******************************************************************************** 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= rrr.txt CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ orf1ab 1.0000 120 S 1.0000 101 orf3 1.0000 25 orf4a 1.0000 55 orf5 1.0000 89 E 1.0000 14 M 1.0000 67 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 rrr.txt -dna -oc . -nostatus -time 14400 -mod zoops -nmotifs 3 -minw 6 -maxw 50 -objfun classic -revcomp -markov_order 0 model: mod= zoops nmotifs= 3 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + - width: minw= 6 maxw= 50 nsites: minsites= 2 maxsites= 9 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= 671 N= 9 sample: seed= 0 hsfrac= 0 searchsize= 671 norand= no csites= 1000 Letter frequencies in dataset: A 0.299 C 0.201 G 0.201 T 0.299 Background letter frequencies (from file dataset with add-one prior applied): A 0.299 C 0.201 G 0.201 T 0.299 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AACGAACT MEME-1 width = 8 sites = 9 llr = 81 E-value = 1.7e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif AACGAACT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 8a::99:: pos.-specific C 2:a:1:92 probability G :::a:1:: matrix T ::::::18 bits 2.3 ** 2.1 ** 1.9 *** * 1.6 *** * Relative 1.4 ****** Entropy 1.2 ******** (12.9 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel AACGAACT consensus C C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACGAACT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- M + 52 1.94e-05 GAGTGGGTTT AACGAACT CCTTCATA E + 7 1.94e-05 ATGGAA AACGAACT orf5 + 82 1.94e-05 CCAGGATTTT AACGAACT orf4a + 46 1.94e-05 TCAGTTAATT AACGAACT CT orf3 + 14 1.94e-05 TTCACTAATT AACGAACT ATTA S + 50 1.94e-05 GAGTCAAATT AACGAACT CGTAATATCT orf8b + 2 1.44e-04 C CACGAGCT GCACCAAATA N + 79 2.04e-04 AATTGATTTT AACGAATC TCAATTTCAT orf1ab - 96 2.04e-04 CCCGAATTGC CACGCACC GGACGAAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACGAACT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- M 1.9e-05 51_[+1]_8 E 1.9e-05 6_[+1] orf5 1.9e-05 81_[+1] orf4a 1.9e-05 45_[+1]_2 orf3 1.9e-05 13_[+1]_4 S 1.9e-05 49_[+1]_44 orf8b 0.00014 1_[+1]_91 N 0.0002 78_[+1]_14 orf1ab 0.0002 95_[-1]_17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACGAACT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AACGAACT width=8 seqs=9 M ( 52) AACGAACT 1 E ( 7) AACGAACT 1 orf5 ( 82) AACGAACT 1 orf4a ( 46) AACGAACT 1 orf3 ( 14) AACGAACT 1 S ( 50) AACGAACT 1 orf8b ( 2) CACGAGCT 1 N ( 79) AACGAATC 1 orf1ab ( 96) CACGCACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACGAACT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 608 bayes= 6.05649 E= 1.7e-004 138 14 -982 -982 174 -982 -982 -982 -982 231 -982 -982 -982 -982 231 -982 157 -86 -982 -982 157 -982 -86 -982 -982 214 -982 -142 -982 14 -982 138 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACGAACT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 1.7e-004 0.777778 0.222222 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.888889 0.000000 0.111111 0.000000 0.000000 0.888889 0.000000 0.111111 0.000000 0.222222 0.000000 0.777778 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACGAACT MEME-1 regular expression -------------------------------------------------------------------------------- [AC]ACGAAC[TC] -------------------------------------------------------------------------------- Time 0.31 secs. ******************************************************************************** ******************************************************************************** MOTIF GCAGGG MEME-2 width = 6 sites = 2 llr = 18 E-value = 9.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCAGGG MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::a::: pos.-specific C :a:::: probability G a::aaa matrix T :::::: bits 2.3 ** *** 2.1 ** *** 1.9 ****** 1.6 ****** Relative 1.4 ****** Entropy 1.2 ****** (13.3 bits) 0.9 ****** 0.7 ****** 0.5 ****** 0.2 ****** 0.0 ------ Multilevel GCAGGG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGGG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ orf8b + 84 9.81e-05 TTCCACCTGG GCAGGG TGTACCTCTT S + 76 9.81e-05 CTCTCCTGTC GCAGGG TAAGTTACTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGGG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- orf8b 9.8e-05 83_[+2]_11 S 9.8e-05 75_[+2]_20 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGGG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCAGGG width=6 seqs=2 orf8b ( 84) GCAGGG 1 S ( 76) GCAGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGGG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 626 bayes= 8.2854 E= 9.4e+003 -765 -765 231 -765 -765 231 -765 -765 174 -765 -765 -765 -765 -765 231 -765 -765 -765 231 -765 -765 -765 231 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGGG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 2 E= 9.4e+003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGGG MEME-2 regular expression -------------------------------------------------------------------------------- GCAGGG -------------------------------------------------------------------------------- Time 0.58 secs. ******************************************************************************** ******************************************************************************** MOTIF CACTGGG MEME-3 width = 7 sites = 2 llr = 21 E-value = 1.0e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CACTGGG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :a::::: pos.-specific C a:a:::: probability G ::::aaa matrix T :::a::: bits 2.3 * * *** 2.1 * * *** 1.9 ******* 1.6 ******* Relative 1.4 ******* Entropy 1.2 ******* (15.1 bits) 0.9 ******* 0.7 ******* 0.5 ******* 0.2 ******* 0.0 ------- Multilevel CACTGGG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACTGGG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------- orf8b + 36 2.93e-05 TCTCTTGGTA CACTGGG CTTACCCAAC orf1ab + 9 2.93e-05 ATGCTCAA CACTGGG TATAATTCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACTGGG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- orf8b 2.9e-05 35_[+3]_58 orf1ab 2.9e-05 8_[+3]_105 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACTGGG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CACTGGG width=7 seqs=2 orf8b ( 36) CACTGGG 1 orf1ab ( 9) CACTGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACTGGG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 617 bayes= 8.26444 E= 1.0e+004 -765 231 -765 -765 174 -765 -765 -765 -765 231 -765 -765 -765 -765 -765 174 -765 -765 231 -765 -765 -765 231 -765 -765 -765 231 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACTGGG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 2 E= 1.0e+004 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACTGGG MEME-3 regular expression -------------------------------------------------------------------------------- CACTGGG -------------------------------------------------------------------------------- Time 0.84 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- orf1ab 1.05e-02 8_[+3(2.93e-05)]_105 S 8.41e-04 49_[+1(1.94e-05)]_18_[+2(9.81e-05)]_\ 20 orf3 2.16e-02 13_[+1(1.94e-05)]_4 orf4a 3.26e-02 45_[+1(1.94e-05)]_2 orf5 2.57e-02 81_[+1(1.94e-05)] E 1.16e-02 6_[+1(1.94e-05)] M 2.81e-02 51_[+1(1.94e-05)]_8 N 3.58e-01 100 orf8b 2.58e-04 35_[+3(2.93e-05)]_41_[+2(9.81e-05)]_\ 11 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************