******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.5.1 (Release date: Sun Jan 29 10:33:12 2023 -0800) 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= promotors.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 promotors.fasta -dna -nmotifs 3 -minw 15 -maxw 35 model: mod= zoops nmotifs= 3 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 15 maxw= 35 nsites: minsites= 2 maxsites= 5447 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= 544700 N= 5447 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.184 C 0.315 G 0.317 T 0.184 Background letter frequencies (from file dataset with add-one prior applied): A 0.184 C 0.315 G 0.317 T 0.184 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GCKGCNGCBSBWSCKSCDCVASBNGCKGC MEME-1 width = 29 sites = 357 llr = 3229 E-value = 1.1e-029 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCKGCNGCBSBWSCKSCDCVASBNGCKGC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :12:121:2:15::1112:27::3::1:: pos.-specific C 262262262441372361741543:7126 probability G 812823733531713533231532a1372 matrix T :25:13:14:24:14114:1::22:2511 bits 2.4 2.2 2.0 1.7 Relative 1.5 * Entropy 1.2 * (13.0 bits) 1.0 * * 0.7 * * ** ** * 0.5 * * ** * *** * ** **** 0.2 ***** **** ******** *** ***** 0.0 ----------------------------- Multilevel GCTGCTGCTGCAGCTGCTCCACCCGCTGC consensus CTG GCGGCGTC GCGGGG GGA G G sequence A C A A TG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCKGCNGCBSBWSCKSCDCVASBNGCKGC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 392184 bayes= 11.9809 E= 1.1e-029 -603 -40 126 -1512 -90 93 -178 19 -23 -95 -47 129 -323 -103 131 -223 -48 89 -104 -52 18 -84 -11 80 -128 -46 113 -1512 -1512 96 -9 -100 -23 -58 -19 95 -371 48 78 -1512 -103 25 10 9 144 -217 -224 98 -403 8 105 -1512 -213 119 -109 -104 -57 -101 -14 123 -157 -1 77 -113 -133 82 -24 -83 43 -168 -12 98 -323 117 -36 -287 32 16 12 -134 190 -132 -112 -213 -1512 77 54 -1512 -345 49 -2 30 72 -2 -54 -13 -1512 -349 162 -1512 -223 114 -161 -18 -90 -149 -7 140 -323 -75 115 -104 -195 102 -45 -118 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCKGCNGCBSBWSCKSCDCVASBNGCKGC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 357 E= 1.1e-029 0.002801 0.238095 0.759104 0.000000 0.098039 0.599440 0.092437 0.210084 0.156863 0.162465 0.229692 0.450980 0.019608 0.154062 0.787115 0.039216 0.131653 0.585434 0.154062 0.128852 0.207283 0.176471 0.294118 0.322129 0.075630 0.229692 0.694678 0.000000 0.000000 0.610644 0.296919 0.092437 0.156863 0.210084 0.277311 0.355742 0.014006 0.439776 0.546218 0.000000 0.089636 0.375350 0.338936 0.196078 0.498599 0.070028 0.067227 0.364146 0.011204 0.333333 0.655462 0.000000 0.042017 0.719888 0.148459 0.089636 0.123249 0.156863 0.288515 0.431373 0.061625 0.313725 0.540616 0.084034 0.072829 0.554622 0.268908 0.103641 0.246499 0.098039 0.291317 0.364146 0.019608 0.708683 0.246499 0.025210 0.229692 0.352941 0.344538 0.072829 0.686275 0.126050 0.145658 0.042017 0.000000 0.537815 0.462185 0.000000 0.016807 0.442577 0.313725 0.226891 0.302521 0.310924 0.218487 0.168067 0.000000 0.028011 0.971989 0.000000 0.039216 0.694678 0.103641 0.162465 0.098039 0.112045 0.302521 0.487395 0.019608 0.187675 0.703081 0.089636 0.047619 0.638655 0.232493 0.081232 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCKGCNGCBSBWSCKSCDCVASBNGCKGC MEME-1 regular expression -------------------------------------------------------------------------------- [GC][CT][TG]GC[TGA][GC][CG][TGC][GC][CG][AT][GC]C[TG][GC][CG][TGA][CG][CGA]A[CG][CGT][CAG]GC[TG]G[CG] -------------------------------------------------------------------------------- Time 215.16 secs. ******************************************************************************** ******************************************************************************** MOTIF CGMSGNCRYSGBCGMSGMSSTSVKCRMCRMSGYCG MEME-2 width = 35 sites = 221 llr = 2186 E-value = 9.5e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGMSGNCRYSGBCGMSGMSSTSVKCRMCRMSGYCG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :24:12:32:21:15214:22121:44:3311112 pos.-specific C 8136336137337134245324328:472451361 probability G 17135235235229136:54154216:35236227 matrix T ::2113:14::4:::1:2:15125::1::212511 bits 2.4 2.2 2.0 1.7 Relative 1.5 Entropy 1.2 (14.3 bits) 1.0 * * 0.7 ** * ** **** 0.5 ** * * * *** *** * **** * * 0.2 ***** ********* *** ** ****** ***** 0.0 ----------------------------------- Multilevel CGACGTCGTCGTCGACGCGGTGGTCGACGCCGTCG consensus ACGCCGACGCCG CGCACCCCCG ACGAAGTCG sequence G G T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGMSGNCRYSGBCGMSGMSSTSVKCRMCRMSGYCG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 35 n= 359502 bayes= 11.8793 E= 9.5e-004 -376 135 -109 -254 18 -212 118 -1443 113 -31 -109 8 -302 93 -2 -154 -39 -29 73 -126 -2 -21 -38 72 -276 103 -9 -254 72 -137 65 -126 -13 -26 -92 113 -1443 105 14 -1443 -13 -26 74 -218 -134 13 -58 101 -302 123 -46 -435 -134 -254 143 -335 144 11 -113 -335 -21 46 -15 -59 -48 -45 101 -1443 94 48 -1443 17 -434 52 70 -303 12 -24 48 -103 -9 -48 -167 144 -153 29 54 -103 12 -31 28 -18 -95 -69 -35 132 -276 139 -132 -303 105 -380 91 -1443 127 49 -513 -83 -434 113 -6 -1443 79 -57 54 -435 49 34 -85 -14 -76 79 -18 -144 -134 -121 89 14 -164 -24 -74 139 -164 93 -35 -103 -13 -154 105 -144 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGMSGNCRYSGBCGMSGMSSTSVKCRMCRMSGYCG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 35 nsites= 221 E= 9.5e-004 0.013575 0.805430 0.149321 0.031674 0.208145 0.072398 0.719457 0.000000 0.402715 0.253394 0.149321 0.194570 0.022624 0.601810 0.312217 0.063348 0.140271 0.257919 0.524887 0.076923 0.180995 0.271493 0.244344 0.303167 0.027149 0.642534 0.298643 0.031674 0.303167 0.122172 0.497738 0.076923 0.167421 0.262443 0.167421 0.402715 0.000000 0.651584 0.348416 0.000000 0.167421 0.262443 0.529412 0.040724 0.072398 0.343891 0.212670 0.371041 0.022624 0.737557 0.230769 0.009050 0.072398 0.054299 0.855204 0.018100 0.497738 0.339367 0.144796 0.018100 0.158371 0.434389 0.285068 0.122172 0.131222 0.230769 0.638009 0.000000 0.352941 0.438914 0.000000 0.208145 0.009050 0.452489 0.515837 0.022624 0.199095 0.266968 0.443439 0.090498 0.171946 0.226244 0.099548 0.502262 0.063348 0.384615 0.461538 0.090498 0.199095 0.253394 0.384615 0.162896 0.095023 0.194570 0.248869 0.461538 0.027149 0.823529 0.126697 0.022624 0.380090 0.022624 0.597285 0.000000 0.443439 0.443439 0.009050 0.104072 0.009050 0.687783 0.303167 0.000000 0.316742 0.212670 0.461538 0.009050 0.257919 0.398190 0.176471 0.167421 0.108597 0.542986 0.280543 0.067873 0.072398 0.135747 0.588235 0.203620 0.058824 0.266968 0.190045 0.484163 0.058824 0.601810 0.248869 0.090498 0.167421 0.108597 0.656109 0.067873 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGMSGNCRYSGBCGMSGMSSTSVKCRMCRMSGYCG MEME-2 regular expression -------------------------------------------------------------------------------- C[GA][AC][CG][GC][TCG][CG][GA][TC][CG][GC][TCG][CG]G[AC][CG][GC][CAT][GC][GC][TC][GC][GC][TG]C[GA][AC][CG][GAC][CA][CG][GT][TC][CG]G -------------------------------------------------------------------------------- Time 346.91 secs. ******************************************************************************** ******************************************************************************** MOTIF CCGCWTCGGCSCGCKBCGCCCAGCGGYGG MEME-3 width = 29 sites = 12 llr = 283 E-value = 2.5e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCGCWTCGGCSCGCKBCGCCCAGCGGYGG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :11:5:2:::1:3:::1::::71::::11 pos.-specific C a8:8:381:a69:9:38:a8a1:a2:712 probability G :191:::9a:31817319:3:29:8a:88 matrix T :::158::::::::34:1:::1::::31: bits 2.4 2.2 2.0 1.7 * ** * * * * Relative 1.5 * ** ** * * * * Entropy 1.2 * * ****** * * ** * ** * (34.0 bits) 1.0 ********** **** *** * ***** 0.7 ********** **** *********** * 0.5 ***************************** 0.2 ***************************** 0.0 ----------------------------- Multilevel CCGCATCGGCCCGCGTCGCCCAGCGGCGG consensus TC G A TC G T sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCWTCGGCSCGCKBCGCCCAGCGGYGG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 392184 bayes= 15.4436 E= 2.5e-003 -1023 167 -1023 -1023 -114 140 -192 -1023 -114 -1023 153 -1023 -1023 140 -192 -115 144 -1023 -1023 144 -1023 -33 -1023 202 -14 140 -1023 -1023 -1023 -191 153 -1023 -1023 -1023 166 -1023 -1023 167 -1023 -1023 -114 89 7 -1023 -1023 154 -192 -1023 45 -1023 124 -1023 -1023 154 -192 -1023 -1023 -1023 107 85 -1023 8 -34 117 -114 140 -192 -1023 -1023 -1023 153 -115 -1023 167 -1023 -1023 -1023 125 -34 -1023 -1023 167 -1023 -1023 186 -191 -93 -115 -114 -1023 153 -1023 -1023 167 -1023 -1023 -1023 -92 139 -1023 -1023 -1023 166 -1023 -1023 108 -1023 85 -114 -191 124 -115 -114 -92 124 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCWTCGGCSCGCKBCGCCCAGCGGYGG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 12 E= 2.5e-003 0.000000 1.000000 0.000000 0.000000 0.083333 0.833333 0.083333 0.000000 0.083333 0.000000 0.916667 0.000000 0.000000 0.833333 0.083333 0.083333 0.500000 0.000000 0.000000 0.500000 0.000000 0.250000 0.000000 0.750000 0.166667 0.833333 0.000000 0.000000 0.000000 0.083333 0.916667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.083333 0.583333 0.333333 0.000000 0.000000 0.916667 0.083333 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.916667 0.083333 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.333333 0.250000 0.416667 0.083333 0.833333 0.083333 0.000000 0.000000 0.000000 0.916667 0.083333 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.083333 0.166667 0.083333 0.083333 0.000000 0.916667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.083333 0.083333 0.750000 0.083333 0.083333 0.166667 0.750000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCWTCGGCSCGCKBCGCCCAGCGGYGG MEME-3 regular expression -------------------------------------------------------------------------------- CCGC[AT][TC]CGGC[CG]C[GA]C[GT][TCG]CGC[CG]CAGCGG[CT]GG -------------------------------------------------------------------------------- Time 474.20 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************