******************************************************************************** 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 oops -nmotifs 1 -minw 16 -maxw 16 -revcomp -psp priors.psp model: mod= oops 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= 15 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 = 15 llr = 175 E-value = 2.8e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :149951131::12:: pos.-specific C 7:3::28::11:8312 probability G 391:11192:1711:2 matrix T 1:21:1::5993:496 bits 2.2 2.0 1.7 * * 1.5 * ** * * Relative 1.3 * ** ** ** * Entropy 1.1 ** ** ** **** * (16.9 bits) 0.9 ** ** ** **** * 0.7 ** ** ** **** ** 0.4 ** ** ******* ** 0.2 **************** 0.0 ---------------- Multilevel CGAAAACGTTTGCTTT consensus G C C A T C C sequence T G A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------------- purM + 122 1.07e-09 AAAGCAGTCT CGCAAACGTTTGCTTT CCCTGTTAGA codB + 119 3.32e-09 TATTTCCCCA CGAAAACGATTGCTTT TTATCTTCAG cvpA + 130 9.99e-09 GAAATCCCTA CGCAAACGTTTTCTTT TTCTGTTAGA purR - 139 2.28e-08 AAAATCGCAA GGTAAACGTTTGCCTT TACACACCTT purE + 115 4.10e-08 TTCACAGCCA CGCAACCGTTTTCCTT GCTCTCTTTC pyrC - 133 1.27e-07 AAAGGATAAG CGGAAACGTTTTCCTT TGCACGAAAA purL - 108 2.29e-07 GATGCGCTGA CGAAACCGTTTGCGTG GAAATAAAAT guaB - 131 4.17e-07 TTATACAGAG CGTAACCGATTGCATC TACCCCTTTT purA + 80 6.85e-07 TACATGTTGA GGAAAACGATTGGCTG AACAAAAAAC glnB - 117 2.57e-06 ATTCATTCCT TGAAATCGTTTGCATC CAGCTCGTGT carA - 91 9.78e-06 ACGAATTTCT GGCAAACGGCGGCATT CTGGAGATAT folD + 87 1.05e-05 GCCTCACCTT CGCAAGAGGTCGCTTC ACGCGATAAA rpiA + 74 1.75e-05 ATTTGCGGGG CGAAAGGGGATGCCTG CCATTGCGCG pdhR - 160 1.44e-04 AGCCACTTGC CGAAGTCAATTGGTCT TACCAATTTC fixA + 143 2.95e-04 CAATATTGGT GATTAAAGTTTTATTT CAAAATTAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- purM 1.1e-09 121_[+1]_63 codB 3.3e-09 118_[+1]_66 cvpA 1e-08 129_[+1]_55 purR 2.3e-08 138_[-1]_46 purE 4.1e-08 114_[+1]_70 pyrC 1.3e-07 132_[-1]_52 purL 2.3e-07 107_[-1]_77 guaB 4.2e-07 130_[-1]_54 purA 6.8e-07 79_[+1]_105 glnB 2.6e-06 116_[-1]_68 carA 9.8e-06 90_[-1]_94 folD 1e-05 86_[+1]_98 rpiA 1.8e-05 73_[+1]_111 pdhR 0.00014 159_[-1]_25 fixA 0.00029 142_[+1]_42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=15 purM ( 122) CGCAAACGTTTGCTTT 1 codB ( 119) CGAAAACGATTGCTTT 1 cvpA ( 130) CGCAAACGTTTTCTTT 1 purR ( 139) GGTAAACGTTTGCCTT 1 purE ( 115) CGCAACCGTTTTCCTT 1 pyrC ( 133) CGGAAACGTTTTCCTT 1 purL ( 108) CGAAACCGTTTGCGTG 1 guaB ( 131) CGTAACCGATTGCATC 1 purA ( 80) GGAAAACGATTGGCTG 1 glnB ( 117) TGAAATCGTTTGCATC 1 carA ( 91) GGCAAACGGCGGCATT 1 folD ( 87) CGCAAGAGGTCGCTTC 1 rpiA ( 74) CGAAAGGGGATGCCTG 1 pdhR ( 160) CGAAGTCAATTGGTCT 1 fixA ( 143) GATTAAAGTTTTATTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 2775 bayes= 7.52356 E= 2.8e-009 -1055 159 27 -206 -206 -1055 207 -1055 52 59 -173 -48 174 -1055 -1055 -206 174 -1055 -173 -1055 94 -15 -73 -106 -106 185 -173 -1055 -206 -1055 207 -1055 -6 -1055 -15 94 -206 -173 -1055 164 -1055 -173 -173 164 -1055 -1055 173 -6 -206 185 -73 -1055 -48 59 -173 52 -1055 -173 -1055 174 -1055 -15 -15 111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 15 E= 2.8e-009 0.000000 0.666667 0.266667 0.066667 0.066667 0.000000 0.933333 0.000000 0.400000 0.333333 0.066667 0.200000 0.933333 0.000000 0.000000 0.066667 0.933333 0.000000 0.066667 0.000000 0.533333 0.200000 0.133333 0.133333 0.133333 0.800000 0.066667 0.000000 0.066667 0.000000 0.933333 0.000000 0.266667 0.000000 0.200000 0.533333 0.066667 0.066667 0.000000 0.866667 0.000000 0.066667 0.066667 0.866667 0.000000 0.000000 0.733333 0.266667 0.066667 0.800000 0.133333 0.000000 0.200000 0.333333 0.066667 0.400000 0.000000 0.066667 0.000000 0.933333 0.000000 0.200000 0.200000 0.600000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG]G[ACT]AA[AC]CG[TAG]TT[GT]C[TCA]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 1.23e-06 118_[+1(3.32e-09)]_66 purE 1.52e-05 114_[+1(4.10e-08)]_70 pyrC 4.71e-05 132_[-1(1.27e-07)]_52 purR 8.44e-06 138_[-1(2.28e-08)]_46 cvpA 3.70e-06 129_[+1(9.99e-09)]_55 purM 3.95e-07 121_[+1(1.07e-09)]_63 guaB 1.54e-04 130_[-1(4.17e-07)]_54 glnB 9.51e-04 116_[-1(2.57e-06)]_68 purL 8.46e-05 107_[-1(2.29e-07)]_77 purA 2.53e-04 79_[+1(6.85e-07)]_105 folD 3.87e-03 86_[+1(1.05e-05)]_98 rpiA 6.46e-03 73_[+1(1.75e-05)]_111 carA 3.61e-03 90_[-1(9.78e-06)]_94 pdhR 5.20e-02 200 fixA 1.03e-01 200 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: compute-0-2.local ********************************************************************************