******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.3.3 (Release date: Sun Feb 7 15:39:52 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= upstream_all.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ "orf1ab" 1.0000 278 "S" 1.0000 100 "orf3" 1.0000 100 "orf4a" 1.0000 100 "orf4b" 1.0000 100 "orf5" 1.0000 100 "E" 1.0000 100 "M" 1.0000 100 "N" 1.0000 100 "orf8b" 1.0000 100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme upstream_all.fasta -dna -oc . -nostatus -time 14400 -mod zoops -nmotifs 1 -minw 8 -maxw 9 -objfun classic -minsites 3 -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= 8 maxw= 9 nsites: minsites= 3 maxsites= 10 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= 1178 N= 10 sample: seed= 0 hsfrac= 0 searchsize= 1178 norand= no csites= 1000 Letter frequencies in dataset: A 0.261 C 0.222 G 0.199 T 0.318 Background letter frequencies (from file dataset with add-one prior applied): A 0.261 C 0.222 G 0.199 T 0.318 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTAACGAAC MEME-1 width = 9 sites = 10 llr = 99 E-value = 5.7e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTAACGAAC MEME-1 Description -------------------------------------------------------------------------------- Simplified A 11a8::aa: pos.-specific C :1:1a1::8 probability G :::1:9::: matrix T 98::::::2 bits 2.3 2.1 * 1.9 * **** 1.6 * **** Relative 1.4 * ***** Entropy 1.2 * ******* (14.3 bits) 0.9 * ******* 0.7 ********* 0.5 ********* 0.2 ********* 0.0 --------- Multilevel TTAACGAAC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTAACGAAC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------- "M" 83 4.60e-06 acgagtgggt ttaacgaac tccttcata "orf5" 91 4.60e-06 atccaggatt ttaacgaac t "orf4a" 89 4.60e-06 actcagttaa ttaacgaac tct "orf3" 87 4.60e-06 tgttcactaa ttaacgaac tatta "S" 47 4.60e-06 gagagtcaaa ttaacgaac tcgtaatatc "orf1ab" 60 4.60e-06 aactttgatt ttaacgaac ttaaataaaa "N" 77 1.44e-05 ttaattgatt ttaacgaat ctcaatttca "E" 91 8.37e-05 ggacatatgg aaaacgaac t "orf8b" 44 1.07e-04 tacactgggc ttacccaac acgggaaagt "orf4b" 72 1.15e-04 aggacgcagc tcagcgaat cgcttggttg -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTAACGAAC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "M" 4.6e-06 82_[+1]_9 "orf5" 4.6e-06 90_[+1]_1 "orf4a" 4.6e-06 88_[+1]_3 "orf3" 4.6e-06 86_[+1]_5 "S" 4.6e-06 46_[+1]_45 "orf1ab" 4.6e-06 59_[+1]_210 "N" 1.4e-05 76_[+1]_15 "E" 8.4e-05 90_[+1]_1 "orf8b" 0.00011 43_[+1]_48 "orf4b" 0.00011 71_[+1]_20 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTAACGAAC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTAACGAAC width=9 seqs=10 "M" ( 83) TTAACGAAC 1 "orf5" ( 91) TTAACGAAC 1 "orf4a" ( 89) TTAACGAAC 1 "orf3" ( 87) TTAACGAAC 1 "S" ( 47) TTAACGAAC 1 "orf1ab" ( 60) TTAACGAAC 1 "N" ( 77) TTAACGAAT 1 "E" ( 91) AAAACGAAC 1 "orf8b" ( 44) TTACCCAAC 1 "orf4b" ( 72) TCAGCGAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTAACGAAC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 9 n= 1098 bayes= 7.32617 E= 5.7e-010 -138 -997 -997 150 -138 -115 -997 133 194 -997 -997 -997 162 -115 -99 -997 -997 217 -997 -997 -997 -115 218 -997 194 -997 -997 -997 194 -997 -997 -997 -997 185 -997 -67 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTAACGAAC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 9 nsites= 10 E= 5.7e-010 0.100000 0.000000 0.000000 0.900000 0.100000 0.100000 0.000000 0.800000 1.000000 0.000000 0.000000 0.000000 0.800000 0.100000 0.100000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.100000 0.900000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTAACGAAC MEME-1 regular expression -------------------------------------------------------------------------------- TTAACGAA[CT] -------------------------------------------------------------------------------- Time 0.25 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "orf1ab" 1.24e-03 59_[+1(4.60e-06)]_210 "S" 4.23e-04 46_[+1(4.60e-06)]_45 "orf3" 4.23e-04 86_[+1(4.60e-06)]_5 "orf4a" 4.23e-04 88_[+1(4.60e-06)]_3 "orf4b" 1.05e-02 100 "orf5" 4.23e-04 90_[+1(4.60e-06)]_1 "E" 7.67e-03 90_[+1(8.37e-05)]_1 "M" 4.23e-04 82_[+1(4.60e-06)]_9 "N" 1.32e-03 76_[+1(1.44e-05)]_15 "orf8b" 9.81e-03 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (1) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************