******************************************************************************** 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/495/495.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 12040 1.0000 500 12047 1.0000 500 25843 1.0000 500 25844 1.0000 500 25847 1.0000 500 25848 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/495/495.seqs.fa -oc motifs/495 -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 0.289 C 0.233 G 0.218 T 0.260 Background letter frequencies (from dataset with add-one prior applied): A 0.289 C 0.233 G 0.218 T 0.260 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 6 llr = 126 E-value = 3.1e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 773::a:3:33:::a:::3:a pos.-specific C 33::::::::::37::7:5:: probability G ::77a::3a77a:3:3:a:a: matrix T :::3::a3::::7::73:2:: bits 2.2 * * * * * 2.0 * * * * * * 1.8 *** * * * * ** 1.5 *** * * * * ** Relative 1.3 *** * * ** * ** Entropy 1.1 ***** ********** ** (30.3 bits) 0.9 ******* ********** ** 0.7 ******* ********** ** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel AAGGGATAGGGGTCATCGCGA consensus CCAT G AA CG GT A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 25843 57 5.28e-12 CCAAAACACT AAGTGATAGGGGTCATCGCGA TTGAGGCACG 12047 58 5.28e-12 CCAAAACACA AAGTGATAGGGGTCATCGCGA TTGAGGCACG 25848 261 3.27e-10 CTATTTTTGC CCGGGATTGAGGTCATTGAGA CGGTACTCAA 12040 421 3.27e-10 CTATTTTTGC CCGGGATTGAGGTCATTGAGA CGGTTCTCAA 25847 190 4.51e-10 CACGACGACA AAAGGATGGGAGCGAGCGCGA AACGACTGAC 25844 398 1.02e-09 CACGAAGACA AAAGGATGGGAGCGAGCGTGA AACGACTGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25843 5.3e-12 56_[+1]_423 12047 5.3e-12 57_[+1]_422 25848 3.3e-10 260_[+1]_219 12040 3.3e-10 420_[+1]_59 25847 4.5e-10 189_[+1]_290 25844 1e-09 397_[+1]_82 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=6 25843 ( 57) AAGTGATAGGGGTCATCGCGA 1 12047 ( 58) AAGTGATAGGGGTCATCGCGA 1 25848 ( 261) CCGGGATTGAGGTCATTGAGA 1 12040 ( 421) CCGGGATTGAGGTCATTGAGA 1 25847 ( 190) AAAGGATGGGAGCGAGCGCGA 1 25844 ( 398) AAAGGATGGGAGCGAGCGTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2880 bayes= 8.90388 E= 3.1e-009 121 51 -923 -923 121 51 -923 -923 21 -923 161 -923 -923 -923 161 36 -923 -923 220 -923 179 -923 -923 -923 -923 -923 -923 194 21 -923 61 36 -923 -923 220 -923 21 -923 161 -923 21 -923 161 -923 -923 -923 220 -923 -923 51 -923 136 -923 151 61 -923 179 -923 -923 -923 -923 -923 61 136 -923 151 -923 36 -923 -923 220 -923 21 110 -923 -64 -923 -923 220 -923 179 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 3.1e-009 0.666667 0.333333 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.333333 0.333333 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.333333 0.500000 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC][AC][GA][GT]GAT[AGT]G[GA][GA]G[TC][CG]A[TG][CT]G[CA]GA -------------------------------------------------------------------------------- Time 0.35 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 6 llr = 121 E-value = 4.9e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :28:::::::77::a3::7aa pos.-specific C :::387:a2a::35:3773:: probability G a::7:3::::3::5::3:::: matrix T :82:2:a:8::37::3:3::: bits 2.2 * * * 2.0 * ** * 1.8 * ** * * ** 1.5 * ** * * ** Relative 1.3 ** ******* * * ** Entropy 1.1 *********** *** ** ** (29.2 bits) 0.9 *************** ***** 0.7 *************** ***** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GTAGCCTCTCAATCAACCAAA consensus C G GTCG CGTC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 25843 230 1.51e-11 TCGTGATCTG GTAGCCTCTCAACCAACCAAA CCCGCTCACA 12047 231 1.51e-11 TCGTGAACTG GTAGCCTCTCAACCAACCAAA CCCGCACAAC 25847 133 3.30e-10 AGTCAATTGA GTACCGTCTCAATGACCTCAA TCCCGGGCAA 12040 319 7.04e-10 TTATGCCATC GTAGTCTCTCGTTGATGCAAA AGTCAAGGAT 25844 341 1.53e-09 AGTCAATTGA GAACCGTCTCAATGACCTCAA TCCCGGGCAA 25848 155 1.88e-09 CTATTATGCC GTTGCCTCCCGTTCATGCAAA GGTCTCAAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25843 1.5e-11 229_[+2]_250 12047 1.5e-11 230_[+2]_249 25847 3.3e-10 132_[+2]_347 12040 7e-10 318_[+2]_161 25844 1.5e-09 340_[+2]_139 25848 1.9e-09 154_[+2]_325 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=6 25843 ( 230) GTAGCCTCTCAACCAACCAAA 1 12047 ( 231) GTAGCCTCTCAACCAACCAAA 1 25847 ( 133) GTACCGTCTCAATGACCTCAA 1 12040 ( 319) GTAGTCTCTCGTTGATGCAAA 1 25844 ( 341) GAACCGTCTCAATGACCTCAA 1 25848 ( 155) GTTGCCTCCCGTTCATGCAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2880 bayes= 8.90388 E= 4.9e-007 -923 -923 220 -923 -79 -923 -923 168 153 -923 -923 -64 -923 51 161 -923 -923 183 -923 -64 -923 151 61 -923 -923 -923 -923 194 -923 210 -923 -923 -923 -48 -923 168 -923 210 -923 -923 121 -923 61 -923 121 -923 -923 36 -923 51 -923 136 -923 110 120 -923 179 -923 -923 -923 21 51 -923 36 -923 151 61 -923 -923 151 -923 36 121 51 -923 -923 179 -923 -923 -923 179 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 4.9e-007 0.000000 0.000000 1.000000 0.000000 0.166667 0.000000 0.000000 0.833333 0.833333 0.000000 0.000000 0.166667 0.000000 0.333333 0.666667 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.333333 0.000000 0.666667 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.333333 0.000000 0.333333 0.000000 0.666667 0.333333 0.000000 0.000000 0.666667 0.000000 0.333333 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GTA[GC]C[CG]TCTC[AG][AT][TC][CG]A[ACT][CG][CT][AC]AA -------------------------------------------------------------------------------- Time 0.66 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 6 llr = 121 E-value = 3.8e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::7:::5::::::::3::7: pos.-specific C :3::::a:a:7:7:3:737:: probability G ::7::3:3:33::a:7::33: matrix T a733a7:2:7:a3:73:7::a bits 2.2 * * * 2.0 * * * * * * * 1.8 * * * * * * * 1.5 * * * * * * * Relative 1.3 * * * * ** * * * Entropy 1.1 *** *** ************* (29.1 bits) 0.9 ******* ************* 0.7 ******* ************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TTGATTCACTCTCGTGCTCAT consensus CTT G G GG T CTACGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 25843 23 5.45e-13 TTTGGCCAAA TTGATTCACTCTCGTGCTCGT GCCCCAAAAC 12047 24 5.45e-13 TTTGGCCAAA TTGATTCACTCTCGTGCTCGT GCCCCAAAAC 12040 365 1.06e-09 TGGTCGTCAG TCGTTTCACGCTCGCTCCCAT CCTTTTGTCT 25848 205 1.22e-09 TGGTCGTCAG TCGTTTCGCGCTCGCTCCCAT CCTTTTGTCG 25844 240 1.74e-09 AGGCTTTGAG TTTATGCGCTGTTGTGATGAT TGACAAGCAG 25847 5 2.68e-09 TGAA TTTATGCTCTGTTGTGATGAT TGACAAGCAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25843 5.5e-13 22_[+3]_457 12047 5.5e-13 23_[+3]_456 12040 1.1e-09 364_[+3]_115 25848 1.2e-09 204_[+3]_275 25844 1.7e-09 239_[+3]_240 25847 2.7e-09 4_[+3]_475 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=6 25843 ( 23) TTGATTCACTCTCGTGCTCGT 1 12047 ( 24) TTGATTCACTCTCGTGCTCGT 1 12040 ( 365) TCGTTTCACGCTCGCTCCCAT 1 25848 ( 205) TCGTTTCGCGCTCGCTCCCAT 1 25844 ( 240) TTTATGCGCTGTTGTGATGAT 1 25847 ( 5) TTTATGCTCTGTTGTGATGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2880 bayes= 8.90388 E= 3.8e-006 -923 -923 -923 194 -923 51 -923 136 -923 -923 161 36 121 -923 -923 36 -923 -923 -923 194 -923 -923 61 136 -923 210 -923 -923 79 -923 61 -64 -923 210 -923 -923 -923 -923 61 136 -923 151 61 -923 -923 -923 -923 194 -923 151 -923 36 -923 -923 220 -923 -923 51 -923 136 -923 -923 161 36 21 151 -923 -923 -923 51 -923 136 -923 151 61 -923 121 -923 61 -923 -923 -923 -923 194 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 3.8e-006 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.666667 0.333333 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.333333 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.666667 0.333333 0.333333 0.666667 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.666667 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[TC][GT][AT]T[TG]C[AG]C[TG][CG]T[CT]G[TC][GT][CA][TC][CG][AG]T -------------------------------------------------------------------------------- Time 0.98 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 12040 2.87e-17 318_[+2(7.04e-10)]_25_\ [+3(1.06e-09)]_35_[+1(3.27e-10)]_59 12047 9.11e-24 23_[+3(5.45e-13)]_13_[+1(5.28e-12)]_\ 127_[+1(5.32e-05)]_4_[+2(1.51e-11)]_249 25843 9.11e-24 22_[+3(5.45e-13)]_13_[+1(5.28e-12)]_\ 152_[+2(1.51e-11)]_250 25844 2.86e-16 239_[+3(1.74e-09)]_80_\ [+2(1.53e-09)]_36_[+1(1.02e-09)]_82 25847 4.59e-17 4_[+3(2.68e-09)]_107_[+2(3.30e-10)]_\ 36_[+1(4.51e-10)]_290 25848 8.36e-17 154_[+2(1.88e-09)]_29_\ [+3(1.22e-09)]_35_[+1(3.27e-10)]_219 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************