******************************************************************************** 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/324/324.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 13078 1.0000 500 46998 1.0000 500 50235 1.0000 500 44003 1.0000 500 44492 1.0000 500 44932 1.0000 500 12894 1.0000 500 43856 1.0000 500 32113 1.0000 500 43746 1.0000 500 50358 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/324/324.seqs.fa -oc motifs/324 -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= 11 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= 5500 N= 11 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.268 C 0.232 G 0.231 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.268 C 0.232 G 0.231 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 10 llr = 107 E-value = 2.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 12:1:8:::::6 pos.-specific C :2::8:71:27: probability G :5::::::a:14 matrix T 91a92239:82: bits 2.1 * 1.9 * * 1.7 * * 1.5 * ** ** Relative 1.3 * ******** Entropy 1.1 * ******** * (15.4 bits) 0.8 * ********** 0.6 * ********** 0.4 * ********** 0.2 ************ 0.0 ------------ Multilevel TGTTCACTGTCA consensus A TTT CTG sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 12894 122 6.74e-08 AAGATTCCTT TGTTCACTGTCA AACACAGTCA 43856 50 1.26e-07 ATAGTATCCA TGTTCACTGTCG TCATACGTTT 50358 394 3.50e-07 CAAATAATCC TATTCACTGTCA ATACTGCAGC 46998 212 3.96e-06 AAGGGTTGCG TTTTCATTGTCA GTAGTTCATT 43746 357 5.28e-06 ACCGCAGGTA ACTTCACTGTCA TTATCCTGTT 13078 440 1.13e-05 GTTCGTTCGT TCTTCACTGCTG CATCCTTGTC 50235 190 1.23e-05 GGACGTTGGA TGTATACTGTCG GCGTCTGTCA 44492 342 1.57e-05 TGGCAGGAAG TATTTTCTGTCG GGTCACTACG 32113 440 1.67e-05 TCGCGTCTCG TGTTCTTTGTGA ATCATTTCCA 44932 21 4.17e-05 CTTCGCTGCA TGTTCATCGCTA TTGTTAGTAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 12894 6.7e-08 121_[+1]_367 43856 1.3e-07 49_[+1]_439 50358 3.5e-07 393_[+1]_95 46998 4e-06 211_[+1]_277 43746 5.3e-06 356_[+1]_132 13078 1.1e-05 439_[+1]_49 50235 1.2e-05 189_[+1]_299 44492 1.6e-05 341_[+1]_147 32113 1.7e-05 439_[+1]_49 44932 4.2e-05 20_[+1]_468 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=10 12894 ( 122) TGTTCACTGTCA 1 43856 ( 50) TGTTCACTGTCG 1 50358 ( 394) TATTCACTGTCA 1 46998 ( 212) TTTTCATTGTCA 1 43746 ( 357) ACTTCACTGTCA 1 13078 ( 440) TCTTCACTGCTG 1 50235 ( 190) TGTATACTGTCG 1 44492 ( 342) TATTTTCTGTCG 1 32113 ( 440) TGTTCTTTGTGA 1 44932 ( 21) TGTTCATCGCTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5379 bayes= 10.0132 E= 2.4e+001 -142 -997 -997 174 -42 -21 111 -143 -997 -997 -997 189 -142 -997 -997 174 -997 179 -997 -43 158 -997 -997 -43 -997 159 -997 16 -997 -121 -997 174 -997 -997 211 -997 -997 -21 -997 157 -997 159 -121 -43 116 -997 79 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 10 E= 2.4e+001 0.100000 0.000000 0.000000 0.900000 0.200000 0.200000 0.500000 0.100000 0.000000 0.000000 0.000000 1.000000 0.100000 0.000000 0.000000 0.900000 0.000000 0.800000 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.000000 0.700000 0.000000 0.300000 0.000000 0.100000 0.000000 0.900000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.700000 0.100000 0.200000 0.600000 0.000000 0.400000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[GAC]TT[CT][AT][CT]TG[TC][CT][AG] -------------------------------------------------------------------------------- Time 1.07 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 11 llr = 120 E-value = 2.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :436812393294:78 pos.-specific C 4::12125:::129:1 probability G 637::862176:3131 matrix T :4:3:::1::2:2::: bits 2.1 1.9 1.7 * 1.5 * * * Relative 1.3 * * ** ** * * Entropy 1.1 * * ** ** * *** (15.7 bits) 0.8 * * *** ** * *** 0.6 * ***** **** *** 0.4 ******* **** *** 0.2 ************ *** 0.0 ---------------- Multilevel GAGAAGGCAGGAACAA consensus CTAT A A G G sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 44492 300 1.54e-09 TTGTTCAGCT GTGAAGGCAGGACCAA TCCTTCACGC 50358 24 4.57e-07 ACCGCCGTCC GTGAAGCCAAGAGCGA AACGAGCAGC 43746 316 6.38e-07 GAGAGCAATT CGGAAGAGAGGACCAA AACCTGCTAC 46998 430 2.15e-06 AACCCATCGA GAGTAGGAAGGAGCGC TATCCTGAAC 50235 392 3.07e-06 TTCTGCCATT GGGTAGGTAGGCACAA AGGAAAGAAT 13078 331 3.36e-06 TCCTCTACCT CTGTCGGAAGAAGCAA GCGCGATACC 12894 407 5.12e-06 AAGATCTGCT GAGAAAGCGGGAACGA TGGTCGGAAG 44932 86 5.12e-06 GTGACGGTGC GAGAAGGGAGGAAGAG GCTGGCAGCC 43856 404 1.02e-05 GCTTGCTTCC GAACAGGCAATATCAA AACAAATCGC 32113 326 1.65e-05 CCGGTGGCAA CGAAACCCAGAAACAA GACTGCTATG 44003 67 4.96e-05 CAAAAGAGAA CTAACGAAAATATCAA ACACATGACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44492 1.5e-09 299_[+2]_185 50358 4.6e-07 23_[+2]_461 43746 6.4e-07 315_[+2]_169 46998 2.2e-06 429_[+2]_55 50235 3.1e-06 391_[+2]_93 13078 3.4e-06 330_[+2]_154 12894 5.1e-06 406_[+2]_78 44932 5.1e-06 85_[+2]_399 43856 1e-05 403_[+2]_81 32113 1.6e-05 325_[+2]_159 44003 5e-05 66_[+2]_418 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=11 44492 ( 300) GTGAAGGCAGGACCAA 1 50358 ( 24) GTGAAGCCAAGAGCGA 1 43746 ( 316) CGGAAGAGAGGACCAA 1 46998 ( 430) GAGTAGGAAGGAGCGC 1 50235 ( 392) GGGTAGGTAGGCACAA 1 13078 ( 331) CTGTCGGAAGAAGCAA 1 12894 ( 407) GAGAAAGCGGGAACGA 1 44932 ( 86) GAGAAGGGAGGAAGAG 1 43856 ( 404) GAACAGGCAATATCAA 1 32113 ( 326) CGAAACCCAGAAACAA 1 44003 ( 67) CTAACGAAAATATCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 5335 bayes= 8.91886 E= 2.7e+002 -1010 65 146 -1010 44 -1010 24 43 3 -1010 165 -1010 125 -135 -1010 2 161 -35 -1010 -1010 -156 -135 182 -1010 -56 -35 146 -1010 3 97 -35 -156 176 -1010 -135 -1010 3 -1010 165 -1010 -56 -1010 146 -57 176 -135 -1010 -1010 44 -35 24 -57 -1010 197 -135 -1010 144 -1010 24 -1010 161 -135 -135 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 11 E= 2.7e+002 0.000000 0.363636 0.636364 0.000000 0.363636 0.000000 0.272727 0.363636 0.272727 0.000000 0.727273 0.000000 0.636364 0.090909 0.000000 0.272727 0.818182 0.181818 0.000000 0.000000 0.090909 0.090909 0.818182 0.000000 0.181818 0.181818 0.636364 0.000000 0.272727 0.454545 0.181818 0.090909 0.909091 0.000000 0.090909 0.000000 0.272727 0.000000 0.727273 0.000000 0.181818 0.000000 0.636364 0.181818 0.909091 0.090909 0.000000 0.000000 0.363636 0.181818 0.272727 0.181818 0.000000 0.909091 0.090909 0.000000 0.727273 0.000000 0.272727 0.000000 0.818182 0.090909 0.090909 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GC][ATG][GA][AT]AGG[CA]A[GA]GA[AG]C[AG]A -------------------------------------------------------------------------------- Time 2.08 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 11 llr = 107 E-value = 1.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 792:::882113 pos.-specific C ::::2221:31: probability G 21::87:::67: matrix T 1:8a:1:18:17 bits 2.1 1.9 * 1.7 * 1.5 * ** Relative 1.3 **** * * Entropy 1.1 ******** * (14.1 bits) 0.8 ************ 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel AATTGGAATGGT consensus C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 44932 166 6.71e-07 AGACGATTGC AATTCGAATGGT TGCTGGACTC 43746 48 1.13e-06 AACGAACAAA AATTGGAATAGT TTCTTGGGGA 13078 239 4.97e-06 TTCGTGGCAG AATTGGCATCGA AAGGTCGGAA 43856 130 6.46e-06 TCCGTCCATT GATTGGAATGTT GCTGGATGCT 50235 39 6.46e-06 GCAGGGTCGC AATTGCAATGCT GCGCTGACAG 44492 397 1.03e-05 GAAGCCCCCA AAATGGATTGGT GAAAGTGAAA 12894 274 1.73e-05 TTTCCTTTCC AATTCGCAAGGT TTCGATCGAG 50358 291 1.96e-05 TCAATCTTGA TATTGCAATGGA ATATTGGCAA 32113 84 2.65e-05 ACGATCGATG GGATGGAATGGT TGTACGAAAC 46998 113 3.55e-05 GTATGACTAC AATTGTACTCGT TGTTGATTCG 44003 488 4.66e-05 AGTAACGGTT AATTGGAAACAA C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44932 6.7e-07 165_[+3]_323 43746 1.1e-06 47_[+3]_441 13078 5e-06 238_[+3]_250 43856 6.5e-06 129_[+3]_359 50235 6.5e-06 38_[+3]_450 44492 1e-05 396_[+3]_92 12894 1.7e-05 273_[+3]_215 50358 2e-05 290_[+3]_198 32113 2.6e-05 83_[+3]_405 46998 3.5e-05 112_[+3]_376 44003 4.7e-05 487_[+3]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=11 44932 ( 166) AATTCGAATGGT 1 43746 ( 48) AATTGGAATAGT 1 13078 ( 239) AATTGGCATCGA 1 43856 ( 130) GATTGGAATGTT 1 50235 ( 39) AATTGCAATGCT 1 44492 ( 397) AAATGGATTGGT 1 12894 ( 274) AATTCGCAAGGT 1 50358 ( 291) TATTGCAATGGA 1 32113 ( 84) GGATGGAATGGT 1 46998 ( 113) AATTGTACTCGT 1 44003 ( 488) AATTGGAAACAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5379 bayes= 9.28648 E= 1.6e+003 144 -1010 -35 -156 176 -1010 -135 -1010 -56 -1010 -1010 160 -1010 -1010 -1010 189 -1010 -35 182 -1010 -1010 -35 165 -156 161 -35 -1010 -1010 161 -135 -1010 -156 -56 -1010 -1010 160 -156 24 146 -1010 -156 -135 165 -156 3 -1010 -1010 143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 11 E= 1.6e+003 0.727273 0.000000 0.181818 0.090909 0.909091 0.000000 0.090909 0.000000 0.181818 0.000000 0.000000 0.818182 0.000000 0.000000 0.000000 1.000000 0.000000 0.181818 0.818182 0.000000 0.000000 0.181818 0.727273 0.090909 0.818182 0.181818 0.000000 0.000000 0.818182 0.090909 0.000000 0.090909 0.181818 0.000000 0.000000 0.818182 0.090909 0.272727 0.636364 0.000000 0.090909 0.090909 0.727273 0.090909 0.272727 0.000000 0.000000 0.727273 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- AATTGGAAT[GC]G[TA] -------------------------------------------------------------------------------- Time 3.01 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 13078 3.81e-06 238_[+3(4.97e-06)]_80_\ [+2(3.36e-06)]_93_[+1(1.13e-05)]_49 46998 5.76e-06 112_[+3(3.55e-05)]_87_\ [+1(3.96e-06)]_206_[+2(2.15e-06)]_55 50235 4.77e-06 38_[+3(6.46e-06)]_139_\ [+1(1.23e-05)]_190_[+2(3.07e-06)]_93 44003 1.52e-02 66_[+2(4.96e-05)]_405_\ [+3(4.66e-05)]_1 44492 9.19e-09 299_[+2(1.54e-09)]_26_\ [+1(1.57e-05)]_43_[+3(1.03e-05)]_92 44932 2.95e-06 20_[+1(4.17e-05)]_53_[+2(5.12e-06)]_\ 64_[+3(6.71e-07)]_323 12894 1.68e-07 121_[+1(6.74e-08)]_140_\ [+3(1.73e-05)]_121_[+2(5.12e-06)]_78 43856 2.26e-07 49_[+1(1.26e-07)]_68_[+3(6.46e-06)]_\ 262_[+2(1.02e-05)]_81 32113 9.42e-05 83_[+3(2.65e-05)]_230_\ [+2(1.65e-05)]_98_[+1(1.67e-05)]_49 43746 1.12e-07 47_[+3(1.13e-06)]_256_\ [+2(6.38e-07)]_25_[+1(5.28e-06)]_132 50358 9.37e-08 23_[+2(4.57e-07)]_251_\ [+3(1.96e-05)]_91_[+1(3.50e-07)]_95 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************