******************************************************************************** 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/305/305.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 13255 1.0000 500 48634 1.0000 500 48636 1.0000 500 49346 1.0000 500 44582 1.0000 500 44705 1.0000 500 27817 1.0000 500 43460 1.0000 500 54574 1.0000 500 44607 1.0000 500 49237 1.0000 500 49088 1.0000 500 45895 1.0000 500 48148 1.0000 500 45130 1.0000 500 49729 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/305/305.seqs.fa -oc motifs/305 -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= 16 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= 8000 N= 16 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.281 C 0.234 G 0.213 T 0.272 Background letter frequencies (from dataset with add-one prior applied): A 0.281 C 0.234 G 0.213 T 0.272 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 15 llr = 141 E-value = 7.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 3:88:21::779 pos.-specific C 19::1:::911: probability G 2121:4::1221 matrix T 5::1949a:::: bits 2.2 2.0 1.8 * 1.6 * *** Relative 1.3 * * *** * Entropy 1.1 ** * *** * (13.6 bits) 0.9 **** **** * 0.7 **** ****** 0.4 *********** 0.2 ************ 0.0 ------------ Multilevel TCAATGTTCAAA consensus A G T GG sequence G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 48634 126 4.58e-07 TTGTTGTTAA ACAATGTTCAAA GTCAAGTCGT 48636 278 1.23e-06 TGCCTACGAA TCAATTTTCAGA TATACAAAAT 44705 157 3.26e-06 ATGGCAGCTG CCAATGTTCAAA CCAAACACTG 49346 245 4.90e-06 GAGGATGAGC GCAATGTTCACA GGGCACCATG 13255 232 6.69e-06 CAGCTGACTG AGAATGTTCAAA ATGCTATTAT 44607 274 1.08e-05 TATATGTCGG TCATTTTTCAAA ATAGTCGTAG 49088 197 1.17e-05 CGAATCATTG TCAGTTTTCGAA ACATATTATT 54574 240 1.50e-05 GAGGGGCTGT GCAGTATTCAAA CTGGACAGCC 45895 357 1.95e-05 CCTTCATTTT TCGATGTTCCAA GCAAAACCAT 45130 489 2.81e-05 TTTAAACAGT TCAATATTGAGA 43460 379 3.40e-05 ACGACACTGC TCGATTTTCAGG GTACGCCCCA 44582 57 3.40e-05 AAAATTCAAC TCAATTATCGAA CCGATTCGCT 48148 434 6.53e-05 CTAACACGAA ACAACATTCACA GTAGACATAC 49729 54 8.21e-05 TTTATTTGGA GGAATGTTCGAG AAGCACCAGA 27817 265 1.12e-04 AATAGCGAGA ACGACTTTGAAA CGACATTTAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48634 4.6e-07 125_[+1]_363 48636 1.2e-06 277_[+1]_211 44705 3.3e-06 156_[+1]_332 49346 4.9e-06 244_[+1]_244 13255 6.7e-06 231_[+1]_257 44607 1.1e-05 273_[+1]_215 49088 1.2e-05 196_[+1]_292 54574 1.5e-05 239_[+1]_249 45895 2e-05 356_[+1]_132 45130 2.8e-05 488_[+1] 43460 3.4e-05 378_[+1]_110 44582 3.4e-05 56_[+1]_432 48148 6.5e-05 433_[+1]_55 49729 8.2e-05 53_[+1]_435 27817 0.00011 264_[+1]_224 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=15 48634 ( 126) ACAATGTTCAAA 1 48636 ( 278) TCAATTTTCAGA 1 44705 ( 157) CCAATGTTCAAA 1 49346 ( 245) GCAATGTTCACA 1 13255 ( 232) AGAATGTTCAAA 1 44607 ( 274) TCATTTTTCAAA 1 49088 ( 197) TCAGTTTTCGAA 1 54574 ( 240) GCAGTATTCAAA 1 45895 ( 357) TCGATGTTCCAA 1 45130 ( 489) TCAATATTGAGA 1 43460 ( 379) TCGATTTTCAGG 1 44582 ( 57) TCAATTATCGAA 1 48148 ( 434) ACAACATTCACA 1 49729 ( 54) GGAATGTTCGAG 1 27817 ( 265) ACGACTTTGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7824 bayes= 9.6993 E= 7.3e+000 -7 -181 -9 78 -1055 189 -68 -1055 151 -1055 -9 -1055 151 -1055 -68 -203 -1055 -81 -1055 167 -49 -1055 91 56 -207 -1055 -1055 178 -1055 -1055 -1055 188 -1055 189 -68 -1055 139 -181 -9 -1055 125 -81 -9 -1055 163 -1055 -68 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 15 E= 7.3e+000 0.266667 0.066667 0.200000 0.466667 0.000000 0.866667 0.133333 0.000000 0.800000 0.000000 0.200000 0.000000 0.800000 0.000000 0.133333 0.066667 0.000000 0.133333 0.000000 0.866667 0.200000 0.000000 0.400000 0.400000 0.066667 0.000000 0.000000 0.933333 0.000000 0.000000 0.000000 1.000000 0.000000 0.866667 0.133333 0.000000 0.733333 0.066667 0.200000 0.000000 0.666667 0.133333 0.200000 0.000000 0.866667 0.000000 0.133333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TAG]C[AG]AT[GTA]TTC[AG][AG]A -------------------------------------------------------------------------------- Time 2.19 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 5 llr = 95 E-value = 1.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::2:2::2:::2a4:::6::: pos.-specific C 2:4::8:::::::2:4::86: probability G :a22:2a:2::6:2:4a2::8 matrix T 8:288::88aa2:2a2:2242 bits 2.2 * * * 2.0 * * * 1.8 * * ** * * * 1.6 * * ** * * * Relative 1.3 * * ** *** * * * * * Entropy 1.1 ** ******** * * * *** (27.3 bits) 0.9 ** ******** * * * *** 0.7 ** ********** *** *** 0.4 ** ********** ******* 0.2 ** ********** ******* 0.0 --------------------- Multilevel TGCTTCGTTTTGAATCGACCG consensus C AGAG AG A C G GTTT sequence G T G T T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 27817 473 3.31e-11 TCTTTCATCT TGCTTCGTTTTGAGTCGGCTG CCGAAAT 44582 229 7.45e-10 AATGTACAAT CGATTCGTTTTTACTGGACCG TTGGCGGGTA 43460 27 1.92e-09 ATGTACATAG TGCGTGGTGTTGAATCGTCCG GTTCCGTGAC 49346 361 2.42e-09 TTCCTGGGTA TGTTTCGATTTAAATTGACTG AGAAGCGATG 45895 84 5.08e-09 TCTGTGACAA TGGTACGTTTTGATTGGATCT AAAGTAGATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 27817 3.3e-11 472_[+2]_7 44582 7.5e-10 228_[+2]_251 43460 1.9e-09 26_[+2]_453 49346 2.4e-09 360_[+2]_119 45895 5.1e-09 83_[+2]_396 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 27817 ( 473) TGCTTCGTTTTGAGTCGGCTG 1 44582 ( 229) CGATTCGTTTTTACTGGACCG 1 43460 ( 27) TGCGTGGTGTTGAATCGTCCG 1 49346 ( 361) TGTTTCGATTTAAATTGACTG 1 45895 ( 84) TGGTACGTTTTGATTGGATCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7680 bayes= 10.018 E= 1.4e+002 -897 -23 -897 155 -897 -897 223 -897 -49 77 -9 -44 -897 -897 -9 155 -49 -897 -897 155 -897 177 -9 -897 -897 -897 223 -897 -49 -897 -897 155 -897 -897 -9 155 -897 -897 -897 188 -897 -897 -897 188 -49 -897 149 -44 183 -897 -897 -897 51 -23 -9 -44 -897 -897 -897 188 -897 77 91 -44 -897 -897 223 -897 109 -897 -9 -44 -897 177 -897 -44 -897 136 -897 55 -897 -897 191 -44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 1.4e+002 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 0.200000 0.400000 0.200000 0.200000 0.000000 0.000000 0.200000 0.800000 0.200000 0.000000 0.000000 0.800000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.200000 0.000000 0.600000 0.200000 1.000000 0.000000 0.000000 0.000000 0.400000 0.200000 0.200000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.400000 0.200000 0.000000 0.000000 1.000000 0.000000 0.600000 0.000000 0.200000 0.200000 0.000000 0.800000 0.000000 0.200000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.800000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TC]G[CAGT][TG][TA][CG]G[TA][TG]TT[GAT]A[ACGT]T[CGT]G[AGT][CT][CT][GT] -------------------------------------------------------------------------------- Time 4.36 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 12 llr = 130 E-value = 1.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :14413::2:27::2 pos.-specific C :9:331:a3:333:7 probability G ::5351::381:881 matrix T a:1:25a:324::21 bits 2.2 2.0 * 1.8 * ** 1.6 ** ** * * Relative 1.3 ** ** * ** Entropy 1.1 ** ** * ** (15.6 bits) 0.9 ** ** * *** 0.7 *** ** * **** 0.4 ***** ** * **** 0.2 ******** ****** 0.0 --------------- Multilevel TCGAGTTCTGTAGGC consensus ACCA C CCC sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 48148 340 4.29e-08 CGCCATCCCA TCGGGTTCCGTCGGC ACACAATCGT 49729 195 7.24e-08 CGAGACCTCT TCGCGATCTGCCGGC AAACGTGACA 44705 464 4.95e-07 AAGCATTAAT TCAAGATCCGCACGC TTGCGACTGA 27817 348 1.16e-06 TCCAAGAAAT TCGATTTCGGACGGC CGGCGCAAAA 45895 224 1.61e-06 CTTCTCCTGA TAACGTTCGGTAGGC ACGGGACTCT 49237 35 2.92e-06 GACATCTTTG TCGCGCTCGGTAGTC AGTCCATATG 44582 336 7.07e-06 TCCATATATC TCAACTTCTTGAGGC TACTTTCCAA 49346 394 9.63e-06 AAGCGATGAA TCGACATCTTTCCGC TTTGAGGCAT 54574 162 1.12e-05 TTCCTTTTCC TCTATTTCTGTAGGA AGTAGGGAAT 48636 164 1.20e-05 GCATTGCCAC TCACGGTCAGCAGGT CTCCCGGCTA 43460 413 1.69e-05 CCACTCACAA TCGGCATCCGCAGTG ATCGCATCCC 45130 302 4.87e-05 GAAAGACAGA TCAGATTCAGAACGA TTTCAGGTAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48148 4.3e-08 339_[+3]_146 49729 7.2e-08 194_[+3]_291 44705 4.9e-07 463_[+3]_22 27817 1.2e-06 347_[+3]_138 45895 1.6e-06 223_[+3]_262 49237 2.9e-06 34_[+3]_451 44582 7.1e-06 335_[+3]_150 49346 9.6e-06 393_[+3]_92 54574 1.1e-05 161_[+3]_324 48636 1.2e-05 163_[+3]_322 43460 1.7e-05 412_[+3]_73 45130 4.9e-05 301_[+3]_184 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=12 48148 ( 340) TCGGGTTCCGTCGGC 1 49729 ( 195) TCGCGATCTGCCGGC 1 44705 ( 464) TCAAGATCCGCACGC 1 27817 ( 348) TCGATTTCGGACGGC 1 45895 ( 224) TAACGTTCGGTAGGC 1 49237 ( 35) TCGCGCTCGGTAGTC 1 44582 ( 336) TCAACTTCTTGAGGC 1 49346 ( 394) TCGACATCTTTCCGC 1 54574 ( 162) TCTATTTCTGTAGGA 1 48636 ( 164) TCACGGTCAGCAGGT 1 43460 ( 413) TCGGCATCCGCAGTG 1 45130 ( 302) TCAGATTCAGAACGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 7776 bayes= 10.4383 E= 1.4e+002 -1023 -1023 -1023 188 -175 197 -1023 -1023 57 -1023 123 -170 57 51 23 -1023 -175 10 123 -71 25 -149 -135 88 -1023 -1023 -1023 188 -1023 209 -1023 -1023 -75 10 23 29 -1023 -1023 197 -71 -75 51 -135 61 125 51 -1023 -1023 -1023 10 181 -1023 -1023 -1023 197 -71 -75 151 -135 -170 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 12 E= 1.4e+002 0.000000 0.000000 0.000000 1.000000 0.083333 0.916667 0.000000 0.000000 0.416667 0.000000 0.500000 0.083333 0.416667 0.333333 0.250000 0.000000 0.083333 0.250000 0.500000 0.166667 0.333333 0.083333 0.083333 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.250000 0.250000 0.333333 0.000000 0.000000 0.833333 0.166667 0.166667 0.333333 0.083333 0.416667 0.666667 0.333333 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.833333 0.166667 0.166667 0.666667 0.083333 0.083333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TC[GA][ACG][GC][TA]TC[TCG]G[TC][AC][GC]GC -------------------------------------------------------------------------------- Time 6.71 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 13255 3.50e-02 231_[+1(6.69e-06)]_257 48634 8.37e-03 125_[+1(4.58e-07)]_363 48636 9.75e-05 163_[+3(1.20e-05)]_99_\ [+1(1.23e-06)]_211 49346 4.41e-09 244_[+1(4.90e-06)]_104_\ [+2(2.42e-09)]_12_[+3(9.63e-06)]_92 44582 6.65e-09 56_[+1(3.40e-05)]_160_\ [+2(7.45e-10)]_86_[+3(7.07e-06)]_150 44705 4.25e-05 156_[+1(3.26e-06)]_295_\ [+3(4.95e-07)]_22 27817 2.06e-10 347_[+3(1.16e-06)]_110_\ [+2(3.31e-11)]_7 43460 3.52e-08 26_[+2(1.92e-09)]_331_\ [+1(3.40e-05)]_22_[+3(1.69e-05)]_73 54574 2.07e-03 161_[+3(1.12e-05)]_63_\ [+1(1.50e-05)]_249 44607 5.30e-02 273_[+1(1.08e-05)]_215 49237 1.30e-03 34_[+3(2.92e-06)]_35_[+2(3.38e-05)]_\ 395 49088 8.96e-02 196_[+1(1.17e-05)]_292 45895 6.01e-09 83_[+2(5.08e-09)]_119_\ [+3(1.61e-06)]_118_[+1(1.95e-05)]_132 48148 8.10e-06 339_[+3(4.29e-08)]_79_\ [+1(6.53e-05)]_55 45130 1.11e-02 301_[+3(4.87e-05)]_172_\ [+1(2.81e-05)] 49729 1.03e-04 53_[+1(8.21e-05)]_129_\ [+3(7.24e-08)]_291 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************