******************************************************************************** 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/449/449.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 50322 1.0000 500 45496 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/449/449.seqs.fa -oc motifs/449 -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= 2 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= 1000 N= 2 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.248 C 0.246 G 0.236 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.248 C 0.246 G 0.236 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 2 llr = 32 E-value = 3.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::5:a::aa: pos.-specific C a::a5::a:::: probability G :a:::a::a::a matrix T ::a::::::::: bits 2.1 ** * ******* 1.9 **** ******* 1.7 **** ******* 1.5 **** ******* Relative 1.2 **** ******* Entropy 1.0 ************ (23.3 bits) 0.8 ************ 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CGTCAGACGAAG consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 45496 409 9.40e-08 TCTTATTTAT CGTCAGACGAAG AGGATTTAGG 50322 451 9.40e-08 TAAATAATCA CGTCCGACGAAG GCTTGGACCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45496 9.4e-08 408_[+1]_80 50322 9.4e-08 450_[+1]_38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=2 45496 ( 409) CGTCAGACGAAG 1 50322 ( 451) CGTCCGACGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 978 bayes= 8.93074 E= 3.3e+002 -765 202 -765 -765 -765 -765 208 -765 -765 -765 -765 188 -765 202 -765 -765 101 102 -765 -765 -765 -765 208 -765 201 -765 -765 -765 -765 202 -765 -765 -765 -765 208 -765 201 -765 -765 -765 201 -765 -765 -765 -765 -765 208 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 2 E= 3.3e+002 0.000000 1.000000 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 0.500000 0.500000 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 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CGTC[AC]GACGAAG -------------------------------------------------------------------------------- Time 0.04 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 14 sites = 2 llr = 35 E-value = 6.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::aa5:::::a:: pos.-specific C a:a:::::55::aa probability G :a:::5aa:5a::: matrix T ::::::::5::::: bits 2.1 ***** ** **** 1.9 ***** ** **** 1.7 ***** ** **** 1.5 ***** ** **** Relative 1.2 ***** ** **** Entropy 1.0 ************** (25.5 bits) 0.8 ************** 0.6 ************** 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel CGCAAAGGCCGACC consensus G TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 45496 340 9.95e-09 CGTGCCGCTT CGCAAGGGTGGACC GAAGGTCAAA 50322 347 1.80e-08 AAAGAGCCAA CGCAAAGGCCGACC ATGGTTAGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45496 9.9e-09 339_[+2]_147 50322 1.8e-08 346_[+2]_140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=14 seqs=2 45496 ( 340) CGCAAGGGTGGACC 1 50322 ( 347) CGCAAAGGCCGACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 974 bayes= 8.92481 E= 6.0e+002 -765 202 -765 -765 -765 -765 208 -765 -765 202 -765 -765 201 -765 -765 -765 201 -765 -765 -765 101 -765 108 -765 -765 -765 208 -765 -765 -765 208 -765 -765 102 -765 89 -765 102 108 -765 -765 -765 208 -765 201 -765 -765 -765 -765 202 -765 -765 -765 202 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 2 E= 6.0e+002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 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 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CGCAA[AG]GG[CT][CG]GACC -------------------------------------------------------------------------------- Time 0.10 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 2 llr = 30 E-value = 7.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A a::::a:5:::: pos.-specific C :a::5::::::5 probability G ::aa5::5aaa5 matrix T ::::::a::::: bits 2.1 **** * *** 1.9 **** ** *** 1.7 **** ** *** 1.5 **** ** *** Relative 1.2 **** ** *** Entropy 1.0 ************ (21.5 bits) 0.8 ************ 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel ACGGCATAGGGC consensus G G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 50322 215 1.63e-07 ACCTCGACGG ACGGGATAGGGG AGATAGCCTC 45496 167 2.91e-07 CTGAATATTT ACGGCATGGGGC ATTGGAATGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50322 1.6e-07 214_[+3]_274 45496 2.9e-07 166_[+3]_322 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=2 50322 ( 215) ACGGGATAGGGG 1 45496 ( 167) ACGGCATGGGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 978 bayes= 8.93074 E= 7.7e+002 201 -765 -765 -765 -765 202 -765 -765 -765 -765 208 -765 -765 -765 208 -765 -765 102 108 -765 201 -765 -765 -765 -765 -765 -765 188 101 -765 108 -765 -765 -765 208 -765 -765 -765 208 -765 -765 -765 208 -765 -765 102 108 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 2 E= 7.7e+002 1.000000 0.000000 0.000000 0.000000 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 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.500000 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 0.000000 0.500000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- ACGG[CG]AT[AG]GGG[CG] -------------------------------------------------------------------------------- Time 0.13 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50322 1.65e-11 214_[+3(1.63e-07)]_120_\ [+2(1.80e-08)]_90_[+1(9.40e-08)]_38 45496 1.63e-11 166_[+3(2.91e-07)]_161_\ [+2(9.95e-09)]_55_[+1(9.40e-08)]_80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************