******************************************************************************** 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= --none-- 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 common/crp0.s -oc results/meme1 -mod oops -dna -revcomp -nmotifs 2 -objfun classic -minw 8 -nostatus -mpi model: mod= oops nmotifs= 2 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + - width: minw= 8 maxw= 50 nsites: minsites= 18 maxsites= 18 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= 1890 N= 18 sample: seed= 0 hsfrac= 0 searchsize= 1890 norand= no csites= 1000 Letter frequencies in dataset: A 0.304 C 0.196 G 0.196 T 0.304 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 TGTGAMRTNGHTCAC MEME-1 width = 15 sites = 18 llr = 170 E-value = 9.6e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGTGAMRTNGHTCAC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :1119231314:172 pos.-specific C 11:1:412213:8:7 probability G :9:8124227:2:31 matrix T 9:91:22532381:: bits 2.4 2.1 1.9 1.6 * Relative 1.4 * ** * Entropy 1.2 ***** ** * (13.6 bits) 0.9 ***** **** 0.7 ***** * **** 0.5 ***** * **** 0.2 ******** ****** 0.0 --------------- Multilevel TGTGACGTTGATCAC consensus AACA TG GA sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGAMRTNGHTCAC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------- lac + 12 5.04e-07 ACGCAATTAA TGTGAGTTAGCTCAC TCATTAGGCA ara - 59 1.52e-06 CATAGCAAAG TGTGACGCCGTGCAA ATAATCAATG malt + 44 3.31e-06 GATTTGGAAT TGTGACACAGTGCAA ATTCAGACAC pbr322 + 56 6.76e-06 CCATATGCGG TGTGAAATACCGCAC AGATGCGTAA uxu1 + 20 7.45e-06 GTGAAATTGT TGTGATGTGGTTAAC CCAATTAGAA male + 17 9.01e-06 CCGCCAATTC TGTAACAGAGATCAC ACAAAGCGAC cya + 53 1.09e-05 ATCAGCAAGG TGTTAAATTGATCAC GTTTTAGACC trn9cat + 87 1.43e-05 TTGGCGAAAA TGAGACGTTGATCGG CACG deop2 + 63 1.43e-05 TTTCCTTAAT TGTGATGTGTATCGA AGTGTGTTGC crp - 67 1.43e-05 TGCACGGTAA TGTGACGTCCTTTGC ATACATGCAG ce1cg - 65 1.43e-05 CTTCCATTTT TGTGAAAACGATCAA AAAAACAGTC tdc + 81 1.85e-05 AAAGTTAATT TGTGAGTGGTCGCAC ATATCCTGTT ompa + 51 1.85e-05 TTTTCATATG CCTGACGGAGTTCAC ACTTGTAAGT ilv - 43 1.85e-05 AAGGGAAAAT TGAGGGGTTGATCAC GTTTTGTACT tnaa - 75 2.20e-05 ATTGTTTAAA TGTGAATCGAATCAC AATCGTTCGG malk + 64 2.59e-05 TAAGGAATTT CGTGATGTTGCTTGC AAAAATCGTG gale + 54 3.88e-05 ATTTATTCCA TGTCACACTTTTCGC ATCTTTGTTA bglr1 - 80 5.71e-05 TTGATAAAAA TATGACCATGCTCAC AGTTATTAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGAMRTNGHTCAC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- lac 5e-07 11_[+1]_79 ara 1.5e-06 58_[-1]_32 malt 3.3e-06 43_[+1]_47 pbr322 6.8e-06 55_[+1]_35 uxu1 7.5e-06 19_[+1]_71 male 9e-06 16_[+1]_74 cya 1.1e-05 52_[+1]_38 trn9cat 1.4e-05 86_[+1]_4 deop2 1.4e-05 62_[+1]_28 crp 1.4e-05 66_[-1]_24 ce1cg 1.4e-05 64_[-1]_26 tdc 1.9e-05 80_[+1]_10 ompa 1.9e-05 50_[+1]_40 ilv 1.9e-05 42_[-1]_48 tnaa 2.2e-05 74_[-1]_16 malk 2.6e-05 63_[+1]_27 gale 3.9e-05 53_[+1]_37 bglr1 5.7e-05 79_[-1]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGAMRTNGHTCAC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGTGAMRTNGHTCAC width=15 seqs=18 lac ( 12) TGTGAGTTAGCTCAC 1 ara ( 59) TGTGACGCCGTGCAA 1 malt ( 44) TGTGACACAGTGCAA 1 pbr322 ( 56) TGTGAAATACCGCAC 1 uxu1 ( 20) TGTGATGTGGTTAAC 1 male ( 17) TGTAACAGAGATCAC 1 cya ( 53) TGTTAAATTGATCAC 1 trn9cat ( 87) TGAGACGTTGATCGG 1 deop2 ( 63) TGTGATGTGTATCGA 1 crp ( 67) TGTGACGTCCTTTGC 1 ce1cg ( 65) TGTGAAAACGATCAA 1 tdc ( 81) TGTGAGTGGTCGCAC 1 ompa ( 51) CCTGACGGAGTTCAC 1 ilv ( 43) TGAGGGGTTGATCAC 1 tnaa ( 75) TGTGAATCGAATCAC 1 malk ( 64) CGTGATGTTGCTTGC 1 gale ( 54) TGTCACACTTTTCGC 1 bglr1 ( 80) TATGACCATGCTCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGAMRTNGHTCAC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1638 bayes= 6.49185 E= 9.6e-007 -1081 -82 -1081 155 -245 -182 218 -1081 -145 -1081 -1081 155 -245 -182 209 -245 163 -1081 -182 -1081 -45 118 -23 -87 13 -182 118 -87 -145 18 -23 72 -13 -23 18 13 -245 -82 177 -87 35 50 -1081 13 -1081 -1081 18 135 -245 209 -1081 -145 125 -1081 50 -1081 -45 188 -182 -1081 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGAMRTNGHTCAC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 18 E= 9.6e-007 0.000000 0.111111 0.000000 0.888889 0.055556 0.055556 0.888889 0.000000 0.111111 0.000000 0.000000 0.888889 0.055556 0.055556 0.833333 0.055556 0.944444 0.000000 0.055556 0.000000 0.222222 0.444444 0.166667 0.166667 0.333333 0.055556 0.444444 0.166667 0.111111 0.222222 0.166667 0.500000 0.277778 0.166667 0.222222 0.333333 0.055556 0.111111 0.666667 0.166667 0.388889 0.277778 0.000000 0.333333 0.000000 0.000000 0.222222 0.777778 0.055556 0.833333 0.000000 0.111111 0.722222 0.000000 0.277778 0.000000 0.222222 0.722222 0.055556 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGAMRTNGHTCAC MEME-1 regular expression -------------------------------------------------------------------------------- TGTGA[CA][GA][TC][TAG]G[ATC][TG]C[AG][CA] -------------------------------------------------------------------------------- Time 0.22 secs. ******************************************************************************** ******************************************************************************** MOTIF CTTTACAR MEME-2 width = 8 sites = 18 llr = 109 E-value = 2.4e+008 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTTTACAR MEME-2 Description -------------------------------------------------------------------------------- Simplified A :2:28194 pos.-specific C a1:128:1 probability G :111::14 matrix T :697:1:2 bits 2.4 * 2.1 * 1.9 * 1.6 * Relative 1.4 * ** Entropy 1.2 * * *** (8.8 bits) 0.9 * * *** 0.7 * * *** 0.5 * ***** 0.2 ******** 0.0 -------- Multilevel CTTTACAA consensus A C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTTACAR MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- ilv - 94 1.95e-05 ACAG CTTTACAG GGGAGACAAT tdc - 58 6.25e-05 ACTTTCAATA CTTTCCAG AGTATCGTTA deop2 + 24 8.20e-05 AACCAGATCG CATTACAG TGATGCAAAC ompa + 94 1.45e-04 ACGTTGTAGA CTTTACAT CGCC male - 65 3.29e-04 ACGGCAACCT CTTTCCAT CCTCCTTGCC lac + 44 3.29e-04 GCACCCCAGG CTTTACAC TTTATGCTTC ce1cg + 98 4.06e-04 AGTCCACAGT CTTGACAG cya + 32 5.39e-04 GCGCATCTTT CTTTACGG TCAATCAGCA uxu1 + 61 6.30e-04 ATTGACATGT CTTACCAA AAGGTAGAAC crp + 90 6.30e-04 CATTACCGTG CAGTACAG TTGATAGC gale - 73 8.47e-04 ATAACCATAG CATAACAA AGATGCGAAA bglr1 + 43 8.47e-04 TTATATATAA CTTTATAA ATTCCTAAAA pbr322 - 30 9.49e-04 GGTGCACTCT CAGTACAA TCTGCTCTGA ara + 11 1.05e-03 GACAAAAACG CGTAACAA AAGTGTCTAT malk - 51 1.09e-03 TCACGAAATT CCTTACAT GACCTCGGTT trn9cat - 1 1.30e-03 AGTGATCTTC CGTCACAG tnaa + 37 1.36e-03 AATTTATAAT CTTTAAAA AAAGCATTTA malt - 92 1.50e-03 AGAAAC CTTTCTAA TGCAAGCGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTTACAR MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ilv 2e-05 93_[-2]_4 tdc 6.2e-05 57_[-2]_40 deop2 8.2e-05 23_[+2]_74 ompa 0.00014 93_[+2]_4 male 0.00033 64_[-2]_33 lac 0.00033 43_[+2]_54 ce1cg 0.00041 97_[+2] cya 0.00054 31_[+2]_66 uxu1 0.00063 60_[+2]_37 crp 0.00063 89_[+2]_8 gale 0.00085 72_[-2]_25 bglr1 0.00085 42_[+2]_55 pbr322 0.00095 29_[-2]_68 ara 0.001 10_[+2]_87 malk 0.0011 50_[-2]_47 trn9cat 0.0013 [-2]_97 tnaa 0.0014 36_[+2]_61 malt 0.0015 91_[-2]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTTACAR MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTTTACAR width=8 seqs=18 ilv ( 94) CTTTACAG 1 tdc ( 58) CTTTCCAG 1 deop2 ( 24) CATTACAG 1 ompa ( 94) CTTTACAT 1 male ( 65) CTTTCCAT 1 lac ( 44) CTTTACAC 1 ce1cg ( 98) CTTGACAG 1 cya ( 32) CTTTACGG 1 uxu1 ( 61) CTTACCAA 1 crp ( 90) CAGTACAG 1 gale ( 73) CATAACAA 1 bglr1 ( 43) CTTTATAA 1 pbr322 ( 30) CAGTACAA 1 ara ( 11) CGTAACAA 1 malk ( 51) CCTTACAT 1 trn9cat ( 1) CGTCACAG 1 tnaa ( 37) CTTTAAAA 1 malt ( 92) CTTTCTAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTTACAR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1764 bayes= 6.59991 E= 2.4e+008 -1081 235 -1081 -1081 -45 -182 -82 101 -1081 -1081 -82 155 -87 -182 -182 125 135 18 -1081 -1081 -245 209 -1081 -145 163 -1081 -182 -1081 35 -182 99 -87 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTTACAR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 18 E= 2.4e+008 0.000000 1.000000 0.000000 0.000000 0.222222 0.055556 0.111111 0.611111 0.000000 0.000000 0.111111 0.888889 0.166667 0.055556 0.055556 0.722222 0.777778 0.222222 0.000000 0.000000 0.055556 0.833333 0.000000 0.111111 0.944444 0.000000 0.055556 0.000000 0.388889 0.055556 0.388889 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTTACAR MEME-2 regular expression -------------------------------------------------------------------------------- C[TA]TT[AC]CA[AG] -------------------------------------------------------------------------------- Time 0.39 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ce1cg 1.89e-03 64_[-1(1.43e-05)]_26 ara 5.57e-04 58_[-1(1.52e-06)]_32 bglr1 1.18e-02 79_[-1(5.71e-05)]_11 crp 2.75e-03 66_[-1(1.43e-05)]_24 cya 1.89e-03 52_[+1(1.09e-05)]_38 deop2 4.59e-04 23_[+2(8.20e-05)]_31_[+1(1.43e-05)]_\ 28 gale 8.44e-03 53_[+1(3.88e-05)]_37 ilv 1.58e-04 42_[-1(1.85e-05)]_36_[-2(1.95e-05)]_\ 4 lac 7.49e-05 11_[+1(5.04e-07)]_79 male 1.04e-03 16_[+1(9.01e-06)]_74 malk 7.26e-03 63_[+1(2.59e-05)]_27 malt 1.50e-03 43_[+1(3.31e-06)]_47 ompa 9.66e-04 50_[+1(1.85e-05)]_40 tnaa 7.46e-03 74_[-1(2.20e-05)]_16 uxu1 1.54e-03 19_[+1(7.45e-06)]_71 pbr322 1.98e-03 55_[+1(6.76e-06)]_35 trn9cat 4.92e-03 86_[+1(1.43e-05)]_4 tdc 4.55e-04 57_[-2(6.25e-05)]_15_[+1(1.85e-05)]_\ 10 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************