******************************************************************************** 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= shrew_cov.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ upstream_region_"ORF1ab" 1.0000 338 "S" 1.0000 100 "E" 1.0000 85 "M" 1.0000 100 "N" 1.0000 107 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme shrew_cov.fasta -dna -oc . -nostatus -time 14400 -mod zoops -nmotifs 3 -minw 6 -maxw 15 -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= 15 nsites: minsites= 2 maxsites= 5 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= 730 N= 5 sample: seed= 0 hsfrac= 0 searchsize= 730 norand= no csites= 1000 Letter frequencies in dataset: A 0.332 C 0.2 G 0.193 T 0.275 Background letter frequencies (from file dataset with add-one prior applied): A 0.332 C 0.2 G 0.193 T 0.275 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TACCMGGTGTTA MEME-1 width = 12 sites = 3 llr = 48 E-value = 2.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TACCMGGTGTTA MEME-1 Description -------------------------------------------------------------------------------- Simplified A :a::7::::::a pos.-specific C ::aa3::::::: probability G :::::aa:a::: matrix T a::::::a:aa: bits 2.4 ** ** * 2.1 ** ** * 1.9 * ** ****** 1.7 **** ******* Relative 1.4 **** ******* Entropy 1.2 **** ******* (23.3 bits) 0.9 ************ 0.7 ************ 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel TACCAGGTGTTA consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TACCMGGTGTTA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ "N" 22 6.02e-08 ATTATAATAG TACCAGGTGTTA AAGGCTACAA "M" 15 6.02e-08 ATTATAATAG TACCAGGTGTTA AAGGCTACAA upstream_region_"ORF1ab" 26 9.64e-08 CCTTTCTACC TACCCGGTGTTA GGCTCTCTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TACCMGGTGTTA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "N" 6e-08 21_[+1]_74 "M" 6e-08 14_[+1]_74 upstream_region_"ORF1ab" 9.6e-08 25_[+1]_301 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TACCMGGTGTTA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TACCMGGTGTTA width=12 seqs=3 "N" ( 22) TACCAGGTGTTA 1 "M" ( 15) TACCAGGTGTTA 1 upstream_region_"ORF1ab" ( 26) TACCCGGTGTTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TACCMGGTGTTA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 675 bayes= 7.4646 E= 2.6e-001 -823 -823 -823 186 159 -823 -823 -823 -823 232 -823 -823 -823 232 -823 -823 101 74 -823 -823 -823 -823 237 -823 -823 -823 237 -823 -823 -823 -823 186 -823 -823 237 -823 -823 -823 -823 186 -823 -823 -823 186 159 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TACCMGGTGTTA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 3 E= 2.6e-001 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TACCMGGTGTTA MEME-1 regular expression -------------------------------------------------------------------------------- TACC[AC]GGTGTTA -------------------------------------------------------------------------------- Time 0.31 secs. ******************************************************************************** ******************************************************************************** MOTIF RSTCTAAACYAAA MEME-2 width = 13 sites = 4 llr = 57 E-value = 6.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif RSTCTAAACYAAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 5::::aaa::aaa pos.-specific C :5:a::::85::: probability G 55::::::::::: matrix T ::a:a:::35::: bits 2.4 * 2.1 * 1.9 *** 1.7 ****** *** Relative 1.4 ******** *** Entropy 1.2 ************ (20.4 bits) 0.9 ************* 0.7 ************* 0.5 ************* 0.2 ************* 0.0 ------------- Multilevel ACTCTAAACCAAA consensus GG TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RSTCTAAACYAAA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------- "N" 95 6.15e-08 ATGTTTGCTT GGTCTAAACCAAA "M" 88 6.15e-08 ATGTTTGCTT GGTCTAAACCAAA upstream_region_"ORF1ab" 67 3.97e-07 GGGGAACTAA ACTCTAAACTAAA ATCGGGGTTG "S" 85 9.43e-07 TGCTTTAAGA ACTCTAAATTAAA ATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RSTCTAAACYAAA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "N" 6.1e-08 94_[+2] "M" 6.1e-08 87_[+2] upstream_region_"ORF1ab" 4e-07 66_[+2]_259 "S" 9.4e-07 84_[+2]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RSTCTAAACYAAA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RSTCTAAACYAAA width=13 seqs=4 "N" ( 95) GGTCTAAACCAAA 1 "M" ( 88) GGTCTAAACCAAA 1 upstream_region_"ORF1ab" ( 67) ACTCTAAACTAAA 1 "S" ( 85) ACTCTAAATTAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RSTCTAAACYAAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 670 bayes= 7.11461 E= 6.9e-001 59 -865 137 -865 -865 132 137 -865 -865 -865 -865 186 -865 232 -865 -865 -865 -865 -865 186 159 -865 -865 -865 159 -865 -865 -865 159 -865 -865 -865 -865 190 -865 -14 -865 132 -865 86 159 -865 -865 -865 159 -865 -865 -865 159 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RSTCTAAACYAAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 4 E= 6.9e-001 0.500000 0.000000 0.500000 0.000000 0.000000 0.500000 0.500000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.500000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RSTCTAAACYAAA MEME-2 regular expression -------------------------------------------------------------------------------- [AG][CG]TCTAAA[CT][CT]AAA -------------------------------------------------------------------------------- Time 0.61 secs. ******************************************************************************** ******************************************************************************** MOTIF GTTTMTMAACA MEME-3 width = 11 sites = 5 llr = 56 E-value = 9.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTTTMTMAACA MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::2:6:6aa2a pos.-specific C ::::4:4::8: probability G 8:::::::::: matrix T 2a8a:a::::: bits 2.4 2.1 1.9 * * * 1.7 ** * * ** * Relative 1.4 ** * * **** Entropy 1.2 **** * **** (16.3 bits) 0.9 *********** 0.7 *********** 0.5 *********** 0.2 *********** 0.0 ----------- Multilevel GTTTATAAACA consensus T A C C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTTMTMAACA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- upstream_region_"ORF1ab" 185 3.23e-07 GGCGCGGGGG GTTTCTCAACA CCCCTCGTTG "N" 57 2.29e-06 AATTTCTAGA GTTTATAAACA AGTAATACCC "M" 50 2.29e-06 AATTTCTAGA GTTTATAAACA AGTAATACCC "S" 35 1.06e-05 TGCAAGAACT GTTTCTAAAAA CAGTAATGAT "E" 57 1.45e-05 GGTAAGTTAC TTATATCAACA GATTCATTAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTTMTMAACA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- upstream_region_"ORF1ab" 3.2e-07 184_[+3]_143 "N" 2.3e-06 56_[+3]_40 "M" 2.3e-06 49_[+3]_40 "S" 1.1e-05 34_[+3]_55 "E" 1.5e-05 56_[+3]_18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTTMTMAACA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTTTMTMAACA width=11 seqs=5 upstream_region_"ORF1ab" ( 185) GTTTCTCAACA 1 "N" ( 57) GTTTATAAACA 1 "M" ( 50) GTTTATAAACA 1 "S" ( 35) GTTTCTAAAAA 1 "E" ( 57) TTATATCAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTTMTMAACA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 680 bayes= 7.33006 E= 9.9e-001 -897 -897 205 -46 -897 -897 -897 186 -73 -897 -897 154 -897 -897 -897 186 85 100 -897 -897 -897 -897 -897 186 85 100 -897 -897 159 -897 -897 -897 159 -897 -897 -897 -73 200 -897 -897 159 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTTMTMAACA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 5 E= 9.9e-001 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 1.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.600000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.600000 0.400000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTTMTMAACA MEME-3 regular expression -------------------------------------------------------------------------------- [GT]T[TA]T[AC]T[AC]AA[CA]A -------------------------------------------------------------------------------- Time 0.90 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- upstream_region_"ORF1ab" 1.88e-10 25_[+1(9.64e-08)]_29_[+2(3.97e-07)]_\ 105_[+3(3.23e-07)]_143 "S" 9.09e-06 34_[+3(1.06e-05)]_39_[+2(9.43e-07)]_\ 3 "E" 5.29e-03 56_[+3(1.45e-05)]_18 "M" 3.40e-12 14_[+1(6.02e-08)]_23_[+3(2.29e-06)]_\ 27_[+2(6.15e-08)] "N" 4.21e-12 21_[+1(6.02e-08)]_23_[+3(2.29e-06)]_\ 27_[+2(6.15e-08)] -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************