******************************************************************************** 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/139/139.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 43274 1.0000 500 5769 1.0000 500 48580 1.0000 500 48895 1.0000 500 25204 1.0000 500 8451 1.0000 500 9731 1.0000 500 5512 1.0000 500 41417 1.0000 500 44561 1.0000 500 34493 1.0000 500 11850 1.0000 500 46154 1.0000 500 50043 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/139/139.seqs.fa -oc motifs/139 -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= 14 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= 7000 N= 14 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.241 C 0.276 G 0.238 T 0.245 Background letter frequencies (from dataset with add-one prior applied): A 0.241 C 0.276 G 0.238 T 0.245 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 12 llr = 139 E-value = 2.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A a5268:382a1:84:a pos.-specific C :1432a::5:38214: probability G :131::83::41152: matrix T :321::::3:31::4: bits 2.1 * * * 1.9 * * * * 1.7 * * * * 1.5 * ** * * Relative 1.2 * **** * * Entropy 1.0 * **** * ** * (16.7 bits) 0.8 * **** * ** * 0.6 * **** * *** * 0.4 ** ******* ***** 0.2 ** ************* 0.0 ---------------- Multilevel AACAACGACAGCAGCA consensus TGC AGT C AT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 11850 63 4.58e-09 TTCATATAAT AACAACGACATCAGCA AGGGACTGCA 9731 469 4.34e-08 GGCAACAAAG AAGAACAACAGCAGCA ACAAACGCCG 5512 474 3.92e-07 GAGTAGTAGC AATACCGATAGCAATA CCAATCCGGA 44561 393 1.02e-06 CTAGTCGCTT ATCAACAACATCCGTA CTCTATTGGT 46154 46 1.51e-06 GATACGAAAA AGCCACGATACCAACA CTACAATTGG 43274 335 1.66e-06 TCTTTCCAGT AACAACGAAAGGAAGA ACACGAGAGG 41417 358 2.35e-06 ACAACGTACA ACGAACGGTACCAATA TCCACAACCG 48580 226 2.55e-06 CTGTAAACCA AAAAACGACATCGAGA TACGTCGCAA 25204 66 3.84e-06 AGTCTGACGC ATGCACGAAAGTAGCA CAACTCATGG 50043 336 4.47e-06 CACCAGAACC ATCCACGACAACACCA ACGATTTTCG 5769 178 1.35e-05 CCGTCGAACA ATTTACGGCACCCGTA TGTTTGCCAA 48895 164 1.68e-05 CGTGGTACCG AAAGCCAGTAGCAGTA GTAGTAGTAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11850 4.6e-09 62_[+1]_422 9731 4.3e-08 468_[+1]_16 5512 3.9e-07 473_[+1]_11 44561 1e-06 392_[+1]_92 46154 1.5e-06 45_[+1]_439 43274 1.7e-06 334_[+1]_150 41417 2.4e-06 357_[+1]_127 48580 2.6e-06 225_[+1]_259 25204 3.8e-06 65_[+1]_419 50043 4.5e-06 335_[+1]_149 5769 1.4e-05 177_[+1]_307 48895 1.7e-05 163_[+1]_321 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=12 11850 ( 63) AACAACGACATCAGCA 1 9731 ( 469) AAGAACAACAGCAGCA 1 5512 ( 474) AATACCGATAGCAATA 1 44561 ( 393) ATCAACAACATCCGTA 1 46154 ( 46) AGCCACGATACCAACA 1 43274 ( 335) AACAACGAAAGGAAGA 1 41417 ( 358) ACGAACGGTACCAATA 1 48580 ( 226) AAAAACGACATCGAGA 1 25204 ( 66) ATGCACGAAAGTAGCA 1 50043 ( 336) ATCCACGACAACACCA 1 5769 ( 178) ATTTACGGCACCCGTA 1 48895 ( 164) AAAGCCAGTAGCAGTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6790 bayes= 9.58982 E= 2.5e+000 205 -1023 -1023 -1023 105 -173 -151 45 -53 59 7 -55 127 -14 -151 -155 179 -73 -1023 -1023 -1023 185 -1023 -1023 5 -1023 166 -1023 164 -1023 7 -1023 -53 86 -1023 45 205 -1023 -1023 -1023 -153 -14 81 3 -1023 159 -151 -155 164 -73 -151 -1023 79 -173 107 -1023 -1023 59 -51 77 205 -1023 -1023 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 12 E= 2.5e+000 1.000000 0.000000 0.000000 0.000000 0.500000 0.083333 0.083333 0.333333 0.166667 0.416667 0.250000 0.166667 0.583333 0.250000 0.083333 0.083333 0.833333 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.750000 0.000000 0.250000 0.000000 0.166667 0.500000 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 0.083333 0.250000 0.416667 0.250000 0.000000 0.833333 0.083333 0.083333 0.750000 0.166667 0.083333 0.000000 0.416667 0.083333 0.500000 0.000000 0.000000 0.416667 0.166667 0.416667 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[AT][CG][AC]AC[GA][AG][CT]A[GCT]CA[GA][CT]A -------------------------------------------------------------------------------- Time 1.95 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 18 sites = 5 llr = 85 E-value = 2.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::a::82:a:24:42::8 pos.-specific C a::a2264:8:2::22:: probability G :a::8:26::82a:28a2 matrix T :::::::::2:2:64::: bits 2.1 ** * * * 1.9 **** * * * 1.7 **** * * * 1.5 **** * * * Relative 1.2 ****** *** * *** Entropy 1.0 ****** **** ** *** (24.6 bits) 0.8 ****** **** ** *** 0.6 *********** ** *** 0.4 *********** ** *** 0.2 *********** ** *** 0.0 ------------------ Multilevel CGACGACGACGAGTTGGA consensus CCAC TAC AAC G sequence G G C T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ 5512 137 1.15e-10 CCATGACCGA CGACGACGACGAGTCGGA CGGGATTCTT 44561 235 1.87e-09 GGAGACAGAC CGACCACGACGGGTTGGA TGGACGAACC 34493 326 1.24e-08 CGCCGGCGGA CGACGCGGACGCGATGGA CGAGGACGCG 43274 135 2.37e-08 AGCCACTACG CGACGACCATGAGAACGA GTACTCGCAG 8451 359 5.63e-08 AAACTCCGTA CGACGAACACATGTGGGG CAACGCCGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5512 1.1e-10 136_[+2]_346 44561 1.9e-09 234_[+2]_248 34493 1.2e-08 325_[+2]_157 43274 2.4e-08 134_[+2]_348 8451 5.6e-08 358_[+2]_124 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=18 seqs=5 5512 ( 137) CGACGACGACGAGTCGGA 1 44561 ( 235) CGACCACGACGGGTTGGA 1 34493 ( 326) CGACGCGGACGCGATGGA 1 43274 ( 135) CGACGACCATGAGAACGA 1 8451 ( 359) CGACGAACACATGTGGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 6762 bayes= 10.6519 E= 2.8e+002 -897 185 -897 -897 -897 -897 207 -897 205 -897 -897 -897 -897 185 -897 -897 -897 -46 175 -897 173 -46 -897 -897 -27 112 -25 -897 -897 53 133 -897 205 -897 -897 -897 -897 153 -897 -29 -27 -897 175 -897 73 -46 -25 -29 -897 -897 207 -897 73 -897 -897 129 -27 -46 -25 71 -897 -46 175 -897 -897 -897 207 -897 173 -897 -25 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 5 E= 2.8e+002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.800000 0.200000 0.000000 0.000000 0.200000 0.600000 0.200000 0.000000 0.000000 0.400000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.200000 0.000000 0.800000 0.000000 0.400000 0.200000 0.200000 0.200000 0.000000 0.000000 1.000000 0.000000 0.400000 0.000000 0.000000 0.600000 0.200000 0.200000 0.200000 0.400000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CGAC[GC][AC][CAG][GC]A[CT][GA][ACGT]G[TA][TACG][GC]G[AG] -------------------------------------------------------------------------------- Time 3.87 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 14 llr = 128 E-value = 6.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 9:::7:4:21a8 pos.-specific C :6:3:81:11:1 probability G :315:22a:6:1 matrix T 11923:3:71:: bits 2.1 * * 1.9 * * 1.7 * * 1.5 * * * * Relative 1.2 * * ** * * Entropy 1.0 * * ** * ** (13.2 bits) 0.8 *** ** ** ** 0.6 *** ** ** ** 0.4 ****** ***** 0.2 ************ 0.0 ------------ Multilevel ACTGACAGTGAA consensus G CTGT A sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 9731 275 5.01e-08 CATTTGCGAC ACTGACAGTGAA AAGCCGGAGC 48895 141 1.01e-07 TAGGGTTACT ACTGACTGTGAA CCGTGGTACC 25204 95 3.78e-06 CTCATGGGCA ACTTACAGTAAA GTGCAAATGA 43274 387 5.08e-06 TTAGTTACCC AGTGACTGTAAA CTATATACTT 46154 192 1.48e-05 ACCGTGGCCA ACTGTGAGAGAA AGTCCGTACT 34493 389 1.48e-05 GTGTGGGACA AGTTACGGAGAA GGTGGAACAA 5512 318 2.84e-05 TTCGAGTAGC ACGCACAGTCAA ACCTGCCTCA 8451 152 2.84e-05 AAACTGGTTT ACTCACAGTTAC TACCATAACG 44561 16 3.61e-05 TTGGTCGTGA ACGGACGGTGAC TTGGGAATCG 50043 100 5.80e-05 TGTCTGACTG ACTCTGCGTGAA TGTGTATGCG 41417 142 5.80e-05 CCAGCCAACG TCTGTCTGTCAA TCTCTCACCG 48580 88 1.08e-04 TTGCTTTCCC AGTTAGTGCGAA TATTACTTAT 5769 295 1.38e-04 CTGGCGTAAA ATTGACAGTTAG TGGTTATCCA 11850 39 1.45e-04 AAATGATTTC TGTCTCGGAGAA ATTTCATATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9731 5e-08 274_[+3]_214 48895 1e-07 140_[+3]_348 25204 3.8e-06 94_[+3]_394 43274 5.1e-06 386_[+3]_102 46154 1.5e-05 191_[+3]_297 34493 1.5e-05 388_[+3]_100 5512 2.8e-05 317_[+3]_171 8451 2.8e-05 151_[+3]_337 44561 3.6e-05 15_[+3]_473 50043 5.8e-05 99_[+3]_389 41417 5.8e-05 141_[+3]_347 48580 0.00011 87_[+3]_401 5769 0.00014 294_[+3]_194 11850 0.00014 38_[+3]_450 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=14 9731 ( 275) ACTGACAGTGAA 1 48895 ( 141) ACTGACTGTGAA 1 25204 ( 95) ACTTACAGTAAA 1 43274 ( 387) AGTGACTGTAAA 1 46154 ( 192) ACTGTGAGAGAA 1 34493 ( 389) AGTTACGGAGAA 1 5512 ( 318) ACGCACAGTCAA 1 8451 ( 152) ACTCACAGTTAC 1 44561 ( 16) ACGGACGGTGAC 1 50043 ( 100) ACTCTGCGTGAA 1 41417 ( 142) TCTGTCTGTCAA 1 48580 ( 88) AGTTAGTGCGAA 1 5769 ( 295) ATTGACAGTTAG 1 11850 ( 39) TGTCTCGGAGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6846 bayes= 8.93074 E= 6.5e+002 183 -1045 -1045 -78 -1045 122 27 -177 -1045 -1045 -73 181 -1045 5 107 -19 157 -1045 -1045 22 -1045 151 -15 -1045 83 -195 -15 22 -1045 -1045 207 -1045 -17 -195 -1045 154 -76 -95 126 -78 205 -1045 -1045 -1045 170 -95 -173 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 14 E= 6.5e+002 0.857143 0.000000 0.000000 0.142857 0.000000 0.642857 0.285714 0.071429 0.000000 0.000000 0.142857 0.857143 0.000000 0.285714 0.500000 0.214286 0.714286 0.000000 0.000000 0.285714 0.000000 0.785714 0.214286 0.000000 0.428571 0.071429 0.214286 0.285714 0.000000 0.000000 1.000000 0.000000 0.214286 0.071429 0.000000 0.714286 0.142857 0.142857 0.571429 0.142857 1.000000 0.000000 0.000000 0.000000 0.785714 0.142857 0.071429 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- A[CG]T[GCT][AT][CG][ATG]G[TA]GAA -------------------------------------------------------------------------------- Time 5.79 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43274 7.44e-09 134_[+2(2.37e-08)]_182_\ [+1(1.66e-06)]_36_[+3(5.08e-06)]_102 5769 1.32e-02 177_[+1(1.35e-05)]_307 48580 2.04e-03 225_[+1(2.55e-06)]_259 48895 4.72e-05 140_[+3(1.01e-07)]_11_\ [+1(1.68e-05)]_13_[+3(1.10e-05)]_296 25204 2.87e-04 65_[+1(3.84e-06)]_13_[+3(3.78e-06)]_\ 394 8451 2.82e-05 151_[+3(2.84e-05)]_195_\ [+2(5.63e-08)]_124 9731 5.85e-08 274_[+3(5.01e-08)]_182_\ [+1(4.34e-08)]_16 5512 6.78e-11 136_[+2(1.15e-10)]_163_\ [+3(2.84e-05)]_144_[+1(3.92e-07)]_11 41417 9.85e-04 141_[+3(5.80e-05)]_204_\ [+1(2.35e-06)]_127 44561 2.77e-09 15_[+3(3.61e-05)]_207_\ [+2(1.87e-09)]_4_[+2(6.87e-05)]_118_[+1(1.02e-06)]_92 34493 5.83e-06 325_[+2(1.24e-08)]_45_\ [+3(1.48e-05)]_100 11850 1.19e-05 62_[+1(4.58e-09)]_422 46154 4.23e-04 45_[+1(1.51e-06)]_130_\ [+3(1.48e-05)]_297 50043 5.40e-04 99_[+3(5.80e-05)]_224_\ [+1(4.47e-06)]_149 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************