******************************************************************************** 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/377/377.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 32401 1.0000 500 46400 1.0000 500 46496 1.0000 500 15134 1.0000 500 43298 1.0000 500 43665 1.0000 500 40273 1.0000 500 40822 1.0000 500 41348 1.0000 500 41349 1.0000 500 33342 1.0000 500 45110 1.0000 500 45305 1.0000 500 54409 1.0000 500 42518 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/377/377.seqs.fa -oc motifs/377 -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 0.267 C 0.243 G 0.223 T 0.266 Background letter frequencies (from dataset with add-one prior applied): A 0.267 C 0.243 G 0.223 T 0.266 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 6 llr = 93 E-value = 7.3e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::::::35::7::: pos.-specific C a:3:25:77:a::2a: probability G :82322a::::a:::a matrix T :25773:3:5::38:: bits 2.2 * * * 1.9 * * ** ** 1.7 * * ** ** 1.5 ** * ** ** Relative 1.3 ** * ** *** Entropy 1.1 ** * *** ****** (22.3 bits) 0.9 ** * ********** 0.6 ** ************* 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CGTTTCGCCACGATCG consensus CG T TAT T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 43665 193 1.09e-09 GTGCGCTCGC CGTTTTGCCACGATCG CGCTTACGGT 40822 95 5.22e-09 TTAACGTGCT CGCTTCGTCTCGATCG CGTCCGTACG 41348 152 6.05e-08 TCTCCTGTTA CGTGTCGCCACGTCCG TCGCCGGACC 40273 284 7.73e-08 AACGGAACAA CTTTTTGCCTCGTTCG ACAACAACGG 41349 395 1.43e-07 GCTACTGGAT CGCGGCGTATCGATCG AAGTGTTTGG 46400 335 1.90e-07 TTTCGCGGAT CGGTCGGCAACGATCG AATTCCTGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43665 1.1e-09 192_[+1]_292 40822 5.2e-09 94_[+1]_390 41348 6e-08 151_[+1]_333 40273 7.7e-08 283_[+1]_201 41349 1.4e-07 394_[+1]_90 46400 1.9e-07 334_[+1]_150 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=6 43665 ( 193) CGTTTTGCCACGATCG 1 40822 ( 95) CGCTTCGTCTCGATCG 1 41348 ( 152) CGTGTCGCCACGTCCG 1 40273 ( 284) CTTTTTGCCTCGTTCG 1 41349 ( 395) CGCGGCGTATCGATCG 1 46400 ( 335) CGGTCGGCAACGATCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 7275 bayes= 10.6904 E= 7.3e+001 -923 204 -923 -923 -923 -923 190 -68 -923 45 -42 91 -923 -923 58 132 -923 -54 -42 132 -923 104 -42 32 -923 -923 216 -923 -923 145 -923 32 32 145 -923 -923 90 -923 -923 91 -923 204 -923 -923 -923 -923 216 -923 132 -923 -923 32 -923 -54 -923 164 -923 204 -923 -923 -923 -923 216 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 6 E= 7.3e+001 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.333333 0.166667 0.500000 0.000000 0.000000 0.333333 0.666667 0.000000 0.166667 0.166667 0.666667 0.000000 0.500000 0.166667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.333333 0.666667 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.166667 0.000000 0.833333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CG[TC][TG]T[CT]G[CT][CA][AT]CG[AT]TCG -------------------------------------------------------------------------------- Time 1.83 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 7 llr = 99 E-value = 8.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 719:1:::613:1a6: pos.-specific C :::94:::113:7:1a probability G :9:1:a:a144a::1: matrix T 3:1:4:a:13::1:1: bits 2.2 * * * 1.9 *** * * * 1.7 *** * * * 1.5 * * *** * * * Relative 1.3 *** *** * * * Entropy 1.1 **** *** * * * (20.3 bits) 0.9 **** *** *** * 0.6 **** *** *** * 0.4 ******** **** * 0.2 **************** 0.0 ---------------- Multilevel AGACCGTGAGGGCAAC consensus T T TA sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 40273 252 6.07e-09 GGATCACGAT TGACTGTGAGCGCAAC CGCGGAAACG 33342 173 1.12e-08 ACTTCATGCT AGACTGTGAGGGAAAC TGACGGCGAG 43298 256 5.10e-08 AGAACATCGC AGACAGTGACAGCAAC TGCGAATTGT 32401 341 1.63e-07 TAGATCAATA AAACCGTGGTGGCAAC GCACTGCAAA 45110 362 2.67e-07 AAGGCAGTAC AGAGCGTGCGGGCAGC TCATTTTTTC 43665 349 8.73e-07 TTTGCGGAAG AGTCTGTGTTCGCATC CATACGCGAC 41349 87 9.21e-07 TTCCACGAAT TGACCGTGAAAGTACC CGTATGTGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 40273 6.1e-09 251_[+2]_233 33342 1.1e-08 172_[+2]_312 43298 5.1e-08 255_[+2]_229 32401 1.6e-07 340_[+2]_144 45110 2.7e-07 361_[+2]_123 43665 8.7e-07 348_[+2]_136 41349 9.2e-07 86_[+2]_398 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=7 40273 ( 252) TGACTGTGAGCGCAAC 1 33342 ( 173) AGACTGTGAGGGAAAC 1 43298 ( 256) AGACAGTGACAGCAAC 1 32401 ( 341) AAACCGTGGTGGCAAC 1 45110 ( 362) AGAGCGTGCGGGCAGC 1 43665 ( 349) AGTCTGTGTTCGCATC 1 41349 ( 87) TGACCGTGAAAGTACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 7275 bayes= 10.6262 E= 8.6e+001 142 -945 -945 10 -90 -945 194 -945 168 -945 -945 -90 -945 182 -64 -945 -90 82 -945 69 -945 -945 216 -945 -945 -945 -945 191 -945 -945 216 -945 110 -77 -64 -90 -90 -77 94 10 10 23 94 -945 -945 -945 216 -945 -90 155 -945 -90 190 -945 -945 -945 110 -77 -64 -90 -945 204 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 7 E= 8.6e+001 0.714286 0.000000 0.000000 0.285714 0.142857 0.000000 0.857143 0.000000 0.857143 0.000000 0.000000 0.142857 0.000000 0.857143 0.142857 0.000000 0.142857 0.428571 0.000000 0.428571 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.571429 0.142857 0.142857 0.142857 0.142857 0.142857 0.428571 0.285714 0.285714 0.285714 0.428571 0.000000 0.000000 0.000000 1.000000 0.000000 0.142857 0.714286 0.000000 0.142857 1.000000 0.000000 0.000000 0.000000 0.571429 0.142857 0.142857 0.142857 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AT]GAC[CT]GTGA[GT][GAC]GCAAC -------------------------------------------------------------------------------- Time 3.89 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 6 llr = 105 E-value = 4.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :5:2::::2::::5:2:::: pos.-specific C 2:2:::5:2a3::32:::2a probability G 8583a22:3::382:2::5: matrix T :::5:83a3:772:87aa3: bits 2.2 * 1.9 * * * ** * 1.7 * * * ** * 1.5 * * * * * * ** * Relative 1.3 * * ** * * * * ** * Entropy 1.1 *** ** * **** * ** * (25.2 bits) 0.9 *** ** * **** * ** * 0.6 *** **** **** ****** 0.4 ******** *********** 0.2 ******** *********** 0.0 -------------------- Multilevel GAGTGTCTGCTTGATTTTGC consensus G G T T CG C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 42518 191 7.32e-11 GTAGAGAGGG GGGGGTCTGCCTGCTTTTGC TGGTAGTGAA 46400 48 1.06e-09 TCAAGGGTGT GAGGGTTTGCTGGATTTTCC AACGACTGGC 45110 68 3.09e-09 CGCTTTCCTA GAGTGGGTCCTTGATTTTGC CAAAAGTAAG 46496 280 3.09e-09 TCCAAAGGAA CGGTGTCTTCCTGCTTTTTC GAAAATAAGT 54409 263 1.45e-08 GATATTTCCA GAGAGTCTTCTTGACATTTC GAAAAAGCGA 45305 124 7.76e-08 AACAGGGCAG GGCTGTTTACTGTGTGTTGC ACTTTTCACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42518 7.3e-11 190_[+3]_290 46400 1.1e-09 47_[+3]_433 45110 3.1e-09 67_[+3]_413 46496 3.1e-09 279_[+3]_201 54409 1.4e-08 262_[+3]_218 45305 7.8e-08 123_[+3]_357 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=6 42518 ( 191) GGGGGTCTGCCTGCTTTTGC 1 46400 ( 48) GAGGGTTTGCTGGATTTTCC 1 45110 ( 68) GAGTGGGTCCTTGATTTTGC 1 46496 ( 280) CGGTGTCTTCCTGCTTTTTC 1 54409 ( 263) GAGAGTCTTCTTGACATTTC 1 45305 ( 124) GGCTGTTTACTGTGTGTTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 7215 bayes= 10.6784 E= 4.2e+001 -923 -54 190 -923 90 -923 116 -923 -923 -54 190 -923 -68 -923 58 91 -923 -923 216 -923 -923 -923 -42 164 -923 104 -42 32 -923 -923 -923 191 -68 -54 58 32 -923 204 -923 -923 -923 45 -923 132 -923 -923 58 132 -923 -923 190 -68 90 45 -42 -923 -923 -54 -923 164 -68 -923 -42 132 -923 -923 -923 191 -923 -923 -923 191 -923 -54 116 32 -923 204 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 4.2e+001 0.000000 0.166667 0.833333 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.166667 0.833333 0.000000 0.166667 0.000000 0.333333 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.500000 0.166667 0.333333 0.000000 0.000000 0.000000 1.000000 0.166667 0.166667 0.333333 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.833333 0.166667 0.500000 0.333333 0.166667 0.000000 0.000000 0.166667 0.000000 0.833333 0.166667 0.000000 0.166667 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.500000 0.333333 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[AG]G[TG]GT[CT]T[GT]C[TC][TG]G[AC]TTTT[GT]C -------------------------------------------------------------------------------- Time 6.25 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 32401 1.92e-03 340_[+2(1.63e-07)]_144 46400 1.06e-08 47_[+3(1.06e-09)]_267_\ [+1(1.90e-07)]_150 46496 1.85e-05 279_[+3(3.09e-09)]_201 15134 1.45e-02 219_[+3(2.17e-05)]_261 43298 6.71e-04 255_[+2(5.10e-08)]_229 43665 2.17e-08 75_[+1(5.08e-06)]_101_\ [+1(1.09e-09)]_140_[+2(8.73e-07)]_136 40273 2.22e-08 251_[+2(6.07e-09)]_16_\ [+1(7.73e-08)]_201 40822 7.16e-05 94_[+1(5.22e-09)]_390 41348 1.18e-03 151_[+1(6.05e-08)]_333 41349 8.65e-07 86_[+2(9.21e-07)]_292_\ [+1(1.43e-07)]_90 33342 2.98e-04 172_[+2(1.12e-08)]_312 45110 1.33e-08 67_[+3(3.09e-09)]_274_\ [+2(2.67e-07)]_123 45305 6.31e-04 123_[+3(7.76e-08)]_357 54409 3.77e-04 262_[+3(1.45e-08)]_218 42518 2.99e-06 190_[+3(7.32e-11)]_290 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************