******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.11.3 (Release date: Fri Feb 19 13:23:06 2016 -0800) 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= common/crp0.s 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 common/crp0.s -oc results/meme3 -mod tcm -dna -revcomp -nmotifs 2 -minw 8 -nostatus model: mod= tcm nmotifs= 2 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= 50 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 WWWATKTGAHCNABNTCACA MEME-1 width = 20 sites = 18 llr = 198 E-value = 4.8e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif WWWATKTGAHCNABNTCACA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 453511:27413713:19:9 pos.-specific C 1::2312:3272:3229:a: probability G :1:216:7:223223::1:1 matrix T 4472638112121438:1:: bits 2.4 * 2.1 * * 1.9 * * 1.6 * * Relative 1.4 * ** Entropy 1.2 * ***** (15.9 bits) 0.9 ** * ***** 0.7 * **** * * ***** 0.5 *** ***** * * ***** 0.2 ********* * ** ***** 0.0 -------------------- Multilevel AATATGTGAACGATATCACA consensus TTA CTCACC A CG sequence T C GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWATKTGAHCNABNTCACA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------------------- ara + 54 4.15e-08 GTCCACATTG ATTATTTGCACGGCGTCACA CTTTGCTATG deop2 + 6 5.85e-07 AGTGA ATTATTTGAACCAGATCGCA TTACAGTGAT crp + 62 7.31e-07 ATGTACTGCA TGTATGCAAAGGACGTCACA TTACCGTGCA ce1cg - 20 9.08e-07 CACCACGCGC TATTCTCGCCCGATGCCACA AAAACCAGCA ce1cg + 60 1.38e-06 TGAAAGACTG TTTTTTTGATCGTTTTCACA AAAATGGAAG malt - 44 1.69e-06 TTTATGTGTC TGAATTTGCACTGTGTCACA ATTCCAAATC pbr322 - 56 1.86e-06 TCTCCTTACG CATCTGTGCGGTATTTCACA CCGCATATGG ompa + 47 1.86e-06 TTTTTTTTCA TATGCCTGACGGAGTTCACA CTTGTAAGTT cya - 53 2.72e-06 AAAATGGTCT AAAACGTGATCAATTTAACA CCTTGCTGAT uxu1 - 20 2.98e-06 CCGAATTCTA ATTGGGTTAACCACATCACA ACAATTTCAC male + 13 3.27e-06 ATTACCGCCA ATTCTGTAACAGAGATCACA CAAAGCGACG lac - 12 4.65e-06 TGGGGTGCCT AATGAGTGAGCTAACTCACA TTAATTGCGT ilv + 38 5.52e-06 AATTCAGTAC AAAACGTGATCAACCCCTCA ATTTTCCCTT bglr1 - 79 6.01e-06 ATTGATA AAAATATGACCATGCTCACA GTTATTAACT tnaa - 74 6.52e-06 TGAAATTGTT TAAATGTGAATCGAATCACA ATCGTTCGGG lac - 76 6.52e-06 GTGAAATTGT TATCCGCTCACAATTCCACA CAACATACGA malk - 64 1.23e-05 ATCGCCACGA TTTTTGCAAGCAACATCACG AAATTCCTTA gale + 41 1.53e-05 AACGATTCCA CTAATTTATTCCATGTCACA CTTTTCGCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWATKTGAHCNABNTCACA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ara 4.1e-08 53_[+1]_32 deop2 5.8e-07 5_[+1]_80 crp 7.3e-07 61_[+1]_24 ce1cg 9.1e-07 19_[-1]_20_[+1]_26 malt 1.7e-06 43_[-1]_42 pbr322 1.9e-06 55_[-1]_30 ompa 1.9e-06 46_[+1]_39 cya 2.7e-06 52_[-1]_33 uxu1 3e-06 19_[-1]_66 male 3.3e-06 12_[+1]_73 lac 4.7e-06 11_[-1]_44_[-1]_10 ilv 5.5e-06 37_[+1]_48 bglr1 6e-06 78_[-1]_7 tnaa 6.5e-06 73_[-1]_12 malk 1.2e-05 63_[-1]_22 gale 1.5e-05 40_[+1]_45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWATKTGAHCNABNTCACA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF WWWATKTGAHCNABNTCACA width=20 seqs=18 ara ( 54) ATTATTTGCACGGCGTCACA 1 deop2 ( 6) ATTATTTGAACCAGATCGCA 1 crp ( 62) TGTATGCAAAGGACGTCACA 1 ce1cg ( 20) TATTCTCGCCCGATGCCACA 1 ce1cg ( 60) TTTTTTTGATCGTTTTCACA 1 malt ( 44) TGAATTTGCACTGTGTCACA 1 pbr322 ( 56) CATCTGTGCGGTATTTCACA 1 ompa ( 47) TATGCCTGACGGAGTTCACA 1 cya ( 53) AAAACGTGATCAATTTAACA 1 uxu1 ( 20) ATTGGGTTAACCACATCACA 1 male ( 13) ATTCTGTAACAGAGATCACA 1 lac ( 12) AATGAGTGAGCTAACTCACA 1 ilv ( 38) AAAACGTGATCAACCCCTCA 1 bglr1 ( 79) AAAATATGACCATGCTCACA 1 tnaa ( 74) TAAATGTGAATCGAATCACA 1 lac ( 76) TATCCGCTCACAATTCCACA 1 malk ( 64) TTTTTGCAAGCAACATCACG 1 gale ( 41) CTAATTTATTCCATGTCACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWATKTGAHCNABNTCACA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1548 bayes= 6.5452 E= 4.8e-004 55 -82 -1081 55 72 -1081 -82 35 13 -1081 -1081 113 72 -23 -23 -87 -245 50 -182 101 -245 -182 150 13 -1081 18 -1081 135 -45 -1081 177 -145 113 50 -1081 -245 35 18 -23 -45 -245 188 -23 -245 -13 18 77 -87 125 -1081 -23 -145 -145 50 18 35 -13 -23 50 -13 -1081 -23 -1081 145 -245 227 -1081 -1081 155 -1081 -182 -245 -1081 235 -1081 -1081 163 -1081 -182 -1081 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWATKTGAHCNABNTCACA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 18 E= 4.8e-004 0.444444 0.111111 0.000000 0.444444 0.500000 0.000000 0.111111 0.388889 0.333333 0.000000 0.000000 0.666667 0.500000 0.166667 0.166667 0.166667 0.055556 0.277778 0.055556 0.611111 0.055556 0.055556 0.555556 0.333333 0.000000 0.222222 0.000000 0.777778 0.222222 0.000000 0.666667 0.111111 0.666667 0.277778 0.000000 0.055556 0.388889 0.222222 0.166667 0.222222 0.055556 0.722222 0.166667 0.055556 0.277778 0.222222 0.333333 0.166667 0.722222 0.000000 0.166667 0.111111 0.111111 0.277778 0.222222 0.388889 0.277778 0.166667 0.277778 0.277778 0.000000 0.166667 0.000000 0.833333 0.055556 0.944444 0.000000 0.000000 0.888889 0.000000 0.055556 0.055556 0.000000 1.000000 0.000000 0.000000 0.944444 0.000000 0.055556 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWATKTGAHCNABNTCACA MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AT][TA]A[TC][GT][TC][GA][AC][ACT]C[GAC]A[TCG][AGT]TCACA -------------------------------------------------------------------------------- Time 0.50 secs. ******************************************************************************** ******************************************************************************** MOTIF CGGYGGGG MEME-2 width = 8 sites = 2 llr = 24 E-value = 1.6e+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= 1.6e+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= 1.6e+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 0.83 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ce1cg 9.14e-04 19_[-1(9.08e-07)]_20_[+1(1.38e-06)]_\ 26 ara 7.87e-05 53_[+1(4.15e-08)]_32 bglr1 7.92e-03 78_[-1(6.01e-06)]_7 crp 1.08e-03 61_[+1(7.31e-07)]_24 cya 3.50e-03 52_[-1(2.72e-06)]_33 deop2 6.14e-04 5_[+1(5.85e-07)]_80 gale 1.82e-02 40_[+1(1.53e-05)]_45 ilv 6.37e-06 4_[+2(2.18e-06)]_25_[+1(5.52e-06)]_\ 48 lac 3.95e-03 11_[-1(4.65e-06)]_44_[-1(6.52e-06)]_\ 10 male 9.36e-06 12_[+1(3.27e-06)]_8_[+2(5.56e-06)]_\ 57 malk 3.60e-03 63_[-1(1.23e-05)]_22 malt 2.29e-03 43_[-1(1.69e-06)]_42 ompa 2.49e-03 46_[+1(1.86e-06)]_39 tnaa 3.58e-03 73_[-1(6.52e-06)]_12 uxu1 2.66e-03 19_[-1(2.98e-06)]_66 pbr322 1.17e-03 55_[-1(1.86e-06)]_30 trn9cat 9.86e-01 105 tdc 1.63e-01 105 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-iMac.rd.unr.edu ********************************************************************************