******************************************************************************** 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/99/99.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 263826 1.0000 500 263827 1.0000 500 264748 1.0000 500 264751 1.0000 500 8879 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/99/99.seqs.fa -oc motifs/99 -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= 5 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= 2500 N= 5 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.235 C 0.208 G 0.248 T 0.310 Background letter frequencies (from dataset with add-one prior applied): A 0.235 C 0.208 G 0.248 T 0.310 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 5 llr = 129 E-value = 3.2e-015 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::::::aa2::::::::aa pos.-specific C 2:2::::::::a::a8:88:: probability G 8:8aa8aa::8::::2::2:: matrix T :a:::2::::::aa::a2::: bits 2.3 * * 2.0 ** **** * * ** 1.8 ** **** * * ** 1.6 * ** **** ****** *** Relative 1.4 ***** *************** Entropy 1.1 ********************* (37.4 bits) 0.9 ********************* 0.7 ********************* 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GTGGGGGGAAGCTTCCTCCAA consensus C C T A G TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 264751 226 1.57e-13 TCGAATGCTG GTGGGGGGAAGCTTCCTCCAA GCATGAGTCA 264748 226 1.57e-13 TCGAATGCTG GTGGGGGGAAGCTTCCTCCAA GCTTGAGTCA 263827 226 1.57e-13 TCGAATGCTG GTGGGGGGAAGCTTCCTCCAA GCTTGAGTCA 263826 226 1.57e-13 TCGAATGCTG GTGGGGGGAAGCTTCCTCCAA GTATGAGTCA 8879 322 1.48e-10 TTAGACGTAT CTCGGTGGAAACTTCGTTGAA ATTGAATATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 264751 1.6e-13 225_[+1]_254 264748 1.6e-13 225_[+1]_254 263827 1.6e-13 225_[+1]_254 263826 1.6e-13 225_[+1]_254 8879 1.5e-10 321_[+1]_158 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=5 264751 ( 226) GTGGGGGGAAGCTTCCTCCAA 1 264748 ( 226) GTGGGGGGAAGCTTCCTCCAA 1 263827 ( 226) GTGGGGGGAAGCTTCCTCCAA 1 263826 ( 226) GTGGGGGGAAGCTTCCTCCAA 1 8879 ( 322) CTCGGTGGAAACTTCGTTGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2400 bayes= 8.90388 E= 3.2e-015 -897 -5 169 -897 -897 -897 -897 169 -897 -5 169 -897 -897 -897 201 -897 -897 -897 201 -897 -897 -897 169 -63 -897 -897 201 -897 -897 -897 201 -897 209 -897 -897 -897 209 -897 -897 -897 -23 -897 169 -897 -897 227 -897 -897 -897 -897 -897 169 -897 -897 -897 169 -897 227 -897 -897 -897 194 -31 -897 -897 -897 -897 169 -897 194 -897 -63 -897 194 -31 -897 209 -897 -897 -897 209 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 3.2e-015 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GC]T[GC]GG[GT]GGAA[GA]CTTC[CG]T[CT][CG]AA -------------------------------------------------------------------------------- Time 0.27 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 4 llr = 120 E-value = 1.3e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::a::a::a:::a:aa:::: pos.-specific C :a:::::aa::a::::::a:a probability G a:a:a:::::::a:a::a::: matrix T :::::a::::a::::::::a: bits 2.3 * ** * * * 2.0 ***** **** ******** * 1.8 ***** **** ******** * 1.6 ********************* Relative 1.4 ********************* Entropy 1.1 ********************* (43.3 bits) 0.9 ********************* 0.7 ********************* 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GCGAGTACCATCGAGAAGCTC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 264751 373 9.45e-14 GACTGGACGT GCGAGTACCATCGAGAAGCTC TTTTTACACT 264748 373 9.45e-14 GAATGGACGT GCGAGTACCATCGAGAAGCTC TTTTTACACT 263827 373 9.45e-14 GAATGGACGT GCGAGTACCATCGAGAAGCTC TTTTTACACT 263826 373 9.45e-14 GACTGGACTT GCGAGTACCATCGAGAAGCTC TTTTTACACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 264751 9.5e-14 372_[+2]_107 264748 9.5e-14 372_[+2]_107 263827 9.5e-14 372_[+2]_107 263826 9.5e-14 372_[+2]_107 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=4 264751 ( 373) GCGAGTACCATCGAGAAGCTC 1 264748 ( 373) GCGAGTACCATCGAGAAGCTC 1 263827 ( 373) GCGAGTACCATCGAGAAGCTC 1 263826 ( 373) GCGAGTACCATCGAGAAGCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2400 bayes= 9.22641 E= 1.3e-014 -865 -865 201 -865 -865 226 -865 -865 -865 -865 201 -865 209 -865 -865 -865 -865 -865 201 -865 -865 -865 -865 169 209 -865 -865 -865 -865 226 -865 -865 -865 226 -865 -865 209 -865 -865 -865 -865 -865 -865 169 -865 226 -865 -865 -865 -865 201 -865 209 -865 -865 -865 -865 -865 201 -865 209 -865 -865 -865 209 -865 -865 -865 -865 -865 201 -865 -865 226 -865 -865 -865 -865 -865 169 -865 226 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 1.3e-014 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GCGAGTACCATCGAGAAGCTC -------------------------------------------------------------------------------- Time 0.50 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 5 llr = 128 E-value = 2.5e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :aa:2a:a:822a:a28:::: pos.-specific C :::2::::a2:::2:82::a: probability G a::88::::::::8:::a::a matrix T ::::::a:::88::::::a:: bits 2.3 * * 2.0 *** * ** * * * ** 1.8 *** * ** * * * ** 1.6 *** **** * ** **** Relative 1.4 ********** ********* Entropy 1.1 ********************* (36.9 bits) 0.9 ********************* 0.7 ********************* 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GAAGGATACATTAGACAGTCG consensus CA CAA C AC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 264751 176 1.80e-13 TGGATAGGTT GAAGGATACATTAGACAGTCG AATGGATAGG 264748 176 1.80e-13 TGGATAGGTT GAAGGATACATTAGACAGTCG AATGGATAGG 263827 176 1.80e-13 TGGATAGGTT GAAGGATACATTAGACAGTCG AATGGATAGG 263826 176 1.80e-13 TGGATAGGTT GAAGGATACATTAGACAGTCG AATGGATAGG 8879 464 2.10e-10 CGTTACAAGA GAACAATACCAAACAACGTCG TCCGAGTCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 264751 1.8e-13 175_[+3]_304 264748 1.8e-13 175_[+3]_304 263827 1.8e-13 175_[+3]_304 263826 1.8e-13 175_[+3]_304 8879 2.1e-10 463_[+3]_16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=5 264751 ( 176) GAAGGATACATTAGACAGTCG 1 264748 ( 176) GAAGGATACATTAGACAGTCG 1 263827 ( 176) GAAGGATACATTAGACAGTCG 1 263826 ( 176) GAAGGATACATTAGACAGTCG 1 8879 ( 464) GAACAATACCAAACAACGTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2400 bayes= 8.90388 E= 2.5e-014 -897 -897 201 -897 209 -897 -897 -897 209 -897 -897 -897 -897 -5 169 -897 -23 -897 169 -897 209 -897 -897 -897 -897 -897 -897 169 209 -897 -897 -897 -897 227 -897 -897 177 -5 -897 -897 -23 -897 -897 137 -23 -897 -897 137 209 -897 -897 -897 -897 -5 169 -897 209 -897 -897 -897 -23 194 -897 -897 177 -5 -897 -897 -897 -897 201 -897 -897 -897 -897 169 -897 227 -897 -897 -897 -897 201 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 2.5e-014 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.800000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GAA[GC][GA]ATAC[AC][TA][TA]A[GC]A[CA][AC]GTCG -------------------------------------------------------------------------------- Time 0.74 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263826 7.50e-28 175_[+3(1.80e-13)]_29_\ [+1(1.57e-13)]_126_[+2(9.45e-14)]_107 263827 7.50e-28 175_[+3(1.80e-13)]_29_\ [+1(1.57e-13)]_126_[+2(9.45e-14)]_107 264748 7.50e-28 175_[+3(1.80e-13)]_29_\ [+1(1.57e-13)]_126_[+2(9.45e-14)]_107 264751 7.50e-28 175_[+3(1.80e-13)]_29_\ [+1(1.57e-13)]_126_[+2(9.45e-14)]_107 8879 2.89e-12 321_[+1(1.48e-10)]_121_\ [+3(2.10e-10)]_16 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************