******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.1 (Release date: Sat Aug 21 19:23:23 2021 -0700) 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= upstreams.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ upstream_0 1.0000 40 upstream_1 1.0000 40 upstream_2 1.0000 40 upstream_3 1.0000 40 upstream_4 1.0000 40 upstream_5 1.0000 40 upstream_6 1.0000 40 upstream_7 1.0000 40 upstream_8 1.0000 40 upstream_9 1.0000 40 upstream_10 1.0000 40 upstream_11 1.0000 40 upstream_12 1.0000 40 upstream_13 1.0000 40 upstream_14 1.0000 40 upstream_15 1.0000 40 upstream_16 1.0000 40 upstream_17 1.0000 40 upstream_18 1.0000 40 upstream_19 1.0000 40 upstream_20 1.0000 40 upstream_21 1.0000 40 upstream_22 1.0000 40 upstream_23 1.0000 40 upstream_24 1.0000 40 upstream_25 1.0000 40 upstream_26 1.0000 40 upstream_27 1.0000 40 upstream_28 1.0000 40 upstream_29 1.0000 40 upstream_30 1.0000 40 upstream_31 1.0000 40 upstream_32 1.0000 40 upstream_33 1.0000 40 upstream_34 1.0000 40 upstream_35 1.0000 40 upstream_36 1.0000 40 upstream_37 1.0000 40 upstream_38 1.0000 40 upstream_39 1.0000 40 upstream_40 1.0000 40 upstream_41 1.0000 40 upstream_42 1.0000 40 upstream_43 1.0000 40 upstream_44 1.0000 40 upstream_45 1.0000 40 upstream_46 1.0000 40 upstream_47 1.0000 40 upstream_48 1.0000 40 upstream_49 1.0000 40 16S_rev_comp 1.0000 40 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme upstreams.fasta -dna -oc . -nostatus -time 14400 -mod zoops -nmotifs 1 -minw 5 -maxw 9 -objfun classic -markov_order 0 model: mod= zoops nmotifs= 1 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 5 maxw= 9 nsites: minsites= 2 maxsites= 51 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= 2040 N= 51 sample: seed= 0 hsfrac= 0 searchsize= 2040 norand= no csites= 1000 Letter frequencies in dataset: A 0.342 C 0.146 G 0.258 T 0.254 Background letter frequencies (from file dataset with add-one prior applied): A 0.342 C 0.146 G 0.258 T 0.254 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GGAGGTGAK MEME-1 width = 9 sites = 26 llr = 173 E-value = 5.4e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGAGGTGAK MEME-1 Description -------------------------------------------------------------------------------- Simplified A 237::::71 pos.-specific C :::::1::: probability G 773aa1924 matrix T 1:1::8125 bits 2.8 2.5 2.2 1.9 * Relative 1.7 ** * Entropy 1.4 ** * (9.6 bits) 1.1 **** 0.8 ** **** 0.6 ********* 0.3 ********* 0.0 --------- Multilevel GGAGGTGAT consensus AG G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGTGAK MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------- 16S_rev_comp 2 8.63e-06 A GGAGGTGAT CGAGCCGTAG upstream_24 29 1.74e-05 GAGGAAGTTA GGAGGTGAG CAA upstream_33 28 3.05e-05 AAGGCTAGCT GGGGGTGAG TGAG upstream_23 29 3.05e-05 TCTAAGATTG GGGGGTGAG TGA upstream_45 28 5.49e-05 GCTCTTTTGA GGAGGTGGT TGAG upstream_19 29 5.49e-05 AAATAATAGA GGAGGTGTT AGG upstream_39 29 8.82e-05 AAGTGAAGAT GAGGGTGAT AAA upstream_40 28 1.30e-04 AAATTAAATT AGAGGTGAT ACTC upstream_47 28 1.71e-04 AATTATCCAA GGAGGCGAG AAAA upstream_20 30 1.71e-04 GGCCAAGCAG GGTGGTGAG GC upstream_3 28 1.80e-04 TTCATAAGAA GGAGGGGAG ATTT upstream_8 29 2.17e-04 GTACCTCACG TGAGGTGAT AAT upstream_37 27 2.35e-04 GCCTAAAGGC GGGGGCGAT ATGAA upstream_5 28 2.93e-04 CGATGAAATA AGGGGTGAG TGAA upstream_34 28 3.37e-04 ATCAGCCATT GAGGGTGTT ATAA upstream_11 31 3.71e-04 TAGAGTAGGT AAAGGTGAT T upstream_1 29 5.43e-04 GAAATAGAAT AGAGGTGGG AGC upstream_7 27 6.00e-04 CGAGAACAGG GGAGGTGGA GATAA upstream_36 26 6.47e-04 TAAATTCCTA TGAGGTGGT CCCGAG upstream_4 29 7.05e-04 CATTCATTTG GAGGGGGAT AAA upstream_27 28 7.94e-04 AAATCCTAAG GGAGGTTTT TAGG upstream_10 27 7.94e-04 ATATAGTGCT CAAGGTGAG CGGGA upstream_16 20 8.58e-04 ATGCGTTCGA GAAGGTTAG GGAGGGAGAG upstream_46 31 1.01e-03 TTCAATTATA GGTGGTGAA G upstream_30 28 1.33e-03 ACAAAAACGG GAAGGGGTG CAAA upstream_43 2 1.47e-03 T GAAAGTGAT AAGAAAAATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGTGAK MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 16S_rev_comp 8.6e-06 1_[+1]_30 upstream_24 1.7e-05 28_[+1]_3 upstream_33 3.1e-05 27_[+1]_4 upstream_23 3.1e-05 28_[+1]_3 upstream_45 5.5e-05 27_[+1]_4 upstream_19 5.5e-05 28_[+1]_3 upstream_39 8.8e-05 28_[+1]_3 upstream_40 0.00013 27_[+1]_4 upstream_47 0.00017 27_[+1]_4 upstream_20 0.00017 29_[+1]_2 upstream_3 0.00018 27_[+1]_4 upstream_8 0.00022 28_[+1]_3 upstream_37 0.00023 26_[+1]_5 upstream_5 0.00029 27_[+1]_4 upstream_34 0.00034 27_[+1]_4 upstream_11 0.00037 30_[+1]_1 upstream_1 0.00054 28_[+1]_3 upstream_7 0.0006 26_[+1]_5 upstream_36 0.00065 25_[+1]_6 upstream_4 0.0007 28_[+1]_3 upstream_27 0.00079 27_[+1]_4 upstream_10 0.00079 26_[+1]_5 upstream_16 0.00086 19_[+1]_12 upstream_46 0.001 30_[+1]_1 upstream_30 0.0013 27_[+1]_4 upstream_43 0.0015 1_[+1]_30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGTGAK MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGAGGTGAK width=9 seqs=26 16S_rev_comp ( 2) GGAGGTGAT 1 upstream_24 ( 29) GGAGGTGAG 1 upstream_33 ( 28) GGGGGTGAG 1 upstream_23 ( 29) GGGGGTGAG 1 upstream_45 ( 28) GGAGGTGGT 1 upstream_19 ( 29) GGAGGTGTT 1 upstream_39 ( 29) GAGGGTGAT 1 upstream_40 ( 28) AGAGGTGAT 1 upstream_47 ( 28) GGAGGCGAG 1 upstream_20 ( 30) GGTGGTGAG 1 upstream_3 ( 28) GGAGGGGAG 1 upstream_8 ( 29) TGAGGTGAT 1 upstream_37 ( 27) GGGGGCGAT 1 upstream_5 ( 28) AGGGGTGAG 1 upstream_34 ( 28) GAGGGTGTT 1 upstream_11 ( 31) AAAGGTGAT 1 upstream_1 ( 29) AGAGGTGGG 1 upstream_7 ( 27) GGAGGTGGA 1 upstream_36 ( 26) TGAGGTGGT 1 upstream_4 ( 29) GAGGGGGAT 1 upstream_27 ( 28) GGAGGTTTT 1 upstream_10 ( 27) CAAGGTGAG 1 upstream_16 ( 20) GAAGGTTAG 1 upstream_46 ( 31) GGTGGTGAA 1 upstream_30 ( 28) GAAGGGGTG 1 upstream_43 ( 2) GAAAGTGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGTGAK MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 9 n= 1632 bayes= 7.12608 E= 5.4e-004 -115 -192 150 -172 -15 -1134 142 -1134 94 -1134 6 -172 -315 -1134 190 -1134 -1134 -1134 196 -1134 -1134 -92 -116 167 -1134 -1134 184 -172 102 -1134 -74 -73 -215 -1134 71 97 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGTGAK MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 9 nsites= 26 E= 5.4e-004 0.153846 0.038462 0.730769 0.076923 0.307692 0.000000 0.692308 0.000000 0.653846 0.000000 0.269231 0.076923 0.038462 0.000000 0.961538 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.076923 0.115385 0.807692 0.000000 0.000000 0.923077 0.076923 0.692308 0.000000 0.153846 0.153846 0.076923 0.000000 0.423077 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGTGAK MEME-1 regular expression -------------------------------------------------------------------------------- G[GA][AG]GGTGA[TG] -------------------------------------------------------------------------------- Time 0.48 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- upstream_0 2.27e-01 40 upstream_1 1.72e-02 40 upstream_2 6.36e-01 40 upstream_3 5.75e-03 40 upstream_4 2.23e-02 40 upstream_5 9.34e-03 40 upstream_6 8.77e-01 40 upstream_7 1.90e-02 40 upstream_8 6.94e-03 40 upstream_9 4.48e-01 40 upstream_10 2.51e-02 40 upstream_11 1.18e-02 40 upstream_12 3.04e-01 40 upstream_13 4.91e-01 40 upstream_14 8.64e-01 40 upstream_15 8.00e-01 40 upstream_16 2.71e-02 40 upstream_17 9.91e-01 40 upstream_18 5.83e-01 40 upstream_19 1.75e-03 28_[+1(5.49e-05)]_3 upstream_20 5.47e-03 40 upstream_21 6.19e-01 40 upstream_22 9.97e-01 40 upstream_23 9.76e-04 28_[+1(3.05e-05)]_3 upstream_24 5.56e-04 28_[+1(1.74e-05)]_3 upstream_25 3.32e-01 40 upstream_26 4.74e-01 40 upstream_27 2.51e-02 40 upstream_28 4.74e-01 40 upstream_29 5.11e-01 40 upstream_30 4.17e-02 40 upstream_31 6.45e-01 40 upstream_32 6.93e-01 40 upstream_33 9.76e-04 27_[+1(3.05e-05)]_4 upstream_34 1.07e-02 40 upstream_35 2.80e-01 40 upstream_36 2.05e-02 40 upstream_37 7.48e-03 40 upstream_38 9.71e-01 40 upstream_39 2.82e-03 28_[+1(8.82e-05)]_3 upstream_40 4.14e-03 40 upstream_41 1.57e-01 40 upstream_42 6.52e-01 40 upstream_43 4.59e-02 40 upstream_44 9.75e-01 40 upstream_45 1.75e-03 27_[+1(5.49e-05)]_4 upstream_46 3.17e-02 40 upstream_47 5.47e-03 40 upstream_48 4.28e-01 40 upstream_49 9.69e-01 40 16S_rev_comp 2.76e-04 1_[+1(8.63e-06)]_30 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (1) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************