******************************************************************************** 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/meme2 -mod zoops -dna -revcomp -nmotifs 2 -objfun classic -minw 8 -nostatus -mpi model: mod= zoops 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 AWDTGTGANVTNGNTCACA MEME-1 width = 19 sites = 17 llr = 183 E-value = 1.8e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif AWDTGTGANVTNGNTCACA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 7521:1:8221224:1827 pos.-specific C ::11:::1222412:8:61 probability G :13:a:9135:2521:212 matrix T 3449:91:21632392:1: bits 2.4 * 2.1 * 1.9 * * 1.6 * * Relative 1.4 * * Entropy 1.2 **** *** (15.5 bits) 0.9 * ***** *** 0.7 * ***** * ***** 0.5 ** ***** ** * ***** 0.2 ** ***** **** ***** 0.0 ------------------- Multilevel AATTGTGAGGTCGATCACA consensus TTG AACT T GA sequence A CC T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWDTGTGANVTNGNTCACA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------------- ara - 58 1.40e-07 TGGCATAGCA AAGTGTGACGCCGTGCAAA TAATCAATGT deop2 + 60 8.95e-07 AGATTTCCTT AATTGTGATGTGTATCGAA GTGTGTTGCG pbr322 - 56 1.53e-06 CTCCTTACGC ATCTGTGCGGTATTTCACA CCGCATATGG ompa - 51 1.53e-06 GAAAACTTAC AAGTGTGAACTCCGTCAGG CATATGAAAA ilv - 42 1.88e-06 GCAAAGGGAA AATTGAGGGGTTGATCACG TTTTGTACTG tdc - 81 2.30e-06 AACAGG ATATGTGCGACCACTCACA AATTAACTTT crp - 66 2.30e-06 TACTGCACGG TAATGTGACGTCCTTTGCA TACATGCAGT male - 17 2.79e-06 CACCGTCGCT TTGTGTGATCTCTGTTACA GAATTGGCGG ce1cg - 64 2.79e-06 GGACTTCCAT TTTTGTGAAAACGATCAAA AAAACAGTCT malt + 41 3.71e-06 AAAGATTTGG AATTGTGACACAGTGCAAA TTCAGACACA tnaa - 74 4.45e-06 GAAATTGTTT AAATGTGAATCGAATCACA ATCGTTCGGG lac - 12 4.45e-06 GGGGTGCCTA ATGAGTGAGCTAACTCACA TTAATTGCGT bglr1 + 76 5.32e-06 CAAAGTTAAT AACTGTGAGCATGGTCATA TTTTTATCAA trn9cat + 84 7.52e-06 CTTTTGGCGA AAATGAGACGTTGATCGGC ACG cya + 50 1.04e-05 TCAATCAGCA AGGTGTTAAATTGATCACG TTTTAGACCA malk + 61 1.32e-05 ATGTAAGGAA TTTCGTGATGTTGCTTGCA AAAATCGTGG uxu1 + 17 1.54e-05 AGAGTGAAAT TGTTGTGATGTGGTTAACC CAATTAGAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWDTGTGANVTNGNTCACA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ara 1.4e-07 57_[-1]_29 deop2 8.9e-07 59_[+1]_27 pbr322 1.5e-06 55_[-1]_31 ompa 1.5e-06 50_[-1]_36 ilv 1.9e-06 41_[-1]_45 tdc 2.3e-06 80_[-1]_6 crp 2.3e-06 65_[-1]_21 male 2.8e-06 16_[-1]_70 ce1cg 2.8e-06 63_[-1]_23 malt 3.7e-06 40_[+1]_46 tnaa 4.5e-06 73_[-1]_13 lac 4.5e-06 11_[-1]_75 bglr1 5.3e-06 75_[+1]_11 trn9cat 7.5e-06 83_[+1]_3 cya 1e-05 49_[+1]_37 malk 1.3e-05 60_[+1]_26 uxu1 1.5e-05 16_[+1]_70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWDTGTGANVTNGNTCACA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AWDTGTGANVTNGNTCACA width=19 seqs=17 ara ( 58) AAGTGTGACGCCGTGCAAA 1 deop2 ( 60) AATTGTGATGTGTATCGAA 1 pbr322 ( 56) ATCTGTGCGGTATTTCACA 1 ompa ( 51) AAGTGTGAACTCCGTCAGG 1 ilv ( 42) AATTGAGGGGTTGATCACG 1 tdc ( 81) ATATGTGCGACCACTCACA 1 crp ( 66) TAATGTGACGTCCTTTGCA 1 male ( 17) TTGTGTGATCTCTGTTACA 1 ce1cg ( 64) TTTTGTGAAAACGATCAAA 1 malt ( 41) AATTGTGACACAGTGCAAA 1 tnaa ( 74) AAATGTGAATCGAATCACA 1 lac ( 12) ATGAGTGAGCTAACTCACA 1 bglr1 ( 76) AACTGTGAGCATGGTCATA 1 trn9cat ( 84) AAATGAGACGTTGATCGGC 1 cya ( 50) AGGTGTTAAATTGATCACG 1 malk ( 61) TTTCGTGATGTTGCTTGCA 1 uxu1 ( 17) TGTTGTGATGTGGTTAACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWDTGTGANVTNGNTCACA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 1566 bayes= 6.9004 E= 1.8e-007 121 -1073 -1073 -5 80 -1073 -73 21 -37 -73 59 21 -237 -173 -1073 154 -1073 -1073 235 -1073 -137 -1073 -1073 154 -1073 -1073 226 -237 144 -73 -173 -1073 -37 26 59 -37 -37 26 126 -237 -137 26 -1073 109 -78 85 -15 -5 -78 -73 143 -78 21 -15 -15 -5 -1073 -1073 -73 154 -237 196 -1073 -78 133 -1073 26 -1073 -37 159 -73 -237 121 -73 -15 -1073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWDTGTGANVTNGNTCACA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 17 E= 1.8e-007 0.705882 0.000000 0.000000 0.294118 0.529412 0.000000 0.117647 0.352941 0.235294 0.117647 0.294118 0.352941 0.058824 0.058824 0.000000 0.882353 0.000000 0.000000 1.000000 0.000000 0.117647 0.000000 0.000000 0.882353 0.000000 0.000000 0.941176 0.058824 0.823529 0.117647 0.058824 0.000000 0.235294 0.235294 0.294118 0.235294 0.235294 0.235294 0.470588 0.058824 0.117647 0.235294 0.000000 0.647059 0.176471 0.352941 0.176471 0.294118 0.176471 0.117647 0.529412 0.176471 0.352941 0.176471 0.176471 0.294118 0.000000 0.000000 0.117647 0.882353 0.058824 0.764706 0.000000 0.176471 0.764706 0.000000 0.235294 0.000000 0.235294 0.588235 0.117647 0.058824 0.705882 0.117647 0.176471 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWDTGTGANVTNGNTCACA MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AT][TGA]TGTGA[GACT][GAC][TC][CT]G[AT]TC[AG][CA]A -------------------------------------------------------------------------------- Time 0.26 secs. ******************************************************************************** ******************************************************************************** MOTIF ASGRGSMRGRAGSAT MEME-2 width = 15 sites = 3 llr = 53 E-value = 2.5e+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= 2.5e+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= 2.5e+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 0.47 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ce1cg 3.97e-03 16_[+1(5.92e-05)]_28_[-1(2.79e-06)]_\ 23 ara 2.80e-04 57_[-1(1.40e-07)]_29 bglr1 3.50e-03 75_[+1(5.32e-06)]_11 crp 1.65e-03 65_[-1(2.30e-06)]_21 cya 4.05e-03 49_[+1(1.04e-05)]_37 deop2 1.29e-03 59_[+1(8.95e-07)]_27 gale 4.31e-02 26_[-1(4.35e-05)]_60 ilv 2.90e-03 41_[-1(1.88e-06)]_45 lac 4.47e-08 11_[-1(4.45e-06)]_24_[-2(1.51e-08)]_\ 36 male 2.86e-08 16_[-1(2.79e-06)]_16_[+2(1.51e-08)]_\ 39 malk 9.54e-09 2_[+2(1.01e-09)]_43_[+1(1.32e-05)]_\ 26 malt 5.29e-03 40_[+1(3.71e-06)]_46 ompa 2.03e-03 50_[-1(1.53e-06)]_36 tnaa 2.44e-03 73_[-1(4.45e-06)]_13 uxu1 1.80e-02 16_[+1(1.54e-05)]_70 pbr322 1.08e-03 55_[-1(1.53e-06)]_31 trn9cat 4.49e-03 83_[+1(7.52e-06)]_3 tdc 3.42e-03 80_[-1(2.30e-06)]_6 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************