******************************************************************************** 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-centered 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-centered -oc meme_out -mod zoops -nmotifs 50 -minw 6 -maxw 15 -bfile ./background -dna -searchsize 100000 -time 2919 -revcomp -nostatus model: mod= zoops nmotifs= 50 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= 15 nsites: minsites= 2 maxsites= 3019 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= 301900 N= 3019 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.189 C 0.311 G 0.311 T 0.189 Background letter frequencies (from file ./background): A 0.179 C 0.321 G 0.321 T 0.179 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF TCARTACATMAMAAA MEME-1 width = 15 sites = 30 llr = 458 E-value = 8.8e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCARTACATMAMAAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A :193:816:3938a7 pos.-specific C :7::1182:5:7::: probability G :::7::1:::::::2 matrix T a11:91:3a11:2:: bits 2.5 * * 2.2 * * * 2.0 * * * * 1.7 * * * * * ** Relative 1.5 * * ** * * ** Entropy 1.2 * * ** * * *** (22.0 bits) 1.0 * **** ** ***** 0.7 ****** ******** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel TCAGTACATCACAAA consensus A T A AT G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCARTACATMAMAAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 259634 bayes= 14.7844 E= 8.8e-010 -242 -1155 -1155 243 -42 119 -1155 -42 233 -326 -1155 -142 90 -1155 105 -1155 -242 -168 -1155 228 216 -227 -1155 -42 -142 126 -127 -242 166 -95 -1155 58 -1155 -1155 -1155 248 90 73 -1155 -42 228 -1155 -326 -84 90 105 -1155 -1155 216 -1155 -1155 16 248 -1155 -1155 -1155 203 -326 -68 -242 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCARTACATMAMAAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 30 E= 8.8e-010 0.033333 0.000000 0.000000 0.966667 0.133333 0.733333 0.000000 0.133333 0.900000 0.033333 0.000000 0.066667 0.333333 0.000000 0.666667 0.000000 0.033333 0.100000 0.000000 0.866667 0.800000 0.066667 0.000000 0.133333 0.066667 0.766667 0.133333 0.033333 0.566667 0.166667 0.000000 0.266667 0.000000 0.000000 0.000000 1.000000 0.333333 0.533333 0.000000 0.133333 0.866667 0.000000 0.033333 0.100000 0.333333 0.666667 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 1.000000 0.000000 0.000000 0.000000 0.733333 0.033333 0.200000 0.033333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCARTACATMAMAAA MEME-1 regular expression -------------------------------------------------------------------------------- TCA[GA]TAC[AT]T[CA]A[CA][AT]A[AG] -------------------------------------------------------------------------------- Time 430.84 secs. ******************************************************************************** ******************************************************************************** MOTIF KCGTCGSTCAT MEME-2 width = 11 sites = 367 llr = 3353 E-value = 2.7e-028 ******************************************************************************** -------------------------------------------------------------------------------- Motif KCGTCGSTCAT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1:1::2:::a: pos.-specific C :53:7:519:: probability G 3262:64:1:: matrix T 63:821:9::a bits 2.5 ** 2.2 ** 2.0 * ** 1.7 * ** Relative 1.5 * * ** Entropy 1.2 * **** (13.2 bits) 1.0 * ** **** 0.7 * ** **** 0.5 * ********* 0.2 *********** 0.0 ----------- Multilevel TCGTCGCTCAT consensus GTCGT G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCGTCGSTCAT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 271710 bayes= 11.6216 E= 2.7e-028 -79 -1516 5 166 -258 76 -88 50 -75 -21 94 -1516 -1516 -1516 -37 207 -1516 122 -488 42 -1 -279 101 -45 -323 75 33 -223 -1516 -230 -1516 239 -1516 152 -202 -1516 248 -1516 -1516 -1516 -1516 -1516 -1516 248 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCGTCGSTCAT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 367 E= 2.7e-028 0.103542 0.000000 0.332425 0.564033 0.029973 0.542234 0.174387 0.253406 0.106267 0.277929 0.615804 0.000000 0.000000 0.000000 0.247956 0.752044 0.000000 0.749319 0.010899 0.239782 0.177112 0.046322 0.645777 0.130790 0.019074 0.539510 0.403270 0.038147 0.000000 0.065395 0.000000 0.934605 0.000000 0.920981 0.079019 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCGTCGSTCAT MEME-2 regular expression -------------------------------------------------------------------------------- [TG][CT][GC][TG][CT]G[CG]TCAT -------------------------------------------------------------------------------- Time 788.80 secs. ******************************************************************************** ******************************************************************************** MOTIF WAAKVSTTDT MEME-3 width = 10 sites = 121 llr = 1225 E-value = 1.3e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif WAAKVSTTDT MEME-3 Description -------------------------------------------------------------------------------- Simplified A 5aa:31::3: pos.-specific C :::233:::1 probability G :::435::4: matrix T 5::31:aa39 bits 2.5 ** ** 2.2 ** ** 2.0 ** ** * 1.7 ** ** * Relative 1.5 *** ** * Entropy 1.2 *** ** * (14.6 bits) 1.0 *** ** * 0.7 *** ** * 0.5 **** **** 0.2 **** ***** 0.0 ---------- Multilevel AAAGGGTTGT consensus T TAC A sequence CC T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAKVSTTDT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 274729 bayes= 13.3782 E= 1.3e-002 152 -1356 -1356 145 248 -1356 -1356 -1356 248 -1356 -1356 -1356 -1356 -58 47 92 61 -24 1 -44 -27 -7 63 -185 -1356 -1356 -1356 248 -1356 -1356 -1356 248 81 -1356 24 77 -1356 -196 -1356 236 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAKVSTTDT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 121 E= 1.3e-002 0.512397 0.000000 0.000000 0.487603 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.214876 0.446281 0.338843 0.272727 0.272727 0.322314 0.132231 0.148760 0.305785 0.495868 0.049587 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.314050 0.000000 0.380165 0.305785 0.000000 0.082645 0.000000 0.917355 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAKVSTTDT MEME-3 regular expression -------------------------------------------------------------------------------- [AT]AA[GTC][GAC][GC]TT[GAT]T -------------------------------------------------------------------------------- Time 1137.32 secs. ******************************************************************************** ******************************************************************************** MOTIF WSGWCGWCCTCSWCG MEME-4 width = 15 sites = 372 llr = 3206 E-value = 2.4e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif WSGWCGWCCTCSWCG MEME-4 Description -------------------------------------------------------------------------------- Simplified A 4:26126232:25:1 pos.-specific C :61:71:77:84:82 probability G :45115:1::13:17 matrix T 6:13123::8:151: bits 2.5 2.2 2.0 1.7 * Relative 1.5 * * * * Entropy 1.2 * * * * (12.4 bits) 1.0 * * * ** * 0.7 * * ***** ** 0.5 ** ** ***** *** 0.2 *********** *** 0.0 --------------- Multilevel TCGACGACCTCCTCG consensus AGAT ATAAA GA sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WSGWCGWCCTCSWCG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 259634 bayes= 11.0127 E= 2.4e-004 131 -690 -690 162 -373 91 26 -1518 17 -158 77 -33 164 -320 -238 94 -166 121 -141 -115 21 -238 77 3 183 -431 -1518 95 44 112 -238 -1518 80 105 -1518 -289 25 -531 -690 212 -306 135 -117 -347 17 34 -35 -36 137 -1518 -1518 159 -605 137 -144 -181 -50 -104 109 -236 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WSGWCGWCCTCSWCG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 372 E= 2.4e-004 0.443548 0.002688 0.002688 0.551075 0.013441 0.602151 0.384409 0.000000 0.201613 0.107527 0.548387 0.142473 0.559140 0.034946 0.061828 0.344086 0.056452 0.741935 0.120968 0.080645 0.206989 0.061828 0.548387 0.182796 0.637097 0.016129 0.000000 0.346774 0.241935 0.696237 0.061828 0.000000 0.311828 0.663978 0.000000 0.024194 0.212366 0.008065 0.002688 0.776882 0.021505 0.819892 0.142473 0.016129 0.201613 0.405914 0.252688 0.139785 0.462366 0.000000 0.000000 0.537634 0.002688 0.827957 0.118280 0.051075 0.126344 0.155914 0.682796 0.034946 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WSGWCGWCCTCSWCG MEME-4 regular expression -------------------------------------------------------------------------------- [TA][CG][GA][AT]C[GA][AT][CA][CA][TA]C[CGA][TA]CG -------------------------------------------------------------------------------- Time 1481.55 secs. ******************************************************************************** ******************************************************************************** MOTIF GTCTGCTTGCTGAAG MEME-5 width = 15 sites = 9 llr = 190 E-value = 8.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTCTGCTTGCTGAAG MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::::::::::::aa: pos.-specific C ::a::a:::a::::: probability G a:::a:::a::a::a matrix T :a:a::aa::a:::: bits 2.5 * * ** * ** 2.2 * * ** * ** 2.0 * * ** * ** 1.7 *************** Relative 1.5 *************** Entropy 1.2 *************** (30.5 bits) 1.0 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GTCTGCTTGCTGAAG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTCTGCTTGCTGAAG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 259634 bayes= 14.9505 E= 8.5e+000 -982 -982 164 -982 -982 -982 -982 248 -982 164 -982 -982 -982 -982 -982 248 -982 -982 164 -982 -982 164 -982 -982 -982 -982 -982 248 -982 -982 -982 248 -982 -982 164 -982 -982 164 -982 -982 -982 -982 -982 248 -982 -982 164 -982 248 -982 -982 -982 248 -982 -982 -982 -982 -982 164 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTCTGCTTGCTGAAG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 8.5e+000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTCTGCTTGCTGAAG MEME-5 regular expression -------------------------------------------------------------------------------- GTCTGCTTGCTGAAG -------------------------------------------------------------------------------- Time 1811.61 secs. ******************************************************************************** ******************************************************************************** MOTIF AGASTAWAGAACKTA MEME-6 width = 15 sites = 6 llr = 104 E-value = 9.9e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGASTAWAGAACKTA MEME-6 Description -------------------------------------------------------------------------------- Simplified A 82822a7a:a8:::8 pos.-specific C :::3::::2::8::: probability G :825::::8::23:2 matrix T 2:::8:3:::2:7a: bits 2.5 * * * * 2.2 * * * * 2.0 * * * * 1.7 * * ** * ** ** Relative 1.5 * * **** ** ** Entropy 1.2 *** **** ** *** (25.1 bits) 1.0 *** *********** 0.7 *** *********** 0.5 *** *********** 0.2 *************** 0.0 --------------- Multilevel AGAGTAAAGAACTTA consensus C T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGASTAWAGAACKTA MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 259634 bayes= 16.5007 E= 9.9e+004 222 -923 -923 -10 -10 -923 137 -923 222 -923 -94 -923 -10 5 64 -923 -10 -923 -923 222 248 -923 -923 -923 190 -923 -923 90 248 -923 -923 -923 -923 -94 137 -923 248 -923 -923 -923 222 -923 -923 -10 -923 137 -94 -923 -923 -923 5 190 -923 -923 -923 248 222 -923 -94 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGASTAWAGAACKTA MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 6 E= 9.9e+004 0.833333 0.000000 0.000000 0.166667 0.166667 0.000000 0.833333 0.000000 0.833333 0.000000 0.166667 0.000000 0.166667 0.333333 0.500000 0.000000 0.166667 0.000000 0.000000 0.833333 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.833333 0.000000 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGASTAWAGAACKTA MEME-6 regular expression -------------------------------------------------------------------------------- AGA[GC]TA[AT]AGAAC[TG]TA -------------------------------------------------------------------------------- Time 2141.46 secs. ******************************************************************************** ******************************************************************************** MOTIF GCCTGTTAGTTGAGA MEME-7 width = 15 sites = 4 llr = 87 E-value = 1.1e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCCTGTTAGTTGAGA MEME-7 Description -------------------------------------------------------------------------------- Simplified A :::::::a::::a:a pos.-specific C :aa:::::::::::: probability G a:::a:::a::a:a: matrix T :::a:aa::aa:::: bits 2.5 * *** ** * * 2.2 * *** ** * * 2.0 * *** ** * * 1.7 *************** Relative 1.5 *************** Entropy 1.2 *************** (31.3 bits) 1.0 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GCCTGTTAGTTGAGA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCTGTTAGTTGAGA MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 259634 bayes= 15.9861 E= 1.1e+005 -865 -865 164 -865 -865 164 -865 -865 -865 164 -865 -865 -865 -865 -865 248 -865 -865 164 -865 -865 -865 -865 248 -865 -865 -865 248 248 -865 -865 -865 -865 -865 164 -865 -865 -865 -865 248 -865 -865 -865 248 -865 -865 164 -865 248 -865 -865 -865 -865 -865 164 -865 248 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCTGTTAGTTGAGA MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 4 E= 1.1e+005 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCTGTTAGTTGAGA MEME-7 regular expression -------------------------------------------------------------------------------- GCCTGTTAGTTGAGA -------------------------------------------------------------------------------- Time 2472.08 secs. ******************************************************************************** ******************************************************************************** MOTIF CTTAGCTCAGMCTGG MEME-8 width = 15 sites = 4 llr = 81 E-value = 6.5e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTTAGCTCAGMCTGG MEME-8 Description -------------------------------------------------------------------------------- Simplified A :::a::::a:5:::: pos.-specific C a::::a:a::5a::: probability G ::::a::::a:::aa matrix T :aa:::a:::::a:: bits 2.5 *** * * * 2.2 *** * * * 2.0 *** * * * 1.7 ********** **** Relative 1.5 ********** **** Entropy 1.2 ********** **** (29.1 bits) 1.0 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel CTTAGCTCAGACTGG consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTAGCTCAGMCTGG MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 259634 bayes= 15.9861 E= 6.5e+005 -865 164 -865 -865 -865 -865 -865 248 -865 -865 -865 248 248 -865 -865 -865 -865 -865 164 -865 -865 164 -865 -865 -865 -865 -865 248 -865 164 -865 -865 248 -865 -865 -865 -865 -865 164 -865 148 64 -865 -865 -865 164 -865 -865 -865 -865 -865 248 -865 -865 164 -865 -865 -865 164 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTAGCTCAGMCTGG MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 4 E= 6.5e+005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTAGCTCAGMCTGG MEME-8 regular expression -------------------------------------------------------------------------------- CTTAGCTCAG[AC]CTGG -------------------------------------------------------------------------------- Time 2801.60 secs. ******************************************************************************** ******************************************************************************** Stopped because MEME would probably exceed the allowed time (2919.00 secs) before finding the next motif. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************