******************************************************************************** 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/bcd_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ bcd_chr2R_5489683_548969 1.0000 9 bcd_chr2R_20730481_20730 1.0000 34 bcd_chr3L_8640857_864086 1.0000 7 bcd_chr3R_26676964_26676 1.0000 15 bcd_chr3L_8641121_864113 1.0000 10 bcd_chr3R_26676842_26676 1.0000 15 bcd_chr3L_8639735_863974 1.0000 9 bcd_chr3L_20631237_20631 1.0000 17 bcd_chr2L_11456122_11456 1.0000 12 bcd_chr3L_8639370_863937 1.0000 9 bcd_chr3R_4520555_452056 1.0000 9 bcd_chr2R_5490045_549005 1.0000 11 bcd_chr3R_26676864_26676 1.0000 15 bcd_chr3R_4520377_452038 1.0000 13 bcd_chr2R_5489662_548967 1.0000 9 bcd_chr3R_26677097_26677 1.0000 29 bcd_chr2R_20730540_20730 1.0000 44 bcd_chr3L_8641218_864122 1.0000 7 bcd_chr3R_4522594_452261 1.0000 20 bcd_chr2L_11455737_11455 1.0000 13 bcd_chr3R_4520526_452053 1.0000 9 bcd_chr3R_26676939_26676 1.0000 15 bcd_chr3R_26677189_26677 1.0000 20 bcd_chr3R_4520539_452054 1.0000 9 bcd_chr2R_5489927_548993 1.0000 9 bcd_chr3R_26677067_26677 1.0000 15 bcd_chr3L_8639162_863917 1.0000 9 bcd_chr3L_20631195_20631 1.0000 38 bcd_chr3R_9720615_972062 1.0000 14 bcd_chr2L_11455793_11455 1.0000 9 bcd_chr3L_8639266_863927 1.0000 9 bcd_chr2R_20730888_20730 1.0000 25 bcd_chr3L_8639420_863942 1.0000 9 bcd_chr2L_11455854_11455 1.0000 12 bcd_chr3R_4520590_452060 1.0000 15 bcd_chr3R_4520483_452049 1.0000 14 bcd_chr2L_11455823_11455 1.0000 13 bcd_chr3L_8639430_863943 1.0000 9 bcd_chr2R_20730451_20730 1.0000 24 bcd_chr3R_9720583_972059 1.0000 16 bcd_chr3R_26676912_26676 1.0000 15 bcd_chr2L_11455773_11455 1.0000 9 bcd_chr2R_5489834_548984 1.0000 9 bcd_chr3L_8639675_863968 1.0000 9 bcd_chr2L_11455643_11455 1.0000 13 bcd_chr3R_4520452_452046 1.0000 14 bcd_chr3R_4520506_452051 1.0000 6 bcd_chr3R_4522643_452265 1.0000 13 ******************************************************************************** ******************************************************************************** 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/bcd_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= 48 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 688 N= 48 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.307 C 0.193 G 0.193 T 0.307 Background letter frequencies (from dataset with add-one prior applied): A 0.306 C 0.194 G 0.194 T 0.306 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 6 sites = 48 llr = 230 E-value = 7.3e-032 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 29a::1 pos.-specific C 1:::96 probability G :::3:1 matrix T 8::7:3 bits 2.4 2.1 1.9 * 1.7 * Information 1.4 * * content 1.2 ** * (6.9 bits) 0.9 **** 0.7 ****** 0.5 ****** 0.2 ****** 0.0 ------ Multilevel TAATCC consensus G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ bcd_chr2L_11455643_11455 - 6 3.30e-04 TA TAATCC CTTCG bcd_chr2R_20730451_20730 - 11 3.30e-04 AAAAAATT TAATCC GTTTCTGAAG bcd_chr3R_4520483_452049 - 5 3.30e-04 GCTC TAATCC AGAA bcd_chr3R_4520590_452060 - 8 3.30e-04 CG TAATCC CCATAGA bcd_chr2R_5489927_548993 - 2 3.30e-04 GC TAATCC C bcd_chr3R_4522594_452261 - 5 3.30e-04 TAATCACCTT TAATCC CAAG bcd_chr2R_5489662_548967 + 3 3.30e-04 GT TAATCC G bcd_chr3R_4520377_452038 - 6 3.30e-04 TC TAATCC CTTGA bcd_chr2R_5490045_549005 - 5 3.30e-04 C TAATCC CTTC bcd_chr2R_20730481_20730 + 3 3.30e-04 AA TAATCC AGCCTTAAGC bcd_chr3L_8639675_863968 + 3 5.39e-04 CT TAAGCC G bcd_chr2L_11455854_11455 - 4 5.39e-04 CGA TAAGCC GGA bcd_chr2R_20730888_20730 - 11 5.39e-04 CAAGAATCC TAAGCC GGATTTAGTT bcd_chr3R_9720615_972062 - 2 5.39e-04 CAAAAGT TAAGCC A bcd_chr2R_20730540_20730 - 35 5.39e-04 GCTC TAAGCC GGAGATTAAC bcd_chr3L_20631237_20631 - 10 5.39e-04 CC TAAGCC AGCGATTTC bcd_chr3L_8641121_864113 - 3 5.39e-04 TT TAAGCC TT bcd_chr3L_8640857_864086 + 2 5.39e-04 T TAAGCC bcd_chr3R_4522643_452265 - 6 1.06e-03 GC TAATCT GATGA bcd_chr3R_26676912_26676 - 6 1.06e-03 CCTC TAATCT CGCTT bcd_chr3L_8639266_863927 - 2 1.06e-03 TT TAATCT T bcd_chr3L_20631195_20631 + 2 1.06e-03 A TAATCT GCAGCTTAGG bcd_chr3R_26676842_26676 + 7 1.06e-03 AATCCG TAATCT GCT bcd_chr3R_26676964_26676 + 6 1.06e-03 ACGCC TAATCT GGCT bcd_chr2R_5489683_548969 - 2 1.06e-03 AA TAATCT C bcd_chr2L_11455773_11455 - 1 1.72e-03 TGC AAATCC bcd_chr3R_9720583_972059 + 4 1.72e-03 TTT AAATCC GTTTTGA bcd_chr2L_11455823_11455 - 4 1.72e-03 GGAC AAATCC TTT bcd_chr2L_11455793_11455 - 1 1.72e-03 TGC AAATCC bcd_chr3R_4520539_452054 - 1 1.72e-03 CGC TAAGCT bcd_chr3R_26676864_26676 - 3 1.72e-03 CTCGACT TAAGCT CG bcd_chr3R_4520555_452056 - 1 1.72e-03 TGC TAAGCT bcd_chr3R_4520452_452046 - 6 2.14e-03 CCT CAATCC GCGAT bcd_chr2R_5489834_548984 + 3 2.47e-03 TA TAATCG C bcd_chr3L_8639162_863917 + 3 4.73e-03 GT CAATCT G bcd_chr3R_26677097_26677 + 20 4.73e-03 ATTAAAAACG CAATCT GAGC bcd_chr3R_26676939_26676 + 1 5.26e-03 . GAATCC TAAAGGCTC bcd_chr2L_11455737_11455 + 4 5.26e-03 AAT TAAGCA TGGC bcd_chr3R_4520526_452053 - 2 5.81e-03 GA TCATCC A bcd_chr3L_8639430_863943 + 3 8.00e-03 AC AAATCG C bcd_chr3L_8639735_863974 - 2 8.00e-03 AT TAGTCT T bcd_chr3L_8639420_863942 + 2 1.08e-02 T TTAGCC TT bcd_chr3R_4520506_452051 - 1 1.39e-02 . TAATTT bcd_chr3R_26677067_26677 + 6 1.39e-02 TAAAA TAATTT TATT bcd_chr3R_26677189_26677 + 1 2.08e-02 . AAATGC AAATATTTGT bcd_chr3L_8639370_863937 + 2 2.69e-02 A TGATCA AC bcd_chr3L_8641218_864122 + 1 4.28e-02 . AAGTCA A bcd_chr2L_11456122_11456 - 5 4.82e-02 GA AAAACG GCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bcd_chr2L_11455643_11455 0.00033 5_[-1]_2 bcd_chr2R_20730451_20730 0.00033 10_[-1]_8 bcd_chr3R_4520483_452049 0.00033 4_[-1]_4 bcd_chr3R_4520590_452060 0.00033 7_[-1]_2 bcd_chr2R_5489927_548993 0.00033 1_[-1]_2 bcd_chr3R_4522594_452261 0.00033 4_[-1]_10 bcd_chr2R_5489662_548967 0.00033 2_[+1]_1 bcd_chr3R_4520377_452038 0.00033 5_[-1]_2 bcd_chr2R_5490045_549005 0.00033 4_[-1]_1 bcd_chr2R_20730481_20730 0.00033 2_[+1]_26 bcd_chr3L_8639675_863968 0.00054 2_[+1]_1 bcd_chr2L_11455854_11455 0.00054 3_[-1]_3 bcd_chr2R_20730888_20730 0.00054 10_[-1]_9 bcd_chr3R_9720615_972062 0.00054 1_[-1]_7 bcd_chr2R_20730540_20730 0.00054 34_[-1]_4 bcd_chr3L_20631237_20631 0.00054 9_[-1]_2 bcd_chr3L_8641121_864113 0.00054 2_[-1]_2 bcd_chr3L_8640857_864086 0.00054 1_[+1] bcd_chr3R_4522643_452265 0.0011 5_[-1]_2 bcd_chr3R_26676912_26676 0.0011 5_[-1]_4 bcd_chr3L_8639266_863927 0.0011 1_[-1]_2 bcd_chr3L_20631195_20631 0.0011 1_[+1]_31 bcd_chr3R_26676842_26676 0.0011 6_[+1]_3 bcd_chr3R_26676964_26676 0.0011 5_[+1]_4 bcd_chr2R_5489683_548969 0.0011 1_[-1]_2 bcd_chr2L_11455773_11455 0.0017 [-1]_3 bcd_chr3R_9720583_972059 0.0017 3_[+1]_7 bcd_chr2L_11455823_11455 0.0017 3_[-1]_4 bcd_chr2L_11455793_11455 0.0017 [-1]_3 bcd_chr3R_4520539_452054 0.0017 [-1]_3 bcd_chr3R_26676864_26676 0.0017 2_[-1]_7 bcd_chr3R_4520555_452056 0.0017 [-1]_3 bcd_chr3R_4520452_452046 0.0021 5_[-1]_3 bcd_chr2R_5489834_548984 0.0025 2_[+1]_1 bcd_chr3L_8639162_863917 0.0047 2_[+1]_1 bcd_chr3R_26677097_26677 0.0047 19_[+1]_4 bcd_chr3R_26676939_26676 0.0053 [+1]_9 bcd_chr2L_11455737_11455 0.0053 3_[+1]_4 bcd_chr3R_4520526_452053 0.0058 1_[-1]_2 bcd_chr3L_8639430_863943 0.008 2_[+1]_1 bcd_chr3L_8639735_863974 0.008 1_[-1]_2 bcd_chr3L_8639420_863942 0.011 1_[+1]_2 bcd_chr3R_4520506_452051 0.014 [-1] bcd_chr3R_26677067_26677 0.014 5_[+1]_4 bcd_chr3R_26677189_26677 0.021 [+1]_14 bcd_chr3L_8639370_863937 0.027 1_[+1]_2 bcd_chr3L_8641218_864122 0.043 [+1]_1 bcd_chr2L_11456122_11456 0.048 4_[-1]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=6 seqs=48 bcd_chr2L_11455643_11455 ( 6) TAATCC 1 bcd_chr2R_20730451_20730 ( 11) TAATCC 1 bcd_chr3R_4520483_452049 ( 5) TAATCC 1 bcd_chr3R_4520590_452060 ( 8) TAATCC 1 bcd_chr2R_5489927_548993 ( 2) TAATCC 1 bcd_chr3R_4522594_452261 ( 5) TAATCC 1 bcd_chr2R_5489662_548967 ( 3) TAATCC 1 bcd_chr3R_4520377_452038 ( 6) TAATCC 1 bcd_chr2R_5490045_549005 ( 5) TAATCC 1 bcd_chr2R_20730481_20730 ( 3) TAATCC 1 bcd_chr3L_8639675_863968 ( 3) TAAGCC 1 bcd_chr2L_11455854_11455 ( 4) TAAGCC 1 bcd_chr2R_20730888_20730 ( 11) TAAGCC 1 bcd_chr3R_9720615_972062 ( 2) TAAGCC 1 bcd_chr2R_20730540_20730 ( 35) TAAGCC 1 bcd_chr3L_20631237_20631 ( 10) TAAGCC 1 bcd_chr3L_8641121_864113 ( 3) TAAGCC 1 bcd_chr3L_8640857_864086 ( 2) TAAGCC 1 bcd_chr3R_4522643_452265 ( 6) TAATCT 1 bcd_chr3R_26676912_26676 ( 6) TAATCT 1 bcd_chr3L_8639266_863927 ( 2) TAATCT 1 bcd_chr3L_20631195_20631 ( 2) TAATCT 1 bcd_chr3R_26676842_26676 ( 7) TAATCT 1 bcd_chr3R_26676964_26676 ( 6) TAATCT 1 bcd_chr2R_5489683_548969 ( 2) TAATCT 1 bcd_chr2L_11455773_11455 ( 1) AAATCC 1 bcd_chr3R_9720583_972059 ( 4) AAATCC 1 bcd_chr2L_11455823_11455 ( 4) AAATCC 1 bcd_chr2L_11455793_11455 ( 1) AAATCC 1 bcd_chr3R_4520539_452054 ( 1) TAAGCT 1 bcd_chr3R_26676864_26676 ( 3) TAAGCT 1 bcd_chr3R_4520555_452056 ( 1) TAAGCT 1 bcd_chr3R_4520452_452046 ( 6) CAATCC 1 bcd_chr2R_5489834_548984 ( 3) TAATCG 1 bcd_chr3L_8639162_863917 ( 3) CAATCT 1 bcd_chr3R_26677097_26677 ( 20) CAATCT 1 bcd_chr3R_26676939_26676 ( 1) GAATCC 1 bcd_chr2L_11455737_11455 ( 4) TAAGCA 1 bcd_chr3R_4520526_452053 ( 2) TCATCC 1 bcd_chr3L_8639430_863943 ( 3) AAATCG 1 bcd_chr3L_8639735_863974 ( 2) TAGTCT 1 bcd_chr3L_8639420_863942 ( 2) TTAGCC 1 bcd_chr3R_4520506_452051 ( 1) TAATTT 1 bcd_chr3R_26677067_26677 ( 6) TAATTT 1 bcd_chr3R_26677189_26677 ( 1) AAATGC 1 bcd_chr3L_8639370_863937 ( 2) TGATCA 1 bcd_chr3L_8641218_864122 ( 1) AAGTCA 1 bcd_chr2L_11456122_11456 ( 5) AAAACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 448 bayes= 4.75489 E= 7.3e-032 -88 -163 -321 129 161 -321 -321 -387 165 -1223 -222 -1223 -387 -1223 48 121 -1223 228 -321 -288 -229 154 -163 3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 48 E= 7.3e-032 0.166667 0.062500 0.020833 0.750000 0.937500 0.020833 0.020833 0.020833 0.958333 0.000000 0.041667 0.000000 0.020833 0.000000 0.270833 0.708333 0.000000 0.937500 0.020833 0.041667 0.062500 0.562500 0.062500 0.312500 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TAA[TG]C[CT] -------------------------------------------------------------------------------- Time 0.31 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bcd_chr2R_5489683_548969 8.46e-03 9 bcd_chr2R_20730481_20730 1.90e-02 34 bcd_chr3L_8640857_864086 2.15e-03 7 bcd_chr3R_26676964_26676 2.10e-02 15 bcd_chr3L_8641121_864113 5.38e-03 10 bcd_chr3R_26676842_26676 2.10e-02 15 bcd_chr3L_8639735_863974 6.22e-02 9 bcd_chr3L_20631237_20631 1.29e-02 17 bcd_chr2L_11456122_11456 4.99e-01 12 bcd_chr3L_8639370_863937 1.96e-01 9 bcd_chr3R_4520555_452056 1.37e-02 9 bcd_chr2R_5490045_549005 3.96e-03 11 bcd_chr3R_26676864_26676 3.39e-02 15 bcd_chr3R_4520377_452038 5.27e-03 13 bcd_chr2R_5489662_548967 2.64e-03 9 bcd_chr3R_26677097_26677 2.03e-01 29 bcd_chr2R_20730540_20730 4.12e-02 44 bcd_chr3L_8641218_864122 1.60e-01 7 bcd_chr3R_4522594_452261 9.86e-03 20 bcd_chr2L_11455737_11455 8.10e-02 13 bcd_chr3R_4520526_452053 4.56e-02 9 bcd_chr3R_26676939_26676 1.00e-01 15 bcd_chr3R_26677189_26677 4.67e-01 20 bcd_chr3R_4520539_452054 1.37e-02 9 bcd_chr2R_5489927_548993 2.64e-03 9 bcd_chr3R_26677067_26677 2.44e-01 15 bcd_chr3L_8639162_863917 3.72e-02 9 bcd_chr3L_20631195_20631 6.77e-02 38 bcd_chr3R_9720615_972062 9.66e-03 14 bcd_chr2L_11455793_11455 1.37e-02 9 bcd_chr3L_8639266_863927 8.46e-03 9 bcd_chr2R_20730888_20730 2.13e-02 25 bcd_chr3L_8639420_863942 8.34e-02 9 bcd_chr2L_11455854_11455 7.52e-03 12 bcd_chr3R_4520590_452060 6.59e-03 15 bcd_chr3R_4520483_452049 5.93e-03 14 bcd_chr2L_11455823_11455 2.72e-02 13 bcd_chr3L_8639430_863943 6.22e-02 9 bcd_chr2R_20730451_20730 1.25e-02 24 bcd_chr3R_9720583_972059 3.72e-02 16 bcd_chr3R_26676912_26676 2.10e-02 15 bcd_chr2L_11455773_11455 1.37e-02 9 bcd_chr2R_5489834_548984 1.96e-02 9 bcd_chr3L_8639675_863968 4.30e-03 9 bcd_chr2L_11455643_11455 5.27e-03 13 bcd_chr3R_4520452_452046 3.78e-02 14 bcd_chr3R_4520506_452051 2.76e-02 6 bcd_chr3R_4522643_452265 1.69e-02 13 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************