******************************************************************************** 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/157/157.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 47350 1.0000 500 30578 1.0000 500 50500 1.0000 500 16982 1.0000 500 50361 1.0000 500 33087 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/157/157.seqs.fa -oc motifs/157 -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= 6 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= 3000 N= 6 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.261 C 0.224 G 0.228 T 0.288 Background letter frequencies (from dataset with add-one prior applied): A 0.261 C 0.224 G 0.228 T 0.288 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 5 llr = 71 E-value = 3.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 22:228aa4:8a::: pos.-specific C :22:62:::2:::6a probability G 86282::::82::4: matrix T ::6:::::6:::a:: bits 2.2 * 1.9 ** * * 1.7 ** ** * 1.5 ** * ** * Relative 1.3 * * *** **** * Entropy 1.1 * * *** ****** (20.6 bits) 0.9 * * ********** 0.6 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel GGTGCAAATGAATCC consensus AACAAC ACG G sequence CG G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 30578 94 2.57e-09 CACGGCTTCC GGTGCAAATGAATGC TATTACTGCC 47350 188 6.11e-08 AGTTCTTGAA GCTGAAAATGAATCC CTACGCGTTG 50361 148 6.93e-08 GTCCGTCTTG GAGGCAAAAGAATCC ATACTTCAAT 16982 63 4.42e-07 AACGTATGTT GGTACCAATGGATCC AAAAAGGATT 33087 426 1.20e-06 GAGGGGAGAA AGCGGAAAACAATGC TCAATTTGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 30578 2.6e-09 93_[+1]_392 47350 6.1e-08 187_[+1]_298 50361 6.9e-08 147_[+1]_338 16982 4.4e-07 62_[+1]_423 33087 1.2e-06 425_[+1]_60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=5 30578 ( 94) GGTGCAAATGAATGC 1 47350 ( 188) GCTGAAAATGAATCC 1 50361 ( 148) GAGGCAAAAGAATCC 1 16982 ( 63) GGTACCAATGGATCC 1 33087 ( 426) AGCGGAAAACAATGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 2916 bayes= 9.43731 E= 3.2e+002 -38 -897 181 -897 -38 -16 140 -897 -897 -16 -19 106 -38 -897 181 -897 -38 142 -19 -897 162 -16 -897 -897 194 -897 -897 -897 194 -897 -897 -897 62 -897 -897 106 -897 -16 181 -897 162 -897 -19 -897 194 -897 -897 -897 -897 -897 -897 179 -897 142 81 -897 -897 216 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 5 E= 3.2e+002 0.200000 0.000000 0.800000 0.000000 0.200000 0.200000 0.600000 0.000000 0.000000 0.200000 0.200000 0.600000 0.200000 0.000000 0.800000 0.000000 0.200000 0.600000 0.200000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.600000 0.000000 0.200000 0.800000 0.000000 0.800000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.400000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GA][GAC][TCG][GA][CAG][AC]AA[TA][GC][AG]AT[CG]C -------------------------------------------------------------------------------- Time 0.51 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 5 llr = 72 E-value = 2.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::22::2:8:4:::: pos.-specific C ::6:2a:a::6:::: probability G 6a:22:8:2::2:8: matrix T 4:266::::a:8a2a bits 2.2 * * * 1.9 * * * 1.7 * * * * * * 1.5 * * * * * * Relative 1.3 * ***** *** Entropy 1.1 ** ********** (20.9 bits) 0.9 ** ********** 0.6 *** *********** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel GGCTTCGCATCTTGT consensus T AAC A G AG T sequence TGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 50500 142 9.08e-09 CATTCGGTGA GGCTTCGCATCGTGT ACGGGGCGAC 47350 285 2.05e-08 TCCAGGTCGT GGCATCGCATATTGT CTCTCCTTCT 33087 108 6.44e-08 AATGCCGCTT TGCGCCGCATCTTGT CCGCAACGTA 30578 186 4.22e-07 CGGATTAGTT TGTTTCGCATATTTT TGTGGTGCGG 16982 155 7.17e-07 ATCGAATACC GGATGCACGTCTTGT TTATCTATAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50500 9.1e-09 141_[+2]_344 47350 2e-08 284_[+2]_201 33087 6.4e-08 107_[+2]_378 30578 4.2e-07 185_[+2]_300 16982 7.2e-07 154_[+2]_331 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=5 50500 ( 142) GGCTTCGCATCGTGT 1 47350 ( 285) GGCATCGCATATTGT 1 33087 ( 108) TGCGCCGCATCTTGT 1 30578 ( 186) TGTTTCGCATATTTT 1 16982 ( 155) GGATGCACGTCTTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 2916 bayes= 9.43731 E= 2.9e+002 -897 -897 140 47 -897 -897 213 -897 -38 142 -897 -52 -38 -897 -19 106 -897 -16 -19 106 -897 216 -897 -897 -38 -897 181 -897 -897 216 -897 -897 162 -897 -19 -897 -897 -897 -897 179 62 142 -897 -897 -897 -897 -19 147 -897 -897 -897 179 -897 -897 181 -52 -897 -897 -897 179 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 5 E= 2.9e+002 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 1.000000 0.000000 0.200000 0.600000 0.000000 0.200000 0.200000 0.000000 0.200000 0.600000 0.000000 0.200000 0.200000 0.600000 0.000000 1.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 1.000000 0.400000 0.600000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT]G[CAT][TAG][TCG]C[GA]C[AG]T[CA][TG]T[GT]T -------------------------------------------------------------------------------- Time 0.82 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 14 sites = 6 llr = 74 E-value = 5.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :3:2:2::2235:: pos.-specific C ::8::::8:8::3a probability G 272828:22:::3: matrix T 8:::8:a:7:753: bits 2.2 * 1.9 * 1.7 * * 1.5 ** *** * * Relative 1.3 * ****** * * Entropy 1.1 ******** * * (17.8 bits) 0.9 ******** *** * 0.6 ************ * 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel TGCGTGTCTCTACC consensus A ATG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 50361 301 4.93e-08 TTATGATAAA TACGTGTCTCTACC TCACGAAATA 16982 319 8.49e-08 ACCAATCTGT TGCGTGTCGCTTCC AATACCAGCT 33087 56 8.94e-07 GGGGAAGTGA TACGGGTCTCATGC TGATCTTACA 50500 424 9.70e-07 ACCGTTGTTC GGGGTGTCTCTAGC CTGCATTGTA 30578 237 2.33e-06 CGTAAGCTTT TGCATGTCTATTTC TCGTTGGCGT 47350 35 7.89e-06 TCTCGATGAA TGCGTATGACAATC TTTTCTACTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50361 4.9e-08 300_[+3]_186 16982 8.5e-08 318_[+3]_168 33087 8.9e-07 55_[+3]_431 50500 9.7e-07 423_[+3]_63 30578 2.3e-06 236_[+3]_250 47350 7.9e-06 34_[+3]_452 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=14 seqs=6 50361 ( 301) TACGTGTCTCTACC 1 16982 ( 319) TGCGTGTCGCTTCC 1 33087 ( 56) TACGGGTCTCATGC 1 50500 ( 424) GGGGTGTCTCTAGC 1 30578 ( 237) TGCATGTCTATTTC 1 47350 ( 35) TGCGTATGACAATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 2922 bayes= 8.92481 E= 5.1e+002 -923 -923 -45 153 35 -923 155 -923 -923 190 -45 -923 -64 -923 187 -923 -923 -923 -45 153 -64 -923 187 -923 -923 -923 -923 179 -923 190 -45 -923 -64 -923 -45 121 -64 190 -923 -923 35 -923 -923 121 94 -923 -923 80 -923 57 55 21 -923 216 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 6 E= 5.1e+002 0.000000 0.000000 0.166667 0.833333 0.333333 0.000000 0.666667 0.000000 0.000000 0.833333 0.166667 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.000000 0.166667 0.833333 0.166667 0.000000 0.833333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.833333 0.166667 0.000000 0.166667 0.000000 0.166667 0.666667 0.166667 0.833333 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.500000 0.000000 0.000000 0.500000 0.000000 0.333333 0.333333 0.333333 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[GA]CGTGTCTC[TA][AT][CGT]C -------------------------------------------------------------------------------- Time 1.20 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47350 4.61e-10 34_[+3(7.89e-06)]_139_\ [+1(6.11e-08)]_82_[+2(2.05e-08)]_201 30578 1.29e-10 93_[+1(2.57e-09)]_77_[+2(4.22e-07)]_\ 36_[+3(2.33e-06)]_87_[+1(6.29e-05)]_148 50500 2.47e-08 141_[+2(9.08e-09)]_237_\ [+1(8.48e-05)]_15_[+3(9.70e-07)]_63 16982 1.17e-09 62_[+1(4.42e-07)]_77_[+2(7.17e-07)]_\ 149_[+3(8.49e-08)]_168 50361 1.39e-07 147_[+1(6.93e-08)]_138_\ [+3(4.93e-08)]_186 33087 2.80e-09 55_[+3(8.94e-07)]_38_[+2(6.44e-08)]_\ 303_[+1(1.20e-06)]_60 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************