******************************************************************************** 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/286/286.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11666 1.0000 500 1621 1.0000 500 24395 1.0000 500 25551 1.0000 500 25698 1.0000 500 260998 1.0000 500 2645 1.0000 500 27773 1.0000 500 31881 1.0000 500 5579 1.0000 500 6291 1.0000 500 7610 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/286/286.seqs.fa -oc motifs/286 -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= 12 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= 6000 N= 12 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.254 C 0.225 G 0.242 T 0.279 Background letter frequencies (from dataset with add-one prior applied): A 0.254 C 0.225 G 0.242 T 0.278 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 11 llr = 157 E-value = 8.0e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 19144322262:2724a318: pos.-specific C 2:94274:52195283:59:9 probability G 61:32::522714::3:3:2: matrix T 1:::3:541::::1:1::::1 bits 2.2 1.9 * 1.7 * * * * * 1.5 ** * * * * * Relative 1.3 ** * * * * *** Entropy 1.1 ** * * * * *** (20.6 bits) 0.9 ** * ** ** * *** 0.6 *** * ****** * *** 0.4 **** ********** ***** 0.2 **** **************** 0.0 --------------------- Multilevel GACAACTGCAGCCACAACCAC consensus CTACT G C A sequence G G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 24395 305 7.78e-12 ACGTATCAAC GACAGCTGCAGCCACAACCAC TTCTTTGCGG 11666 305 7.78e-12 ACGTATCAAC GACAGCTGCAGCCACAACCAC TTCTTTGCGG 6291 464 7.72e-09 TATTCCCCCC GACCTCTTCAGCATCCACCAC TCGCAGTCTG 25551 318 9.57e-08 CCTGTCGATC GACCCAATGCGCGACCAACAC AACAACACAG 5579 474 1.24e-07 ACCGCACACC GACCACCGACACGACGAACGC AGACTC 25698 283 2.01e-07 CCGTCTCAGT TGCAACTGCACCCACAAGCAC CAGCAGCCAA 31881 425 4.26e-07 ACCGTCACAA CACACCAGCAGCCCACAACGC CATACCCACC 2645 402 5.62e-07 TATGATTTTG AACGTCCTGAGCCCCGACAAC AAAGCCTCGC 7610 434 6.43e-07 GTCTAGGCTG CACCAACTTGGCAACTACCAC ACCTCTCTCT 27773 459 9.47e-07 GTGCATTGAT GAAGTCCAAAGCGACAAGCAT TCGCGATGTT 1621 197 2.51e-06 GAAAGAATTG GACGAATACGAGGAAGAGCAC AAGAATGATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24395 7.8e-12 304_[+1]_175 11666 7.8e-12 304_[+1]_175 6291 7.7e-09 463_[+1]_16 25551 9.6e-08 317_[+1]_162 5579 1.2e-07 473_[+1]_6 25698 2e-07 282_[+1]_197 31881 4.3e-07 424_[+1]_55 2645 5.6e-07 401_[+1]_78 7610 6.4e-07 433_[+1]_46 27773 9.5e-07 458_[+1]_21 1621 2.5e-06 196_[+1]_283 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=11 24395 ( 305) GACAGCTGCAGCCACAACCAC 1 11666 ( 305) GACAGCTGCAGCCACAACCAC 1 6291 ( 464) GACCTCTTCAGCATCCACCAC 1 25551 ( 318) GACCCAATGCGCGACCAACAC 1 5579 ( 474) GACCACCGACACGACGAACGC 1 25698 ( 283) TGCAACTGCACCCACAAGCAC 1 31881 ( 425) CACACCAGCAGCCCACAACGC 1 2645 ( 402) AACGTCCTGAGCCCCGACAAC 1 7610 ( 434) CACCAACTTGGCAACTACCAC 1 27773 ( 459) GAAGTCCAAAGCGACAAGCAT 1 1621 ( 197) GACGAATACGAGGAAGAGCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5760 bayes= 9.38536 E= 8.0e-005 -148 -31 139 -161 184 -1010 -141 -1010 -148 201 -1010 -1010 52 69 17 -1010 52 -31 -41 -3 10 169 -1010 -1010 -48 69 -1010 71 -48 -1010 91 38 -48 128 -41 -161 132 -31 -41 -1010 -48 -131 159 -1010 -1010 201 -141 -1010 -48 101 59 -1010 151 -31 -1010 -161 -48 186 -1010 -1010 52 28 17 -161 197 -1010 -1010 -1010 10 101 17 -1010 -148 201 -1010 -1010 168 -1010 -41 -1010 -1010 201 -1010 -161 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 11 E= 8.0e-005 0.090909 0.181818 0.636364 0.090909 0.909091 0.000000 0.090909 0.000000 0.090909 0.909091 0.000000 0.000000 0.363636 0.363636 0.272727 0.000000 0.363636 0.181818 0.181818 0.272727 0.272727 0.727273 0.000000 0.000000 0.181818 0.363636 0.000000 0.454545 0.181818 0.000000 0.454545 0.363636 0.181818 0.545455 0.181818 0.090909 0.636364 0.181818 0.181818 0.000000 0.181818 0.090909 0.727273 0.000000 0.000000 0.909091 0.090909 0.000000 0.181818 0.454545 0.363636 0.000000 0.727273 0.181818 0.000000 0.090909 0.181818 0.818182 0.000000 0.000000 0.363636 0.272727 0.272727 0.090909 1.000000 0.000000 0.000000 0.000000 0.272727 0.454545 0.272727 0.000000 0.090909 0.909091 0.000000 0.000000 0.818182 0.000000 0.181818 0.000000 0.000000 0.909091 0.000000 0.090909 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GAC[ACG][AT][CA][TC][GT]CAGC[CG]AC[ACG]A[CAG]CAC -------------------------------------------------------------------------------- Time 1.19 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 9 llr = 121 E-value = 4.6e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::11:::::8:11:: pos.-specific C :917329119139::9 probability G 91::::132::1:911 matrix T 1:9268:67116::9: bits 2.2 1.9 1.7 * * * * * 1.5 ** * * ** * Relative 1.3 *** * * **** Entropy 1.1 *** ** ** **** (19.5 bits) 0.9 **** ** ** **** 0.6 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel GCTCTTCTTCATCGTC consensus TCC GG C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 24395 358 8.64e-10 TCTTCCTTGT GCTCTTCGTCATCGTC GTATGCCTCA 11666 358 8.64e-10 TCTTCCTTGT GCTCTTCGTCATCGTC GTATGCCTCA 5579 441 1.30e-08 TGAAGCCGAT GCTCCTCTCCACCGTC CTCGTTCACC 6291 289 7.53e-08 CTGCAAGGGT TCTTTTCTTCATCGTC GTCTCAGAGG 31881 405 8.91e-07 TCAATCACAC GCTCACGTGCACCGTC ACAACACACC 25698 235 8.91e-07 GTGGCCGCAA GCTCCTCCTCACCAGC CCCACGCCCC 7610 46 2.05e-06 TCTCTCTTTT GCTATCCTTTCTCGTC AGGCATGTGA 25551 444 2.05e-06 CGTATCACTC GCTTTTCTTCTGAGTC CATTGACGAA 2645 89 3.26e-06 CTCTATGACA GGCCCTCGGCATCGTG TGGTGGAGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24395 8.6e-10 357_[+2]_127 11666 8.6e-10 357_[+2]_127 5579 1.3e-08 440_[+2]_44 6291 7.5e-08 288_[+2]_196 31881 8.9e-07 404_[+2]_80 25698 8.9e-07 234_[+2]_250 7610 2e-06 45_[+2]_439 25551 2e-06 443_[+2]_41 2645 3.3e-06 88_[+2]_396 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=9 24395 ( 358) GCTCTTCGTCATCGTC 1 11666 ( 358) GCTCTTCGTCATCGTC 1 5579 ( 441) GCTCCTCTCCACCGTC 1 6291 ( 289) TCTTTTCTTCATCGTC 1 31881 ( 405) GCTCACGTGCACCGTC 1 25698 ( 235) GCTCCTCCTCACCAGC 1 7610 ( 46) GCTATCCTTTCTCGTC 1 25551 ( 444) GCTTTTCTTCTGAGTC 1 2645 ( 89) GGCCCTCGGCATCGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 5820 bayes= 9.46915 E= 4.6e-003 -982 -982 187 -132 -982 198 -112 -982 -982 -102 -982 167 -119 157 -982 -33 -119 57 -982 100 -982 -2 -982 148 -982 198 -112 -982 -982 -102 46 100 -982 -102 -12 126 -982 198 -982 -132 161 -102 -982 -132 -982 57 -112 100 -119 198 -982 -982 -119 -982 187 -982 -982 -982 -112 167 -982 198 -112 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 9 E= 4.6e-003 0.000000 0.000000 0.888889 0.111111 0.000000 0.888889 0.111111 0.000000 0.000000 0.111111 0.000000 0.888889 0.111111 0.666667 0.000000 0.222222 0.111111 0.333333 0.000000 0.555556 0.000000 0.222222 0.000000 0.777778 0.000000 0.888889 0.111111 0.000000 0.000000 0.111111 0.333333 0.555556 0.000000 0.111111 0.222222 0.666667 0.000000 0.888889 0.000000 0.111111 0.777778 0.111111 0.000000 0.111111 0.000000 0.333333 0.111111 0.555556 0.111111 0.888889 0.000000 0.000000 0.111111 0.000000 0.888889 0.000000 0.000000 0.000000 0.111111 0.888889 0.000000 0.888889 0.111111 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GCT[CT][TC][TC]C[TG][TG]CA[TC]CGTC -------------------------------------------------------------------------------- Time 2.36 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 12 llr = 142 E-value = 5.8e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 3:::61::::4:833: pos.-specific C :3:::1:112::111: probability G 71:a128:48:813:8 matrix T :7a:37295:63:473 bits 2.2 * 1.9 ** 1.7 ** 1.5 ** * * Relative 1.3 ** ** * * * Entropy 1.1 * ** ** * ** * (17.1 bits) 0.9 * ** ** **** * 0.6 ***** ******* ** 0.4 ************* ** 0.2 **************** 0.0 ---------------- Multilevel GTTGATGTTGTGATTG consensus AC T G AT AAT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 25551 291 1.65e-09 AGGCCTGTCC GTTGATGTTGAGATTG GCCTGTCGAT 24395 136 1.04e-07 ATTGGTGGCT GTTGTTGTGCTGATTG GTCGTTCTTG 11666 136 1.04e-07 ATTGGTGGCT GTTGTTGTGCTGATTG GTCGTTCTTG 25698 58 1.99e-07 ACCGCCACTC ATTGTTGTTGTTATTG AGTGTGTAGA 5579 157 3.09e-07 AAGTGAATCT GCTGATGTTGTGATAT CGTGAATGCG 1621 125 5.30e-07 GTGTGTGCCC ATTGAAGTGGAGAATG TTGCAAACTT 31881 31 1.83e-06 GATGAGAGTG AGTGATGTTGAGAGTT GAGACACGAG 260998 302 3.71e-06 CTCAGAGCTC ACTGATGTCGTGAACG CTTCCACCGT 6291 266 4.96e-06 AGCTGTAAGC GCTGATGTTGTTGCTG CAAGGGTTCT 2645 137 9.51e-06 ACCAAGTTGG GTTGGGTTGGAGAGAG ACTGTGGCAA 27773 220 1.01e-05 ATGCCGTGCA GTTGTCGCTGAGAGTT ATGAACTGTG 7610 146 2.21e-05 AGTTTCATCC GTTGAGTTGGTTCAAG TCTCACCTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25551 1.7e-09 290_[+3]_194 24395 1e-07 135_[+3]_349 11666 1e-07 135_[+3]_349 25698 2e-07 57_[+3]_427 5579 3.1e-07 156_[+3]_328 1621 5.3e-07 124_[+3]_360 31881 1.8e-06 30_[+3]_454 260998 3.7e-06 301_[+3]_183 6291 5e-06 265_[+3]_219 2645 9.5e-06 136_[+3]_348 27773 1e-05 219_[+3]_265 7610 2.2e-05 145_[+3]_339 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=12 25551 ( 291) GTTGATGTTGAGATTG 1 24395 ( 136) GTTGTTGTGCTGATTG 1 11666 ( 136) GTTGTTGTGCTGATTG 1 25698 ( 58) ATTGTTGTTGTTATTG 1 5579 ( 157) GCTGATGTTGTGATAT 1 1621 ( 125) ATTGAAGTGGAGAATG 1 31881 ( 31) AGTGATGTTGAGAGTT 1 260998 ( 302) ACTGATGTCGTGAACG 1 6291 ( 266) GCTGATGTTGTTGCTG 1 2645 ( 137) GTTGGGTTGGAGAGAG 1 27773 ( 220) GTTGTCGCTGAGAGTT 1 7610 ( 146) GTTGAGTTGGTTCAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 5820 bayes= 9.36712 E= 5.8e-003 39 -1023 146 -1023 -1023 15 -154 126 -1023 -1023 -1023 184 -1023 -1023 204 -1023 120 -1023 -154 26 -161 -143 -54 126 -1023 -1023 178 -74 -1023 -143 -1023 172 -1023 -143 78 84 -1023 -43 178 -1023 71 -1023 -1023 107 -1023 -1023 163 -16 171 -143 -154 -1023 -2 -143 5 58 -2 -143 -1023 126 -1023 -1023 163 -16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 12 E= 5.8e-003 0.333333 0.000000 0.666667 0.000000 0.000000 0.250000 0.083333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.583333 0.000000 0.083333 0.333333 0.083333 0.083333 0.166667 0.666667 0.000000 0.000000 0.833333 0.166667 0.000000 0.083333 0.000000 0.916667 0.000000 0.083333 0.416667 0.500000 0.000000 0.166667 0.833333 0.000000 0.416667 0.000000 0.000000 0.583333 0.000000 0.000000 0.750000 0.250000 0.833333 0.083333 0.083333 0.000000 0.250000 0.083333 0.250000 0.416667 0.250000 0.083333 0.000000 0.666667 0.000000 0.000000 0.750000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA][TC]TG[AT]TGT[TG]G[TA][GT]A[TAG][TA][GT] -------------------------------------------------------------------------------- Time 3.54 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11666 7.97e-17 135_[+3(1.04e-07)]_153_\ [+1(7.78e-12)]_32_[+2(8.64e-10)]_127 1621 3.89e-05 124_[+3(5.30e-07)]_56_\ [+1(2.51e-06)]_283 24395 7.97e-17 135_[+3(1.04e-07)]_153_\ [+1(7.78e-12)]_32_[+2(8.64e-10)]_127 25551 1.87e-11 290_[+3(1.65e-09)]_11_\ [+1(9.57e-08)]_5_[+1(6.03e-05)]_79_[+2(2.05e-06)]_41 25698 1.50e-09 57_[+3(1.99e-07)]_161_\ [+2(8.91e-07)]_32_[+1(2.01e-07)]_197 260998 1.15e-02 301_[+3(3.71e-06)]_183 2645 4.35e-07 88_[+2(3.26e-06)]_32_[+3(9.51e-06)]_\ 249_[+1(5.62e-07)]_78 27773 1.40e-04 219_[+3(1.01e-05)]_223_\ [+1(9.47e-07)]_21 31881 2.32e-08 30_[+3(1.83e-06)]_201_\ [+1(4.64e-05)]_136_[+2(8.91e-07)]_4_[+1(4.26e-07)]_55 5579 2.79e-11 156_[+3(3.09e-07)]_193_\ [+3(1.49e-05)]_59_[+2(1.30e-08)]_17_[+1(1.24e-07)]_6 6291 1.44e-10 265_[+3(4.96e-06)]_7_[+2(7.53e-08)]_\ 159_[+1(7.72e-09)]_16 7610 6.91e-07 45_[+2(2.05e-06)]_84_[+3(2.21e-05)]_\ 272_[+1(6.43e-07)]_46 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************