******************************************************************************** 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/465/465.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 32183 1.0000 500 29736 1.0000 500 39556 1.0000 500 10988 1.0000 500 34551 1.0000 500 35713 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/465/465.seqs.fa -oc motifs/465 -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= 6 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= 3000 N= 6 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.269 C 0.252 G 0.226 T 0.253 Background letter frequencies (from dataset with add-one prior applied): A 0.269 C 0.252 G 0.226 T 0.253 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 4 llr = 77 E-value = 1.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::3:535:::3:::::::: pos.-specific C :3::3::::::::a3:33:a probability G :8:88:83:3a58::8::3: matrix T a:a::5:3a8:33:83888: bits 2.1 * 1.9 * * * * * * 1.7 * * * * * * 1.5 * * * * * * Relative 1.3 ***** * *** ** * ** Entropy 1.1 ***** * *** ******** (27.7 bits) 0.9 ******* *** ******** 0.6 ******* ************ 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TGTGGAGATTGGGCTGTTTC consensus C ACTAG G AT CTCCG sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 39556 131 8.48e-12 CTTTGGTGTA TGTGGAGATGGGGCTGTTTC CCGTTGGGGA 32183 2 6.69e-10 A TGTGGTGGTTGTTCCGTTTC ACGTTTAGCG 35713 387 3.93e-09 CTTAGAAGCT TCTGGAATTTGGGCTTCTTC GTATGAGGCG 10988 340 4.15e-09 ATACGAGCTC TGTACTGATTGAGCTGTCGC CATTGTTCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 39556 8.5e-12 130_[+1]_350 32183 6.7e-10 1_[+1]_479 35713 3.9e-09 386_[+1]_94 10988 4.2e-09 339_[+1]_141 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=4 39556 ( 131) TGTGGAGATGGGGCTGTTTC 1 32183 ( 2) TGTGGTGGTTGTTCCGTTTC 1 35713 ( 387) TCTGGAATTTGGGCTTCTTC 1 10988 ( 340) TGTACTGATTGAGCTGTCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 2886 bayes= 9.49285 E= 1.7e+002 -865 -865 -865 198 -865 -1 173 -865 -865 -865 -865 198 -10 -865 173 -865 -865 -1 173 -865 89 -865 -865 98 -10 -865 173 -865 89 -865 14 -2 -865 -865 -865 198 -865 -865 14 157 -865 -865 214 -865 -10 -865 114 -2 -865 -865 173 -2 -865 199 -865 -865 -865 -1 -865 157 -865 -865 173 -2 -865 -1 -865 157 -865 -1 -865 157 -865 -865 14 157 -865 199 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 4 E= 1.7e+002 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 0.500000 0.000000 0.000000 0.500000 0.250000 0.000000 0.750000 0.000000 0.500000 0.000000 0.250000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.500000 0.250000 0.000000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.750000 0.250000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[GC]T[GA][GC][AT][GA][AGT]T[TG]G[GAT][GT]C[TC][GT][TC][TC][TG]C -------------------------------------------------------------------------------- Time 0.43 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 6 llr = 94 E-value = 2.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 32:22222:::2:87::553 pos.-specific C ::a7:32:2::7a:::335: probability G :2:282::::5::2:a5::: matrix T 77:::3788a52::3:22:7 bits 2.1 * 1.9 * * * * 1.7 * * * * 1.5 * * * * * Relative 1.3 * * *** ** * Entropy 1.1 * * * **** **** * (22.7 bits) 0.9 * * * **** **** ** 0.6 ***** *********** ** 0.4 ***** ************** 0.2 ***** ************** 0.0 -------------------- Multilevel TTCCGCTTTTGCCAAGGAAT consensus A T T T CCCA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 35713 8 2.08e-11 CGTACAT TTCCGTTTTTGCCAAGCAAT TTCCTTCCGC 29736 233 1.36e-08 CCGGAGTCTC TTCCGCCATTGCCATGGCCT ATTCGGAAGA 34551 462 2.41e-08 AGTACTACAA ATCCGGTTCTTACAAGGACT GCCGTGAGGG 10988 479 4.34e-08 CCTTGCTCGG TGCCATTTTTGCCATGCAAA AT 39556 245 1.20e-07 CCGTGCAAGT TTCGGAATTTTCCGAGGTCT CGTTCGGAGG 32183 475 2.81e-07 AGTATACTCG AACAGCTTTTTTCAAGTCAA TCAAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35713 2.1e-11 7_[+2]_473 29736 1.4e-08 232_[+2]_248 34551 2.4e-08 461_[+2]_19 10988 4.3e-08 478_[+2]_2 39556 1.2e-07 244_[+2]_236 32183 2.8e-07 474_[+2]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=6 35713 ( 8) TTCCGTTTTTGCCAAGCAAT 1 29736 ( 233) TTCCGCCATTGCCATGGCCT 1 34551 ( 462) ATCCGGTTCTTACAAGGACT 1 10988 ( 479) TGCCATTTTTGCCATGCAAA 1 39556 ( 245) TTCGGAATTTTCCGAGGTCT 1 32183 ( 475) AACAGCTTTTTTCAAGTCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 2886 bayes= 8.90689 E= 2.1e+002 31 -923 -923 140 -69 -923 -44 140 -923 199 -923 -923 -69 140 -44 -923 -69 -923 188 -923 -69 40 -44 40 -69 -60 -923 140 -69 -923 -923 172 -923 -60 -923 172 -923 -923 -923 198 -923 -923 114 98 -69 140 -923 -60 -923 199 -923 -923 163 -923 -44 -923 131 -923 -923 40 -923 -923 214 -923 -923 40 114 -60 90 40 -923 -60 90 99 -923 -923 31 -923 -923 140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 2.1e+002 0.333333 0.000000 0.000000 0.666667 0.166667 0.000000 0.166667 0.666667 0.000000 1.000000 0.000000 0.000000 0.166667 0.666667 0.166667 0.000000 0.166667 0.000000 0.833333 0.000000 0.166667 0.333333 0.166667 0.333333 0.166667 0.166667 0.000000 0.666667 0.166667 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.166667 0.666667 0.000000 0.166667 0.000000 1.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.500000 0.166667 0.500000 0.333333 0.000000 0.166667 0.500000 0.500000 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TA]TCCG[CT]TTTT[GT]CCA[AT]G[GC][AC][AC][TA] -------------------------------------------------------------------------------- Time 0.75 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 6 llr = 94 E-value = 5.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 8a22:::5::25:::228::2 pos.-specific C ::3237:238:22:2232:2: probability G 2:55::a3:28::282::338 matrix T :::273::7::388:55:75: bits 2.1 * 1.9 * * 1.7 * * 1.5 * * * * * Relative 1.3 ** * ** *** * * Entropy 1.1 ** *** *** *** ** * (22.5 bits) 0.9 ** *** *** *** ** * 0.6 *** *** *** *** **** 0.4 *** *********** ***** 0.2 ********************* 0.0 --------------------- Multilevel AAGGTCGATCGATTGTTATTG consensus C CT GC T C GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 10988 118 4.67e-09 CAAAAAAGAA AACGCCGATCGTTTGTACTTG GCGTTGACGT 35713 232 1.08e-08 ATGCCAGTAC AAGTTCGCTCGATTGCCATCG ATCGGGGATA 29736 183 2.30e-08 GAACTCCAAC AACGTCGGTGGATGGATAGTG GCGTTGGTGG 34551 14 4.87e-08 TCTGATCAGT AAACTCGACCGCTTCTTATGG AATATGCGAT 32183 408 5.26e-08 CCTATTCATT GAGGTTGATCATCTGTCATTG ACACTGCCTC 39556 350 1.16e-07 CAATGAAAAA AAGACTGGCCGATTGGTAGGA ATCCAAAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10988 4.7e-09 117_[+3]_362 35713 1.1e-08 231_[+3]_248 29736 2.3e-08 182_[+3]_297 34551 4.9e-08 13_[+3]_466 32183 5.3e-08 407_[+3]_72 39556 1.2e-07 349_[+3]_130 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=6 10988 ( 118) AACGCCGATCGTTTGTACTTG 1 35713 ( 232) AAGTTCGCTCGATTGCCATCG 1 29736 ( 183) AACGTCGGTGGATGGATAGTG 1 34551 ( 14) AAACTCGACCGCTTCTTATGG 1 32183 ( 408) GAGGTTGATCATCTGTCATTG 1 39556 ( 350) AAGACTGGCCGATTGGTAGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2880 bayes= 8.90388 E= 5.4e+002 163 -923 -44 -923 189 -923 -923 -923 -69 40 114 -923 -69 -60 114 -60 -923 40 -923 140 -923 140 -923 40 -923 -923 214 -923 90 -60 56 -923 -923 40 -923 140 -923 172 -44 -923 -69 -923 188 -923 90 -60 -923 40 -923 -60 -923 172 -923 -923 -44 172 -923 -60 188 -923 -69 -60 -44 98 -69 40 -923 98 163 -60 -923 -923 -923 -923 56 140 -923 -60 56 98 -69 -923 188 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 5.4e+002 0.833333 0.000000 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.333333 0.500000 0.000000 0.166667 0.166667 0.500000 0.166667 0.000000 0.333333 0.000000 0.666667 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.500000 0.166667 0.333333 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.833333 0.166667 0.000000 0.166667 0.000000 0.833333 0.000000 0.500000 0.166667 0.000000 0.333333 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.166667 0.833333 0.000000 0.166667 0.833333 0.000000 0.166667 0.166667 0.166667 0.500000 0.166667 0.333333 0.000000 0.500000 0.833333 0.166667 0.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.166667 0.333333 0.500000 0.166667 0.000000 0.833333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- AA[GC]G[TC][CT]G[AG][TC]CG[AT]TTGT[TC]A[TG][TG]G -------------------------------------------------------------------------------- Time 1.18 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 32183 6.90e-13 1_[+1(6.69e-10)]_386_[+3(5.26e-08)]_\ 46_[+2(2.81e-07)]_6 29736 1.75e-08 182_[+3(2.30e-08)]_29_\ [+2(1.36e-08)]_248 39556 1.04e-14 130_[+1(8.48e-12)]_94_\ [+2(1.20e-07)]_85_[+3(1.16e-07)]_130 10988 6.72e-14 117_[+3(4.67e-09)]_201_\ [+1(4.15e-09)]_119_[+2(4.34e-08)]_2 34551 3.29e-08 13_[+3(4.87e-08)]_202_\ [+2(8.10e-05)]_205_[+2(2.41e-08)]_19 35713 9.86e-17 7_[+2(2.08e-11)]_204_[+3(1.08e-08)]_\ 134_[+1(3.93e-09)]_94 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************