******************************************************************************** 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 -minsites 3 -maxsites 17 common/crp0.s -oc results/meme3 -mod anr -dna -revcomp -nmotifs 2 -objfun classic -minw 8 -nostatus -mpi model: mod= anr 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= 3 maxsites= 17 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 WWTAYKTGAWCNAYDTCACAM MEME-1 width = 21 sites = 17 llr = 195 E-value = 5.8e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif WWTAYKTGAWCNAYDTCACAM MEME-1 Description -------------------------------------------------------------------------------- Simplified A 45351::26412813:19:94 pos.-specific C 1::2312:3272:3129:a:4 probability G :1:216:6:224223::1:1: matrix T 5472648112121438:1::2 bits 2.4 * 2.1 * 1.9 * * 1.6 * * Relative 1.4 * ** Entropy 1.2 * ***** (16.6 bits) 0.9 * *** * * ***** 0.7 * **** * * ***** 0.5 *** ***** * * ****** 0.2 *** ***** **** ****** 0.0 --------------------- Multilevel TATATGTGAACGATATCACAA consensus ATA CTCACT A CG C sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTAYKTGAWCNAYDTCACAM MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------------- ara + 54 6.23e-09 GTCCACATTG ATTATTTGCACGGCGTCACAC TTTGCTATGC ce1cg - 19 4.24e-07 CACCACGCGC TATTCTCGCCCGATGCCACAA AAACCAGCAC pbr322 - 55 5.29e-07 TCTCCTTACG CATCTGTGCGGTATTTCACAC CGCATATGGT ompa + 47 8.08e-07 TTTTTTTTCA TATGCCTGACGGAGTTCACAC TTGTAAGTTT malt - 43 8.96e-07 TTTATGTGTC TGAATTTGCACTGTGTCACAA TTCCAAATCT crp + 62 8.96e-07 ATGTACTGCA TGTATGCAAAGGACGTCACAT TACCGTGCAG uxu1 - 19 1.33e-06 CCGAATTCTA ATTGGGTTAACCACATCACAA CAATTTCACT deop2 + 6 1.47e-06 AGTGA ATTATTTGAACCAGATCGCAT TACAGTGATG ce1cg + 60 1.47e-06 TGAAAGACTG TTTTTTTGATCGTTTTCACAA AAATGGAAGT lac - 75 1.77e-06 GTGAAATTGT TATCCGCTCACAATTCCACAC AACATACGAG cya - 52 1.77e-06 AAAATGGTCT AAAACGTGATCAATTTAACAC CTTGCTGATT male + 13 2.13e-06 ATTACCGCCA ATTCTGTAACAGAGATCACAC AAAGCGACGG tnaa - 73 4.60e-06 TGAAATTGTT TAAATGTGAATCGAATCACAA TCGTTCGGGG malk - 63 6.32e-06 ATCGCCACGA TTTTTGCAAGCAACATCACGA AATTCCTTAC ilv + 38 6.82e-06 AATTCAGTAC AAAACGTGATCAACCCCTCAA TTTTCCCTTT gale + 41 6.82e-06 AACGATTCCA CTAATTTATTCCATGTCACAC TTTTCGCATC lac - 11 8.55e-06 TGGGGTGCCT AATGAGTGAGCTAACTCACAT TAATTGCGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTAYKTGAWCNAYDTCACAM MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ara 6.2e-09 53_[+1]_31 ce1cg 4.2e-07 18_[-1]_20_[+1]_25 pbr322 5.3e-07 54_[-1]_30 ompa 8.1e-07 46_[+1]_38 malt 9e-07 42_[-1]_42 crp 9e-07 61_[+1]_23 uxu1 1.3e-06 18_[-1]_66 deop2 1.5e-06 5_[+1]_79 lac 8.5e-06 10_[-1]_43_[-1]_10 cya 1.8e-06 51_[-1]_33 male 2.1e-06 12_[+1]_72 tnaa 4.6e-06 72_[-1]_12 malk 6.3e-06 62_[-1]_22 ilv 6.8e-06 37_[+1]_47 gale 6.8e-06 40_[+1]_44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTAYKTGAWCNAYDTCACAM MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF WWTAYKTGAWCNAYDTCACAM width=21 seqs=17 ara ( 54) ATTATTTGCACGGCGTCACAC 1 ce1cg ( 19) TATTCTCGCCCGATGCCACAA 1 pbr322 ( 55) CATCTGTGCGGTATTTCACAC 1 ompa ( 47) TATGCCTGACGGAGTTCACAC 1 malt ( 43) TGAATTTGCACTGTGTCACAA 1 crp ( 62) TGTATGCAAAGGACGTCACAT 1 uxu1 ( 19) ATTGGGTTAACCACATCACAA 1 deop2 ( 6) ATTATTTGAACCAGATCGCAT 1 ce1cg ( 60) TTTTTTTGATCGTTTTCACAA 1 lac ( 75) TATCCGCTCACAATTCCACAC 1 cya ( 52) AAAACGTGATCAATTTAACAC 1 male ( 13) ATTCTGTAACAGAGATCACAC 1 tnaa ( 73) TAAATGTGAATCGAATCACAA 1 malk ( 63) TTTTTGCAAGCAACATCACGA 1 ilv ( 38) AAAACGTGATCAACCCCTCAA 1 gale ( 41) CTAATTTATTCCATGTCACAC 1 lac ( 11) AATGAGTGAGCTAACTCACAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTAYKTGAWCNAYDTCACAM MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1530 bayes= 6.47573 E= 5.8e-004 44 -73 -1073 63 63 -1073 -73 44 -5 -1073 -1073 121 63 -15 -15 -78 -237 59 -173 95 -1073 -173 159 21 -1073 26 -1073 133 -37 -1073 172 -137 109 59 -1073 -237 44 -15 -15 -37 -237 185 -15 -237 -37 26 85 -78 133 -1073 -15 -237 -137 59 -15 44 -5 -73 59 -5 -1073 -15 -1073 144 -237 226 -1073 -1073 154 -1073 -173 -237 -1073 235 -1073 -1073 163 -1073 -173 -1073 44 107 -1073 -78 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTAYKTGAWCNAYDTCACAM MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 17 E= 5.8e-004 0.411765 0.117647 0.000000 0.470588 0.470588 0.000000 0.117647 0.411765 0.294118 0.000000 0.000000 0.705882 0.470588 0.176471 0.176471 0.176471 0.058824 0.294118 0.058824 0.588235 0.000000 0.058824 0.588235 0.352941 0.000000 0.235294 0.000000 0.764706 0.235294 0.000000 0.647059 0.117647 0.647059 0.294118 0.000000 0.058824 0.411765 0.176471 0.176471 0.235294 0.058824 0.705882 0.176471 0.058824 0.235294 0.235294 0.352941 0.176471 0.764706 0.000000 0.176471 0.058824 0.117647 0.294118 0.176471 0.411765 0.294118 0.117647 0.294118 0.294118 0.000000 0.176471 0.000000 0.823529 0.058824 0.941176 0.000000 0.000000 0.882353 0.000000 0.058824 0.058824 0.000000 1.000000 0.000000 0.000000 0.941176 0.000000 0.058824 0.000000 0.411765 0.411765 0.000000 0.176471 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTAYKTGAWCNAYDTCACAM MEME-1 regular expression -------------------------------------------------------------------------------- [TA][AT][TA]A[TC][GT][TC][GA][AC][AT]C[GAC]A[TC][AGT]TCACA[AC] -------------------------------------------------------------------------------- Time 0.29 secs. ******************************************************************************** ******************************************************************************** MOTIF ASGRGSMRGRAGSAT MEME-2 width = 15 sites = 3 llr = 53 E-value = 3.0e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif ASGRGSMRGRAGSAT MEME-2 Description -------------------------------------------------------------------------------- Simplified A a::7::33:3a::a: pos.-specific C :3:::77:::::3:: probability G :7a3a3:7a7:a7:: matrix T ::::::::::::::a bits 2.4 * * * * 2.1 * * * * 1.9 * * * * 1.6 * * * * ** ** Relative 1.4 *** ** * ***** Entropy 1.2 *** *********** (25.3 bits) 0.9 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel AGGAGCCGGGAGGAT consensus C G GAA A C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ASGRGSMRGRAGSAT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------- malk + 3 1.01e-09 GG AGGAGGCGGGAGGAT GAGAACACGG male + 52 1.51e-08 GGTGGGGCGT AGGGGCAAGGAGGAT GGAAAGAGGT lac - 55 1.51e-08 CACACAACAT ACGAGCCGGAAGCAT AAAGTGTAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ASGRGSMRGRAGSAT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- malk 1e-09 2_[+2]_88 male 1.5e-08 51_[+2]_39 lac 1.5e-08 54_[-2]_36 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ASGRGSMRGRAGSAT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ASGRGSMRGRAGSAT width=15 seqs=3 malk ( 3) AGGAGGCGGGAGGAT 1 male ( 52) AGGGGCAAGGAGGAT 1 lac ( 55) ACGAGCCGGAAGCAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ASGRGSMRGRAGSAT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1638 bayes= 9.09011 E= 3.0e+004 171 -823 -823 -823 -823 77 176 -823 -823 -823 235 -823 113 -823 77 -823 -823 -823 235 -823 -823 176 77 -823 13 176 -823 -823 13 -823 176 -823 -823 -823 235 -823 13 -823 176 -823 171 -823 -823 -823 -823 -823 235 -823 -823 77 176 -823 171 -823 -823 -823 -823 -823 -823 171 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ASGRGSMRGRAGSAT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 3 E= 3.0e+004 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ASGRGSMRGRAGSAT MEME-2 regular expression -------------------------------------------------------------------------------- A[GC]G[AG]G[CG][CA][GA]G[GA]AG[GC]AT -------------------------------------------------------------------------------- Time 0.53 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ce1cg 7.17e-04 18_[-1(4.24e-07)]_20_[+1(1.47e-06)]_\ 25 ara 1.54e-05 53_[+1(6.23e-09)]_31 bglr1 1.56e-01 105 crp 6.93e-04 61_[+1(8.96e-07)]_23 cya 8.11e-04 51_[-1(1.77e-06)]_33 deop2 1.97e-03 5_[+1(1.47e-06)]_79 gale 8.72e-03 40_[+1(6.82e-06)]_44 ilv 8.84e-03 37_[+1(6.82e-06)]_47 lac 1.81e-08 10_[-1(8.55e-06)]_23_[-2(1.51e-08)]_\ 5_[-1(1.77e-06)]_10 male 2.16e-08 12_[+1(2.13e-06)]_18_[+2(1.51e-08)]_\ 39 malk 4.60e-09 2_[+2(1.01e-09)]_45_[-1(6.32e-06)]_\ 22 malt 1.46e-03 42_[-1(8.96e-07)]_42 ompa 1.12e-03 46_[+1(8.08e-07)]_38 tnaa 2.46e-03 72_[-1(4.60e-06)]_12 uxu1 2.06e-03 18_[-1(1.33e-06)]_66 pbr322 4.05e-04 54_[-1(5.29e-07)]_30 trn9cat 7.68e-01 105 tdc 1.16e-01 105 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************