******************************************************************************** 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= upstream.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ up_orf1ab 1.0000 591 up_S 1.0000 101 up_E 1.0000 101 up_M 1.0000 101 up_NS6 1.0000 101 up_n 1.0000 101 up_NS7a 1.0000 101 up_NS7b 1.0000 101 up_NS7c 1.0000 101 ******************************************************************************** ******************************************************************************** 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 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= 1399 N= 9 sample: seed= 0 hsfrac= 0 searchsize= 1399 norand= no csites= 1000 Letter frequencies in dataset: A 0.268 C 0.214 G 0.206 T 0.312 Background letter frequencies (from file dataset with add-one prior applied): A 0.268 C 0.214 G 0.206 T 0.312 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GACACCMANCC MEME-1 width = 11 sites = 7 llr = 73 E-value = 2.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GACACCMANCC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :a3a::6a31: pos.-specific C ::7:793:36a probability G 9:::311:11: matrix T 1:::::::31: bits 2.3 * 2.1 * 1.8 * * * * 1.6 ** * * * * Relative 1.4 ****** * * Entropy 1.1 ****** * * (14.9 bits) 0.9 ****** * * 0.7 ******** * 0.5 ******** ** 0.2 ******** ** 0.0 ----------- Multilevel GACACCAAACC consensus A G C C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACACCMANCC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- up_n 88 2.30e-07 ATGTTAATTT GACACCAAACC AAT up_orf1ab 64 3.79e-07 GTCCGATTCC GACACCAATCC AGGTGCGTTG up_E 64 4.89e-06 GAGAAAATTT GACAGCGACCC GACACCAGTT up_NS7a 70 6.61e-06 CTTCTGCATA GACACCCAAAC CTTTAAAATT up_S 45 1.71e-05 AGCTTGAAAA GAAACCAATTC TTAAGTATCT up_M 35 2.66e-05 TATAGTGTAC TACAGCAAGCC CAATCCTACT up_NS6 74 4.72e-05 TCAGATTCAG GAAACGCACGC CTGTATAAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACACCMANCC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- up_n 2.3e-07 87_[+1]_3 up_orf1ab 3.8e-07 63_[+1]_517 up_E 4.9e-06 63_[+1]_27 up_NS7a 6.6e-06 69_[+1]_21 up_S 1.7e-05 44_[+1]_46 up_M 2.7e-05 34_[+1]_56 up_NS6 4.7e-05 73_[+1]_17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACACCMANCC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GACACCMANCC width=11 seqs=7 up_n ( 88) GACACCAAACC 1 up_orf1ab ( 64) GACACCAATCC 1 up_E ( 64) GACAGCGACCC 1 up_NS7a ( 70) GACACCCAAAC 1 up_S ( 45) GAAACCAATTC 1 up_M ( 35) TACAGCAAGCC 1 up_NS6 ( 74) GAAACGCACGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACACCMANCC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1309 bayes= 8.14754 E= 2.5e-001 -945 -945 206 -112 190 -945 -945 -945 9 173 -945 -945 190 -945 -945 -945 -945 173 47 -945 -945 200 -53 -945 109 41 -53 -945 190 -945 -945 -945 9 41 -53 -13 -91 141 -53 -112 -945 222 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACACCMANCC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 7 E= 2.5e-001 0.000000 0.000000 0.857143 0.142857 1.000000 0.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.714286 0.285714 0.000000 0.000000 0.857143 0.142857 0.000000 0.571429 0.285714 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.285714 0.142857 0.285714 0.142857 0.571429 0.142857 0.142857 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACACCMANCC MEME-1 regular expression -------------------------------------------------------------------------------- GA[CA]A[CG]C[AC]A[ACT]CC -------------------------------------------------------------------------------- Time 0.52 secs. ******************************************************************************** ******************************************************************************** MOTIF GARSAAGAKT MEME-2 width = 10 sites = 6 llr = 61 E-value = 7.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif GARSAAGAKT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 283:a8:a2: pos.-specific C :::7:::::: probability G 8:73::a:3: matrix T :2:::2::5a bits 2.3 * 2.1 * 1.8 * ** 1.6 * * ** * Relative 1.4 * ** ** * Entropy 1.1 ******** * (14.8 bits) 0.9 ******** * 0.7 ******** * 0.5 ********** 0.2 ********** 0.0 ---------- Multilevel GAGCAAGATT consensus AG G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARSAAGAKT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------- up_NS7b 46 1.56e-06 TAATTGGGAG GAGCAAGATT TTACTTCTCA up_M 59 3.06e-06 TCCTACTCCA GAGGAAGAGT TTGTTAAAAT up_orf1ab 112 1.23e-05 CCGGTGAGTG GTGCAAGAGT TTGATCACGC up_NS7a 50 1.53e-05 TTTTGAAATA AAGCAAGATT CTTCTGCATA up_n 70 2.18e-05 AGTTATTCTT GAAGAAGAAT GTTAATTTGA up_NS7c 46 2.84e-05 ACTAACTTAA GAACATGATT AGTATTGGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARSAAGAKT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- up_NS7b 1.6e-06 45_[+2]_46 up_M 3.1e-06 58_[+2]_33 up_orf1ab 1.2e-05 111_[+2]_470 up_NS7a 1.5e-05 49_[+2]_42 up_n 2.2e-05 69_[+2]_22 up_NS7c 2.8e-05 45_[+2]_46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARSAAGAKT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GARSAAGAKT width=10 seqs=6 up_NS7b ( 46) GAGCAAGATT 1 up_M ( 59) GAGGAAGAGT 1 up_orf1ab ( 112) GTGCAAGAGT 1 up_NS7a ( 50) AAGCAAGATT 1 up_n ( 70) GAAGAAGAAT 1 up_NS7c ( 46) GAACATGATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARSAAGAKT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 1318 bayes= 7.42979 E= 7.6e+000 -68 -923 201 -923 163 -923 -923 -90 31 -923 169 -923 -923 163 69 -923 190 -923 -923 -923 163 -923 -923 -90 -923 -923 228 -923 190 -923 -923 -923 -68 -923 69 68 -923 -923 -923 168 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARSAAGAKT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 6 E= 7.6e+000 0.166667 0.000000 0.833333 0.000000 0.833333 0.000000 0.000000 0.166667 0.333333 0.000000 0.666667 0.000000 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.333333 0.500000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARSAAGAKT MEME-2 regular expression -------------------------------------------------------------------------------- GA[GA][CG]AAGA[TG]T -------------------------------------------------------------------------------- Time 0.97 secs. ******************************************************************************** ******************************************************************************** MOTIF AGAGTGGGA MEME-3 width = 9 sites = 2 llr = 26 E-value = 8.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGAGTGGGA MEME-3 Description -------------------------------------------------------------------------------- Simplified A a:a:::::a pos.-specific C ::::::::: probability G :a:a:aaa: matrix T ::::a:::: bits 2.3 * * *** 2.1 * * *** 1.8 **** **** 1.6 ********* Relative 1.4 ********* Entropy 1.1 ********* (18.8 bits) 0.9 ********* 0.7 ********* 0.5 ********* 0.2 ********* 0.0 --------- Multilevel AGAGTGGGA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGTGGGA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------- up_NS7a 25 2.23e-06 CTGCTGACTT AGAGTGGGA TGATGCTTTT up_orf1ab 236 2.23e-06 CCACTCATTT AGAGTGGGA GTTTCCACAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGTGGGA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- up_NS7a 2.2e-06 24_[+3]_68 up_orf1ab 2.2e-06 235_[+3]_347 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGTGGGA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGAGTGGGA width=9 seqs=2 up_NS7a ( 25) AGAGTGGGA 1 up_orf1ab ( 236) AGAGTGGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGTGGGA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 9 n= 1327 bayes= 9.37178 E= 8.4e+002 189 -765 -765 -765 -765 -765 227 -765 189 -765 -765 -765 -765 -765 227 -765 -765 -765 -765 168 -765 -765 227 -765 -765 -765 227 -765 -765 -765 227 -765 189 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGTGGGA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 9 nsites= 2 E= 8.4e+002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGTGGGA MEME-3 regular expression -------------------------------------------------------------------------------- AGAGTGGGA -------------------------------------------------------------------------------- Time 1.34 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- up_orf1ab 4.49e-07 63_[+1(3.79e-07)]_37_[+2(1.23e-05)]_\ 114_[+3(2.23e-06)]_347 up_S 1.98e-02 44_[+1(1.71e-05)]_46 up_E 1.13e-03 63_[+1(4.89e-06)]_27 up_M 2.62e-05 34_[+1(2.66e-05)]_13_[+2(3.06e-06)]_\ 33 up_NS6 5.06e-02 73_[+1(4.72e-05)]_17 up_n 3.70e-06 69_[+2(2.18e-05)]_8_[+1(2.30e-07)]_\ 3 up_NS7a 4.85e-08 24_[+3(2.23e-06)]_16_[+2(1.53e-05)]_\ 10_[+1(6.61e-06)]_21 up_NS7b 2.78e-03 45_[+2(1.56e-06)]_46 up_NS7c 3.98e-02 45_[+2(2.84e-05)]_46 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: ip-172-31-5-241 ********************************************************************************