******************************************************************************** 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= MEME15.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 folD 1.0000 200 rpiA 1.0000 200 carA 1.0000 200 pdhR 1.0000 200 fixA 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 MEME15.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= 15 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= 3000 N= 15 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.279 C 0.222 G 0.222 T 0.279 Background letter frequencies (from dataset with add-one prior applied): A 0.278 C 0.222 G 0.222 T 0.278 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 12 llr = 169 E-value = 1.4e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::2aa61:2::::3:: pos.-specific C 716::29::11:a3:4 probability G 391::1:a3:16:1:: matrix T 1:2::2::6984:3a6 bits 2.2 * * 2.0 * * 1.7 * ** ** * * 1.5 * ** ** * * * Relative 1.3 * ** ** * * * Entropy 1.1 * ** ** **** ** (20.4 bits) 0.9 ** ** ** **** ** 0.7 ** ** ** **** ** 0.4 ***** ******* ** 0.2 **************** 0.0 ---------------- Multilevel CGCAAACGTTTGCCTT consensus G G T T C sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------------- purM + 122 6.42e-10 AAAGCAGTCT CGCAAACGTTTGCTTT CCCTGTTAGA cvpA + 130 2.64e-09 GAAATCCCTA CGCAAACGTTTTCTTT TTCTGTTAGA purE + 115 1.21e-08 TTCACAGCCA CGCAACCGTTTTCCTT GCTCTCTTTC purR - 139 3.96e-08 AAAATCGCAA GGTAAACGTTTGCCTT TACACACCTT pyrC - 133 4.86e-08 AAAGGATAAG CGGAAACGTTTTCCTT TGCACGAAAA purL + 110 5.65e-08 TTTATTTCCA CGCAAACGGTTTCGTC AGCGCATCAG codB + 119 6.91e-08 TATTTCCCCA CGAAAACGATTGCTTT TTATCTTCAG guaB - 131 3.13e-07 TTATACAGAG CGTAACCGATTGCATC TACCCCTTTT purA - 78 6.77e-07 TTTTTGTTCA GCCAATCGTTTTCCTC AACATGTAGT glnB - 117 8.72e-07 ATTCATTCCT TGAAATCGTTTGCATC CAGCTCGTGT carA - 91 1.36e-06 ACGAATTTCT GGCAAACGGCGGCATT CTGGAGATAT folD + 87 2.38e-06 GCCTCACCTT CGCAAGAGGTCGCTTC ACGCGATAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- purM 6.4e-10 121_[+1]_63 cvpA 2.6e-09 129_[+1]_55 purE 1.2e-08 114_[+1]_70 purR 4e-08 138_[-1]_46 pyrC 4.9e-08 132_[-1]_52 purL 5.6e-08 109_[+1]_75 codB 6.9e-08 118_[+1]_66 guaB 3.1e-07 130_[-1]_54 purA 6.8e-07 77_[-1]_107 glnB 8.7e-07 116_[-1]_68 carA 1.4e-06 90_[-1]_94 folD 2.4e-06 86_[+1]_98 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=12 purM ( 122) CGCAAACGTTTGCTTT 1 cvpA ( 130) CGCAAACGTTTTCTTT 1 purE ( 115) CGCAACCGTTTTCCTT 1 purR ( 139) GGTAAACGTTTGCCTT 1 pyrC ( 133) CGGAAACGTTTTCCTT 1 purL ( 110) CGCAAACGGTTTCGTC 1 codB ( 119) CGAAAACGATTGCTTT 1 guaB ( 131) CGTAACCGATTGCATC 1 purA ( 78) GCCAATCGTTTTCCTC 1 glnB ( 117) TGAAATCGTTTGCATC 1 carA ( 91) GGCAAACGGCGGCATT 1 folD ( 87) CGCAAGAGGTCGCTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 2775 bayes= 8.29619 E= 1.4e-012 -1023 159 17 -174 -1023 -141 205 -1023 -74 140 -141 -74 184 -1023 -1023 -1023 184 -1023 -1023 -1023 107 -41 -141 -74 -174 205 -1023 -1023 -1023 -1023 217 -1023 -74 -1023 17 107 -1023 -141 -1023 172 -1023 -141 -141 158 -1023 -1023 140 58 -1023 217 -1023 -1023 -16 59 -141 26 -1023 -1023 -1023 184 -1023 91 -1023 107 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 12 E= 1.4e-012 0.000000 0.666667 0.250000 0.083333 0.000000 0.083333 0.916667 0.000000 0.166667 0.583333 0.083333 0.166667 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.583333 0.166667 0.083333 0.166667 0.083333 0.916667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.000000 0.250000 0.583333 0.000000 0.083333 0.000000 0.916667 0.000000 0.083333 0.083333 0.833333 0.000000 0.000000 0.583333 0.416667 0.000000 1.000000 0.000000 0.000000 0.250000 0.333333 0.083333 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.416667 0.000000 0.583333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG]GCAAACG[TG]TT[GT]C[CTA]T[TC] -------------------------------------------------------------------------------- Time 0.29 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- codB 2.56e-05 118_[+1(6.91e-08)]_66 purE 4.48e-06 114_[+1(1.21e-08)]_70 pyrC 1.80e-05 132_[-1(4.86e-08)]_52 purR 1.46e-05 138_[-1(3.96e-08)]_46 cvpA 9.78e-07 129_[+1(2.64e-09)]_55 purM 2.38e-07 55_[+1(4.91e-05)]_50_[+1(6.42e-10)]_\ 63 guaB 1.16e-04 130_[-1(3.13e-07)]_54 glnB 3.22e-04 116_[-1(8.72e-07)]_68 purL 2.09e-05 109_[+1(5.65e-08)]_75 purA 2.50e-04 77_[-1(6.77e-07)]_107 folD 8.80e-04 86_[+1(2.38e-06)]_98 rpiA 4.68e-01 200 carA 5.03e-04 90_[-1(1.36e-06)]_94 pdhR 8.98e-01 200 fixA 8.32e-01 200 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: compute-0-2.local ********************************************************************************