******************************************************************************** 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/250/250.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10403 1.0000 500 23330 1.0000 500 261251 1.0000 500 2951 1.0000 500 35764 1.0000 500 4701 1.0000 500 5224 1.0000 500 6343 1.0000 500 957 1.0000 500 bd898 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/250/250.seqs.fa -oc motifs/250 -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= 10 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= 5000 N= 10 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.262 C 0.230 G 0.230 T 0.278 Background letter frequencies (from dataset with add-one prior applied): A 0.262 C 0.230 G 0.230 T 0.278 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 10 llr = 119 E-value = 3.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :a::42:5:2212:2: pos.-specific C 9:69169278418:39 probability G ::::51:2::35::21 matrix T 1:41:1113:13:a3: bits 2.1 1.9 * * 1.7 ** * * * * 1.5 ** * * * * Relative 1.3 ** * * * ** * Entropy 1.1 **** * ** ** * (17.2 bits) 0.8 **** * ** ** * 0.6 ***** * ** ** * 0.4 ******* ** *** * 0.2 ************** * 0.0 ---------------- Multilevel CACCGCCACCCGCTCC consensus T AA CTAGTA T sequence G A A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 2951 464 4.65e-08 GAACTTCAAA CACCAACACCCTCTCC TTCCTAAGAT 35764 22 1.17e-07 TACCATCCAT CATCACCACCCGATGC AGTGGTCTAT 957 448 1.32e-07 AGACATTAAA CACCGCCGCCGACTTC CACCTGCCTG bd898 111 4.36e-07 GTTTTTGAAT CATCGGCATCCGCTGC ATCCATCATC 261251 2 7.73e-07 C CATCACCATCGGATAC GTTGGCAAAT 5224 368 1.68e-06 ACTCTTCCGC CACCGCCATAGCCTAC CAAGCAACAC 10403 228 2.30e-06 ACAGCTTGCC CATCAACGCACTCTTC TTCAATTCAG 6343 173 3.58e-06 GAGCAAGGAG TACCGTCCCCAGCTCC TTGGAGAGTT 4701 447 5.03e-06 CGCAAGTCTT CACCCCTCCCATCTCC TTCCACCGCG 23330 385 1.67e-05 AGCTCCCGAG CACTGCCTCCTGCTTG ATCATACAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2951 4.7e-08 463_[+1]_21 35764 1.2e-07 21_[+1]_463 957 1.3e-07 447_[+1]_37 bd898 4.4e-07 110_[+1]_374 261251 7.7e-07 1_[+1]_483 5224 1.7e-06 367_[+1]_117 10403 2.3e-06 227_[+1]_257 6343 3.6e-06 172_[+1]_312 4701 5e-06 446_[+1]_38 23330 1.7e-05 384_[+1]_100 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=10 2951 ( 464) CACCAACACCCTCTCC 1 35764 ( 22) CATCACCACCCGATGC 1 957 ( 448) CACCGCCGCCGACTTC 1 bd898 ( 111) CATCGGCATCCGCTGC 1 261251 ( 2) CATCACCATCGGATAC 1 5224 ( 368) CACCGCCATAGCCTAC 1 10403 ( 228) CATCAACGCACTCTTC 1 6343 ( 173) TACCGTCCCCAGCTCC 1 4701 ( 447) CACCCCTCCCATCTCC 1 23330 ( 385) CACTGCCTCCTGCTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 4850 bayes= 8.91886 E= 3.8e-001 -997 197 -997 -147 193 -997 -997 -997 -997 138 -997 52 -997 197 -997 -147 61 -120 112 -997 -39 138 -120 -147 -997 197 -997 -147 93 -20 -20 -147 -997 161 -997 11 -39 180 -997 -997 -39 80 38 -147 -139 -120 112 11 -39 180 -997 -997 -997 -997 -997 185 -39 38 -20 11 -997 197 -120 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 3.8e-001 0.000000 0.900000 0.000000 0.100000 1.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.900000 0.000000 0.100000 0.400000 0.100000 0.500000 0.000000 0.200000 0.600000 0.100000 0.100000 0.000000 0.900000 0.000000 0.100000 0.500000 0.200000 0.200000 0.100000 0.000000 0.700000 0.000000 0.300000 0.200000 0.800000 0.000000 0.000000 0.200000 0.400000 0.300000 0.100000 0.100000 0.100000 0.500000 0.300000 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.200000 0.300000 0.200000 0.300000 0.000000 0.900000 0.100000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CA[CT]C[GA][CA]C[ACG][CT][CA][CGA][GT][CA]T[CTAG]C -------------------------------------------------------------------------------- Time 0.99 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 9 llr = 126 E-value = 8.8e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :2::9:7112:944:9223:2 pos.-specific C :421:127:2a:33::::24: probability G 1124:7:1:1:::19::8::8 matrix T 9264121194:121118:46: bits 2.1 * 1.9 * 1.7 * 1.5 * ** ** Relative 1.3 * * * ** ** * * Entropy 1.1 * * * ** **** ** (20.1 bits) 0.8 * ** * ** **** ** 0.6 * ******* ** **** ** 0.4 * ******* *** ******* 0.2 ********************* 0.0 --------------------- Multilevel TCTGAGACTTCAAAGATGTTG consensus ACT TC A CC AAACA sequence TG C T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 35764 472 3.25e-11 TGCAACATCT TCTTAGACTACAACGATGTTG CTTCCTAT 261251 202 1.76e-09 GTCTTTCAAC TCTTAGACTTCTCCGATGATG CATGGAAGGA 4701 183 1.40e-07 TCCGCGCTCG TCCGACCCTCCACAGATGCCA ACAAACAAAA 957 229 3.14e-07 CGTATGATGA TATGAGATAGCATAGATGATG ATTCAGTTAT 23330 421 3.39e-07 TTTGCTTGAT TCCCATTCTTCAAAGAAGCCG CTCATCCTAA 5224 194 3.93e-07 AGTTATCCCC TGTGAGAGTTCAAGGAAATCG TAAAAGTCCC 10403 301 4.23e-07 GACGTTGTCG TTGTTGCCTCCACCGATGATA TTGATGGCGT 6343 240 6.94e-07 GAGTTATTTG GATGAGACTTCATATTTGTTG CGAGAGGGAG bd898 422 1.10e-06 TGTGAGTTCA TTGTATAATACAATGATATCG ATTGTTCATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35764 3.3e-11 471_[+2]_8 261251 1.8e-09 201_[+2]_278 4701 1.4e-07 182_[+2]_297 957 3.1e-07 228_[+2]_251 23330 3.4e-07 420_[+2]_59 5224 3.9e-07 193_[+2]_286 10403 4.2e-07 300_[+2]_179 6343 6.9e-07 239_[+2]_240 bd898 1.1e-06 421_[+2]_58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=9 35764 ( 472) TCTTAGACTACAACGATGTTG 1 261251 ( 202) TCTTAGACTTCTCCGATGATG 1 4701 ( 183) TCCGACCCTCCACAGATGCCA 1 957 ( 229) TATGAGATAGCATAGATGATG 1 23330 ( 421) TCCCATTCTTCAAAGAAGCCG 1 5224 ( 194) TGTGAGAGTTCAAGGAAATCG 1 10403 ( 301) TTGTTGCCTCCACCGATGATA 1 6343 ( 240) GATGAGACTTCATATTTGTTG 1 bd898 ( 422) TTGTATAATACAATGATATCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4800 bayes= 9.19073 E= 8.8e+001 -982 -982 -105 168 -24 95 -105 -32 -982 -5 -5 100 -982 -105 95 68 176 -982 -982 -132 -982 -105 153 -32 135 -5 -982 -132 -124 154 -105 -132 -124 -982 -982 168 -24 -5 -105 68 -982 212 -982 -982 176 -982 -982 -132 76 54 -982 -32 76 54 -105 -132 -982 -982 195 -132 176 -982 -982 -132 -24 -982 -982 148 -24 -982 176 -982 35 -5 -982 68 -982 95 -982 100 -24 -982 176 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 8.8e+001 0.000000 0.000000 0.111111 0.888889 0.222222 0.444444 0.111111 0.222222 0.000000 0.222222 0.222222 0.555556 0.000000 0.111111 0.444444 0.444444 0.888889 0.000000 0.000000 0.111111 0.000000 0.111111 0.666667 0.222222 0.666667 0.222222 0.000000 0.111111 0.111111 0.666667 0.111111 0.111111 0.111111 0.000000 0.000000 0.888889 0.222222 0.222222 0.111111 0.444444 0.000000 1.000000 0.000000 0.000000 0.888889 0.000000 0.000000 0.111111 0.444444 0.333333 0.000000 0.222222 0.444444 0.333333 0.111111 0.111111 0.000000 0.000000 0.888889 0.111111 0.888889 0.000000 0.000000 0.111111 0.222222 0.000000 0.000000 0.777778 0.222222 0.000000 0.777778 0.000000 0.333333 0.222222 0.000000 0.444444 0.000000 0.444444 0.000000 0.555556 0.222222 0.000000 0.777778 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[CAT][TCG][GT]A[GT][AC]CT[TAC]CA[ACT][AC]GA[TA][GA][TAC][TC][GA] -------------------------------------------------------------------------------- Time 1.85 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 3 llr = 67 E-value = 2.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::3:::::a:::::::3::: pos.-specific C :::3::3::3:::::::7a: probability G aa73a:3a:3aaa7aa33:a matrix T :::3:a3::3:::3::3::: bits 2.1 ** * * *** ** ** 1.9 ** ** ** *** ** ** 1.7 ** ** ** *** ** ** 1.5 ** ** ** *** ** ** Relative 1.3 ** ** ** *** ** *** Entropy 1.1 *** ** ** ****** *** (32.3 bits) 0.8 *** ** ** ****** *** 0.6 *** ** ** ****** *** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GGGCGTCGACGGGGGGACCG consensus AG G G T GG sequence T T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 261251 79 9.76e-12 ATCATTATGT GGGCGTCGACGGGGGGTCCG ATGCCTCCTT 2951 121 1.16e-10 CAGAAAAGCC GGGTGTTGATGGGTGGGCCG TATCTGTTGC 10403 447 1.19e-10 TTGCGGTGTG GGAGGTGGAGGGGGGGAGCG TTGTGTCTAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 261251 9.8e-12 78_[+3]_402 2951 1.2e-10 120_[+3]_360 10403 1.2e-10 446_[+3]_34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=3 261251 ( 79) GGGCGTCGACGGGGGGTCCG 1 2951 ( 121) GGGTGTTGATGGGTGGGCCG 1 10403 ( 447) GGAGGTGGAGGGGGGGAGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 4810 bayes= 11.0937 E= 2.9e+002 -823 -823 212 -823 -823 -823 212 -823 35 -823 153 -823 -823 53 53 26 -823 -823 212 -823 -823 -823 -823 184 -823 53 53 26 -823 -823 212 -823 193 -823 -823 -823 -823 53 53 26 -823 -823 212 -823 -823 -823 212 -823 -823 -823 212 -823 -823 -823 153 26 -823 -823 212 -823 -823 -823 212 -823 35 -823 53 26 -823 153 53 -823 -823 212 -823 -823 -823 -823 212 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 3 E= 2.9e+002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.333333 0.333333 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.333333 0.333333 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.333333 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.333333 0.333333 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GG[GA][CGT]GT[CGT]GA[CGT]GGG[GT]GG[AGT][CG]CG -------------------------------------------------------------------------------- Time 2.71 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10403 7.05e-12 227_[+1(2.30e-06)]_57_\ [+2(4.23e-07)]_125_[+3(1.19e-10)]_34 23330 9.97e-05 384_[+1(1.67e-05)]_20_\ [+2(3.39e-07)]_59 261251 1.32e-15 1_[+1(7.73e-07)]_61_[+3(9.76e-12)]_\ 103_[+2(1.76e-09)]_278 2951 5.02e-10 120_[+3(1.16e-10)]_323_\ [+1(4.65e-08)]_21 35764 3.67e-11 21_[+1(1.17e-07)]_434_\ [+2(3.25e-11)]_8 4701 9.27e-06 182_[+2(1.40e-07)]_243_\ [+1(5.03e-06)]_38 5224 4.70e-06 193_[+2(3.93e-07)]_153_\ [+1(1.68e-06)]_117 6343 2.87e-05 172_[+1(3.58e-06)]_51_\ [+2(6.94e-07)]_240 957 1.75e-06 228_[+2(3.14e-07)]_198_\ [+1(1.32e-07)]_37 bd898 1.54e-05 110_[+1(4.36e-07)]_295_\ [+2(1.10e-06)]_58 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************