******************************************************************************** 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/AT1G49480_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/AT1G49480_peak_sequences.fasta -dna -oc out/AT1G49480 -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= 9640 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= 2693257 N= 9640 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.377 C 0.123 G 0.123 T 0.377 Background letter frequencies (from file dataset with add-one prior applied): A 0.377 C 0.123 G 0.123 T 0.377 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF NAAAAAAAAAAAAAAAAAAAA MEME-1 width = 21 sites = 9541 llr = 91719 E-value = 1.3e-525 ******************************************************************************** -------------------------------------------------------------------------------- Motif NAAAAAAAAAAAAAAAAAAAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2677999999999a7766665 pos.-specific C 22221:::1:::::1111:12 probability G 21:1:1:1::1:::1:21112 matrix T 321:1::::1::::1222231 bits 3.0 2.7 2.4 2.1 Relative 1.8 Entropy 1.5 (13.9 bits) 1.2 **** 0.9 *********** 0.6 ************ * 0.3 ******************* * 0.0 --------------------- Multilevel TAAAAAAAAAAAAAAAAAAAA consensus A TTG sequence C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NAAAAAAAAAAAAAAAAAAAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2500455 bayes= 10.3164 E= 1.3e-525 -62 91 87 -33 59 36 -34 -110 95 62 -1019 -223 99 62 -97 -1986 120 -89 -317 -275 125 -920 -51 -432 130 -444 -130 -475 128 -238 -102 -1986 128 -115 -1986 -369 122 -580 -235 -198 129 -434 -81 -1181 133 -256 -1986 -354 130 -147 -236 -949 135 -820 -199 -566 99 -59 -73 -195 98 -49 -436 -120 65 -53 37 -120 70 16 -46 -123 61 -161 24 -65 64 -44 -84 -58 47 65 71 -220 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NAAAAAAAAAAAAAAAAAAAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9541 E= 1.3e-525 0.244733 0.230374 0.225553 0.299340 0.569332 0.158369 0.096845 0.175453 0.730531 0.188869 0.000105 0.080495 0.748035 0.189079 0.062886 0.000000 0.864165 0.066345 0.013625 0.055864 0.894770 0.000210 0.086154 0.018866 0.930406 0.005660 0.049890 0.014045 0.915522 0.023687 0.060790 0.000000 0.915522 0.055340 0.000000 0.029137 0.877895 0.002201 0.024106 0.095797 0.923698 0.006079 0.070118 0.000105 0.946651 0.020857 0.000000 0.032491 0.931034 0.044440 0.024002 0.000524 0.961115 0.000419 0.031024 0.007442 0.746777 0.081648 0.074311 0.097264 0.742480 0.087622 0.005974 0.163924 0.592286 0.084897 0.158579 0.164239 0.612619 0.137826 0.089299 0.160256 0.574363 0.040247 0.145687 0.239702 0.588093 0.090661 0.068861 0.252384 0.523949 0.192957 0.201132 0.081962 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NAAAAAAAAAAAAAAAAAAAA MEME-1 regular expression -------------------------------------------------------------------------------- [TACG]AAAAAAAAAAAAAAAAA[AT][AT][AG] -------------------------------------------------------------------------------- Time 121.75 secs. ******************************************************************************** ******************************************************************************** MOTIF RARAAAAARAAARARARARAAAARAAAAA MEME-2 width = 29 sites = 1085 llr = 13073 E-value = 7.6e-038 ******************************************************************************** -------------------------------------------------------------------------------- Motif RARAAAAARAAARARARARAAAARAAAAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 57577778465558675658676566666 pos.-specific C 1:1:1::1:1111::111::1::112:12 probability G 4232222:412241323242332322232 matrix T :11::1111212::::111:::1:1:1:: bits 3.0 2.7 2.4 2.1 Relative 1.8 Entropy 1.5 (17.4 bits) 1.2 0.9 * * *** * * 0.6 * ******* ***** ****** * ** 0.3 ***************************** 0.0 ----------------------------- Multilevel AAAAAAAAAAAAAAAAAAAAAAAAAAAAA consensus G GGG G G GGG GGG GGGGGGGG GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARAAAAARAAARARARARAAAARAAAAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 2423335 bayes= 13.4049 E= 7.6e-038 35 25 159 -1673 80 -133 38 -147 53 -120 135 -208 97 -206 92 -1673 84 -28 86 -1673 98 -1673 48 -215 85 -706 88 -202 110 -37 -1673 -192 24 -1673 182 -162 79 3 -83 -128 42 28 80 -153 33 19 85 -119 49 -23 158 -1673 116 -267 18 -1673 75 -1673 148 -415 91 -125 71 -318 52 -20 126 -275 78 -23 58 -253 49 -706 157 -186 102 -225 75 -867 60 -25 119 -306 97 -1673 109 -1673 73 -1673 89 -136 51 2 131 -355 72 -46 79 -234 67 39 95 -1673 77 -181 49 -135 64 11 117 -867 64 67 80 -867 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARAAAAARAAARARARARAAAARAAAAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 1085 E= 7.6e-038 0.482028 0.146544 0.371429 0.000000 0.654378 0.048848 0.160369 0.136406 0.543779 0.053456 0.313364 0.089401 0.737327 0.029493 0.233180 0.000000 0.675576 0.101382 0.223041 0.000000 0.743779 0.000000 0.171429 0.084793 0.680184 0.000922 0.225806 0.093088 0.805530 0.094931 0.000000 0.099539 0.444240 0.000000 0.433180 0.122581 0.649770 0.125346 0.069124 0.155760 0.505069 0.149309 0.214747 0.130876 0.473733 0.140092 0.221198 0.164977 0.528111 0.105069 0.366820 0.000000 0.841475 0.019355 0.139171 0.000000 0.635023 0.000000 0.343779 0.021198 0.705991 0.051613 0.200922 0.041475 0.541935 0.106912 0.294931 0.056221 0.645161 0.105069 0.184332 0.065438 0.530876 0.000922 0.364055 0.104147 0.766820 0.025806 0.206452 0.000922 0.570507 0.103226 0.281106 0.045161 0.737327 0.000000 0.262673 0.000000 0.624885 0.000000 0.228571 0.146544 0.537327 0.124424 0.305991 0.032258 0.623041 0.089401 0.212903 0.074654 0.600922 0.161290 0.237788 0.000000 0.644240 0.035023 0.172350 0.148387 0.588940 0.132719 0.277419 0.000922 0.588940 0.195392 0.214747 0.000922 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARAAAAARAAARARARARAAAARAAAAA MEME-2 regular expression -------------------------------------------------------------------------------- [AG]A[AG][AG][AG]A[AG]A[AG]A[AG][AG][AG]A[AG][AG][AG]A[AG][AG][AG][AG][AG][AG][AG][AG]A[AG][AG] -------------------------------------------------------------------------------- Time 232.30 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************