******************************************************************************** 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-Z2_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ br-Z2_chr2L_19115566_191 1.0000 14 br-Z2_chr3L_9354397_9354 1.0000 23 br-Z2_chr2L_19116819_191 1.0000 11 br-Z2_chr2L_19115597_191 1.0000 12 br-Z2_chr2L_19115545_191 1.0000 14 br-Z2_chr3L_9354463_9354 1.0000 24 br-Z2_chrX_3105730_31057 1.0000 17 br-Z2_chr2L_19115454_191 1.0000 20 br-Z2_chrX_3105596_31056 1.0000 20 br-Z2_chr3L_9354293_9354 1.0000 18 br-Z2_chrX_3105633_31056 1.0000 37 br-Z2_chrX_3105784_31058 1.0000 32 br-Z2_chr2L_19115439_191 1.0000 14 br-Z2_chr3L_9354222_9354 1.0000 26 br-Z2_chrX_3105966_31059 1.0000 18 br-Z2_chr2L_19116751_191 1.0000 11 br-Z2_chrX_3105708_31057 1.0000 20 br-Z2_chrX_3105444_31054 1.0000 24 br-Z2_chr2L_19116908_191 1.0000 25 br-Z2_chrX_3105530_31055 1.0000 33 br-Z2_chrX_3105915_31059 1.0000 15 ******************************************************************************** ******************************************************************************** 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-Z2_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= 21 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 428 N= 21 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.335 C 0.165 G 0.165 T 0.335 Background letter frequencies (from dataset with add-one prior applied): A 0.334 C 0.166 G 0.166 T 0.334 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 10 sites = 5 llr = 51 E-value = 3.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :64842:86: pos.-specific C a4:::8a242 probability G :::26::::8 matrix T ::6::::::: bits 2.6 * * 2.3 * * 2.1 * * 1.8 * * * Information 1.6 * ** * content 1.3 * *** * (14.7 bits) 1.0 ** ******* 0.8 ** ******* 0.5 ********** 0.3 ********** 0.0 ---------- Multilevel CATAGCCAAG consensus CAGAA CCC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- br-Z2_chr3L_9354293_9354 + 9 1.42e-06 TGTGGTTA CATAGCCAAG br-Z2_chrX_3105784_31058 + 22 9.48e-06 AAATAATAAA CAAAACCACG A br-Z2_chrX_3105444_31054 + 15 1.35e-05 AGTAAAAGCT CCAGACCACG br-Z2_chr2L_19116908_191 - 13 1.41e-05 CAA CCTAGCCCAC TTCCCCTAGC br-Z2_chrX_3105633_31056 - 12 2.11e-05 GATGGTTAGA CATAGACAAG ACTCAACTAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- br-Z2_chr3L_9354293_9354 1.4e-06 8_[+1] br-Z2_chrX_3105784_31058 9.5e-06 21_[+1]_1 br-Z2_chrX_3105444_31054 1.3e-05 14_[+1] br-Z2_chr2L_19116908_191 1.4e-05 12_[-1]_3 br-Z2_chrX_3105633_31056 2.1e-05 11_[-1]_16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=10 seqs=5 br-Z2_chr3L_9354293_9354 ( 9) CATAGCCAAG 1 br-Z2_chrX_3105784_31058 ( 22) CAAAACCACG 1 br-Z2_chrX_3105444_31054 ( 15) CCAGACCACG 1 br-Z2_chr2L_19116908_191 ( 13) CCTAGCCCAC 1 br-Z2_chrX_3105633_31056 ( 12) CATAGACAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 239 bayes= 6.50657 E= 3.7e+003 -897 259 -897 -897 84 127 -897 -897 26 -897 -897 84 126 -897 27 -897 26 -897 186 -897 -74 227 -897 -897 -897 259 -897 -897 126 27 -897 -897 84 127 -897 -897 -897 27 227 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 5 E= 3.7e+003 0.000000 1.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.400000 0.000000 0.000000 0.600000 0.800000 0.000000 0.200000 0.000000 0.400000 0.000000 0.600000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AC][TA][AG][GA][CA]C[AC][AC][GC] -------------------------------------------------------------------------------- Time 0.24 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- br-Z2_chr2L_19115566_191 7.30e-01 14 br-Z2_chr3L_9354397_9354 4.09e-01 23 br-Z2_chr2L_19116819_191 9.74e-01 11 br-Z2_chr2L_19115597_191 9.97e-01 12 br-Z2_chr2L_19115545_191 2.09e-01 14 br-Z2_chr3L_9354463_9354 7.68e-01 24 br-Z2_chrX_3105730_31057 8.78e-02 17 br-Z2_chr2L_19115454_191 9.98e-01 20 br-Z2_chrX_3105596_31056 8.23e-01 20 br-Z2_chr3L_9354293_9354 2.55e-05 8_[+1(1.42e-06)] br-Z2_chrX_3105633_31056 1.18e-03 11_[-1(2.11e-05)]_16 br-Z2_chrX_3105784_31058 4.36e-04 21_[+1(9.48e-06)]_1 br-Z2_chr2L_19115439_191 7.55e-01 14 br-Z2_chr3L_9354222_9354 7.68e-01 26 br-Z2_chrX_3105966_31059 4.61e-01 18 br-Z2_chr2L_19116751_191 9.70e-01 11 br-Z2_chrX_3105708_31057 4.27e-01 20 br-Z2_chrX_3105444_31054 4.05e-04 14_[+1(1.35e-05)] br-Z2_chr2L_19116908_191 4.52e-04 12_[-1(1.41e-05)]_3 br-Z2_chrX_3105530_31055 3.05e-01 33 br-Z2_chrX_3105915_31059 3.80e-01 15 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************