******************************************************************************** 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/Trl_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Trl_chr3L_14723092_14723 1.0000 19 Trl_chr3L_14722846_14722 1.0000 16 Trl_chr3L_14722510_14722 1.0000 7 Trl_chr3R_7782325_778234 1.0000 18 Trl_chr3R_2912768_291279 1.0000 28 Trl_chr3R_12589559_12589 1.0000 20 Trl_chr3L_14722415_14722 1.0000 19 Trl_chr3R_12589585_12589 1.0000 21 Trl_chr2R_20734155_20734 1.0000 12 Trl_chr3L_17584614_17584 1.0000 18 Trl_chr3R_2912848_291286 1.0000 14 Trl_chr2R_20734172_20734 1.0000 13 Trl_chr3L_14723706_14723 1.0000 13 Trl_chr3R_7782373_778240 1.0000 33 Trl_chr3R_12589906_12589 1.0000 13 Trl_chr3R_2912222_291223 1.0000 16 Trl_chr3R_12560279_12560 1.0000 18 Trl_chr3L_9351644_935166 1.0000 18 Trl_chr2L_21517250_21517 1.0000 13 Trl_chr3R_12560232_12560 1.0000 16 Trl_chr3R_12589526_12589 1.0000 20 Trl_chr3L_14723210_14723 1.0000 22 Trl_chr3L_14722636_14722 1.0000 22 Trl_chr3L_14723011_14723 1.0000 8 Trl_chr3R_12589730_12589 1.0000 33 Trl_chr2R_20734303_20734 1.0000 16 Trl_chr3R_12589608_12589 1.0000 11 Trl_chr3R_7782300_778231 1.0000 11 Trl_chr3L_14723240_14723 1.0000 18 Trl_chr3R_12589944_12589 1.0000 7 Trl_chr3L_17584708_17584 1.0000 16 Trl_chr3L_14723422_14723 1.0000 13 Trl_chr3R_12589864_12589 1.0000 13 Trl_chr3L_14722950_14722 1.0000 12 Trl_chr3L_17584756_17584 1.0000 26 Trl_chr3L_14723376_14723 1.0000 15 Trl_chr3L_14722540_14722 1.0000 20 Trl_chr3R_12589950_12589 1.0000 24 Trl_chr3R_2912203_291221 1.0000 13 Trl_chr2L_21441906_21441 1.0000 27 Trl_chr3L_14723789_14723 1.0000 9 Trl_chr3R_12590056_12590 1.0000 17 Trl_chr3L_14722699_14722 1.0000 18 Trl_chr3R_7782411_778243 1.0000 20 Trl_chr2L_14615550_14615 1.0000 30 Trl_chr3L_14722582_14722 1.0000 8 Trl_chr3L_9351436_935144 1.0000 13 Trl_chr3L_14723037_14723 1.0000 15 Trl_chr3L_9351685_935170 1.0000 22 Trl_chr3R_12560330_12560 1.0000 15 Trl_chr3L_14723469_14723 1.0000 21 Trl_chr3R_2912811_291282 1.0000 12 Trl_chr2L_14615337_14615 1.0000 33 Trl_chr3R_26677844_26677 1.0000 13 Trl_chr2R_20734273_20734 1.0000 14 Trl_chr3R_12589860_12589 1.0000 44 Trl_chr3R_12560184_12560 1.0000 21 Trl_chr3L_14723401_14723 1.0000 13 Trl_chr3L_14723144_14723 1.0000 15 Trl_chr3L_14722611_14722 1.0000 14 Trl_chr3L_17584662_17584 1.0000 11 Trl_chr3L_9351404_935142 1.0000 25 Trl_chr3L_14722977_14722 1.0000 10 Trl_chr3R_12590367_12590 1.0000 27 Trl_chr2R_20734356_20734 1.0000 12 Trl_chr2R_20734105_20734 1.0000 15 Trl_chr3R_2912174_291219 1.0000 17 Trl_chr3L_17584728_17584 1.0000 16 Trl_chr3L_14723440_14723 1.0000 12 Trl_chr3R_12589983_12590 1.0000 23 Trl_chr3L_14723286_14723 1.0000 16 Trl_chr3L_14722665_14722 1.0000 21 Trl_chr3L_14722469_14722 1.0000 8 Trl_chr2L_2454725_245473 1.0000 8 Trl_chr3L_17584678_17584 1.0000 18 Trl_chr3R_12590719_12590 1.0000 34 Trl_chr3L_14722884_14722 1.0000 14 Trl_chr3R_12589700_12589 1.0000 27 Trl_chr3R_12589987_12589 1.0000 7 ******************************************************************************** ******************************************************************************** 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/Trl_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= 79 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 1380 N= 79 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.254 C 0.246 G 0.246 T 0.254 Background letter frequencies (from dataset with add-one prior applied): A 0.254 C 0.246 G 0.246 T 0.254 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 6 sites = 73 llr = 398 E-value = 3.1e-050 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 7:a:62 pos.-specific C 1:::31 probability G 1a:a:7 matrix T 2:::1: bits 2.0 * 1.8 * * 1.6 *** 1.4 *** Information 1.2 *** content 1.0 *** (7.9 bits) 0.8 ***** 0.6 ****** 0.4 ****** 0.2 ****** 0.0 ------ Multilevel AGAGAG consensus CA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ Trl_chr3R_12589987_12589 + 2 2.44e-04 G AGAGAG Trl_chr3R_12589983_12590 - 10 2.44e-04 TCAAAAAG AGAGAG GGCTATTCC Trl_chr3L_17584728_17584 + 3 2.44e-04 TA AGAGAG CGGAATGC Trl_chr2R_20734356_20734 - 4 2.44e-04 GGT AGAGAG ATT Trl_chr3L_9351404_935142 + 1 2.44e-04 . AGAGAG AGAGAAGAGA Trl_chr3R_12589860_12589 + 12 2.44e-04 GCGACTGCGG AGAGAG GGAGAGATAC Trl_chr3L_9351436_935144 + 2 2.44e-04 C AGAGAG AAAAAA Trl_chr3R_12590056_12590 + 6 2.44e-04 GGCCT AGAGAG CAGTAG Trl_chr2L_21441906_21441 - 3 2.44e-04 AGAGAGAGAG AGAGAG AA Trl_chr3R_2912203_291221 + 3 2.44e-04 TT AGAGAG ACCAA Trl_chr3L_17584756_17584 + 13 2.44e-04 GGAGAGCCAA AGAGAG TAGGGAGC Trl_chr3R_12589864_12589 - 7 2.44e-04 G AGAGAG GGAGAG Trl_chr3L_17584708_17584 + 3 2.44e-04 GT AGAGAG CGCAAGCG Trl_chr3R_12589730_12589 + 1 2.44e-04 . AGAGAG CACCAAACAA Trl_chr3L_14722636_14722 - 3 2.44e-04 AGAGAGAGAG AGAGAG CT Trl_chr3R_12560232_12560 + 7 2.44e-04 AGAAAC AGAGAG CCAG Trl_chr2L_21517250_21517 + 4 2.44e-04 CCG AGAGAG TACG Trl_chr3L_9351644_935166 + 7 2.44e-04 TGAGTG AGAGAG CCGAAG Trl_chr3R_12560279_12560 - 10 2.44e-04 AAG AGAGAG CGCAAGAGC Trl_chr3R_7782373_778240 - 21 2.44e-04 CAGAGTG AGAGAG CAATAGTACA Trl_chr3R_12589585_12589 + 10 2.44e-04 ATACGAGTT AGAGAG AGTCCC Trl_chr3R_12589559_12589 - 5 2.44e-04 TGCTAGAGCG AGAGAG CAGC Trl_chr3R_2912768_291279 + 19 2.44e-04 GAAAATGGCG AGAGAG TAAA Trl_chr3R_7782325_778234 + 7 2.44e-04 GCTTCG AGAGAG CGCGCC Trl_chr3L_17584678_17584 - 5 4.80e-04 TGAAGTTC AGAGCG TGAA Trl_chr3L_14722665_14722 - 12 4.80e-04 TGCG AGAGCG GGAGAGTGAG Trl_chr3L_14723401_14723 - 4 4.80e-04 TCAA AGAGCG TTG Trl_chr3L_9351685_935170 + 8 4.80e-04 TCTAGAA AGAGCG CAAAAGAAA Trl_chr3L_14722699_14722 + 1 4.80e-04 . AGAGCG CGCGAGAGCG Trl_chr3R_12589950_12589 - 12 4.80e-04 GTGCGTA AGAGCG AGATACAGAT Trl_chr3R_7782300_778231 + 3 4.80e-04 AA AGAGCG CCG Trl_chr3R_12589906_12589 - 3 4.80e-04 AAGCG AGAGCG AT Trl_chr2R_20734172_20734 + 7 4.80e-04 CGAGAC AGAGCG T Trl_chr3R_12589700_12589 + 9 7.32e-04 AACCAGCG AGAGAA GAAAGAGCAA Trl_chr3L_14723286_14723 - 1 7.32e-04 CTCCCCGAGT AGAGAA Trl_chr3L_17584662_17584 + 2 7.32e-04 C AGAGAA ACGC Trl_chr3L_14723144_14723 - 3 7.32e-04 AAGAGAA AGAGAA GG Trl_chr3R_7782411_778243 - 6 7.32e-04 AAAACGAAT AGAGAA TAACG Trl_chr3L_14723376_14723 + 7 7.32e-04 TCTATG AGAGAA GTG Trl_chr3R_2912848_291286 - 2 9.76e-04 GTGCGAG TGAGAG A Trl_chr2L_2454725_245473 + 3 1.22e-03 GA AGAGCA Trl_chr3R_2912811_291282 + 5 1.22e-03 AAGT AGAGCA AA Trl_chr3L_14723469_14723 + 9 1.22e-03 TGGAGAGG AGAGCA AGACGGC Trl_chr3L_14722540_14722 - 8 1.22e-03 AAGAGGA AGAGCA AAGGGAG Trl_chr2R_20734105_20734 + 5 1.69e-03 CGTG TGAGCG GGAGA Trl_chr3L_14723037_14723 - 1 1.69e-03 TGCGCTCCG TGAGCG Trl_chr3R_12589526_12589 + 9 1.69e-03 TGCGGTAT GGAGAG ATGCGC Trl_chr3R_2912222_291223 - 5 1.69e-03 GAAGTG GGAGAG GTAA Trl_chr3L_17584614_17584 - 6 1.69e-03 GTGTGCG TGAGCG GGTCT Trl_chr3L_14723706_14723 - 4 1.94e-03 ATTC AGAGTG GAG Trl_chr3L_14723011_14723 - 1 2.18e-03 CA AGAGAC Trl_chr2L_14615337_14615 - 18 2.67e-03 GAAAGTGCAC TGAGAA ACAAATAAGT Trl_chr3R_12560330_12560 - 5 2.67e-03 ATGAA CGAGAG GCGC Trl_chr3R_12589608_12589 + 2 2.67e-03 G CGAGAG CTTT Trl_chr2R_20734155_20734 + 4 2.67e-03 GAG TGAGAA TCT Trl_chr3L_14723440_14723 + 4 2.89e-03 GAT GGAGCG CAG Trl_chr3L_14723092_14723 + 11 2.89e-03 TCTTCTCACC GGAGCG CAA Trl_chr3R_26677844_26677 - 7 3.85e-03 T TGAGCA AGGAAC Trl_chr3L_14723422_14723 + 4 3.85e-03 TGT CGAGCG GCAT Trl_chr3R_12590719_12590 - 9 4.10e-03 TTATCTCATA AGAGTA ACTCGAAA Trl_chr3L_14722611_14722 + 5 4.10e-03 AAAA AGAGTA CAGA Trl_chr3R_12590367_12590 - 17 4.34e-03 TTTTA TGAGTG CATCCAAAGT Trl_chr3L_14722977_14722 - 2 4.34e-03 AAC TGAGTG A Trl_chr3R_12560184_12560 - 15 4.59e-03 G AGTGAG TTGAGTCGGC Trl_chr2L_14615550_14615 - 14 5.31e-03 ACAACTGCAC TGAGAC AATAATGCAT Trl_chr3L_14722950_14722 + 2 5.31e-03 A TGAGAC ACGCA Trl_chr3L_14723240_14723 - 13 5.31e-03 . GGAGCA GCGAAATTCG Trl_chr3L_14723210_14723 + 9 5.31e-03 ACTCGAAC TGAGAC TGAGTAAA Trl_chr3L_14722415_14722 - 11 6.98e-03 GTT GGAGAC AAATAGCAGC Trl_chr3L_14722846_14722 + 1 8.67e-03 . AGCGCG CCACATTTAA Trl_chr3L_14722884_14722 - 1 1.08e-02 TCTGAGTT TGTGCG Trl_chr2R_20734273_20734 + 5 1.18e-02 ACCG CGAGTA ATAT Trl_chr3L_14722469_14722 - 2 1.47e-02 T GAAGAG A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Trl_chr3R_12589987_12589 0.00024 1_[+1] Trl_chr3R_12589983_12590 0.00024 9_[-1]_8 Trl_chr3L_17584728_17584 0.00024 2_[+1]_8 Trl_chr2R_20734356_20734 0.00024 3_[-1]_3 Trl_chr3L_9351404_935142 0.00024 [+1]_19 Trl_chr3R_12589860_12589 0.00024 11_[+1]_27 Trl_chr3L_9351436_935144 0.00024 1_[+1]_6 Trl_chr3R_12590056_12590 0.00024 5_[+1]_6 Trl_chr2L_21441906_21441 0.00024 2_[-1]_19 Trl_chr3R_2912203_291221 0.00024 2_[+1]_5 Trl_chr3L_17584756_17584 0.00024 12_[+1]_8 Trl_chr3R_12589864_12589 0.00024 6_[-1]_1 Trl_chr3L_17584708_17584 0.00024 2_[+1]_8 Trl_chr3R_12589730_12589 0.00024 [+1]_27 Trl_chr3L_14722636_14722 0.00024 2_[-1]_14 Trl_chr3R_12560232_12560 0.00024 6_[+1]_4 Trl_chr2L_21517250_21517 0.00024 3_[+1]_4 Trl_chr3L_9351644_935166 0.00024 6_[+1]_6 Trl_chr3R_12560279_12560 0.00024 9_[-1]_3 Trl_chr3R_7782373_778240 0.00024 20_[-1]_7 Trl_chr3R_12589585_12589 0.00024 9_[+1]_6 Trl_chr3R_12589559_12589 0.00024 4_[-1]_10 Trl_chr3R_2912768_291279 0.00024 18_[+1]_4 Trl_chr3R_7782325_778234 0.00024 6_[+1]_6 Trl_chr3L_17584678_17584 0.00048 4_[-1]_8 Trl_chr3L_14722665_14722 0.00048 11_[-1]_4 Trl_chr3L_14723401_14723 0.00048 3_[-1]_4 Trl_chr3L_9351685_935170 0.00048 7_[+1]_9 Trl_chr3L_14722699_14722 0.00048 [+1]_12 Trl_chr3R_12589950_12589 0.00048 11_[-1]_7 Trl_chr3R_7782300_778231 0.00048 2_[+1]_3 Trl_chr3R_12589906_12589 0.00048 2_[-1]_5 Trl_chr2R_20734172_20734 0.00048 6_[+1]_1 Trl_chr3R_12589700_12589 0.00073 8_[+1]_13 Trl_chr3L_14723286_14723 0.00073 [-1]_10 Trl_chr3L_17584662_17584 0.00073 1_[+1]_4 Trl_chr3L_14723144_14723 0.00073 2_[-1]_7 Trl_chr3R_7782411_778243 0.00073 5_[-1]_9 Trl_chr3L_14723376_14723 0.00073 6_[+1]_3 Trl_chr3R_2912848_291286 0.00098 1_[-1]_7 Trl_chr2L_2454725_245473 0.0012 2_[+1] Trl_chr3R_2912811_291282 0.0012 4_[+1]_2 Trl_chr3L_14723469_14723 0.0012 8_[+1]_7 Trl_chr3L_14722540_14722 0.0012 7_[-1]_7 Trl_chr2R_20734105_20734 0.0017 4_[+1]_5 Trl_chr3L_14723037_14723 0.0017 [-1]_9 Trl_chr3R_12589526_12589 0.0017 8_[+1]_6 Trl_chr3R_2912222_291223 0.0017 4_[-1]_6 Trl_chr3L_17584614_17584 0.0017 5_[-1]_7 Trl_chr3L_14723706_14723 0.0019 3_[-1]_4 Trl_chr3L_14723011_14723 0.0022 [-1]_2 Trl_chr2L_14615337_14615 0.0027 17_[-1]_10 Trl_chr3R_12560330_12560 0.0027 4_[-1]_5 Trl_chr3R_12589608_12589 0.0027 1_[+1]_4 Trl_chr2R_20734155_20734 0.0027 3_[+1]_3 Trl_chr3L_14723440_14723 0.0029 3_[+1]_3 Trl_chr3L_14723092_14723 0.0029 10_[+1]_3 Trl_chr3R_26677844_26677 0.0038 6_[-1]_1 Trl_chr3L_14723422_14723 0.0038 3_[+1]_4 Trl_chr3R_12590719_12590 0.0041 8_[-1]_20 Trl_chr3L_14722611_14722 0.0041 4_[+1]_4 Trl_chr3R_12590367_12590 0.0043 16_[-1]_5 Trl_chr3L_14722977_14722 0.0043 1_[-1]_3 Trl_chr3R_12560184_12560 0.0046 14_[-1]_1 Trl_chr2L_14615550_14615 0.0053 13_[-1]_11 Trl_chr3L_14722950_14722 0.0053 1_[+1]_5 Trl_chr3L_14723240_14723 0.0053 12_[-1] Trl_chr3L_14723210_14723 0.0053 8_[+1]_8 Trl_chr3L_14722415_14722 0.007 10_[-1]_3 Trl_chr3L_14722846_14722 0.0087 [+1]_10 Trl_chr3L_14722884_14722 0.011 [-1]_8 Trl_chr2R_20734273_20734 0.012 4_[+1]_4 Trl_chr3L_14722469_14722 0.015 1_[-1]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=6 seqs=73 Trl_chr3R_12589987_12589 ( 2) AGAGAG 1 Trl_chr3R_12589983_12590 ( 10) AGAGAG 1 Trl_chr3L_17584728_17584 ( 3) AGAGAG 1 Trl_chr2R_20734356_20734 ( 4) AGAGAG 1 Trl_chr3L_9351404_935142 ( 1) AGAGAG 1 Trl_chr3R_12589860_12589 ( 12) AGAGAG 1 Trl_chr3L_9351436_935144 ( 2) AGAGAG 1 Trl_chr3R_12590056_12590 ( 6) AGAGAG 1 Trl_chr2L_21441906_21441 ( 3) AGAGAG 1 Trl_chr3R_2912203_291221 ( 3) AGAGAG 1 Trl_chr3L_17584756_17584 ( 13) AGAGAG 1 Trl_chr3R_12589864_12589 ( 7) AGAGAG 1 Trl_chr3L_17584708_17584 ( 3) AGAGAG 1 Trl_chr3R_12589730_12589 ( 1) AGAGAG 1 Trl_chr3L_14722636_14722 ( 3) AGAGAG 1 Trl_chr3R_12560232_12560 ( 7) AGAGAG 1 Trl_chr2L_21517250_21517 ( 4) AGAGAG 1 Trl_chr3L_9351644_935166 ( 7) AGAGAG 1 Trl_chr3R_12560279_12560 ( 10) AGAGAG 1 Trl_chr3R_7782373_778240 ( 21) AGAGAG 1 Trl_chr3R_12589585_12589 ( 10) AGAGAG 1 Trl_chr3R_12589559_12589 ( 5) AGAGAG 1 Trl_chr3R_2912768_291279 ( 19) AGAGAG 1 Trl_chr3R_7782325_778234 ( 7) AGAGAG 1 Trl_chr3L_17584678_17584 ( 5) AGAGCG 1 Trl_chr3L_14722665_14722 ( 12) AGAGCG 1 Trl_chr3L_14723401_14723 ( 4) AGAGCG 1 Trl_chr3L_9351685_935170 ( 8) AGAGCG 1 Trl_chr3L_14722699_14722 ( 1) AGAGCG 1 Trl_chr3R_12589950_12589 ( 12) AGAGCG 1 Trl_chr3R_7782300_778231 ( 3) AGAGCG 1 Trl_chr3R_12589906_12589 ( 3) AGAGCG 1 Trl_chr2R_20734172_20734 ( 7) AGAGCG 1 Trl_chr3R_12589700_12589 ( 9) AGAGAA 1 Trl_chr3L_14723286_14723 ( 1) AGAGAA 1 Trl_chr3L_17584662_17584 ( 2) AGAGAA 1 Trl_chr3L_14723144_14723 ( 3) AGAGAA 1 Trl_chr3R_7782411_778243 ( 6) AGAGAA 1 Trl_chr3L_14723376_14723 ( 7) AGAGAA 1 Trl_chr3R_2912848_291286 ( 2) TGAGAG 1 Trl_chr2L_2454725_245473 ( 3) AGAGCA 1 Trl_chr3R_2912811_291282 ( 5) AGAGCA 1 Trl_chr3L_14723469_14723 ( 9) AGAGCA 1 Trl_chr3L_14722540_14722 ( 8) AGAGCA 1 Trl_chr2R_20734105_20734 ( 5) TGAGCG 1 Trl_chr3L_14723037_14723 ( 1) TGAGCG 1 Trl_chr3R_12589526_12589 ( 9) GGAGAG 1 Trl_chr3R_2912222_291223 ( 5) GGAGAG 1 Trl_chr3L_17584614_17584 ( 6) TGAGCG 1 Trl_chr3L_14723706_14723 ( 4) AGAGTG 1 Trl_chr3L_14723011_14723 ( 1) AGAGAC 1 Trl_chr2L_14615337_14615 ( 18) TGAGAA 1 Trl_chr3R_12560330_12560 ( 5) CGAGAG 1 Trl_chr3R_12589608_12589 ( 2) CGAGAG 1 Trl_chr2R_20734155_20734 ( 4) TGAGAA 1 Trl_chr3L_14723440_14723 ( 4) GGAGCG 1 Trl_chr3L_14723092_14723 ( 11) GGAGCG 1 Trl_chr3R_26677844_26677 ( 7) TGAGCA 1 Trl_chr3L_14723422_14723 ( 4) CGAGCG 1 Trl_chr3R_12590719_12590 ( 9) AGAGTA 1 Trl_chr3L_14722611_14722 ( 5) AGAGTA 1 Trl_chr3R_12590367_12590 ( 17) TGAGTG 1 Trl_chr3L_14722977_14722 ( 2) TGAGTG 1 Trl_chr3R_12560184_12560 ( 15) AGTGAG 1 Trl_chr2L_14615550_14615 ( 14) TGAGAC 1 Trl_chr3L_14722950_14722 ( 2) TGAGAC 1 Trl_chr3L_14723240_14723 ( 13) GGAGCA 1 Trl_chr3L_14723210_14723 ( 9) TGAGAC 1 Trl_chr3L_14722415_14722 ( 11) GGAGAC 1 Trl_chr3L_14722846_14722 ( 1) AGCGCG 1 Trl_chr3L_14722884_14722 ( 1) TGTGCG 1 Trl_chr2R_20734273_20734 ( 5) CGAGTA 1 Trl_chr3L_14722469_14722 ( 2) GAAGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 985 bayes= 4.55474 E= 3.1e-050 140 -216 -136 -51 -421 -1283 201 -1283 191 -416 -1283 -321 -1283 -1283 203 -1283 124 36 -1283 -163 -13 -184 151 -1283 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 73 E= 3.1e-050 0.671233 0.054795 0.095890 0.178082 0.013699 0.000000 0.986301 0.000000 0.958904 0.013699 0.000000 0.027397 0.000000 0.000000 1.000000 0.000000 0.602740 0.315068 0.000000 0.082192 0.232877 0.068493 0.698630 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- AGAG[AC][GA] -------------------------------------------------------------------------------- Time 1.22 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Trl_chr3L_14723092_14723 7.21e-02 19 Trl_chr3L_14722846_14722 1.74e-01 16 Trl_chr3L_14722510_14722 2.50e-01 7 Trl_chr3R_7782325_778234 6.32e-03 18 Trl_chr3R_2912768_291279 1.12e-02 28 Trl_chr3R_12589559_12589 7.29e-03 20 Trl_chr3L_14722415_14722 1.78e-01 19 Trl_chr3R_12589585_12589 7.78e-03 21 Trl_chr2R_20734155_20734 3.67e-02 12 Trl_chr3L_17584614_17584 4.31e-02 18 Trl_chr3R_2912848_291286 1.74e-02 14 Trl_chr2R_20734172_20734 7.64e-03 13 Trl_chr3L_14723706_14723 3.05e-02 13 Trl_chr3R_7782373_778240 1.36e-02 33 Trl_chr3R_12589906_12589 7.64e-03 13 Trl_chr3R_2912222_291223 3.66e-02 16 Trl_chr3R_12560279_12560 6.32e-03 18 Trl_chr3L_9351644_935166 6.32e-03 18 Trl_chr2L_21517250_21517 3.90e-03 13 Trl_chr3R_12560232_12560 5.35e-03 16 Trl_chr3R_12589526_12589 4.95e-02 20 Trl_chr3L_14723210_14723 1.66e-01 22 Trl_chr3L_14722636_14722 8.26e-03 22 Trl_chr3L_14723011_14723 1.30e-02 8 Trl_chr3R_12589730_12589 1.36e-02 33 Trl_chr2R_20734303_20734 4.12e-01 16 Trl_chr3R_12589608_12589 3.15e-02 11 Trl_chr3R_7782300_778231 5.74e-03 11 Trl_chr3L_14723240_14723 1.29e-01 18 Trl_chr3R_12589944_12589 2.34e-01 7 Trl_chr3L_17584708_17584 5.35e-03 16 Trl_chr3L_14723422_14723 5.98e-02 13 Trl_chr3R_12589864_12589 3.90e-03 13 Trl_chr3L_14722950_14722 7.18e-02 12 Trl_chr3L_17584756_17584 1.02e-02 26 Trl_chr3L_14723376_14723 1.45e-02 15 Trl_chr3L_14722540_14722 3.60e-02 20 Trl_chr3R_12589950_12589 1.81e-02 24 Trl_chr3R_2912203_291221 3.90e-03 13 Trl_chr2L_21441906_21441 1.07e-02 27 Trl_chr3L_14723789_14723 5.57e-01 9 Trl_chr3R_12590056_12590 5.84e-03 17 Trl_chr3L_14722699_14722 1.24e-02 18 Trl_chr3R_7782411_778243 2.17e-02 20 Trl_chr2L_14615550_14615 2.34e-01 30 Trl_chr3L_14722582_14722 5.63e-01 8 Trl_chr3L_9351436_935144 3.90e-03 13 Trl_chr3L_14723037_14723 3.33e-02 15 Trl_chr3L_9351685_935170 1.62e-02 22 Trl_chr3R_12560330_12560 5.20e-02 15 Trl_chr3L_14723469_14723 3.83e-02 21 Trl_chr3R_2912811_291282 1.69e-02 12 Trl_chr2L_14615337_14615 1.39e-01 33 Trl_chr3R_26677844_26677 5.98e-02 13 Trl_chr2R_20734273_20734 1.92e-01 14 Trl_chr3R_12589860_12589 1.88e-02 44 Trl_chr3R_12560184_12560 1.37e-01 21 Trl_chr3L_14723401_14723 7.64e-03 13 Trl_chr3L_14723144_14723 1.45e-02 15 Trl_chr3L_14722611_14722 7.13e-02 14 Trl_chr3L_17584662_17584 8.75e-03 11 Trl_chr3L_9351404_935142 9.71e-03 25 Trl_chr3L_14722977_14722 4.26e-02 10 Trl_chr3R_12590367_12590 1.74e-01 27 Trl_chr2R_20734356_20734 3.41e-03 12 Trl_chr2R_20734105_20734 3.33e-02 15 Trl_chr3R_2912174_291219 9.50e-01 17 Trl_chr3L_17584728_17584 5.35e-03 16 Trl_chr3L_14723440_14723 3.98e-02 12 Trl_chr3R_12589983_12590 8.74e-03 23 Trl_chr3L_14723286_14723 1.60e-02 16 Trl_chr3L_14722665_14722 1.52e-02 21 Trl_chr3L_14722469_14722 8.49e-02 8 Trl_chr2L_2454725_245473 7.30e-03 8 Trl_chr3L_17584678_17584 1.24e-02 18 Trl_chr3R_12590719_12590 2.12e-01 34 Trl_chr3L_14722884_14722 1.78e-01 14 Trl_chr3R_12589700_12589 3.17e-02 27 Trl_chr3R_12589987_12589 9.76e-04 7 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************