******************************************************************************** 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/297/297.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42658 1.0000 500 42929 1.0000 500 42930 1.0000 500 43086 1.0000 500 46483 1.0000 500 14345 1.0000 500 1745 1.0000 500 48918 1.0000 500 25739 1.0000 500 11953 1.0000 500 45848 1.0000 500 12887 1.0000 500 49888 1.0000 500 34891 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/297/297.seqs.fa -oc motifs/297 -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= 14 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= 7000 N= 14 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.274 C 0.236 G 0.225 T 0.265 Background letter frequencies (from dataset with add-one prior applied): A 0.274 C 0.236 G 0.225 T 0.265 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 8 llr = 94 E-value = 8.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 6::::::::8:: pos.-specific C :4a::9:13151 probability G 41:a::a::14: matrix T :5::a1:98:19 bits 2.2 ** * 1.9 *** * 1.7 *** * 1.5 ***** Relative 1.3 ****** * Entropy 1.1 * ******* * (16.9 bits) 0.9 * ******** * 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel ATCGTCGTTACT consensus GC C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 49888 232 1.86e-07 GAATGCAAGT ACCGTCGTTACT GTTAGTAGGG 43086 51 1.86e-07 AACTGTTAAC ATCGTCGTTAGT ACTAGCTAGC 14345 384 7.08e-07 TGCCGGGGAA GTCGTCGTCACT TACGCCGAAA 12887 178 1.55e-06 CAGTGTCGGT GTCGTCGTTATT GAAACTCACG 48918 434 2.36e-06 TTTTTCAGCT ACCGTCGTTCGT AAACGGGAAC 46483 111 4.86e-06 GTCATATATT AGCGTCGTTACC ATGGACATCT 1745 336 5.21e-06 GAGTGCAGAC GCCGTCGTCGCT GATACCGAGG 42930 126 1.04e-05 GATAGCCTGC ATCGTTGCTAGT AGAGTCTGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49888 1.9e-07 231_[+1]_257 43086 1.9e-07 50_[+1]_438 14345 7.1e-07 383_[+1]_105 12887 1.6e-06 177_[+1]_311 48918 2.4e-06 433_[+1]_55 46483 4.9e-06 110_[+1]_378 1745 5.2e-06 335_[+1]_153 42930 1e-05 125_[+1]_363 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=8 49888 ( 232) ACCGTCGTTACT 1 43086 ( 51) ATCGTCGTTAGT 1 14345 ( 384) GTCGTCGTCACT 1 12887 ( 178) GTCGTCGTTATT 1 48918 ( 434) ACCGTCGTTCGT 1 46483 ( 111) AGCGTCGTTACC 1 1745 ( 336) GCCGTCGTCGCT 1 42930 ( 126) ATCGTTGCTAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6846 bayes= 9.73936 E= 8.4e+001 119 -965 74 -965 -965 67 -85 92 -965 208 -965 -965 -965 -965 215 -965 -965 -965 -965 192 -965 189 -965 -108 -965 -965 215 -965 -965 -91 -965 172 -965 8 -965 150 145 -91 -85 -965 -965 108 74 -108 -965 -91 -965 172 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 8 E= 8.4e+001 0.625000 0.000000 0.375000 0.000000 0.000000 0.375000 0.125000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.000000 1.000000 0.000000 0.000000 0.125000 0.000000 0.875000 0.000000 0.250000 0.000000 0.750000 0.750000 0.125000 0.125000 0.000000 0.000000 0.500000 0.375000 0.125000 0.000000 0.125000 0.000000 0.875000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AG][TC]CGTCGT[TC]A[CG]T -------------------------------------------------------------------------------- Time 1.93 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 14 llr = 143 E-value = 1.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 4:1::1:121691121 pos.-specific C 4:121917442::159 probability G :11:3:2:441:::1: matrix T 19686:71::11972: bits 2.2 1.9 1.7 * 1.5 * * * * Relative 1.3 * * * ** * Entropy 1.1 * * * ** * (14.7 bits) 0.9 * * *** *** * 0.6 * ***** * *** * 0.4 ************** * 0.2 **************** 0.0 ---------------- Multilevel ATTTTCTCCCAATTCC consensus C CG G GGC A sequence A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 45848 130 1.43e-07 ACCGCGAAAA ATCTTCTCCGAATTTC ATTCGTGTTC 43086 388 1.43e-07 GGAAGGTCGC CTCTTCGCCCAATTCC CGAAAACACC 12887 72 6.07e-07 CACCCGAGGC ATTTTCCCGGCATTCC GGAACCTGCC 42929 392 2.10e-06 CAGCACCATT CTTTTCTCCATTTTCC GATATTGATG 25739 215 3.42e-06 CGTTTAGCAG ATGTTCTACGAATACC AGCTGTCTGA 11953 111 3.78e-06 TCGTCCACAA CGTTTCTCAGAATACC TATCTAGCTC 34891 381 7.20e-06 GTGTCATACC TTTTCCTCGCCATTCA CAATCTCATC 1745 479 7.20e-06 ATCCCGACGA CTTTGCGCGCAAATAC GTTCCA 14345 69 7.88e-06 CGGTCAACGA ATTCGCTTCCAATTGC CCCTCGCTCT 46483 5 8.57e-06 TCAT ATTTCCTTCGAATCTC GGTTTTTGAC 42930 439 1.19e-05 CTGTTGCTTC CTTCGCTCGCTTTTTC ATTCGCGCAT 48918 116 1.78e-05 AGTATTTTGC ATTCTATCGACATTCC ACGTGTGTCG 42658 442 2.58e-05 CTGCTTTGTT TTATGCGCAGAATTAC ATTACACAGC 49888 114 2.53e-04 AGTCTGGTGA CTGTTCTAACGATCAA CAGGTCCGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45848 1.4e-07 129_[+2]_355 43086 1.4e-07 387_[+2]_97 12887 6.1e-07 71_[+2]_413 42929 2.1e-06 391_[+2]_93 25739 3.4e-06 214_[+2]_270 11953 3.8e-06 110_[+2]_374 34891 7.2e-06 380_[+2]_104 1745 7.2e-06 478_[+2]_6 14345 7.9e-06 68_[+2]_416 46483 8.6e-06 4_[+2]_480 42930 1.2e-05 438_[+2]_46 48918 1.8e-05 115_[+2]_369 42658 2.6e-05 441_[+2]_43 49888 0.00025 113_[+2]_371 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=14 45848 ( 130) ATCTTCTCCGAATTTC 1 43086 ( 388) CTCTTCGCCCAATTCC 1 12887 ( 72) ATTTTCCCGGCATTCC 1 42929 ( 392) CTTTTCTCCATTTTCC 1 25739 ( 215) ATGTTCTACGAATACC 1 11953 ( 111) CGTTTCTCAGAATACC 1 34891 ( 381) TTTTCCTCGCCATTCA 1 1745 ( 479) CTTTGCGCGCAAATAC 1 14345 ( 69) ATTCGCTTCCAATTGC 1 46483 ( 5) ATTTCCTTCGAATCTC 1 42930 ( 439) CTTCGCTCGCTTTTTC 1 48918 ( 116) ATTCTATCGACATTCC 1 42658 ( 442) TTATGCGCAGAATTAC 1 49888 ( 114) CTGTTCTAACGATCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6790 bayes= 8.91886 E= 1.4e+003 64 86 -1045 -89 -1045 -1045 -165 181 -194 -72 -65 128 -1045 -14 -1045 157 -1045 -72 35 111 -194 198 -1045 -1045 -1045 -172 -7 143 -94 160 -1045 -89 -36 86 67 -1045 -94 86 93 -1045 106 -14 -165 -89 164 -1045 -1045 -89 -194 -1045 -1045 181 -94 -72 -1045 143 -36 108 -165 -31 -94 186 -1045 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 14 E= 1.4e+003 0.428571 0.428571 0.000000 0.142857 0.000000 0.000000 0.071429 0.928571 0.071429 0.142857 0.142857 0.642857 0.000000 0.214286 0.000000 0.785714 0.000000 0.142857 0.285714 0.571429 0.071429 0.928571 0.000000 0.000000 0.000000 0.071429 0.214286 0.714286 0.142857 0.714286 0.000000 0.142857 0.214286 0.428571 0.357143 0.000000 0.142857 0.428571 0.428571 0.000000 0.571429 0.214286 0.071429 0.142857 0.857143 0.000000 0.000000 0.142857 0.071429 0.000000 0.000000 0.928571 0.142857 0.142857 0.000000 0.714286 0.214286 0.500000 0.071429 0.214286 0.142857 0.857143 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AC]TT[TC][TG]C[TG]C[CGA][CG][AC]ATT[CAT]C -------------------------------------------------------------------------------- Time 3.58 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 2 llr = 42 E-value = 2.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::::5:::::a::::: pos.-specific C a:::5::::::55::: probability G :aaa:aa:a::55aa: matrix T :::::::a:a:::::a bits 2.2 **** ** * ** 1.9 **** ****** *** 1.7 **** ****** *** 1.5 **** ****** *** Relative 1.3 **** ****** *** Entropy 1.1 **************** (30.1 bits) 0.9 **************** 0.6 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CGGGAGGTGTACCGGT consensus C GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 14345 13 2.93e-10 GCCTTACTAG CGGGCGGTGTACGGGT CCTCGTCACC 25739 356 7.36e-10 GAGTGATTCC CGGGAGGTGTAGCGGT AGTAGCTGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 14345 2.9e-10 12_[+3]_472 25739 7.4e-10 355_[+3]_129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=2 14345 ( 13) CGGGCGGTGTACGGGT 1 25739 ( 356) CGGGAGGTGTAGCGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6790 bayes= 11.7288 E= 2.7e+003 -765 208 -765 -765 -765 -765 215 -765 -765 -765 215 -765 -765 -765 215 -765 86 108 -765 -765 -765 -765 215 -765 -765 -765 215 -765 -765 -765 -765 191 -765 -765 215 -765 -765 -765 -765 191 186 -765 -765 -765 -765 108 115 -765 -765 108 115 -765 -765 -765 215 -765 -765 -765 215 -765 -765 -765 -765 191 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 2 E= 2.7e+003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CGGG[AC]GGTGTA[CG][CG]GGT -------------------------------------------------------------------------------- Time 5.23 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42658 4.21e-02 441_[+2(2.58e-05)]_43 42929 1.15e-03 355_[+1(3.22e-05)]_24_\ [+2(2.10e-06)]_93 42930 1.85e-03 125_[+1(1.04e-05)]_301_\ [+2(1.19e-05)]_46 43086 8.56e-07 50_[+1(1.86e-07)]_325_\ [+2(1.43e-07)]_97 46483 7.61e-04 4_[+2(8.57e-06)]_90_[+1(4.86e-06)]_\ 378 14345 8.61e-11 12_[+3(2.93e-10)]_40_[+2(7.88e-06)]_\ 299_[+1(7.08e-07)]_105 1745 4.69e-04 335_[+1(5.21e-06)]_131_\ [+2(7.20e-06)]_6 48918 3.88e-04 115_[+2(1.78e-05)]_302_\ [+1(2.36e-06)]_55 25739 5.42e-08 214_[+2(3.42e-06)]_125_\ [+3(7.36e-10)]_129 11953 1.63e-02 110_[+2(3.78e-06)]_374 45848 1.45e-03 129_[+2(1.43e-07)]_355 12887 6.65e-06 71_[+2(6.07e-07)]_90_[+1(1.55e-06)]_\ 311 49888 8.02e-04 231_[+1(1.86e-07)]_257 34891 5.09e-02 380_[+2(7.20e-06)]_104 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************