******************************************************************************** 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.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ E 1.0000 31 M 1.0000 31 N 1.0000 20 NS6 1.0000 21 NS7a 1.0000 21 NS7b 1.0000 21 S 1.0000 12 orf1 1.0000 35 ******************************************************************************** ******************************************************************************** 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.fasta -dna -oc . -nostatus -time 14400 -mod zoops -nmotifs 1 -minw 3 -maxw 7 -objfun classic -revcomp -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= 3 maxw= 7 nsites: minsites= 2 maxsites= 8 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= 192 N= 8 sample: seed= 0 hsfrac= 0 searchsize= 192 norand= no csites= 1000 Letter frequencies in dataset: A 0.289 C 0.211 G 0.211 T 0.289 Background letter frequencies (from file dataset with add-one prior applied): A 0.289 C 0.211 G 0.211 T 0.289 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AMACCA MEME-1 width = 6 sites = 7 llr = 51 E-value = 1.9e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif AMACCA MEME-1 Description -------------------------------------------------------------------------------- Simplified A a3a::a pos.-specific C :6:aa: probability G :1:::: matrix T :::::: bits 2.2 ** 2.0 ** 1.8 * **** 1.6 * **** Relative 1.3 * **** Entropy 1.1 * **** (10.6 bits) 0.9 * **** 0.7 ****** 0.4 ****** 0.2 ****** 0.0 ------ Multilevel ACACCA consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMACCA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ orf1 + 3 2.27e-04 AT ACACCA ACTCTGTAAA N + 7 2.27e-04 TACTTG ACACCA AACCAATT M + 18 2.27e-04 TTGTAAAAAT ACACCA ATTTCCAA E + 15 2.27e-04 CAGTGAACCG ACACCA GTCTCATTTA NS7b + 1 5.37e-04 . AAACCA CAACAGAAGA NS7a + 4 5.37e-04 ACC AAACCA ATTATGACAG S + 2 7.64e-04 G AGACCA CCGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMACCA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- orf1 0.00023 2_[+1]_27 N 0.00023 6_[+1]_8 M 0.00023 17_[+1]_8 E 0.00023 14_[+1]_11 NS7b 0.00054 [+1]_15 NS7a 0.00054 3_[+1]_12 S 0.00076 1_[+1]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMACCA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AMACCA width=6 seqs=7 orf1 ( 3) ACACCA 1 N ( 7) ACACCA 1 M ( 18) ACACCA 1 E ( 15) ACACCA 1 NS7b ( 1) AAACCA 1 NS7a ( 4) AAACCA 1 S ( 2) AGACCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMACCA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 152 bayes= 5.00196 E= 1.9e-002 179 -945 -945 -945 -2 144 -56 -945 179 -945 -945 -945 -945 224 -945 -945 -945 224 -945 -945 179 -945 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMACCA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 7 E= 1.9e-002 1.000000 0.000000 0.000000 0.000000 0.285714 0.571429 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMACCA MEME-1 regular expression -------------------------------------------------------------------------------- A[CA]ACCA -------------------------------------------------------------------------------- Time 0.23 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- E 1.17e-02 31 M 1.17e-02 31 N 6.78e-03 20 NS6 7.51e-01 21 NS7a 1.71e-02 21 NS7b 1.71e-02 21 S 1.06e-02 12 orf1 1.35e-02 35 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (1) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************