******************************************************************************** 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/br-Z3_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ br-Z3_chrX_3105939_31059 1.0000 16 br-Z3_chrX_3106077_31060 1.0000 15 br-Z3_chrX_3105444_31054 1.0000 24 br-Z3_chrX_3105708_31057 1.0000 20 br-Z3_chr2L_19115597_191 1.0000 13 br-Z3_chrX_3105544_31055 1.0000 19 br-Z3_chrX_3106130_31061 1.0000 20 br-Z3_chr2L_19115566_191 1.0000 17 br-Z3_chrX_3106219_31062 1.0000 19 br-Z3_chrX_3105633_31056 1.0000 20 br-Z3_chr3L_9354463_9354 1.0000 24 br-Z3_chr2L_19115461_191 1.0000 15 br-Z3_chrX_3105784_31058 1.0000 32 br-Z3_chr3L_9354222_9354 1.0000 26 br-Z3_chrX_3105730_31057 1.0000 17 br-Z3_chrX_3105849_31058 1.0000 17 ******************************************************************************** ******************************************************************************** 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/br-Z3_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= 25 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 16 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 314 N= 16 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.354 C 0.146 G 0.146 T 0.354 Background letter frequencies (from dataset with add-one prior applied): A 0.352 C 0.148 G 0.148 T 0.352 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 16 llr = 79 E-value = 1.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 844a1:31 pos.-specific C 162:13:4 probability G 1:::8:21 matrix T ::4::764 bits 2.8 2.5 2.2 1.9 Information 1.7 * content 1.4 ** (7.2 bits) 1.1 * *** 0.8 ** *** 0.6 ** *** * 0.3 ******** 0.0 -------- Multilevel ACAAGTTC consensus AT CAT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- br-Z3_chrX_3105544_31055 - 5 3.08e-06 ACCAATC ACCAGCTC TATT br-Z3_chrX_3105939_31059 + 8 4.39e-05 GTGAAAG ACAAGTTC G br-Z3_chrX_3105849_31058 - 8 1.37e-04 GC ACCAGCTT TAGTTTA br-Z3_chrX_3105730_31057 + 3 1.95e-04 CA ACTAGTAC ACGCAAT br-Z3_chrX_3106077_31060 + 3 2.76e-04 CA ACAAGTTT ATCAT br-Z3_chrX_3105444_31054 + 8 3.77e-04 TTATAGT AAAAGCTC CAGACCACG br-Z3_chr2L_19115597_191 + 4 1.80e-03 ATT AATAGTTT AA br-Z3_chrX_3105708_31057 - 2 1.80e-03 GAGCAAATCA AATAGTTT T br-Z3_chrX_3106219_31062 - 3 2.88e-03 CTTTATATA CCCACTGC AT br-Z3_chrX_3105633_31056 + 1 3.61e-03 . CCTAGTTG AGTCTTGTCT br-Z3_chr2L_19115461_191 + 2 3.82e-03 A GATAGTGC TAATCA br-Z3_chr2L_19115566_191 + 4 4.52e-03 GAT AATAGTTA TAATAA br-Z3_chrX_3105784_31058 + 23 5.42e-03 AATAATAAAC AAAACCAC GA br-Z3_chr3L_9354222_9354 - 4 6.53e-03 GTATGTAGAT ACAAATGT ATA br-Z3_chrX_3106130_31061 - 3 8.08e-03 TGAAGAAACT AAAAGTAA GC br-Z3_chr3L_9354463_9354 - 17 8.66e-03 . ACAAACAT ACTATATAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- br-Z3_chrX_3105544_31055 3.1e-06 4_[-1]_7 br-Z3_chrX_3105939_31059 4.4e-05 7_[+1]_1 br-Z3_chrX_3105849_31058 0.00014 7_[-1]_2 br-Z3_chrX_3105730_31057 0.0002 2_[+1]_7 br-Z3_chrX_3106077_31060 0.00028 2_[+1]_5 br-Z3_chrX_3105444_31054 0.00038 7_[+1]_9 br-Z3_chr2L_19115597_191 0.0018 3_[+1]_2 br-Z3_chrX_3105708_31057 0.0018 1_[-1]_11 br-Z3_chrX_3106219_31062 0.0029 2_[-1]_9 br-Z3_chrX_3105633_31056 0.0036 [+1]_12 br-Z3_chr2L_19115461_191 0.0038 1_[+1]_6 br-Z3_chr2L_19115566_191 0.0045 3_[+1]_6 br-Z3_chrX_3105784_31058 0.0054 22_[+1]_2 br-Z3_chr3L_9354222_9354 0.0065 3_[-1]_15 br-Z3_chrX_3106130_31061 0.0081 2_[-1]_10 br-Z3_chr3L_9354463_9354 0.0087 16_[-1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=16 br-Z3_chrX_3105544_31055 ( 5) ACCAGCTC 1 br-Z3_chrX_3105939_31059 ( 8) ACAAGTTC 1 br-Z3_chrX_3105849_31058 ( 8) ACCAGCTT 1 br-Z3_chrX_3105730_31057 ( 3) ACTAGTAC 1 br-Z3_chrX_3106077_31060 ( 3) ACAAGTTT 1 br-Z3_chrX_3105444_31054 ( 8) AAAAGCTC 1 br-Z3_chr2L_19115597_191 ( 4) AATAGTTT 1 br-Z3_chrX_3105708_31057 ( 2) AATAGTTT 1 br-Z3_chrX_3106219_31062 ( 3) CCCACTGC 1 br-Z3_chrX_3105633_31056 ( 1) CCTAGTTG 1 br-Z3_chr2L_19115461_191 ( 2) GATAGTGC 1 br-Z3_chr2L_19115566_191 ( 4) AATAGTTA 1 br-Z3_chrX_3105784_31058 ( 23) AAAACCAC 1 br-Z3_chr3L_9354222_9354 ( 4) ACAAATGT 1 br-Z3_chrX_3106130_31061 ( 3) AAAAGTAA 1 br-Z3_chr3L_9354463_9354 ( 17) ACAAACAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 202 bayes= 3.53916 E= 1.5e+001 121 -24 -124 -1064 31 193 -1064 -1064 31 34 -1064 9 150 -1064 -1064 -1064 -149 -24 234 -1064 -1064 108 -1064 96 -49 -1064 34 68 -149 157 -124 9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 16 E= 1.5e+001 0.812500 0.125000 0.062500 0.000000 0.437500 0.562500 0.000000 0.000000 0.437500 0.187500 0.000000 0.375000 1.000000 0.000000 0.000000 0.000000 0.125000 0.125000 0.750000 0.000000 0.000000 0.312500 0.000000 0.687500 0.250000 0.000000 0.187500 0.562500 0.125000 0.437500 0.062500 0.375000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[CA][AT]AG[TC][TA][CT] -------------------------------------------------------------------------------- Time 0.13 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- br-Z3_chrX_3105939_31059 7.90e-04 7_[+1(4.39e-05)]_1 br-Z3_chrX_3106077_31060 4.40e-03 15 br-Z3_chrX_3105444_31054 1.27e-02 24 br-Z3_chrX_3105708_31057 4.58e-02 20 br-Z3_chr2L_19115597_191 2.14e-02 13 br-Z3_chrX_3105544_31055 7.39e-05 4_[-1(3.08e-06)]_7 br-Z3_chrX_3106130_31061 1.90e-01 20 br-Z3_chr2L_19115566_191 8.66e-02 17 br-Z3_chrX_3106219_31062 6.68e-02 19 br-Z3_chrX_3105633_31056 8.98e-02 20 br-Z3_chr3L_9354463_9354 2.56e-01 24 br-Z3_chr2L_19115461_191 5.94e-02 15 br-Z3_chrX_3105784_31058 2.38e-01 32 br-Z3_chr3L_9354222_9354 2.20e-01 26 br-Z3_chrX_3105730_31057 3.90e-03 17 br-Z3_chrX_3105849_31058 2.73e-03 17 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************