******************************************************************************** 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/sd_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ sd_chr2R_19849909_198499 1.0000 26 sd_chrX_7375676_7375690_ 1.0000 15 sd_chr3L_20640984_206409 1.0000 9 sd_chr2R_8412503_8412516 1.0000 14 sd_chr2R_8412777_8412788 1.0000 12 sd_chr2L_11454657_114546 1.0000 24 sd_chrX_7375593_7375606_ 1.0000 14 sd_chr3L_20641161_206411 1.0000 9 sd_chr3L_20641044_206410 1.0000 9 sd_chr2R_8412379_8412389 1.0000 11 sd_chr2R_8412416_8412429 1.0000 14 sd_chr3L_20640792_206408 1.0000 18 sd_chr2L_11454576_114545 1.0000 7 sd_chrX_7376024_7376046_ 1.0000 23 sd_chrX_7375697_7375723_ 1.0000 27 sd_chrX_7375797_7375813_ 1.0000 17 sd_chrX_7375625_7375636_ 1.0000 12 sd_chrX_7375895_7375904_ 1.0000 10 sd_chr3L_20641091_206410 1.0000 9 ******************************************************************************** ******************************************************************************** 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/sd_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= 19 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 280 N= 19 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.330 C 0.170 G 0.170 T 0.330 Background letter frequencies (from dataset with add-one prior applied): A 0.329 C 0.171 G 0.171 T 0.329 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 18 llr = 88 E-value = 1.3e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 2629:1:3 pos.-specific C 126:::55 probability G 51:1:1:1 matrix T 212:a951 bits 2.5 2.3 2.0 1.8 Information 1.5 * content 1.3 ** (7.0 bits) 1.0 **** 0.8 ***** 0.5 * ****** 0.3 ******** 0.0 -------- Multilevel GACATTCC consensus ACA TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- sd_chr2L_11454657_114546 + 4 1.18e-04 ATG GACATTCG TGGGATTCCA sd_chr2R_8412777_8412788 - 5 1.18e-04 . AACATTCC AAAC sd_chr2R_19849909_198499 + 4 1.57e-04 TAA GAAATTCC TGGCATAGTT sd_chrX_7375895_7375904_ - 1 1.97e-04 AT CCCATTCC sd_chr2R_8412503_8412516 - 6 5.00e-04 T GCCATGCC GCGTG sd_chr2R_8412416_8412429 + 3 5.96e-04 TG GGAATTCC ACGG sd_chr2R_8412379_8412389 - 2 6.63e-04 AA GATATTTC C sd_chrX_7376024_7376046_ - 13 9.11e-04 GAC GACATTTT TCGAATTACA sd_chr3L_20641044_206410 - 1 9.11e-04 C GACATTTT sd_chr3L_20641091_206410 - 1 1.12e-03 A CGCATTTC sd_chrX_7375625_7375636_ + 2 1.70e-03 T AACATTTA ATT sd_chrX_7375797_7375813_ - 10 3.07e-03 . GTAATTTC AATAATTTT sd_chr3L_20640792_206408 + 1 3.07e-03 . TACATTTG TCGCATAGTT sd_chrX_7375697_7375723_ - 15 4.56e-03 TAGAG AAAATTCA TTTAAAAAAA sd_chr3L_20641161_206411 - 2 4.56e-03 . ACTATTTC T sd_chrX_7375593_7375606_ - 5 5.14e-03 AC TTCATTCA CAAA sd_chr3L_20640984_206409 + 2 1.23e-02 A TACATACA sd_chrX_7375676_7375690_ - 3 1.60e-02 ACACT GCTGTTTA TC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- sd_chr2L_11454657_114546 0.00012 3_[+1]_13 sd_chr2R_8412777_8412788 0.00012 4_[-1] sd_chr2R_19849909_198499 0.00016 3_[+1]_15 sd_chrX_7375895_7375904_ 0.0002 [-1]_2 sd_chr2R_8412503_8412516 0.0005 5_[-1]_1 sd_chr2R_8412416_8412429 0.0006 2_[+1]_4 sd_chr2R_8412379_8412389 0.00066 1_[-1]_2 sd_chrX_7376024_7376046_ 0.00091 12_[-1]_3 sd_chr3L_20641044_206410 0.00091 [-1]_1 sd_chr3L_20641091_206410 0.0011 [-1]_1 sd_chrX_7375625_7375636_ 0.0017 1_[+1]_3 sd_chrX_7375797_7375813_ 0.0031 9_[-1] sd_chr3L_20640792_206408 0.0031 [+1]_10 sd_chrX_7375697_7375723_ 0.0046 14_[-1]_5 sd_chr3L_20641161_206411 0.0046 1_[-1] sd_chrX_7375593_7375606_ 0.0051 4_[-1]_2 sd_chr3L_20640984_206409 0.012 1_[+1] sd_chrX_7375676_7375690_ 0.016 2_[-1]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=18 sd_chr2L_11454657_114546 ( 4) GACATTCG 1 sd_chr2R_8412777_8412788 ( 5) AACATTCC 1 sd_chr2R_19849909_198499 ( 4) GAAATTCC 1 sd_chrX_7375895_7375904_ ( 1) CCCATTCC 1 sd_chr2R_8412503_8412516 ( 6) GCCATGCC 1 sd_chr2R_8412416_8412429 ( 3) GGAATTCC 1 sd_chr2R_8412379_8412389 ( 2) GATATTTC 1 sd_chrX_7376024_7376046_ ( 13) GACATTTT 1 sd_chr3L_20641044_206410 ( 1) GACATTTT 1 sd_chr3L_20641091_206410 ( 1) CGCATTTC 1 sd_chrX_7375625_7375636_ ( 2) AACATTTA 1 sd_chrX_7375797_7375813_ ( 10) GTAATTTC 1 sd_chr3L_20640792_206408 ( 1) TACATTTG 1 sd_chrX_7375697_7375723_ ( 15) AAAATTCA 1 sd_chr3L_20641161_206411 ( 2) ACTATTTC 1 sd_chrX_7375593_7375606_ ( 5) TTCATTCA 1 sd_chr3L_20640984_206409 ( 2) TACATACA 1 sd_chrX_7375676_7375690_ ( 3) GCTGTTTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 147 bayes= 2.99339 E= 1.3e-003 -57 -62 155 -98 75 38 -62 -157 -57 184 -1081 -98 152 -1081 -162 -1081 -1081 -1081 -1081 160 -256 -1081 -162 143 -1081 155 -1081 60 -24 155 -62 -157 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 18 E= 1.3e-003 0.222222 0.111111 0.500000 0.166667 0.555556 0.222222 0.111111 0.111111 0.222222 0.611111 0.000000 0.166667 0.944444 0.000000 0.055556 0.000000 0.000000 0.000000 0.000000 1.000000 0.055556 0.000000 0.055556 0.888889 0.000000 0.500000 0.000000 0.500000 0.277778 0.500000 0.111111 0.111111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GA][AC][CA]ATT[CT][CA] -------------------------------------------------------------------------------- Time 0.10 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- sd_chr2R_19849909_198499 5.96e-03 26 sd_chrX_7375676_7375690_ 2.28e-01 15 sd_chr3L_20640984_206409 4.84e-02 9 sd_chr2R_8412503_8412516 6.98e-03 14 sd_chr2R_8412777_8412788 1.18e-03 12 sd_chr2L_11454657_114546 4.01e-03 24 sd_chrX_7375593_7375606_ 6.96e-02 14 sd_chr3L_20641161_206411 1.81e-02 9 sd_chr3L_20641044_206410 3.64e-03 9 sd_chr2R_8412379_8412389 5.29e-03 11 sd_chr2R_8412416_8412429 8.32e-03 14 sd_chr3L_20640792_206408 6.55e-02 18 sd_chr2L_11454576_114545 1.00e+00 7 sd_chrX_7376024_7376046_ 2.87e-02 23 sd_chrX_7375697_7375723_ 1.67e-01 27 sd_chrX_7375797_7375813_ 5.97e-02 17 sd_chrX_7375625_7375636_ 1.68e-02 12 sd_chrX_7375895_7375904_ 1.18e-03 10 sd_chr3L_20641091_206410 4.45e-03 9 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************