******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 3.5.4 (Release date: ) 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= ../data/oreganno_data/processed_data/regulons_for_one_factor/ap_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ ap_chr3R_22997763_229977 1.0000 8 ap_chr3R_22997008_229970 1.0000 8 ap_chr3R_22997413_229974 1.0000 10 ap_chr3R_22997731_229977 1.0000 13 ap_chr3R_22997200_229972 1.0000 13 ap_chr3R_22997594_229976 1.0000 11 ap_chr3R_22997027_229970 1.0000 8 ap_chr3R_22997214_229972 1.0000 10 ap_chr3R_22997776_229977 1.0000 7 ap_chr3R_22997753_229977 1.0000 7 ap_chr3R_22997018_229970 1.0000 8 ap_chr3R_22997174_229971 1.0000 15 ap_chr3R_22997058_229970 1.0000 8 ap_chr3R_22997795_229978 1.0000 8 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme ../data/oreganno_data/processed_data/regulons_for_one_factor/ap_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values width: minw= 6 maxw= 15 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 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 134 N= 14 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.373 C 0.127 G 0.127 T 0.373 Background letter frequencies (from dataset with add-one prior applied): A 0.370 C 0.130 G 0.130 T 0.370 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 6 sites = 14 llr = 50 E-value = 2.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 139::5 pos.-specific C 111::1 probability G :31::3 matrix T 94:aa1 bits 2.9 2.6 2.4 2.1 Information 1.8 content 1.5 ** (5.1 bits) 1.2 ** 0.9 * *** 0.6 * *** 0.3 * **** 0.0 ------ Multilevel TTATTA consensus A G sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ ap_chr3R_22997174_229971 - 5 3.17e-04 TCGCT TGATTG TGGC ap_chr3R_22997731_229977 + 4 3.17e-04 AGA TGATTG CCAA ap_chr3R_22997776_229977 + 1 1.22e-03 . TGATTA A ap_chr3R_22997594_229976 - 1 3.33e-03 TGCGC TAATTG ap_chr3R_22997795_229978 - 2 5.88e-03 A TTATTA C ap_chr3R_22997027_229970 + 3 5.88e-03 GA TTATTA ap_chr3R_22997413_229974 + 5 9.98e-03 ATTT TAATTA ap_chr3R_22997763_229977 - 1 1.09e-02 TA TAATTC ap_chr3R_22997058_229970 - 3 1.18e-02 . TCATTA AG ap_chr3R_22997200_229972 + 7 1.34e-02 ATTTTC TGCTTC A ap_chr3R_22997018_229970 + 3 1.62e-02 TA CAATTG ap_chr3R_22997214_229972 - 1 1.92e-02 TGTG TTGTTA ap_chr3R_22997008_229970 - 3 2.89e-02 . TTATTT AG ap_chr3R_22997753_229977 + 1 3.67e-02 . ATATTA T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ap_chr3R_22997174_229971 0.00032 4_[-1]_5 ap_chr3R_22997731_229977 0.00032 3_[+1]_4 ap_chr3R_22997776_229977 0.0012 [+1]_1 ap_chr3R_22997594_229976 0.0033 [-1]_5 ap_chr3R_22997795_229978 0.0059 1_[-1]_1 ap_chr3R_22997027_229970 0.0059 2_[+1] ap_chr3R_22997413_229974 0.01 4_[+1] ap_chr3R_22997763_229977 0.011 [-1]_2 ap_chr3R_22997058_229970 0.012 2_[-1] ap_chr3R_22997200_229972 0.013 6_[+1]_1 ap_chr3R_22997018_229970 0.016 2_[+1] ap_chr3R_22997214_229972 0.019 [-1]_4 ap_chr3R_22997008_229970 0.029 2_[-1] ap_chr3R_22997753_229977 0.037 [+1]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=6 seqs=14 ap_chr3R_22997174_229971 ( 5) TGATTG 1 ap_chr3R_22997731_229977 ( 4) TGATTG 1 ap_chr3R_22997776_229977 ( 1) TGATTA 1 ap_chr3R_22997594_229976 ( 1) TAATTG 1 ap_chr3R_22997795_229978 ( 2) TTATTA 1 ap_chr3R_22997027_229970 ( 3) TTATTA 1 ap_chr3R_22997413_229974 ( 5) TAATTA 1 ap_chr3R_22997763_229977 ( 1) TAATTC 1 ap_chr3R_22997058_229970 ( 3) TCATTA 1 ap_chr3R_22997200_229972 ( 7) TGCTTC 1 ap_chr3R_22997018_229970 ( 3) CAATTG 1 ap_chr3R_22997214_229972 ( 1) TTGTTA 1 ap_chr3R_22997008_229970 ( 3) TTATTT 1 ap_chr3R_22997753_229977 ( 1) ATATTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 64 bayes= 2.57447 E= 2.3e+000 -237 -87 -1045 121 -37 -87 113 -5 121 -87 -87 -1045 -1045 -1045 -1045 144 -1045 -1045 -1045 144 44 13 113 -237 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 14 E= 2.3e+000 0.071429 0.071429 0.000000 0.857143 0.285714 0.071429 0.285714 0.357143 0.857143 0.071429 0.071429 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.142857 0.285714 0.071429 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[TAG]ATT[AG] -------------------------------------------------------------------------------- Time 0.04 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ap_chr3R_22997763_229977 6.35e-02 8 ap_chr3R_22997008_229970 1.62e-01 8 ap_chr3R_22997413_229974 9.54e-02 10 ap_chr3R_22997731_229977 5.07e-03 13 ap_chr3R_22997200_229972 1.94e-01 13 ap_chr3R_22997594_229976 3.93e-02 11 ap_chr3R_22997027_229970 3.48e-02 8 ap_chr3R_22997214_229972 1.76e-01 10 ap_chr3R_22997776_229977 4.86e-03 7 ap_chr3R_22997753_229977 1.39e-01 7 ap_chr3R_22997018_229970 9.33e-02 8 ap_chr3R_22997174_229971 6.33e-03 15 ap_chr3R_22997058_229970 6.86e-02 8 ap_chr3R_22997795_229978 3.48e-02 8 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************