******************************************************************************** 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/394/394.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 21954 1.0000 500 22714 1.0000 500 22777 1.0000 500 23120 1.0000 500 23668 1.0000 500 23766 1.0000 500 25349 1.0000 500 262879 1.0000 500 268890 1.0000 500 268988 1.0000 500 3323 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/394/394.seqs.fa -oc motifs/394 -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= 11 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= 5500 N= 11 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.267 C 0.228 G 0.257 T 0.247 Background letter frequencies (from dataset with add-one prior applied): A 0.267 C 0.228 G 0.257 T 0.247 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 6 llr = 108 E-value = 4.4e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::2::53::73:3723:::: pos.-specific C aa:a32:7a::8:3273:a: probability G ::::5273:2723:5:7::a matrix T ::8:22:::2::3:2::a:: bits 2.1 ** * * * 1.9 ** * * *** 1.7 ** * * *** 1.5 ** * * * *** Relative 1.3 **** * * *** Entropy 1.1 **** *** ** * ***** (25.9 bits) 0.9 **** *** ** * ***** 0.6 ***** ****** * ***** 0.4 ***** ******** ***** 0.2 ******************** 0.0 -------------------- Multilevel CCTCGAGCCAGCAAGCGTCG consensus C AG A GC AC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 268988 384 3.28e-11 GGCGAAACAG CCTCGTGCCAGCAAGCGTCG TTGACTCGTT 23120 348 5.69e-10 AGTCACTCCT CCTCCAGCCAGCTCTCCTCG ACCAGGTCGT 21954 450 7.42e-10 TCGTGCCCGG CCTCCGGCCTGCGAGCGTCG ACCCCAGCAG 25349 251 8.67e-09 GACGGACTGC CCTCGAGGCGACGACAGTCG AACCCGCCAC 262879 447 1.20e-08 AACACTCTTG CCTCTCACCAGCACACCTCG ACAGAAACCC 22714 105 2.91e-08 GACCGACGGC CCACGAAGCAAGTAGAGTCG CTGCAGCTAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 268988 3.3e-11 383_[+1]_97 23120 5.7e-10 347_[+1]_133 21954 7.4e-10 449_[+1]_31 25349 8.7e-09 250_[+1]_230 262879 1.2e-08 446_[+1]_34 22714 2.9e-08 104_[+1]_376 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=6 268988 ( 384) CCTCGTGCCAGCAAGCGTCG 1 23120 ( 348) CCTCCAGCCAGCTCTCCTCG 1 21954 ( 450) CCTCCGGCCTGCGAGCGTCG 1 25349 ( 251) CCTCGAGGCGACGACAGTCG 1 262879 ( 447) CCTCTCACCAGCACACCTCG 1 22714 ( 105) CCACGAAGCAAGTAGAGTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 5291 bayes= 10.8831 E= 4.4e-002 -923 213 -923 -923 -923 213 -923 -923 -68 -923 -923 175 -923 213 -923 -923 -923 54 96 -57 90 -45 -62 -57 32 -923 137 -923 -923 154 38 -923 -923 213 -923 -923 132 -923 -62 -57 32 -923 137 -923 -923 187 -62 -923 32 -923 38 43 132 54 -923 -923 -68 -45 96 -57 32 154 -923 -923 -923 54 137 -923 -923 -923 -923 201 -923 213 -923 -923 -923 -923 196 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 4.4e-002 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.833333 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.500000 0.166667 0.500000 0.166667 0.166667 0.166667 0.333333 0.000000 0.666667 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.166667 0.166667 0.333333 0.000000 0.666667 0.000000 0.000000 0.833333 0.166667 0.000000 0.333333 0.000000 0.333333 0.333333 0.666667 0.333333 0.000000 0.000000 0.166667 0.166667 0.500000 0.166667 0.333333 0.666667 0.000000 0.000000 0.000000 0.333333 0.666667 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CCTC[GC]A[GA][CG]CA[GA]C[AGT][AC]G[CA][GC]TCG -------------------------------------------------------------------------------- Time 1.12 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 11 llr = 114 E-value = 4.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1:11::6::13: pos.-specific C :27:874:a:53 probability G 9:2311:::91: matrix T :8:612:a::27 bits 2.1 * 1.9 ** 1.7 ** 1.5 * *** Relative 1.3 ** * *** * Entropy 1.1 *** ****** * (15.0 bits) 0.9 ********** * 0.6 ********** * 0.4 ********** * 0.2 ************ 0.0 ------------ Multilevel GTCTCCATCGCT consensus G C AC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 23766 113 4.72e-07 TCGGTCAAAG GCCTCCATCGCT GACGTCGTGA 262879 185 5.62e-07 TTGTTTATCC GTGTCCATCGCT GCCTTCCTAT 3323 63 3.10e-06 TCCAATACTG GTATCCATCGAT AATAAATCCA 21954 66 3.10e-06 CACTTTTCTG GTCTCGATCGAT CATTAGAAAC 22714 444 4.67e-06 CAGCCGACCC ATCGCCATCGCT GTGTCGCTCT 268988 425 5.20e-06 ATCACCGCCT GTCACCCTCGCC CATTCTCACC 25349 47 5.66e-06 GTCGGAATGG GTCTCTCTCGAC CGCTCGCTGC 23668 321 7.89e-06 AGCTCATACT GTCTTCCTCGTT GGCGTGACCA 22777 33 1.06e-05 CATATCGTAC GTCTCCATCAGT TCCGTTTTGG 23120 173 2.00e-05 CACGTGTTTT GCGGCCATCGCC CTTTATTGTG 268890 78 5.58e-05 TTCGTGGGCC GTCGGTCTCGTT TCTGCACAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23766 4.7e-07 112_[+2]_376 262879 5.6e-07 184_[+2]_304 3323 3.1e-06 62_[+2]_426 21954 3.1e-06 65_[+2]_423 22714 4.7e-06 443_[+2]_45 268988 5.2e-06 424_[+2]_64 25349 5.7e-06 46_[+2]_442 23668 7.9e-06 320_[+2]_168 22777 1.1e-05 32_[+2]_456 23120 2e-05 172_[+2]_316 268890 5.6e-05 77_[+2]_411 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=11 23766 ( 113) GCCTCCATCGCT 1 262879 ( 185) GTGTCCATCGCT 1 3323 ( 63) GTATCCATCGAT 1 21954 ( 66) GTCTCGATCGAT 1 22714 ( 444) ATCGCCATCGCT 1 268988 ( 425) GTCACCCTCGCC 1 25349 ( 47) GTCTCTCTCGAC 1 23668 ( 321) GTCTTCCTCGTT 1 22777 ( 33) GTCTCCATCAGT 1 23120 ( 173) GCGGCCATCGCC 1 268890 ( 78) GTCGGTCTCGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5379 bayes= 9.28648 E= 4.6e-001 -155 -1010 182 -1010 -1010 -33 -1010 173 -155 167 -50 -1010 -155 -1010 9 136 -1010 184 -150 -144 -1010 167 -150 -44 125 67 -1010 -1010 -1010 -1010 -1010 201 -1010 213 -1010 -1010 -155 -1010 182 -1010 3 99 -150 -44 -1010 26 -1010 156 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 11 E= 4.6e-001 0.090909 0.000000 0.909091 0.000000 0.000000 0.181818 0.000000 0.818182 0.090909 0.727273 0.181818 0.000000 0.090909 0.000000 0.272727 0.636364 0.000000 0.818182 0.090909 0.090909 0.000000 0.727273 0.090909 0.181818 0.636364 0.363636 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.090909 0.000000 0.909091 0.000000 0.272727 0.454545 0.090909 0.181818 0.000000 0.272727 0.000000 0.727273 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GTC[TG]CC[AC]TCG[CA][TC] -------------------------------------------------------------------------------- Time 2.29 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 19 sites = 3 llr = 62 E-value = 6.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::::::aa::::::3:::: pos.-specific C 7a:37a::a:77:7:a:7a probability G :::73::::a::733:a:: matrix T 3:a:::::::333:3::3: bits 2.1 * * * * * 1.9 ** ***** ** * 1.7 ** ***** ** * 1.5 ** ***** ** * Relative 1.3 *** ******* **** Entropy 1.1 ************** **** (29.9 bits) 0.9 ************** **** 0.6 ************** **** 0.4 ******************* 0.2 ******************* 0.0 ------------------- Multilevel CCTGCCAACGCCGCACGCC consensus T CG TTTGG T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 3323 430 1.67e-10 GTGTTAAATG CCTGCCAACGTCGGTCGCC GAAGTAGTAG 22714 390 1.67e-10 CAACCAGCTC TCTGCCAACGCTGCACGCC ACCACGACCA 23120 295 6.73e-10 GCAGTGGTGG CCTCGCAACGCCTCGCGTC GTGGTATTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3323 1.7e-10 429_[+3]_52 22714 1.7e-10 389_[+3]_92 23120 6.7e-10 294_[+3]_187 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=19 seqs=3 3323 ( 430) CCTGCCAACGTCGGTCGCC 1 22714 ( 390) TCTGCCAACGCTGCACGCC 1 23120 ( 295) CCTCGCAACGCCTCGCGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 5302 bayes= 10.4453 E= 6.1e+002 -823 154 -823 43 -823 213 -823 -823 -823 -823 -823 201 -823 54 137 -823 -823 154 37 -823 -823 213 -823 -823 190 -823 -823 -823 190 -823 -823 -823 -823 213 -823 -823 -823 -823 196 -823 -823 154 -823 43 -823 154 -823 43 -823 -823 137 43 -823 154 37 -823 32 -823 37 43 -823 213 -823 -823 -823 -823 196 -823 -823 154 -823 43 -823 213 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 3 E= 6.1e+002 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.666667 0.333333 0.000000 0.666667 0.333333 0.000000 0.333333 0.000000 0.333333 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT]CT[GC][CG]CAACG[CT][CT][GT][CG][AGT]CG[CT]C -------------------------------------------------------------------------------- Time 3.40 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21954 4.97e-08 65_[+2(3.10e-06)]_372_\ [+1(7.42e-10)]_31 22714 1.54e-12 104_[+1(2.91e-08)]_114_\ [+2(4.70e-05)]_139_[+3(1.67e-10)]_35_[+2(4.67e-06)]_45 22777 7.37e-02 32_[+2(1.06e-05)]_456 23120 5.50e-13 172_[+2(2.00e-05)]_110_\ [+3(6.73e-10)]_34_[+1(5.69e-10)]_133 23668 6.48e-02 320_[+2(7.89e-06)]_168 23766 5.19e-03 112_[+2(4.72e-07)]_376 25349 1.14e-06 46_[+2(5.66e-06)]_192_\ [+1(8.67e-09)]_230 262879 3.22e-08 184_[+2(5.62e-07)]_250_\ [+1(1.20e-08)]_34 268890 5.57e-02 77_[+2(5.58e-05)]_411 268988 5.00e-09 383_[+1(3.28e-11)]_21_\ [+2(5.20e-06)]_64 3323 4.44e-09 62_[+2(3.10e-06)]_355_\ [+3(1.67e-10)]_52 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************