******************************************************************************** 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 3-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/meme20 -mod zoops -dna -revcomp -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus -mpi model: mod= zoops nmotifs= 2 evt= inf objective function: em= Differential Enrichment 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 KGMGYDDKBTCA MEME-1 width = 12 sites = 7 llr = 64 p-value = 7.5e-001 E-value = 7.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif KGMGYDDKBTCA MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::6::33::::a pos.-specific C 114:3:::4:a: probability G 39:9134633:: matrix T 6::1643437:: bits 2.4 * 2.1 * 1.9 * 1.6 * * ** Relative 1.4 * * ** Entropy 1.2 * * * ** (13.2 bits) 0.9 *** * *** 0.7 ***** ***** 0.5 ***** ****** 0.2 ************ 0.0 ------------ Multilevel TGAGTTGGCTCA consensus G C CAATGG sequence GT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGMGYDDKBTCA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ lac + 14 2.45e-06 GCAATTAATG TGAGTTAGCTCA CTCATTAGGC tdc + 83 4.36e-06 AGTTAATTTG TGAGTGGTCGCA CATATCCTGT male + 47 6.93e-06 GCGACGGTGG GGCGTAGGGGCA AGGAGGATGG bglr1 + 81 1.69e-05 TTAATAACTG TGAGCATGGTCA TATTTTTATC pbr322 - 58 6.55e-05 TACGCATCTG TGCGGTATTTCA CACCGCATAT malk - 17 6.96e-05 GTTCACAGAA GCCGTGTTCTCA TCCTCCCGCC deop2 - 12 1.25e-04 CACTGTAATG CGATCTGGTTCA AATAATTCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGMGYDDKBTCA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- lac 2.4e-06 13_[+1]_80 tdc 4.4e-06 82_[+1]_11 male 6.9e-06 46_[+1]_47 bglr1 1.7e-05 80_[+1]_13 pbr322 6.5e-05 57_[-1]_36 malk 7e-05 16_[-1]_77 deop2 0.00012 11_[-1]_82 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGMGYDDKBTCA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF KGMGYDDKBTCA width=12 seqs=7 lac ( 14) TGAGTTAGCTCA 1 tdc ( 83) TGAGTGGTCGCA 1 male ( 47) GGCGTAGGGGCA 1 bglr1 ( 81) TGAGCATGGTCA 1 pbr322 ( 58) TGCGGTATTTCA 1 malk ( 17) GCCGTGTTCTCA 1 deop2 ( 12) CGATCTGGTTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGMGYDDKBTCA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 7.91118 E= 7.5e-001 -945 -45 54 91 -945 -45 213 -945 91 113 -945 -945 -945 -945 213 -109 -945 54 -45 91 -9 -945 54 49 -9 -945 113 -9 -945 -945 154 49 -945 113 54 -9 -945 -945 54 123 -945 235 -945 -945 172 -945 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGMGYDDKBTCA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 7.5e-001 0.000000 0.142857 0.285714 0.571429 0.000000 0.142857 0.857143 0.000000 0.571429 0.428571 0.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.285714 0.142857 0.571429 0.285714 0.000000 0.285714 0.428571 0.285714 0.000000 0.428571 0.285714 0.000000 0.000000 0.571429 0.428571 0.000000 0.428571 0.285714 0.285714 0.000000 0.000000 0.285714 0.714286 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGMGYDDKBTCA MEME-1 regular expression -------------------------------------------------------------------------------- [TG]G[AC]G[TC][TAG][GAT][GT][CGT][TG]CA -------------------------------------------------------------------------------- Time 0.20 secs. ******************************************************************************** ******************************************************************************** MOTIF TSTKTAAYTGTG MEME-2 width = 12 sites = 7 llr = 67 p-value = 9.9e-001 E-value = 9.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TSTKTAAYTGTG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :1:::aa11113 pos.-specific C :33::::3:::: probability G 16:41::::7:7 matrix T 9:769::6919: bits 2.4 2.1 1.9 1.6 ** Relative 1.4 ** * Entropy 1.2 * *** * ** (13.9 bits) 0.9 ******* **** 0.7 ******* **** 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel TGTTTAATTGTG consensus CCG C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTKTAAYTGTG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ deop2 + 55 1.37e-06 TAAGTAGATT TCCTTAATTGTG ATGTGTATCG lac + 76 1.68e-06 TCGTATGTTG TGTGGAATTGTG AGCGGATAAC tnaa - 86 2.47e-06 TCTGAAAT TGTTTAAATGTG AATCGAATCA tdc + 35 2.01e-05 TATTTAAAGG TATTTAATTGTA ATAACGATAC bglr1 - 56 2.27e-05 TTATTAACTT TGTGTAATTTTA GGAATTTATA pbr322 + 3 5.33e-05 CT GGCTTAACTATG CGGCATCAGA male + 15 6.90e-05 TACCGCCAAT TCTGTAACAGAG ATCACACAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTKTAAYTGTG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- deop2 1.4e-06 54_[+2]_39 lac 1.7e-06 75_[+2]_18 tnaa 2.5e-06 85_[-2]_8 tdc 2e-05 34_[+2]_59 bglr1 2.3e-05 55_[-2]_38 pbr322 5.3e-05 2_[+2]_91 male 6.9e-05 14_[+2]_79 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTKTAAYTGTG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TSTKTAAYTGTG width=12 seqs=7 deop2 ( 55) TCCTTAATTGTG 1 lac ( 76) TGTGGAATTGTG 1 tnaa ( 86) TGTTTAAATGTG 1 tdc ( 35) TATTTAATTGTA 1 bglr1 ( 56) TGTGTAATTTTA 1 pbr322 ( 3) GGCTTAACTATG 1 male ( 15) TCTGTAACAGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTKTAAYTGTG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 8.08695 E= 9.9e-001 -945 -945 -45 149 -109 54 154 -945 -945 54 -945 123 -945 -945 113 91 -945 -945 -45 149 172 -945 -945 -945 172 -945 -945 -945 -109 54 -945 91 -109 -945 -945 149 -109 -945 187 -109 -109 -945 -945 149 -9 -945 187 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTKTAAYTGTG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 9.9e-001 0.000000 0.000000 0.142857 0.857143 0.142857 0.285714 0.571429 0.000000 0.000000 0.285714 0.000000 0.714286 0.000000 0.000000 0.428571 0.571429 0.000000 0.000000 0.142857 0.857143 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.285714 0.000000 0.571429 0.142857 0.000000 0.000000 0.857143 0.142857 0.000000 0.714286 0.142857 0.142857 0.000000 0.000000 0.857143 0.285714 0.000000 0.714286 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTKTAAYTGTG MEME-2 regular expression -------------------------------------------------------------------------------- T[GC][TC][TG]TAA[TC]TGT[GA] -------------------------------------------------------------------------------- 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 1.24e-01 105 ara 8.12e-02 105 bglr1 1.65e-04 55_[-2(2.27e-05)]_13_[+1(1.69e-05)]_\ 13 crp 6.63e-01 105 cya 5.28e-01 105 deop2 7.78e-05 54_[+2(1.37e-06)]_39 gale 8.11e-01 105 ilv 4.41e-01 105 lac 2.43e-06 13_[+1(2.45e-06)]_50_[+2(1.68e-06)]_\ 18 male 2.01e-04 14_[+2(6.90e-05)]_20_[+1(6.93e-06)]_\ 47 malk 6.51e-02 16_[-1(6.96e-05)]_77 malt 3.99e-02 105 ompa 4.17e-01 105 tnaa 1.88e-03 85_[-2(2.47e-06)]_8 uxu1 6.49e-01 105 pbr322 1.22e-03 2_[+2(5.33e-05)]_43_[-1(6.55e-05)]_\ 36 trn9cat 5.52e-01 105 tdc 4.22e-05 34_[+2(2.01e-05)]_36_[+1(4.36e-06)]_\ 11 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************