******************************************************************************** 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/6/6.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 9251 1.0000 500 9355 1.0000 500 48408 1.0000 500 23598 1.0000 500 44844 1.0000 500 35314 1.0000 500 7208 1.0000 500 33484 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/6/6.seqs.fa -oc motifs/6 -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= 8 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= 4000 N= 8 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.271 C 0.239 G 0.218 T 0.272 Background letter frequencies (from dataset with add-one prior applied): A 0.271 C 0.239 G 0.218 T 0.272 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 7 llr = 109 E-value = 1.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :39::a49:1:11:41:6::: pos.-specific C :4:19:1:4::16914134:: probability G a311::3:4:6::1419117a matrix T :::71:1119473::3::43: bits 2.2 * * 2.0 * * * 1.8 * * * 1.5 * ** * * * Relative 1.3 * * ** * * * * ** Entropy 1.1 * * ** * ** * * ** (22.4 bits) 0.9 * **** * ** * * ** 0.7 * **** ******** ***** 0.4 ****** ******** ***** 0.2 ********************* 0.0 --------------------- Multilevel GCATCAAACTGTCCACGACGG consensus A G G T T GT CTT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 7208 113 8.67e-10 ATGTCCGAAT GGATCAAACTTTCCGCCACGG CTATGGTAGC 33484 385 2.19e-09 TTAACAATGT GCGTCAAAGTGTACACGATGG TTTTATCATT 9355 221 2.48e-09 CACCTACTAG GCATCACAGTGATCGCGACGG AGAATTCCTC 35314 185 2.80e-09 CAATGAGTTT GAATCAGACTGTCCCGGCCGG GAGGAGATGC 48408 342 2.77e-07 TTCTGACTGT GAAGTAAACTTTCCAAGAGTG TGGCAACGTT 9251 477 3.27e-07 CTCGAACATT GGACCAGAGAGCCCGTGGTTG AAA 44844 461 4.27e-07 ATGAGGATTG GCATCATTTTTTTGATGCTGG GCGTCATCAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7208 8.7e-10 112_[+1]_367 33484 2.2e-09 384_[+1]_95 9355 2.5e-09 220_[+1]_259 35314 2.8e-09 184_[+1]_295 48408 2.8e-07 341_[+1]_138 9251 3.3e-07 476_[+1]_3 44844 4.3e-07 460_[+1]_19 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=7 7208 ( 113) GGATCAAACTTTCCGCCACGG 1 33484 ( 385) GCGTCAAAGTGTACACGATGG 1 9355 ( 221) GCATCACAGTGATCGCGACGG 1 35314 ( 185) GAATCAGACTGTCCCGGCCGG 1 48408 ( 342) GAAGTAAACTTTCCAAGAGTG 1 9251 ( 477) GGACCAGAGAGCCCGTGGTTG 1 44844 ( 461) GCATCATTTTTTTGATGCTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3840 bayes= 9.70353 E= 1.5e+001 -945 -945 220 -945 8 84 39 -945 166 -945 -61 -945 -945 -74 -61 139 -945 184 -945 -93 188 -945 -945 -945 66 -74 39 -93 166 -945 -945 -93 -945 84 97 -93 -92 -945 -945 165 -945 -945 139 66 -92 -74 -945 139 -92 126 -945 7 -945 184 -61 -945 66 -74 97 -945 -92 84 -61 7 -945 -74 197 -945 108 26 -61 -945 -945 84 -61 66 -945 -945 171 7 -945 -945 220 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 1.5e+001 0.000000 0.000000 1.000000 0.000000 0.285714 0.428571 0.285714 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 0.142857 0.142857 0.714286 0.000000 0.857143 0.000000 0.142857 1.000000 0.000000 0.000000 0.000000 0.428571 0.142857 0.285714 0.142857 0.857143 0.000000 0.000000 0.142857 0.000000 0.428571 0.428571 0.142857 0.142857 0.000000 0.000000 0.857143 0.000000 0.000000 0.571429 0.428571 0.142857 0.142857 0.000000 0.714286 0.142857 0.571429 0.000000 0.285714 0.000000 0.857143 0.142857 0.000000 0.428571 0.142857 0.428571 0.000000 0.142857 0.428571 0.142857 0.285714 0.000000 0.142857 0.857143 0.000000 0.571429 0.285714 0.142857 0.000000 0.000000 0.428571 0.142857 0.428571 0.000000 0.000000 0.714286 0.285714 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[CAG]ATCA[AG]A[CG]T[GT]T[CT]C[AG][CT]G[AC][CT][GT]G -------------------------------------------------------------------------------- Time 0.56 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 5 llr = 73 E-value = 5.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::42::2:::86::4: pos.-specific C 222:8:::::222:4: probability G 882622::aa::8a28 matrix T ::22:88a:::2:::2 bits 2.2 ** * 2.0 *** * 1.8 *** * 1.5 ** *** ** Relative 1.3 ** ** *** ** * Entropy 1.1 ** ******* ** * (21.0 bits) 0.9 ** ******* ** * 0.7 ** ******** ** * 0.4 ** ************* 0.2 ** ************* 0.0 ---------------- Multilevel GGAGCTTTGGAAGGAG consensus CCCAGGA CCC CT sequence GT T G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 9355 14 2.71e-09 CAGATTCACA GGAGCTTTGGCAGGAG CTGGAACAGC 7208 199 8.30e-08 ATCGTAAGTG GGCGCTATGGAAGGCT GAACCCGAGC 9251 220 1.03e-07 CCTGAAATGG GGTGGTTTGGATGGGG CCAGAACGAA 33484 101 1.90e-07 AAAATGATAC GCGTCTTTGGACGGAG AACAGACGGC 44844 162 4.45e-07 CCGACCAGTT CGAACGTTGGAACGCG AATGGGGTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9355 2.7e-09 13_[+2]_471 7208 8.3e-08 198_[+2]_286 9251 1e-07 219_[+2]_265 33484 1.9e-07 100_[+2]_384 44844 4.5e-07 161_[+2]_323 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=5 9355 ( 14) GGAGCTTTGGCAGGAG 1 7208 ( 199) GGCGCTATGGAAGGCT 1 9251 ( 220) GGTGGTTTGGATGGGG 1 33484 ( 101) GCGTCTTTGGACGGAG 1 44844 ( 162) CGAACGTTGGAACGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 3880 bayes= 9.84989 E= 5.3e+002 -897 -26 187 -897 -897 -26 187 -897 56 -26 -12 -44 -44 -897 146 -44 -897 174 -12 -897 -897 -897 -12 155 -44 -897 -897 155 -897 -897 -897 188 -897 -897 220 -897 -897 -897 220 -897 156 -26 -897 -897 115 -26 -897 -44 -897 -26 187 -897 -897 -897 220 -897 56 74 -12 -897 -897 -897 187 -44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 5 E= 5.3e+002 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.800000 0.000000 0.400000 0.200000 0.200000 0.200000 0.200000 0.000000 0.600000 0.200000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.200000 0.800000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.600000 0.200000 0.000000 0.200000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.400000 0.200000 0.000000 0.000000 0.000000 0.800000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GC][GC][ACGT][GAT][CG][TG][TA]TGG[AC][ACT][GC]G[ACG][GT] -------------------------------------------------------------------------------- Time 1.14 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 4 llr = 78 E-value = 1.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 8:::::::33:3:::3::::: pos.-specific C 3:::5:::::a:3:333883a probability G ::83:8aa:8:5:a:35338: matrix T :a3853::8::38:833:::: bits 2.2 ** * 2.0 * ** * * * 1.8 * ** * * * 1.5 * ** * * * Relative 1.3 ** *** ** * **** Entropy 1.1 **** ****** *** **** (28.1 bits) 0.9 *********** *** **** 0.7 *********** *** ***** 0.4 *************** ***** 0.2 *************** ***** 0.0 --------------------- Multilevel ATGTCGGGTGCGTGTAGCCGC consensus C TGTT AA AC CCCGGC sequence T GT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 48408 467 2.47e-13 AACGATTTCG ATGTTGGGTGCGTGTGGCCGC CGTGCAACTG 33484 442 2.12e-09 ATTGCAAGTG CTGGCGGGTACGTGCTTCCGC AACAACTTTG 9355 303 2.53e-09 TGCAAAGGAG ATTTTGGGTGCTCGTACCGGC CAACAACTAA 23598 85 3.17e-09 CTCCGGGTAA ATGTCTGGAGCATGTCGGCCC TCTGTCGATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48408 2.5e-13 466_[+3]_13 33484 2.1e-09 441_[+3]_38 9355 2.5e-09 302_[+3]_177 23598 3.2e-09 84_[+3]_395 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=4 48408 ( 467) ATGTTGGGTGCGTGTGGCCGC 1 33484 ( 442) CTGGCGGGTACGTGCTTCCGC 1 9355 ( 303) ATTTTGGGTGCTCGTACCGGC 1 23598 ( 85) ATGTCTGGAGCATGTCGGCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3840 bayes= 9.90539 E= 1.1e+003 147 6 -865 -865 -865 -865 -865 188 -865 -865 178 -12 -865 -865 20 146 -865 106 -865 88 -865 -865 178 -12 -865 -865 219 -865 -865 -865 219 -865 -12 -865 -865 146 -12 -865 178 -865 -865 206 -865 -865 -12 -865 120 -12 -865 6 -865 146 -865 -865 219 -865 -865 6 -865 146 -12 6 20 -12 -865 6 120 -12 -865 165 20 -865 -865 165 20 -865 -865 6 178 -865 -865 206 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 1.1e+003 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.250000 0.750000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.500000 0.250000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.250000 0.250000 0.250000 0.250000 0.000000 0.250000 0.500000 0.250000 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AC]T[GT][TG][CT][GT]GG[TA][GA]C[GAT][TC]G[TC][ACGT][GCT][CG][CG][GC]C -------------------------------------------------------------------------------- Time 1.64 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9251 8.23e-07 219_[+2(1.03e-07)]_241_\ [+1(3.27e-07)]_3 9355 1.66e-15 13_[+2(2.71e-09)]_191_\ [+1(2.48e-09)]_61_[+3(2.53e-09)]_177 48408 8.28e-12 341_[+1(2.77e-07)]_104_\ [+3(2.47e-13)]_13 23598 1.05e-04 84_[+3(3.17e-09)]_395 44844 1.99e-06 161_[+2(4.45e-07)]_283_\ [+1(4.27e-07)]_19 35314 9.91e-05 184_[+1(2.80e-09)]_295 7208 3.78e-09 112_[+1(8.67e-10)]_65_\ [+2(8.30e-08)]_286 33484 7.10e-14 100_[+2(1.90e-07)]_268_\ [+1(2.19e-09)]_36_[+3(2.12e-09)]_38 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************