******************************************************************************** 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/kni_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ kni_chr3L_8638757_863876 1.0000 10 kni_chr3L_8639165_863917 1.0000 8 kni_chr3R_12598893_12598 1.0000 9 kni_chr3L_8640869_864091 1.0000 45 kni_chr3L_8639837_863984 1.0000 8 kni_chr3L_8641321_864133 1.0000 10 kni_chr2R_5487392_548740 1.0000 15 kni_chr3L_8639855_863986 1.0000 8 kni_chr2R_5487348_548736 1.0000 14 kni_chr3L_8639618_863962 1.0000 8 kni_chr3L_8640806_864082 1.0000 20 kni_chr3R_12600037_12600 1.0000 9 kni_chr3L_8639485_863949 1.0000 8 kni_chr2R_5487415_548742 1.0000 15 kni_chr3R_12599333_12599 1.0000 19 kni_chr3L_8639911_863992 1.0000 10 kni_chr3L_8638865_863889 1.0000 32 kni_chr3L_8640835_864085 1.0000 23 kni_chr3L_8639054_863906 1.0000 8 kni_chr3L_8639669_863967 1.0000 8 kni_chr3L_8639403_863941 1.0000 8 kni_chr3R_12598704_12598 1.0000 9 kni_chr2R_5487618_548762 1.0000 11 kni_chr3L_8639070_863907 1.0000 8 kni_chr2R_5487573_548758 1.0000 13 kni_chr3L_8638573_863859 1.0000 24 kni_chr3L_8639096_863910 1.0000 8 kni_chr2R_20730884_20730 1.0000 16 kni_chr3R_12599841_12599 1.0000 9 kni_chr3L_8639205_863921 1.0000 8 kni_chr3L_8639539_863954 1.0000 8 kni_chr3L_8638500_863850 1.0000 10 kni_chr3L_8639264_863927 1.0000 8 ******************************************************************************** ******************************************************************************** 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/kni_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= 33 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 427 N= 33 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.286 C 0.214 G 0.214 T 0.286 Background letter frequencies (from dataset with add-one prior applied): A 0.285 C 0.215 G 0.215 T 0.285 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 33 llr = 107 E-value = 1.3e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 252:1533 pos.-specific C 122a1221 probability G 7:1:1131 matrix T 125:7226 bits 2.2 * 2.0 * 1.8 * 1.6 * Information 1.3 * content 1.1 * (4.7 bits) 0.9 * 0.7 * * 0.4 ** ** * 0.2 ***** * 0.0 -------- Multilevel GATCTAAT consensus TA CGA sequence C TC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- kni_chr2R_5487348_548736 - 6 1.87e-05 T GATCTAGT TTTCT kni_chr2R_5487573_548758 - 6 6.23e-05 . GATCTACT TTCCT kni_chr3L_8638573_863859 + 15 7.64e-05 TCAATGTTCT GATCTCGT TC kni_chr3L_8639669_863967 + 1 2.89e-04 . GCTCTACT kni_chr3L_8639911_863992 - 1 2.89e-04 GC GCTCTACT kni_chr3L_8638865_863889 + 23 4.72e-04 CCCATTTTTT GTTCTAAT TA kni_chr3L_8639837_863984 + 1 1.04e-03 . GATCTGGA kni_chr2R_20730884_20730 + 4 1.44e-03 ACT GAACTAAA TCCGG kni_chr2R_5487392_548740 + 7 2.57e-03 CCCGGT GCTCTCTT T kni_chr3L_8639205_863921 - 1 2.98e-03 . GCCCTCAT kni_chr3L_8640869_864091 - 32 2.98e-03 GACACC GAACTGAT TTGAACTGAA kni_chr3R_12598893_12598 - 2 2.98e-03 . GTTCCAGT T kni_chr3L_8641321_864133 - 3 3.84e-03 . GATCGTCT TT kni_chr2R_5487618_548762 + 3 4.39e-03 CT GCGCTAGT T kni_chr3L_8639855_863986 + 1 6.19e-03 . GAACTAGG kni_chr3L_8639264_863927 - 1 6.87e-03 . AATCTTGA kni_chr2R_5487415_548742 + 8 7.79e-03 TGGCCGC GTTCCCAT kni_chr3L_8640806_864082 - 13 7.79e-03 . GATCGTAA AAAACTGCGA kni_chr3L_8638500_863850 + 1 8.68e-03 . GACCGAAA TA kni_chr3L_8639165_863917 + 1 9.58e-03 . AATCTGGA kni_chr3R_12598704_12598 + 1 1.09e-02 . GACCCATT T kni_chr3L_8639485_863949 + 1 1.09e-02 . AACCTAAA kni_chr3L_8640835_864085 + 7 1.30e-02 TTTTAC GACCTCCG TCCGTTTTT kni_chr3L_8639539_863954 + 1 3.04e-02 . ATACTCGA kni_chr3R_12600037_12600 + 2 3.04e-02 A GCTCATTT kni_chr3L_8639054_863906 + 1 4.33e-02 . TTTCTTTT kni_chr3L_8639070_863907 - 1 4.60e-02 . CCACTTCT kni_chr3R_12599333_12599 - 1 5.20e-02 AATATGAAAC AATCATAA kni_chr3L_8639403_863941 - 1 5.82e-02 . ATTCTGGC kni_chr3L_8639618_863962 - 1 5.82e-02 . TTACTCCA kni_chr3L_8638757_863876 + 1 6.17e-02 . GAGCGACC TG kni_chr3R_12599841_12599 + 1 6.82e-02 . TTCCCAAT T kni_chr3L_8639096_863910 - 1 9.33e-02 . CAACAATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- kni_chr2R_5487348_548736 1.9e-05 5_[-1]_1 kni_chr2R_5487573_548758 6.2e-05 5_[-1] kni_chr3L_8638573_863859 7.6e-05 14_[+1]_2 kni_chr3L_8639669_863967 0.00029 [+1] kni_chr3L_8639911_863992 0.00029 [-1]_2 kni_chr3L_8638865_863889 0.00047 22_[+1]_2 kni_chr3L_8639837_863984 0.001 [+1] kni_chr2R_20730884_20730 0.0014 3_[+1]_5 kni_chr2R_5487392_548740 0.0026 6_[+1]_1 kni_chr3L_8639205_863921 0.003 [-1] kni_chr3L_8640869_864091 0.003 31_[-1]_6 kni_chr3R_12598893_12598 0.003 1_[-1] kni_chr3L_8641321_864133 0.0038 2_[-1] kni_chr2R_5487618_548762 0.0044 2_[+1]_1 kni_chr3L_8639855_863986 0.0062 [+1] kni_chr3L_8639264_863927 0.0069 [-1] kni_chr2R_5487415_548742 0.0078 7_[+1] kni_chr3L_8640806_864082 0.0078 12_[-1] kni_chr3L_8638500_863850 0.0087 [+1]_2 kni_chr3L_8639165_863917 0.0096 [+1] kni_chr3R_12598704_12598 0.011 [+1]_1 kni_chr3L_8639485_863949 0.011 [+1] kni_chr3L_8640835_864085 0.013 6_[+1]_9 kni_chr3L_8639539_863954 0.03 [+1] kni_chr3R_12600037_12600 0.03 1_[+1] kni_chr3L_8639054_863906 0.043 [+1] kni_chr3L_8639070_863907 0.046 [-1] kni_chr3R_12599333_12599 0.052 [-1]_11 kni_chr3L_8639403_863941 0.058 [-1] kni_chr3L_8639618_863962 0.058 [-1] kni_chr3L_8638757_863876 0.062 [+1]_2 kni_chr3R_12599841_12599 0.068 [+1]_1 kni_chr3L_8639096_863910 0.093 [-1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=33 kni_chr2R_5487348_548736 ( 6) GATCTAGT 1 kni_chr2R_5487573_548758 ( 6) GATCTACT 1 kni_chr3L_8638573_863859 ( 15) GATCTCGT 1 kni_chr3L_8639669_863967 ( 1) GCTCTACT 1 kni_chr3L_8639911_863992 ( 1) GCTCTACT 1 kni_chr3L_8638865_863889 ( 23) GTTCTAAT 1 kni_chr3L_8639837_863984 ( 1) GATCTGGA 1 kni_chr2R_20730884_20730 ( 4) GAACTAAA 1 kni_chr2R_5487392_548740 ( 7) GCTCTCTT 1 kni_chr3L_8639205_863921 ( 1) GCCCTCAT 1 kni_chr3L_8640869_864091 ( 32) GAACTGAT 1 kni_chr3R_12598893_12598 ( 2) GTTCCAGT 1 kni_chr3L_8641321_864133 ( 3) GATCGTCT 1 kni_chr2R_5487618_548762 ( 3) GCGCTAGT 1 kni_chr3L_8639855_863986 ( 1) GAACTAGG 1 kni_chr3L_8639264_863927 ( 1) AATCTTGA 1 kni_chr2R_5487415_548742 ( 8) GTTCCCAT 1 kni_chr3L_8640806_864082 ( 13) GATCGTAA 1 kni_chr3L_8638500_863850 ( 1) GACCGAAA 1 kni_chr3L_8639165_863917 ( 1) AATCTGGA 1 kni_chr3R_12598704_12598 ( 1) GACCCATT 1 kni_chr3L_8639485_863949 ( 1) AACCTAAA 1 kni_chr3L_8640835_864085 ( 7) GACCTCCG 1 kni_chr3L_8639539_863954 ( 1) ATACTCGA 1 kni_chr3R_12600037_12600 ( 2) GCTCATTT 1 kni_chr3L_8639054_863906 ( 1) TTTCTTTT 1 kni_chr3L_8639070_863907 ( 1) CCACTTCT 1 kni_chr3R_12599333_12599 ( 1) AATCATAA 1 kni_chr3L_8639403_863941 ( 1) ATTCTGGC 1 kni_chr3L_8639618_863962 ( 1) TTACTCCA 1 kni_chr3L_8638757_863876 ( 1) GAGCGACC 1 kni_chr3R_12599841_12599 ( 1) TTCCCAAT 1 kni_chr3L_8639096_863910 ( 1) CAACAATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 196 bayes= 2.3468 E= 1.3e-006 -65 -182 163 -165 93 -2 -1169 -24 -43 -24 -182 93 -1169 222 -1169 -1169 -165 -82 -82 122 67 -2 -82 -43 9 18 50 -91 9 -182 -182 101 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 1.3e-006 0.181818 0.060606 0.666667 0.090909 0.545455 0.212121 0.000000 0.242424 0.212121 0.181818 0.060606 0.545455 0.000000 1.000000 0.000000 0.000000 0.090909 0.121212 0.121212 0.666667 0.454545 0.212121 0.121212 0.212121 0.303030 0.242424 0.303030 0.151515 0.303030 0.060606 0.060606 0.575758 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[ATC][TA]CT[ACT][AGC][TA] -------------------------------------------------------------------------------- Time 0.18 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- kni_chr3L_8638757_863876 3.18e-01 10 kni_chr3L_8639165_863917 1.91e-02 8 kni_chr3R_12598893_12598 1.18e-02 9 kni_chr3L_8640869_864091 2.03e-01 45 kni_chr3L_8639837_863984 2.09e-03 8 kni_chr3L_8641321_864133 2.28e-02 10 kni_chr2R_5487392_548740 4.03e-02 15 kni_chr3L_8639855_863986 1.23e-02 8 kni_chr2R_5487348_548736 2.62e-04 5_[-1(1.87e-05)]_1 kni_chr3L_8639618_863962 1.13e-01 8 kni_chr3L_8640806_864082 1.84e-01 20 kni_chr3R_12600037_12600 1.16e-01 9 kni_chr3L_8639485_863949 2.17e-02 8 kni_chr2R_5487415_548742 1.18e-01 15 kni_chr3R_12599333_12599 7.22e-01 19 kni_chr3L_8639911_863992 1.73e-03 10 kni_chr3L_8638865_863889 2.33e-02 32 kni_chr3L_8640835_864085 3.42e-01 23 kni_chr3L_8639054_863906 8.47e-02 8 kni_chr3L_8639669_863967 5.77e-04 8 kni_chr3L_8639403_863941 1.13e-01 8 kni_chr3R_12598704_12598 4.29e-02 9 kni_chr2R_5487618_548762 3.46e-02 11 kni_chr3L_8639070_863907 9.00e-02 8 kni_chr2R_5487573_548758 7.48e-04 5_[-1(6.23e-05)] kni_chr3L_8638573_863859 2.59e-03 14_[+1(7.64e-05)]_2 kni_chr3L_8639096_863910 1.78e-01 8 kni_chr2R_20730884_20730 2.56e-02 16 kni_chr3R_12599841_12599 2.46e-01 9 kni_chr3L_8639205_863921 5.94e-03 8 kni_chr3L_8639539_863954 5.99e-02 8 kni_chr3L_8638500_863850 5.09e-02 10 kni_chr3L_8639264_863927 1.37e-02 8 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************