******************************************************************************** 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/meme30 -mod anr -dna -revcomp -nmotifs 2 -objfun se -w 12 -hsfrac 0.6 -shuf 2 -nostatus -mpi model: mod= anr nmotifs= 2 evt= inf objective function: em= Selective 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= 0.6 searchsize= 1890 norand= no csites= -1 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 CAVATCACAWWW MEME-1 width = 12 sites = 11 llr = 98 p-value = 4.6e-001 E-value = 4.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAVATCACAWWW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 17471:6:9545 pos.-specific C 72431a2a:2:: probability G 113:::2:1::: matrix T 1:::8::::365 bits 2.4 * * 2.1 * * 1.9 * * 1.6 * * Relative 1.4 * ** Entropy 1.2 * ** (12.8 bits) 0.9 * *** ** 0.7 ** ****** ** 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel CAAATCACAATA consensus CC TAT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAVATCACAWWW MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ deop2 - 60 2.15e-07 CACTTCGATA CACATCACAATT AAGGAAATCT bglr1 - 21 4.69e-06 TTATATATAA CAAATCCCAATA ATTAAGTTAT bglr1 + 2 4.69e-06 A CAAATCCCAATA ACTTAATTAT deop2 + 17 9.63e-06 TTATTTGAAC CAGATCGCATTA CAGTGATGCA lac - 81 1.06e-05 AAATTGTTAT CCGCTCACAATT CCACACAACA tdc - 78 2.47e-05 ATATGTGCGA CCACTCACAAAT TAACTTTCAA male + 24 6.47e-05 TTCTGTAACA GAGATCACACAA AGCGACGGTG pbr322 - 48 1.00e-04 TGCGGTATTT CACACCGCATAT GGTGCACTCT lac - 9 1.00e-04 ATGAGTGAGC TAACTCACATTA ATTGCGTT deop2 - 77 1.56e-04 ACATCTACTC CGCAACACACTT CGATACACAT malk - 61 1.83e-04 TTTTGCAAGC AACATCACGAAA TTCCTTACAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAVATCACAWWW MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- deop2 0.00016 16_[+1]_31_[-1]_5_[-1]_17 bglr1 4.7e-06 1_[+1]_7_[-1]_73 lac 0.0001 8_[-1]_60_[-1]_13 tdc 2.5e-05 77_[-1]_16 male 6.5e-05 23_[+1]_70 pbr322 0.0001 47_[-1]_46 malk 0.00018 60_[-1]_33 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAVATCACAWWW MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAVATCACAWWW width=12 seqs=11 deop2 ( 60) CACATCACAATT 1 bglr1 ( 21) CAAATCCCAATA 1 bglr1 ( 2) CAAATCCCAATA 1 deop2 ( 17) CAGATCGCATTA 1 lac ( 81) CCGCTCACAATT 1 tdc ( 78) CCACTCACAAAT 1 male ( 24) GAGATCACACAA 1 pbr322 ( 48) CACACCGCATAT 1 lac ( 9) TAACTCACATTA 1 deop2 ( 77) CGCAACACACTT 1 malk ( 61) AACATCACGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAVATCACAWWW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 7.36529 E= 4.6e-001 -174 189 -111 -174 126 -11 -111 -1010 26 89 48 -1010 126 48 -1010 -1010 -174 -111 -1010 143 -1010 235 -1010 -1010 106 -11 -11 -1010 -1010 235 -1010 -1010 158 -1010 -111 -1010 84 -11 -1010 -16 26 -1010 -1010 106 84 -1010 -1010 58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAVATCACAWWW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 11 E= 4.6e-001 0.090909 0.727273 0.090909 0.090909 0.727273 0.181818 0.090909 0.000000 0.363636 0.363636 0.272727 0.000000 0.727273 0.272727 0.000000 0.000000 0.090909 0.090909 0.000000 0.818182 0.000000 1.000000 0.000000 0.000000 0.636364 0.181818 0.181818 0.000000 0.000000 1.000000 0.000000 0.000000 0.909091 0.000000 0.090909 0.000000 0.545455 0.181818 0.000000 0.272727 0.363636 0.000000 0.000000 0.636364 0.545455 0.000000 0.000000 0.454545 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAVATCACAWWW MEME-1 regular expression -------------------------------------------------------------------------------- CA[ACG][AC]TCACA[AT][TA][AT] -------------------------------------------------------------------------------- Time 0.21 secs. ******************************************************************************** ******************************************************************************** MOTIF ABSCSKAAKSAK MEME-2 width = 12 sites = 12 llr = 97 p-value = 3.2e-001 E-value = 3.2e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif ABSCSKAAKSAK MEME-2 Description -------------------------------------------------------------------------------- Simplified A 8:::::68::8: pos.-specific C :3484221:331 probability G 3363553:56:6 matrix T :4::13:151:3 bits 2.4 2.1 1.9 1.6 * Relative 1.4 ** Entropy 1.2 * ** * (11.7 bits) 0.9 * *** ***** 0.7 * ********** 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel ATGCGGAAGGAG consensus GCCGCTG TCCT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ABSCSKAAKSAK MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ pbr322 + 73 1.34e-06 TACCGCACAG ATGCGTAAGGAG AAAATACCGC malk + 6 6.50e-06 GGAGG AGGCGGGAGGAT GAGAACACGG pbr322 + 12 1.20e-05 TGGCTTAACT ATGCGGCATCAG AGCAGATTGT lac - 55 1.58e-05 ACAACATACG AGCCGGAAGCAT AAAGTGTAAA lac - 26 1.82e-05 AAAGCCTGGG GTGCCTAATGAG TGAGCTAACT male + 52 2.34e-05 GGTGGGGCGT AGGGGCAAGGAG GATGGAAAGA pbr322 - 92 6.11e-05 GA GCGCCTGATGCG GTATTTTCTC ilv - 2 6.11e-05 ATAACAAAAA ACCCCGCCGGAG C trn9cat + 54 2.28e-04 CCCTGTTGAT ACCGGGAAGCCC TGGGCCAACT uxu1 - 41 3.26e-04 AGACATGTCA ATCCCGAATTCT AATTGGGTTA cya + 36 3.83e-04 ATCTTTCTTT ACGGTCAATCAG CAAGGTGTTA trn9cat + 42 6.29e-04 AAATCCTGGT GTCCCTGTTGAT ACCGGGAAGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ABSCSKAAKSAK MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- pbr322 6.1e-05 11_[+2]_49_[+2]_7_[-2]_2 malk 6.5e-06 5_[+2]_88 lac 1.6e-05 25_[-2]_17_[-2]_39 male 2.3e-05 51_[+2]_42 ilv 6.1e-05 1_[-2]_92 trn9cat 0.00023 41_[+2]_[+2]_40 uxu1 0.00033 40_[-2]_53 cya 0.00038 35_[+2]_58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ABSCSKAAKSAK MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ABSCSKAAKSAK width=12 seqs=12 pbr322 ( 73) ATGCGTAAGGAG 1 malk ( 6) AGGCGGGAGGAT 1 pbr322 ( 12) ATGCGGCATCAG 1 lac ( 55) AGCCGGAAGCAT 1 lac ( 26) GTGCCTAATGAG 1 male ( 52) AGGGGCAAGGAG 1 pbr322 ( 92) GCGCCTGATGCG 1 ilv ( 2) ACCCCGCCGGAG 1 trn9cat ( 54) ACCGGGAAGCCC 1 uxu1 ( 41) ATCCCGAATTCT 1 cya ( 36) ACGGTCAATCAG 1 trn9cat ( 42) GTCCCTGTTGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ABSCSKAAKSAK MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 7.71768 E= 3.2e-001 130 -1023 35 -1023 -1023 77 35 45 -1023 109 157 -1023 -1023 194 35 -1023 -1023 109 135 -186 -1023 -23 135 13 94 -23 35 -1023 145 -123 -1023 -186 -1023 -1023 135 72 -1023 77 157 -186 130 35 -1023 -1023 -1023 -123 157 13 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ABSCSKAAKSAK MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 12 E= 3.2e-001 0.750000 0.000000 0.250000 0.000000 0.000000 0.333333 0.250000 0.416667 0.000000 0.416667 0.583333 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.416667 0.500000 0.083333 0.000000 0.166667 0.500000 0.333333 0.583333 0.166667 0.250000 0.000000 0.833333 0.083333 0.000000 0.083333 0.000000 0.000000 0.500000 0.500000 0.000000 0.333333 0.583333 0.083333 0.750000 0.250000 0.000000 0.000000 0.000000 0.083333 0.583333 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ABSCSKAAKSAK MEME-2 regular expression -------------------------------------------------------------------------------- [AG][TCG][GC][CG][GC][GT][AG]A[GT][GC][AC][GT] -------------------------------------------------------------------------------- Time 0.38 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ce1cg 1.56e-01 105 ara 3.21e-01 105 bglr1 6.98e-03 1_[+1(4.69e-06)]_7_[-1(4.69e-06)]_\ 73 crp 1.71e-01 105 cya 1.50e-01 105 deop2 2.93e-04 16_[+1(9.63e-06)]_31_[-1(2.15e-07)]_\ 34 gale 8.81e-01 105 ilv 1.19e-02 1_[-2(6.11e-05)]_92 lac 7.71e-05 8_[-1(1.00e-04)]_5_[-2(1.82e-05)]_\ 17_[-2(1.58e-05)]_14_[-1(1.06e-05)]_13 male 5.76e-04 23_[+1(6.47e-05)]_16_[+2(2.34e-05)]_\ 42 malk 4.58e-04 5_[+2(6.50e-06)]_88 malt 4.68e-01 105 ompa 3.65e-01 105 tnaa 4.13e-01 105 uxu1 3.47e-02 105 pbr322 6.23e-05 11_[+2(1.20e-05)]_24_[-1(1.00e-04)]_\ 13_[+2(1.34e-06)]_7_[-2(6.11e-05)]_2 trn9cat 1.28e-01 105 tdc 2.62e-02 77_[-1(2.47e-05)]_16 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************