******************************************************************************** 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/432/432.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42523 1.0000 500 42736 1.0000 500 9171 1.0000 500 32454 1.0000 500 6732 1.0000 500 46863 1.0000 500 7934 1.0000 500 48747 1.0000 500 49501 1.0000 500 10356 1.0000 500 41496 1.0000 500 10902 1.0000 500 46002 1.0000 500 46567 1.0000 500 34164 1.0000 500 45937 1.0000 500 40338 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/432/432.seqs.fa -oc motifs/432 -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= 17 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= 8500 N= 17 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.276 C 0.234 G 0.219 T 0.271 Background letter frequencies (from dataset with add-one prior applied): A 0.276 C 0.234 G 0.219 T 0.271 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 9 llr = 133 E-value = 3.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::697::::2:1::389: pos.-specific C :3:2:1:1::22:3::3::3 probability G 77282:::748131a82216 matrix T 3:8:2:3936:474:21::1 bits 2.2 * 2.0 * 1.8 * 1.5 * Relative 1.3 * * * * * ** * Entropy 1.1 **** * **** * ** ** (21.3 bits) 0.9 **** ****** * ** *** 0.7 **** ****** * ** *** 0.4 *********** * ** *** 0.2 ******************** 0.0 -------------------- Multilevel GGTGAAATGTGTTTGGAAAG consensus TCGCG T TGCAGC TCG C sequence T C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 7934 78 4.93e-10 GGACGTTTTT GGTGAATTGGGTTCGGCGAG CTTACTGTAT 40338 360 3.00e-09 AATTATTTTC GGTGAAATTGGTTTGGTAAC AGTAAACTGT 42523 232 3.51e-08 AAAATTGTTC TGGGAAATGGGATAGGGAAG AACAAACGAA 34164 66 7.60e-08 GGCCGGAATG GCTGGATTGTCCGTGGCAAC GCTGTTCATG 42736 475 9.07e-08 TGGCCAAGTG GGTGTATTTTGATCGTGAAG CGGCAC 32454 302 9.89e-08 TTCCCCATGC TCTGAAATGTCTTGGGAGAG CATGGCATGC 10902 223 3.30e-07 CATTCGTCTC TGTCGAACGTGGGTGGAAAG GCTCCCAAGG 46002 116 3.52e-07 CCCGGCACAA GCGGAAATTGGTTCGTCAGC ACAAAGTATA 46863 31 5.09e-07 TTTAGAGTGC GGTCTCATGTGCGTGGAAAT GTCCGGTATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7934 4.9e-10 77_[+1]_403 40338 3e-09 359_[+1]_121 42523 3.5e-08 231_[+1]_249 34164 7.6e-08 65_[+1]_415 42736 9.1e-08 474_[+1]_6 32454 9.9e-08 301_[+1]_179 10902 3.3e-07 222_[+1]_258 46002 3.5e-07 115_[+1]_365 46863 5.1e-07 30_[+1]_450 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=9 7934 ( 78) GGTGAATTGGGTTCGGCGAG 1 40338 ( 360) GGTGAAATTGGTTTGGTAAC 1 42523 ( 232) TGGGAAATGGGATAGGGAAG 1 34164 ( 66) GCTGGATTGTCCGTGGCAAC 1 42736 ( 475) GGTGTATTTTGATCGTGAAG 1 32454 ( 302) TCTGAAATGTCTTGGGAGAG 1 10902 ( 223) TGTCGAACGTGGGTGGAAAG 1 46002 ( 116) GCGGAAATTGGTTCGTCAGC 1 46863 ( 31) GGTCTCATGTGCGTGGAAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 8177 bayes= 9.96028 E= 3.9e+000 -982 -982 160 30 -982 51 160 -982 -982 -982 2 152 -982 -8 183 -982 101 -982 2 -29 169 -107 -982 -982 127 -982 -982 30 -982 -107 -982 171 -982 -982 160 30 -982 -982 102 104 -982 -8 183 -982 -31 -8 -98 71 -982 -982 60 130 -131 51 -98 71 -982 -982 219 -982 -982 -982 183 -29 27 51 2 -128 150 -982 2 -982 169 -982 -98 -982 -982 51 134 -128 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.9e+000 0.000000 0.000000 0.666667 0.333333 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.222222 0.777778 0.000000 0.222222 0.777778 0.000000 0.555556 0.000000 0.222222 0.222222 0.888889 0.111111 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.111111 0.000000 0.888889 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.444444 0.555556 0.000000 0.222222 0.777778 0.000000 0.222222 0.222222 0.111111 0.444444 0.000000 0.000000 0.333333 0.666667 0.111111 0.333333 0.111111 0.444444 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.777778 0.222222 0.333333 0.333333 0.222222 0.111111 0.777778 0.000000 0.222222 0.000000 0.888889 0.000000 0.111111 0.000000 0.000000 0.333333 0.555556 0.111111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GT][GC][TG][GC][AGT]A[AT]T[GT][TG][GC][TAC][TG][TC]G[GT][ACG][AG]A[GC] -------------------------------------------------------------------------------- Time 2.86 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 11 llr = 151 E-value = 4.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 164:3:3::11:1::2:321 pos.-specific C :4::1:12:223:::57:5: probability G 6:2::11:2163:::2:3:: matrix T 3:5a695886159aa13539 bits 2.2 2.0 * ** 1.8 * ** 1.5 * * *** * Relative 1.3 * * ** *** * Entropy 1.1 * * * ** *** * * (19.8 bits) 0.9 ** * * ** *** * * 0.7 ** *** ** * *** * ** 0.4 ****** ************* 0.2 ******************** 0.0 -------------------- Multilevel GATTTTTTTTGTTTTCCTCT consensus TCA A A C TAT sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 46002 264 1.22e-08 CAGCCCGACG TAGTTTTTGTGTTTTCCACT ACCATGGTTC 9171 290 1.75e-08 GACGCTACAA GCTTTTTCTTCGTTTCCACT TGTTTTTCCT 7934 436 6.47e-08 ATCCACGTGA GCTTATTCTTCTTTTGCTCT TGTATAGACA 46567 82 7.89e-08 TAAACAGCAA GCTTATTTTTGTTTTCCGAA ATTGATCACC 49501 79 9.57e-08 TCAAGTACTC GAGTTTTTTGGGTTTGTGCT GATTCTACGA 34164 124 1.66e-07 CTGTAGACCC GAATTTGTGTGGATTCCTCT CCGGTCGGTG 40338 283 2.16e-07 CAAACAAAGG TATTTTATTTATTTTACTTT TTTCCCGAAC 42736 15 2.55e-07 TTCTCGTTCA TCATCTATTCGTTTTCCTTT CTTAGTTTGT 41496 189 3.82e-07 ACTCGTGAAT GAATTTTTTATCTTTACACT GGGATATCAC 10356 263 1.26e-06 ATGGTACGTT GATTTGCTTCGCTTTCTGAT TCCGACAATT 32454 383 1.61e-06 GGGTTACTCA AAATATATTTGCTTTTTTTT TCGACCCGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46002 1.2e-08 263_[+2]_217 9171 1.8e-08 289_[+2]_191 7934 6.5e-08 435_[+2]_45 46567 7.9e-08 81_[+2]_399 49501 9.6e-08 78_[+2]_402 34164 1.7e-07 123_[+2]_357 40338 2.2e-07 282_[+2]_198 42736 2.6e-07 14_[+2]_466 41496 3.8e-07 188_[+2]_292 10356 1.3e-06 262_[+2]_218 32454 1.6e-06 382_[+2]_98 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=11 46002 ( 264) TAGTTTTTGTGTTTTCCACT 1 9171 ( 290) GCTTTTTCTTCGTTTCCACT 1 7934 ( 436) GCTTATTCTTCTTTTGCTCT 1 46567 ( 82) GCTTATTTTTGTTTTCCGAA 1 49501 ( 79) GAGTTTTTTGGGTTTGTGCT 1 34164 ( 124) GAATTTGTGTGGATTCCTCT 1 40338 ( 283) TATTTTATTTATTTTACTTT 1 42736 ( 15) TCATCTATTCGTTTTCCTTT 1 41496 ( 189) GAATTTTTTATCTTTACACT 1 10356 ( 263) GATTTGCTTCGCTTTCTGAT 1 32454 ( 383) AAATATATTTGCTTTTTTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 8177 bayes= 9.8915 E= 4.0e+000 -160 -1010 154 1 121 63 -1010 -1010 40 -1010 -27 75 -1010 -1010 -1010 188 -1 -136 -1010 123 -1010 -1010 -127 175 -1 -136 -127 101 -1010 -37 -1010 159 -1010 -1010 -27 159 -160 -37 -127 123 -160 -37 154 -157 -1010 22 32 75 -160 -1010 -1010 175 -1010 -1010 -1010 188 -1010 -1010 -1010 188 -60 122 -27 -157 -1010 163 -1010 1 -1 -1010 32 75 -60 122 -1010 1 -160 -1010 -1010 175 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 11 E= 4.0e+000 0.090909 0.000000 0.636364 0.272727 0.636364 0.363636 0.000000 0.000000 0.363636 0.000000 0.181818 0.454545 0.000000 0.000000 0.000000 1.000000 0.272727 0.090909 0.000000 0.636364 0.000000 0.000000 0.090909 0.909091 0.272727 0.090909 0.090909 0.545455 0.000000 0.181818 0.000000 0.818182 0.000000 0.000000 0.181818 0.818182 0.090909 0.181818 0.090909 0.636364 0.090909 0.181818 0.636364 0.090909 0.000000 0.272727 0.272727 0.454545 0.090909 0.000000 0.000000 0.909091 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.181818 0.545455 0.181818 0.090909 0.000000 0.727273 0.000000 0.272727 0.272727 0.000000 0.272727 0.454545 0.181818 0.545455 0.000000 0.272727 0.090909 0.000000 0.000000 0.909091 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][AC][TA]T[TA]T[TA]TTTG[TCG]TTTC[CT][TAG][CT]T -------------------------------------------------------------------------------- Time 5.40 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 17 llr = 156 E-value = 5.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A a36961596947 pos.-specific C :61::9:13152 probability G :131::4:1:1: matrix T ::::4:1::::1 bits 2.2 2.0 1.8 * * 1.5 * * * Relative 1.3 * * * * * Entropy 1.1 * * * * * (13.2 bits) 0.9 * **** * * 0.7 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel ACAAACAAAACA consensus AG T G C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 42736 196 1.03e-06 AGCAACGAGC ACAATCGAAACA ACACGCTGTT 46863 297 2.27e-06 AACAATTTTA ACGATCAAAACA GTAGCTGAAA 7934 126 2.90e-06 TGCGTAGAAA ACAAACGAAACC CACGAATGCC 34164 480 5.62e-06 GGGTATCTCG ACAAACAACACC CTCTCCAAA 9171 326 7.18e-06 TCCTACGAGC AGAAACAAAAAA TACTATGTGG 42523 325 9.02e-06 GGCGCGTCGC ACAGACAAAAAA CGATCCTTGC 10356 312 1.28e-05 GCTTTGGTAA AAAATCAACAAA ATGGACACCG 49501 245 1.28e-05 TTAGGATATG ACGGACGAAACA TGAATTCGTG 41496 478 2.45e-05 GTCAATTTTT ACAAAAGAAACA CTCACGGCAC 32454 158 2.45e-05 AATTCTAGAT AAAATCGAGACA AATCTAGTGT 6732 177 3.21e-05 CGCCACTTCC ACAATCAACAAT TCAAATGAAG 10902 130 4.01e-05 GCTACCGACA AAGAACAACAAC TGGATGCTGC 45937 149 4.39e-05 GTTGTTATTG AAGAACACAAAA CGACGATGGA 48747 384 4.39e-05 AAAATTGTGG AAAAACTACACA CACTCCCTTT 40338 456 8.27e-05 TTGTAGCACA AGGAACGCAAAA AAGGCTCCTT 46567 205 1.27e-04 ATTGCCAGAC ACAATCGAACCT AAACCCAAAG 46002 429 1.95e-04 ACGCTGTGAA ACCAACAAGAGA CACGCAGTAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42736 1e-06 195_[+3]_293 46863 2.3e-06 296_[+3]_192 7934 2.9e-06 125_[+3]_363 34164 5.6e-06 479_[+3]_9 9171 7.2e-06 325_[+3]_163 42523 9e-06 324_[+3]_164 10356 1.3e-05 311_[+3]_177 49501 1.3e-05 244_[+3]_244 41496 2.4e-05 477_[+3]_11 32454 2.4e-05 157_[+3]_331 6732 3.2e-05 176_[+3]_312 10902 4e-05 129_[+3]_359 45937 4.4e-05 148_[+3]_340 48747 4.4e-05 383_[+3]_105 40338 8.3e-05 455_[+3]_33 46567 0.00013 204_[+3]_284 46002 0.00019 428_[+3]_60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=17 42736 ( 196) ACAATCGAAACA 1 46863 ( 297) ACGATCAAAACA 1 7934 ( 126) ACAAACGAAACC 1 34164 ( 480) ACAAACAACACC 1 9171 ( 326) AGAAACAAAAAA 1 42523 ( 325) ACAGACAAAAAA 1 10356 ( 312) AAAATCAACAAA 1 49501 ( 245) ACGGACGAAACA 1 41496 ( 478) ACAAAAGAAACA 1 32454 ( 158) AAAATCGAGACA 1 6732 ( 177) ACAATCAACAAT 1 10902 ( 130) AAGAACAACAAC 1 45937 ( 149) AAGAACACAAAA 1 48747 ( 384) AAAAACTACACA 1 40338 ( 456) AGGAACGCAAAA 1 46567 ( 205) ACAATCGAACCT 1 46002 ( 429) ACCAACAAGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 8313 bayes= 8.93074 E= 5.1e+000 186 -1073 -1073 -1073 9 133 -90 -1073 123 -199 42 -1073 168 -1073 -90 -1073 123 -1073 -1073 38 -222 201 -1073 -1073 94 -1073 91 -220 168 -99 -1073 -1073 109 33 -90 -1073 177 -199 -1073 -1073 58 118 -190 -1073 136 -41 -1073 -120 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 17 E= 5.1e+000 1.000000 0.000000 0.000000 0.000000 0.294118 0.588235 0.117647 0.000000 0.647059 0.058824 0.294118 0.000000 0.882353 0.000000 0.117647 0.000000 0.647059 0.000000 0.000000 0.352941 0.058824 0.941176 0.000000 0.000000 0.529412 0.000000 0.411765 0.058824 0.882353 0.117647 0.000000 0.000000 0.588235 0.294118 0.117647 0.000000 0.941176 0.058824 0.000000 0.000000 0.411765 0.529412 0.058824 0.000000 0.705882 0.176471 0.000000 0.117647 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- A[CA][AG]A[AT]C[AG]A[AC]A[CA]A -------------------------------------------------------------------------------- Time 7.96 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42523 8.28e-06 231_[+1(3.51e-08)]_1_[+3(3.72e-05)]_\ 60_[+3(9.02e-06)]_164 42736 1.03e-09 14_[+2(2.55e-07)]_161_\ [+3(1.03e-06)]_267_[+1(9.07e-08)]_6 9171 1.55e-06 289_[+2(1.75e-08)]_16_\ [+3(7.18e-06)]_163 32454 1.12e-07 157_[+3(2.45e-05)]_132_\ [+1(9.89e-08)]_61_[+2(1.61e-06)]_98 6732 1.40e-01 176_[+3(3.21e-05)]_312 46863 3.37e-06 30_[+1(5.09e-07)]_246_\ [+3(2.27e-06)]_123_[+3(5.45e-05)]_57 7934 5.77e-12 3_[+3(2.25e-05)]_62_[+1(4.93e-10)]_\ 28_[+3(2.90e-06)]_298_[+2(6.47e-08)]_45 48747 7.08e-02 383_[+3(4.39e-05)]_105 49501 3.55e-05 78_[+2(9.57e-08)]_146_\ [+3(1.28e-05)]_178_[+2(6.83e-05)]_46 10356 5.52e-05 262_[+2(1.26e-06)]_29_\ [+3(1.28e-05)]_177 41496 1.94e-04 188_[+2(3.82e-07)]_269_\ [+3(2.45e-05)]_11 10902 6.56e-05 129_[+3(4.01e-05)]_81_\ [+1(3.30e-07)]_258 46002 2.63e-08 115_[+1(3.52e-07)]_128_\ [+2(1.22e-08)]_217 46567 3.46e-05 81_[+2(7.89e-08)]_399 34164 2.83e-09 65_[+1(7.60e-08)]_38_[+2(1.66e-07)]_\ 336_[+3(5.62e-06)]_9 45937 1.36e-02 148_[+3(4.39e-05)]_340 40338 2.14e-09 282_[+2(2.16e-07)]_57_\ [+1(3.00e-09)]_76_[+3(8.27e-05)]_33 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************