******************************************************************************** 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_BCG_TRIM1_3_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_BCG_TRIM1_3_peaks/seqs-centered -oc /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_D1_BCG_TRIM1_3_peaks/meme_out -mod zoops -nmotifs 10 -minw 5 -maxw 20 -bfile /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_D1_BCG_TRIM1_3_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= 17887 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= 1788700 N= 17887 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.203 C 0.297 G 0.297 T 0.203 Background letter frequencies (from file /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_D1_BCG_TRIM1_3_peaks/background): A 0.201 C 0.299 G 0.299 T 0.201 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF TCTCWAMWAAAAAWAMAAAA MEME-1 width = 20 sites = 1887 llr = 27572 E-value = 2.5e-295 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCTCWAMWAAAAAWAMAAAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 11124945888884748888 pos.-specific C :7:6::5:1111:114111: probability G :1:1::1:::::1:11:11: matrix T 918161141:1125111111 bits 2.3 2.1 1.9 1.6 * * Relative 1.4 * * * **** Entropy 1.2 * * ** ***** **** (21.1 bits) 0.9 * * ** ******** **** 0.7 * * ** ******** **** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TCTCTACAAAAAATAAAAAA consensus A AT A C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTCWAMWAAAAAWAMAAAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1448847 bayes= 11.5597 E= 2.5e-295 -89 -386 -714 212 -63 117 -139 -131 -60 -286 -419 201 -13 108 -196 -91 96 -414 -814 156 210 -714 -356 -82 96 60 -197 -137 121 -259 -277 114 193 -257 -275 -51 206 -188 -284 -221 205 -220 -314 -150 204 -224 -336 -133 199 -633 -257 -40 116 -243 -326 121 179 -157 -239 -43 114 31 -246 -63 195 -173 -393 -78 190 -236 -211 -72 193 -224 -224 -86 194 -259 -273 -58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTCWAMWAAAAAWAMAAAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 1887 E= 2.5e-295 0.108108 0.020668 0.002120 0.869104 0.129306 0.675146 0.114467 0.081081 0.132485 0.041335 0.016428 0.809751 0.183890 0.632750 0.076842 0.106518 0.388977 0.016958 0.001060 0.593005 0.858506 0.002120 0.025437 0.113937 0.391097 0.455220 0.076312 0.077371 0.464229 0.049815 0.043985 0.441971 0.764176 0.050344 0.044515 0.140964 0.833598 0.081081 0.041865 0.043455 0.829889 0.065183 0.033916 0.071012 0.827239 0.063593 0.029147 0.080021 0.794383 0.003710 0.050344 0.151563 0.448331 0.055644 0.031267 0.464759 0.693164 0.100689 0.057234 0.148914 0.443561 0.372019 0.054584 0.129836 0.773185 0.090090 0.019608 0.117117 0.750397 0.058294 0.069422 0.121887 0.762586 0.063593 0.063593 0.110228 0.771065 0.049815 0.045045 0.134075 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTCWAMWAAAAAWAMAAAA MEME-1 regular expression -------------------------------------------------------------------------------- TCTC[TA]A[CA][AT]AAAAA[TA]A[AC]AAAA -------------------------------------------------------------------------------- Time 420.08 secs. ******************************************************************************** ******************************************************************************** MOTIF CTCCCAARKWGCTGGGATTA MEME-2 width = 20 sites = 932 llr = 19333 E-value = 3.1e-275 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTCCCAARKWGCTGGGATTA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::6a5:5:::11:a::a pos.-specific C 9:9a8::::::9:::::2:: probability G :::::3:55:9::999:::: matrix T :a::2:::55:1a::::89: bits 2.3 * 2.1 * * * * * 1.9 * * * * ** 1.6 * * * * ** Relative 1.4 **** * ********** Entropy 1.2 **** * *********** (29.9 bits) 0.9 ******** *********** 0.7 ******************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel CTCCCAAAGAGCTGGGATTA consensus G GTT C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCCAARKWGCTGGGATTA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1448847 bayes= 12.7383 E= 3.1e-275 -754 166 -580 -205 -474 -366 -1651 227 -474 165 -712 -202 -596 168 -812 -255 -296 139 -612 -13 169 -373 10 -496 226 -712 -322 -522 136 -580 66 -474 -322 -380 68 125 129 -422 -495 127 -269 -532 166 -346 -655 165 -512 -196 -754 -532 -654 230 -187 -1651 166 -754 -157 -812 162 -455 -215 -532 166 -754 230 -812 -495 -596 -754 -41 -554 194 -496 -295 -495 224 226 -712 -327 -455 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCCAARKWGCTGGGATTA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 932 E= 3.1e-275 0.001073 0.945279 0.005365 0.048283 0.007511 0.023605 0.000000 0.968884 0.007511 0.940987 0.002146 0.049356 0.003219 0.961373 0.001073 0.034335 0.025751 0.786481 0.004292 0.183476 0.649142 0.022532 0.321888 0.006438 0.960300 0.002146 0.032189 0.005365 0.515021 0.005365 0.472103 0.007511 0.021459 0.021459 0.478541 0.478541 0.489270 0.016094 0.009657 0.484979 0.031116 0.007511 0.943133 0.018240 0.002146 0.937768 0.008584 0.051502 0.001073 0.007511 0.003219 0.988197 0.054721 0.000000 0.944206 0.001073 0.067597 0.001073 0.922747 0.008584 0.045064 0.007511 0.946352 0.001073 0.986052 0.001073 0.009657 0.003219 0.001073 0.225322 0.006438 0.767167 0.006438 0.038627 0.009657 0.945279 0.958155 0.002146 0.031116 0.008584 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCCAARKWGCTGGGATTA MEME-2 regular expression -------------------------------------------------------------------------------- CTCCC[AG]A[AG][GT][AT]GCTGGGA[TC]TA -------------------------------------------------------------------------------- Time 774.01 secs. ******************************************************************************** ******************************************************************************** MOTIF TSSASWCCAGCCTGGSCAAC MEME-3 width = 20 sites = 862 llr = 15659 E-value = 1.8e-175 ******************************************************************************** -------------------------------------------------------------------------------- Motif TSSASWCCAGCCTGGSCAAC MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::29:6::a:::::1::7a: pos.-specific C :44:4:9a::aa:::47::9 probability G :44:6::::9:::a95:2:: matrix T a2:::4:::1::a:::2::1 bits 2.3 * * 2.1 * * * 1.9 * * * * * 1.6 * * * * * Relative 1.4 * * **** ***** * Entropy 1.2 * * ********** *** (26.2 bits) 0.9 * * ********** **** 0.7 * ************ **** 0.5 * ***************** 0.2 ******************** 0.0 -------------------- Multilevel TCGAGACCAGCCTGGGCAAC consensus GC CT CTG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSSASWCCAGCCTGGSCAAC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1448847 bayes= 12.364 E= 1.8e-175 -1640 -801 -1640 232 -335 47 40 -23 -20 29 49 -239 224 -431 -392 -363 -273 44 91 -585 157 -701 -701 100 -643 165 -455 -219 -411 168 -601 -311 232 -1640 -1640 -1640 -268 -455 152 -106 -743 169 -543 -279 -426 167 -701 -258 -485 -431 -1640 229 -253 -1640 167 -385 -113 -569 159 -643 -243 46 82 -311 -335 126 -401 27 189 -520 -33 -411 225 -401 -337 -1640 -273 157 -420 -158 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSSASWCCAGCCTGGSCAAC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 862 E= 1.8e-175 0.000000 0.001160 0.000000 0.998840 0.019722 0.415313 0.394432 0.170534 0.175174 0.366589 0.419954 0.038283 0.948956 0.015081 0.019722 0.016241 0.030162 0.404872 0.561485 0.003480 0.595128 0.002320 0.002320 0.400232 0.002320 0.940835 0.012761 0.044084 0.011601 0.960557 0.004640 0.023202 1.000000 0.000000 0.000000 0.000000 0.031323 0.012761 0.859629 0.096288 0.001160 0.962877 0.006961 0.029002 0.010441 0.953596 0.002320 0.033643 0.006961 0.015081 0.000000 0.977958 0.034803 0.000000 0.951276 0.013921 0.091647 0.005800 0.900232 0.002320 0.037123 0.410673 0.529002 0.023202 0.019722 0.719258 0.018561 0.242459 0.742459 0.008121 0.237819 0.011601 0.952436 0.018561 0.029002 0.000000 0.030162 0.886311 0.016241 0.067285 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSSASWCCAGCCTGGSCAAC MEME-3 regular expression -------------------------------------------------------------------------------- T[CG][GC]A[GC][AT]CCAGCCTGG[GC][CT][AG]AC -------------------------------------------------------------------------------- Time 1122.01 secs. ******************************************************************************** ******************************************************************************** MOTIF GCYGAGGCRGGAGRATCRCT MEME-4 width = 20 sites = 871 llr = 15353 E-value = 2.1e-163 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCYGAGGCRGGAGRATCRCT MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::2a:::6:1614a::6:: pos.-specific C :a4::::7:::2::::7:92 probability G 9::8:aa:499:96::14:1 matrix T ::6::::2:::2:::a2:16 bits 2.3 ** 2.1 * ** 1.9 * ** 1.6 ** ** Relative 1.4 ** *** * ** Entropy 1.2 *** *** ** * ** * (25.4 bits) 0.9 *********** **** ** 0.7 ******************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GCTGAGGCAGGAGGATCACT consensus C TG C A G C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCYGAGGCRGGAGRATCRCT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1448847 bayes= 12.6499 E= 2.1e-163 -264 -503 166 -386 -645 167 -403 -280 -645 27 -457 164 -11 -444 140 -413 230 -1641 -457 -745 -259 -802 169 -645 -209 -802 167 -1641 -306 132 -544 14 158 -522 34 -413 -245 -403 161 -275 -172 -486 163 -745 150 -50 -403 1 -45 -802 151 -1641 111 -802 92 -1641 232 -1641 -802 -1641 -586 -702 -1641 231 -336 129 -192 -23 152 -422 38 -345 -413 160 -544 -143 -232 -55 -121 164 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCYGAGGCRGGAGRATCRCT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 871 E= 2.1e-163 0.032147 0.009185 0.944891 0.013777 0.002296 0.950631 0.018370 0.028703 0.002296 0.361653 0.012629 0.623421 0.185993 0.013777 0.788749 0.011481 0.986223 0.000000 0.012629 0.001148 0.033295 0.001148 0.963261 0.002296 0.047072 0.001148 0.951780 0.000000 0.024110 0.748565 0.006889 0.220436 0.601607 0.008037 0.378875 0.011481 0.036739 0.018370 0.915040 0.029851 0.060850 0.010333 0.927669 0.001148 0.568312 0.211251 0.018370 0.202067 0.146958 0.001148 0.851894 0.000000 0.433984 0.001148 0.564868 0.000000 0.998852 0.000000 0.001148 0.000000 0.003444 0.002296 0.000000 0.994259 0.019518 0.730195 0.079219 0.171068 0.575201 0.016073 0.390356 0.018370 0.011481 0.907003 0.006889 0.074627 0.040184 0.204363 0.129736 0.625718 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCYGAGGCRGGAGRATCRCT MEME-4 regular expression -------------------------------------------------------------------------------- GC[TC]GAGG[CT][AG]GG[ACT]G[GA]ATC[AG]C[TC] -------------------------------------------------------------------------------- Time 1465.84 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCRYGGTGGCKCAYGCCTG MEME-5 width = 20 sites = 864 llr = 14836 E-value = 1.8e-154 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCRYGGTGGCKCAYGCCTG MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::4:2:::::2:7:3:::1 pos.-specific C ::7:4:::::8:7:6:99:: probability G a9:6:89:aa:323:7:::9 matrix T ::3:6::a::251:4:::a: bits 2.3 2.1 * * 1.9 * * 1.6 * *** * Relative 1.4 ** **** **** Entropy 1.2 ** * ***** * **** (24.8 bits) 0.9 *** ******* * ***** 0.7 *********** ******* 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GGCGTGGTGGCTCACGCCTG consensus TAC TG GTA sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCRYGGTGGCKCAYGCCTG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1448847 bayes= 12.3619 E= 1.8e-154 -263 -1640 169 -1640 -244 -431 166 -743 -274 123 -543 37 93 -431 97 -374 -1640 26 -1640 168 -7 -411 138 -427 -219 -543 166 -1640 -511 -411 -543 227 -244 -1640 168 -644 -1640 -1640 173 -444 -1640 141 -1640 2 8 -431 3 122 -363 118 -81 -60 174 -1640 15 -1640 -304 94 -411 93 38 -1640 126 -304 -1640 166 -469 -231 -463 166 -601 -223 -444 -501 -701 229 -139 -469 161 -1640 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCRYGGTGGCKCAYGCCTG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 864 E= 1.8e-154 0.032407 0.000000 0.967593 0.000000 0.037037 0.015046 0.946759 0.001157 0.030093 0.703704 0.006944 0.259259 0.383102 0.015046 0.586806 0.015046 0.000000 0.357639 0.000000 0.642361 0.190972 0.017361 0.781250 0.010417 0.043981 0.006944 0.949074 0.000000 0.005787 0.017361 0.006944 0.969907 0.037037 0.000000 0.960648 0.002315 0.000000 0.000000 0.990741 0.009259 0.000000 0.796296 0.000000 0.203704 0.211806 0.015046 0.305556 0.467593 0.016204 0.680556 0.171296 0.131944 0.667824 0.000000 0.332176 0.000000 0.024306 0.575231 0.017361 0.383102 0.260417 0.000000 0.715278 0.024306 0.000000 0.947917 0.011574 0.040509 0.008102 0.944444 0.004630 0.042824 0.009259 0.009259 0.002315 0.979167 0.076389 0.011574 0.912037 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCRYGGTGGCKCAYGCCTG MEME-5 regular expression -------------------------------------------------------------------------------- GG[CT][GA][TC]GGTGG[CT][TGA]C[AG][CT][GA]CCTG -------------------------------------------------------------------------------- Time 1806.28 secs. ******************************************************************************** ******************************************************************************** MOTIF GAGGTTGCAGTGAGCYGAGA MEME-6 width = 20 sites = 463 llr = 9260 E-value = 1.1e-063 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAGGTTGCAGTGAGCYGAGA MEME-6 Description -------------------------------------------------------------------------------- Simplified A 1a:1::1:9:::a:::38:9 pos.-specific C :::12::9::::::96:::: probability G 9:98::9:1a:a:a::6:91 matrix T ::::8a:1::a::::3:2:: bits 2.3 2.1 * * * 1.9 * * * * * 1.6 * * * * * * Relative 1.4 ** ** ******* *** Entropy 1.2 *** *********** *** (28.9 bits) 0.9 *** *********** *** 0.7 ******************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GAGGTTGCAGTGAGCCGAGA consensus TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGGTTGCAGTGAGCYGAGA MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1448847 bayes= 13.8844 E= 1.1e-063 -122 -553 159 -495 225 -611 -311 -554 -214 -611 166 -495 -184 -136 142 -284 -495 -72 -479 200 -554 -331 -453 225 -178 -611 160 -273 -354 161 -611 -158 217 -353 -236 -373 -263 -711 167 -421 -554 -431 -553 228 -245 -553 167 -495 226 -1550 -341 -454 -337 -553 169 -421 -421 165 -611 -214 -245 105 -379 67 67 -431 110 -308 198 -553 -366 -18 -229 -379 164 -554 219 -553 -221 -395 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGGTTGCAGTGAGCYGAGA MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 463 E= 1.1e-063 0.086393 0.006479 0.900648 0.006479 0.956803 0.004320 0.034557 0.004320 0.045356 0.004320 0.943844 0.006479 0.056156 0.116631 0.799136 0.028078 0.006479 0.181425 0.010799 0.801296 0.004320 0.030238 0.012959 0.952484 0.058315 0.004320 0.907127 0.030238 0.017279 0.911447 0.004320 0.066955 0.900648 0.025918 0.058315 0.015119 0.032397 0.002160 0.954644 0.010799 0.004320 0.015119 0.006479 0.974082 0.036717 0.006479 0.950324 0.006479 0.963283 0.000000 0.028078 0.008639 0.019438 0.006479 0.963283 0.010799 0.010799 0.939525 0.004320 0.045356 0.036717 0.622030 0.021598 0.319654 0.319654 0.015119 0.641469 0.023758 0.792657 0.006479 0.023758 0.177106 0.041037 0.021598 0.933045 0.004320 0.915767 0.006479 0.064795 0.012959 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGGTTGCAGTGAGCYGAGA MEME-6 regular expression -------------------------------------------------------------------------------- GAGGTTGCAGTGAGC[CT][GA]AGA -------------------------------------------------------------------------------- Time 2144.65 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCGGSGGCSGSGGCGGSGG MEME-7 width = 20 sites = 2566 llr = 23728 E-value = 8.4e-092 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCGGSGGCSGSGGCGGSGG MEME-7 Description -------------------------------------------------------------------------------- Simplified A 111111::1211::1:111: pos.-specific C 2:62242273:6:1613522 probability G 692774883593a8376477 matrix T ::1::1:::::::111:::: bits 2.3 2.1 1.9 1.6 Relative 1.4 * * Entropy 1.2 * * (13.3 bits) 0.9 * ** * * 0.7 * * *** * ** * * 0.5 ** ** ************** 0.2 ******************** 0.0 -------------------- Multilevel GGCGGCGGCGGCGGCGGCGG consensus C C G GC G G CG C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGSGGCSGSGGCGGSGG MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1448847 bayes= 11.427 E= 8.4e-092 -65 -27 106 -1797 -171 -1797 162 -328 -128 106 -64 -99 -56 -54 113 -900 -108 -86 129 -442 -67 57 30 -172 -286 -93 144 -801 -601 -69 144 -1797 -180 116 -13 -1797 -9 3 75 -1797 -189 -303 153 -219 -90 94 8 -1797 -520 -321 168 -1797 -269 -122 138 -176 -182 106 -18 -185 -260 -115 130 -110 -70 -18 98 -317 -199 70 53 -280 -105 -59 121 -405 -410 -45 131 -305 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGSGGCSGSGGCGGSGG MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 2566 E= 8.4e-092 0.127825 0.248636 0.623539 0.000000 0.061185 0.000000 0.918161 0.020655 0.082619 0.623928 0.192518 0.100935 0.136399 0.206157 0.657054 0.000390 0.094700 0.164458 0.731489 0.009353 0.126267 0.444661 0.368277 0.060795 0.027670 0.157054 0.814497 0.000779 0.003118 0.185892 0.810990 0.000000 0.057677 0.669135 0.273188 0.000000 0.189010 0.305924 0.505066 0.000000 0.054170 0.036633 0.865160 0.044037 0.107560 0.576383 0.316056 0.000000 0.005456 0.032346 0.962198 0.000000 0.031177 0.128215 0.781372 0.059236 0.056898 0.622369 0.265004 0.055729 0.033125 0.135230 0.738114 0.093531 0.123149 0.263445 0.591193 0.022214 0.050663 0.486750 0.433749 0.028839 0.097038 0.199143 0.691738 0.012081 0.011691 0.219797 0.744349 0.024162 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGSGGCSGSGGCGGSGG MEME-7 regular expression -------------------------------------------------------------------------------- [GC]GC[GC]G[CG]GG[CG][GC]G[CG]GG[CG]G[GC][CG]G[GC] -------------------------------------------------------------------------------- Time 2504.89 secs. ******************************************************************************** ******************************************************************************** MOTIF TGARSYCAGGAG MEME-8 width = 12 sites = 957 llr = 11334 E-value = 4.3e-053 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGARSYCAGGAG MEME-8 Description -------------------------------------------------------------------------------- Simplified A ::a4:::7::a: pos.-specific C 1:::568::::: probability G :a:64::3a9:a matrix T 9::::41::::: bits 2.3 * 2.1 * * 1.9 * * * 1.6 *** * ** Relative 1.4 *** **** Entropy 1.2 *** ****** (17.1 bits) 0.9 **** ******* 0.7 ************ 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel TGAGCCCAGGAG consensus AGT G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGARSYCAGGAG MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1591943 bayes= 12.6797 E= 4.3e-053 -558 -246 -426 221 -368 -1655 172 -1655 228 -616 -384 -1655 88 -516 103 -426 -1655 86 54 -326 -1655 101 -1655 99 -500 147 -416 -45 184 -1655 -20 -326 -300 -1655 170 -1655 -234 -658 167 -478 230 -1655 -1655 -400 -294 -535 169 -1655 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGARSYCAGGAG MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 957 E= 4.3e-053 0.004180 0.054336 0.015674 0.925810 0.015674 0.000000 0.984326 0.000000 0.974922 0.004180 0.020899 0.000000 0.369906 0.008359 0.611285 0.010449 0.000000 0.542320 0.436782 0.020899 0.000000 0.602926 0.000000 0.397074 0.006270 0.829676 0.016719 0.147335 0.718913 0.000000 0.260188 0.020899 0.025078 0.000000 0.974922 0.000000 0.039707 0.003135 0.949843 0.007315 0.987461 0.000000 0.000000 0.012539 0.026123 0.007315 0.966562 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGARSYCAGGAG MEME-8 regular expression -------------------------------------------------------------------------------- TGA[GA][CG][CT]C[AG]GGAG -------------------------------------------------------------------------------- Time 2828.37 secs. ******************************************************************************** ******************************************************************************** MOTIF ATGGTGAAACCC MEME-9 width = 12 sites = 464 llr = 6406 E-value = 1.7e-038 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATGGTGAAACCC MEME-9 Description -------------------------------------------------------------------------------- Simplified A a:2::1a9a::: pos.-specific C :2::2::::a99 probability G ::8a:9:1:::: matrix T :8::8:::::11 bits 2.3 * * * 2.1 * * * 1.9 * **** 1.6 * * **** Relative 1.4 ** ** ****** Entropy 1.2 ************ (19.9 bits) 0.9 ************ 0.7 ************ 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel ATGGTGAAACCC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATGGTGAAACCC MEME-9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1591943 bayes= 13.97 E= 1.7e-038 232 -1550 -1550 -1550 -237 -99 -1550 201 -31 -612 148 -1550 -229 -1550 168 -1550 -202 -81 -1550 196 -61 -1550 154 -1550 232 -1550 -1550 -1550 221 -1550 -203 -1550 231 -512 -1550 -1550 -1550 174 -1550 -1550 -1550 161 -1550 -125 -1550 164 -1550 -159 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATGGTGAAACCC MEME-9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 464 E= 1.7e-038 1.000000 0.000000 0.000000 0.000000 0.038793 0.150862 0.000000 0.810345 0.161638 0.004310 0.834052 0.000000 0.040948 0.000000 0.959052 0.000000 0.049569 0.170259 0.000000 0.780172 0.131466 0.000000 0.868534 0.000000 1.000000 0.000000 0.000000 0.000000 0.926724 0.000000 0.073276 0.000000 0.991379 0.008621 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.915948 0.000000 0.084052 0.000000 0.933190 0.000000 0.066810 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATGGTGAAACCC MEME-9 regular expression -------------------------------------------------------------------------------- ATGGTGAAACCC -------------------------------------------------------------------------------- Time 3151.19 secs. ******************************************************************************** ******************************************************************************** MOTIF RWWWWWHHWWTTMTTYHHTW MEME-10 width = 20 sites = 984 llr = 9814 E-value = 4.4e-018 ******************************************************************************** -------------------------------------------------------------------------------- Motif RWWWWWHHWWTTMTTYHHTW MEME-10 Description -------------------------------------------------------------------------------- Simplified A 45433534232:533:4214 pos.-specific C 1:111:3222125::3232: probability G 3:112:11:::2:::21::1 matrix T 153545335576:7753475 bits 2.3 2.1 1.9 1.6 Relative 1.4 ** Entropy 1.2 * * * *** * (14.4 bits) 0.9 * * * *** * 0.7 * * ***** ** 0.5 * * * ************* 0.2 ******************** 0.0 -------------------- Multilevel AAATTTTATTTTATTTATTT consensus GTTAAACTAAA CAACTCCA sequence ACCC CA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RWWWWWHHWWTTMTTYHHTW MEME-10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1448847 bayes= 12.7548 E= 4.4e-018 109 -110 7 -74 136 -1659 -430 123 98 -101 -114 67 72 -207 -140 127 32 -121 -78 115 119 -307 -820 133 38 4 -173 76 101 -40 -253 67 30 -41 -281 128 32 -40 -316 128 9 -190 -1659 182 -1659 -61 -63 161 142 63 -1659 -1659 41 -820 -1659 187 47 -1659 -1659 185 -1659 22 -80 126 109 -28 -232 41 20 -10 -285 116 -190 -27 -1659 180 81 -1659 -101 132 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RWWWWWHHWWTTMTTYHHTW MEME-10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 984 E= 4.4e-018 0.425813 0.139228 0.315041 0.119919 0.513211 0.000000 0.015244 0.471545 0.395325 0.148374 0.136179 0.320122 0.331301 0.071138 0.113821 0.483740 0.250000 0.129065 0.174797 0.446138 0.458333 0.035569 0.001016 0.505081 0.261179 0.307927 0.090447 0.340447 0.403455 0.226626 0.051829 0.318089 0.246951 0.224593 0.042683 0.485772 0.251016 0.226626 0.033537 0.488821 0.213415 0.080285 0.000000 0.706301 0.000000 0.196138 0.193089 0.610772 0.536585 0.463415 0.000000 0.000000 0.267276 0.001016 0.000000 0.731707 0.277439 0.000000 0.000000 0.722561 0.000000 0.348577 0.171748 0.479675 0.425813 0.246951 0.059959 0.267276 0.230691 0.279472 0.041667 0.448171 0.053862 0.248984 0.000000 0.697154 0.350610 0.000000 0.148374 0.501016 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RWWWWWHHWWTTMTTYHHTW MEME-10 regular expression -------------------------------------------------------------------------------- [AG][AT][AT][TA][TA][TA][TCA][ATC][TAC][TAC][TA]T[AC][TA][TA][TC][ATC][TCA][TC][TA] -------------------------------------------------------------------------------- Time 3473.05 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (10) found. ******************************************************************************** CPU: cn45 ********************************************************************************