******************************************************************************** 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/AT2G22430_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/AT2G22430_peak_sequences.fasta -dna -oc out/AT2G22430 -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= 9369 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= 2983145 N= 9369 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.371 C 0.129 G 0.129 T 0.371 Background letter frequencies (from file dataset with add-one prior applied): A 0.371 C 0.129 G 0.129 T 0.371 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HHAATAATTDA MEME-1 width = 11 sites = 9294 llr = 62851 E-value = 1.3e-026 ******************************************************************************** -------------------------------------------------------------------------------- Motif HHAATAATTDA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 33aa:7a::35 pos.-specific C 24:::2:::11 probability G 1:::::::132 matrix T 33::a::a822 bits 3.0 2.7 2.4 2.1 Relative 1.8 Entropy 1.5 *** ** (9.8 bits) 1.2 *** ** 0.9 ******* 0.6 ******** 0.3 ********* 0.0 ----------- Multilevel ACAATAATTAA consensus TT C GT sequence CA T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HHAATAATTDA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 2889454 bayes= 10.4221 E= 1.3e-026 -13 91 11 -41 -48 173 -380 -31 143 -1983 -1983 -1983 143 -1983 -1983 -1017 -1983 -1983 -1983 143 101 92 -480 -743 143 -1983 -1022 -1175 -1017 -1022 -1983 143 -315 -537 15 113 -14 -24 138 -77 50 -68 36 -69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HHAATAATTDA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 9294 E= 1.3e-026 0.340219 0.241231 0.139230 0.279320 0.265655 0.425651 0.009253 0.299440 1.000000 0.000000 0.000000 0.000000 0.999677 0.000000 0.000000 0.000323 0.000000 0.000000 0.000000 1.000000 0.749731 0.243490 0.004627 0.002152 0.999785 0.000000 0.000108 0.000108 0.000323 0.000108 0.000000 0.999570 0.041855 0.003120 0.142457 0.812567 0.337745 0.108672 0.335485 0.218098 0.524747 0.080482 0.165053 0.229718 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HHAATAATTDA MEME-1 regular expression -------------------------------------------------------------------------------- [ATC][CTA]AAT[AC]ATT[AGT][AT] -------------------------------------------------------------------------------- Time 123.32 secs. ******************************************************************************** ******************************************************************************** MOTIF GCCAGTGGCAGCCAYTGTAAATAARTCYCAACTCCAGGA MEME-2 width = 39 sites = 21 llr = 712 E-value = 2.9e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCCAGTGGCAGCCAYTGTAAATAARTCYCAACTCCAGGA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1::8:1::181227:1::a99:a84::1187:11:83:8 pos.-specific C :77:::1:7::87:4::1:1:1:1::748:18188:1:1 probability G 71119:9a:28:122:a1:::1:16::11:22::2268: matrix T 212::9::2:1::148:8:::7:::a33:2::81:::11 bits 3.0 2.7 * * 2.4 * ** * 2.1 * ** * Relative 1.8 * ** ** * * * * * Entropy 1.5 ** * ** ** * * * * * ** * (48.9 bits) 1.2 *** * *** *** * * * *** * * ** ** 0.9 ************* * ***** ***** * ** ***** 0.6 ************* ************************* 0.3 *************************************** 0.0 --------------------------------------- Multilevel GCCAGTGGCAGCCATTGTAAATAAGTCCCAACTCCAGGA consensus T A C A TT T A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCAGTGGCAGCCAYTGTAAATAARTCYCAACTCCAGGA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 39 n= 2627122 bayes= 18.4375 E= 2.9e-006 -196 -1104 247 -96 -296 247 -43 -138 -296 237 -43 -96 112 -1104 15 -296 -296 -143 281 -1104 -196 -1104 -143 121 -1104 15 273 -1104 -296 -1104 289 -1104 -196 237 -1104 -64 112 -1104 57 -1104 -196 -1104 265 -196 -64 257 -1104 -1104 -96 237 -43 -296 84 -143 57 -196 -1104 157 57 21 -138 -143 -1104 112 -296 -1104 289 -1104 -1104 -43 15 104 136 -1104 -143 -1104 121 -43 -143 -1104 121 -143 -143 -296 -296 -43 15 94 136 -1104 -1104 -296 104 15 -43 -1104 4 -1104 227 -1104 -1104 -1104 -143 136 -296 237 -1104 -38 -196 174 15 -16 -196 257 15 -1104 104 -1104 -1104 -64 94 -43 57 -1104 -1104 257 57 -296 -196 -43 -1104 112 -196 257 -1104 -138 -1104 257 57 -296 112 -1104 57 -1104 -38 -43 227 -1104 -296 -143 265 -196 104 15 -1104 -196 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCAGTGGCAGCCAYTGTAAATAARTCYCAACTCCAGGA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 39 nsites= 21 E= 2.9e-006 0.095238 0.000000 0.714286 0.190476 0.047619 0.714286 0.095238 0.142857 0.047619 0.666667 0.095238 0.190476 0.809524 0.000000 0.142857 0.047619 0.047619 0.047619 0.904762 0.000000 0.095238 0.000000 0.047619 0.857143 0.000000 0.142857 0.857143 0.000000 0.047619 0.000000 0.952381 0.000000 0.095238 0.666667 0.000000 0.238095 0.809524 0.000000 0.190476 0.000000 0.095238 0.000000 0.809524 0.095238 0.238095 0.761905 0.000000 0.000000 0.190476 0.666667 0.095238 0.047619 0.666667 0.047619 0.190476 0.095238 0.000000 0.380952 0.190476 0.428571 0.142857 0.047619 0.000000 0.809524 0.047619 0.000000 0.952381 0.000000 0.000000 0.095238 0.142857 0.761905 0.952381 0.000000 0.047619 0.000000 0.857143 0.095238 0.047619 0.000000 0.857143 0.047619 0.047619 0.047619 0.047619 0.095238 0.142857 0.714286 0.952381 0.000000 0.000000 0.047619 0.761905 0.142857 0.095238 0.000000 0.380952 0.000000 0.619048 0.000000 0.000000 0.000000 0.047619 0.952381 0.047619 0.666667 0.000000 0.285714 0.095238 0.428571 0.142857 0.333333 0.095238 0.761905 0.142857 0.000000 0.761905 0.000000 0.000000 0.238095 0.714286 0.095238 0.190476 0.000000 0.000000 0.761905 0.190476 0.047619 0.095238 0.095238 0.000000 0.809524 0.095238 0.761905 0.000000 0.142857 0.000000 0.761905 0.190476 0.047619 0.809524 0.000000 0.190476 0.000000 0.285714 0.095238 0.619048 0.000000 0.047619 0.047619 0.809524 0.095238 0.761905 0.142857 0.000000 0.095238 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCAGTGGCAGCCAYTGTAAATAARTCYCAACTCCAGGA MEME-2 regular expression -------------------------------------------------------------------------------- GCCAGTGG[CT]AG[CA]CA[TC]TGTAAATAA[GA]T[CT][CT]C[AT]ACTCCA[GA]GA -------------------------------------------------------------------------------- Time 236.83 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************