * ************* 0.7 * ************* 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GGCTCAAGTGATCCT consensus ACT G C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RSYTCAAGYGATYCT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 878748 bayes= 13.3087 E= 4.3e-065 97 -1517 102 -1517 -180 17 91 -412 -1517 79 -684 128 -1517 -526 -584 239 -1517 163 -584 -280 238 -385 -1517 -1517 200 -1517 -34 -1517 -212 -1517 162 -1517 -1517 44 -339 154 -14 -452 137 -453 241 -1517 -1517 -1517 -1517 -385 -1517 238 -1517 78 -1517 131 -612 138 -484 -10 -10 -426 -78 173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RSYTCAAGYGATYCT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 369 E= 4.3e-065 0.368564 0.000000 0.631436 0.000000 0.054201 0.349593 0.585366 0.010840 0.000000 0.539295 0.002710 0.457995 0.000000 0.008130 0.005420 0.986450 0.000000 0.967480 0.005420 0.027100 0.978320 0.021680 0.000000 0.000000 0.753388 0.000000 0.246612 0.000000 0.043360 0.000000 0.956640 0.000000 0.000000 0.422764 0.029810 0.547425 0.170732 0.013550 0.807588 0.008130 1.000000 0.000000 0.000000 0.000000 0.000000 0.021680 0.000000 0.978320 0.000000 0.533875 0.000000 0.466125 0.002710 0.810298 0.010840 0.176152 0.176152 0.016260 0.181572 0.626016 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RSYTCAAGYGATYCT MEME-5 regular expression -------------------------------------------------------------------------------- [GA][GC][CT]TCA[AG]G[TC]GAT[CT]CT -------------------------------------------------------------------------------- Time 1236.79 secs. ******************************************************************************** ******************************************************************************** MOTIF AGGCRTGAGCCACCR MEME-6 width = 15 sites = 337 llr = 4897 E-value = 2.1e-055 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGGCRTGAGCCACCR MEME-6 Description -------------------------------------------------------------------------------- Simplified A a:::4:171::a::5 pos.-specific C :::7:1:2:aa:a8: probability G :aa:6:9:9:::::4 matrix T :::3:9:2:::::2: bits 2.4 * * 2.2 * * 1.9 * * * 1.7 * * * * Relative 1.4 *** * **** Entropy 1.2 *** ** ***** (21.0 bits) 1.0 **** ********** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel AGGCGTGAGCCACCA consensus TA TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGCRTGAGCCACCR MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 878748 bayes= 13.2058 E= 2.1e-055 239 -1504 -471 -1504 -267 -1504 163 -599 -1504 -1504 168 -1504 -340 117 -1504 57 101 -354 89 -367 -1504 -207 -391 226 -160 -271 151 -1504 180 -93 -1504 -6 -46 -1504 147 -1504 -1504 164 -571 -299 -1504 161 -1504 -199 239 -1504 -1504 -399 -1504 162 -1504 -208 -1504 127 -513 35 153 -1504 48 -318 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGCRTGAGCCACCR MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 337 E= 2.1e-055 0.988131 0.000000 0.011869 0.000000 0.029674 0.000000 0.967359 0.002967 0.000000 0.000000 1.000000 0.000000 0.017804 0.703264 0.000000 0.278932 0.379822 0.026706 0.578635 0.014837 0.000000 0.074184 0.020772 0.905045 0.062315 0.047478 0.890208 0.000000 0.655786 0.163205 0.000000 0.181009 0.136499 0.000000 0.863501 0.000000 0.000000 0.970326 0.005935 0.023739 0.000000 0.952522 0.000000 0.047478 0.988131 0.000000 0.000000 0.011869 0.000000 0.955490 0.000000 0.044510 0.000000 0.750742 0.008902 0.240356 0.543027 0.000000 0.436202 0.020772 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGCRTGAGCCACCR MEME-6 regular expression -------------------------------------------------------------------------------- AGG[CT][GA]TGAGCCAC[CT][AG] -------------------------------------------------------------------------------- Time 1463.64 secs. ******************************************************************************** ******************************************************************************** MOTIF GGGTYTCRCYMTGTT MEME-7 width = 15 sites = 481 llr = 6621 E-value = 2.5e-047 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGTYTCRCYMTGTT MEME-7 Description -------------------------------------------------------------------------------- Simplified A 131::::6::5:1:: pos.-specific C ::::4:8:9531::3 probability G 979::::3::1:9:: matrix T :::a6a2::5:9:a7 bits 2.4 * 2.2 * * * 1.9 * * * * 1.7 * * * * Relative 1.4 * * * * * Entropy 1.2 ** * * * ** (19.9 bits) 1.0 ******* ** **** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GGGTTTCACCATGTT consensus A C TG TC C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTYTCRCYMTGTT MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 878748 bayes= 13.1098 E= 2.5e-047 -101 -391 149 -392 77 -1555 109 -369 -159 -623 156 -392 -650 -406 -523 237 -550 44 -523 158 -650 -722 -564 239 -550 131 -464 16 164 -277 8 -233 -369 160 -722 -241 -492 71 -623 135 150 13 -150 -369 -450 -223 -491 228 -122 -391 150 -333 -650 -406 -722 238 -1555 -21 -491 193 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTYTCRCYMTGTT MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 481 E= 2.5e-047 0.093555 0.020790 0.873181 0.012474 0.320166 0.000000 0.665281 0.014553 0.062370 0.004158 0.920998 0.012474 0.002079 0.018711 0.008316 0.970894 0.004158 0.424116 0.008316 0.563410 0.002079 0.002079 0.006237 0.989605 0.004158 0.773389 0.012474 0.209979 0.588358 0.045738 0.328482 0.037422 0.014553 0.948025 0.002079 0.035343 0.006237 0.509356 0.004158 0.480249 0.534304 0.340956 0.110187 0.014553 0.008316 0.066528 0.010395 0.914761 0.081081 0.020790 0.879418 0.018711 0.002079 0.018711 0.002079 0.977131 0.000000 0.270270 0.010395 0.719335 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTYTCRCYMTGTT MEME-7 regular expression -------------------------------------------------------------------------------- G[GA]GT[TC]T[CT][AG]C[CT][AC]TGT[TC] -------------------------------------------------------------------------------- Time 1689.37 secs. ******************************************************************************** ******************************************************************************** MOTIF AGTGAGCYGAGATYG MEME-8 width = 15 sites = 187 llr = 2946 E-value = 4.0e-035 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGTGAGCYGAGATYG MEME-8 Description -------------------------------------------------------------------------------- Simplified A 9:::a:::38:a::3 pos.-specific C ::::::a6::::16: probability G 1a:a:a::7:a::16 matrix T ::a::::4:2::93: bits 2.4 * 2.2 * * ** 1.9 * * * ** 1.7 * * * * ** Relative 1.4 ******* **** Entropy 1.2 ******* **** (22.7 bits) 1.0 ******* ***** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel AGTGAGCCGAGATCG consensus TA TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGAGCYGAGATYG MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 878748 bayes= 14.2922 E= 4.0e-035 226 -1419 -206 -314 -233 -1419 163 -1419 -355 -586 -1419 238 -414 -1419 166 -514 239 -1419 -486 -1419 -214 -1419 161 -514 -1419 161 -428 -255 -197 86 -586 101 77 -1419 110 -414 212 -1419 -586 -9 -282 -586 163 -514 236 -1419 -328 -1419 -1419 -254 -1419 233 -514 96 -206 74 74 -1419 105 -233 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGAGCYGAGATYG MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 187 E= 4.0e-035 0.903743 0.000000 0.074866 0.021390 0.037433 0.000000 0.962567 0.000000 0.016043 0.005348 0.000000 0.978610 0.010695 0.000000 0.983957 0.005348 0.989305 0.000000 0.010695 0.000000 0.042781 0.000000 0.951872 0.005348 0.000000 0.951872 0.016043 0.032086 0.048128 0.566845 0.005348 0.379679 0.320856 0.000000 0.668449 0.010695 0.818182 0.000000 0.005348 0.176471 0.026738 0.005348 0.962567 0.005348 0.967914 0.000000 0.032086 0.000000 0.000000 0.053476 0.000000 0.946524 0.005348 0.604278 0.074866 0.315508 0.315508 0.000000 0.647059 0.037433 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGAGCYGAGATYG MEME-8 regular expression -------------------------------------------------------------------------------- AGTGAGC[CT][GA]AGAT[CT][GA] -------------------------------------------------------------------------------- Time 1914.69 secs. ******************************************************************************** ******************************************************************************** MOTIF CCCCGCCCCCGSCCC MEME-9 width = 15 sites = 1244 llr = 10882 E-value = 9.7e-034 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCCCGCCCCCGSCCC MEME-9 Description -------------------------------------------------------------------------------- Simplified A :::1:1::::1:1:: pos.-specific C a879:788a725967 probability G :13:9112:255133 matrix T :11:1:::::21:1: bits 2.4 2.2 1.9 1.7 Relative 1.4 * * Entropy 1.2 * ** * (12.6 bits) 1.0 ** ** *** * 0.7 ***** **** * * 0.5 ********** **** 0.2 *************** 0.0 --------------- Multilevel CCCCGCCCCCGCCCC consensus G GCG GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCCGCCCCCGSCCC MEME-9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 878748 bayes= 11.5158 E= 9.7e-034 -1692 165 -1692 -312 -1692 144 -164 -181 -1692 116 -31 -181 -141 151 -284 -1692 -323 -1692 148 -77 -47 116 -120 -255 -1692 137 -109 -199 -1692 137 -68 -1692 -1692 162 -579 -248 -429 125 -34 -1692 -72 -58 72 -19 -1692 57 56 -127 -185 148 -197 -1692 -251 100 -10 -181 -1692 114 -14 -270 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCCGCCCCCGSCCC MEME-9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1244 E= 9.7e-034 0.000000 0.978296 0.000000 0.021704 0.000000 0.846463 0.099678 0.053859 0.000000 0.694534 0.251608 0.053859 0.070740 0.885852 0.043408 0.000000 0.020096 0.000000 0.869775 0.110129 0.135852 0.696141 0.135852 0.032154 0.000000 0.806270 0.146302 0.047428 0.000000 0.805466 0.194534 0.000000 0.000000 0.960611 0.005627 0.033762 0.009646 0.743569 0.246785 0.000000 0.114148 0.208199 0.512862 0.164791 0.000000 0.461415 0.460611 0.077974 0.052251 0.868167 0.079582 0.000000 0.032958 0.622186 0.290997 0.053859 0.000000 0.688907 0.282154 0.028939 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCCGCCCCCGSCCC MEME-9 regular expression -------------------------------------------------------------------------------- CC[CG]CGCCCC[CG][GC][CG]C[CG][CG] -------------------------------------------------------------------------------- Time 2139.58 secs. ******************************************************************************** ******************************************************************************** MOTIF AWAWHTTTAWDWYHW MEME-10 width = 15 sites = 387 llr = 3935 E-value = 7.7e-019 ******************************************************************************** -------------------------------------------------------------------------------- Motif AWAWHTTTAWDWYHW MEME-10 Description -------------------------------------------------------------------------------- Simplified A 75634:::8534233 pos.-specific C 1212322:::::531 probability G 1::::::2113:::: matrix T 133548881446346 bits 2.4 2.2 1.9 1.7 Relative 1.4 *** * Entropy 1.2 **** * (14.7 bits) 1.0 * ***** * * 0.7 ************ ** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel AAATTTTTAATTCTT consensus TTAAC G TAATAA sequence C C G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWAWHTTTAWDWYHW MEME-10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 878748 bayes= 13.2499 E= 7.7e-019 181 -133 -227 -33 128 -61 -1524 85 174 -136 -1524 41 77 -69 -1524 137 94 -19 -1524 95 -1524 -33 -1524 200 -360 -67 -1524 207 -1524 -591 -39 201 202 -1524 -139 -70 131 -1524 -139 113 67 -1524 -15 115 93 -1524 -1524 177 8 70 -1524 65 71 -17 -1524 114 70 -152 -374 158 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWAWHTTTAWDWYHW MEME-10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 387 E= 7.7e-019 0.661499 0.124031 0.064599 0.149871 0.457364 0.204134 0.000000 0.338501 0.627907 0.121447 0.000000 0.250646 0.320413 0.193798 0.000000 0.485788 0.361757 0.273902 0.000000 0.364341 0.000000 0.248062 0.000000 0.751938 0.015504 0.196382 0.000000 0.788114 0.000000 0.005168 0.237726 0.757106 0.764858 0.000000 0.118863 0.116279 0.467700 0.000000 0.118863 0.413437 0.299742 0.000000 0.281654 0.418605 0.359173 0.000000 0.000000 0.640827 0.198966 0.506460 0.000000 0.294574 0.307494 0.276486 0.000000 0.416021 0.304910 0.108527 0.023256 0.563307 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWAWHTTTAWDWYHW MEME-10 regular expression -------------------------------------------------------------------------------- A[ATC][AT][TA][TAC][TC]T[TG]A[AT][TAG][TA][CT][TAC][TA] -------------------------------------------------------------------------------- Time 2357.42 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (10) found. ******************************************************************************** CPU: cn45 ********************************************************************************