******************************************************************************** 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/278/278.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11343 1.0000 500 11504 1.0000 500 11505 1.0000 500 11962 1.0000 500 36686 1.0000 500 3734 1.0000 500 4215 1.0000 500 7145 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/278/278.seqs.fa -oc motifs/278 -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= 8 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= 4000 N= 8 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.252 C 0.228 G 0.246 T 0.273 Background letter frequencies (from dataset with add-one prior applied): A 0.252 C 0.228 G 0.247 T 0.273 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 6 llr = 106 E-value = 9.3e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 872::a3:7:82:383753a pos.-specific C :3828::a3a2835:5:27: probability G ::::::2:::::::223::: matrix T 2::82:5:::::72:::3:: bits 2.1 * * 1.9 * * * * 1.7 * * * * 1.5 * ** * * * * Relative 1.3 * **** * *** * * Entropy 1.1 ****** ****** * * ** (25.6 bits) 0.9 ****** ****** * * ** 0.6 ****** ********** ** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel AACTCATCACACTCACAACA consensus C A C CA AGTA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 11505 475 3.24e-11 CATTCACCGC AACTCAACACACCAACAACA TCAGCC 11504 475 9.37e-11 CATTCATCGC AACTCAACACACCAAAAACA TCAACC 7145 367 4.87e-10 CGCCAAATCA ACCTCAGCCCACTCACATCA AAAATTACCG 36686 471 3.73e-09 CCCCCCCCCA TACCCATCACACTCACATAA CACCTCATCA 4215 417 5.35e-08 TATGCCTCAT ACATCATCACAATCAGGCAA CGATTGATGC 3734 376 5.79e-08 GGACATGCGA AACTTATCCCCCTTGAGACA GGCGGCCCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11505 3.2e-11 474_[+1]_6 11504 9.4e-11 474_[+1]_6 7145 4.9e-10 366_[+1]_114 36686 3.7e-09 470_[+1]_10 4215 5.3e-08 416_[+1]_64 3734 5.8e-08 375_[+1]_105 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=6 11505 ( 475) AACTCAACACACCAACAACA 1 11504 ( 475) AACTCAACACACCAAAAACA 1 7145 ( 367) ACCTCAGCCCACTCACATCA 1 36686 ( 471) TACCCATCACACTCACATAA 1 4215 ( 417) ACATCATCACAATCAGGCAA 1 3734 ( 376) AACTTATCCCCCTTGAGACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 3848 bayes= 8.98104 E= 9.3e-002 172 -923 -923 -71 140 55 -923 -923 -60 187 -923 -923 -923 -45 -923 161 -923 187 -923 -71 199 -923 -923 -923 40 -923 -56 87 -923 213 -923 -923 140 55 -923 -923 -923 213 -923 -923 172 -45 -923 -923 -60 187 -923 -923 -923 55 -923 129 40 113 -923 -71 172 -923 -56 -923 40 113 -56 -923 140 -923 43 -923 99 -45 -923 29 40 155 -923 -923 199 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 9.3e-002 0.833333 0.000000 0.000000 0.166667 0.666667 0.333333 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.833333 0.000000 0.166667 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.166667 0.500000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.333333 0.500000 0.000000 0.166667 0.833333 0.000000 0.166667 0.000000 0.333333 0.500000 0.166667 0.000000 0.666667 0.000000 0.333333 0.000000 0.500000 0.166667 0.000000 0.333333 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[AC]CTCA[TA]C[AC]CAC[TC][CA]A[CA][AG][AT][CA]A -------------------------------------------------------------------------------- Time 0.64 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 4 llr = 87 E-value = 5.7e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::::3:::3a88:::8:35: pos.-specific C :::a888aa::33::8388:8 probability G 8:3:::3::8:::aa3:3::3 matrix T 3a8:3::::::::::::::5: bits 2.1 * ** 1.9 * * ** * ** 1.7 * * ** * ** 1.5 * * ** * ** Relative 1.3 * **************** * Entropy 1.1 ******************* * (31.3 bits) 0.9 ********************* 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GTTCCCCCCGAAAGGCACCAC consensus T G TAG A CC GCGATG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 11504 388 1.07e-13 GTTTCTTCCT GTTCCCCCCGAAAGGCACCAC CTCCTCCTAA 11505 373 3.09e-12 TCCAGTGTCA GTTCCCGCCGAAAGGCACCTC GACCCCTGAC 11962 88 6.33e-10 AAACGCAAGC GTTCCCCCCAACCGGGCCCAG TGGGAATCAG 11343 244 1.08e-09 GAGCAATATA TTGCTACCCGAAAGGCAGATC TCGTAATTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11504 1.1e-13 387_[+2]_92 11505 3.1e-12 372_[+2]_107 11962 6.3e-10 87_[+2]_392 11343 1.1e-09 243_[+2]_236 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=4 11504 ( 388) GTTCCCCCCGAAAGGCACCAC 1 11505 ( 373) GTTCCCGCCGAAAGGCACCTC 1 11962 ( 88) GTTCCCCCCAACCGGGCCCAG 1 11343 ( 244) TTGCTACCCGAAAGGCAGATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3840 bayes= 9.90539 E= 5.7e-001 -865 -865 160 -13 -865 -865 -865 187 -865 -865 2 145 -865 213 -865 -865 -865 172 -865 -13 -1 172 -865 -865 -865 172 2 -865 -865 213 -865 -865 -865 213 -865 -865 -1 -865 160 -865 198 -865 -865 -865 157 13 -865 -865 157 13 -865 -865 -865 -865 202 -865 -865 -865 202 -865 -865 172 2 -865 157 13 -865 -865 -865 172 2 -865 -1 172 -865 -865 99 -865 -865 87 -865 172 2 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 5.7e-001 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.250000 0.750000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.250000 0.750000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.750000 0.250000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT]T[TG]C[CT][CA][CG]CC[GA]A[AC][AC]GG[CG][AC][CG][CA][AT][CG] -------------------------------------------------------------------------------- Time 1.36 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 8 llr = 86 E-value = 3.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 34::a:399:8: pos.-specific C ::::::3::1:: probability G 858a:a311936 matrix T :13:::3::::4 bits 2.1 1.9 *** 1.7 *** 1.5 *** *** Relative 1.3 * *** **** Entropy 1.1 * **** ***** (15.6 bits) 0.9 * **** ***** 0.6 ****** ***** 0.4 ****** ***** 0.2 ****** ***** 0.0 ------------ Multilevel GGGGAGAAAGAG consensus AAT C GT sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 11505 345 2.26e-07 TGTAATTGGC GGGGAGTAAGAG AAAAGTTCCA 36686 323 1.77e-06 AGTGGGAAAC AAGGAGCAAGAG TGAGAGCAGC 11962 5 2.06e-06 GCTG AAGGAGAAAGAG AGCTTATTGT 3734 218 5.66e-06 ATAAGCAAGC GAGGAGCGAGAG GTTGGCTTGT 7145 214 6.26e-06 ATGGTAGTAG GGTGAGGAAGGG GTGGAAATGA 11343 115 8.27e-06 AACACAGACG GGGGAGGAGGAT GTATGTGCAA 4215 260 1.00e-05 TACATTGTGG GGTGAGAAAGGT GGCTGTTGTG 11504 125 2.47e-05 CCGTAGTAAT GTGGAGTAACAT AGAAAAGTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11505 2.3e-07 344_[+3]_144 36686 1.8e-06 322_[+3]_166 11962 2.1e-06 4_[+3]_484 3734 5.7e-06 217_[+3]_271 7145 6.3e-06 213_[+3]_275 11343 8.3e-06 114_[+3]_374 4215 1e-05 259_[+3]_229 11504 2.5e-05 124_[+3]_364 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=8 11505 ( 345) GGGGAGTAAGAG 1 36686 ( 323) AAGGAGCAAGAG 1 11962 ( 5) AAGGAGAAAGAG 1 3734 ( 218) GAGGAGCGAGAG 1 7145 ( 214) GGTGAGGAAGGG 1 11343 ( 115) GGGGAGGAGGAT 1 4215 ( 260) GGTGAGAAAGGT 1 11504 ( 125) GTGGAGTAACAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 3912 bayes= 8.93074 E= 3.9e+001 -1 -965 160 -965 57 -965 102 -113 -965 -965 160 -13 -965 -965 202 -965 199 -965 -965 -965 -965 -965 202 -965 -1 13 2 -13 179 -965 -98 -965 179 -965 -98 -965 -965 -87 183 -965 157 -965 2 -965 -965 -965 134 46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 8 E= 3.9e+001 0.250000 0.000000 0.750000 0.000000 0.375000 0.000000 0.500000 0.125000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.250000 0.250000 0.250000 0.875000 0.000000 0.125000 0.000000 0.875000 0.000000 0.125000 0.000000 0.000000 0.125000 0.875000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 0.625000 0.375000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA][GA][GT]GAG[ACGT]AAG[AG][GT] -------------------------------------------------------------------------------- Time 2.01 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11343 4.01e-07 114_[+3(8.27e-06)]_117_\ [+2(1.08e-09)]_236 11504 2.95e-17 124_[+3(2.47e-05)]_251_\ [+2(1.07e-13)]_66_[+1(9.37e-11)]_6 11505 3.00e-18 344_[+3(2.26e-07)]_16_\ [+2(3.09e-12)]_81_[+1(3.24e-11)]_6 11962 2.47e-08 4_[+3(2.06e-06)]_71_[+2(6.33e-10)]_\ 392 36686 3.13e-07 322_[+3(1.77e-06)]_136_\ [+1(3.73e-09)]_10 3734 1.13e-05 186_[+3(7.55e-05)]_19_\ [+3(5.66e-06)]_146_[+1(5.79e-08)]_105 4215 1.73e-05 259_[+3(1.00e-05)]_145_\ [+1(5.35e-08)]_64 7145 1.60e-07 213_[+3(6.26e-06)]_5_[+3(4.89e-05)]_\ 124_[+1(4.87e-10)]_114 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************