******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.1 (Release date: Sat Aug 21 19:23:23 2021 -0700) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** PRIMARY SEQUENCES= /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d1_beta_glu_TRIM1_2_peaks/seqs-centered CONTROL SEQUENCES= --none-- ALPHABET= ACGT ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d1_beta_glu_TRIM1_2_peaks/seqs-centered -oc /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d1_beta_glu_TRIM1_2_peaks/meme_out -mod zoops -nmotifs 10 -minw 5 -maxw 20 -bfile /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d1_beta_glu_TRIM1_2_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= 16853 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= 1685300 N= 16853 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.201 C 0.299 G 0.299 T 0.201 Background letter frequencies (from file /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d1_beta_glu_TRIM1_2_peaks/background): A 0.198 C 0.302 G 0.302 T 0.198 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF AHWAAAAAWAMAAAAAWWAR MEME-1 width = 20 sites = 2823 llr = 34182 E-value = 3.6e-338 ******************************************************************************** -------------------------------------------------------------------------------- Motif AHWAAAAAWAMAAAAAWWAR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 64377879474878775565 pos.-specific C 14111:1::14::1111:11 probability G 1:1:121:11111::11:13 matrix T 32421:1:512111213522 bits 2.3 2.1 * 1.9 * 1.6 * Relative 1.4 * * Entropy 1.2 * * * * * (17.5 bits) 0.9 * *** * **** * 0.7 * ******* ***** ** 0.5 ********** ******** 0.2 ******************** 0.0 -------------------- Multilevel AATAAAAATACAAAAAAAAA consensus TCAT A A TTTG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AHWAAAAAWAMAAAAAWWAR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1365093 bayes= 10.9983 E= 3.6e-338 158 -254 -220 54 102 36 -973 8 81 -104 -215 114 173 -193 -270 14 190 -195 -219 -77 202 -615 -95 -251 177 -131 -105 -179 226 -265 -693 -912 99 -282 -215 133 179 -179 -105 -124 83 33 -167 -19 201 -277 -254 -90 189 -297 -148 -74 193 -232 -278 -50 181 -152 -272 -35 179 -148 -126 -129 126 -139 -220 80 133 -773 -290 122 154 -194 -148 25 120 -159 -6 -36 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AHWAAAAAWAMAAAAAWWAR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 2823 E= 3.6e-338 0.593695 0.052072 0.065887 0.288346 0.402763 0.387885 0.000354 0.208998 0.348211 0.147007 0.068013 0.436769 0.657102 0.078994 0.046405 0.217499 0.739284 0.078286 0.066242 0.116188 0.804463 0.004251 0.156571 0.034715 0.675522 0.121502 0.145590 0.057386 0.948990 0.048176 0.002480 0.000354 0.392844 0.042862 0.068013 0.496281 0.682961 0.087141 0.146298 0.083599 0.351399 0.380446 0.094934 0.173220 0.797379 0.044279 0.052072 0.106270 0.734679 0.038611 0.108395 0.118314 0.755579 0.060574 0.043925 0.139922 0.692880 0.105561 0.045696 0.155863 0.684733 0.108041 0.126107 0.081119 0.473964 0.115480 0.065887 0.344669 0.498406 0.001417 0.040383 0.459795 0.577400 0.078640 0.108395 0.235565 0.455544 0.100248 0.290117 0.154091 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AHWAAAAAWAMAAAAAWWAR MEME-1 regular expression -------------------------------------------------------------------------------- [AT][ACT][TA][AT]AAAA[TA]A[CA]AAAAA[AT][AT][AT][AG] -------------------------------------------------------------------------------- Time 420.52 secs. ******************************************************************************** ******************************************************************************** MOTIF RARKWGCTGGGATTACAGGC MEME-2 width = 20 sites = 880 llr = 17916 E-value = 2.9e-219 ******************************************************************************** -------------------------------------------------------------------------------- Motif RARKWGCTGGGATTACAGGC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 6a5:5:::111a::a:a::: pos.-specific C ::::::9:::::3::9:::7 probability G 3:55:9::999::::::99: matrix T :::55::a::::7a:1:::3 bits 2.3 2.1 * * * ** * 1.9 * * * ** * 1.6 * * * ** * Relative 1.4 * ********** *** Entropy 1.2 * *************** (29.4 bits) 0.9 *** *************** 0.7 ******************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel AAATAGCTGGGATTACAGGC consensus G GGT C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARKWGCTGGGATTACAGGC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1365093 bayes= 12.5525 E= 2.9e-219 165 -359 11 -280 229 -605 -366 -586 135 -573 69 -1643 -249 -435 58 133 138 -473 -505 122 -269 -415 165 -544 -444 163 -505 -216 -486 -388 -805 229 -136 -805 161 -644 -186 -805 164 -544 -164 -647 162 -486 230 -1643 -397 -586 -544 -27 -647 190 -544 -330 -705 228 229 -805 -347 -644 -399 159 -605 -147 229 -473 -459 -512 -236 -705 165 -427 -220 -488 163 -444 -305 118 -415 47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARKWGCTGGGATTACAGGC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 880 E= 2.9e-219 0.621591 0.025000 0.325000 0.028409 0.968182 0.004545 0.023864 0.003409 0.505682 0.005682 0.488636 0.000000 0.035227 0.014773 0.452273 0.497727 0.517045 0.011364 0.009091 0.462500 0.030682 0.017045 0.947727 0.004545 0.009091 0.937500 0.009091 0.044318 0.006818 0.020455 0.001136 0.971591 0.077273 0.001136 0.919318 0.002273 0.054545 0.001136 0.939773 0.004545 0.063636 0.003409 0.926136 0.006818 0.977273 0.000000 0.019318 0.003409 0.004545 0.251136 0.003409 0.740909 0.004545 0.030682 0.002273 0.962500 0.969318 0.001136 0.027273 0.002273 0.012500 0.911364 0.004545 0.071591 0.970455 0.011364 0.012500 0.005682 0.038636 0.002273 0.948864 0.010227 0.043182 0.010227 0.937500 0.009091 0.023864 0.684091 0.017045 0.275000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARKWGCTGGGATTACAGGC MEME-2 regular expression -------------------------------------------------------------------------------- [AG]A[AG][TG][AT]GCTGGGA[TC]TACAGG[CT] -------------------------------------------------------------------------------- Time 766.88 secs. ******************************************************************************** ******************************************************************************** MOTIF YMTGTTGSCCAGGCTGGWS MEME-3 width = 19 sites = 616 llr = 11390 E-value = 1.3e-145 ******************************************************************************** -------------------------------------------------------------------------------- Motif YMTGTTGSCCAGGCTGGWS MEME-3 Description -------------------------------------------------------------------------------- Simplified A :5:1::2:::a::1:::4: pos.-specific C 53:::2:59a:::9::::6 probability G :1:9::85:::aa::aa:4 matrix T 41a:a8::1:::::a::6: bits 2.3 * * * 2.1 * * * * 1.9 * * * * 1.6 * * *** * Relative 1.4 **** **** *** Entropy 1.2 **** ********** (26.7 bits) 0.9 * ***** ********** 0.7 * ***** *********** 0.5 ******************* 0.2 ******************* 0.0 ------------------- Multilevel CATGTTGCCCAGGCTGGTC consensus TC CAG AG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YMTGTTGSCCAGGCTGGWS MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 1381946 bayes= 12.9518 E= 1.3e-145 -393 86 -1591 115 144 -1 -192 -126 -1591 -354 -1591 230 -168 -1591 163 -493 -493 -1591 -1591 233 -693 -38 -1591 195 2 -554 136 -361 -1591 77 58 -261 -1591 155 -1591 -78 -593 169 -1591 -302 234 -1591 -1591 -1591 -261 -1591 168 -1591 -268 -654 168 -1591 -84 153 -1591 -335 -1591 -1591 -1591 234 -218 -1591 166 -534 -261 -454 166 -1591 89 -422 -1591 164 -434 100 28 -335 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YMTGTTGSCCAGGCTGGWS MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 616 E= 1.3e-145 0.012987 0.548701 0.000000 0.438312 0.537338 0.300325 0.079545 0.082792 0.000000 0.025974 0.000000 0.974026 0.061688 0.000000 0.931818 0.006494 0.006494 0.000000 0.000000 0.993506 0.001623 0.232143 0.000000 0.766234 0.201299 0.006494 0.775974 0.016234 0.000000 0.514610 0.452922 0.032468 0.000000 0.884740 0.000000 0.115260 0.003247 0.972403 0.000000 0.024351 1.000000 0.000000 0.000000 0.000000 0.032468 0.000000 0.967532 0.000000 0.030844 0.003247 0.965909 0.000000 0.110390 0.870130 0.000000 0.019481 0.000000 0.000000 0.000000 1.000000 0.043831 0.000000 0.951299 0.004870 0.032468 0.012987 0.954545 0.000000 0.366883 0.016234 0.000000 0.616883 0.009740 0.603896 0.366883 0.019481 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YMTGTTGSCCAGGCTGGWS MEME-3 regular expression -------------------------------------------------------------------------------- [CT][AC]TGT[TC][GA][CG]CCAGGCTGG[TA][CG] -------------------------------------------------------------------------------- Time 1109.75 secs. ******************************************************************************** ******************************************************************************** MOTIF AMCTCCTGRSYTCAAGYGAT MEME-4 width = 20 sites = 684 llr = 12700 E-value = 1.4e-135 ******************************************************************************** -------------------------------------------------------------------------------- Motif AMCTCCTGRSYTCAAGYGAT MEME-4 Description -------------------------------------------------------------------------------- Simplified A 75:::::241:::a81:2a: pos.-specific C :49:9a3::46:a:::4::: probability G 3::::::865::::29:8:: matrix T ::1a::7:::4a::::5::a bits 2.3 * 2.1 * * * * 1.9 * * * ** 1.6 * * * ** Relative 1.4 **** ***** ** Entropy 1.2 * ***** ***** ** (26.8 bits) 0.9 * ******* ****** *** 0.7 ********* ********** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel AACTCCTGGGCTCAAGTGAT consensus GC C ACT G CA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMCTCCTGRSYTCAAGYGAT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1365093 bayes= 13.037 E= 1.4e-135 186 -610 -18 -391 146 39 -378 -238 -362 161 -769 -176 -550 -378 -537 229 -476 165 -769 -217 -708 166 -610 -244 -427 1 -769 179 -17 -469 139 -338 94 -669 103 -608 -176 34 85 -391 -450 102 -569 91 -708 -569 -669 232 -550 166 -769 -244 228 -437 -469 -376 192 -669 -32 -608 -191 -469 163 -708 -233 40 -369 144 3 -352 134 -450 227 -610 -305 -476 -427 -488 -510 229 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMCTCCTGRSYTCAAGYGAT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 684 E= 1.4e-135 0.716374 0.004386 0.266082 0.013158 0.545322 0.394737 0.021930 0.038012 0.016082 0.923977 0.001462 0.058480 0.004386 0.021930 0.007310 0.966374 0.007310 0.947368 0.001462 0.043860 0.001462 0.957602 0.004386 0.036550 0.010234 0.304094 0.001462 0.684211 0.175439 0.011696 0.793860 0.019006 0.378655 0.002924 0.615497 0.002924 0.058480 0.383041 0.545322 0.013158 0.008772 0.612573 0.005848 0.372807 0.001462 0.005848 0.002924 0.989766 0.004386 0.957602 0.001462 0.036550 0.959064 0.014620 0.011696 0.014620 0.751462 0.002924 0.242690 0.002924 0.052632 0.011696 0.934211 0.001462 0.039474 0.399123 0.023392 0.538012 0.201754 0.026316 0.763158 0.008772 0.951754 0.004386 0.036550 0.007310 0.010234 0.010234 0.008772 0.970760 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMCTCCTGRSYTCAAGYGAT MEME-4 regular expression -------------------------------------------------------------------------------- [AG][AC]CTCC[TC]G[GA][GC][CT]TCA[AG]G[TC][GA]AT -------------------------------------------------------------------------------- Time 1450.47 secs. ******************************************************************************** ******************************************************************************** MOTIF CCYGCCTCRGCCTCCC MEME-5 width = 16 sites = 1242 llr = 16300 E-value = 1.0e-092 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCYGCCTCRGCCTCCC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::2::::51:::::: pos.-specific C 894:9918::99:998 probability G 1::7::::39:::::: matrix T 11511:921:119112 bits 2.3 2.1 1.9 * 1.6 * * Relative 1.4 *** ***** Entropy 1.2 * *** ****** (18.9 bits) 0.9 ** **** ******* 0.7 *** ************ 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel CCTGCCTCAGCCTCCC consensus CA G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCYGCCTCRGCCTCCC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 1432505 bayes= 12.3518 E= 1.0e-092 -562 147 -204 -119 -413 154 -364 -123 -211 57 -655 135 9 -309 112 -104 -377 163 -855 -196 -1692 165 -755 -201 -394 -169 -755 217 -694 142 -303 -36 142 -264 21 -147 -190 -696 158 -224 -636 161 -555 -147 -694 161 -655 -142 -319 -277 -696 223 -562 164 -696 -192 -636 164 -1692 -183 -477 131 -269 -2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCYGCCTCRGCCTCCC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 1242 E= 1.0e-092 0.004026 0.835749 0.073269 0.086957 0.011272 0.880032 0.024155 0.084541 0.045894 0.447665 0.003221 0.503221 0.210145 0.035427 0.657810 0.096618 0.014493 0.933977 0.000805 0.050725 0.000000 0.949275 0.001610 0.049114 0.012882 0.093398 0.001610 0.892110 0.001610 0.806763 0.037037 0.154589 0.530596 0.048309 0.349436 0.071659 0.053140 0.002415 0.902576 0.041868 0.002415 0.919485 0.006441 0.071659 0.001610 0.921095 0.003221 0.074074 0.021739 0.044283 0.002415 0.931562 0.004026 0.941224 0.002415 0.052335 0.002415 0.942029 0.000000 0.055556 0.007246 0.751208 0.046699 0.194847 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCYGCCTCRGCCTCCC MEME-5 regular expression -------------------------------------------------------------------------------- CC[TC][GA]CCTC[AG]GCCTCCC -------------------------------------------------------------------------------- Time 1787.08 secs. ******************************************************************************** ******************************************************************************** MOTIF CYRGGCRYGGTGGCKC MEME-6 width = 16 sites = 694 llr = 9329 E-value = 5.1e-070 ******************************************************************************** -------------------------------------------------------------------------------- Motif CYRGGCRYGGTGGCKC MEME-6 Description -------------------------------------------------------------------------------- Simplified A ::3:1:4:2:::::2: pos.-specific C a6:::7:3:::::8:6 probability G ::699:6:8a:aa:32 matrix T :4:::3:7::a::251 bits 2.3 * 2.1 * 1.9 * 1.6 * * * Relative 1.4 * ** **** Entropy 1.2 * ** ******* (19.4 bits) 0.9 ************** 0.7 *************** 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel CCGGGCGTGGTGGCTC consensus TA TACA GG sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYRGGCRYGGTGGCKC MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 1432505 bayes= 12.8801 E= 5.1e-070 -510 171 -539 -1608 -364 94 -1608 103 77 -471 111 -1608 -220 -490 165 -1608 -182 -1608 162 -378 -610 123 -425 46 91 -1608 106 -1608 -452 14 -539 172 2 -513 139 -1608 -278 -671 167 -510 -1608 -771 -1608 233 -220 -1608 166 -1608 -1608 -571 170 -410 -1608 141 -1608 -1 17 -1608 -1 127 -340 110 -54 -64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYRGGCRYGGTGGCKC MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 694 E= 5.1e-070 0.005764 0.987032 0.007205 0.000000 0.015850 0.579251 0.000000 0.404899 0.338617 0.011527 0.649856 0.000000 0.043228 0.010086 0.946686 0.000000 0.056196 0.000000 0.929395 0.014409 0.002882 0.708934 0.015850 0.272334 0.371758 0.000000 0.628242 0.000000 0.008646 0.332853 0.007205 0.651297 0.200288 0.008646 0.791066 0.000000 0.028818 0.002882 0.962536 0.005764 0.000000 0.001441 0.000000 0.998559 0.043228 0.000000 0.956772 0.000000 0.000000 0.005764 0.982709 0.011527 0.000000 0.804035 0.000000 0.195965 0.223343 0.000000 0.299712 0.476945 0.018732 0.646974 0.207493 0.126801 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYRGGCRYGGTGGCKC MEME-6 regular expression -------------------------------------------------------------------------------- C[CT][GA]GG[CT][GA][TC][GA]GTGGC[TGA][CG] -------------------------------------------------------------------------------- Time 2120.77 secs. ******************************************************************************** ******************************************************************************** MOTIF AGAGAYRGGGTTTCAC MEME-7 width = 16 sites = 572 llr = 9056 E-value = 1.4e-068 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGAGAYRGGGTTTCAC MEME-7 Description -------------------------------------------------------------------------------- Simplified A 8:a:a:4121::::6: pos.-specific C :::::7:::::2:8:9 probability G :9:a::6989::::3: matrix T 2::::3::::a8a21: bits 2.3 * * 2.1 * * * * 1.9 * * * * 1.6 * * * * Relative 1.4 ***** *** Entropy 1.2 ***** * ***** * (22.8 bits) 0.9 ************** * 0.7 **************** 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel AGAGACGGGGTTTCAC consensus TA A C TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGAYRGGGTTTCAC MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 1432505 bayes= 13.0784 E= 1.4e-068 197 -462 -311 -17 -424 -334 165 -402 232 -643 -485 -1580 -250 -643 167 -682 233 -743 -643 -1580 -450 111 -511 74 83 -743 108 -482 -124 -643 156 -336 6 -643 135 -336 -165 -462 158 -312 -1580 -643 -462 231 -424 -43 -1580 195 -682 -1580 -743 233 -1580 138 -1580 10 165 -318 -12 -154 -312 160 -443 -207 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGAYRGGGTTTCAC MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 572 E= 1.4e-068 0.776224 0.012238 0.034965 0.176573 0.010490 0.029720 0.947552 0.012238 0.986014 0.003497 0.010490 0.000000 0.034965 0.003497 0.959790 0.001748 0.994755 0.001748 0.003497 0.000000 0.008741 0.652098 0.008741 0.330420 0.351399 0.001748 0.639860 0.006993 0.083916 0.003497 0.893357 0.019231 0.206294 0.003497 0.770979 0.019231 0.062937 0.012238 0.902098 0.022727 0.000000 0.003497 0.012238 0.984266 0.010490 0.223776 0.000000 0.765734 0.001748 0.000000 0.001748 0.996503 0.000000 0.788462 0.000000 0.211538 0.620629 0.033217 0.277972 0.068182 0.022727 0.916084 0.013986 0.047203 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGAYRGGGTTTCAC MEME-7 regular expression -------------------------------------------------------------------------------- AGAGA[CT][GA]G[GA]GT[TC]T[CT][AG]C -------------------------------------------------------------------------------- Time 2451.38 secs. ******************************************************************************** ******************************************************************************** MOTIF GAGGTTGCAGTGAGCY MEME-8 width = 16 sites = 301 llr = 5357 E-value = 6.6e-039 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAGGTTGCAGTGAGCY MEME-8 Description -------------------------------------------------------------------------------- Simplified A 1a::::1:a:::a::: pos.-specific C :::12::9::::::a6 probability G 9:a9::9::a:a:a:: matrix T ::::8a:1::a::::4 bits 2.3 * 2.1 * * * * * 1.9 * * * * * 1.6 * * * *** Relative 1.4 *** *********** Entropy 1.2 *** *********** (25.7 bits) 0.9 **************** 0.7 **************** 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel GAGGTTGCAGTGAGCC consensus C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGGTTGCAGTGAGCY MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 1432505 bayes= 14.0271 E= 6.6e-039 -144 -1488 162 -1488 233 -1488 -650 -1488 -290 -650 168 -589 -390 -186 153 -273 -589 -44 -650 196 -589 -370 -1488 230 -173 -1488 161 -331 -331 161 -650 -181 228 -650 -451 -331 -244 -550 166 -1488 -390 -650 -1488 231 -390 -1488 171 -1488 231 -1488 -418 -1488 -244 -1488 166 -431 -490 168 -451 -431 -273 103 -650 83 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGGTTGCAGTGAGCY MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 301 E= 6.6e-039 0.073090 0.000000 0.926910 0.000000 0.996678 0.000000 0.003322 0.000000 0.026578 0.003322 0.966777 0.003322 0.013289 0.083056 0.873754 0.029900 0.003322 0.222591 0.003322 0.770764 0.003322 0.023256 0.000000 0.973422 0.059801 0.000000 0.920266 0.019934 0.019934 0.920266 0.003322 0.056478 0.963455 0.003322 0.013289 0.019934 0.036545 0.006645 0.956811 0.000000 0.013289 0.003322 0.000000 0.983389 0.013289 0.000000 0.986711 0.000000 0.983389 0.000000 0.016611 0.000000 0.036545 0.000000 0.953488 0.009967 0.006645 0.970100 0.013289 0.009967 0.029900 0.614618 0.003322 0.352159 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGGTTGCAGTGAGCY MEME-8 regular expression -------------------------------------------------------------------------------- GAGG[TC]TGCAGTGAGC[CT] -------------------------------------------------------------------------------- Time 2781.09 secs. ******************************************************************************** ******************************************************************************** MOTIF AGATCGYGCCACTGCA MEME-9 width = 16 sites = 293 llr = 4928 E-value = 5.2e-032 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGATCGYGCCACTGCA MEME-9 Description -------------------------------------------------------------------------------- Simplified A 8:a::3:3::a::::a pos.-specific C ::::6:6:aa:8::9: probability G :a::16:7:::::9:: matrix T 1::a3:3::::2a:1: bits 2.3 * * * 2.1 ** * * * 1.9 ** * * * 1.6 * ** ** * * Relative 1.4 **** *** **** Entropy 1.2 **** ******** (24.3 bits) 0.9 **** ********** 0.7 **** *********** 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel AGATCGCGCCACTGCA consensus TATA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATCGYGCCACTGCA MEME-9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 1432505 bayes= 14.4277 E= 5.2e-032 210 -1484 -547 -43 -254 -447 166 -1484 229 -1484 -330 -1484 -1484 -266 -1484 227 -254 107 -230 45 67 -315 107 -354 -269 106 -1484 79 67 -1484 115 -386 -327 166 -1484 -305 -1484 172 -1484 -486 234 -1484 -1484 -1484 -1484 148 -1484 -33 -486 -1484 -646 232 -205 -547 163 -386 -1484 161 -1484 -133 234 -1484 -1484 -1484 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATCGYGCCACTGCA MEME-9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 293 E= 5.2e-032 0.846416 0.000000 0.006826 0.146758 0.034130 0.013652 0.952218 0.000000 0.969283 0.000000 0.030717 0.000000 0.000000 0.047782 0.000000 0.952218 0.034130 0.634812 0.061433 0.269625 0.313993 0.034130 0.634812 0.017065 0.030717 0.627986 0.000000 0.341297 0.313993 0.000000 0.672355 0.013652 0.020478 0.955631 0.000000 0.023891 0.000000 0.993174 0.000000 0.006826 1.000000 0.000000 0.000000 0.000000 0.000000 0.843003 0.000000 0.156997 0.006826 0.000000 0.003413 0.989761 0.047782 0.006826 0.931741 0.013652 0.000000 0.921502 0.000000 0.078498 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATCGYGCCACTGCA MEME-9 regular expression -------------------------------------------------------------------------------- AGAT[CT][GA][CT][GA]CCACTGCA -------------------------------------------------------------------------------- Time 3111.02 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCGGCGGCGGCGGCG MEME-10 width = 16 sites = 829 llr = 8779 E-value = 6.6e-032 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCGGCGGCGGCGGCG MEME-10 Description -------------------------------------------------------------------------------- Simplified A :1111:1111::1::2 pos.-specific C 2:92:8::9128:27: probability G 88:79199:7718836 matrix T :1:::1:::1:11::2 bits 2.3 2.1 1.9 1.6 Relative 1.4 * * * Entropy 1.2 * * *** (15.3 bits) 0.9 *** * *** ** * 0.7 *** ***** ****** 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel GGCGGCGGCGGCGGCG consensus C C GA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCGGCGGCGGCG MEME-10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 1432505 bayes= 13.022 E= 6.6e-032 -1634 -32 133 -1634 -153 -268 144 -160 -187 162 -406 -1634 -115 -69 122 -336 -177 -1634 164 -1634 -1634 136 -156 -69 -67 -1634 154 -1634 -84 -1634 156 -1634 -155 157 -1634 -255 -153 -137 128 -134 -1634 -50 130 -215 -1634 145 -146 -166 -177 -638 147 -95 -284 -74 136 -366 -1634 131 -26 -1634 6 -1634 101 -9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCGGCGGCGGCG MEME-10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 829 E= 6.6e-032 0.000000 0.241255 0.758745 0.000000 0.068758 0.047045 0.819059 0.065139 0.054282 0.927624 0.018094 0.000000 0.089264 0.186972 0.704463 0.019300 0.057901 0.000000 0.942099 0.000000 0.000000 0.774427 0.102533 0.123040 0.124246 0.000000 0.875754 0.000000 0.110977 0.000000 0.889023 0.000000 0.067551 0.898673 0.000000 0.033776 0.068758 0.117008 0.735826 0.078408 0.000000 0.213510 0.741858 0.044632 0.000000 0.827503 0.109771 0.062726 0.057901 0.003619 0.835947 0.102533 0.027744 0.180941 0.775633 0.015682 0.000000 0.747889 0.252111 0.000000 0.206273 0.000000 0.607961 0.185766 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCGGCGGCGGCG MEME-10 regular expression -------------------------------------------------------------------------------- [GC]GCGGCGGCG[GC]CGG[CG][GA] -------------------------------------------------------------------------------- Time 3441.67 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (10) found. ******************************************************************************** CPU: cn45 ********************************************************************************