******************************************************************************** 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/pan_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ pan_chr2R_5497589_549760 1.0000 13 pan_chr2R_5497302_549731 1.0000 11 pan_chr3R_22997606_22997 1.0000 19 pan_chr2L_3823277_382329 1.0000 20 pan_chr2L_3824297_382432 1.0000 26 pan_chr3R_22997264_22997 1.0000 22 pan_chr2L_3824209_382422 1.0000 18 pan_chr2R_5497500_549751 1.0000 16 pan_chr2L_3823211_382323 1.0000 26 pan_chr2R_5497348_549736 1.0000 14 pan_chr2R_5497184_549719 1.0000 14 pan_chr2L_3824346_382436 1.0000 21 pan_chr3R_22997687_22997 1.0000 22 pan_chr3R_22997065_22997 1.0000 19 pan_chr2L_3824023_382404 1.0000 26 pan_chr2R_5497525_549753 1.0000 14 pan_chr2L_3824173_382419 1.0000 23 pan_chr3R_22997245_22997 1.0000 16 pan_chr2R_5497332_549734 1.0000 11 pan_chr3R_22997591_22997 1.0000 10 pan_chr2L_3823447_382346 1.0000 23 pan_chr2L_3823994_382401 1.0000 25 pan_chr3R_22997400_22997 1.0000 18 pan_chr3R_22997721_22997 1.0000 15 pan_chr3R_22997361_22997 1.0000 25 ******************************************************************************** ******************************************************************************** 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/pan_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= 25 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 467 N= 25 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.318 C 0.182 G 0.182 T 0.318 Background letter frequencies (from dataset with add-one prior applied): A 0.317 C 0.183 G 0.183 T 0.317 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 25 llr = 108 E-value = 4.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 63:99843 pos.-specific C :19:::12 probability G 1:::::44 matrix T 26:1:121 bits 2.5 2.2 2.0 * 1.7 * Information 1.5 * content 1.2 ** (6.2 bits) 1.0 **** 0.7 **** 0.5 ***** 0.2 ******** 0.0 -------- Multilevel ATCAAAGG consensus TA AA sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- pan_chr2L_3823994_382401 - 9 3.92e-05 GACAAAACA ATCAAAGC AGCAACAA pan_chr2R_5497302_549731 + 1 3.92e-05 . ATCAAAGC GAC pan_chr3R_22997721_22997 + 5 7.33e-05 TTAT ATCAAAAG ATG pan_chr2L_3823211_382323 + 11 1.47e-04 ATATATAATT TTCAAAGG TCTTACGA pan_chr3R_22997065_22997 - 7 3.59e-04 TCAAG ATCAAAAA ATATTT pan_chr2L_3824023_382404 + 11 5.03e-04 TGTCTAAGAT ATCAAACG CACAGTGC pan_chr2L_3824346_382436 - 4 5.03e-04 ATCCTTTGGG ATCAAACG AAG pan_chr3R_22997245_22997 - 6 6.45e-04 TCG AACAAAAC GAAAT pan_chr2L_3824173_382419 + 11 6.45e-04 CAATTGTTCT AACAAAAC ATGCC pan_chr3R_22997606_22997 + 3 1.35e-03 AT TTCAAATG CGATCGCCG pan_chr2R_5497500_549751 - 5 1.40e-03 GGCA TCCAAAGG ATCG pan_chr2L_3824297_382432 + 11 1.65e-03 AAGTCCGGAC TTCAAAGT CCATTTCG pan_chr3R_22997400_22997 - 6 2.28e-03 AAAAT ACCAAAAA GAGCC pan_chr2L_3823447_382346 - 6 2.28e-03 TGACAACCGC GACAAAAC TAATT pan_chr3R_22997361_22997 - 17 2.79e-03 A AACTAAGC TCAGCGGATG pan_chr2R_5497525_549753 - 7 4.63e-03 . ATTAAAGG ACAACT pan_chr2R_5497184_549719 + 4 6.34e-03 GCC ATCAATTA GCA pan_chr2R_5497589_549760 + 4 7.44e-03 CTG ATCTAAAT AC pan_chr2L_3824209_382422 + 11 8.06e-03 ACACTATGGA CACAAAAA pan_chr3R_22997591_22997 + 2 1.28e-02 A TTCAATTA G pan_chr2R_5497332_549734 + 4 1.41e-02 CAC TTCACAGT pan_chr3R_22997687_22997 + 6 1.50e-02 GATGG AAAAAAGA GTCCGCAAG pan_chr2R_5497348_549736 - 5 2.11e-02 AT ATCTTAAG TGCC pan_chr2L_3823277_382329 - 3 2.42e-02 AAAAGATGAA GACAATTA TA pan_chr3R_22997264_22997 - 8 2.71e-02 AAATTTC GTCAGCGG TAAACTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- pan_chr2L_3823994_382401 3.9e-05 8_[-1]_9 pan_chr2R_5497302_549731 3.9e-05 [+1]_3 pan_chr3R_22997721_22997 7.3e-05 4_[+1]_3 pan_chr2L_3823211_382323 0.00015 10_[+1]_8 pan_chr3R_22997065_22997 0.00036 6_[-1]_5 pan_chr2L_3824023_382404 0.0005 10_[+1]_8 pan_chr2L_3824346_382436 0.0005 3_[-1]_10 pan_chr3R_22997245_22997 0.00064 5_[-1]_3 pan_chr2L_3824173_382419 0.00064 10_[+1]_5 pan_chr3R_22997606_22997 0.0013 2_[+1]_9 pan_chr2R_5497500_549751 0.0014 4_[-1]_4 pan_chr2L_3824297_382432 0.0017 10_[+1]_8 pan_chr3R_22997400_22997 0.0023 5_[-1]_5 pan_chr2L_3823447_382346 0.0023 5_[-1]_10 pan_chr3R_22997361_22997 0.0028 16_[-1]_1 pan_chr2R_5497525_549753 0.0046 6_[-1] pan_chr2R_5497184_549719 0.0063 3_[+1]_3 pan_chr2R_5497589_549760 0.0074 3_[+1]_2 pan_chr2L_3824209_382422 0.0081 10_[+1] pan_chr3R_22997591_22997 0.013 1_[+1]_1 pan_chr2R_5497332_549734 0.014 3_[+1] pan_chr3R_22997687_22997 0.015 5_[+1]_9 pan_chr2R_5497348_549736 0.021 4_[-1]_2 pan_chr2L_3823277_382329 0.024 2_[-1]_10 pan_chr3R_22997264_22997 0.027 7_[-1]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=25 pan_chr2L_3823994_382401 ( 9) ATCAAAGC 1 pan_chr2R_5497302_549731 ( 1) ATCAAAGC 1 pan_chr3R_22997721_22997 ( 5) ATCAAAAG 1 pan_chr2L_3823211_382323 ( 11) TTCAAAGG 1 pan_chr3R_22997065_22997 ( 7) ATCAAAAA 1 pan_chr2L_3824023_382404 ( 11) ATCAAACG 1 pan_chr2L_3824346_382436 ( 4) ATCAAACG 1 pan_chr3R_22997245_22997 ( 6) AACAAAAC 1 pan_chr2L_3824173_382419 ( 11) AACAAAAC 1 pan_chr3R_22997606_22997 ( 3) TTCAAATG 1 pan_chr2R_5497500_549751 ( 5) TCCAAAGG 1 pan_chr2L_3824297_382432 ( 11) TTCAAAGT 1 pan_chr3R_22997400_22997 ( 6) ACCAAAAA 1 pan_chr2L_3823447_382346 ( 6) GACAAAAC 1 pan_chr3R_22997361_22997 ( 17) AACTAAGC 1 pan_chr2R_5497525_549753 ( 7) ATTAAAGG 1 pan_chr2R_5497184_549719 ( 4) ATCAATTA 1 pan_chr2R_5497589_549760 ( 4) ATCTAAAT 1 pan_chr2L_3824209_382422 ( 11) CACAAAAA 1 pan_chr3R_22997591_22997 ( 2) TTCAATTA 1 pan_chr2R_5497332_549734 ( 4) TTCACAGT 1 pan_chr3R_22997687_22997 ( 6) AAAAAAGA 1 pan_chr2R_5497348_549736 ( 5) ATCTTAAG 1 pan_chr2L_3823277_382329 ( 3) GACAATTA 1 pan_chr3R_22997264_22997 ( 8) GTCAGCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 292 bayes= 3.41684 E= 4.6e+000 92 -219 -61 -40 -18 -119 -1129 101 -298 233 -1129 -298 147 -1129 -1129 -140 147 -219 -219 -298 140 -219 -1129 -140 18 -119 113 -99 -18 39 98 -140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 4.6e+000 0.600000 0.040000 0.120000 0.240000 0.280000 0.080000 0.000000 0.640000 0.040000 0.920000 0.000000 0.040000 0.880000 0.000000 0.000000 0.120000 0.880000 0.040000 0.040000 0.040000 0.840000 0.040000 0.000000 0.120000 0.360000 0.080000 0.400000 0.160000 0.280000 0.240000 0.360000 0.120000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT][TA]CAAA[GA][GAC] -------------------------------------------------------------------------------- Time 0.23 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- pan_chr2R_5497589_549760 8.57e-02 13 pan_chr2R_5497302_549731 3.14e-04 [+1(3.92e-05)]_3 pan_chr3R_22997606_22997 3.18e-02 19 pan_chr2L_3823277_382329 4.70e-01 20 pan_chr2L_3824297_382432 6.09e-02 26 pan_chr3R_22997264_22997 5.62e-01 22 pan_chr2L_3824209_382422 1.63e-01 18 pan_chr2R_5497500_549751 2.50e-02 16 pan_chr2L_3823211_382323 5.56e-03 26 pan_chr2R_5497348_549736 2.58e-01 14 pan_chr2R_5497184_549719 8.52e-02 14 pan_chr2L_3824346_382436 1.40e-02 21 pan_chr3R_22997687_22997 3.64e-01 22 pan_chr3R_22997065_22997 8.57e-03 19 pan_chr2L_3824023_382404 1.89e-02 26 pan_chr2R_5497525_549753 6.29e-02 14 pan_chr2L_3824173_382419 2.04e-02 23 pan_chr3R_22997245_22997 1.15e-02 16 pan_chr2R_5497332_549734 1.07e-01 11 pan_chr3R_22997591_22997 7.45e-02 10 pan_chr2L_3823447_382346 7.04e-02 23 pan_chr2L_3823994_382401 1.41e-03 8_[-1(3.92e-05)]_9 pan_chr3R_22997400_22997 4.90e-02 18 pan_chr3R_22997721_22997 1.17e-03 4_[+1(7.33e-05)]_3 pan_chr3R_22997361_22997 9.56e-02 25 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************