******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.12.0 (Release date: Tue Jun 27 16:22:50 2017 -0700) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org . This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://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 ******************************************************************************** DATAFILE= common/crp0.s 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 -oc results/motif.meme.crp0 -nostatus -dna -nmotifs 3 common/crp0.s model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 50 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 18 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 1890 N= 18 shuffle= -1 strands: + sample: seed= 0 ctfrac= -1 maxwords= -1 Letter frequencies in dataset: A 0.303 C 0.183 G 0.209 T 0.306 Background letter frequencies (from dataset with add-one prior applied): A 0.303 C 0.183 G 0.209 T 0.306 ******************************************************************************** ******************************************************************************** MOTIF TGTGANVBWGNTCACAYWW MEME-1 width = 19 sites = 17 llr = 175 E-value = 4.1e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGTGANVBWGNTCACAYWW MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::28331512:1818244 pos.-specific C 211:1242:2219:914:1 probability G :6:8:2242631:2:11:: matrix T 8391141331381111466 bits 2.5 2.2 2.0 1.7 * * Relative 1.5 * * * Entropy 1.2 * ** * * (14.8 bits) 1.0 ***** ** * 0.7 ***** * ***** * 0.5 ***** * ***** ** 0.2 ***** **** ******** 0.0 ------------------- Multilevel TGTGATCGAGGTCACACTT consensus T AATTCT TAA sequence GC C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGANVBWGNTCACAYWW MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- ompa 51 3.13e-07 TTTTCATATG CCTGACGGAGTTCACACTT GTAAGTTTTC male 17 3.13e-07 CCGCCAATTC TGTAACAGAGATCACACAA AGCGACGGTG deop2 10 5.00e-07 AGTGAATTA TTTGAACCAGATCGCATTA CAGTGATGCA ara 58 7.01e-07 ACATTGATTA TTTGCACGGCGTCACACTT TGCTATGCCA lac 12 1.33e-06 ACGCAATTAA TGTGAGTTAGCTCACTCAT TAGGCACCCC tdc 79 2.68e-06 TGAAAGTTAA TTTGTGAGTGGTCGCACAT ATCCTGTT bglr1 79 2.95e-06 AGTTAATAAC TGTGAGCATGGTCATATTT TTATCAAT tnaa 74 3.24e-06 CCCGAACGAT TGTGATTCGATTCACATTT AAACAATTTC ce1cg 64 3.24e-06 AGACTGTTTT TTTGATCGTTTTCACAAAA ATGGAAGTCC pbr322 56 3.56e-06 CCATATGCGG TGTGAAATACCGCACAGAT GCGTAAGGAG crp 66 5.14e-06 ACTGCATGTA TGCAAAGGACGTCACATTA CCGTGCAGTA gale 45 7.31e-06 ATTCCACTAA TTTATTCCATGTCACACTT TTCGCATCTT uxu1 20 2.29e-05 GTGAAATTGT TGTGATGTGGTTAACCCAA TTAGAATTCG malt 44 3.32e-05 GATTTGGAAT TGTGACACAGTGCAAATTC AGACACATAA cya 53 3.32e-05 ATCAGCAAGG TGTTAAATTGATCACGTTT TAGACCATTT malk 64 5.10e-05 TAAGGAATTT CGTGATGTTGCTTGCAAAA ATCGTGGCGA ilv 42 5.46e-05 CAGTACAAAA CGTGATCAACCCCTCAATT TTCCCTTTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGANVBWGNTCACAYWW MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ompa 3.1e-07 50_[+1]_36 male 3.1e-07 16_[+1]_70 deop2 5e-07 9_[+1]_77 ara 7e-07 57_[+1]_29 lac 1.3e-06 11_[+1]_75 tdc 2.7e-06 78_[+1]_8 bglr1 2.9e-06 78_[+1]_8 tnaa 3.2e-06 73_[+1]_13 ce1cg 3.2e-06 63_[+1]_23 pbr322 3.6e-06 55_[+1]_31 crp 5.1e-06 65_[+1]_21 gale 7.3e-06 44_[+1]_42 uxu1 2.3e-05 19_[+1]_67 malt 3.3e-05 43_[+1]_43 cya 3.3e-05 52_[+1]_34 malk 5.1e-05 63_[+1]_23 ilv 5.5e-05 41_[+1]_45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGANVBWGNTCACAYWW MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGTGANVBWGNTCACAYWW width=19 seqs=17 ompa ( 51) CCTGACGGAGTTCACACTT 1 male ( 17) TGTAACAGAGATCACACAA 1 deop2 ( 10) TTTGAACCAGATCGCATTA 1 ara ( 58) TTTGCACGGCGTCACACTT 1 lac ( 12) TGTGAGTTAGCTCACTCAT 1 tdc ( 79) TTTGTGAGTGGTCGCACAT 1 bglr1 ( 79) TGTGAGCATGGTCATATTT 1 tnaa ( 74) TGTGATTCGATTCACATTT 1 ce1cg ( 64) TTTGATCGTTTTCACAAAA 1 pbr322 ( 56) TGTGAAATACCGCACAGAT 1 crp ( 66) TGCAAAGGACGTCACATTA 1 gale ( 45) TTTATTCCATGTCACACTT 1 uxu1 ( 20) TGTGATGTGGTTAACCCAA 1 malt ( 44) TGTGACACAGTGCAAATTC 1 cya ( 53) TGTTAAATTGATCACGTTT 1 malk ( 64) CGTGATGTTGCTTGCAAAA 1 ilv ( 42) CGTGATCAACCCCTCAATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGANVBWGNTCACAYWW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 1566 bayes= 6.57994 E= 4.1e-009 -1073 -5 -1073 143 -1073 -163 163 -6 -1073 -163 -1073 162 -78 -1073 187 -237 144 -163 -1073 -138 -4 -5 -24 21 -4 95 17 -138 -136 36 76 -6 81 -1073 -24 -6 -236 36 149 -138 -78 36 49 -6 -1073 -163 -83 143 -236 227 -1073 -237 134 -1073 -24 -237 -236 227 -1073 -237 144 -163 -183 -237 -78 117 -183 21 44 -1073 -1073 94 22 -163 -1073 94 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGANVBWGNTCACAYWW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 17 E= 4.1e-009 0.000000 0.176471 0.000000 0.823529 0.000000 0.058824 0.647059 0.294118 0.000000 0.058824 0.000000 0.941176 0.176471 0.000000 0.764706 0.058824 0.823529 0.058824 0.000000 0.117647 0.294118 0.176471 0.176471 0.352941 0.294118 0.352941 0.235294 0.117647 0.117647 0.235294 0.352941 0.294118 0.529412 0.000000 0.176471 0.294118 0.058824 0.235294 0.588235 0.117647 0.176471 0.235294 0.294118 0.294118 0.000000 0.058824 0.117647 0.823529 0.058824 0.882353 0.000000 0.058824 0.764706 0.000000 0.176471 0.058824 0.058824 0.882353 0.000000 0.058824 0.823529 0.058824 0.058824 0.058824 0.176471 0.411765 0.058824 0.352941 0.411765 0.000000 0.000000 0.588235 0.352941 0.058824 0.000000 0.588235 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGANVBWGNTCACAYWW MEME-1 regular expression -------------------------------------------------------------------------------- T[GT]TGA[TA][CAG][GTC][AT][GC][GTC]TCACA[CT][TA][TA] -------------------------------------------------------------------------------- Time 0.61 secs. ******************************************************************************** ******************************************************************************** MOTIF GSMGARAATACSRC MEME-2 width = 14 sites = 6 llr = 75 E-value = 1.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GSMGARAATACSRC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :25:a7aa272:3: pos.-specific C :33:::::2:75:a probability G a5:8:3::22257: matrix T ::22::::52:::: bits 2.5 * 2.2 * * 2.0 * * 1.7 * * ** * Relative 1.5 * ** ** * * Entropy 1.2 * ** ** *** (17.9 bits) 1.0 * ***** **** 0.7 ** ***** **** 0.5 ******** ***** 0.2 ************** 0.0 -------------- Multilevel GGAGAAAATACCGC consensus CC G GA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSMGARAATACSRC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- pbr322 81 6.35e-09 AGATGCGTAA GGAGAAAATACCGC ATCAGGCGCT ce1cg 30 2.70e-07 TGTGGCATCG GGCGAGAATAGCGC GTGGTGTGAA gale 3 1.88e-06 GC GCATAAAAAACGGC TAAATTCTTG malk 15 2.01e-06 GAGGCGGGAG GATGAGAACACGGC TTCTGTGAAC ara 36 2.01e-06 TATAATCACG GCAGAAAAGTCCAC ATTGATTATT trn9cat 79 3.09e-06 GCCAACTTTT GGCGAAAATGAGAC GTTGATCGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSMGARAATACSRC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- pbr322 6.4e-09 80_[+2]_11 ce1cg 2.7e-07 29_[+2]_62 gale 1.9e-06 2_[+2]_89 malk 2e-06 14_[+2]_77 ara 2e-06 35_[+2]_56 trn9cat 3.1e-06 78_[+2]_13 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSMGARAATACSRC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GSMGARAATACSRC width=14 seqs=6 pbr322 ( 81) GGAGAAAATACCGC 1 ce1cg ( 30) GGCGAGAATAGCGC 1 gale ( 3) GCATAAAAAACGGC 1 malk ( 15) GATGAGAACACGGC 1 ara ( 36) GCAGAAAAGTCCAC 1 trn9cat ( 79) GGCGAAAATGAGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSMGARAATACSRC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 1656 bayes= 7.76085 E= 1.2e+002 -923 -923 226 -923 -86 87 126 -923 72 87 -923 -87 -923 -923 199 -87 172 -923 -923 -923 114 -923 67 -923 172 -923 -923 -923 172 -923 -923 -923 -86 -13 -33 71 114 -923 -33 -87 -86 187 -33 -923 -923 145 126 -923 14 -923 167 -923 -923 245 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSMGARAATACSRC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 6 E= 1.2e+002 0.000000 0.000000 1.000000 0.000000 0.166667 0.333333 0.500000 0.000000 0.500000 0.333333 0.000000 0.166667 0.000000 0.000000 0.833333 0.166667 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.166667 0.166667 0.500000 0.666667 0.000000 0.166667 0.166667 0.166667 0.666667 0.166667 0.000000 0.000000 0.500000 0.500000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSMGARAATACSRC MEME-2 regular expression -------------------------------------------------------------------------------- G[GC][AC]GA[AG]AATAC[CG][GA]C -------------------------------------------------------------------------------- Time 0.98 secs. ******************************************************************************** ******************************************************************************** MOTIF CCMCAGKCTTKACA MEME-3 width = 14 sites = 2 llr = 36 E-value = 1.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCMCAGKCTTKACA MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::5:a::::::a:a pos.-specific C aa5a:::a::::a: probability G :::::a5:::5::: matrix T ::::::5:aa5::: bits 2.5 ** * * * 2.2 ** * * * * 2.0 ** * * * * 1.7 ** *** *** *** Relative 1.5 ** *** *** *** Entropy 1.2 ** *** *** *** (26.2 bits) 1.0 ************** 0.7 ************** 0.5 ************** 0.2 ************** 0.0 -------------- Multilevel CCACAGGCTTGACA consensus C T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCMCAGKCTTKACA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- lac 37 3.51e-09 TCATTAGGCA CCCCAGGCTTTACA CTTTATGCTT ce1cg 91 1.12e-08 AAATGGAAGT CCACAGTCTTGACA G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCMCAGKCTTKACA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- lac 3.5e-09 36_[+3]_55 ce1cg 1.1e-08 90_[+3]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCMCAGKCTTKACA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCMCAGKCTTKACA width=14 seqs=2 lac ( 37) CCCCAGGCTTTACA 1 ce1cg ( 91) CCACAGTCTTGACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCMCAGKCTTKACA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 1656 bayes= 9.69174 E= 1.2e+003 -765 245 -765 -765 -765 245 -765 -765 72 145 -765 -765 -765 245 -765 -765 172 -765 -765 -765 -765 -765 225 -765 -765 -765 125 71 -765 245 -765 -765 -765 -765 -765 170 -765 -765 -765 170 -765 -765 125 71 172 -765 -765 -765 -765 245 -765 -765 172 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCMCAGKCTTKACA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 2 E= 1.2e+003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCMCAGKCTTKACA MEME-3 regular expression -------------------------------------------------------------------------------- CC[AC]CAG[GT]CTT[GT]ACA -------------------------------------------------------------------------------- Time 1.30 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ce1cg 4.08e-12 29_[+2(2.70e-07)]_20_[+1(3.24e-06)]_\ 8_[+3(1.12e-08)]_1 ara 7.20e-07 35_[+2(2.01e-06)]_8_[+1(7.01e-07)]_\ 29 bglr1 4.08e-04 78_[+1(2.95e-06)]_8 crp 5.36e-03 65_[+1(5.14e-06)]_21 cya 2.01e-02 52_[+1(3.32e-05)]_34 deop2 1.87e-03 9_[+1(5.00e-07)]_77 gale 5.23e-06 2_[+2(1.88e-06)]_28_[+1(7.31e-06)]_\ 42 ilv 3.26e-02 41_[+1(5.46e-05)]_45 lac 7.56e-09 11_[+1(1.33e-06)]_6_[+3(3.51e-09)]_\ 55 male 3.40e-04 16_[+1(3.13e-07)]_70 malk 5.59e-05 14_[+2(2.01e-06)]_35_[+1(5.10e-05)]_\ 23 malt 1.50e-02 43_[+1(3.32e-05)]_43 ompa 2.46e-04 50_[+1(3.13e-07)]_36 tnaa 4.93e-03 73_[+1(3.24e-06)]_13 uxu1 4.61e-03 19_[+1(2.29e-05)]_67 pbr322 4.79e-08 55_[+1(3.56e-06)]_6_[+2(6.35e-09)]_\ 11 trn9cat 9.01e-03 78_[+2(3.09e-06)]_13 tdc 4.92e-03 78_[+1(2.68e-06)]_8 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: sh-ln04.stanford.edu ********************************************************************************