******************************************************************************** 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/197/197.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 17184 1.0000 500 7848 1.0000 500 48731 1.0000 500 39466 1.0000 500 9910 1.0000 500 49167 1.0000 500 44117 1.0000 500 44132 1.0000 500 34217 1.0000 500 27067 1.0000 500 35319 1.0000 500 46074 1.0000 500 46122 1.0000 500 46523 1.0000 500 47624 1.0000 500 49921 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/197/197.seqs.fa -oc motifs/197 -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 0.269 C 0.240 G 0.234 T 0.256 Background letter frequencies (from dataset with add-one prior applied): A 0.269 C 0.240 G 0.235 T 0.256 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 7 llr = 117 E-value = 9.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::3461:99377336:::3a1 pos.-specific C 6111:9:1::3:7147::6:7 probability G 49631:a::7:1:6::a9::: matrix T :::13:::1::1:::3:11:1 bits 2.1 * * 1.9 * * * 1.7 * * * 1.5 * ** ** * Relative 1.3 * ***** *** * Entropy 1.0 ** ****** * **** * (24.1 bits) 0.8 ** ******** **** ** 0.6 *** ***************** 0.4 *** ***************** 0.2 ********************* 0.0 --------------------- Multilevel CGGAACGAAGAACGACGGCAC consensus G AGT AC AACT A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 27067 351 2.99e-11 TTCCGACGGT CGGGACGAAGAACGACGGTAC TGGGAAGCCG 35319 124 7.36e-10 GGTGAGATAA CGAAACGAAGAAAAATGGCAC CACGTCGTGA 7848 133 1.50e-08 GACGACCATG GGGATCGCAACGCGACGGCAC TCGGGCACAC 9910 347 1.62e-08 ACCGCTTAAC GGCGGCGAAGCACGCTGGAAC GCTCGACAGC 46122 421 2.07e-08 TTCTTCGGGA GGGTTCGATGAACACCGGCAT TCCACTTCGA 39466 51 5.55e-08 AATGGTATCC CCGAAAGAAGAAAGCCGGAAA GGGGCCGTGC 49167 33 7.11e-08 CCATGTCAAG CGACACGAAAATCCACGTCAC ATACGGGTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 27067 3e-11 350_[+1]_129 35319 7.4e-10 123_[+1]_356 7848 1.5e-08 132_[+1]_347 9910 1.6e-08 346_[+1]_133 46122 2.1e-08 420_[+1]_59 39466 5.6e-08 50_[+1]_429 49167 7.1e-08 32_[+1]_447 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=7 27067 ( 351) CGGGACGAAGAACGACGGTAC 1 35319 ( 124) CGAAACGAAGAAAAATGGCAC 1 7848 ( 133) GGGATCGCAACGCGACGGCAC 1 9910 ( 347) GGCGGCGAAGCACGCTGGAAC 1 46122 ( 421) GGGTTCGATGAACACCGGCAT 1 39466 ( 51) CCGAAAGAAGAAAGCCGGAAA 1 49167 ( 33) CGACACGAAAATCCACGTCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7680 bayes= 9.94195 E= 9.1e+001 -945 125 87 -945 -945 -75 187 -945 9 -75 128 -945 67 -75 28 -84 109 -945 -71 16 -91 183 -945 -945 -945 -945 209 -945 167 -75 -945 -945 167 -945 -945 -84 9 -945 161 -945 141 25 -945 -945 141 -945 -71 -84 9 157 -945 -945 9 -75 128 -945 109 83 -945 -945 -945 157 -945 16 -945 -945 209 -945 -945 -945 187 -84 9 125 -945 -84 189 -945 -945 -945 -91 157 -945 -84 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 9.1e+001 0.000000 0.571429 0.428571 0.000000 0.000000 0.142857 0.857143 0.000000 0.285714 0.142857 0.571429 0.000000 0.428571 0.142857 0.285714 0.142857 0.571429 0.000000 0.142857 0.285714 0.142857 0.857143 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.857143 0.000000 0.000000 0.142857 0.285714 0.000000 0.714286 0.000000 0.714286 0.285714 0.000000 0.000000 0.714286 0.000000 0.142857 0.142857 0.285714 0.714286 0.000000 0.000000 0.285714 0.142857 0.571429 0.000000 0.571429 0.428571 0.000000 0.000000 0.000000 0.714286 0.000000 0.285714 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.285714 0.571429 0.000000 0.142857 1.000000 0.000000 0.000000 0.000000 0.142857 0.714286 0.000000 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG]G[GA][AG][AT]CGAA[GA][AC]A[CA][GA][AC][CT]GG[CA]AC -------------------------------------------------------------------------------- Time 2.22 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 6 llr = 91 E-value = 4.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::::::5:5:25::: pos.-specific C 785:2a::a:a8::82 probability G :252::85:3::5228 matrix T 3::88:2::2:::8:: bits 2.1 * * * 1.9 * * * 1.7 * * * 1.5 * ** * ** ** Relative 1.3 * **** * ** *** Entropy 1.0 ********* ****** (21.9 bits) 0.8 ********* ****** 0.6 ********* ****** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CCCTTCGACACCATCG consensus T G G G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 46074 300 7.48e-09 GGAACGGGTA CCGGTCGGCACCGTCG TTCCATCGAC 49167 232 2.79e-08 TGGAGTTTTC CCGTTCGACGCCATGG AACTCTTCGG 35319 386 3.25e-08 TCCAAACCAA TCCTTCGGCACCGTCC CTCAGACCCC 27067 176 5.94e-08 CTGAAGGAGA TCCTTCGGCGCAATCG AGATTTCCGT 47624 454 9.69e-08 TCCGGCCTTA CCGTTCTACACCAGCG GTACACCTTT 9910 470 2.12e-07 AACTCTACGG CGCTCCGACTCCGTCG AACGCCGCTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46074 7.5e-09 299_[+2]_185 49167 2.8e-08 231_[+2]_253 35319 3.3e-08 385_[+2]_99 27067 5.9e-08 175_[+2]_309 47624 9.7e-08 453_[+2]_31 9910 2.1e-07 469_[+2]_15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=6 46074 ( 300) CCGGTCGGCACCGTCG 1 49167 ( 232) CCGTTCGACGCCATGG 1 35319 ( 386) TCCTTCGGCACCGTCC 1 27067 ( 176) TCCTTCGGCGCAATCG 1 47624 ( 454) CCGTTCTACACCAGCG 1 9910 ( 470) CGCTCCGACTCCGTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 7760 bayes= 9.99443 E= 4.0e+002 -923 147 -923 38 -923 179 -49 -923 -923 106 109 -923 -923 -923 -49 170 -923 -53 -923 170 -923 206 -923 -923 -923 -923 183 -62 89 -923 109 -923 -923 206 -923 -923 89 -923 51 -62 -923 206 -923 -923 -69 179 -923 -923 89 -923 109 -923 -923 -923 -49 170 -923 179 -49 -923 -923 -53 183 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 6 E= 4.0e+002 0.000000 0.666667 0.000000 0.333333 0.000000 0.833333 0.166667 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.166667 0.000000 0.833333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.333333 0.166667 0.000000 1.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.833333 0.166667 0.000000 0.000000 0.166667 0.833333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT]C[CG]TTCG[AG]C[AG]CC[AG]TCG -------------------------------------------------------------------------------- Time 4.76 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 6 llr = 101 E-value = 1.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 823::::::5:3::87:3::: pos.-specific C ::2233:2:2822a::::2:: probability G 282573a:82:38:22a27:: matrix T ::33:3:82222:::2:52aa bits 2.1 * * * 1.9 * * * ** 1.7 * * * ** 1.5 * * * * ** * ** Relative 1.3 ** * *** * *** * ** Entropy 1.0 ** * *** * *** * ** (24.2 bits) 0.8 ** * *** * *** * *** 0.6 ** ** *** * ***** *** 0.4 ** ****** * ********* 0.2 ** ******** ********* 0.0 --------------------- Multilevel AGAGGCGTGACAGCAAGTGTT consensus TTCG G A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 46122 131 4.20e-11 GTCCCGGTTG AGAGGGGTGACGGCAGGTGTT CGTCGCGATC 27067 386 6.67e-09 AAGCCGAAAA AGTGCGGCGGCTGCAAGAGTT GGAAGATTCA 49167 70 1.54e-08 GTATGACCCT AAGCGCGTGACCGCAAGGGTT TGCTCGTCCG 46523 115 1.66e-08 TCCTTAAATC AGCGGTGTGATGCCATGTGTT TCCGGACGAT 49921 465 2.08e-08 ACGTGCCTCT AGATCCGTTTCAGCAAGTCTT CTTTCATTCT 46074 169 4.92e-08 GAGTGGATGT GGTTGTGTGCCAGCGAGATTT GAAAGCTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46122 4.2e-11 130_[+3]_349 27067 6.7e-09 385_[+3]_94 49167 1.5e-08 69_[+3]_410 46523 1.7e-08 114_[+3]_365 49921 2.1e-08 464_[+3]_15 46074 4.9e-08 168_[+3]_311 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=6 46122 ( 131) AGAGGGGTGACGGCAGGTGTT 1 27067 ( 386) AGTGCGGCGGCTGCAAGAGTT 1 49167 ( 70) AAGCGCGTGACCGCAAGGGTT 1 46523 ( 115) AGCGGTGTGATGCCATGTGTT 1 49921 ( 465) AGATCCGTTTCAGCAAGTCTT 1 46074 ( 169) GGTTGTGTGCCAGCGAGATTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7680 bayes= 10.7686 E= 1.0e+003 163 -923 -49 -923 -69 -923 183 -923 31 -53 -49 38 -923 -53 109 38 -923 47 151 -923 -923 47 51 38 -923 -923 209 -923 -923 -53 -923 170 -923 -923 183 -62 89 -53 -49 -62 -923 179 -923 -62 31 -53 51 -62 -923 -53 183 -923 -923 206 -923 -923 163 -923 -49 -923 131 -923 -49 -62 -923 -923 209 -923 31 -923 -49 96 -923 -53 151 -62 -923 -923 -923 196 -923 -923 -923 196 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 1.0e+003 0.833333 0.000000 0.166667 0.000000 0.166667 0.000000 0.833333 0.000000 0.333333 0.166667 0.166667 0.333333 0.000000 0.166667 0.500000 0.333333 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.333333 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.833333 0.166667 0.500000 0.166667 0.166667 0.166667 0.000000 0.833333 0.000000 0.166667 0.333333 0.166667 0.333333 0.166667 0.000000 0.166667 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.666667 0.000000 0.166667 0.166667 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.166667 0.500000 0.000000 0.166667 0.666667 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- AG[AT][GT][GC][CGT]GTGAC[AG]GCAAG[TA]GTT -------------------------------------------------------------------------------- Time 6.70 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17184 1.29e-01 500 7848 1.62e-04 132_[+1(1.50e-08)]_347 48731 6.78e-01 500 39466 7.07e-04 50_[+1(5.55e-08)]_429 9910 1.13e-07 346_[+1(1.62e-08)]_102_\ [+2(2.12e-07)]_15 49167 2.01e-12 32_[+1(7.11e-08)]_16_[+3(1.54e-08)]_\ 141_[+2(2.79e-08)]_253 44117 8.79e-01 500 44132 6.04e-01 500 34217 5.30e-02 500 27067 1.18e-15 175_[+2(5.94e-08)]_159_\ [+1(2.99e-11)]_14_[+3(6.67e-09)]_94 35319 1.25e-09 123_[+1(7.36e-10)]_241_\ [+2(3.25e-08)]_99 46074 1.61e-08 168_[+3(4.92e-08)]_110_\ [+2(7.48e-09)]_185 46122 4.94e-11 130_[+3(4.20e-11)]_269_\ [+1(2.07e-08)]_59 46523 1.38e-05 114_[+3(1.66e-08)]_365 47624 1.63e-03 453_[+2(9.69e-08)]_31 49921 1.20e-04 464_[+3(2.08e-08)]_15 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************