******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) 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= motifs/453/453.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 48666 1.0000 500 48983 1.0000 500 45161 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/453/453.seqs.fa -oc motifs/453 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 3 wnsites= 0.8 theta: prob= 1 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= 1500 N= 3 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.277 C 0.249 G 0.211 T 0.263 Background letter frequencies (from dataset with add-one prior applied): A 0.277 C 0.249 G 0.211 T 0.263 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 3 llr = 63 E-value = 2.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A a7:7:33::::::::33:::a pos.-specific C :::::73:::a:3:::3a:a: probability G :373a::3a7:73aa:3:7:: matrix T ::3:::37:3:33::7::3:: bits 2.2 * * ** 2.0 * * * ** * * 1.8 * * * * ** * ** 1.6 * * * * ** * ** Relative 1.3 * * * * ** * ** Entropy 1.1 ****** ***** ** **** (30.1 bits) 0.9 ****** ***** *** **** 0.7 ****** ***** *** **** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel AAGAGCATGGCGCGGTACGCA consensus GTG ACG T TG AC T sequence T T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 45161 321 1.98e-11 GTTAACAGTA AAGGGCAGGGCGGGGTCCGCA TACATCCAAA 48666 262 2.86e-11 GGCACCTAAG AAGAGCCTGTCGCGGTACGCA TTTCATACGG 48983 56 1.39e-09 TAGAATACTT AGTAGATTGGCTTGGAGCTCA ATAGAACATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45161 2e-11 320_[+1]_159 48666 2.9e-11 261_[+1]_218 48983 1.4e-09 55_[+1]_424 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=3 45161 ( 321) AAGGGCAGGGCGGGGTCCGCA 1 48666 ( 262) AAGAGCCTGTCGCGGTACGCA 1 48983 ( 56) AGTAGATTGGCTTGGAGCTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1440 bayes= 8.90388 E= 2.2e+002 185 -823 -823 -823 126 -823 66 -823 -823 -823 166 34 126 -823 66 -823 -823 -823 224 -823 26 142 -823 -823 26 42 -823 34 -823 -823 66 134 -823 -823 224 -823 -823 -823 166 34 -823 200 -823 -823 -823 -823 166 34 -823 42 66 34 -823 -823 224 -823 -823 -823 224 -823 26 -823 -823 134 26 42 66 -823 -823 200 -823 -823 -823 -823 166 34 -823 200 -823 -823 185 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 3 E= 2.2e+002 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 0.666667 0.333333 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.333333 0.000000 0.333333 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.333333 0.333333 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.333333 0.333333 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[AG][GT][AG]G[CA][ACT][TG]G[GT]C[GT][CGT]GG[TA][ACG]C[GT]CA -------------------------------------------------------------------------------- Time 0.10 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 13 sites = 3 llr = 44 E-value = 3.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::::::a:37:a pos.-specific C :37::a:::::a: probability G a:3aa:7:773:: matrix T :7::::3:3:::: bits 2.2 * ** 2.0 * *** * 1.8 * *** * ** 1.6 * *** * ** Relative 1.3 * *** * ** Entropy 1.1 ************* (21.4 bits) 0.9 ************* 0.7 ************* 0.4 ************* 0.2 ************* 0.0 ------------- Multilevel GTCGGCGAGGACA consensus CG T TAG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------- 48983 387 1.99e-08 GATGCTGGCT GTGGGCGAGGACA AAAGCTCTCG 45161 455 1.51e-07 CGGTATTCTT GCCGGCGAGAACA ACATTAAAAA 48666 202 2.60e-07 CTCTCCACCC GTCGGCTATGGCA TAAAATTGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48983 2e-08 386_[+2]_101 45161 1.5e-07 454_[+2]_33 48666 2.6e-07 201_[+2]_286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=13 seqs=3 48983 ( 387) GTGGGCGAGGACA 1 45161 ( 455) GCCGGCGAGAACA 1 48666 ( 202) GTCGGCTATGGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 1464 bayes= 9.37603 E= 3.1e+002 -823 -823 224 -823 -823 42 -823 134 -823 142 66 -823 -823 -823 224 -823 -823 -823 224 -823 -823 200 -823 -823 -823 -823 166 34 185 -823 -823 -823 -823 -823 166 34 26 -823 166 -823 126 -823 66 -823 -823 200 -823 -823 185 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 3 E= 3.1e+002 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.333333 0.000000 0.666667 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[TC][CG]GGC[GT]A[GT][GA][AG]CA -------------------------------------------------------------------------------- Time 0.19 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 3 llr = 43 E-value = 3.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :a7:::7::a:: pos.-specific C a:33::3a3::: probability G :::7:a::7::a matrix T ::::a:::::a: bits 2.2 * * 2.0 * ** * ** 1.8 ** ** * *** 1.6 ** ** * *** Relative 1.3 ** *** ***** Entropy 1.1 ** *** ***** (20.5 bits) 0.9 ************ 0.7 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CAAGTGACGATG consensus CC C C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 48983 369 1.40e-07 CCAGGATAGC CAAGTGCCGATG CTGGCTGTGG 48666 86 1.40e-07 CGAGCCTCAG CACGTGACGATG AGGCACCCAA 45161 196 5.81e-07 ATTATACAGG CAACTGACCATG AAAGTGAAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48983 1.4e-07 368_[+3]_120 48666 1.4e-07 85_[+3]_403 45161 5.8e-07 195_[+3]_293 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=3 48983 ( 369) CAAGTGCCGATG 1 48666 ( 86) CACGTGACGATG 1 45161 ( 196) CAACTGACCATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1467 bayes= 8.93074 E= 3.7e+002 -823 200 -823 -823 185 -823 -823 -823 126 42 -823 -823 -823 42 166 -823 -823 -823 -823 192 -823 -823 224 -823 126 42 -823 -823 -823 200 -823 -823 -823 42 166 -823 185 -823 -823 -823 -823 -823 -823 192 -823 -823 224 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 3 E= 3.7e+002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CA[AC][GC]TG[AC]C[GC]ATG -------------------------------------------------------------------------------- Time 0.27 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48666 8.47e-14 85_[+3(1.40e-07)]_104_\ [+2(2.60e-07)]_47_[+1(2.86e-11)]_218 48983 2.92e-13 55_[+1(1.39e-09)]_292_\ [+3(1.40e-07)]_6_[+2(1.99e-08)]_101 45161 1.37e-13 195_[+3(5.81e-07)]_113_\ [+1(1.98e-11)]_113_[+2(1.51e-07)]_33 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net 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