******************************************************************************** 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= MEME14.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 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme MEME14.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= 14 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= 2800 N= 14 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.273 C 0.227 G 0.227 T 0.273 Background letter frequencies (from dataset with add-one prior applied): A 0.273 C 0.227 G 0.227 T 0.273 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 11 llr = 162 E-value = 5.8e-013 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 6a3:5996::2::2:1 pos.-specific C ::1:51:2a::::193 probability G 4:4a::1::a2::516 matrix T ::3::::2::6aa2:: bits 2.1 * ** 1.9 * * ** ** 1.7 * * ** ** * 1.5 * * ** ** ** * Relative 1.3 * * ** ** ** * Entropy 1.1 ** **** ** ** * (21.3 bits) 0.9 ** **** ** ** ** 0.6 ** ********** ** 0.4 ** ************* 0.2 **************** 0.0 ---------------- Multilevel AAGGCAAACGTTTGCG consensus G A A C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------------- purM - 122 1.18e-09 TCTAACAGGG AAAGCAAACGTTTGCG AGACTGCTTT cvpA - 130 2.68e-09 TCTAACAGAA AAAGAAAACGTTTGCG TAGGGATTTC purE - 115 7.31e-09 GAAAGAGAGC AAGGAAAACGGTTGCG TGGCTGTGAA purR + 139 2.43e-08 AAGGTGTGTA AAGGCAAACGTTTACC TTGCGATTTT pyrC + 133 2.68e-08 TTTTCGTGCA AAGGAAAACGTTTCCG CTTATCCTTT codB - 119 6.64e-08 CTGAAGATAA AAAGCAATCGTTTTCG TGGGGAAATA purL - 110 8.73e-08 CTGATGCGCT GACGAAACCGTTTGCG TGGAAATAAA guaB + 131 2.50e-07 AAAAGGGGTA GATGCAATCGGTTACG CTCTGTATAA purA + 78 4.56e-07 ACTACATGTT GAGGAAAACGATTGGC TGAACAAAAA glnB + 117 5.41e-07 ACACGAGCTG GATGCAAACGATTTCA AGGAATGAAT carA + 91 1.00e-06 ATATCTCCAG AATGCCGCCGTTTGCC AGAAATTCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- purM 1.2e-09 121_[-1]_63 cvpA 2.7e-09 129_[-1]_55 purE 7.3e-09 114_[-1]_70 purR 2.4e-08 138_[+1]_46 pyrC 2.7e-08 132_[+1]_52 codB 6.6e-08 118_[-1]_66 purL 8.7e-08 109_[-1]_75 guaB 2.5e-07 130_[+1]_54 purA 4.6e-07 77_[+1]_107 glnB 5.4e-07 116_[+1]_68 carA 1e-06 90_[+1]_94 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=11 purM ( 122) AAAGCAAACGTTTGCG 1 cvpA ( 130) AAAGAAAACGTTTGCG 1 purE ( 115) AAGGAAAACGGTTGCG 1 purR ( 139) AAGGCAAACGTTTACC 1 pyrC ( 133) AAGGAAAACGTTTCCG 1 codB ( 119) AAAGCAATCGTTTTCG 1 purL ( 110) GACGAAACCGTTTGCG 1 guaB ( 131) GATGCAATCGGTTACG 1 purA ( 78) GAGGAAAACGATTGGC 1 glnB ( 117) GATGCAAACGATTTCA 1 carA ( 91) AATGCCGCCGTTTGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 2590 bayes= 8.90277 E= 5.8e-013 122 -1010 68 -1010 187 -1010 -1010 -1010 0 -132 68 0 -1010 -1010 214 -1010 73 127 -1010 -1010 173 -132 -1010 -1010 173 -1010 -132 -1010 122 -32 -1010 -59 -1010 214 -1010 -1010 -1010 -1010 214 -1010 -59 -1010 -32 122 -1010 -1010 -1010 187 -1010 -1010 -1010 187 -59 -132 127 -59 -1010 200 -132 -1010 -159 27 149 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 11 E= 5.8e-013 0.636364 0.000000 0.363636 0.000000 1.000000 0.000000 0.000000 0.000000 0.272727 0.090909 0.363636 0.272727 0.000000 0.000000 1.000000 0.000000 0.454545 0.545455 0.000000 0.000000 0.909091 0.090909 0.000000 0.000000 0.909091 0.000000 0.090909 0.000000 0.636364 0.181818 0.000000 0.181818 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.181818 0.000000 0.181818 0.636364 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.181818 0.090909 0.545455 0.181818 0.000000 0.909091 0.090909 0.000000 0.090909 0.272727 0.636364 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AG]A[GAT]G[CA]AAACGTTTGC[GC] -------------------------------------------------------------------------------- Time 0.27 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- codB 2.46e-05 118_[-1(6.64e-08)]_66 purE 2.71e-06 114_[-1(7.31e-09)]_70 pyrC 9.93e-06 132_[+1(2.68e-08)]_52 purR 8.99e-06 138_[+1(2.43e-08)]_46 cvpA 9.93e-07 129_[-1(2.68e-09)]_55 purM 4.38e-07 121_[-1(1.18e-09)]_63 guaB 9.25e-05 130_[+1(2.50e-07)]_54 glnB 2.00e-04 116_[+1(5.41e-07)]_68 purL 3.23e-05 109_[-1(8.73e-08)]_19_\ [+1(6.19e-05)]_40 purA 1.69e-04 77_[+1(4.56e-07)]_107 folD 1.41e-01 200 rpiA 3.67e-01 200 carA 3.71e-04 90_[+1(1.00e-06)]_94 pdhR 8.16e-01 200 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: compute-0-2.local ********************************************************************************