******************************************************************************** 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= 3017 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= 301700 N= 3017 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.168 C 0.332 G 0.332 T 0.168 Background letter frequencies (from file ./background): A 0.172 C 0.328 G 0.328 T 0.172 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF CGHCGVCGASG MEME-1 width = 11 sites = 1642 llr = 12674 E-value = 9.0e-282 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGHCGVCGASG MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::41:4::8:: pos.-specific C a:38248:251 probability G :9::732a:49 matrix T :1311::::1: bits 2.5 2.3 2.0 1.8 Relative 1.5 * ** Entropy 1.3 * ** * (11.1 bits) 1.0 ** * *** * 0.8 ***** *** * 0.5 *********** 0.3 *********** 0.0 ----------- Multilevel CGACGACGACG consensus T C G sequence C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGHCGVCGASG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 271530 bayes= 9.58126 E= 9.0e-282 -1733 159 -443 -814 -814 -275 145 -160 138 -34 -1733 77 -83 133 -1733 -118 -1733 -94 119 -111 115 17 -38 -1733 -1733 135 -99 -1733 -1733 -1733 161 -1733 222 -75 -1733 -1733 -1733 62 38 -136 -1733 -225 151 -1733 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGHCGVCGASG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 1642 E= 9.0e-282 0.000000 0.984166 0.015225 0.000609 0.000609 0.048721 0.894032 0.056638 0.448234 0.258222 0.000000 0.293544 0.096833 0.827040 0.000000 0.076127 0.000000 0.171133 0.749086 0.079781 0.380633 0.367844 0.251523 0.000000 0.000000 0.834348 0.165652 0.000000 0.000000 0.000000 1.000000 0.000000 0.804507 0.195493 0.000000 0.000000 0.000000 0.504872 0.428136 0.066991 0.000000 0.068819 0.931181 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGHCGVCGASG MEME-1 regular expression -------------------------------------------------------------------------------- CG[ATC]CG[ACG]CGA[CG]G -------------------------------------------------------------------------------- Time 442.62 secs. ******************************************************************************** ******************************************************************************** MOTIF GAGSAGTTCGW MEME-2 width = 11 sites = 141 llr = 1466 E-value = 1.2e-020 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAGSAGTTCGW MEME-2 Description -------------------------------------------------------------------------------- Simplified A 2a1:7::2::7 pos.-specific C :::5:::191: probability G 8:75:9:1:9: matrix T ::2:31a71:3 bits 2.5 * * 2.3 * * 2.0 * * 1.8 * * Relative 1.5 * * * * Entropy 1.3 * * * * * (15.0 bits) 1.0 ** ******* 0.8 *** ******* 0.5 *********** 0.3 *********** 0.0 ----------- Multilevel GAGGAGTTCGA consensus CT T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGSAGTTCGW MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 271530 bayes= 12.9379 E= 1.2e-020 -2 -1378 134 -1378 254 -1378 -1378 -1378 -21 -1378 104 4 -1378 49 72 -1378 200 -1378 -1378 86 -1378 -1378 138 -21 -1378 -1378 -1378 254 -8 -136 -253 192 -1378 146 -1378 -79 -1378 -162 140 -260 194 -1378 -1378 98 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGSAGTTCGW MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 141 E= 1.2e-020 0.170213 0.000000 0.829787 0.000000 1.000000 0.000000 0.000000 0.000000 0.148936 0.000000 0.673759 0.177305 0.000000 0.460993 0.539007 0.000000 0.687943 0.000000 0.000000 0.312057 0.000000 0.000000 0.851064 0.148936 0.000000 0.000000 0.000000 1.000000 0.163121 0.127660 0.056738 0.652482 0.000000 0.900709 0.000000 0.099291 0.000000 0.106383 0.865248 0.028369 0.659574 0.000000 0.000000 0.340426 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGSAGTTCGW MEME-2 regular expression -------------------------------------------------------------------------------- GAG[GC][AT]GTTCG[AT] -------------------------------------------------------------------------------- Time 779.03 secs. ******************************************************************************** ******************************************************************************** MOTIF TTATTTGATAT MEME-3 width = 11 sites = 11 llr = 150 E-value = 8.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTATTTGATAT MEME-3 Description -------------------------------------------------------------------------------- Simplified A :1821:29:a1 pos.-specific C 1:::::::1:3 probability G :::22:8:::: matrix T 99267a:19:6 bits 2.5 * * 2.3 * * 2.0 ** * *** 1.8 *** * *** Relative 1.5 *** * *** Entropy 1.3 *** ** *** (19.6 bits) 1.0 *********** 0.8 *********** 0.5 *********** 0.3 *********** 0.0 ----------- Multilevel TTATTTGATAT consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTATTTGATAT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 271530 bayes= 15.6178 E= 8.1e+003 -1010 -185 -1010 240 -92 -1010 -1010 240 225 -1010 -1010 8 8 -1010 -85 189 -92 -1010 -85 208 -1010 -1010 -1010 254 8 -1010 132 -1010 240 -1010 -1010 -92 -1010 -185 -1010 240 254 -1010 -1010 -1010 -92 -27 -1010 189 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTATTTGATAT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 11 E= 8.1e+003 0.000000 0.090909 0.000000 0.909091 0.090909 0.000000 0.000000 0.909091 0.818182 0.000000 0.000000 0.181818 0.181818 0.000000 0.181818 0.636364 0.090909 0.000000 0.181818 0.727273 0.000000 0.000000 0.000000 1.000000 0.181818 0.000000 0.818182 0.000000 0.909091 0.000000 0.000000 0.090909 0.000000 0.090909 0.000000 0.909091 1.000000 0.000000 0.000000 0.000000 0.090909 0.272727 0.000000 0.636364 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTATTTGATAT MEME-3 regular expression -------------------------------------------------------------------------------- TTATTTGATA[TC] -------------------------------------------------------------------------------- Time 1116.57 secs. ******************************************************************************** ******************************************************************************** MOTIF AATTTGGGTCTAATT MEME-4 width = 15 sites = 2 llr = 48 E-value = 3.4e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif AATTTGGGTCTAATT MEME-4 Description -------------------------------------------------------------------------------- Simplified A aa:::::::::aa:: pos.-specific C :::::::::a::::: probability G :::::aaa::::::: matrix T ::aaa:::a:a::aa bits 2.5 ***** * ***** 2.3 ***** * ***** 2.0 ***** * ***** 1.8 ***** * ***** Relative 1.5 *************** Entropy 1.3 *************** (34.4 bits) 1.0 *************** 0.8 *************** 0.5 *************** 0.3 *************** 0.0 --------------- Multilevel AATTTGGGTCTAATT consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATTTGGGTCTAATT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 259462 bayes= 16.9852 E= 3.4e+005 253 -765 -765 -765 253 -765 -765 -765 -765 -765 -765 253 -765 -765 -765 253 -765 -765 -765 253 -765 -765 160 -765 -765 -765 160 -765 -765 -765 160 -765 -765 -765 -765 253 -765 160 -765 -765 -765 -765 -765 253 253 -765 -765 -765 253 -765 -765 -765 -765 -765 -765 253 -765 -765 -765 253 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATTTGGGTCTAATT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 2 E= 3.4e+005 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATTTGGGTCTAATT MEME-4 regular expression -------------------------------------------------------------------------------- AATTTGGGTCTAATT -------------------------------------------------------------------------------- Time 1446.60 secs. ******************************************************************************** ******************************************************************************** MOTIF AAVAATAATTA MEME-5 width = 11 sites = 5 llr = 81 E-value = 1.2e+006 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAVAATAATTA MEME-5 Description -------------------------------------------------------------------------------- Simplified A 8a4aa:8a::a pos.-specific C ::2:::::2:: probability G ::4:::::::: matrix T 2::::a2:8a: bits 2.5 * *** * ** 2.3 * *** * ** 2.0 * *** * ** 1.8 ** ***** ** Relative 1.5 ** ******** Entropy 1.3 ** ******** (23.5 bits) 1.0 ** ******** 0.8 ** ******** 0.5 *********** 0.3 *********** 0.0 ----------- Multilevel AAAAATAATTA consensus T G T C sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAVAATAATTA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 271530 bayes= 16.6722 E= 1.2e+006 221 -897 -897 22 254 -897 -897 -897 122 -71 29 -897 254 -897 -897 -897 254 -897 -897 -897 -897 -897 -897 254 221 -897 -897 22 254 -897 -897 -897 -897 -71 -897 221 -897 -897 -897 254 254 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAVAATAATTA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 5 E= 1.2e+006 0.800000 0.000000 0.000000 0.200000 1.000000 0.000000 0.000000 0.000000 0.400000 0.200000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.800000 0.000000 0.000000 0.200000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAVAATAATTA MEME-5 regular expression -------------------------------------------------------------------------------- [AT]A[AGC]AAT[AT]A[TC]TA -------------------------------------------------------------------------------- Time 1781.48 secs. ******************************************************************************** ******************************************************************************** MOTIF TAATAGTT MEME-6 width = 8 sites = 2 llr = 27 E-value = 6.6e+006 ******************************************************************************** -------------------------------------------------------------------------------- Motif TAATAGTT MEME-6 Description -------------------------------------------------------------------------------- Simplified A :aa:a::: pos.-specific C :::::::: probability G :::::a:: matrix T a::a::aa bits 2.5 ***** ** 2.3 ***** ** 2.0 ***** ** 1.8 ***** ** Relative 1.5 ******** Entropy 1.3 ******** (19.4 bits) 1.0 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel TAATAGTT consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAATAGTT MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 280581 bayes= 17.098 E= 6.6e+006 -765 -765 -765 253 253 -765 -765 -765 253 -765 -765 -765 -765 -765 -765 253 253 -765 -765 -765 -765 -765 160 -765 -765 -765 -765 253 -765 -765 -765 253 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAATAGTT MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 6.6e+006 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAATAGTT MEME-6 regular expression -------------------------------------------------------------------------------- TAATAGTT -------------------------------------------------------------------------------- Time 2123.03 secs. ******************************************************************************** ******************************************************************************** MOTIF ATTTTT MEME-7 width = 6 sites = 7 llr = 74 E-value = 1.3e+007 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATTTTT MEME-7 Description -------------------------------------------------------------------------------- Simplified A a::::: pos.-specific C :::::: probability G :::::: matrix T :aaaaa bits 2.5 ****** 2.3 ****** 2.0 ****** 1.8 ****** Relative 1.5 ****** Entropy 1.3 ****** (15.2 bits) 1.0 ****** 0.8 ****** 0.5 ****** 0.3 ****** 0.0 ------ Multilevel ATTTTT consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTTT MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 286615 bayes= 16.5438 E= 1.3e+007 254 -945 -945 -945 -945 -945 -945 254 -945 -945 -945 254 -945 -945 -945 254 -945 -945 -945 254 -945 -945 -945 254 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTTT MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 7 E= 1.3e+007 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTTT MEME-7 regular expression -------------------------------------------------------------------------------- ATTTTT -------------------------------------------------------------------------------- Time 2457.98 secs. ******************************************************************************** ******************************************************************************** MOTIF AWTTAT MEME-8 width = 6 sites = 4 llr = 39 E-value = 1.3e+007 ******************************************************************************** -------------------------------------------------------------------------------- Motif AWTTAT MEME-8 Description -------------------------------------------------------------------------------- Simplified A a5::a: pos.-specific C :::::: probability G :::::: matrix T :5aa:a bits 2.5 * **** 2.3 * **** 2.0 * **** 1.8 * **** Relative 1.5 ****** Entropy 1.3 ****** (14.2 bits) 1.0 ****** 0.8 ****** 0.5 ****** 0.3 ****** 0.0 ------ Multilevel AATTAT consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWTTAT MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 286615 bayes= 16.8657 E= 1.3e+007 254 -865 -865 -865 154 -865 -865 154 -865 -865 -865 254 -865 -865 -865 254 254 -865 -865 -865 -865 -865 -865 254 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWTTAT MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 4 E= 1.3e+007 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 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 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWTTAT MEME-8 regular expression -------------------------------------------------------------------------------- A[AT]TTAT -------------------------------------------------------------------------------- Time 2788.33 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 ********************************************************************************