******************************************************************************** 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/Kr_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Kr_chr2R_5490139_5490149 1.0000 11 Kr_chr3L_8639465_8639474 1.0000 10 Kr_chr2R_5489851_5489860 1.0000 10 Kr_chr2R_5489954_5489999 1.0000 46 Kr_chr3L_8644209_8644261 1.0000 53 Kr_chr2R_5490096_5490105 1.0000 10 Kr_chr2R_5489784_5489792 1.0000 9 Kr_chr3R_12636469_126364 1.0000 23 Kr_chr3L_21022078_210220 1.0000 11 Kr_chr2R_5489821_5489830 1.0000 10 Kr_chr3L_8639521_8639530 1.0000 10 Kr_chr3R_4520681_4520692 1.0000 12 Kr_chr2L_11456018_114560 1.0000 37 Kr_chr3L_8644087_8644106 1.0000 20 Kr_chr3L_8640920_8640929 1.0000 10 Kr_chr3L_20630442_206304 1.0000 24 Kr_chr2L_11455642_114556 1.0000 13 Kr_chr2R_5490045_5490055 1.0000 11 Kr_chr3L_21022228_210222 1.0000 12 Kr_chr2L_11455800_114558 1.0000 34 Kr_chr3L_8639587_8639596 1.0000 10 Kr_chr3L_20630373_206303 1.0000 18 Kr_chr3L_8640829_8640838 1.0000 10 Kr_chr2R_5489528_5489537 1.0000 10 Kr_chr3L_8640882_8640891 1.0000 10 Kr_chr3L_8641146_8641155 1.0000 10 Kr_chr3L_8641120_8641129 1.0000 10 Kr_chr2L_11455986_114560 1.0000 20 Kr_chr3R_12598980_125989 1.0000 10 Kr_chr2R_5489926_5489946 1.0000 21 Kr_chr3L_8639823_8639832 1.0000 10 Kr_chr2R_5489810_5489818 1.0000 9 Kr_chr3L_21021993_210220 1.0000 13 Kr_chr3L_20630560_206305 1.0000 21 Kr_chr3L_8641004_8641011 1.0000 8 Kr_chr3L_8640857_8640866 1.0000 10 Kr_chr2R_5489663_5489672 1.0000 10 Kr_chr3L_8641253_8641262 1.0000 10 Kr_chr3L_20630537_206305 1.0000 19 Kr_chr3R_4520998_4521009 1.0000 12 Kr_chr2R_7044648_7044657 1.0000 10 Kr_chr3L_8639315_8639324 1.0000 10 Kr_chr3L_20630505_206305 1.0000 20 Kr_chr2R_5489612_5489622 1.0000 11 Kr_chr2R_5489577_5489585 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/Kr_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= 45 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 687 N= 45 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.287 C 0.213 G 0.213 T 0.287 Background letter frequencies (from dataset with add-one prior applied): A 0.287 C 0.213 G 0.213 T 0.287 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 44 llr = 241 E-value = 5.5e-040 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 78:1:11: pos.-specific C 1:8892:1 probability G 1:1::32: matrix T 1111:479 bits 2.2 2.0 1.8 * 1.6 * Information 1.3 *** content 1.1 **** * (7.9 bits) 0.9 **** * 0.7 **** ** 0.4 ***** ** 0.2 ******** 0.0 -------- Multilevel AACCCTTT consensus G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- Kr_chr3L_20630505_206305 + 7 1.88e-05 CTGTTT AACCCTTT TATGCC Kr_chr3L_20630537_206305 + 5 1.88e-05 GCTT AACCCTTT TATGGGC Kr_chr3L_8641253_8641262 - 1 1.88e-05 AA AACCCTTT Kr_chr3L_20630560_206305 - 10 1.88e-05 GAAC AACCCTTT TGGTACAAT Kr_chr3L_8639823_8639832 - 1 1.88e-05 CG AACCCTTT Kr_chr3L_20630373_206303 + 3 1.88e-05 GT AACCCTTT TAAAAGTC Kr_chr3L_8639587_8639596 + 3 1.88e-05 GA AACCCTTT Kr_chr3L_8640829_8640838 - 1 3.28e-05 AA AACCCGTT Kr_chr2R_5490139_5490149 + 3 3.28e-05 TT AACCCGTT T Kr_chr2R_5489851_5489860 - 1 8.98e-05 GC AACCCGGT Kr_chr2L_11455800_114558 + 8 1.19e-04 CAGCCAT TACCCTTT TGTTGGCCAA Kr_chr3L_21022228_210222 - 3 1.19e-04 AT TACCCTTT TT Kr_chr3L_21022078_210220 + 3 1.19e-04 TC TACCCTTT T Kr_chr3R_12598980_125989 - 1 1.47e-04 GT GACCCTTT Kr_chr3R_12636469_126364 - 9 1.47e-04 GTAGCTT CACCCTTT CACGCACT Kr_chr3L_8640882_8640891 + 3 2.14e-04 CT GACCCGTT Kr_chr2R_5489663_5489672 + 3 3.50e-04 TT AATCCGTT Kr_chr3L_8640857_8640866 + 3 3.93e-04 TT AAGCCTTT Kr_chr3L_8641120_8641129 - 1 3.93e-04 TT AAGCCTTT Kr_chr2R_5490045_5490055 - 2 4.40e-04 CT AATCCCTT C Kr_chr2L_11455642_114556 - 4 4.40e-04 AT AATCCCTT CGA Kr_chr2R_5490096_5490105 - 1 4.40e-04 AT AACCCAGT Kr_chr3L_20630442_206304 + 4 4.79e-04 CTT AACTCTTT TTATGAATAT Kr_chr3L_8644087_8644106 + 6 4.79e-04 GTAAA AACTCTTT GCGAATC Kr_chr2R_5489926_5489946 - 12 5.26e-04 TC AAGCCCTT GGCTAATCCC Kr_chr2R_5489577_5489585 + 2 7.20e-04 T TACCCGGT Kr_chr2L_11456018_114560 - 23 7.20e-04 AGAATTT CACCCATT TCTATGACAC Kr_chr2R_5489528_5489537 + 3 9.96e-04 AT AACCCAAT Kr_chr3L_8644209_8644261 + 36 1.28e-03 TCCCAGAGAG AACCTCTT TCGGCGCGAG Kr_chr2L_11455986_114560 + 12 1.40e-03 AAATTTGTGC CATCCTTT T Kr_chr3L_21021993_210220 - 3 1.94e-03 ACA GTCCCCTT TT Kr_chr2R_7044648_7044657 + 3 2.17e-03 TT AACCAGTT Kr_chr2R_5489954_5489999 + 5 2.17e-03 TCCA ATCCCGAT CCCTAGCCCG Kr_chr3L_8639315_8639324 + 3 3.12e-03 GT CACTCCTT Kr_chr3R_4520998_4521009 - 1 3.12e-03 TAAA TGCCCCTT Kr_chr3L_8640920_8640929 - 1 4.65e-03 AG AACCCGAA Kr_chr2R_5489612_5489622 - 3 9.03e-03 T GTCCCAGT TA Kr_chr3L_8641004_8641011 - 1 9.03e-03 . AACATTTT Kr_chr2R_5489810_5489818 - 2 9.03e-03 . ATTCCGTC T Kr_chr2R_5489784_5489792 + 2 9.03e-03 T AACACGCT Kr_chr3L_8639521_8639530 + 2 1.29e-02 T TTCCCTGC C Kr_chr3L_8639465_8639474 + 3 1.46e-02 TT AACTCAGC Kr_chr3L_8641146_8641155 - 1 2.92e-02 TT AACACCAA Kr_chr3R_4520681_4520692 - 2 2.92e-02 TTA AGTCCCGC A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Kr_chr3L_20630505_206305 1.9e-05 6_[+1]_6 Kr_chr3L_20630537_206305 1.9e-05 4_[+1]_7 Kr_chr3L_8641253_8641262 1.9e-05 [-1]_2 Kr_chr3L_20630560_206305 1.9e-05 9_[-1]_4 Kr_chr3L_8639823_8639832 1.9e-05 [-1]_2 Kr_chr3L_20630373_206303 1.9e-05 2_[+1]_8 Kr_chr3L_8639587_8639596 1.9e-05 2_[+1] Kr_chr3L_8640829_8640838 3.3e-05 [-1]_2 Kr_chr2R_5490139_5490149 3.3e-05 2_[+1]_1 Kr_chr2R_5489851_5489860 9e-05 [-1]_2 Kr_chr2L_11455800_114558 0.00012 7_[+1]_19 Kr_chr3L_21022228_210222 0.00012 2_[-1]_2 Kr_chr3L_21022078_210220 0.00012 2_[+1]_1 Kr_chr3R_12598980_125989 0.00015 [-1]_2 Kr_chr3R_12636469_126364 0.00015 8_[-1]_7 Kr_chr3L_8640882_8640891 0.00021 2_[+1] Kr_chr2R_5489663_5489672 0.00035 2_[+1] Kr_chr3L_8640857_8640866 0.00039 2_[+1] Kr_chr3L_8641120_8641129 0.00039 [-1]_2 Kr_chr2R_5490045_5490055 0.00044 1_[-1]_2 Kr_chr2L_11455642_114556 0.00044 3_[-1]_2 Kr_chr2R_5490096_5490105 0.00044 [-1]_2 Kr_chr3L_20630442_206304 0.00048 3_[+1]_13 Kr_chr3L_8644087_8644106 0.00048 5_[+1]_7 Kr_chr2R_5489926_5489946 0.00053 11_[-1]_2 Kr_chr2R_5489577_5489585 0.00072 1_[+1] Kr_chr2L_11456018_114560 0.00072 22_[-1]_7 Kr_chr2R_5489528_5489537 0.001 2_[+1] Kr_chr3L_8644209_8644261 0.0013 35_[+1]_10 Kr_chr2L_11455986_114560 0.0014 11_[+1]_1 Kr_chr3L_21021993_210220 0.0019 2_[-1]_3 Kr_chr2R_7044648_7044657 0.0022 2_[+1] Kr_chr2R_5489954_5489999 0.0022 4_[+1]_34 Kr_chr3L_8639315_8639324 0.0031 2_[+1] Kr_chr3R_4520998_4521009 0.0031 [-1]_4 Kr_chr3L_8640920_8640929 0.0047 [-1]_2 Kr_chr2R_5489612_5489622 0.009 2_[-1]_1 Kr_chr3L_8641004_8641011 0.009 [-1] Kr_chr2R_5489810_5489818 0.009 1_[-1] Kr_chr2R_5489784_5489792 0.009 1_[+1] Kr_chr3L_8639521_8639530 0.013 1_[+1]_1 Kr_chr3L_8639465_8639474 0.015 2_[+1] Kr_chr3L_8641146_8641155 0.029 [-1]_2 Kr_chr3R_4520681_4520692 0.029 1_[-1]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=44 Kr_chr3L_20630505_206305 ( 7) AACCCTTT 1 Kr_chr3L_20630537_206305 ( 5) AACCCTTT 1 Kr_chr3L_8641253_8641262 ( 1) AACCCTTT 1 Kr_chr3L_20630560_206305 ( 10) AACCCTTT 1 Kr_chr3L_8639823_8639832 ( 1) AACCCTTT 1 Kr_chr3L_20630373_206303 ( 3) AACCCTTT 1 Kr_chr3L_8639587_8639596 ( 3) AACCCTTT 1 Kr_chr3L_8640829_8640838 ( 1) AACCCGTT 1 Kr_chr2R_5490139_5490149 ( 3) AACCCGTT 1 Kr_chr2R_5489851_5489860 ( 1) AACCCGGT 1 Kr_chr2L_11455800_114558 ( 8) TACCCTTT 1 Kr_chr3L_21022228_210222 ( 3) TACCCTTT 1 Kr_chr3L_21022078_210220 ( 3) TACCCTTT 1 Kr_chr3R_12598980_125989 ( 1) GACCCTTT 1 Kr_chr3R_12636469_126364 ( 9) CACCCTTT 1 Kr_chr3L_8640882_8640891 ( 3) GACCCGTT 1 Kr_chr2R_5489663_5489672 ( 3) AATCCGTT 1 Kr_chr3L_8640857_8640866 ( 3) AAGCCTTT 1 Kr_chr3L_8641120_8641129 ( 1) AAGCCTTT 1 Kr_chr2R_5490045_5490055 ( 2) AATCCCTT 1 Kr_chr2L_11455642_114556 ( 4) AATCCCTT 1 Kr_chr2R_5490096_5490105 ( 1) AACCCAGT 1 Kr_chr3L_20630442_206304 ( 4) AACTCTTT 1 Kr_chr3L_8644087_8644106 ( 6) AACTCTTT 1 Kr_chr2R_5489926_5489946 ( 12) AAGCCCTT 1 Kr_chr2R_5489577_5489585 ( 2) TACCCGGT 1 Kr_chr2L_11456018_114560 ( 23) CACCCATT 1 Kr_chr2R_5489528_5489537 ( 3) AACCCAAT 1 Kr_chr3L_8644209_8644261 ( 36) AACCTCTT 1 Kr_chr2L_11455986_114560 ( 12) CATCCTTT 1 Kr_chr3L_21021993_210220 ( 3) GTCCCCTT 1 Kr_chr2R_7044648_7044657 ( 3) AACCAGTT 1 Kr_chr2R_5489954_5489999 ( 5) ATCCCGAT 1 Kr_chr3L_8639315_8639324 ( 3) CACTCCTT 1 Kr_chr3R_4520998_4521009 ( 1) TGCCCCTT 1 Kr_chr3L_8640920_8640929 ( 1) AACCCGAA 1 Kr_chr2R_5489612_5489622 ( 3) GTCCCAGT 1 Kr_chr3L_8641004_8641011 ( 1) AACATTTT 1 Kr_chr2R_5489810_5489818 ( 2) ATTCCGTC 1 Kr_chr2R_5489784_5489792 ( 2) AACACGCT 1 Kr_chr3L_8639521_8639530 ( 2) TTCCCTGC 1 Kr_chr3L_8639465_8639474 ( 3) AACTCAGC 1 Kr_chr3L_8641146_8641155 ( 1) AACACCAA 1 Kr_chr3R_4520681_4520692 ( 2) AGTCCCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 372 bayes= 3.29483 E= 5.5e-040 125 -123 -123 -107 155 -1210 -223 -134 -1210 190 -164 -107 -207 198 -1210 -166 -366 213 -1210 -266 -134 -6 23 59 -166 -322 -42 134 -266 -123 -1210 159 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 5.5e-040 0.681818 0.090909 0.090909 0.136364 0.840909 0.000000 0.045455 0.113636 0.000000 0.795455 0.068182 0.136364 0.068182 0.840909 0.000000 0.090909 0.022727 0.931818 0.000000 0.045455 0.113636 0.204545 0.250000 0.431818 0.090909 0.022727 0.159091 0.727273 0.045455 0.090909 0.000000 0.863636 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- AACCC[TGC]TT -------------------------------------------------------------------------------- Time 0.33 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Kr_chr2R_5490139_5490149 2.62e-04 2_[+1(3.28e-05)]_1 Kr_chr3L_8639465_8639474 8.47e-02 10 Kr_chr2R_5489851_5489860 5.39e-04 [-1(8.98e-05)]_2 Kr_chr2R_5489954_5489999 1.56e-01 46 Kr_chr3L_8644209_8644261 1.11e-01 53 Kr_chr2R_5490096_5490105 2.64e-03 10 Kr_chr2R_5489784_5489792 3.56e-02 9 Kr_chr3R_12636469_126364 4.69e-03 23 Kr_chr3L_21022078_210220 9.52e-04 11 Kr_chr2R_5489821_5489830 6.23e-01 10 Kr_chr3L_8639521_8639530 7.48e-02 10 Kr_chr3R_4520681_4520692 2.57e-01 12 Kr_chr2L_11456018_114560 4.23e-02 37 Kr_chr3L_8644087_8644106 1.24e-02 20 Kr_chr3L_8640920_8640929 2.76e-02 10 Kr_chr3L_20630442_206304 1.62e-02 24 Kr_chr2L_11455642_114556 5.27e-03 13 Kr_chr2R_5490045_5490055 3.51e-03 11 Kr_chr3L_21022228_210222 1.19e-03 12 Kr_chr2L_11455800_114558 6.41e-03 34 Kr_chr3L_8639587_8639596 1.13e-04 2_[+1(1.88e-05)] Kr_chr3L_20630373_206303 4.14e-04 2_[+1(1.88e-05)]_8 Kr_chr3L_8640829_8640838 1.97e-04 [-1(3.28e-05)]_2 Kr_chr2R_5489528_5489537 5.96e-03 10 Kr_chr3L_8640882_8640891 1.28e-03 10 Kr_chr3L_8641146_8641155 1.63e-01 10 Kr_chr3L_8641120_8641129 2.36e-03 10 Kr_chr2L_11455986_114560 3.58e-02 20 Kr_chr3R_12598980_125989 8.81e-04 10 Kr_chr2R_5489926_5489946 1.46e-02 21 Kr_chr3L_8639823_8639832 1.13e-04 [-1(1.88e-05)]_2 Kr_chr2R_5489810_5489818 3.56e-02 9 Kr_chr3L_21021993_210220 2.31e-02 13 Kr_chr3L_20630560_206305 5.27e-04 9_[-1(1.88e-05)]_4 Kr_chr3L_8641004_8641011 1.80e-02 8 Kr_chr3L_8640857_8640866 2.36e-03 10 Kr_chr2R_5489663_5489672 2.10e-03 10 Kr_chr3L_8641253_8641262 1.13e-04 [-1(1.88e-05)]_2 Kr_chr3L_20630537_206305 4.52e-04 4_[+1(1.88e-05)]_7 Kr_chr3R_4520998_4521009 3.08e-02 12 Kr_chr2R_7044648_7044657 1.29e-02 10 Kr_chr3L_8639315_8639324 1.86e-02 10 Kr_chr3L_20630505_206305 4.90e-04 6_[+1(1.88e-05)]_6 Kr_chr2R_5489612_5489622 7.00e-02 11 Kr_chr2R_5489577_5489585 2.88e-03 9 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************