******************************************************************************** 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/dl_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ dl_chr2L_2456352_2456369 1.0000 18 dl_chr2L_15475919_154759 1.0000 17 dl_chr2L_2456485_2456500 1.0000 16 dl_chr3R_2581102_2581111 1.0000 10 dl_chr2L_2456179_2456195 1.0000 17 dl_chr2L_15475754_154757 1.0000 16 dl_chr2L_15475288_154753 1.0000 19 dl_chr2L_2457291_2457304 1.0000 14 dl_chr3L_1445616_1445626 1.0000 11 dl_chr2R_18553742_185537 1.0000 11 dl_chr2L_2456209_2456223 1.0000 15 dl_chr2L_15476025_154760 1.0000 16 dl_chr3R_2581220_2581229 1.0000 10 dl_chr2L_2456446_2456465 1.0000 20 dl_chr2R_18552822_185528 1.0000 20 dl_chr2L_15475642_154756 1.0000 16 dl_chr2R_18553624_185536 1.0000 11 dl_chr3L_1445374_1445384 1.0000 11 dl_chr2L_2456749_2456764 1.0000 16 dl_chr2L_2456607_2456624 1.0000 18 dl_chr2L_15475721_154757 1.0000 16 dl_chr2L_15475985_154760 1.0000 16 dl_chr3L_1445569_1445579 1.0000 11 dl_chr2L_2456426_2456439 1.0000 14 dl_chr2L_2456800_2456816 1.0000 17 dl_chr2L_2456997_2457009 1.0000 13 dl_chr2L_2457011_2457028 1.0000 18 dl_chr2L_15476060_154760 1.0000 16 dl_chr2L_15475577_154755 1.0000 16 dl_chr2L_15475489_154755 1.0000 16 dl_chr2R_18553608_185536 1.0000 11 dl_chr3L_1445510_1445520 1.0000 11 dl_chr2R_18552809_185528 1.0000 11 dl_chr2L_2456702_2456718 1.0000 17 dl_chr2R_18552863_185528 1.0000 11 dl_chr2R_18553654_185536 1.0000 11 dl_chr2L_2456823_2456842 1.0000 20 dl_chr3R_2581170_2581180 1.0000 11 ******************************************************************************** ******************************************************************************** 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/dl_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= 20 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 38 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 558 N= 38 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.273 C 0.227 G 0.227 T 0.273 Background letter frequencies (from dataset with add-one prior applied): A 0.273 C 0.227 G 0.227 T 0.273 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 38 llr = 228 E-value = 2.2e-038 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :49994:3 pos.-specific C :::1:156 probability G a61::1:1 matrix T ::1:1441 bits 2.1 1.9 * 1.7 * 1.5 * ** Information 1.3 * ** content 1.1 ***** (8.7 bits) 0.9 ***** * 0.6 ***** * 0.4 ***** ** 0.2 ******** 0.0 -------- Multilevel GGAAAACC consensus A TTA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- dl_chr2L_15476060_154760 + 5 2.95e-05 TTGG GGAAAACC CTTT dl_chr3R_2581220_2581229 - 2 2.95e-05 G GGAAATCC A dl_chr3R_2581102_2581111 - 2 2.95e-05 G GGAAAACC A dl_chr3L_1445510_1445520 - 3 6.50e-05 A GGAAATTC CG dl_chr3L_1445569_1445579 + 2 6.50e-05 G GGAAATTC CC dl_chr2L_2456607_2456624 + 6 6.50e-05 CACGC GGAAATTC CACGG dl_chr2L_2456485_2456500 - 6 6.50e-05 TCA GGAAAATC CGACT dl_chr2L_15475919_154759 + 5 6.50e-05 CGCG GGAAAATC CGCAC dl_chr2R_18552822_185528 - 10 1.00e-04 TCC GAAAATCC AGAAAAATA dl_chr2R_18553654_185536 + 4 1.91e-04 ACA GAAAAATC dl_chr2L_15476025_154760 - 5 1.91e-04 AAGC GGAAAACA CTGG dl_chr2L_2456352_2456369 - 6 1.91e-04 AGGTG GAAAATTC AGGTA dl_chr2L_2456800_2456816 - 9 2.48e-04 C GGAAAATA ATGCGAAA dl_chr2L_15475642_154756 - 5 2.48e-04 GATG GGAAATTA CTTT dl_chr2L_2456179_2456195 - 6 2.48e-04 AAAT GGAAATTA TTCTT dl_chr3L_1445374_1445384 + 3 3.18e-04 GG GAAAAACA C dl_chr3L_1445616_1445626 + 3 3.18e-04 GG GAAAAGCC C dl_chr2L_2457291_2457304 - 4 3.48e-04 CAG GGAAATCG GGG dl_chr2R_18552809_185528 - 1 4.46e-04 AGC GAAAAGTC dl_chr2L_15475721_154757 - 4 4.61e-04 ATATA GAAAACCC CCA dl_chr2R_18553624_185536 + 4 4.61e-04 AGA GAAAACCC dl_chr2R_18553608_185536 - 2 4.97e-04 TG GGAAAATG C dl_chr2R_18552863_185528 - 1 5.74e-04 CGA GAAAATCG dl_chr2L_2456446_2456465 - 7 5.74e-04 GGTAGC GGAAAGTA CGCATT dl_chr2R_18553742_185537 + 4 5.74e-04 CGA GAAAATCG dl_chr2L_15475489_154755 + 5 8.97e-04 GCGC GGAATTCC AATT dl_chr3R_2581170_2581180 + 3 1.16e-03 GG GAGAAACC C dl_chr2L_15475577_154755 - 5 1.16e-03 GCAG GGAAATAC GAAA dl_chr2L_2456209_2456223 - 4 1.39e-03 TCTA GATAAACC AGA dl_chr2L_2456702_2456718 - 4 1.58e-03 TCTTAG GAAAAATT TCA dl_chr2L_2457011_2457028 - 8 1.58e-03 AGC GGGAATCA ACCGGAG dl_chr2L_15475288_154753 - 8 2.16e-03 GTTG GGAAAGTT TCCCATC dl_chr2L_2456823_2456842 + 10 2.68e-03 TATAGGGTC GAACAATA AAG dl_chr2L_2456426_2456439 - 3 2.68e-03 AGTG GGAATATA AA dl_chr2L_15475754_154757 + 5 4.50e-03 GGTG GGTCATCC CGGA dl_chr2L_2456749_2456764 - 5 5.09e-03 AATA TAAAAGCC ATTT dl_chr2L_15475985_154760 - 5 5.85e-03 AGCG GGCCAACC CGAC dl_chr2L_2456997_2457009 + 4 6.48e-03 CTC GGAACCCA AC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- dl_chr2L_15476060_154760 2.9e-05 4_[+1]_4 dl_chr3R_2581220_2581229 2.9e-05 1_[-1]_1 dl_chr3R_2581102_2581111 2.9e-05 1_[-1]_1 dl_chr3L_1445510_1445520 6.5e-05 2_[-1]_1 dl_chr3L_1445569_1445579 6.5e-05 1_[+1]_2 dl_chr2L_2456607_2456624 6.5e-05 5_[+1]_5 dl_chr2L_2456485_2456500 6.5e-05 5_[-1]_3 dl_chr2L_15475919_154759 6.5e-05 4_[+1]_5 dl_chr2R_18552822_185528 0.0001 9_[-1]_3 dl_chr2R_18553654_185536 0.00019 3_[+1] dl_chr2L_15476025_154760 0.00019 4_[-1]_4 dl_chr2L_2456352_2456369 0.00019 5_[-1]_5 dl_chr2L_2456800_2456816 0.00025 8_[-1]_1 dl_chr2L_15475642_154756 0.00025 4_[-1]_4 dl_chr2L_2456179_2456195 0.00025 5_[-1]_4 dl_chr3L_1445374_1445384 0.00032 2_[+1]_1 dl_chr3L_1445616_1445626 0.00032 2_[+1]_1 dl_chr2L_2457291_2457304 0.00035 3_[-1]_3 dl_chr2R_18552809_185528 0.00045 [-1]_3 dl_chr2L_15475721_154757 0.00046 3_[-1]_5 dl_chr2R_18553624_185536 0.00046 3_[+1] dl_chr2R_18553608_185536 0.0005 1_[-1]_2 dl_chr2R_18552863_185528 0.00057 [-1]_3 dl_chr2L_2456446_2456465 0.00057 6_[-1]_6 dl_chr2R_18553742_185537 0.00057 3_[+1] dl_chr2L_15475489_154755 0.0009 4_[+1]_4 dl_chr3R_2581170_2581180 0.0012 2_[+1]_1 dl_chr2L_15475577_154755 0.0012 4_[-1]_4 dl_chr2L_2456209_2456223 0.0014 3_[-1]_4 dl_chr2L_2456702_2456718 0.0016 3_[-1]_6 dl_chr2L_2457011_2457028 0.0016 7_[-1]_3 dl_chr2L_15475288_154753 0.0022 7_[-1]_4 dl_chr2L_2456823_2456842 0.0027 9_[+1]_3 dl_chr2L_2456426_2456439 0.0027 2_[-1]_4 dl_chr2L_15475754_154757 0.0045 4_[+1]_4 dl_chr2L_2456749_2456764 0.0051 4_[-1]_4 dl_chr2L_15475985_154760 0.0058 4_[-1]_4 dl_chr2L_2456997_2457009 0.0065 3_[+1]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=38 dl_chr2L_15476060_154760 ( 5) GGAAAACC 1 dl_chr3R_2581220_2581229 ( 2) GGAAATCC 1 dl_chr3R_2581102_2581111 ( 2) GGAAAACC 1 dl_chr3L_1445510_1445520 ( 3) GGAAATTC 1 dl_chr3L_1445569_1445579 ( 2) GGAAATTC 1 dl_chr2L_2456607_2456624 ( 6) GGAAATTC 1 dl_chr2L_2456485_2456500 ( 6) GGAAAATC 1 dl_chr2L_15475919_154759 ( 5) GGAAAATC 1 dl_chr2R_18552822_185528 ( 10) GAAAATCC 1 dl_chr2R_18553654_185536 ( 4) GAAAAATC 1 dl_chr2L_15476025_154760 ( 5) GGAAAACA 1 dl_chr2L_2456352_2456369 ( 6) GAAAATTC 1 dl_chr2L_2456800_2456816 ( 9) GGAAAATA 1 dl_chr2L_15475642_154756 ( 5) GGAAATTA 1 dl_chr2L_2456179_2456195 ( 6) GGAAATTA 1 dl_chr3L_1445374_1445384 ( 3) GAAAAACA 1 dl_chr3L_1445616_1445626 ( 3) GAAAAGCC 1 dl_chr2L_2457291_2457304 ( 4) GGAAATCG 1 dl_chr2R_18552809_185528 ( 1) GAAAAGTC 1 dl_chr2L_15475721_154757 ( 4) GAAAACCC 1 dl_chr2R_18553624_185536 ( 4) GAAAACCC 1 dl_chr2R_18553608_185536 ( 2) GGAAAATG 1 dl_chr2R_18552863_185528 ( 1) GAAAATCG 1 dl_chr2L_2456446_2456465 ( 7) GGAAAGTA 1 dl_chr2R_18553742_185537 ( 4) GAAAATCG 1 dl_chr2L_15475489_154755 ( 5) GGAATTCC 1 dl_chr3R_2581170_2581180 ( 3) GAGAAACC 1 dl_chr2L_15475577_154755 ( 5) GGAAATAC 1 dl_chr2L_2456209_2456223 ( 4) GATAAACC 1 dl_chr2L_2456702_2456718 ( 4) GAAAAATT 1 dl_chr2L_2457011_2457028 ( 8) GGGAATCA 1 dl_chr2L_15475288_154753 ( 8) GGAAAGTT 1 dl_chr2L_2456823_2456842 ( 10) GAACAATA 1 dl_chr2L_2456426_2456439 ( 3) GGAATATA 1 dl_chr2L_15475754_154757 ( 5) GGTCATCC 1 dl_chr2L_2456749_2456764 ( 5) TAAAAGCC 1 dl_chr2L_15475985_154760 ( 5) GGCCAACC 1 dl_chr2L_2456997_2457009 ( 4) GGAACCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 292 bayes= 3.73484 E= 2.2e-038 -1189 -1189 210 -337 53 -1189 142 -1189 167 -310 -211 -237 175 -152 -1189 -1189 175 -310 -1189 -237 53 -152 -79 53 -337 121 -1189 71 -5 135 -111 -237 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 2.2e-038 0.000000 0.000000 0.973684 0.026316 0.394737 0.000000 0.605263 0.000000 0.868421 0.026316 0.052632 0.052632 0.921053 0.078947 0.000000 0.000000 0.921053 0.026316 0.000000 0.052632 0.394737 0.078947 0.131579 0.394737 0.026316 0.526316 0.000000 0.447368 0.263158 0.578947 0.105263 0.052632 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[GA]AAA[AT][CT][CA] -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- dl_chr2L_2456352_2456369 4.19e-03 18 dl_chr2L_15475919_154759 1.30e-03 4_[+1(6.50e-05)]_5 dl_chr2L_2456485_2456500 1.17e-03 5_[-1(6.50e-05)]_3 dl_chr3R_2581102_2581111 1.77e-04 1_[-1(2.95e-05)]_1 dl_chr2L_2456179_2456195 4.96e-03 17 dl_chr2L_15475754_154757 7.79e-02 16 dl_chr2L_15475288_154753 5.06e-02 19 dl_chr2L_2457291_2457304 4.86e-03 14 dl_chr3L_1445616_1445626 2.54e-03 11 dl_chr2R_18553742_185537 4.59e-03 11 dl_chr2L_2456209_2456223 2.20e-02 15 dl_chr2L_15476025_154760 3.43e-03 16 dl_chr3R_2581220_2581229 1.77e-04 1_[-1(2.95e-05)]_1 dl_chr2L_2456446_2456465 1.48e-02 20 dl_chr2R_18552822_185528 2.61e-03 20 dl_chr2L_15475642_154756 4.46e-03 16 dl_chr2R_18553624_185536 3.68e-03 11 dl_chr3L_1445374_1445384 2.54e-03 11 dl_chr2L_2456749_2456764 8.77e-02 16 dl_chr2L_2456607_2456624 1.43e-03 5_[+1(6.50e-05)]_5 dl_chr2L_15475721_154757 8.27e-03 16 dl_chr2L_15475985_154760 1.00e-01 16 dl_chr3L_1445569_1445579 5.20e-04 1_[+1(6.50e-05)]_2 dl_chr2L_2456426_2456439 3.68e-02 14 dl_chr2L_2456800_2456816 4.96e-03 17 dl_chr2L_2456997_2457009 7.50e-02 13 dl_chr2L_2457011_2457028 3.42e-02 18 dl_chr2L_15476060_154760 5.31e-04 4_[+1(2.95e-05)]_4 dl_chr2L_15475577_154755 2.06e-02 16 dl_chr2L_15475489_154755 1.60e-02 16 dl_chr2R_18553608_185536 3.97e-03 11 dl_chr3L_1445510_1445520 5.20e-04 2_[-1(6.50e-05)]_1 dl_chr2R_18552809_185528 3.57e-03 11 dl_chr2L_2456702_2456718 3.11e-02 17 dl_chr2R_18552863_185528 4.59e-03 11 dl_chr2R_18553654_185536 1.53e-03 11 dl_chr2L_2456823_2456842 6.73e-02 20 dl_chr3R_2581170_2581180 9.22e-03 11 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************