******************************************************************************** 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/AT1G43700_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/AT1G43700_peak_sequences.fasta -dna -oc out/AT1G43700 -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= 1621 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= 296010 N= 1621 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.317 C 0.183 G 0.183 T 0.317 Background letter frequencies (from file dataset with add-one prior applied): A 0.319 C 0.181 G 0.181 T 0.319 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF NHYAGCTGTCA MEME-1 width = 11 sites = 1522 llr = 12635 E-value = 5.6e-451 ******************************************************************************** -------------------------------------------------------------------------------- Motif NHYAGCTGTCA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 34191::::36 pos.-specific C 235:19:::71 probability G 2:219::a3:1 matrix T 233::1a:712 bits 2.5 * 2.2 * * 2.0 * * 1.7 **** Relative 1.5 **** Entropy 1.2 ***** (12.0 bits) 1.0 ******* 0.7 ******* 0.5 ******** 0.2 ********** 0.0 ----------- Multilevel AACAGCTGTCA consensus CCT GAT sequence GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NHYAGCTGTCA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 279800 bayes= 8.61057 E= 5.6e-451 12 44 20 -68 27 72 -255 -16 -170 141 -18 -28 152 -441 -168 -417 -237 -143 225 -534 -1722 239 -810 -264 -1722 -1722 -1722 165 -1722 -1722 247 -1722 -1722 -1722 88 107 -25 189 -578 -248 80 -54 -111 -44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NHYAGCTGTCA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 1522 E= 5.6e-451 0.345598 0.246386 0.208279 0.199737 0.385020 0.298949 0.030880 0.285151 0.097898 0.480289 0.159658 0.262155 0.917214 0.008541 0.056505 0.017740 0.061761 0.067017 0.863338 0.007884 0.000000 0.948095 0.000657 0.051248 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.332457 0.667543 0.268725 0.670828 0.003285 0.057162 0.556505 0.124836 0.084100 0.234560 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NHYAGCTGTCA MEME-1 regular expression -------------------------------------------------------------------------------- [ACG][ACT][CT]AGCTG[TG][CA][AT] -------------------------------------------------------------------------------- Time 124.70 secs. ******************************************************************************** ******************************************************************************** MOTIF NTYYYTYTTYTTYTTYTTYTT MEME-2 width = 21 sites = 256 llr = 2901 E-value = 4.8e-053 ******************************************************************************** -------------------------------------------------------------------------------- Motif NTYYYTYTTYTTYTTYTTYTT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 21111:1:::11:::1::::: pos.-specific C 3134415:34214124315:2 probability G 21:::::11::::11:1:::: matrix T 3765684966775876795a8 bits 2.5 2.2 2.0 1.7 Relative 1.5 * Entropy 1.2 * * * (16.3 bits) 1.0 * * **** 0.7 ****** ********* 0.5 ******************** 0.2 ******************** 0.0 --------------------- Multilevel TTTTTTCTTTTTTTTTTTCTT consensus C CCC T CCC C CCC T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NTYYYTYTTYTTYTTYTTYTT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 263590 bayes= 12.0076 E= 4.8e-053 -71 77 2 -3 -131 -78 -145 113 -196 79 -236 84 -210 115 -353 67 -254 96 -1464 90 -435 -40 -1464 141 -189 145 -1464 39 -1464 -1464 -78 149 -1464 47 -78 101 -635 110 -195 82 -126 25 -1464 103 -110 -58 -221 112 -354 127 -1464 75 -318 -163 -73 132 -1464 27 -107 112 -265 99 -1464 89 -1464 53 -153 108 -1464 -114 -1464 152 -1464 147 -221 53 -335 -1464 -553 160 -1464 42 -453 123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NTYYYTYTTYTTYTTYTTYTT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 256 E= 4.8e-053 0.195312 0.308594 0.183594 0.312500 0.128906 0.105469 0.066406 0.699219 0.082031 0.312500 0.035156 0.570312 0.074219 0.402344 0.015625 0.507812 0.054688 0.351562 0.000000 0.593750 0.015625 0.136719 0.000000 0.847656 0.085938 0.496094 0.000000 0.417969 0.000000 0.000000 0.105469 0.894531 0.000000 0.250000 0.105469 0.644531 0.003906 0.386719 0.046875 0.562500 0.132812 0.214844 0.000000 0.652344 0.148438 0.121094 0.039062 0.691406 0.027344 0.437500 0.000000 0.535156 0.035156 0.058594 0.109375 0.796875 0.000000 0.218750 0.085938 0.695312 0.050781 0.359375 0.000000 0.589844 0.000000 0.261719 0.062500 0.675781 0.000000 0.082031 0.000000 0.917969 0.000000 0.500000 0.039062 0.460938 0.031250 0.000000 0.003906 0.964844 0.000000 0.242188 0.007812 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NTYYYTYTTYTTYTTYTTYTT MEME-2 regular expression -------------------------------------------------------------------------------- [TC]T[TC][TC][TC]T[CT]T[TC][TC][TC]T[TC]T[TC][TC][TC]T[CT]T[TC] -------------------------------------------------------------------------------- Time 234.93 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************