******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.11.4 (Release date: Thu Mar 30 17:02:08 2017 -0700) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org . 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-suite.org . ******************************************************************************** ******************************************************************************** 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= crp0.fna ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ ce1cg 1.0000 105 ara 1.0000 105 bglr1 1.0000 105 crp 1.0000 105 cya 1.0000 105 deop2 1.0000 105 gale 1.0000 105 ilv 1.0000 105 lac 1.0000 105 male 1.0000 105 malk 1.0000 105 malt 1.0000 105 ompa 1.0000 105 tnaa 1.0000 105 uxu1 1.0000 105 pbr322 1.0000 105 trn9cat 1.0000 105 tdc 1.0000 105 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme crp0.fna -oc meme_example_output_files -dna -mod zoops -nmotifs 3 -revcomp model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 50 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 18 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 1890 N= 18 shuffle= -1 strands: + - sample: seed= 0 ctfrac= -1 maxwords= -1 Letter frequencies in dataset: A 0.304 C 0.196 G 0.196 T 0.304 Background letter frequencies (from dataset with add-one prior applied): A 0.304 C 0.196 G 0.196 T 0.304 ******************************************************************************** ******************************************************************************** MOTIF TKTGANCNABNTCACAHWT MEME-1 width = 19 sites = 18 llr = 191 E-value = 4.3e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif TKTGANCNABNTCACAHWT MEME-1 Description -------------------------------------------------------------------------------- Simplified A :1:28322613::9:8333 pos.-specific C 112:1252:431a:a:31: probability G 16:7:2132331:::11:: matrix T 838113222228:1:1367 bits 2.4 * * 2.1 * * 1.9 * * 1.6 * * Relative 1.4 * * Entropy 1.2 * *** (15.3 bits) 0.9 * *** ***** * 0.7 * *** ***** * 0.5 ***** ** ***** ** 0.2 ***** * ** ***** ** 0.0 ------------------- Multilevel TGTGAACGACATCACAATT consensus TCA TAAGGC CAA sequence C TG T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKTGANCNABNTCACAHWT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------------- ara + 58 7.97e-08 ACATTGATTA TTTGCACGGCGTCACACTT TGCTATGCCA deop2 - 60 3.33e-07 CGCAACACAC TTCGATACACATCACAATT AAGGAAATCT pbr322 + 56 1.14e-06 CCATATGCGG TGTGAAATACCGCACAGAT GCGTAAGGAG crp + 66 1.27e-06 ACTGCATGTA TGCAAAGGACGTCACATTA CCGTGCAGTA malt - 41 1.77e-06 TGTGTCTGAA TTTGCACTGTGTCACAATT CCAAATCTTT male + 17 1.97e-06 CCGCCAATTC TGTAACAGAGATCACACAA AGCGACGGTG tdc + 81 3.31e-06 AAAGTTAATT TGTGAGTGGTCGCACATAT CCTGTT tnaa + 74 4.02e-06 CCCGAACGAT TGTGATTCGATTCACATTT AAACAATTTC ompa + 51 4.02e-06 TTTTCATATG CCTGACGGAGTTCACACTT GTAAGTTTTC lac + 12 4.43e-06 ACGCAATTAA TGTGAGTTAGCTCACTCAT TAGGCACCCC ce1cg + 64 4.87e-06 AGACTGTTTT TTTGATCGTTTTCACAAAA ATGGAAGTCC bglr1 - 76 5.35e-06 TTGATAAAAA TATGACCATGCTCACAGTT ATTAACTTTG gale + 45 7.68e-06 ATTCCACTAA TTTATTCCATGTCACACTT TTCGCATCTT ilv + 42 8.39e-06 CAGTACAAAA CGTGATCAACCCCTCAATT TTCCCTTTGC trn9cat - 84 1.08e-05 CGT GCCGATCAACGTCTCATTT TCGCCAAAAG malk - 61 1.18e-05 CCACGATTTT TGCAAGCAACATCACGAAA TTCCTTACAT uxu1 - 17 1.90e-05 ATTCTAATTG GGTTAACCACATCACAACA ATTTCACTCT cya + 53 3.16e-05 ATCAGCAAGG TGTTAAATTGATCACGTTT TAGACCATTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKTGANCNABNTCACAHWT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ara 8e-08 57_[+1]_29 deop2 3.3e-07 59_[-1]_27 pbr322 1.1e-06 55_[+1]_31 crp 1.3e-06 65_[+1]_21 malt 1.8e-06 40_[-1]_46 male 2e-06 16_[+1]_70 tdc 3.3e-06 80_[+1]_6 tnaa 4e-06 73_[+1]_13 ompa 4e-06 50_[+1]_36 lac 4.4e-06 11_[+1]_75 ce1cg 4.9e-06 63_[+1]_23 bglr1 5.3e-06 75_[-1]_11 gale 7.7e-06 44_[+1]_42 ilv 8.4e-06 41_[+1]_45 trn9cat 1.1e-05 83_[-1]_3 malk 1.2e-05 60_[-1]_26 uxu1 1.9e-05 16_[-1]_70 cya 3.2e-05 52_[+1]_34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKTGANCNABNTCACAHWT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TKTGANCNABNTCACAHWT width=19 seqs=18 ara ( 58) TTTGCACGGCGTCACACTT 1 deop2 ( 60) TTCGATACACATCACAATT 1 pbr322 ( 56) TGTGAAATACCGCACAGAT 1 crp ( 66) TGCAAAGGACGTCACATTA 1 malt ( 41) TTTGCACTGTGTCACAATT 1 male ( 17) TGTAACAGAGATCACACAA 1 tdc ( 81) TGTGAGTGGTCGCACATAT 1 tnaa ( 74) TGTGATTCGATTCACATTT 1 ompa ( 51) CCTGACGGAGTTCACACTT 1 lac ( 12) TGTGAGTTAGCTCACTCAT 1 ce1cg ( 64) TTTGATCGTTTTCACAAAA 1 bglr1 ( 76) TATGACCATGCTCACAGTT 1 gale ( 45) TTTATTCCATGTCACACTT 1 ilv ( 42) CGTGATCAACCCCTCAATT 1 trn9cat ( 84) GCCGATCAACGTCTCATTT 1 malk ( 61) TGCAAGCAACATCACGAAA 1 uxu1 ( 17) GGTTAACCACATCACAACA 1 cya ( 53) TGTTAAATTGATCACGTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKTGANCNABNTCACAHWT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 1566 bayes= 7.2817 E= 4.3e-009 -1081 -82 -82 135 -245 -82 150 -13 -1081 18 -1081 135 -45 -1081 177 -145 145 -82 -1081 -245 13 -23 -23 13 -45 135 -82 -87 -45 18 77 -45 101 -1081 18 -87 -245 118 50 -45 -13 50 50 -87 -1081 -182 -82 145 -1081 235 -1081 -1081 155 -1081 -1081 -145 -1081 235 -1081 -1081 145 -1081 -82 -245 13 50 -82 -13 13 -182 -1081 101 -13 -1081 -1081 125 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKTGANCNABNTCACAHWT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 18 E= 4.3e-009 0.000000 0.111111 0.111111 0.777778 0.055556 0.111111 0.555556 0.277778 0.000000 0.222222 0.000000 0.777778 0.222222 0.000000 0.666667 0.111111 0.833333 0.111111 0.000000 0.055556 0.333333 0.166667 0.166667 0.333333 0.222222 0.500000 0.111111 0.166667 0.222222 0.222222 0.333333 0.222222 0.611111 0.000000 0.222222 0.166667 0.055556 0.444444 0.277778 0.222222 0.277778 0.277778 0.277778 0.166667 0.000000 0.055556 0.111111 0.833333 0.000000 1.000000 0.000000 0.000000 0.888889 0.000000 0.000000 0.111111 0.000000 1.000000 0.000000 0.000000 0.833333 0.000000 0.111111 0.055556 0.333333 0.277778 0.111111 0.277778 0.333333 0.055556 0.000000 0.611111 0.277778 0.000000 0.000000 0.722222 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKTGANCNABNTCACAHWT MEME-1 regular expression -------------------------------------------------------------------------------- T[GT][TC][GA]A[AT][CA][GACT][AG][CGT][ACG]TCACA[ACT][TA][TA] -------------------------------------------------------------------------------- Time 1.69 secs. ******************************************************************************** ******************************************************************************** MOTIF CGGYGGGG MEME-2 width = 8 sites = 2 llr = 24 E-value = 1.5e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGGYGGGG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C a::5:::: probability G :aa:aaaa matrix T :::5:::: bits 2.4 *** **** 2.1 *** **** 1.9 *** **** 1.6 *** **** Relative 1.4 *** **** Entropy 1.2 *** **** (17.5 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CGGCGGGG consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGYGGGG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- ilv + 5 2.18e-06 GCTC CGGCGGGG TTTTTTGTTA male + 41 5.56e-06 CACAAAGCGA CGGTGGGG CGTAGGGGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGYGGGG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ilv 2.2e-06 4_[+2]_93 male 5.6e-06 40_[+2]_57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGYGGGG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGGYGGGG width=8 seqs=2 ilv ( 5) CGGCGGGG 1 male ( 41) CGGTGGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGYGGGG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1764 bayes= 9.783 E= 1.5e+004 -765 235 -765 -765 -765 -765 235 -765 -765 -765 235 -765 -765 135 -765 71 -765 -765 235 -765 -765 -765 235 -765 -765 -765 235 -765 -765 -765 235 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGYGGGG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.5e+004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGYGGGG MEME-2 regular expression -------------------------------------------------------------------------------- CGG[CT]GGGG -------------------------------------------------------------------------------- Time 2.72 secs. ******************************************************************************** ******************************************************************************** MOTIF GCATCRGRBSAGA MEME-3 width = 13 sites = 3 llr = 48 E-value = 1.8e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCATCRGRBSAGA MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::a::3:7::a:a pos.-specific C :a::a:::33::: probability G a::::7a337:a: matrix T :::a::::3:::: bits 2.4 ** * * * 2.1 ** * * * 1.9 ** * * * 1.6 ***** * *** Relative 1.4 ***** * **** Entropy 1.2 ******* **** (22.9 bits) 0.9 ******** **** 0.7 ******** **** 0.5 ************* 0.2 ************* 0.0 ------------- Multilevel GCATCGGACGAGA consensus A GGC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCATCRGRBSAGA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------- ce1cg + 24 1.86e-08 GGTTTTTGTG GCATCGGGCGAGA ATAGCGCGTG uxu1 - 89 2.74e-08 GCTT GCATCGGATGAGA TGGCGTATAA pbr322 + 17 1.35e-07 TAACTATGCG GCATCAGAGCAGA TTGTACTGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCATCRGRBSAGA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ce1cg 1.9e-08 23_[+3]_69 uxu1 2.7e-08 88_[-3]_4 pbr322 1.3e-07 16_[+3]_76 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCATCRGRBSAGA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCATCRGRBSAGA width=13 seqs=3 ce1cg ( 24) GCATCGGGCGAGA 1 uxu1 ( 89) GCATCGGATGAGA 1 pbr322 ( 17) GCATCAGAGCAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCATCRGRBSAGA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 1674 bayes= 8.77981 E= 1.8e+004 -823 -823 235 -823 -823 235 -823 -823 171 -823 -823 -823 -823 -823 -823 171 -823 235 -823 -823 13 -823 176 -823 -823 -823 235 -823 113 -823 77 -823 -823 77 77 13 -823 77 176 -823 171 -823 -823 -823 -823 -823 235 -823 171 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCATCRGRBSAGA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 3 E= 1.8e+004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.333333 0.333333 0.333333 0.000000 0.333333 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCATCRGRBSAGA MEME-3 regular expression -------------------------------------------------------------------------------- GCATC[GA]G[AG][CGT][GC]AGA -------------------------------------------------------------------------------- Time 3.79 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ce1cg 3.74e-07 23_[+3(1.86e-08)]_27_[+1(4.87e-06)]_\ 23 ara 1.77e-04 57_[+1(7.97e-08)]_29 bglr1 2.94e-02 75_[-1(5.35e-06)]_11 crp 2.90e-03 65_[+1(1.27e-06)]_21 cya 9.02e-02 52_[+1(3.16e-05)]_34 deop2 5.46e-04 59_[-1(3.33e-07)]_27 gale 3.40e-02 44_[+1(7.68e-06)]_42 ilv 3.87e-05 4_[+2(2.18e-06)]_29_[+1(8.39e-06)]_\ 45 lac 9.54e-03 11_[+1(4.43e-06)]_75 male 2.21e-05 16_[+1(1.97e-06)]_5_[+2(5.56e-06)]_\ 57 malk 9.33e-03 60_[-1(1.18e-05)]_26 malt 7.39e-03 40_[-1(1.77e-06)]_46 ompa 1.58e-02 50_[+1(4.02e-06)]_36 tnaa 2.01e-03 73_[+1(4.02e-06)]_13 uxu1 1.81e-06 16_[-1(1.90e-05)]_53_[-3(2.74e-08)]_\ 4 pbr322 4.03e-07 16_[+3(1.35e-07)]_26_[+1(1.14e-06)]_\ 31 trn9cat 3.77e-02 83_[-1(1.08e-05)]_3 tdc 2.06e-02 80_[+1(3.31e-06)]_6 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: glutamine.gs.washington.edu ********************************************************************************