******************************************************************************** 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/264/264.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 8866 1.0000 500 43047 1.0000 500 54688 1.0000 500 13856 1.0000 500 15324 1.0000 500 43420 1.0000 500 18303 1.0000 500 43900 1.0000 500 10362 1.0000 500 45148 1.0000 500 20066 1.0000 500 45980 1.0000 500 45607 1.0000 500 49992 1.0000 500 35344 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/264/264.seqs.fa -oc motifs/264 -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= 15 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= 7500 N= 15 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.253 C 0.278 G 0.224 T 0.245 Background letter frequencies (from dataset with add-one prior applied): A 0.253 C 0.278 G 0.224 T 0.245 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 14 sites = 8 llr = 112 E-value = 1.8e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :45:::a:8:11a9 pos.-specific C :3:4:8:9:::8:: probability G a4:::::::a:::1 matrix T ::56a3:13:91:: bits 2.2 * * 1.9 * * * * * 1.7 * * * * * 1.5 * * * ** ** Relative 1.3 * * ** ** ** Entropy 1.1 * ********* ** (20.1 bits) 0.9 * ************ 0.6 * ************ 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel GAATTCACAGTCAA consensus GTC T T sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 43420 142 1.54e-08 AACGTTTTCC GAATTCACAGTCAA CGATCTCCAT 35344 436 2.85e-08 CAGAGGGAAG GGTCTCACAGTCAA TAGATTTTTA 45607 436 2.85e-08 CAGAGGGAAG GGTCTCACAGTCAA TAGATTTTTA 43047 126 2.85e-08 TCCAGCGATA GCATTCACAGTCAA CCAAGATGGA 18303 248 3.75e-07 CAGTAAGTTT GATTTTACAGTTAA TTTTTGACCC 13856 79 3.75e-07 AACAACGCTC GCATTTACTGTCAA TCGACTCGAC 49992 129 7.94e-07 ATGAGAAGGA GATCTCACTGTCAG ACGATCCAAC 54688 88 2.15e-06 TGCTGCCAAT GGATTCATAGAAAA CGGGAACTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43420 1.5e-08 141_[+1]_345 35344 2.8e-08 435_[+1]_51 45607 2.8e-08 435_[+1]_51 43047 2.8e-08 125_[+1]_361 18303 3.8e-07 247_[+1]_239 13856 3.8e-07 78_[+1]_408 49992 7.9e-07 128_[+1]_358 54688 2.1e-06 87_[+1]_399 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=14 seqs=8 43420 ( 142) GAATTCACAGTCAA 1 35344 ( 436) GGTCTCACAGTCAA 1 45607 ( 436) GGTCTCACAGTCAA 1 43047 ( 126) GCATTCACAGTCAA 1 18303 ( 248) GATTTTACAGTTAA 1 13856 ( 79) GCATTTACTGTCAA 1 49992 ( 129) GATCTCACTGTCAG 1 54688 ( 88) GGATTCATAGAAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 7305 bayes= 9.83309 E= 1.8e-002 -965 -965 215 -965 57 -15 74 -965 98 -965 -965 103 -965 43 -965 135 -965 -965 -965 203 -965 143 -965 3 198 -965 -965 -965 -965 165 -965 -97 157 -965 -965 3 -965 -965 215 -965 -101 -965 -965 183 -101 143 -965 -97 198 -965 -965 -965 179 -965 -84 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 8 E= 1.8e-002 0.000000 0.000000 1.000000 0.000000 0.375000 0.250000 0.375000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.375000 0.000000 0.625000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 0.000000 0.875000 0.000000 0.125000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.125000 0.000000 0.000000 0.875000 0.125000 0.750000 0.000000 0.125000 1.000000 0.000000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[AGC][AT][TC]T[CT]AC[AT]GTCAA -------------------------------------------------------------------------------- Time 1.92 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 9 llr = 140 E-value = 7.1e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1:12:6412:3:1:::3:::: pos.-specific C 7::394::3a11::1::3:11 probability G 2::1::113:14212::6:4: matrix T :a931:481:44797a71a49 bits 2.2 1.9 * * * * 1.7 * * * * 1.5 ** * * * * * Relative 1.3 ** * * * * * * Entropy 1.1 ** * * * * ** * * (22.4 bits) 0.9 ** ** * * ***** * * 0.6 *** **** * ********** 0.4 *** **** * ********** 0.2 *** ***************** 0.0 --------------------- Multilevel CTTCCAATCCTGTTTTTGTGT consensus G T CT G ATG G AC T sequence A A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 35344 7 8.15e-12 CTTTTC CTTTCATTGCATTTTTTGTGT CACATGCTTC 45607 7 8.15e-12 CTTTTC CTTTCAATGCATTTTTTGTGT CACATGCTTC 54688 310 4.64e-09 TTTTCACATT GTTCCATTACTGTTGTAGTTT GACCAGTGCA 43900 153 6.28e-08 ATCCGCAACA GTTACCAACCTTTTTTTTTTT AATGTAAGTA 13856 305 6.78e-08 CGTGGACAAG CTTTCCGTCCTCGTTTACTGT TAGTTGTCGA 15324 162 8.46e-08 CATGAGCAAT ATACCCATCCTTTTTTACTGT ACTGTAAGAA 43420 361 1.20e-07 CCTCGCTCGC CTTCCAAGACGGTTGTTGTCT TTGCTCACCA 10362 295 4.45e-07 GCGGTCGATC CTTGTCTTGCAGAGTTTCTTT TGGTGTTGAC 18303 103 4.68e-07 TTGTTTTGCA CTTACATTTCCGGTCTTGTTC GGAACAGATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35344 8.1e-12 6_[+2]_473 45607 8.1e-12 6_[+2]_473 54688 4.6e-09 309_[+2]_170 43900 6.3e-08 152_[+2]_327 13856 6.8e-08 304_[+2]_175 15324 8.5e-08 161_[+2]_318 43420 1.2e-07 360_[+2]_119 10362 4.4e-07 294_[+2]_185 18303 4.7e-07 102_[+2]_377 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=9 35344 ( 7) CTTTCATTGCATTTTTTGTGT 1 45607 ( 7) CTTTCAATGCATTTTTTGTGT 1 54688 ( 310) GTTCCATTACTGTTGTAGTTT 1 43900 ( 153) GTTACCAACCTTTTTTTTTTT 1 13856 ( 305) CTTTCCGTCCTCGTTTACTGT 1 15324 ( 162) ATACCCATCCTTTTTTACTGT 1 43420 ( 361) CTTCCAAGACGGTTGTTGTCT 1 10362 ( 295) CTTGTCTTGCAGAGTTTCTTT 1 18303 ( 103) CTTACATTTCCGGTCTTGTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7200 bayes= 9.77651 E= 7.1e-002 -118 126 -1 -982 -982 -982 -982 203 -118 -982 -982 186 -18 26 -101 44 -982 168 -982 -114 114 68 -982 -982 81 -982 -101 86 -118 -982 -101 167 -18 26 57 -114 -982 185 -982 -982 40 -132 -101 86 -982 -132 99 86 -118 -982 -1 144 -982 -982 -101 186 -982 -132 -1 144 -982 -982 -982 203 40 -982 -982 144 -982 26 131 -114 -982 -982 -982 203 -982 -132 99 86 -982 -132 -982 186 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 7.1e-002 0.111111 0.666667 0.222222 0.000000 0.000000 0.000000 0.000000 1.000000 0.111111 0.000000 0.000000 0.888889 0.222222 0.333333 0.111111 0.333333 0.000000 0.888889 0.000000 0.111111 0.555556 0.444444 0.000000 0.000000 0.444444 0.000000 0.111111 0.444444 0.111111 0.000000 0.111111 0.777778 0.222222 0.333333 0.333333 0.111111 0.000000 1.000000 0.000000 0.000000 0.333333 0.111111 0.111111 0.444444 0.000000 0.111111 0.444444 0.444444 0.111111 0.000000 0.222222 0.666667 0.000000 0.000000 0.111111 0.888889 0.000000 0.111111 0.222222 0.666667 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.333333 0.555556 0.111111 0.000000 0.000000 0.000000 1.000000 0.000000 0.111111 0.444444 0.444444 0.000000 0.111111 0.000000 0.888889 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CG]TT[CTA]C[AC][AT]T[CGA]C[TA][GT][TG]T[TG]T[TA][GC]T[GT]T -------------------------------------------------------------------------------- Time 3.90 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 5 llr = 102 E-value = 1.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::28aa44a8a4:64::::2: pos.-specific C ::62:::2:2:::2:::2::: probability G :8::::62:::2a:::46a8: matrix T a22::::2:::4:26a62::a bits 2.2 * * 1.9 * ** * * * * * * 1.7 * ** * * * * * * 1.5 ** ** * * * * * * Relative 1.3 ** *** *** * * *** Entropy 1.1 ** **** *** * *** *** (29.3 bits) 0.9 ** **** *** * *** *** 0.6 ******* *** ********* 0.4 ******* ************* 0.2 ******* ************* 0.0 --------------------- Multilevel TGCAAAGAAAAAGATTTGGGT consensus TAC AC C T CA GC A sequence T G G T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 35344 327 1.90e-12 ATAGGCTGTT TGCAAAGAAAATGAATGGGGT GGCTATTTGG 45607 327 1.90e-12 ATAGGCTGTT TGCAAAGAAAATGAATGGGGT GGCTATTTGG 43420 59 3.37e-10 ATATGTGAAA TGAAAAACAAAAGATTTCGGT CAGAGTACCT 45980 169 2.60e-09 ACGCGGTCAG TGTCAAGGAAAGGCTTTTGGT TCGAAAACCG 49992 256 3.38e-09 AGTATTATTT TTCAAAATACAAGTTTTGGAT TTGCACAGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35344 1.9e-12 326_[+3]_153 45607 1.9e-12 326_[+3]_153 43420 3.4e-10 58_[+3]_421 45980 2.6e-09 168_[+3]_311 49992 3.4e-09 255_[+3]_224 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=5 35344 ( 327) TGCAAAGAAAATGAATGGGGT 1 45607 ( 327) TGCAAAGAAAATGAATGGGGT 1 43420 ( 59) TGAAAAACAAAAGATTTCGGT 1 45980 ( 169) TGTCAAGGAAAGGCTTTTGGT 1 49992 ( 256) TTCAAAATACAAGTTTTGGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7200 bayes= 10.7426 E= 1.1e+000 -897 -897 -897 203 -897 -897 183 -29 -34 111 -897 -29 166 -47 -897 -897 198 -897 -897 -897 198 -897 -897 -897 66 -897 142 -897 66 -47 -17 -29 198 -897 -897 -897 166 -47 -897 -897 198 -897 -897 -897 66 -897 -17 71 -897 -897 215 -897 125 -47 -897 -29 66 -897 -897 129 -897 -897 -897 203 -897 -897 83 129 -897 -47 142 -29 -897 -897 215 -897 -34 -897 183 -897 -897 -897 -897 203 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 1.1e+000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.200000 0.600000 0.000000 0.200000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.400000 0.200000 0.200000 0.200000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.200000 0.400000 0.000000 0.000000 1.000000 0.000000 0.600000 0.200000 0.000000 0.200000 0.400000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.200000 0.600000 0.200000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[GT][CAT][AC]AA[GA][ACGT]A[AC]A[ATG]G[ACT][TA]T[TG][GCT]G[GA]T -------------------------------------------------------------------------------- Time 5.88 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8866 7.01e-01 500 43047 6.86e-04 125_[+1(2.85e-08)]_361 54688 2.48e-07 87_[+1(2.15e-06)]_208_\ [+2(4.64e-09)]_170 13856 1.88e-07 78_[+1(3.75e-07)]_212_\ [+2(6.78e-08)]_175 15324 2.22e-04 161_[+2(8.46e-08)]_318 43420 5.13e-14 58_[+3(3.37e-10)]_62_[+1(1.54e-08)]_\ 205_[+2(1.20e-07)]_119 18303 1.32e-06 102_[+2(4.68e-07)]_124_\ [+1(3.75e-07)]_239 43900 8.99e-05 152_[+2(6.28e-08)]_327 10362 9.60e-03 294_[+2(4.45e-07)]_185 45148 4.39e-01 500 20066 7.10e-01 500 45980 5.86e-05 168_[+3(2.60e-09)]_311 45607 6.77e-20 6_[+2(8.15e-12)]_299_[+3(1.90e-12)]_\ 88_[+1(2.85e-08)]_51 49992 7.43e-08 128_[+1(7.94e-07)]_113_\ [+3(3.38e-09)]_224 35344 6.77e-20 6_[+2(8.15e-12)]_299_[+3(1.90e-12)]_\ 88_[+1(2.85e-08)]_51 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************