******************************************************************************** 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/meme29 -mod zoops -dna -revcomp -nmotifs 2 -objfun se -w 12 -hsfrac 0.6 -shuf 2 -nostatus -mpi model: mod= zoops 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 TGKRMGGWAWTG MEME-1 width = 12 sites = 10 llr = 93 p-value = 1.1e-001 E-value = 1.1e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGKRMGGWAWTG MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::53116a3:: pos.-specific C ::1:51:::::: probability G :734:79::1:7 matrix T a36121:4:6a3 bits 2.4 2.1 1.9 * 1.6 * * * * Relative 1.4 * * * * Entropy 1.2 ** * * ** (13.5 bits) 0.9 ** ** * ** 0.7 **** **** ** 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel TGTACGGAATTG consensus TGGA T A T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGKRMGGWAWTG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ lac + 74 1.33e-06 GCTCGTATGT TGTGTGGAATTG TGAGCGGATA pbr322 - 60 2.44e-06 CTTACGCATC TGTGCGGTATTT CACACCGCAT malk + 52 6.19e-06 ACCGAGGTCA TGTAAGGAATTT CGTGATGTTG ilv - 27 7.46e-06 GATCACGTTT TGTACTGAATTG CAGATAACAA male - 2 8.76e-06 TGTTACAGAA TTGGCGGTAATG T crp - 80 8.76e-06 TCAACTGTAC TGCACGGTAATG TGACGTCCTT tdc + 59 4.42e-05 AACGATACTC TGGAAAGTATTG AAAGTTAATT trn9cat + 77 7.60e-05 GGGCCAACTT TTGGCGAAAATG AGACGTTGAT deop2 + 70 7.60e-05 AATTGTGATG TGTATCGAAGTG TGTTGCGGAG bglr1 - 49 1.04e-04 CTTTGTGTAA TTTTAGGAATTT ATAAAGTTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGKRMGGWAWTG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- lac 1.3e-06 73_[+1]_20 pbr322 2.4e-06 59_[-1]_34 malk 6.2e-06 51_[+1]_42 ilv 7.5e-06 26_[-1]_67 male 8.8e-06 1_[-1]_92 crp 8.8e-06 79_[-1]_14 tdc 4.4e-05 58_[+1]_35 trn9cat 7.6e-05 76_[+1]_17 deop2 7.6e-05 69_[+1]_24 bglr1 0.0001 48_[-1]_45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGKRMGGWAWTG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGKRMGGWAWTG width=12 seqs=10 lac ( 74) TGTGTGGAATTG 1 pbr322 ( 60) TGTGCGGTATTT 1 malk ( 52) TGTAAGGAATTT 1 ilv ( 27) TGTACTGAATTG 1 male ( 2) TTGGCGGTAATG 1 crp ( 80) TGCACGGTAATG 1 tdc ( 59) TGGAAAGTATTG 1 trn9cat ( 77) TTGGCGAAAATG 1 deop2 ( 70) TGTATCGAAGTG 1 bglr1 ( 49) TTTTAGGAATTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGKRMGGWAWTG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 7.95317 E= 1.1e-001 -997 -997 -997 172 -997 -997 184 -2 -997 -97 61 98 72 -997 103 -160 -2 135 -997 -60 -160 -97 184 -160 -160 -997 220 -997 98 -997 -997 40 172 -997 -997 -997 -2 -997 -97 98 -997 -997 -997 172 -997 -997 184 -2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGKRMGGWAWTG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 10 E= 1.1e-001 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.700000 0.300000 0.000000 0.100000 0.300000 0.600000 0.500000 0.000000 0.400000 0.100000 0.300000 0.500000 0.000000 0.200000 0.100000 0.100000 0.700000 0.100000 0.100000 0.000000 0.900000 0.000000 0.600000 0.000000 0.000000 0.400000 1.000000 0.000000 0.000000 0.000000 0.300000 0.000000 0.100000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.700000 0.300000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGKRMGGWAWTG MEME-1 regular expression -------------------------------------------------------------------------------- T[GT][TG][AG][CAT]GG[AT]A[TA]T[GT] -------------------------------------------------------------------------------- Time 0.20 secs. ******************************************************************************** ******************************************************************************** MOTIF AKKYGKAAGKAG MEME-2 width = 12 sites = 7 llr = 65 p-value = 6.8e-001 E-value = 6.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AKKYGKAAGKAG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 9:::::7a::7: pos.-specific C :1:411:::::: probability G 1361933:7637 matrix T :644:6::34:3 bits 2.4 2.1 1.9 1.6 * * Relative 1.4 * ** * Entropy 1.2 * * * *** * (13.4 bits) 0.9 * * * ****** 0.7 ************ 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel ATGCGTAAGGAG consensus GTT GG TTGT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKKYGKAAGKAG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ pbr322 + 73 4.47e-08 TACCGCACAG ATGCGTAAGGAG AAAATACCGC male + 52 8.77e-06 GGTGGGGCGT AGGGGCAAGGAG GATGGAAAGA malk + 6 1.14e-05 GGAGG AGGCGGGAGGAT GAGAACACGG deop2 + 40 1.97e-05 AGTGATGCAA ACTTGTAAGTAG ATTTCCTTAA tdc + 78 2.13e-05 TTGAAAGTTA ATTTGTGAGTGG TCGCACATAT lac - 26 9.09e-05 AAAGCCTGGG GTGCCTAATGAG TGAGCTAACT malt + 35 1.51e-04 GTTAATAAAG ATTTGGAATTGT GACACAGTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKKYGKAAGKAG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- pbr322 4.5e-08 72_[+2]_21 male 8.8e-06 51_[+2]_42 malk 1.1e-05 5_[+2]_88 deop2 2e-05 39_[+2]_54 tdc 2.1e-05 77_[+2]_16 lac 9.1e-05 25_[-2]_68 malt 0.00015 34_[+2]_59 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKKYGKAAGKAG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AKKYGKAAGKAG width=12 seqs=7 pbr322 ( 73) ATGCGTAAGGAG 1 male ( 52) AGGGGCAAGGAG 1 malk ( 6) AGGCGGGAGGAT 1 deop2 ( 40) ACTTGTAAGTAG 1 tdc ( 78) ATTTGTGAGTGG 1 lac ( 26) GTGCCTAATGAG 1 malt ( 35) ATTTGGAATTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKKYGKAAGKAG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 8.28694 E= 6.8e-001 149 -945 -45 -945 -945 -45 54 91 -945 -945 154 49 -945 113 -45 49 -945 -45 213 -945 -945 -45 54 91 123 -945 54 -945 172 -945 -945 -945 -945 -945 187 -9 -945 -945 154 49 123 -945 54 -945 -945 -945 187 -9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKKYGKAAGKAG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 6.8e-001 0.857143 0.000000 0.142857 0.000000 0.000000 0.142857 0.285714 0.571429 0.000000 0.000000 0.571429 0.428571 0.000000 0.428571 0.142857 0.428571 0.000000 0.142857 0.857143 0.000000 0.000000 0.142857 0.285714 0.571429 0.714286 0.000000 0.285714 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.714286 0.285714 0.000000 0.000000 0.571429 0.428571 0.714286 0.000000 0.285714 0.000000 0.000000 0.000000 0.714286 0.285714 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKKYGKAAGKAG MEME-2 regular expression -------------------------------------------------------------------------------- A[TG][GT][CT]G[TG][AG]A[GT][GT][AG][GT] -------------------------------------------------------------------------------- Time 0.37 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ce1cg 1.65e-01 105 ara 1.61e-01 105 bglr1 4.97e-02 105 crp 1.16e-02 79_[-1(8.76e-06)]_14 cya 1.54e-01 105 deop2 5.68e-04 39_[+2(1.97e-05)]_18_[+1(7.60e-05)]_\ 24 gale 8.15e-01 105 ilv 5.16e-03 26_[-1(7.46e-06)]_67 lac 5.68e-05 25_[-2(9.09e-05)]_36_[+1(1.33e-06)]_\ 20 male 3.74e-05 1_[-1(8.76e-06)]_38_[+2(8.77e-06)]_\ 42 malk 3.47e-05 5_[+2(1.14e-05)]_34_[+1(6.19e-06)]_\ 42 malt 7.31e-02 105 ompa 4.14e-01 105 tnaa 8.13e-01 105 uxu1 3.71e-01 105 pbr322 7.87e-08 59_[-1(2.44e-06)]_1_[+2(4.47e-08)]_\ 21 trn9cat 7.23e-02 76_[+1(7.60e-05)]_17 tdc 3.74e-04 58_[+1(4.42e-05)]_7_[+2(2.13e-05)]_\ 16 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************