******************************************************************************** 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/488/488.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 46402 1.0000 500 13424 1.0000 500 37959 1.0000 500 14242 1.0000 500 14898 1.0000 500 18029 1.0000 500 43744 1.0000 500 30246 1.0000 500 50183 1.0000 500 41645 1.0000 500 44323 1.0000 500 44733 1.0000 500 34853 1.0000 500 12217 1.0000 500 8096 1.0000 500 38679 1.0000 500 50456 1.0000 500 48938 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/488/488.seqs.fa -oc motifs/488 -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= 18 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= 9000 N= 18 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.256 C 0.267 G 0.222 T 0.255 Background letter frequencies (from dataset with add-one prior applied): A 0.256 C 0.267 G 0.222 T 0.255 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 15 llr = 166 E-value = 3.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 292a354739671927 pos.-specific C 817:336171339:62 probability G ::::3::2:::1:121 matrix T ::1:13::::1::::1 bits 2.2 2.0 * 1.7 * 1.5 * * * Relative 1.3 ** * * ** Entropy 1.1 ** * ** ** (15.9 bits) 0.9 **** * ** *** 0.7 **** ********** 0.4 **** *********** 0.2 **************** 0.0 ---------------- Multilevel CACAAACACAAACACA consensus A A GCAGA CC AC sequence CT G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 14242 42 8.95e-09 CAAACACACG CACACACACACACACA GATATACACG 50183 122 3.90e-08 GTCCACGCGA CACAATCGCAAACACA GACTGACTCA 46402 359 1.16e-07 TCCATGTATT CACAGTCACACACACC GCTACCTTTC 18029 455 1.52e-07 TCATTCATTA CACACAAGCACACACA CGTCCATTCA 13424 127 1.07e-06 CCCATTCACG CACATACACATACACA CGTGCTCCAC 50456 260 1.31e-06 CGCCTACGGG CACACACACACACAGG TCACATGTGT 30246 318 2.60e-06 GGACCAGCAC CATAGAAAAAACCACA TCAGTCGTAG 34853 449 5.24e-06 CTAGTAGTAC AACAACAACAACAACA ACAACAACAA 44323 323 7.23e-06 CGCAACCTAC CAAAGCAACAAACAAT CAGTCCCAAC 48938 404 8.42e-06 TTTCTTGGTC CACACAAACACGCAAC ACGATAAACA 43744 251 9.08e-06 GTGTTTTTTT CACAAACGCCAACGAA CTCTCTCGTA 44733 474 1.60e-05 ACGTACCACC ACCAGTACCAAACACA ATCATTACAC 38679 322 1.94e-05 CTTTGTGACT CACAGCCCAAACAAGA AAACCCGACG 12217 477 2.07e-05 AAATGCTATC AAAAATCAAAAACGGA ACCTGGGG 37959 293 2.20e-05 GTCAAGTCAG CAAAACCAACACCACC AACAGCGGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 14242 9e-09 41_[+1]_443 50183 3.9e-08 121_[+1]_363 46402 1.2e-07 358_[+1]_126 18029 1.5e-07 454_[+1]_30 13424 1.1e-06 126_[+1]_358 50456 1.3e-06 259_[+1]_225 30246 2.6e-06 317_[+1]_167 34853 5.2e-06 448_[+1]_36 44323 7.2e-06 322_[+1]_162 48938 8.4e-06 403_[+1]_81 43744 9.1e-06 250_[+1]_234 44733 1.6e-05 473_[+1]_11 38679 1.9e-05 321_[+1]_163 12217 2.1e-05 476_[+1]_8 37959 2.2e-05 292_[+1]_192 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=15 14242 ( 42) CACACACACACACACA 1 50183 ( 122) CACAATCGCAAACACA 1 46402 ( 359) CACAGTCACACACACC 1 18029 ( 455) CACACAAGCACACACA 1 13424 ( 127) CACATACACATACACA 1 50456 ( 260) CACACACACACACAGG 1 30246 ( 318) CATAGAAAAAACCACA 1 34853 ( 449) AACAACAACAACAACA 1 44323 ( 323) CAAAGCAACAAACAAT 1 48938 ( 404) CACACAAACACGCAAC 1 43744 ( 251) CACAAACGCCAACGAA 1 44733 ( 474) ACCAGTACCAAACACA 1 38679 ( 322) CACAGCCCAAACAAGA 1 12217 ( 477) AAAAATCAAAAACGGA 1 37959 ( 293) CAAAACCAACACCACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8730 bayes= 9.85755 E= 3.6e+000 -36 158 -1055 -1055 186 -200 -1055 -1055 -36 146 -1055 -193 196 -1055 -1055 -1055 38 0 59 -193 86 0 -1055 6 64 117 -1055 -1055 138 -100 -15 -1055 6 146 -1055 -1055 176 -100 -1055 -1055 123 32 -1055 -193 138 0 -173 -1055 -94 170 -1055 -1055 176 -1055 -73 -1055 -36 117 -15 -1055 138 -42 -173 -193 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 15 E= 3.6e+000 0.200000 0.800000 0.000000 0.000000 0.933333 0.066667 0.000000 0.000000 0.200000 0.733333 0.000000 0.066667 1.000000 0.000000 0.000000 0.000000 0.333333 0.266667 0.333333 0.066667 0.466667 0.266667 0.000000 0.266667 0.400000 0.600000 0.000000 0.000000 0.666667 0.133333 0.200000 0.000000 0.266667 0.733333 0.000000 0.000000 0.866667 0.133333 0.000000 0.000000 0.600000 0.333333 0.000000 0.066667 0.666667 0.266667 0.066667 0.000000 0.133333 0.866667 0.000000 0.000000 0.866667 0.000000 0.133333 0.000000 0.200000 0.600000 0.200000 0.000000 0.666667 0.200000 0.066667 0.066667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA]A[CA]A[AGC][ACT][CA][AG][CA]A[AC][AC]CA[CAG][AC] -------------------------------------------------------------------------------- Time 3.17 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 4 llr = 83 E-value = 2.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :383:::8::3:3:a38::83 pos.-specific C :::3::3:5::::8:::8::: probability G a335aa835a8883:8::a38 matrix T :5:::::::::3::::33::: bits 2.2 * ** * * 2.0 * ** * * * 1.7 * ** * * * 1.5 * ** * * * Relative 1.3 * * **** **** ** *** Entropy 1.1 * * ***************** (29.8 bits) 0.9 * * ***************** 0.7 * ******************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GTAGGGGACGGGGCAGACGAG consensus AGA CGG ATAG ATT GA sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 12217 354 1.70e-12 GGCCAAAGAC GTAGGGGAGGGTGCAGACGAG GGTGATGAAC 46402 263 3.83e-10 TTTGAAAGGC GTACGGCACGGGACAGTCGAG CTAGTAGCGA 41645 317 6.49e-10 CTAGGACGCC GAAAGGGACGAGGCAGATGAA CTGTCAACCC 37959 164 7.44e-10 CTCAACCAAA GGGGGGGGGGGGGGAAACGGG ACACAGGCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 12217 1.7e-12 353_[+2]_126 46402 3.8e-10 262_[+2]_217 41645 6.5e-10 316_[+2]_163 37959 7.4e-10 163_[+2]_316 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=4 12217 ( 354) GTAGGGGAGGGTGCAGACGAG 1 46402 ( 263) GTACGGCACGGGACAGTCGAG 1 41645 ( 317) GAAAGGGACGAGGCAGATGAA 1 37959 ( 164) GGGGGGGGGGGGGGAAACGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 8640 bayes= 11.0761 E= 2.3e+002 -865 -865 217 -865 -4 -865 17 97 155 -865 17 -865 -4 -9 117 -865 -865 -865 217 -865 -865 -865 217 -865 -865 -9 176 -865 155 -865 17 -865 -865 90 117 -865 -865 -865 217 -865 -4 -865 176 -865 -865 -865 176 -3 -4 -865 176 -865 -865 149 17 -865 196 -865 -865 -865 -4 -865 176 -865 155 -865 -865 -3 -865 149 -865 -3 -865 -865 217 -865 155 -865 17 -865 -4 -865 176 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 2.3e+002 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.250000 0.500000 0.750000 0.000000 0.250000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 0.750000 0.250000 0.250000 0.000000 0.750000 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 0.750000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.250000 0.000000 0.750000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[TAG][AG][GAC]GG[GC][AG][CG]G[GA][GT][GA][CG]A[GA][AT][CT]G[AG][GA] -------------------------------------------------------------------------------- Time 6.21 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 14 llr = 137 E-value = 2.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 82:61:a9:499 pos.-specific C :1:151::64:: probability G 23a129::4211 matrix T :4:11::1:::: bits 2.2 * 2.0 * * 1.7 * ** 1.5 * *** * Relative 1.3 * * *** ** Entropy 1.1 * * **** ** (14.1 bits) 0.9 * * **** ** 0.7 * * **** ** 0.4 * ** ******* 0.2 * ********** 0.0 ------------ Multilevel ATGACGAACAAA consensus GG G GC sequence A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 30246 276 6.26e-07 ATAGCGCTAG AGGACGAACGAA CACTGCAAAA 50183 421 7.89e-07 CAATACGAAG AGGACGAAGCAA GAAGTTCCAT 41645 487 2.36e-06 CGTCTCGAAA ATGTCGAACAAA TG 8096 193 3.11e-06 GATGATAAAA ATGATGAAGAAA AAAACCGGTC 38679 97 4.61e-06 CAAGGGCTCG ATGATGAAGCAA TCGCCAGCCT 12217 328 6.42e-06 CGACAGAAGG AAGAAGAAGAAA GATTGGCCAA 43744 480 9.29e-06 CGATGAAGAC AAGGCGAACAAA CGATCCCCC 34853 159 1.15e-05 ACTTACGCCA ACGCCGAACCAA TCCTATGTCC 44733 15 1.63e-05 AGCTTCGATC GGGCCGAACCAA GTAGAAAGAT 50456 86 2.34e-05 ACACGGGGAG AGGAGGATCAAA GGTGGCACGA 48938 334 4.53e-05 GTTTTGGTTC GTGACGAACGGA CACGTTTTAG 44323 74 4.88e-05 GCGATGCCGT GAGAGGAACCAG TATTCGTCCG 13424 255 6.45e-05 AACCTAACAA ACGAGCAAGAAA GTTTTGTTCA 14898 107 7.19e-05 TACAAGGATA ATGTAGAACGAG CGTATTGCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 30246 6.3e-07 275_[+3]_213 50183 7.9e-07 420_[+3]_68 41645 2.4e-06 486_[+3]_2 8096 3.1e-06 192_[+3]_296 38679 4.6e-06 96_[+3]_392 12217 6.4e-06 327_[+3]_161 43744 9.3e-06 479_[+3]_9 34853 1.2e-05 158_[+3]_330 44733 1.6e-05 14_[+3]_474 50456 2.3e-05 85_[+3]_403 48938 4.5e-05 333_[+3]_155 44323 4.9e-05 73_[+3]_415 13424 6.5e-05 254_[+3]_234 14898 7.2e-05 106_[+3]_382 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=14 30246 ( 276) AGGACGAACGAA 1 50183 ( 421) AGGACGAAGCAA 1 41645 ( 487) ATGTCGAACAAA 1 8096 ( 193) ATGATGAAGAAA 1 38679 ( 97) ATGATGAAGCAA 1 12217 ( 328) AAGAAGAAGAAA 1 43744 ( 480) AAGGCGAACAAA 1 34853 ( 159) ACGCCGAACCAA 1 44733 ( 15) GGGCCGAACCAA 1 50456 ( 86) AGGAGGATCAAA 1 48938 ( 334) GTGACGAACGGA 1 44323 ( 74) GAGAGGAACCAG 1 13424 ( 255) ACGAGCAAGAAA 1 14898 ( 107) ATGTAGAACGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 8802 bayes= 9.90047 E= 2.6e+001 162 -1045 -5 -1045 -26 -90 37 48 -1045 -1045 217 -1045 133 -90 -163 -84 -84 91 -5 -84 -1045 -190 207 -1045 196 -1045 -1045 -1045 186 -1045 -1045 -183 -1045 127 69 -1045 74 42 -5 -1045 186 -1045 -163 -1045 174 -1045 -63 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 14 E= 2.6e+001 0.785714 0.000000 0.214286 0.000000 0.214286 0.142857 0.285714 0.357143 0.000000 0.000000 1.000000 0.000000 0.642857 0.142857 0.071429 0.142857 0.142857 0.500000 0.214286 0.142857 0.000000 0.071429 0.928571 0.000000 1.000000 0.000000 0.000000 0.000000 0.928571 0.000000 0.000000 0.071429 0.000000 0.642857 0.357143 0.000000 0.428571 0.357143 0.214286 0.000000 0.928571 0.000000 0.071429 0.000000 0.857143 0.000000 0.142857 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AG][TGA]GA[CG]GAA[CG][ACG]AA -------------------------------------------------------------------------------- Time 9.43 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46402 1.21e-09 262_[+2(3.83e-10)]_75_\ [+1(1.16e-07)]_126 13424 9.21e-04 126_[+1(1.07e-06)]_112_\ [+3(6.45e-05)]_234 37959 7.14e-07 163_[+2(7.44e-10)]_108_\ [+1(2.20e-05)]_192 14242 1.29e-04 41_[+1(8.95e-09)]_443 14898 2.52e-01 106_[+3(7.19e-05)]_382 18029 2.04e-04 289_[+2(8.84e-05)]_144_\ [+1(1.52e-07)]_30 43744 2.25e-04 250_[+1(9.08e-06)]_213_\ [+3(9.29e-06)]_9 30246 2.09e-05 194_[+3(1.63e-05)]_69_\ [+3(6.26e-07)]_30_[+1(2.60e-06)]_167 50183 9.99e-07 121_[+1(3.90e-08)]_283_\ [+3(7.89e-07)]_68 41645 8.56e-08 316_[+2(6.49e-10)]_149_\ [+3(2.36e-06)]_2 44323 4.19e-03 73_[+3(4.88e-05)]_192_\ [+1(6.72e-05)]_29_[+1(7.23e-06)]_162 44733 3.24e-03 14_[+3(1.63e-05)]_447_\ [+1(1.60e-05)]_11 34853 5.30e-04 158_[+3(1.15e-05)]_278_\ [+1(5.24e-06)]_2_[+1(5.24e-06)]_2_[+1(5.24e-06)] 12217 1.34e-11 327_[+3(6.42e-06)]_14_\ [+2(1.70e-12)]_102_[+1(2.07e-05)]_8 8096 5.57e-03 192_[+3(3.11e-06)]_189_\ [+3(2.34e-05)]_95 38679 8.60e-04 96_[+3(4.61e-06)]_64_[+3(3.05e-05)]_\ 137_[+1(1.94e-05)]_163 50456 2.67e-04 85_[+3(2.34e-05)]_162_\ [+1(1.31e-06)]_225 48938 4.19e-03 333_[+3(4.53e-05)]_58_\ [+1(8.42e-06)]_81 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************