******************************************************************************** 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/meme42 -mod zoops -dna -revcomp -nmotifs 2 -objfun nz -w 12 -hsfrac 0.5 -shuf 2 -nostatus -mpi model: mod= zoops 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 GCWTCKKTGSRG MEME-1 width = 12 sites = 17 llr = 102 p-value = 2.6e-001 E-value = 2.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCWTCKKTGSRG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 21521:111131 pos.-specific C 28:19:111411 probability G 512::4515448 matrix T 11361647222: bits 2.4 2.1 1.9 1.6 * Relative 1.4 * Entropy 1.2 * * * (8.6 bits) 0.9 * ** * 0.7 * *** * 0.5 ********** * 0.2 ************ 0.0 ------------ Multilevel GCATCTGTGGGG consensus A TA GT TCA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWTCKKTGSRG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ pbr322 - 65 6.12e-08 TTCTCCTTAC GCATCTGTGCGG TATTTCACAC male + 37 1.70e-06 ATCACACAAA GCGACGGTGGGG CGTAGGGGCA ilv + 1 2.28e-05 . GCTCCGGCGGGG TTTTTTGTTA ce1cg + 24 3.75e-05 GGTTTTTGTG GCATCGGGCGAG AATAGCGCGT uxu1 - 90 1.37e-04 GCTT GCATCGGATGAG ATGGCGTATA malt + 6 1.68e-04 GATCA GCGTCGTTTTAG GTGAGTTGTT malk + 27 3.70e-04 TGAGAACACG GCTTCTGTGAAC TAAACCGAGG tnaa - 64 4.44e-04 AATCGAATCA CAATCGTTCGGG GAGCAATATT gale + 67 4.44e-04 CACACTTTTC GCATCTTTGTTA TGCTATGGTT ompa + 81 4.93e-04 TAAGTTTTCA ACTACGTTGTAG ACTTTACATC trn9cat + 70 6.96e-04 AAGCCCTGGG CCAACTTTTGGC GAAAATGAGA crp - 90 1.61e-03 GCTA TCAACTGTACTG CACGGTAATG cya + 28 2.32e-03 TGTAGCGCAT CTTTCTTTACGG TCAATCAGCA deop2 - 87 3.13e-03 TATTCTA ACATCTACTCCG CAACACACTT tdc - 90 3.82e-03 AACA GGATATGTGCGA CCACTCACAA lac - 35 3.82e-03 ATAAAGTGTA AAGCCTGGGGTG CCTAATGAGT ara - 34 5.00e-03 ATCAATGTGG ACTTTTCTGCCG TGATTATAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWTCKKTGSRG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- pbr322 6.1e-08 64_[-1]_29 male 1.7e-06 36_[+1]_57 ilv 2.3e-05 [+1]_93 ce1cg 3.8e-05 23_[+1]_70 uxu1 0.00014 89_[-1]_4 malt 0.00017 5_[+1]_88 malk 0.00037 26_[+1]_67 tnaa 0.00044 63_[-1]_30 gale 0.00044 66_[+1]_27 ompa 0.00049 80_[+1]_13 trn9cat 0.0007 69_[+1]_24 crp 0.0016 89_[-1]_4 cya 0.0023 27_[+1]_66 deop2 0.0031 86_[-1]_7 tdc 0.0038 89_[-1]_4 lac 0.0038 34_[-1]_59 ara 0.005 33_[-1]_60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWTCKKTGSRG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCWTCKKTGSRG width=12 seqs=17 pbr322 ( 65) GCATCTGTGCGG 1 male ( 37) GCGACGGTGGGG 1 ilv ( 1) GCTCCGGCGGGG 1 ce1cg ( 24) GCATCGGGCGAG 1 uxu1 ( 90) GCATCGGATGAG 1 malt ( 6) GCGTCGTTTTAG 1 malk ( 27) GCTTCTGTGAAC 1 tnaa ( 64) CAATCGTTCGGG 1 gale ( 67) GCATCTTTGTTA 1 ompa ( 81) ACTACGTTGTAG 1 trn9cat ( 70) CCAACTTTTGGC 1 crp ( 90) TCAACTGTACTG 1 cya ( 28) CTTTCTTTACGG 1 deop2 ( 87) ACATCTACTCCG 1 tdc ( 90) GGATATGTGCGA 1 lac ( 35) AAGCCTGGGGTG 1 ara ( 34) ACTTTTCTGCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWTCKKTGSRG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 2444 bayes= 8.39832 E= 2.9e-001 -37 -15 143 -237 -137 196 -173 -237 80 -1073 -15 -5 -37 -73 -1073 109 -237 217 -1073 -237 -1073 -1073 107 95 -237 -173 143 21 -237 -73 -73 121 -137 -73 143 -37 -237 85 107 -78 -5 -73 107 -78 -137 -73 196 -1073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWTCKKTGSRG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 17 E= 2.9e-001 0.235294 0.176471 0.529412 0.058824 0.117647 0.764706 0.058824 0.058824 0.529412 0.000000 0.176471 0.294118 0.235294 0.117647 0.000000 0.647059 0.058824 0.882353 0.000000 0.058824 0.000000 0.000000 0.411765 0.588235 0.058824 0.058824 0.529412 0.352941 0.058824 0.117647 0.117647 0.705882 0.117647 0.117647 0.529412 0.235294 0.058824 0.352941 0.411765 0.176471 0.294118 0.117647 0.411765 0.176471 0.117647 0.117647 0.764706 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWTCKKTGSRG MEME-1 regular expression -------------------------------------------------------------------------------- [GA]C[AT][TA]C[TG][GT]T[GT][GC][GA]G -------------------------------------------------------------------------------- Time 0.21 secs. ******************************************************************************** ******************************************************************************** MOTIF RCRBATAAMAAA MEME-2 width = 12 sites = 14 llr = 119 p-value = 2.7e-001 E-value = 3.1e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif RCRBATAAMAAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 51418:9969a7 pos.-specific C 18:4:21:4::1 probability G 4:621::::1:: matrix T :11318:1:::2 bits 2.4 2.1 1.9 1.6 * Relative 1.4 * ** Entropy 1.2 * *** ** (12.3 bits) 0.9 * ****** 0.7 *** ******** 0.5 *** ******** 0.2 ************ 0.0 ------------ Multilevel ACGCATAAAAAA consensus G AT C C T sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCRBATAAMAAA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ gale + 1 2.85e-07 . GCGCATAAAAAA CGGCTAAATT malt + 65 2.77e-06 GCAAATTCAG ACACATAAAAAA ACGTCATCGC ilv - 16 3.56e-06 GTACTGAATT GCAGATAACAAA AAACCCCGCC lac + 89 6.60e-06 GGAATTGTGA GCGGATAACAAT TTCAC ara + 8 8.68e-06 GACAAAA ACGCGTAACAAA AGTGTCTATA deop2 - 61 4.59e-05 ACACTTCGAT ACACATCACAAT TAAGGAAATC malk - 93 4.95e-05 T GCGCACATAAAA TCGCCACGAT bglr1 - 29 7.12e-05 TTATAAAGTT ATATATAACAAA TCCCAATAAT male + 79 8.24e-05 AAAGAGGTTG CCGTATAAAGAA ACTAGAGTCC ompa + 1 8.77e-05 . GCTGACAAAAAA GATTAAACAT tnaa - 1 1.67e-04 AAGAATTTTA ATGTTTAAAAAA uxu1 - 18 1.77e-04 ATTGGGTTAA CCACATCACAAC AATTTCACTC ce1cg - 61 1.77e-04 TTTTGTGAAA ACGATCAAAAAA ACAGTCTTTC tdc - 2 1.89e-04 CAACAAGTTA AAGTATAAAAAT C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCRBATAAMAAA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- gale 2.8e-07 [+2]_93 malt 2.8e-06 64_[+2]_29 ilv 3.6e-06 15_[-2]_78 lac 6.6e-06 88_[+2]_5 ara 8.7e-06 7_[+2]_86 deop2 4.6e-05 60_[-2]_33 malk 5e-05 92_[-2]_1 bglr1 7.1e-05 28_[-2]_65 male 8.2e-05 78_[+2]_15 ompa 8.8e-05 [+2]_93 tnaa 0.00017 [-2]_93 uxu1 0.00018 17_[-2]_76 ce1cg 0.00018 60_[-2]_33 tdc 0.00019 1_[-2]_92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCRBATAAMAAA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RCRBATAAMAAA width=12 seqs=14 gale ( 1) GCGCATAAAAAA 1 malt ( 65) ACACATAAAAAA 1 ilv ( 16) GCAGATAACAAA 1 lac ( 89) GCGGATAACAAT 1 ara ( 8) ACGCGTAACAAA 1 deop2 ( 61) ACACATCACAAT 1 malk ( 93) GCGCACATAAAA 1 bglr1 ( 29) ATATATAACAAA 1 male ( 79) CCGTATAAAGAA 1 ompa ( 1) GCTGACAAAAAA 1 tnaa ( 1) ATGTTTAAAAAA 1 uxu1 ( 18) CCACATCACAAC 1 ce1cg ( 61) ACGATCAAAAAA 1 tdc ( 2) AAGTATAAAAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCRBATAAMAAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 2444 bayes= 7.08163 E= 3.1e-001 72 -46 87 -1045 -209 200 -1045 -109 23 -1045 154 -209 -209 113 13 -9 137 -1045 -145 -109 -1045 13 -1045 137 149 -46 -1045 -1045 161 -1045 -1045 -209 91 113 -1045 -1045 161 -1045 -145 -1045 172 -1045 -1045 -1045 123 -145 -1045 -50 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCRBATAAMAAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 14 E= 3.1e-001 0.500000 0.142857 0.357143 0.000000 0.071429 0.785714 0.000000 0.142857 0.357143 0.000000 0.571429 0.071429 0.071429 0.428571 0.214286 0.285714 0.785714 0.000000 0.071429 0.142857 0.000000 0.214286 0.000000 0.785714 0.857143 0.142857 0.000000 0.000000 0.928571 0.000000 0.000000 0.071429 0.571429 0.428571 0.000000 0.000000 0.928571 0.000000 0.071429 0.000000 1.000000 0.000000 0.000000 0.000000 0.714286 0.071429 0.000000 0.214286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCRBATAAMAAA MEME-2 regular expression -------------------------------------------------------------------------------- [AG]C[GA][CTG]A[TC]AA[AC]AA[AT] -------------------------------------------------------------------------------- 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 2.16e-03 23_[+1(3.75e-05)]_70 ara 7.87e-03 7_[+2(8.68e-06)]_71_[-2(9.37e-05)]_\ 3 bglr1 6.25e-02 28_[-2(7.12e-05)]_65 crp 2.43e-01 105 cya 4.76e-01 105 deop2 2.51e-02 60_[-2(4.59e-05)]_33 gale 5.73e-05 [+2(2.85e-07)]_93 ilv 3.94e-05 [+1(2.28e-05)]_3_[-2(3.56e-06)]_78 lac 5.31e-03 88_[+2(6.60e-06)]_5 male 6.49e-05 36_[+1(1.70e-06)]_30_[+2(8.24e-05)]_\ 15 malk 5.22e-03 92_[-2(4.95e-05)]_1 malt 1.95e-04 64_[+2(2.77e-06)]_29 ompa 1.09e-02 [+2(8.77e-05)]_93 tnaa 1.73e-02 105 uxu1 6.75e-03 105 pbr322 1.37e-04 64_[-1(6.12e-08)]_29 trn9cat 3.14e-01 105 tdc 8.99e-02 105 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************