******************************************************************************** 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 5 -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= 5 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 GGTGA MEME-1 width = 5 sites = 22 llr = 130 E-value = 1.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGTGA MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::8 pos.-specific C ::::: probability G aa:a2 matrix T ::a:: bits 2.8 2.5 2.2 1.9 ** * Relative 1.7 **** Entropy 1.4 **** (8.5 bits) 1.1 **** 0.8 ***** 0.6 ***** 0.3 ***** 0.0 ----- Multilevel GGTGA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----- 16S_rev_comp 5 1.49e-03 AGGA GGTGA TCGAGCCGTA upstream_46 34 1.49e-03 AATTATAGGT GGTGA AG upstream_40 31 1.49e-03 TTAAATTAGA GGTGA TACTC upstream_39 32 1.49e-03 TGAAGATGAG GGTGA TAAA upstream_33 31 1.49e-03 GCTAGCTGGG GGTGA GTGAG upstream_25 30 1.49e-03 ATAAAGCATG GGTGA CTATAA upstream_24 32 1.49e-03 GAAGTTAGGA GGTGA GCAA upstream_23 32 1.49e-03 AAGATTGGGG GGTGA GTGA upstream_22 36 1.49e-03 ACAACGTCAC GGTGA upstream_20 33 1.49e-03 CAAGCAGGGT GGTGA GGC upstream_13 30 1.49e-03 TATCAAATTT GGTGA CTCAAA upstream_11 34 1.49e-03 AGTAGGTAAA GGTGA TT upstream_10 30 1.49e-03 TAGTGCTCAA GGTGA GCGGGA upstream_8 32 1.49e-03 CCTCACGTGA GGTGA TAAT upstream_6 32 1.49e-03 ATGTGCTCTC GGTGA TAAA upstream_5 31 1.49e-03 TGAAATAAGG GGTGA GTGAA upstream_2 30 1.49e-03 AGGTTATTCT GGTGA AATGCG upstream_45 31 2.62e-03 CTTTTGAGGA GGTGG TTGAG upstream_36 29 2.62e-03 ATTCCTATGA GGTGG TCCCGAG upstream_7 30 2.62e-03 GAACAGGGGA GGTGG AGATAA upstream_1 32 2.62e-03 ATAGAATAGA GGTGG GAGC upstream_32 18 4.63e-03 ACTATATAAA GGAGA AATCTATAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 16S_rev_comp 0.0015 4_[+1]_31 upstream_46 0.0015 33_[+1]_2 upstream_40 0.0015 30_[+1]_5 upstream_39 0.0015 31_[+1]_4 upstream_33 0.0015 30_[+1]_5 upstream_25 0.0015 29_[+1]_6 upstream_24 0.0015 31_[+1]_4 upstream_23 0.0015 31_[+1]_4 upstream_22 0.0015 35_[+1] upstream_20 0.0015 32_[+1]_3 upstream_13 0.0015 29_[+1]_6 upstream_11 0.0015 33_[+1]_2 upstream_10 0.0015 29_[+1]_6 upstream_8 0.0015 31_[+1]_4 upstream_6 0.0015 31_[+1]_4 upstream_5 0.0015 30_[+1]_5 upstream_2 0.0015 29_[+1]_6 upstream_45 0.0026 30_[+1]_5 upstream_36 0.0026 28_[+1]_7 upstream_7 0.0026 29_[+1]_6 upstream_1 0.0026 31_[+1]_4 upstream_32 0.0046 17_[+1]_18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGTGA width=5 seqs=22 16S_rev_comp ( 5) GGTGA 1 upstream_46 ( 34) GGTGA 1 upstream_40 ( 31) GGTGA 1 upstream_39 ( 32) GGTGA 1 upstream_33 ( 31) GGTGA 1 upstream_25 ( 30) GGTGA 1 upstream_24 ( 32) GGTGA 1 upstream_23 ( 32) GGTGA 1 upstream_22 ( 36) GGTGA 1 upstream_20 ( 33) GGTGA 1 upstream_13 ( 30) GGTGA 1 upstream_11 ( 34) GGTGA 1 upstream_10 ( 30) GGTGA 1 upstream_8 ( 32) GGTGA 1 upstream_6 ( 32) GGTGA 1 upstream_5 ( 31) GGTGA 1 upstream_2 ( 30) GGTGA 1 upstream_45 ( 31) GGTGG 1 upstream_36 ( 29) GGTGG 1 upstream_7 ( 30) GGTGG 1 upstream_1 ( 32) GGTGG 1 upstream_32 ( 18) GGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 5 n= 1836 bayes= 6.72443 E= 1.9e+001 -1110 -1110 196 -1110 -1110 -1110 196 -1110 -291 -1110 -1110 191 -1110 -1110 196 -1110 126 -1110 -50 -1110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 5 nsites= 22 E= 1.9e+001 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.045455 0.000000 0.000000 0.954545 0.000000 0.000000 1.000000 0.000000 0.818182 0.000000 0.181818 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGA MEME-1 regular expression -------------------------------------------------------------------------------- GGTGA -------------------------------------------------------------------------------- Time 0.31 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- upstream_0 9.96e-01 40 upstream_1 9.00e-02 40 upstream_2 5.23e-02 40 upstream_3 1.54e-01 40 upstream_4 1.99e-01 40 upstream_5 5.23e-02 40 upstream_6 5.23e-02 40 upstream_7 9.00e-02 40 upstream_8 5.23e-02 40 upstream_9 5.69e-01 40 upstream_10 5.23e-02 40 upstream_11 5.23e-02 40 upstream_12 8.66e-01 40 upstream_13 5.23e-02 40 upstream_14 9.59e-01 40 upstream_15 7.19e-01 40 upstream_16 1.54e-01 40 upstream_17 9.59e-01 40 upstream_18 1.99e-01 40 upstream_19 1.99e-01 40 upstream_20 5.23e-02 40 upstream_21 9.59e-01 40 upstream_22 5.23e-02 40 upstream_23 5.23e-02 40 upstream_24 5.23e-02 40 upstream_25 5.23e-02 40 upstream_26 9.19e-01 40 upstream_27 1.99e-01 40 upstream_28 1.99e-01 40 upstream_29 5.69e-01 40 upstream_30 2.48e-01 40 upstream_31 2.48e-01 40 upstream_32 1.54e-01 40 upstream_33 5.23e-02 40 upstream_34 1.99e-01 40 upstream_35 5.69e-01 40 upstream_36 9.00e-02 40 upstream_37 5.69e-01 40 upstream_38 1.00e+00 40 upstream_39 5.23e-02 40 upstream_40 5.23e-02 40 upstream_41 5.69e-01 40 upstream_42 5.69e-01 40 upstream_43 5.69e-01 40 upstream_44 9.96e-01 40 upstream_45 9.00e-02 40 upstream_46 5.23e-02 40 upstream_47 1.99e-01 40 upstream_48 7.19e-01 40 upstream_49 5.69e-01 40 16S_rev_comp 5.23e-02 40 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (1) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************