******************************************************************************** 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= seqs/AT1G06850_peak_sequences.fasta 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 seqs/AT1G06850_peak_sequences.fasta -dna -oc out/AT1G06850 -nostatus -time 300 -mod zoops -nmotifs 2 -minw 6 -maxw 50 -objfun classic -revcomp -markov_order 0 -mpi model: mod= zoops nmotifs= 2 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + - width: minw= 6 maxw= 50 nsites: minsites= 2 maxsites= 2279 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= 404374 N= 2279 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.315 C 0.185 G 0.185 T 0.315 Background letter frequencies (from file dataset with add-one prior applied): A 0.317 C 0.183 G 0.183 T 0.317 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF NNDNWWDVHCAGCT MEME-1 width = 14 sites = 1902 llr = 10947 E-value = 5.0e-415 ******************************************************************************** -------------------------------------------------------------------------------- Motif NNDNWWDVHCAGCT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 33434323319::: pos.-specific C 2222111345:1a: probability G 22222243:119:: matrix T 3333343132:::a bits 2.4 2.2 * 2.0 ** 1.7 *** Relative 1.5 *** Entropy 1.2 **** (8.3 bits) 1.0 **** 0.7 **** 0.5 ****** 0.2 ******** 0.0 -------------- Multilevel TTATATGACCAGCT consensus AATATATCAT sequence GG GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NNDNWWDVHCAGCT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 374747 bayes= 8.81818 E= 5.0e-415 -15 9 20 -4 -21 11 32 -7 15 -27 -4 1 -5 -9 2 9 21 -43 -18 8 5 -133 -21 48 -69 -145 110 11 -5 60 56 -112 0 114 -844 -19 -135 148 -40 -50 146 -412 -73 -523 -359 -156 231 -643 -1754 242 -1754 -423 -1754 -1754 -1754 166 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NNDNWWDVHCAGCT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 1902 E= 5.0e-415 0.286015 0.194532 0.210831 0.308623 0.272871 0.197687 0.228707 0.300736 0.350683 0.152471 0.178759 0.318086 0.304942 0.171924 0.185594 0.337539 0.366982 0.136172 0.161935 0.334911 0.327550 0.073081 0.158780 0.440589 0.196635 0.067298 0.393270 0.342797 0.305468 0.277077 0.271293 0.146162 0.317035 0.405363 0.000526 0.277077 0.124606 0.512618 0.139327 0.223449 0.870137 0.010515 0.110936 0.008412 0.026288 0.062040 0.907992 0.003680 0.000000 0.983176 0.000000 0.016824 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NNDNWWDVHCAGCT MEME-1 regular expression -------------------------------------------------------------------------------- [TAG][TAG][AT][TA][AT][TA][GT][ACG][CAT][CT]AGCT -------------------------------------------------------------------------------- Time 127.93 secs. ******************************************************************************** ******************************************************************************** MOTIF BTYTYTCTTYTTCTTYTTYTYHTYYYTYW MEME-2 width = 29 sites = 268 llr = 3125 E-value = 7.9e-034 ******************************************************************************** -------------------------------------------------------------------------------- Motif BTYTYTCTTYTTCTTYTTYTYHTYYYTYW MEME-2 Description -------------------------------------------------------------------------------- Simplified A 12::::::::1::1::11:2222111:13 pos.-specific C 41524:71263271352251342332341 probability G 21111:111:11:1::1:11::1112:11 matrix T 37475a28745737756646545555745 bits 2.4 2.2 2.0 1.7 * Relative 1.5 * Entropy 1.2 * * (16.8 bits) 1.0 ** * * * * 0.7 ******** * ** * 0.5 ********* ***** ** * ** 0.2 **************************** 0.0 ----------------------------- Multilevel CTCTTTCTTCTTCTTCTTCTTTTTTTTCT consensus T TCC CTC T CT CT CCCCCCCTA sequence G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BTYTYTCTTYTTCTTYTTYTYHTYYYTYW MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 340562 bayes= 12.0698 E= 7.9e-034 -176 107 14 2 -91 -130 -103 108 -1471 149 -49 16 -1471 34 -181 118 -1471 116 -62 57 -1471 -1471 -1471 166 -482 185 -37 -76 -308 -123 -71 129 -1471 29 -81 109 -360 168 -1471 28 -155 45 -66 73 -295 2 -137 115 -408 184 -1471 4 -128 -49 -153 109 -324 53 -362 112 -1471 147 -1471 64 -160 11 -45 83 -112 38 -330 92 -308 139 -137 37 -79 -33 -116 90 -79 67 -1471 73 -55 94 -362 40 -76 31 -98 64 -171 74 -116 70 -112 63 -181 71 -141 43 -10 55 -408 72 -1471 110 -250 123 -86 39 -26 -45 -57 59 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BTYTYTCTTYTTCTTYTTYTYHTYYYTYW MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 268 E= 7.9e-034 0.093284 0.384328 0.201493 0.320896 0.167910 0.074627 0.089552 0.667910 0.000000 0.514925 0.130597 0.354478 0.000000 0.231343 0.052239 0.716418 0.000000 0.410448 0.119403 0.470149 0.000000 0.000000 0.000000 1.000000 0.011194 0.660448 0.141791 0.186567 0.037313 0.078358 0.111940 0.772388 0.000000 0.223881 0.104478 0.671642 0.026119 0.589552 0.000000 0.384328 0.108209 0.250000 0.115672 0.526119 0.041045 0.186567 0.070896 0.701493 0.018657 0.656716 0.000000 0.324627 0.130597 0.130597 0.063433 0.675373 0.033582 0.264925 0.014925 0.686567 0.000000 0.507463 0.000000 0.492537 0.104478 0.197761 0.134328 0.563433 0.145522 0.238806 0.018657 0.597015 0.037313 0.481343 0.070896 0.410448 0.182836 0.145522 0.082090 0.589552 0.182836 0.291045 0.000000 0.526119 0.216418 0.350746 0.014925 0.417910 0.186567 0.227612 0.093284 0.492537 0.097015 0.305970 0.082090 0.514925 0.145522 0.283582 0.052239 0.518657 0.119403 0.246269 0.171642 0.462687 0.018657 0.302239 0.000000 0.679104 0.055970 0.429104 0.100746 0.414179 0.264925 0.134328 0.123134 0.477612 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BTYTYTCTTYTTCTTYTTYTYHTYYYTYW MEME-2 regular expression -------------------------------------------------------------------------------- [CTG]T[CT][TC][TC]TCT[TC][CT][TC]T[CT]T[TC][CT]T[TC][CT]T[TC][TCA][TC][TC][TC][TC][TC][CT][TA] -------------------------------------------------------------------------------- Time 238.64 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************