******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.0 (Release date: Tue Mar 9 17:38:20 2021 -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= common/crp0.s CONTROL SEQUENCES= Primary sequences shuffled preserving 2-mers ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ ce1cg 1.0000 105 ara 1.0000 105 bglr1 1.0000 105 crp 1.0000 105 cya 1.0000 105 deop2 1.0000 105 gale 1.0000 105 ilv 1.0000 105 lac 1.0000 105 male 1.0000 105 malk 1.0000 105 malt 1.0000 105 ompa 1.0000 105 tnaa 1.0000 105 uxu1 1.0000 105 pbr322 1.0000 105 trn9cat 1.0000 105 tdc 1.0000 105 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -minsites 3 -maxsites 17 common/crp0.s -oc results/meme43 -mod anr -dna -revcomp -nmotifs 2 -objfun nz -w 12 -hsfrac 0.5 -shuf 2 -nostatus -mpi model: mod= anr nmotifs= 2 evt= inf objective function: em= Noise-injected mHG starts= log likelihood ratio (LLR) strands: + - width: minw= 12 maxw= 12 nsites: minsites= 3 maxsites= 17 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 1890 N= 18 sample: seed= 0 hsfrac= 0.5 searchsize= 1890 norand= no csites= -1 Letter frequencies in dataset: A 0.307 C 0.193 G 0.193 T 0.307 Background letter frequencies (from file dataset with add-one prior applied): A 0.304 C 0.196 G 0.196 T 0.304 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AKTGTGATBYGB MEME-1 width = 12 sites = 15 llr = 136 p-value = 8.1e-001 E-value = 1.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif AKTGTGATBYGB MEME-1 Description -------------------------------------------------------------------------------- Simplified A 71::::911::1 pos.-specific C ::::1::33333 probability G 13:a18::4:73 matrix T 25a:821727:3 bits 2.4 * 2.1 * 1.9 * 1.6 ** Relative 1.4 ** ** * Entropy 1.2 ** ** * (13.0 bits) 0.9 ***** ** 0.7 * ****** ** 0.5 *********** 0.2 ************ 0.0 ------------ Multilevel ATTGTGATGTGG consensus TG T CCCCT sequence T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKTGTGATBYGB MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ deop2 + 61 7.81e-07 GATTTCCTTA ATTGTGATGTGT ATCGAAGTGT ara - 64 7.10e-06 GGCATAGCAA AGTGTGACGCCG TGCAAATAAT uxu1 + 18 7.87e-06 GAGTGAAATT GTTGTGATGTGG TTAACCCAAT lac - 89 1.74e-05 GTGAA ATTGTTATCCGC TCACAATTCC gale - 51 2.13e-05 AGATGCGAAA AGTGTGACATGG AATAAATTAG deop2 + 78 2.32e-05 TGTGTATCGA AGTGTGTTGCGG AGTAGATGTT bglr1 + 22 2.54e-05 TAACTTAATT ATTGGGATTTGT TATATATAAC bglr1 - 1 2.54e-05 TAATTAAGTT ATTGGGATTTGT male - 23 2.80e-05 ACCGTCGCTT TGTGTGATCTCT GTTACAGAAT crp - 72 3.31e-05 ACTGCACGGT AATGTGACGTCC TTTGCATACA tnaa + 72 4.22e-05 TCCCCGAACG ATTGTGATTCGA TTCACATTTA deop2 - 16 4.61e-05 GCATCACTGT AATGCGATCTGG TTCAAATAAT ilv + 16 5.02e-05 GGCGGGGTTT TTTGTTATCTGC AATTCAGTAC ompa - 57 5.89e-05 AAAACTTACA AGTGTGAACTCC GTCAGGCATA ara - 8 9.53e-05 TATAGACACT TTTGTTACGCGT TTTTGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKTGTGATBYGB MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- deop2 4.6e-05 15_[-1]_33_[+1]_5_[+1]_16 ara 9.5e-05 7_[-1]_44_[-1]_30 uxu1 7.9e-06 17_[+1]_76 lac 1.7e-05 88_[-1]_5 gale 2.1e-05 50_[-1]_43 bglr1 2.5e-05 [-1]_9_[+1]_72 male 2.8e-05 22_[-1]_71 crp 3.3e-05 71_[-1]_22 tnaa 4.2e-05 71_[+1]_22 ilv 5e-05 15_[+1]_78 ompa 5.9e-05 56_[-1]_37 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKTGTGATBYGB MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AKTGTGATBYGB width=12 seqs=15 deop2 ( 61) ATTGTGATGTGT 1 ara ( 64) AGTGTGACGCCG 1 uxu1 ( 18) GTTGTGATGTGG 1 lac ( 89) ATTGTTATCCGC 1 gale ( 51) AGTGTGACATGG 1 deop2 ( 78) AGTGTGTTGCGG 1 bglr1 ( 22) ATTGGGATTTGT 1 bglr1 ( 1) ATTGGGATTTGT 1 male ( 23) TGTGTGATCTCT 1 crp ( 72) AATGTGACGTCC 1 tnaa ( 72) ATTGTGATTCGA 1 deop2 ( 16) AATGCGATCTGG 1 ilv ( 16) TTTGTTATCTGC 1 ompa ( 57) AGTGTGAACTCC 1 ara ( 8) TTTGTTACGCGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKTGTGATBYGB MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 2444 bayes= 8.08695 E= 1.4e+000 127 -1055 -155 -60 -119 -1055 77 81 -1055 -1055 -1055 172 -1055 -1055 235 -1055 -1055 -155 -55 139 -1055 -1055 203 -60 162 -1055 -1055 -219 -219 44 -1055 113 -219 77 103 -60 -1055 77 -1055 113 -1055 44 190 -1055 -219 44 77 13 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKTGTGATBYGB MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 15 E= 1.4e+000 0.733333 0.000000 0.066667 0.200000 0.133333 0.000000 0.333333 0.533333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.066667 0.133333 0.800000 0.000000 0.000000 0.800000 0.200000 0.933333 0.000000 0.000000 0.066667 0.066667 0.266667 0.000000 0.666667 0.066667 0.333333 0.400000 0.200000 0.000000 0.333333 0.000000 0.666667 0.000000 0.266667 0.733333 0.000000 0.066667 0.266667 0.333333 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKTGTGATBYGB MEME-1 regular expression -------------------------------------------------------------------------------- [AT][TG]TGT[GT]A[TC][GCT][TC][GC][GTC] -------------------------------------------------------------------------------- Time 0.22 secs. ******************************************************************************** ******************************************************************************** MOTIF AAAAAACGKCWT MEME-2 width = 12 sites = 8 llr = 81 p-value = 9.6e-001 E-value = 2.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAAAACGKCWT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 96aa893:::51 pos.-specific C 11::1181:8:: probability G :1:::::943:: matrix T :1::1:::6:59 bits 2.4 2.1 1.9 * 1.6 ** * * Relative 1.4 ** ** * Entropy 1.2 * ** *** * * (14.6 bits) 0.9 * ** ***** * 0.7 * ********** 0.5 * ********** 0.2 ************ 0.0 ------------ Multilevel AAAAAACGTCAT consensus A GGT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAACGKCWT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ malt + 72 3.34e-07 CAGACACATA AAAAAACGTCAT CGCTTGCATT ompa - 32 3.11e-06 AGGCATATGA AAAAAAAGTCTT GTATAAGGTA gale + 7 5.92e-06 GCGCAT AAAAAACGGCTA AATTCTTGTG ilv + 36 6.35e-06 GCAATTCAGT ACAAAACGTGAT CAACCCCTCA malk + 19 9.33e-06 CGGGAGGATG AGAACACGGCTT CTGTGAACTA ce1cg - 53 1.61e-05 AAACGATCAA AAAAACAGTCTT TCACACCACG pbr322 + 85 2.94e-05 GCGTAAGGAG AAAATACCGCAT CAGGCGCTC cya - 63 3.72e-05 AAAAAATGGT CTAAAACGTGAT CAATTTAACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAACGKCWT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- malt 3.3e-07 71_[+2]_22 ompa 3.1e-06 31_[-2]_62 gale 5.9e-06 6_[+2]_87 ilv 6.3e-06 35_[+2]_58 malk 9.3e-06 18_[+2]_75 ce1cg 1.6e-05 52_[-2]_41 pbr322 2.9e-05 84_[+2]_9 cya 3.7e-05 62_[-2]_31 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAACGKCWT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAAAACGKCWT width=12 seqs=8 malt ( 72) AAAAAACGTCAT 1 ompa ( 32) AAAAAAAGTCTT 1 gale ( 7) AAAAAACGGCTA 1 ilv ( 36) ACAAAACGTGAT 1 malk ( 19) AGAACACGGCTT 1 ce1cg ( 53) AAAAACAGTCTT 1 pbr322 ( 85) AAAATACCGCAT 1 cya ( 63) CTAAAACGTGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAACGKCWT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 2444 bayes= 7.71768 E= 2.2e+000 152 -65 -965 -965 104 -65 -65 -128 172 -965 -965 -965 172 -965 -965 -965 130 -65 -965 -128 152 -65 -965 -965 -28 194 -965 -965 -965 -65 216 -965 -965 -965 94 104 -965 194 35 -965 72 -965 -965 72 -128 -965 -965 152 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAACGKCWT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 8 E= 2.2e+000 0.875000 0.125000 0.000000 0.000000 0.625000 0.125000 0.125000 0.125000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.125000 0.000000 0.125000 0.875000 0.125000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 0.000000 0.375000 0.625000 0.000000 0.750000 0.250000 0.000000 0.500000 0.000000 0.000000 0.500000 0.125000 0.000000 0.000000 0.875000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAACGKCWT MEME-2 regular expression -------------------------------------------------------------------------------- AAAAAA[CA]G[TG][CG][AT]T -------------------------------------------------------------------------------- Time 0.41 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ce1cg 1.05e-02 52_[-2(1.61e-05)]_41 ara 1.92e-03 7_[-1(9.53e-05)]_44_[-1(7.10e-06)]_\ 30 bglr1 1.94e-02 [-1(2.54e-05)]_9_[+1(2.54e-05)]_72 crp 2.63e-02 71_[-1(3.31e-05)]_22 cya 2.88e-02 62_[-2(3.72e-05)]_31 deop2 1.30e-03 15_[-1(4.61e-05)]_33_[+1(7.81e-07)]_\ 5_[+1(2.32e-05)]_16 gale 5.92e-05 6_[+2(5.92e-06)]_32_[-1(2.13e-05)]_\ 43 ilv 1.39e-04 15_[+1(5.02e-05)]_8_[+2(6.35e-06)]_\ 58 lac 2.06e-02 88_[-1(1.74e-05)]_5 male 2.88e-02 22_[-1(2.80e-05)]_71 malk 7.84e-03 18_[+2(9.33e-06)]_75 malt 1.98e-04 71_[+2(3.34e-07)]_22 ompa 8.34e-05 31_[-2(3.11e-06)]_13_[-1(5.89e-05)]_\ 37 tnaa 2.60e-02 71_[+1(4.22e-05)]_22 uxu1 2.04e-03 17_[+1(7.87e-06)]_76 pbr322 2.43e-02 84_[+2(2.94e-05)]_9 trn9cat 8.83e-01 105 tdc 7.51e-01 105 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************