******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.1 (Release date: Sat Aug 21 19:23:23 2021 -0700) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** PRIMARY SEQUENCES= /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d6_BCG_TRIM1_7_peaks/seqs-centered CONTROL SEQUENCES= --none-- ALPHABET= ACGT ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d6_BCG_TRIM1_7_peaks/seqs-centered -oc /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d6_BCG_TRIM1_7_peaks/meme_out -mod zoops -nmotifs 10 -minw 5 -maxw 20 -bfile /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d6_BCG_TRIM1_7_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= 20237 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= 2023700 N= 20237 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.214 C 0.286 G 0.286 T 0.214 Background letter frequencies (from file /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d6_BCG_TRIM1_7_peaks/background): A 0.21 C 0.29 G 0.29 T 0.21 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF TAYWAAAAAWAMAAAAAWWA MEME-1 width = 20 sites = 2063 llr = 31859 E-value = 1.7e-400 ******************************************************************************** -------------------------------------------------------------------------------- Motif TAYWAAAAAWAMAAAAAWWA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 26238a98a49488988457 pos.-specific C 12521::1:1:4::11111: probability G :1::1::::1::1::1:1:1 matrix T 72341:11:51211:11442 bits 2.2 2.0 * * 1.8 ** * * 1.6 ** * * Relative 1.3 **** * *** * Entropy 1.1 ***** * ***** (22.3 bits) 0.9 * ***** * ***** ** 0.7 * ******** ***** ** 0.4 ** ***************** 0.2 ******************** 0.0 -------------------- Multilevel TACTAAAAATACAAAAAAAA consensus CTA A A TTT sequence AC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAYWAAAAAWAMAAAAAWWA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1639197 bayes= 11.9115 E= 1.7e-400 -18 -108 -350 163 144 -41 -230 -46 5 70 -287 37 63 -38 -605 109 191 -226 -227 -124 223 -605 -622 -595 212 -642 -532 -143 198 -162 -622 -157 222 -576 -532 -544 90 -203 -235 119 202 -270 -418 -129 95 50 -337 -42 200 -283 -225 -188 200 -285 -311 -132 216 -244 -622 -718 187 -162 -242 -134 198 -239 -590 -90 99 -190 -134 90 118 -195 -542 107 164 -305 -150 -2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAYWAAAAAWAMAAAAAWWA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 2063 E= 1.7e-400 0.186137 0.136694 0.025691 0.651478 0.570044 0.218129 0.058652 0.153175 0.217159 0.471643 0.039748 0.271449 0.324770 0.222492 0.004363 0.448376 0.790111 0.060591 0.060107 0.089190 0.988366 0.004363 0.003878 0.003393 0.911294 0.003393 0.007271 0.078042 0.831314 0.094038 0.003878 0.070771 0.982550 0.005332 0.007271 0.004847 0.393602 0.070771 0.056714 0.478914 0.853127 0.044595 0.015996 0.086282 0.405235 0.409598 0.028114 0.157053 0.841008 0.040717 0.061076 0.057198 0.841978 0.040233 0.033446 0.084343 0.941348 0.053320 0.003878 0.001454 0.768299 0.094523 0.054290 0.082889 0.827436 0.055259 0.004847 0.112458 0.416869 0.077557 0.114397 0.391178 0.477460 0.075133 0.006786 0.440620 0.655356 0.034901 0.102278 0.207465 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAYWAAAAAWAMAAAAAWWA MEME-1 regular expression -------------------------------------------------------------------------------- T[AC][CTA][TAC]AAAAA[TA]A[CA]AAAAA[AT][AT][AT] -------------------------------------------------------------------------------- Time 422.43 secs. ******************************************************************************** ******************************************************************************** MOTIF CCTCCCRARKWGCTGGGATT MEME-2 width = 20 sites = 1346 llr = 24656 E-value = 4.4e-341 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCTCCCRARKWGCTGGGATT MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::::::695:5:::111a:: pos.-specific C 99:998::::::9:::::31 probability G ::::::3:55:9::999::: matrix T :19112:::55:19::::79 bits 2.2 2.0 1.8 * * * * * 1.6 * * * * * Relative 1.3 **** * **** ** * Entropy 1.1 ***** * ********** (26.4 bits) 0.9 ********* ********** 0.7 ******************** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel CCTCCCAAAGAGCTGGGATT consensus TG GTT C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCCCRARKWGCTGGGATT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1639197 bayes= 12.5048 E= 4.4e-341 -324 164 -344 -219 -514 170 -628 -202 -469 -261 -628 216 -514 165 -375 -167 -434 164 -436 -155 -282 138 -444 -7 155 -336 17 -275 215 -340 -344 -424 124 -515 77 -614 -279 -332 70 116 124 -396 -502 118 -229 -444 169 -434 -556 166 -461 -162 -334 -332 -761 217 -158 -428 165 -656 -140 -385 161 -382 -184 -491 166 -362 218 -628 -296 -456 -514 -16 -544 179 -456 -229 -480 213 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCCCRARKWGCTGGGATT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 1346 E= 4.4e-341 0.022288 0.904903 0.026746 0.046062 0.005944 0.938336 0.003715 0.052006 0.008172 0.047548 0.003715 0.940565 0.005944 0.906389 0.021545 0.066122 0.010401 0.903418 0.014116 0.072065 0.029718 0.756315 0.013373 0.200594 0.615156 0.028232 0.325409 0.031204 0.934621 0.027489 0.026746 0.011144 0.495542 0.008172 0.493314 0.002972 0.030461 0.028975 0.470282 0.470282 0.496285 0.018574 0.008915 0.476226 0.043091 0.013373 0.933135 0.010401 0.004458 0.915305 0.011887 0.068351 0.020802 0.028975 0.001486 0.948737 0.070579 0.014859 0.912333 0.002229 0.079495 0.020059 0.885587 0.014859 0.058692 0.009658 0.914562 0.017088 0.950223 0.003715 0.037147 0.008915 0.005944 0.259287 0.006686 0.728083 0.008915 0.059435 0.010401 0.921248 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCCCRARKWGCTGGGATT MEME-2 regular expression -------------------------------------------------------------------------------- CCTCC[CT][AG]A[AG][GT][AT]GCTGGGA[TC]T -------------------------------------------------------------------------------- Time 775.87 secs. ******************************************************************************** ******************************************************************************** MOTIF GTYTCRCYMTGTTGSCCAGG MEME-3 width = 20 sites = 1224 llr = 21809 E-value = 5.0e-271 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTYTCRCYMTGTTGSCCAGG MEME-3 Description -------------------------------------------------------------------------------- Simplified A 1::::6::5:1::2:::a:: pos.-specific C ::4:8:953:::2:599::: probability G 9::::3::1:9::74:::99 matrix T :a6a2115:9:a7:11:::: bits 2.2 2.0 * * * * 1.8 * * * * * 1.6 * * * * * Relative 1.3 * * * * ** ***** Entropy 1.1 ** * * **** ***** (25.7 bits) 0.9 ***** ** ***** ***** 0.7 ******** ***** ***** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GTTTCACCATGTTGCCCAGG consensus C TG TC CAG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTYTCRCYMTGTTGSCCAGG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1639197 bayes= 12.4348 E= 5.0e-271 -182 -430 162 -262 -800 -371 -547 221 -642 59 -588 140 -642 -466 -615 222 -501 138 -366 3 149 -269 8 -188 -376 166 -566 -180 -569 80 -647 121 131 17 -143 -223 -520 -261 -615 216 -128 -371 160 -392 -484 -388 -688 221 -484 -28 -615 183 17 -547 134 -305 -355 76 60 -201 -431 160 -647 -99 -348 168 -688 -213 221 -688 -388 -542 -220 -688 170 -401 -220 -383 167 -431 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTYTCRCYMTGTTGSCCAGG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 1224 E= 5.0e-271 0.059641 0.014706 0.891340 0.034314 0.000817 0.022059 0.006536 0.970588 0.002451 0.437092 0.004902 0.555556 0.002451 0.011438 0.004085 0.982026 0.006536 0.756536 0.022876 0.214052 0.590686 0.044935 0.307190 0.057190 0.015523 0.918301 0.005719 0.060458 0.004085 0.505719 0.003268 0.486928 0.521242 0.325980 0.107843 0.044935 0.005719 0.047386 0.004085 0.942810 0.086601 0.022059 0.877451 0.013889 0.007353 0.019608 0.002451 0.970588 0.007353 0.239379 0.004085 0.749183 0.236111 0.006536 0.732026 0.025327 0.017974 0.491013 0.438725 0.052288 0.010621 0.879902 0.003268 0.106209 0.018791 0.930556 0.002451 0.048203 0.973039 0.002451 0.019608 0.004902 0.045752 0.002451 0.938725 0.013072 0.045752 0.020425 0.923203 0.010621 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTYTCRCYMTGTTGSCCAGG MEME-3 regular expression -------------------------------------------------------------------------------- GT[TC]T[CT][AG]C[CT][AC]TGT[TC][GA][CG]CCAGG -------------------------------------------------------------------------------- Time 1127.66 secs. ******************************************************************************** ******************************************************************************** MOTIF AGGCRGGAGRATCRCTTGAR MEME-4 width = 20 sites = 917 llr = 17202 E-value = 3.6e-225 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGGCRGGAGRATCRCTTGAR MEME-4 Description -------------------------------------------------------------------------------- Simplified A a:::611625a::5::::a5 pos.-specific C :::7:::2::::7:92:::: probability G :a9:499:85::14:::a:5 matrix T :::2:::2:::a2:17a::: bits 2.2 2.0 * ** * * 1.8 * ** * * 1.6 *** ** *** Relative 1.3 *** * ** * *** Entropy 1.1 *** ** * ** * *** (27.1 bits) 0.9 ******* **** ****** 0.7 ******************** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel AGGCAGGAGGATCACTTGAG consensus TG A TG C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGCRGGAGRATCRCTTGAR MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1639197 bayes= 13.0761 E= 3.6e-225 222 -705 -397 -759 -231 -573 171 -759 -216 -705 171 -601 -301 132 -647 24 152 -573 34 -307 -164 -405 163 -342 -181 -647 169 -659 156 -64 -525 -19 -45 -605 153 -527 110 -573 91 -759 219 -459 -366 -659 -601 -320 -805 220 -501 128 -217 9 130 -366 58 -307 -601 169 -525 -204 -378 -35 -281 177 -501 -805 -525 223 -389 -647 176 -559 222 -705 -459 -559 112 -505 88 -759 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGCRGGAGRATCRCTTGAR MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 917 E= 3.6e-225 0.978190 0.002181 0.018539 0.001091 0.042530 0.005453 0.950927 0.001091 0.046892 0.002181 0.947655 0.003272 0.026172 0.723010 0.003272 0.247546 0.601963 0.005453 0.367503 0.025082 0.067612 0.017448 0.895311 0.019629 0.059978 0.003272 0.934569 0.002181 0.621592 0.186478 0.007634 0.184297 0.153762 0.004362 0.836423 0.005453 0.450382 0.005453 0.543075 0.001091 0.962923 0.011996 0.022901 0.002181 0.003272 0.031625 0.001091 0.964013 0.006543 0.705562 0.064340 0.223555 0.517993 0.022901 0.434024 0.025082 0.003272 0.937841 0.007634 0.051254 0.015267 0.227917 0.041439 0.715376 0.006543 0.001091 0.007634 0.984733 0.014177 0.003272 0.978190 0.004362 0.981461 0.002181 0.011996 0.004362 0.456925 0.008724 0.533261 0.001091 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGCRGGAGRATCRCTTGAR MEME-4 regular expression -------------------------------------------------------------------------------- AGG[CT][AG]GGAG[GA]AT[CT][AG]C[TC]TGA[GA] -------------------------------------------------------------------------------- Time 1473.66 secs. ******************************************************************************** ******************************************************************************** MOTIF GGGYGYRGTGGCDCRHKCCT MEME-5 width = 20 sites = 1566 llr = 22299 E-value = 1.4e-203 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGYGYRGTGGCDCRHKCCT MEME-5 Description -------------------------------------------------------------------------------- Simplified A 23::3:41::::3:632:1: pos.-specific C :::5:5:::::8:7:4:a72 probability G 77a:7:69:aa:314:5::: matrix T :::5:5::a::232:33:28 bits 2.2 2.0 * 1.8 * 1.6 * *** * Relative 1.3 * **** * * Entropy 1.1 * ***** * * (20.5 bits) 0.9 *** ******** * *** 0.7 ************ ** *** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GGGCGTGGTGGCGCACGCCT consensus AA TACA TT GTT T sequence A A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGYGYRGTGGCDCRHKCCT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1639197 bayes= 11.9451 E= 1.4e-203 19 -402 131 -301 55 -650 123 -419 -412 -370 173 -636 -297 73 -418 118 55 -782 122 -384 -378 71 -602 127 92 -566 104 -678 -135 -466 164 -836 -678 -350 -1726 221 -243 -782 173 -678 -266 -882 172 -404 -836 142 -882 8 49 -430 27 70 -578 122 -106 -22 140 -343 46 -361 35 51 -366 50 -8 -566 82 44 -436 172 -624 -261 -206 126 -524 25 -404 -64 -437 190 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGYGYRGTGGCDCRHKCCT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 1566 E= 1.4e-203 0.239464 0.017880 0.716475 0.026181 0.307791 0.003193 0.677522 0.011494 0.012133 0.022350 0.962963 0.002554 0.026820 0.480843 0.015964 0.476373 0.308429 0.001277 0.675607 0.014687 0.015326 0.473180 0.004470 0.507024 0.397829 0.005747 0.594508 0.001916 0.082375 0.011494 0.905492 0.000639 0.001916 0.025543 0.000000 0.972542 0.038953 0.001277 0.957854 0.001916 0.033206 0.000639 0.953384 0.012771 0.000639 0.777139 0.000639 0.221584 0.295658 0.014687 0.348659 0.340996 0.003831 0.676245 0.139208 0.180715 0.556194 0.026820 0.399745 0.017241 0.267561 0.411239 0.022989 0.298212 0.199234 0.005747 0.510217 0.284802 0.010217 0.951469 0.003831 0.034483 0.050447 0.692209 0.007663 0.249681 0.012771 0.186462 0.014049 0.786718 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGYGYRGTGGCDCRHKCCT MEME-5 regular expression -------------------------------------------------------------------------------- [GA][GA]G[CT][GA][TC][GA]GTGG[CT][GTA]C[AG][CTA][GT]C[CT]T -------------------------------------------------------------------------------- Time 1814.73 secs. ******************************************************************************** ******************************************************************************** MOTIF CAGGAGTTCRAGACCA MEME-6 width = 16 sites = 679 llr = 11929 E-value = 3.1e-145 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAGGAGTTCRAGACCA MEME-6 Description -------------------------------------------------------------------------------- Simplified A :91:a11::3a:9::a pos.-specific C 9:::::::7::::99: probability G :19a:9:::6:a1::: matrix T ::::::8a3:::::1: bits 2.2 * * 2.0 * * * * 1.8 * * * * * * 1.6 ** ** ** *** * Relative 1.3 ******** ****** Entropy 1.1 ******** ****** (25.3 bits) 0.9 **************** 0.7 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CAGGAGTTCGAGACCA consensus TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGAGTTCRAGACCA MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 1720145 bayes= 13.4987 E= 3.1e-145 -516 171 -762 -216 216 -1605 -230 -715 -170 -462 167 -1605 -235 -762 172 -557 219 -562 -303 -715 -207 -1605 170 -457 -63 -371 -603 199 -1605 -503 -1605 224 -384 124 -337 37 62 -303 114 -616 225 -762 -1605 -715 -616 -530 177 -715 216 -1605 -230 -715 -399 167 -381 -220 -1605 166 -762 -132 220 -603 -323 -715 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGAGTTCRAGACCA MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 679 E= 3.1e-145 0.005891 0.945508 0.001473 0.047128 0.939617 0.000000 0.058910 0.001473 0.064801 0.011782 0.923417 0.000000 0.041237 0.001473 0.952872 0.004418 0.957290 0.005891 0.035346 0.001473 0.050074 0.000000 0.941090 0.008837 0.135493 0.022091 0.004418 0.837997 0.000000 0.008837 0.000000 0.991163 0.014728 0.684831 0.027982 0.272459 0.322533 0.035346 0.639175 0.002946 0.997054 0.001473 0.000000 0.001473 0.002946 0.007364 0.988218 0.001473 0.939617 0.000000 0.058910 0.001473 0.013255 0.920471 0.020619 0.045655 0.000000 0.914580 0.001473 0.083947 0.963181 0.004418 0.030928 0.001473 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGAGTTCRAGACCA MEME-6 regular expression -------------------------------------------------------------------------------- CAGGAGTT[CT][GA]AGACCA -------------------------------------------------------------------------------- Time 2150.60 secs. ******************************************************************************** ******************************************************************************** MOTIF GGSSGCGGSGGCGGSSGSGG MEME-7 width = 20 sites = 3186 llr = 28169 E-value = 2.6e-066 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGSSGCGGSGGCGGSSGSGG MEME-7 Description -------------------------------------------------------------------------------- Simplified A ::11:11:11121::1:1:1 pos.-specific C 21631722422631642522 probability G 79359288576268458486 matrix T ::11::::::11:1:111:: bits 2.2 2.0 1.8 1.6 Relative 1.3 Entropy 1.1 * * (12.8 bits) 0.9 ** * ** * * * 0.7 ** **** * ** * ** 0.4 *** ******* *** * ** 0.2 ******************** 0.0 -------------------- Multilevel GGCGGCGGGGGCGGCGGCGG consensus C GC G CC C GC GCC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGSSGCGGSGGCGGSSGSGG MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1639197 bayes= 11.2168 E= 2.6e-066 -214 -43 135 -1828 -1828 -184 163 -318 -183 101 6 -190 -97 -1 71 -68 -400 -182 163 -493 -60 117 -48 -1828 -174 -95 144 -1828 -245 -56 140 -1828 -93 58 65 -1828 -147 -45 127 -390 -52 -91 116 -200 -44 101 -54 -179 -84 -10 103 -322 -839 -135 149 -152 -1828 99 45 -293 -126 38 68 -156 -1828 -81 138 -137 -124 73 29 -149 -1828 -50 143 -393 -81 -31 116 -1828 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGSSGCGGSGGCGGSSGSGG MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 3186 E= 2.6e-066 0.047709 0.215003 0.737288 0.000000 0.000000 0.080979 0.895794 0.023227 0.059322 0.581921 0.302574 0.056183 0.107659 0.287508 0.473949 0.130885 0.013183 0.082235 0.897677 0.006905 0.138418 0.653484 0.208098 0.000000 0.062775 0.150345 0.786880 0.000000 0.038606 0.196485 0.764909 0.000000 0.110483 0.434087 0.455430 0.000000 0.075957 0.211864 0.698054 0.014124 0.146265 0.154112 0.647207 0.052417 0.155053 0.584746 0.199309 0.060891 0.117389 0.270245 0.589768 0.022599 0.000628 0.113308 0.812932 0.073132 0.000000 0.576271 0.396108 0.027621 0.087884 0.378217 0.462649 0.071249 0.000000 0.165097 0.753610 0.081293 0.089140 0.480854 0.354991 0.075016 0.000000 0.204645 0.781544 0.013810 0.119900 0.233208 0.646893 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGSSGCGGSGGCGGSSGSGG MEME-7 regular expression -------------------------------------------------------------------------------- [GC]G[CG][GC]G[CG]GG[GC][GC]GC[GC]G[CG][GC]G[CG][GC][GC] -------------------------------------------------------------------------------- Time 2487.08 secs. ******************************************************************************** ******************************************************************************** MOTIF AGGYRGAGGTTGCAGTGAGC MEME-8 width = 20 sites = 440 llr = 9419 E-value = 2.0e-065 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGGYRGAGGTTGCAGTGAGC MEME-8 Description -------------------------------------------------------------------------------- Simplified A a11:31a::::::9:::a:: pos.-specific C :::61:::12::9::::::a probability G :99:69:99::a:1a:a:a: matrix T :::3:::::8a:1::a:::: bits 2.2 2.0 * * * * * 1.8 * * * * * * 1.6 * ** ** ******* Relative 1.3 *** *** *********** Entropy 1.1 *** *************** (30.9 bits) 0.9 **** *************** 0.7 **** *************** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel AGGCGGAGGTTGCAGTGAGC consensus TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGYRGAGGTTGCAGTGAGC MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1639197 bayes= 13.8166 E= 2.0e-065 222 -599 -467 -553 -189 -1543 169 -495 -178 -699 168 -453 -553 114 -467 73 73 -241 92 -214 -201 -699 170 -553 222 -699 -467 -453 -221 -699 171 -553 -214 -160 156 -553 -421 -78 -541 195 -495 -541 -599 222 -236 -599 171 -553 -653 169 -699 -178 213 -441 -229 -453 -336 -699 175 -653 -653 -441 -382 220 -453 -499 176 -1543 222 -599 -441 -1543 -307 -599 174 -553 -653 174 -1543 -272 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGYRGAGGTTGCAGTGAGC MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 440 E= 2.0e-065 0.979545 0.004545 0.011364 0.004545 0.056818 0.000000 0.936364 0.006818 0.061364 0.002273 0.927273 0.009091 0.004545 0.636364 0.011364 0.347727 0.347727 0.054545 0.550000 0.047727 0.052273 0.002273 0.940909 0.004545 0.977273 0.002273 0.011364 0.009091 0.045455 0.002273 0.947727 0.004545 0.047727 0.095455 0.852273 0.004545 0.011364 0.168182 0.006818 0.813636 0.006818 0.006818 0.004545 0.981818 0.040909 0.004545 0.950000 0.004545 0.002273 0.934091 0.002273 0.061364 0.918182 0.013636 0.059091 0.009091 0.020455 0.002273 0.975000 0.002273 0.002273 0.013636 0.020455 0.963636 0.009091 0.009091 0.981818 0.000000 0.981818 0.004545 0.013636 0.000000 0.025000 0.004545 0.965909 0.004545 0.002273 0.965909 0.000000 0.031818 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGYRGAGGTTGCAGTGAGC MEME-8 regular expression -------------------------------------------------------------------------------- AGG[CT][GA]GAGGTTGCAGTGAGC -------------------------------------------------------------------------------- Time 2807.44 secs. ******************************************************************************** ******************************************************************************** MOTIF WWDDDWWWAAWRAATDWANW MEME-9 width = 20 sites = 2132 llr = 19131 E-value = 2.2e-028 ******************************************************************************** -------------------------------------------------------------------------------- Motif WWDDDWWWAAWRAATDWANW MEME-9 Description -------------------------------------------------------------------------------- Simplified A 55352554555677234723 pos.-specific C ::1:1::1121::::11:3: probability G :1333212211311231:21 matrix T 53334343224132725336 bits 2.2 2.0 1.8 1.6 Relative 1.3 * * Entropy 1.1 * ** * (12.9 bits) 0.9 ** *** * * 0.7 ** * ** **** ** * 0.4 ** * **** ***** ** * 0.2 ****************** * 0.0 -------------------- Multilevel AATATAAAAAAAAATGTATT consensus TTGTGTTT TTGTT AATCA sequence AGA T A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWDDDWWWAAWRAATDWANW MEME-9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1639197 bayes= 11.824 E= 2.2e-028 135 -1770 -1770 115 136 -1770 -109 62 35 -212 16 70 114 -1770 -14 38 8 -217 15 90 116 -1770 -59 68 115 -1770 -97 87 110 -175 -71 45 128 -130 -65 -18 119 -56 -152 8 114 -150 -190 76 149 -329 16 -190 164 -1770 -189 35 178 -1770 -249 10 -25 -1770 -95 168 71 -162 25 5 93 -190 -222 112 168 -1770 -1770 63 12 -21 -39 52 49 -1770 -116 145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWDDDWWWAAWRAATDWANW MEME-9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 2132 E= 2.2e-028 0.534240 0.000000 0.000000 0.465760 0.540807 0.000000 0.136492 0.322702 0.267355 0.066604 0.324578 0.341463 0.464353 0.000000 0.262664 0.272983 0.222795 0.064259 0.320356 0.392589 0.469512 0.000000 0.192777 0.337711 0.466229 0.000000 0.148218 0.385553 0.449343 0.085835 0.177298 0.287523 0.512195 0.117261 0.184803 0.185741 0.480769 0.196529 0.100844 0.221857 0.463415 0.102251 0.077392 0.356942 0.590994 0.029550 0.323171 0.056285 0.654315 0.000000 0.078330 0.267355 0.722326 0.000000 0.051595 0.226079 0.176829 0.000000 0.150094 0.673077 0.343340 0.094278 0.345216 0.217167 0.401970 0.077392 0.062383 0.458255 0.674953 0.000000 0.000000 0.325047 0.227955 0.250000 0.220919 0.301126 0.295497 0.000000 0.129925 0.574578 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWDDDWWWAAWRAATDWANW MEME-9 regular expression -------------------------------------------------------------------------------- [AT][AT][TGA][ATG][TGA][AT][AT][AT]A[AT][AT][AG][AT][AT]T[GAT][TA][AT][TCAG][TA] -------------------------------------------------------------------------------- Time 3128.16 secs. ******************************************************************************** ******************************************************************************** MOTIF CCCTCCCCBCMCCCCC MEME-10 width = 16 sites = 429 llr = 4669 E-value = 3.8e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCCTCCCCBCMCCCCC MEME-10 Description -------------------------------------------------------------------------------- Simplified A ::::::1:1222:121 pos.-specific C 7a7:996a48469867 probability G ::::::::2:21:1:2 matrix T 3:3a113:3:211:2: bits 2.2 * 2.0 * 1.8 * * 1.6 * * * Relative 1.3 * *** * * Entropy 1.1 ** *** * * ** (15.7 bits) 0.9 ** *** * * ** 0.7 ******** * ** * 0.4 ******** * ***** 0.2 ******** * ***** 0.0 ---------------- Multilevel CCCTCCCCCCCCCCCC consensus T T T TAA TG sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTCCCCBCMCCCCC MEME-10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 1720145 bayes= 13.9144 E= 3.8e-012 -1539 130 -1539 45 -1539 179 -1539 -1539 -417 117 -287 50 -649 -1539 -1539 225 -1539 159 -596 -77 -1539 164 -1539 -110 -77 104 -1539 42 -217 172 -1539 -1539 -61 30 -43 47 0 143 -1539 -417 18 45 -71 -16 -45 116 -115 -159 -1539 156 -1539 -54 -141 154 -187 -1539 -9 93 -1539 25 -91 120 -39 -1539 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTCCCCBCMCCCCC MEME-10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 429 E= 3.8e-012 0.000000 0.713287 0.000000 0.286713 0.000000 1.000000 0.000000 0.000000 0.011655 0.650350 0.039627 0.298368 0.002331 0.000000 0.000000 0.997669 0.000000 0.871795 0.004662 0.123543 0.000000 0.902098 0.000000 0.097902 0.123543 0.594406 0.000000 0.282051 0.046620 0.953380 0.000000 0.000000 0.137529 0.356643 0.214452 0.291375 0.209790 0.778555 0.000000 0.011655 0.237762 0.396270 0.177156 0.188811 0.153846 0.645688 0.130536 0.069930 0.000000 0.855478 0.000000 0.144522 0.079254 0.841492 0.079254 0.000000 0.198135 0.552448 0.000000 0.249417 0.111888 0.666667 0.221445 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTCCCCBCMCCCCC MEME-10 regular expression -------------------------------------------------------------------------------- [CT]C[CT]TCC[CT]C[CTG][CA][CA]CCC[CT][CG] -------------------------------------------------------------------------------- Time 3437.38 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (10) found. ******************************************************************************** CPU: cn45 ********************************************************************************