******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** 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 ******************************************************************************** DATAFILE= MEME10.txt ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ codB 1.0000 200 purE 1.0000 200 pyrC 1.0000 200 purR 1.0000 200 cvpA 1.0000 200 purM 1.0000 200 guaB 1.0000 200 glnB 1.0000 200 purL 1.0000 200 purA 1.0000 200 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme MEME10.txt -dna -oc . -nostatus -time 18000 -maxsize 60000 -mod zoops -nmotifs 1 -minw 16 -maxw 16 -revcomp -psp priors.psp model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values width: minw= 16 maxw= 16 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 10 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 2000 N= 10 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.270 C 0.230 G 0.230 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.270 C 0.230 G 0.230 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 10 llr = 153 E-value = 8.2e-015 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::4aa6::3::::2:: pos.-specific C 7:3::3a:::::94:2 probability G 2a1::::a:::711:2 matrix T 1:2::1::7aa3:3a6 bits 2.1 * ** 1.9 * ** ** ** * 1.7 * ** ** ** * * 1.5 * ** ** ** * * Relative 1.3 * ** ** **** * Entropy 1.1 * ** ******* * (22.1 bits) 0.8 ** ** ******* * 0.6 ** ********** ** 0.4 ** ********** ** 0.2 **************** 0.0 ---------------- Multilevel CGAAAACGTTTGCCTT consensus G C C A T T C sequence T A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------------- purM + 122 1.27e-09 AAAGCAGTCT CGCAAACGTTTGCTTT CCCTGTTAGA codB + 119 5.94e-09 TATTTCCCCA CGAAAACGATTGCTTT TTATCTTCAG cvpA + 130 1.09e-08 GAAATCCCTA CGCAAACGTTTTCTTT TTCTGTTAGA purE + 115 1.21e-08 TTCACAGCCA CGCAACCGTTTTCCTT GCTCTCTTTC purR - 139 2.07e-08 AAAATCGCAA GGTAAACGTTTGCCTT TACACACCTT pyrC - 133 2.89e-08 AAAGGATAAG CGGAAACGTTTTCCTT TGCACGAAAA purL - 108 5.92e-08 GATGCGCTGA CGAAACCGTTTGCGTG GAAATAAAAT guaB - 131 1.50e-07 TTATACAGAG CGTAACCGATTGCATC TACCCCTTTT purA + 80 3.66e-07 TACATGTTGA GGAAAACGATTGGCTG AACAAAAAAC glnB - 117 4.39e-07 ATTCATTCCT TGAAATCGTTTGCATC CAGCTCGTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- purM 1.3e-09 121_[+1]_63 codB 5.9e-09 118_[+1]_66 cvpA 1.1e-08 129_[+1]_55 purE 1.2e-08 114_[+1]_70 purR 2.1e-08 138_[-1]_46 pyrC 2.9e-08 132_[-1]_52 purL 5.9e-08 107_[-1]_77 guaB 1.5e-07 130_[-1]_54 purA 3.7e-07 79_[+1]_105 glnB 4.4e-07 116_[-1]_68 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=10 purM ( 122) CGCAAACGTTTGCTTT 1 codB ( 119) CGAAAACGATTGCTTT 1 cvpA ( 130) CGCAAACGTTTTCTTT 1 purE ( 115) CGCAACCGTTTTCCTT 1 purR ( 139) GGTAAACGTTTGCCTT 1 pyrC ( 133) CGGAAACGTTTTCCTT 1 purL ( 108) CGAAACCGTTTGCGTG 1 guaB ( 131) CGTAACCGATTGCATC 1 purA ( 80) GGAAAACGATTGGCTG 1 glnB ( 117) TGAAATCGTTTGCATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 1850 bayes= 7.52356 E= 8.2e-015 -997 160 -20 -143 -997 -997 212 -997 57 38 -120 -43 189 -997 -997 -997 189 -997 -997 -997 115 38 -997 -143 -997 212 -997 -997 -997 -997 212 -997 15 -997 -997 138 -997 -997 -997 189 -997 -997 -997 189 -997 -997 160 15 -997 197 -120 -997 -43 80 -120 15 -997 -997 -997 189 -997 -20 -20 115 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 8.2e-015 0.000000 0.700000 0.200000 0.100000 0.000000 0.000000 1.000000 0.000000 0.400000 0.300000 0.100000 0.200000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.300000 0.000000 0.100000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.300000 0.000000 0.000000 0.700000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.700000 0.300000 0.000000 0.900000 0.100000 0.000000 0.200000 0.400000 0.100000 0.300000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.200000 0.600000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG]G[ACT]AA[AC]CG[TA]TT[GT]C[CTA]T[TCG] -------------------------------------------------------------------------------- Time 0.16 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- codB 2.20e-06 118_[+1(5.94e-09)]_66 purE 4.48e-06 114_[+1(1.21e-08)]_70 pyrC 1.07e-05 132_[-1(2.89e-08)]_52 purR 7.67e-06 138_[-1(2.07e-08)]_46 cvpA 4.05e-06 129_[+1(1.09e-08)]_55 purM 4.69e-07 121_[+1(1.27e-09)]_63 guaB 5.56e-05 130_[-1(1.50e-07)]_54 glnB 1.62e-04 116_[-1(4.39e-07)]_68 purL 2.19e-05 107_[-1(5.92e-08)]_77 purA 1.35e-04 79_[+1(3.66e-07)]_105 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: compute-0-2.local ********************************************************************************