******************************************************************************** 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 common/crp0.s -oc results/meme41 -mod oops -dna -revcomp -nmotifs 2 -objfun nz -w 12 -hsfrac 0.5 -shuf 2 -nostatus -mpi model: mod= oops nmotifs= 2 evt= inf objective function: em= Noise-injected mHG starts= log likelihood ratio (LLR) strands: + - width: minw= 12 maxw= 12 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 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 DTGTGKMATTGT MEME-1 width = 12 sites = 18 llr = 131 p-value = 4.5e-001 E-value = 4.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif DTGTGKMATTGT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2121216911:: pos.-specific C :::2::3132:1 probability G 318:65::::71 matrix T 48:7242:6738 bits 2.4 2.1 1.9 1.6 * Relative 1.4 * * Entropy 1.2 * * * (10.5 bits) 0.9 * * ** 0.7 ***** ***** 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel TTGTGGAATTGT consensus G CTTC CCT sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DTGTGKMATTGT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ lac + 75 6.94e-08 CTCGTATGTT GTGTGGAATTGT GAGCGGATAA bglr1 - 57 9.34e-06 GTTATTAACT TTGTGTAATTTT AGGAATTTAT gale - 32 2.42e-05 TGGAATAAAT TAGTGGAATCGT TTACACAAGA cya - 1 3.81e-05 CTACATACAA GTGTAGCACCGT ce1cg + 19 5.30e-05 GTGCTGGTTT TTGTGGCATCGG GCGAGAATAG uxu1 + 8 8.05e-05 CCCATGA GAGTGAAATTGT TGTGATGTGG deop2 - 28 9.82e-05 ACTTACAAGT TTGCATCACTGT AATGCGATCT ara - 40 9.82e-05 CAAATAATCA ATGTGGACTTTT CTGCCGTGAT tnaa - 87 1.09e-04 TCTGAAA TTGTTTAAATGT GAATCGAATC tdc + 34 1.31e-04 ATATTTAAAG GTATTTAATTGT AATAACGATA pbr322 - 85 1.31e-04 GAGCGCCTG ATGCGGTATTTT CTCCTTACGC trn9cat + 38 2.08e-04 AAATAAATCC TGGTGTCCCTGT TGATACCGGG crp - 38 2.67e-04 CAGTACATCA ATGTATTACTGT AGCATCCTGA ompa - 11 3.15e-04 TGTATAAGGT ATGTTTAATCTT TTTTGTCAGC malt + 43 3.40e-04 AGATTTGGAA TTGTGACACAGT GCAAATTCAG male - 1 3.97e-04 GTTACAGAAT TGGCGGTAATGT ilv - 26 6.14e-04 ATCACGTTTT GTACTGAATTGC AGATAACAAA malk + 53 1.82e-03 CCGAGGTCAT GTAAGGAATTTC GTGATGTTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DTGTGKMATTGT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- lac 6.9e-08 74_[+1]_19 bglr1 9.3e-06 56_[-1]_37 gale 2.4e-05 31_[-1]_62 cya 3.8e-05 [-1]_93 ce1cg 5.3e-05 18_[+1]_75 uxu1 8.1e-05 7_[+1]_86 deop2 9.8e-05 27_[-1]_66 ara 9.8e-05 39_[-1]_54 tnaa 0.00011 86_[-1]_7 tdc 0.00013 33_[+1]_60 pbr322 0.00013 84_[-1]_9 trn9cat 0.00021 37_[+1]_56 crp 0.00027 37_[-1]_56 ompa 0.00031 10_[-1]_83 malt 0.00034 42_[+1]_51 male 0.0004 [-1]_93 ilv 0.00061 25_[-1]_68 malk 0.0018 52_[+1]_41 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DTGTGKMATTGT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF DTGTGKMATTGT width=12 seqs=18 lac ( 75) GTGTGGAATTGT 1 bglr1 ( 57) TTGTGTAATTTT 1 gale ( 32) TAGTGGAATCGT 1 cya ( 1) GTGTAGCACCGT 1 ce1cg ( 19) TTGTGGCATCGG 1 uxu1 ( 8) GAGTGAAATTGT 1 deop2 ( 28) TTGCATCACTGT 1 ara ( 40) ATGTGGACTTTT 1 tnaa ( 87) TTGTTTAAATGT 1 tdc ( 34) GTATTTAATTGT 1 pbr322 ( 85) ATGCGGTATTTT 1 trn9cat ( 38) TGGTGTCCCTGT 1 crp ( 38) ATGTATTACTGT 1 ompa ( 11) ATGTTTAATCTT 1 malt ( 43) TTGTGACACAGT 1 male ( 1) TGGCGGTAATGT 1 ilv ( 26) GTACTGAATTGC 1 malk ( 53) GTAAGGAATTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DTGTGKMATTGT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 2444 bayes= 6.53916 E= 4.5e-001 -45 -1081 77 55 -145 -1081 -82 135 -87 -1081 209 -1081 -245 18 -1081 125 -87 -1081 164 -45 -145 -1081 135 35 87 50 -1081 -87 155 -82 -1081 -1081 -145 50 -1081 101 -245 18 -1081 125 -1081 -1081 188 -13 -1081 -82 -182 145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DTGTGKMATTGT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 4.5e-001 0.222222 0.000000 0.333333 0.444444 0.111111 0.000000 0.111111 0.777778 0.166667 0.000000 0.833333 0.000000 0.055556 0.222222 0.000000 0.722222 0.166667 0.000000 0.611111 0.222222 0.111111 0.000000 0.500000 0.388889 0.555556 0.277778 0.000000 0.166667 0.888889 0.111111 0.000000 0.000000 0.111111 0.277778 0.000000 0.611111 0.055556 0.222222 0.000000 0.722222 0.000000 0.000000 0.722222 0.277778 0.000000 0.111111 0.055556 0.833333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DTGTGKMATTGT MEME-1 regular expression -------------------------------------------------------------------------------- [TGA]TG[TC][GT][GT][AC]A[TC][TC][GT]T -------------------------------------------------------------------------------- Time 0.22 secs. ******************************************************************************** ******************************************************************************** MOTIF BWSDTCACANWW MEME-2 width = 12 sites = 18 llr = 131 p-value = 1.4e-001 E-value = 1.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif BWSDTCACANWW MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1614::8:8243 pos.-specific C 2132:9:a:3:1 probability G 4152112:22:: matrix T 33129::::366 bits 2.4 * 2.1 * 1.9 * * 1.6 * * Relative 1.4 ** * Entropy 1.2 ***** (10.5 bits) 0.9 ***** 0.7 ***** * 0.5 * * ***** ** 0.2 *** ***** ** 0.0 ------------ Multilevel GAGATCACATTT consensus TTCG GCAA sequence C T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BWSDTCACANWW MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ ompa + 58 7.03e-07 ATGCCTGACG GAGTTCACACTT GTAAGTTTTC male + 24 4.18e-06 TTCTGTAACA GAGATCACACAA AGCGACGGTG crp + 73 1.27e-05 GTATGCAAAG GACGTCACATTA CCGTGCAGTA ara + 65 2.02e-05 TTATTTGCAC GGCGTCACACTT TGCTATGCCA deop2 - 60 3.38e-05 CACTTCGATA CACATCACAATT AAGGAAATCT tdc + 86 5.55e-05 TAATTTGTGA GTGGTCGCACAT ATCCTGTT ilv - 39 7.25e-05 AATTGAGGGG TTGATCACGTTT TGTACTGAAT gale + 52 7.25e-05 TAATTTATTC CATGTCACACTT TTCGCATCTT cya + 60 7.25e-05 AGGTGTTAAA TTGATCACGTTT TAGACCATTT malk - 29 8.14e-05 GACCTCGGTT TAGTTCACAGAA GCCGTGTTCT bglr1 - 76 2.67e-04 AAATATGACC ATGCTCACAGTT ATTAACTTTG trn9cat + 15 3.73e-04 GACGGAAGAT CACTTCGCAGAA TAAATAAATC lac - 9 3.73e-04 ATGAGTGAGC TAACTCACATTA ATTGCGTT uxu1 - 81 5.75e-04 TGCATCGGAT GAGATGGCGTAT AAGTTCTACC pbr322 + 63 6.90e-04 CGGTGTGAAA TACCGCACAGAT GCGTAAGGAG malt - 75 6.90e-04 TCTAATGCAA GCGATGACGTTT TTTTATGTGT ce1cg + 71 7.81e-04 TTTTTTGATC GTTTTCACAAAA ATGGAAGTCC tnaa - 71 1.68e-03 AAATGTGAAT CGAATCACAATC GTTCGGGGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BWSDTCACANWW MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ompa 7e-07 57_[+2]_36 male 4.2e-06 23_[+2]_70 crp 1.3e-05 72_[+2]_21 ara 2e-05 64_[+2]_29 deop2 3.4e-05 59_[-2]_34 tdc 5.5e-05 85_[+2]_8 ilv 7.2e-05 38_[-2]_55 gale 7.2e-05 51_[+2]_42 cya 7.2e-05 59_[+2]_34 malk 8.1e-05 28_[-2]_65 bglr1 0.00027 75_[-2]_18 trn9cat 0.00037 14_[+2]_79 lac 0.00037 8_[-2]_85 uxu1 0.00058 80_[-2]_13 pbr322 0.00069 62_[+2]_31 malt 0.00069 74_[-2]_19 ce1cg 0.00078 70_[+2]_23 tnaa 0.0017 70_[-2]_23 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BWSDTCACANWW MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF BWSDTCACANWW width=12 seqs=18 ompa ( 58) GAGTTCACACTT 1 male ( 24) GAGATCACACAA 1 crp ( 73) GACGTCACATTA 1 ara ( 65) GGCGTCACACTT 1 deop2 ( 60) CACATCACAATT 1 tdc ( 86) GTGGTCGCACAT 1 ilv ( 39) TTGATCACGTTT 1 gale ( 52) CATGTCACACTT 1 cya ( 60) TTGATCACGTTT 1 malk ( 29) TAGTTCACAGAA 1 bglr1 ( 76) ATGCTCACAGTT 1 trn9cat ( 15) CACTTCGCAGAA 1 lac ( 9) TAACTCACATTA 1 uxu1 ( 81) GAGATGGCGTAT 1 pbr322 ( 63) TACCGCACAGAT 1 malt ( 75) GCGATGACGTTT 1 ce1cg ( 71) GTTTTCACAAAA 1 tnaa ( 71) CGAATCACAATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BWSDTCACANWW MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 2444 bayes= 6.53916 E= 1.4e-001 -245 18 118 -13 87 -182 -82 -13 -145 50 135 -145 35 -23 18 -45 -1081 -1081 -182 163 -1081 218 -82 -1081 145 -1081 -23 -1081 -1081 235 -1081 -1081 135 -1081 18 -1081 -87 50 18 13 35 -1081 -1081 101 13 -182 -1081 101 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BWSDTCACANWW MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 1.4e-001 0.055556 0.222222 0.444444 0.277778 0.555556 0.055556 0.111111 0.277778 0.111111 0.277778 0.500000 0.111111 0.388889 0.166667 0.222222 0.222222 0.000000 0.000000 0.055556 0.944444 0.000000 0.888889 0.111111 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.777778 0.000000 0.222222 0.000000 0.166667 0.277778 0.222222 0.333333 0.388889 0.000000 0.000000 0.611111 0.333333 0.055556 0.000000 0.611111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BWSDTCACANWW MEME-2 regular expression -------------------------------------------------------------------------------- [GTC][AT][GC][AGT]TCAC[AG][TCG][TA][TA] -------------------------------------------------------------------------------- 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 1.03e-02 18_[+1(5.30e-05)]_75 ara 7.33e-04 39_[-1(9.82e-05)]_13_[+2(2.02e-05)]_\ 29 bglr1 8.90e-04 56_[-1(9.34e-06)]_37 crp 1.18e-03 72_[+2(1.27e-05)]_21 cya 9.90e-04 [-1(3.81e-05)]_47_[+2(7.25e-05)]_34 deop2 1.16e-03 16_[+2(8.14e-05)]_31_[-2(3.38e-05)]_\ 34 gale 6.56e-04 31_[-1(2.42e-05)]_8_[+2(7.25e-05)]_\ 42 ilv 1.11e-02 38_[-2(7.25e-05)]_55 lac 1.05e-05 74_[+1(6.94e-08)]_19 male 6.10e-04 23_[+2(4.18e-06)]_70 malk 2.83e-02 28_[-2(8.14e-05)]_65 malt 4.44e-02 105 ompa 9.72e-05 57_[+2(7.03e-07)]_36 tnaa 1.33e-02 105 uxu1 1.15e-02 7_[+1(8.05e-05)]_86 pbr322 2.02e-02 105 trn9cat 1.81e-02 105 tdc 2.35e-03 85_[+2(5.55e-05)]_8 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************