******************************************************************************** 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/83/83.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 46347 1.0000 500 27972 1.0000 500 13320 1.0000 500 5419 1.0000 500 47436 1.0000 500 859 1.0000 500 8365 1.0000 500 14636 1.0000 500 14467 1.0000 500 39402 1.0000 500 32733 1.0000 500 49037 1.0000 500 49185 1.0000 500 15844 1.0000 500 15853 1.0000 500 30394 1.0000 500 49686 1.0000 500 23467 1.0000 500 52709 1.0000 500 18549 1.0000 500 10865 1.0000 500 26934 1.0000 500 35464 1.0000 500 54528 1.0000 500 12663 1.0000 500 46251 1.0000 500 42786 1.0000 500 46709 1.0000 500 45342 1.0000 500 49228 1.0000 500 50265 1.0000 500 50330 1.0000 500 50316 1.0000 500 45582 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/83/83.seqs.fa -oc motifs/83 -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= 34 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= 17000 N= 34 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.262 C 0.246 G 0.225 T 0.267 Background letter frequencies (from dataset with add-one prior applied): A 0.262 C 0.246 G 0.225 T 0.267 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 13 llr = 156 E-value = 5.7e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::a17:::a5:1 pos.-specific C :a:91::9::25 probability G :::::9:1:444 matrix T a:::21a::24: bits 2.1 1.9 *** * * 1.7 **** **** 1.5 **** **** Relative 1.3 **** **** Entropy 1.1 **** **** (17.3 bits) 0.9 ********* * 0.6 ********** * 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TCACAGTCAAGC consensus T GTG sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 39402 72 1.16e-07 TGGCCAAGCC TCACAGTCAAGC TAACGGTATT 5419 54 1.16e-07 TAGTAAGCCT TCACAGTCAGGC ATTATATGAA 50265 61 4.85e-07 ATCTCTTAAC TCACAGTCAGTG CCTTACTATC 14467 108 4.85e-07 CAATTGCGGC TCACAGTCAGTG TTCCATCTGG 26934 74 6.11e-07 CAGACCGAAT TCACAGTCAACC GCATTCTAAT 49686 161 1.49e-06 GCTCTGTGTG TCACTGTCAATG ACGAGACACG 23467 436 1.68e-06 GATTCGGTTC TCACTGTCAGCC AGGTTTCGTG 49185 247 1.99e-06 TATCCTCACA TCACAGTCAAGA GAAACCTTAG 15853 38 2.44e-06 CCCCACTCAC TCACCGTCAATC GTAACGAAGC 49228 24 2.78e-06 ACACTCACAA TCACTGTCATGG CGGAAAGACG 46709 356 3.85e-06 GGCTATAATA TCAAAGTCAGTC AGTACATCGC 46347 276 4.80e-06 GGAATCGACG TCACAGTGAACC AACAAGATTT 50330 37 8.57e-06 CCTACTTCTT TCACATTCATGG TCAAACATGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 39402 1.2e-07 71_[+1]_417 5419 1.2e-07 53_[+1]_435 50265 4.8e-07 60_[+1]_428 14467 4.8e-07 107_[+1]_381 26934 6.1e-07 73_[+1]_415 49686 1.5e-06 160_[+1]_328 23467 1.7e-06 435_[+1]_53 49185 2e-06 246_[+1]_242 15853 2.4e-06 37_[+1]_451 49228 2.8e-06 23_[+1]_465 46709 3.9e-06 355_[+1]_133 46347 4.8e-06 275_[+1]_213 50330 8.6e-06 36_[+1]_452 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=13 39402 ( 72) TCACAGTCAAGC 1 5419 ( 54) TCACAGTCAGGC 1 50265 ( 61) TCACAGTCAGTG 1 14467 ( 108) TCACAGTCAGTG 1 26934 ( 74) TCACAGTCAACC 1 49686 ( 161) TCACTGTCAATG 1 23467 ( 436) TCACTGTCAGCC 1 49185 ( 247) TCACAGTCAAGA 1 15853 ( 38) TCACCGTCAATC 1 49228 ( 24) TCACTGTCATGG 1 46709 ( 356) TCAAAGTCAGTC 1 46347 ( 276) TCACAGTGAACC 1 50330 ( 37) TCACATTCATGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 16626 bayes= 10.8504 E= 5.7e-004 -1035 -1035 -1035 190 -1035 202 -1035 -1035 193 -1035 -1035 -1035 -176 191 -1035 -1035 140 -167 -1035 -21 -1035 -1035 203 -179 -1035 -1035 -1035 190 -1035 191 -155 -1035 193 -1035 -1035 -1035 82 -1035 77 -80 -1035 -9 77 53 -176 113 77 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 13 E= 5.7e-004 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.076923 0.923077 0.000000 0.000000 0.692308 0.076923 0.000000 0.230769 0.000000 0.000000 0.923077 0.076923 0.000000 0.000000 0.000000 1.000000 0.000000 0.923077 0.076923 0.000000 1.000000 0.000000 0.000000 0.000000 0.461538 0.000000 0.384615 0.153846 0.000000 0.230769 0.384615 0.384615 0.076923 0.538462 0.384615 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TCAC[AT]GTCA[AG][GTC][CG] -------------------------------------------------------------------------------- Time 9.56 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 4 llr = 94 E-value = 1.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 3a8:55:::5a:::::::::: pos.-specific C ::::3::a:5:3::8::::3: probability G 8:3a35::a::5aa:3aa:8a matrix T ::::::a::::3::38::a:: bits 2.1 * * ** ** * 1.9 * * *** * ** *** * 1.7 * * *** * ** *** * 1.5 * * *** * ** *** * Relative 1.3 ** * *** * *** ***** Entropy 1.1 **** ****** ********* (33.9 bits) 0.9 **** ****** ********* 0.6 **** **************** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GAAGAATCGAAGGGCTGGTGG consensus A G CG C C TG C sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 14467 462 2.06e-13 AGTGCCGAAA GAAGAGTCGAAGGGCTGGTGG AACTCGGCAG 14636 105 2.06e-13 AGTGCCGAAA GAAGAGTCGAAGGGCTGGTGG AACTCGGCAG 54528 204 7.79e-11 TCGCAAAACC AAAGCATCGCATGGTTGGTGG GGAACACGAT 18549 232 9.24e-11 GCCACCGGCG GAGGGATCGCACGGCGGGTCG GCTCGTTCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 14467 2.1e-13 461_[+2]_18 14636 2.1e-13 104_[+2]_375 54528 7.8e-11 203_[+2]_276 18549 9.2e-11 231_[+2]_248 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=4 14467 ( 462) GAAGAGTCGAAGGGCTGGTGG 1 14636 ( 105) GAAGAGTCGAAGGGCTGGTGG 1 54528 ( 204) AAAGCATCGCATGGTTGGTGG 1 18549 ( 232) GAGGGATCGCACGGCGGGTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16320 bayes= 11.994 E= 1.1e+000 -7 -865 173 -865 193 -865 -865 -865 152 -865 15 -865 -865 -865 215 -865 93 2 15 -865 93 -865 115 -865 -865 -865 -865 190 -865 202 -865 -865 -865 -865 215 -865 93 102 -865 -865 193 -865 -865 -865 -865 2 115 -10 -865 -865 215 -865 -865 -865 215 -865 -865 161 -865 -10 -865 -865 15 149 -865 -865 215 -865 -865 -865 215 -865 -865 -865 -865 190 -865 2 173 -865 -865 -865 215 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 1.1e+000 0.250000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.500000 0.000000 0.500000 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 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.500000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA]A[AG]G[ACG][AG]TCG[AC]A[GCT]GG[CT][TG]GGT[GC]G -------------------------------------------------------------------------------- Time 18.77 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 5 llr = 102 E-value = 1.8e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :4a6::4:::4:2:a:::84 pos.-specific C 62::::::a::2:4::aa:6 probability G 44:48:6a:a6884:8::2: matrix T ::::2a:::::::2:2:::: bits 2.1 * * 1.9 * * *** * ** 1.7 * * *** * ** 1.5 * * *** * * ** Relative 1.3 * ** *** ** ***** Entropy 1.1 * *********** ****** (29.3 bits) 0.9 * *********** ****** 0.6 * *********** ****** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel CAAAGTGGCGGGGCAGCCAC consensus GG GT A ACAG T GA sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 14467 384 2.93e-11 GTTCAGTGAA GGAGGTGGCGGGGCAGCCAA AGAATCCAAA 14636 27 2.93e-11 GTTCAGTGAA GGAGGTGGCGGGGCAGCCAA AGAATCCAAA 8365 108 3.32e-10 TACACAACTT CCAAGTAGCGAGGTAGCCAC CGTTTGCAAG 46709 150 1.43e-09 GAGCTCCTTT CAAATTAGCGAGAGAGCCAC CTTTTAAAAC 13320 225 1.52e-09 AATTCCTTCC CAAAGTGGCGGCGGATCCGC ACTACCCGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 14467 2.9e-11 383_[+3]_97 14636 2.9e-11 26_[+3]_454 8365 3.3e-10 107_[+3]_373 46709 1.4e-09 149_[+3]_331 13320 1.5e-09 224_[+3]_256 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=5 14467 ( 384) GGAGGTGGCGGGGCAGCCAA 1 14636 ( 27) GGAGGTGGCGGGGCAGCCAA 1 8365 ( 108) CCAAGTAGCGAGGTAGCCAC 1 46709 ( 150) CAAATTAGCGAGAGAGCCAC 1 13320 ( 225) CAAAGTGGCGGCGGATCCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 16354 bayes= 10.2095 E= 1.8e+001 -897 128 83 -897 61 -30 83 -897 193 -897 -897 -897 120 -897 83 -897 -897 -897 183 -42 -897 -897 -897 190 61 -897 141 -897 -897 -897 215 -897 -897 202 -897 -897 -897 -897 215 -897 61 -897 141 -897 -897 -30 183 -897 -39 -897 183 -897 -897 70 83 -42 193 -897 -897 -897 -897 -897 183 -42 -897 202 -897 -897 -897 202 -897 -897 161 -897 -17 -897 61 128 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 5 E= 1.8e+001 0.000000 0.600000 0.400000 0.000000 0.400000 0.200000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 1.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.200000 0.800000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.400000 0.400000 0.200000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.400000 0.600000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG][AGC]A[AG][GT]T[GA]GCG[GA][GC][GA][CGT]A[GT]CC[AG][CA] -------------------------------------------------------------------------------- Time 28.23 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46347 1.13e-02 275_[+1(4.80e-06)]_213 27972 2.26e-01 500 13320 1.05e-05 224_[+3(1.52e-09)]_256 5419 1.59e-04 53_[+1(1.16e-07)]_240_\ [+2(9.75e-05)]_174 47436 1.71e-02 420_[+2(1.63e-05)]_59 859 1.32e-01 413_[+3(8.78e-05)]_67 8365 4.96e-06 107_[+3(3.32e-10)]_373 14636 9.47e-16 26_[+3(2.93e-11)]_58_[+2(2.06e-13)]_\ 375 14467 4.21e-19 107_[+1(4.85e-07)]_264_\ [+3(2.93e-11)]_58_[+2(2.06e-13)]_18 39402 3.00e-04 71_[+1(1.16e-07)]_417 32733 1.92e-02 234_[+3(3.16e-05)]_246 49037 4.91e-01 500 49185 4.44e-03 246_[+1(1.99e-06)]_242 15844 2.95e-01 500 15853 1.20e-02 37_[+1(2.44e-06)]_451 30394 3.93e-01 500 49686 1.40e-02 160_[+1(1.49e-06)]_328 23467 1.67e-02 435_[+1(1.68e-06)]_53 52709 2.40e-01 500 18549 5.24e-07 231_[+2(9.24e-11)]_248 10865 6.80e-01 500 26934 4.50e-03 73_[+1(6.11e-07)]_415 35464 8.45e-02 329_[+3(2.14e-05)]_151 54528 3.38e-06 203_[+2(7.79e-11)]_276 12663 6.31e-02 422_[+1(3.93e-05)]_66 46251 5.61e-01 500 42786 9.37e-01 500 46709 2.62e-07 149_[+3(1.43e-09)]_186_\ [+1(3.85e-06)]_41_[+1(8.56e-05)]_80 45342 1.83e-01 500 49228 2.40e-02 23_[+1(2.78e-06)]_465 50265 4.95e-03 60_[+1(4.85e-07)]_213_\ [+1(3.28e-05)]_203 50330 4.00e-02 36_[+1(8.57e-06)]_452 50316 6.57e-01 500 45582 2.22e-01 479_[+3(9.38e-05)]_1 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************