******************************************************************************** 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 20 -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= 20 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 STACCMGGTGTTARRSKCT MEME-1 width = 19 sites = 3 llr = 70 E-value = 1.4e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif STACCMGGTGTTARRSKCT MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::a::7::::::a77:::: pos.-specific C 3::aa3:::::::::3:a: probability G 7:::::aa:a:::3377:: matrix T :a::::::a:aa::::3:a bits 2.4 ** ** * * 2.1 ** ** * * 1.9 * ** ****** ** 1.7 **** ******* ** Relative 1.4 ***** ******* * ** Entropy 1.2 ***** ******* **** (33.5 bits) 0.9 ******************* 0.7 ******************* 0.5 ******************* 0.2 ******************* 0.0 ------------------- Multilevel GTACCAGGTGTTAAAGGCT consensus C C GGCT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STACCMGGTGTTARRSKCT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- "N" 21 2.62e-12 AATTATAATA GTACCAGGTGTTAAAGGCT ACAAAACAAT "M" 14 2.62e-12 AATTATAATA GTACCAGGTGTTAAAGGCT ACAAAACAAT upstream_region_"ORF1ab" 25 1.06e-10 TCCTTTCTAC CTACCCGGTGTTAGGCTCT CTCACTCCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STACCMGGTGTTARRSKCT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "N" 2.6e-12 20_[+1]_68 "M" 2.6e-12 13_[+1]_68 upstream_region_"ORF1ab" 1.1e-10 24_[+1]_295 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STACCMGGTGTTARRSKCT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF STACCMGGTGTTARRSKCT width=19 seqs=3 "N" ( 21) GTACCAGGTGTTAAAGGCT 1 "M" ( 14) GTACCAGGTGTTAAAGGCT 1 upstream_region_"ORF1ab" ( 25) CTACCCGGTGTTAGGCTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STACCMGGTGTTARRSKCT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 640 bayes= 7.38734 E= 1.4e-002 -823 74 178 -823 -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 -823 101 -823 78 -823 101 -823 78 -823 -823 74 178 -823 -823 -823 178 28 -823 232 -823 -823 -823 -823 -823 186 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STACCMGGTGTTARRSKCT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 3 E= 1.4e-002 0.000000 0.333333 0.666667 0.000000 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 0.666667 0.000000 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STACCMGGTGTTARRSKCT MEME-1 regular expression -------------------------------------------------------------------------------- [GC]TACC[AC]GGTGTTA[AG][AG][GC][GT]CT -------------------------------------------------------------------------------- Time 0.34 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 0.65 secs. ******************************************************************************** ******************************************************************************** MOTIF CCSRCRCRGGRKGTTTSY MEME-3 width = 18 sites = 3 llr = 64 E-value = 2.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCSRCRCRGGRKGTTTSY MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::7:7:7::7::::::: pos.-specific C aa7:a:a:::::::::37 probability G ::33:3:3aa33a:::7: matrix T :::::::::::7:aaa:3 bits 2.4 ** * * ** * 2.1 ** * * ** * 1.9 ** * * ** **** 1.7 ** * * ** **** Relative 1.4 *** * * ** ***** Entropy 1.2 *** * * ** ******* (30.9 bits) 0.9 ****************** 0.7 ****************** 0.5 ****************** 0.2 ****************** 0.0 ------------------ Multilevel CCCACACAGGATGTTTGC consensus GG G G GG CT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCSRCRCRGGRKGTTTSY MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ "N" 75 6.17e-12 ACAAGTAATA CCCACACAGGATGTTTGC TTGGTCTAAA "M" 68 6.17e-12 ACAAGTAATA CCCACACAGGATGTTTGC TTGGTCTAAA upstream_region_"ORF1ab" 173 6.24e-10 ATTGGCACGG CCGGCGCGGGGGGTTTCT CAACACCCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCSRCRCRGGRKGTTTSY MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "N" 6.2e-12 74_[+3]_15 "M" 6.2e-12 67_[+3]_15 upstream_region_"ORF1ab" 6.2e-10 172_[+3]_148 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCSRCRCRGGRKGTTTSY MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCSRCRCRGGRKGTTTSY width=18 seqs=3 "N" ( 75) CCCACACAGGATGTTTGC 1 "M" ( 68) CCCACACAGGATGTTTGC 1 upstream_region_"ORF1ab" ( 173) CCGGCGCGGGGGGTTTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCSRCRCRGGRKGTTTSY MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 645 bayes= 8.19072 E= 2.8e-001 -823 232 -823 -823 -823 232 -823 -823 -823 173 78 -823 101 -823 78 -823 -823 232 -823 -823 101 -823 78 -823 -823 232 -823 -823 101 -823 78 -823 -823 -823 237 -823 -823 -823 237 -823 101 -823 78 -823 -823 -823 78 127 -823 -823 237 -823 -823 -823 -823 186 -823 -823 -823 186 -823 -823 -823 186 -823 74 178 -823 -823 173 -823 28 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCSRCRCRGGRKGTTTSY MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 3 E= 2.8e-001 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 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 0.000000 1.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.666667 0.000000 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCSRCRCRGGRKGTTTSY MEME-3 regular expression -------------------------------------------------------------------------------- CC[CG][AG]C[AG]C[AG]GG[AG][TG]GTTT[GC][CT] -------------------------------------------------------------------------------- Time 0.96 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" 7.95e-16 24_[+1(1.06e-10)]_23_[+2(3.97e-07)]_\ 93_[+3(6.24e-10)]_148 "S" 2.56e-03 84_[+2(9.43e-07)]_3 "E" 5.61e-01 85 "M" 9.60e-22 13_[+1(2.62e-12)]_35_[+3(6.17e-12)]_\ 2_[+2(6.15e-08)] "N" 1.21e-21 20_[+1(2.62e-12)]_35_[+3(6.17e-12)]_\ 2_[+2(6.15e-08)] -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************