******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.1.1 (Release date: Wed Jan 29 15:00:42 2020 -0800) For further information on how to interpret please access http://meme-suite.org/. To get a copy of the MEME software please access http://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= res.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ orf1ab 1.0000 100 S 1.0000 100 E 1.0000 100 M 1.0000 100 NS6 1.0000 100 N 1.0000 100 NS7a 1.0000 100 NS7b 1.0000 100 NS7c 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 res.fasta -dna -oc . -nostatus -time 18000 -mod zoops -nmotifs 3 -minw 6 -maxw 50 -objfun classic -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= 900 N= 9 sample: seed= 0 hsfrac= 0 searchsize= 900 norand= no csites= 1000 Letter frequencies in dataset: A 0.276 C 0.24 G 0.204 T 0.28 Background letter frequencies (from file dataset with add-one prior applied): A 0.276 C 0.24 G 0.204 T 0.28 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF MTCTVMYAAGGAG MEME-1 width = 13 sites = 9 llr = 84 E-value = 1.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif MTCTVMYAAGGAG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 6:1:26:66:29: pos.-specific C 4:92236212:11 probability G ::::4:::178:9 matrix T :a:8114221::: bits 2.3 2.1 1.8 * * 1.6 ** * Relative 1.4 ** *** Entropy 1.1 *** *** (13.5 bits) 0.9 **** * **** 0.7 **** * **** 0.5 **** *** **** 0.2 ************* 0.0 ------------- Multilevel ATCTGACAAGGAG consensus C CACTCTCA sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MTCTVMYAAGGAG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------- NS7a 11 1.25e-08 ATAGCAAGCC ATCTGACAAGGAG GCCCCTGCTG S 23 9.41e-06 CGCCCATAAT CTCCTCCAAGGAG TTGGAGAAGA M 54 1.29e-05 CTCAAACAGT CTCTGACACTGAG TTTGTAAAGT E 44 1.42e-05 TTGGGCTCTT CTCTCACAACAAG AGAAACACCG NS6 12 1.86e-05 AGCTGTCTTG ATCTATCAGGGAG ACCGCTCCTC orf1ab 10 2.77e-05 GTGTAAGTG ATCTGATCTGGAC GTATCGTGTT NS7c 21 3.51e-05 GAAACAGGGC ATCCGCTCAGGCG ACTGGGAATC NS7b 79 5.84e-05 TATTGAATCA CTCTCCTTTGAAG GCCCTGATT N 69 9.06e-05 AATTATGCAT ATATAATTACGAG TTTGACACCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MTCTVMYAAGGAG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- NS7a 1.3e-08 10_[+1]_77 S 9.4e-06 22_[+1]_65 M 1.3e-05 53_[+1]_34 E 1.4e-05 43_[+1]_44 NS6 1.9e-05 11_[+1]_76 orf1ab 2.8e-05 9_[+1]_78 NS7c 3.5e-05 20_[+1]_67 NS7b 5.8e-05 78_[+1]_9 N 9.1e-05 68_[+1]_19 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MTCTVMYAAGGAG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF MTCTVMYAAGGAG width=13 seqs=9 NS7a ( 11) ATCTGACAAGGAG 1 S ( 23) CTCCTCCAAGGAG 1 M ( 54) CTCTGACACTGAG 1 E ( 44) CTCTCACAACAAG 1 NS6 ( 12) ATCTATCAGGGAG 1 orf1ab ( 10) ATCTGATCTGGAC 1 NS7c ( 21) ATCCGCTCAGGCG 1 NS7b ( 79) CTCTCCTTTGAAG 1 N ( 69) ATATAATTACGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MTCTVMYAAGGAG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 792 bayes= 6.57872 E= 1.3e+000 101 89 -982 -982 -982 -982 -982 184 -131 189 -982 -982 -982 -11 -982 147 -31 -11 112 -133 101 47 -982 -133 -982 121 -982 67 101 -11 -982 -33 101 -111 -88 -33 -982 -11 170 -133 -31 -982 193 -982 169 -111 -982 -982 -982 -111 212 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MTCTVMYAAGGAG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 9 E= 1.3e+000 0.555556 0.444444 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.111111 0.888889 0.000000 0.000000 0.000000 0.222222 0.000000 0.777778 0.222222 0.222222 0.444444 0.111111 0.555556 0.333333 0.000000 0.111111 0.000000 0.555556 0.000000 0.444444 0.555556 0.222222 0.000000 0.222222 0.555556 0.111111 0.111111 0.222222 0.000000 0.222222 0.666667 0.111111 0.222222 0.000000 0.777778 0.000000 0.888889 0.111111 0.000000 0.000000 0.000000 0.111111 0.888889 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MTCTVMYAAGGAG MEME-1 regular expression -------------------------------------------------------------------------------- [AC]TC[TC][GAC][AC][CT][ACT][AT][GC][GA]AG -------------------------------------------------------------------------------- Time 0.29 secs. ******************************************************************************** ******************************************************************************** MOTIF ACACCA MEME-2 width = 6 sites = 9 llr = 59 E-value = 4.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACACCA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 8:9::9 pos.-specific C 2a:8a: probability G ::12:1 matrix T :::::: bits 2.3 2.1 * * 1.8 * * 1.6 * * Relative 1.4 ***** Entropy 1.1 ****** (9.4 bits) 0.9 ****** 0.7 ****** 0.5 ****** 0.2 ****** 0.0 ------ Multilevel ACACCA consensus C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACCA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ NS7c 70 2.91e-04 CACAGTGTTT ACACCA TACCTTCACC NS7a 90 2.91e-04 GGATGCGTAG ACACCA ATCTA N 86 2.91e-04 TACGAGTTTG ACACCA AAACCTATT M 78 2.91e-04 TTGTAAAGTT ACACCA ATTTCCTAGA S 93 7.90e-04 GCTAGTCAGA CCACCA GA orf1ab 41 7.90e-04 TTGCGCAAGT ACAGCA CCCATAGGAG NS6 76 1.22e-03 AATTCTGGCA ACGCCA GGATTTACAA E 61 1.22e-03 AACAAGAGAA ACACCG AGTCCATACC NS7b 5 1.43e-03 CTAA CCAGCA TCTTTTCCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACCA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- NS7c 0.00029 69_[+2]_25 NS7a 0.00029 89_[+2]_5 N 0.00029 85_[+2]_9 M 0.00029 77_[+2]_17 S 0.00079 92_[+2]_2 orf1ab 0.00079 40_[+2]_54 NS6 0.0012 75_[+2]_19 E 0.0012 60_[+2]_34 NS7b 0.0014 4_[+2]_90 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACCA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ACACCA width=6 seqs=9 NS7c ( 70) ACACCA 1 NS7a ( 90) ACACCA 1 N ( 86) ACACCA 1 M ( 78) ACACCA 1 S ( 93) CCACCA 1 orf1ab ( 41) ACAGCA 1 NS6 ( 76) ACGCCA 1 E ( 61) ACACCG 1 NS7b ( 5) CCAGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACCA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 855 bayes= 6.69025 E= 4.4e+000 150 -11 -982 -982 -982 206 -982 -982 169 -982 -88 -982 -982 170 12 -982 -982 206 -982 -982 169 -982 -88 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACCA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 9 E= 4.4e+000 0.777778 0.222222 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.888889 0.000000 0.111111 0.000000 0.000000 0.777778 0.222222 0.000000 0.000000 1.000000 0.000000 0.000000 0.888889 0.000000 0.111111 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACCA MEME-2 regular expression -------------------------------------------------------------------------------- [AC]CA[CG]CA -------------------------------------------------------------------------------- Time 0.47 secs. ******************************************************************************** ******************************************************************************** MOTIF GCAKCTSSSCGCCTG MEME-3 width = 15 sites = 2 llr = 38 E-value = 3.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCAKCTSSSCGCCTG MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::a:::::::::::: pos.-specific C :a::a:555a:aa:: probability G a::5::555:a:::a matrix T :::5:a:::::::a: bits 2.3 * * * 2.1 ** * **** * 1.8 *** ** ****** 1.6 *** ** ****** Relative 1.4 *** ** ****** Entropy 1.1 *************** (27.3 bits) 0.9 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GCAGCTCCCCGCCTG consensus T GGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAKCTSSSCGCCTG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- orf1ab 73 2.20e-09 ATCCTATTCT GCAGCTCCGCGCCTG ATATAGTTTT S 69 4.19e-09 GTATCTTGTT GCATCTGGCCGCCTG CTAGTCAGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAKCTSSSCGCCTG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- orf1ab 2.2e-09 72_[+3]_13 S 4.2e-09 68_[+3]_17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAKCTSSSCGCCTG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCAKCTSSSCGCCTG width=15 seqs=2 orf1ab ( 73) GCAGCTCCGCGCCTG 1 S ( 69) GCATCTGGCCGCCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAKCTSSSCGCCTG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 774 bayes= 8.59246 E= 3.9e+002 -765 -765 228 -765 -765 205 -765 -765 185 -765 -765 -765 -765 -765 129 83 -765 205 -765 -765 -765 -765 -765 183 -765 106 129 -765 -765 106 129 -765 -765 106 129 -765 -765 205 -765 -765 -765 -765 228 -765 -765 205 -765 -765 -765 205 -765 -765 -765 -765 -765 183 -765 -765 228 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAKCTSSSCGCCTG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 2 E= 3.9e+002 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 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAKCTSSSCGCCTG MEME-3 regular expression -------------------------------------------------------------------------------- GCA[GT]CT[CG][CG][CG]CGCCTG -------------------------------------------------------------------------------- Time 0.63 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-08 9_[+1(2.77e-05)]_50_[+3(2.20e-09)]_\ 13 S 7.06e-09 22_[+1(9.41e-06)]_33_[+3(4.19e-09)]_\ 17 E 6.08e-03 43_[+1(1.42e-05)]_44 M 1.72e-03 53_[+1(1.29e-05)]_34 NS6 4.87e-03 11_[+1(1.86e-05)]_76 N 8.79e-03 68_[+1(9.06e-05)]_19 NS7a 1.57e-06 10_[+1(1.25e-08)]_77 NS7b 7.82e-03 78_[+1(5.84e-05)]_9 NS7c 1.77e-03 20_[+1(3.51e-05)]_67 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: ip-172-31-13-134 ********************************************************************************