******************************************************************************** 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/AT1G02250_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/AT1G02250_peak_sequences.fasta -dna -oc out/AT1G02250 -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= 7675 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= 1307782 N= 7675 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.326 C 0.174 G 0.174 T 0.326 Background letter frequencies (from file dataset with add-one prior applied): A 0.327 C 0.173 G 0.173 T 0.327 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TWNCTTVTTHHNYAAGYWWY MEME-1 width = 20 sites = 7634 llr = 64039 E-value = 3.0e-669 ******************************************************************************** -------------------------------------------------------------------------------- Motif TWNCTTVTTHHNYAAGYWWY MEME-1 Description -------------------------------------------------------------------------------- Simplified A 233:::2122332a9:2342 pos.-specific C 112a::4223224:::2113 probability G 112:::3111121::a21:1 matrix T 653:aa2643434:::4554 bits 2.5 2.3 * * 2.0 * * 1.8 * * Relative 1.5 ** * * Entropy 1.3 *** *** (12.1 bits) 1.0 *** *** 0.8 *** *** 0.5 *** *** 0.3 * ***** **** *** 0.0 -------------------- Multilevel TTTCTTCTTTTACAAGTTTT consensus AAA G CCATT CAAC sequence C A AAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TWNCTTVTTHHNYAAGYWWY MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1161957 bayes= 9.18072 E= 3.0e-669 -50 -47 -143 83 -20 -62 -64 59 -13 21 19 -11 -531 249 -1954 -411 -1954 -300 -520 157 -464 -255 -1954 155 -65 108 54 -91 -119 -17 -66 86 -65 31 -35 43 -49 72 -27 5 -20 39 -48 16 9 14 4 -21 -109 114 -78 16 160 -1954 -439 -1954 153 -199 -453 -659 -1954 -567 249 -359 -97 42 -16 45 -29 -29 -154 70 26 -130 -183 58 -83 93 -72 22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TWNCTTVTTHHNYAAGYWWY MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 7634 E= 3.0e-669 0.230941 0.124574 0.064056 0.580430 0.285565 0.112785 0.110689 0.490961 0.299188 0.200419 0.197406 0.302987 0.008253 0.972753 0.000000 0.018994 0.000000 0.021614 0.004716 0.973670 0.013099 0.029473 0.000000 0.957427 0.208017 0.365208 0.252161 0.174614 0.143175 0.153917 0.109772 0.593136 0.208934 0.213911 0.135840 0.441315 0.233167 0.284648 0.143175 0.339010 0.283993 0.226749 0.123657 0.365601 0.348834 0.190726 0.178150 0.282290 0.153262 0.379879 0.100996 0.365863 0.991747 0.000000 0.008253 0.000000 0.945638 0.043490 0.007467 0.003406 0.000000 0.003406 0.969348 0.027247 0.166492 0.231203 0.154310 0.447996 0.266964 0.141865 0.059471 0.531700 0.391538 0.070081 0.048598 0.489783 0.184176 0.328792 0.105318 0.381713 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TWNCTTVTTHHNYAAGYWWY MEME-1 regular expression -------------------------------------------------------------------------------- [TA][TA][TAC]CTT[CGA]T[TCA][TCA][TAC][AT][CT]AAG[TC][TA][TA][TC] -------------------------------------------------------------------------------- Time 131.10 secs. ******************************************************************************** ******************************************************************************** MOTIF YTYTTYTTYTTYTTC MEME-2 width = 15 sites = 1516 llr = 14751 E-value = 3.5e-037 ******************************************************************************** -------------------------------------------------------------------------------- Motif YTYTTYTTYTTYTTC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1::1::::::::::: pos.-specific C 3:61342:7126226 probability G 1:::1::::::::12 matrix T 5948657a3984782 bits 2.5 2.3 2.0 1.8 Relative 1.5 * Entropy 1.3 ** (14.0 bits) 1.0 ** ****** * 0.8 ************** 0.5 ************** 0.3 *************** 0.0 --------------- Multilevel TTCTTTTTCTTCTTC consensus C T CCC T CTC T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTYTTYTTYTTYTTC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1200332 bayes= 11.9354 E= 3.5e-037 -155 81 -79 57 -295 -203 -323 146 -1721 181 -286 18 -159 -64 -1721 125 -695 57 -68 95 -1721 129 -184 69 -317 32 -201 111 -895 -1721 -1721 161 -1721 191 -1721 9 -374 -86 -1721 143 -1721 35 -339 122 -1721 169 -1721 44 -1721 46 -268 117 -1721 -16 -153 126 -595 181 8 -68 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTYTTYTTYTTYTTC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1516 E= 3.5e-037 0.111478 0.302770 0.100264 0.485488 0.042216 0.042216 0.018470 0.897098 0.000000 0.604881 0.023747 0.371372 0.108839 0.110818 0.000000 0.780343 0.002639 0.255937 0.108179 0.633245 0.000000 0.422823 0.048153 0.529024 0.036280 0.215699 0.042876 0.705145 0.000660 0.000000 0.000000 0.999340 0.000000 0.651715 0.000000 0.348285 0.024406 0.094987 0.000000 0.880607 0.000000 0.219657 0.016491 0.763852 0.000000 0.556728 0.000000 0.443272 0.000000 0.237467 0.027045 0.735488 0.000000 0.155013 0.060026 0.784960 0.005277 0.608179 0.182718 0.203826 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTYTTYTTYTTYTTC MEME-2 regular expression -------------------------------------------------------------------------------- [TC]T[CT]T[TC][TC][TC]T[CT]T[TC][CT][TC]T[CT] -------------------------------------------------------------------------------- Time 239.49 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************