******************************************************************************** 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 1 -minw 6 -maxw 50 -objfun classic -markov_order 0 model: mod= zoops nmotifs= 1 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= 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 CAMGWAWWACMCACWSWGGMTSTWYKYKTGGTCYARMMC MEME-1 width = 39 sites = 3 llr = 126 E-value = 1.1e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAMGWAWWACMCACWSWGGMTSTWYKYKTGGTCYARMMC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :a7:3a73a:3:a:7:7::7:::3::::::::::a773: pos.-specific C a:3::::::a7a:a:7:::3:3::3:7:::::a3::37a probability G :::a:::::::::::3:aa::7:::7:3:aa::::3::: matrix T ::::7:37::::::3:3:::a:a77337a::a:7::::: bits 2.4 * * * * * ** ** * * 2.1 * * * * * ** ** * * 1.9 * * * * * ** * * ***** * 1.7 ** * * ** *** ** * * ***** * * Relative 1.4 ** * * ** *** * ** *** ***** * * Entropy 1.2 ** * * ****** * ** *** *********** ** (60.8 bits) 0.9 ****** ******* * ********************** 0.7 *************************************** 0.5 *************************************** 0.2 *************************************** 0.0 --------------------------------------- Multilevel CAAGTAATACCCACACAGGATGTTTGCTTGGTCTAAACC consensus C A TA A TGT C C ACTTG C GCA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAMGWAWWACMCACWSWGGMTSTWYKYKTGGTCYARMMC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------------------------- "N" 66 4.53e-24 AGTTTATAAA CAAGTAATACCCACACAGGATGTTTGCTTGGTCTAAACC AAA "M" 59 4.53e-24 AGTTTATAAA CAAGTAATACCCACACAGGATGTTTGCTTGGTCTAAACC AAA upstream_region_"ORF1ab" 278 2.39e-17 CCGTCGCTGT CACGAATAACACACTGTGGCTCTACTTGTGGTCCAGCAC AAGTATCCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAMGWAWWACMCACWSWGGMTSTWYKYKTGGTCYARMMC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "N" 4.5e-24 65_[+1]_3 "M" 4.5e-24 58_[+1]_3 upstream_region_"ORF1ab" 2.4e-17 277_[+1]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAMGWAWWACMCACWSWGGMTSTWYKYKTGGTCYARMMC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAMGWAWWACMCACWSWGGMTSTWYKYKTGGTCYARMMC width=39 seqs=3 "N" ( 66) CAAGTAATACCCACACAGGATGTTTGCTTGGTCTAAACC 1 "M" ( 59) CAAGTAATACCCACACAGGATGTTTGCTTGGTCTAAACC 1 upstream_region_"ORF1ab" ( 278) CACGAATAACACACTGTGGCTCTACTTGTGGTCCAGCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAMGWAWWACMCACWSWGGMTSTWYKYKTGGTCYARMMC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 39 n= 540 bayes= 7.93342 E= 1.1e-004 -823 232 -823 -823 159 -823 -823 -823 101 74 -823 -823 -823 -823 237 -823 1 -823 -823 127 159 -823 -823 -823 101 -823 -823 28 1 -823 -823 127 159 -823 -823 -823 -823 232 -823 -823 1 173 -823 -823 -823 232 -823 -823 159 -823 -823 -823 -823 232 -823 -823 101 -823 -823 28 -823 173 78 -823 101 -823 -823 28 -823 -823 237 -823 -823 -823 237 -823 101 74 -823 -823 -823 -823 -823 186 -823 74 178 -823 -823 -823 -823 186 1 -823 -823 127 -823 74 -823 127 -823 -823 178 28 -823 173 -823 28 -823 -823 78 127 -823 -823 -823 186 -823 -823 237 -823 -823 -823 237 -823 -823 -823 -823 186 -823 232 -823 -823 -823 74 -823 127 159 -823 -823 -823 101 -823 78 -823 101 74 -823 -823 1 173 -823 -823 -823 232 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAMGWAWWACMCACWSWGGMTSTWYKYKTGGTCYARMMC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 39 nsites= 3 E= 1.1e-004 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.000000 0.666667 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.333333 0.000000 0.000000 0.666667 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 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 0.666667 0.000000 0.000000 0.333333 0.000000 0.666667 0.333333 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.666667 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.333333 0.666667 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.333333 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAMGWAWWACMCACWSWGGMTSTWYKYKTGGTCYARMMC MEME-1 regular expression -------------------------------------------------------------------------------- CA[AC]G[TA]A[AT][TA]AC[CA]CAC[AT][CG][AT]GG[AC]T[GC]T[TA][TC][GT][CT][TG]TGGTC[TC]A[AG][AC][CA]C -------------------------------------------------------------------------------- Time 0.35 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" 7.17e-15 277_[+1(2.39e-17)]_22 "S" 7.94e-01 100 "E" 1.52e-01 85 "M" 2.81e-22 58_[+1(4.53e-24)]_3 "N" 3.13e-22 65_[+1(4.53e-24)]_3 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (1) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************