******************************************************************************** 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/462/462.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 38140 1.0000 500 39186 1.0000 500 48667 1.0000 500 50206 1.0000 500 33756 1.0000 500 45446 1.0000 500 45451 1.0000 500 48199 1.0000 500 40475 1.0000 500 46732 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/462/462.seqs.fa -oc motifs/462 -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 0.282 C 0.223 G 0.216 T 0.279 Background letter frequencies (from dataset with add-one prior applied): A 0.282 C 0.223 G 0.216 T 0.279 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 10 llr = 117 E-value = 7.3e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 78117aa::6a48:51 pos.-specific C 1::1:::533:::827 probability G :226:::561::221: matrix T 2:723:::1::6::22 bits 2.2 2.0 1.8 ** * 1.5 ** * * Relative 1.3 ** * * Entropy 1.1 * *** * ** (16.9 bits) 0.9 * ***** **** * 0.7 *** ********** * 0.4 ************** * 0.2 **************** 0.0 ---------------- Multilevel AATGAAACGAATACAC consensus TGGTT GCC AGGCT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 45451 415 2.15e-09 ACATACGGGA AATGAAACGAAAACAC GGGATGTATT 45446 143 1.30e-07 AATCGCAGTA AATGTAAGGCATGCAC GATTGGCCGT 46732 201 2.11e-07 AGAAATATCG AATGAAACCAATAGCC CTCCTCGAGA 50206 301 2.69e-07 GTTATCAGTT AAGTAAACGCATACAC ATTCGTAGAA 40475 155 1.28e-06 TTCATCATTG TATGAAAGTAATACTC TGGGTTCTCC 39186 230 4.69e-06 TTAGAATGGA AATGTAACGGAAGCAT CATGTCAATC 38140 94 5.39e-06 TCCCAGGCTA TAATAAAGGAAAACCC TTCCTGCTGA 33756 229 8.51e-06 AAAGTCCTAT AGTAAAAGGAAAAGGC GTTATAGGCG 48667 264 8.51e-06 GCTACTTATA AATCTAAGCCATACTT TCTTAAACCT 48199 7 1.27e-05 GAAGGA CGGGAAACCAATACAA TATGCTGGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45451 2.1e-09 414_[+1]_70 45446 1.3e-07 142_[+1]_342 46732 2.1e-07 200_[+1]_284 50206 2.7e-07 300_[+1]_184 40475 1.3e-06 154_[+1]_330 39186 4.7e-06 229_[+1]_255 38140 5.4e-06 93_[+1]_391 33756 8.5e-06 228_[+1]_256 48667 8.5e-06 263_[+1]_221 48199 1.3e-05 6_[+1]_478 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=10 45451 ( 415) AATGAAACGAAAACAC 1 45446 ( 143) AATGTAAGGCATGCAC 1 46732 ( 201) AATGAAACCAATAGCC 1 50206 ( 301) AAGTAAACGCATACAC 1 40475 ( 155) TATGAAAGTAATACTC 1 39186 ( 230) AATGTAACGGAAGCAT 1 38140 ( 94) TAATAAAGGAAAACCC 1 33756 ( 229) AGTAAAAGGAAAAGGC 1 48667 ( 264) AATCTAAGCCATACTT 1 48199 ( 7) CGGGAAACCAATACAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 4850 bayes= 9.17088 E= 7.3e+001 131 -115 -997 -48 150 -997 -11 -997 -149 -997 -11 133 -149 -115 147 -48 131 -997 -997 11 182 -997 -997 -997 182 -997 -997 -997 -997 117 121 -997 -997 43 147 -148 109 43 -111 -997 182 -997 -997 -997 50 -997 -997 111 150 -997 -11 -997 -997 184 -11 -997 82 -16 -111 -48 -149 165 -997 -48 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 7.3e+001 0.700000 0.100000 0.000000 0.200000 0.800000 0.000000 0.200000 0.000000 0.100000 0.000000 0.200000 0.700000 0.100000 0.100000 0.600000 0.200000 0.700000 0.000000 0.000000 0.300000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.300000 0.600000 0.100000 0.600000 0.300000 0.100000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.600000 0.800000 0.000000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.500000 0.200000 0.100000 0.200000 0.100000 0.700000 0.000000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT][AG][TG][GT][AT]AA[CG][GC][AC]A[TA][AG][CG][ACT][CT] -------------------------------------------------------------------------------- Time 0.92 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 5 llr = 75 E-value = 1.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 8::::::::4:2::: pos.-specific C :4a::2:a::6::42 probability G 26::28::a::6:28 matrix T :::a8:a::642a4: bits 2.2 * ** 2.0 * ** 1.8 ** *** * 1.5 ** **** * * Relative 1.3 *** **** * * Entropy 1.1 ********* * * * (21.8 bits) 0.9 *********** * * 0.7 ************* * 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel AGCTTGTCGTCGTCG consensus GC GC ATA TC sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 45451 218 4.49e-09 CCACCGGAAC AGCTTGTCGTTGTCG AGTGCTGGTC 48199 131 6.16e-08 GTCAGAAAAA AGCTTCTCGTTGTTG CTGTACACGA 50206 22 1.22e-07 ATCCCATGAT AGCTGGTCGACTTCG AAAGGCTGGC 48667 369 1.22e-07 CAGAATGTTG ACCTTGTCGACGTGC AGTCGCGGGA 45446 300 1.57e-07 CGACACACTT GCCTTGTCGTCATTG GCTAAGTGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45451 4.5e-09 217_[+2]_268 48199 6.2e-08 130_[+2]_355 50206 1.2e-07 21_[+2]_464 48667 1.2e-07 368_[+2]_117 45446 1.6e-07 299_[+2]_186 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=5 45451 ( 218) AGCTTGTCGTTGTCG 1 48199 ( 131) AGCTTCTCGTTGTTG 1 50206 ( 22) AGCTGGTCGACTTCG 1 48667 ( 369) ACCTTGTCGACGTGC 1 45446 ( 300) GCCTTGTCGTCATTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 4860 bayes= 9.35702 E= 1.8e+002 150 -897 -11 -897 -897 84 147 -897 -897 216 -897 -897 -897 -897 -897 184 -897 -897 -11 152 -897 -16 189 -897 -897 -897 -897 184 -897 216 -897 -897 -897 -897 221 -897 50 -897 -897 110 -897 143 -897 52 -50 -897 147 -48 -897 -897 -897 184 -897 84 -11 52 -897 -16 189 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 5 E= 1.8e+002 0.800000 0.000000 0.200000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.200000 0.800000 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 0.400000 0.000000 0.000000 0.600000 0.000000 0.600000 0.000000 0.400000 0.200000 0.000000 0.600000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.200000 0.400000 0.000000 0.200000 0.800000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AG][GC]CT[TG][GC]TCG[TA][CT][GAT]T[CTG][GC] -------------------------------------------------------------------------------- Time 1.74 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 10 llr = 102 E-value = 2.6e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 337491::::9: pos.-specific C 3:::1::37a:: probability G 473::7::3::4 matrix T :::6:2a7::16 bits 2.2 * 2.0 * 1.8 * * 1.5 * * Relative 1.3 * * *** Entropy 1.1 ** * ****** (14.7 bits) 0.9 *********** 0.7 *********** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GGATAGTTCCAT consensus AAGA T CG G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 48199 40 1.21e-07 GGAAGCAATT GGATAGTTCCAG AATACTCTAC 38140 78 2.70e-06 TGCGGGTTGA CGAAAGTCCCAG GCTATAATAA 45451 310 6.72e-06 ATGTATTTTA AAAAAGTTCCAT GAACCGTTTG 50206 126 7.43e-06 TATCCCCAAC GGATAATTCCAT CAAGAACTTT 39186 350 7.43e-06 TTATGTTCCT GGGTATTTCCAG CGGCTCAGAG 40475 305 1.06e-05 AATTAGCATC AAATAGTTGCAT TGCATGGCTA 33756 148 1.06e-05 GTGTTGATTT GGAAATTCCCAT ATCAGGCCGG 46732 457 1.48e-05 AACCAACAGC CGGAAGTCGCAG CAAACACAAT 45446 207 2.33e-05 TGCTACCGAC CGATAGTTGCTT TTTAACCGTG 48667 145 4.21e-05 AAGTATGTCT AAGTCGTTCCAT CGACCTCCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48199 1.2e-07 39_[+3]_449 38140 2.7e-06 77_[+3]_411 45451 6.7e-06 309_[+3]_179 50206 7.4e-06 125_[+3]_363 39186 7.4e-06 349_[+3]_139 40475 1.1e-05 304_[+3]_184 33756 1.1e-05 147_[+3]_341 46732 1.5e-05 456_[+3]_32 45446 2.3e-05 206_[+3]_282 48667 4.2e-05 144_[+3]_344 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=10 48199 ( 40) GGATAGTTCCAG 1 38140 ( 78) CGAAAGTCCCAG 1 45451 ( 310) AAAAAGTTCCAT 1 50206 ( 126) GGATAATTCCAT 1 39186 ( 350) GGGTATTTCCAG 1 40475 ( 305) AAATAGTTGCAT 1 33756 ( 148) GGAAATTCCCAT 1 46732 ( 457) CGGAAGTCGCAG 1 45446 ( 207) CGATAGTTGCTT 1 48667 ( 145) AAGTCGTTCCAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 4890 bayes= 8.93074 E= 2.6e+002 9 43 89 -997 9 -997 170 -997 131 -997 47 -997 50 -997 -997 111 167 -115 -997 -997 -149 -997 170 -48 -997 -997 -997 184 -997 43 -997 133 -997 165 47 -997 -997 216 -997 -997 167 -997 -997 -148 -997 -997 89 111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 10 E= 2.6e+002 0.300000 0.300000 0.400000 0.000000 0.300000 0.000000 0.700000 0.000000 0.700000 0.000000 0.300000 0.000000 0.400000 0.000000 0.000000 0.600000 0.900000 0.100000 0.000000 0.000000 0.100000 0.000000 0.700000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.300000 0.000000 0.700000 0.000000 0.700000 0.300000 0.000000 0.000000 1.000000 0.000000 0.000000 0.900000 0.000000 0.000000 0.100000 0.000000 0.000000 0.400000 0.600000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GAC][GA][AG][TA]A[GT]T[TC][CG]CA[TG] -------------------------------------------------------------------------------- Time 2.69 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38140 2.03e-04 77_[+3(2.70e-06)]_4_[+1(5.39e-06)]_\ 391 39186 4.34e-04 229_[+1(4.69e-06)]_104_\ [+3(7.43e-06)]_139 48667 1.01e-06 144_[+3(4.21e-05)]_107_\ [+1(8.51e-06)]_89_[+2(1.22e-07)]_117 50206 8.98e-09 21_[+2(1.22e-07)]_89_[+3(7.43e-06)]_\ 163_[+1(2.69e-07)]_184 33756 3.14e-04 147_[+3(1.06e-05)]_69_\ [+1(8.51e-06)]_256 45446 1.66e-08 142_[+1(1.30e-07)]_48_\ [+3(2.33e-05)]_81_[+2(1.57e-07)]_58_[+3(9.43e-05)]_116 45451 4.19e-12 217_[+2(4.49e-09)]_77_\ [+3(6.72e-06)]_93_[+1(2.15e-09)]_70 48199 3.74e-09 6_[+1(1.27e-05)]_17_[+3(1.21e-07)]_\ 79_[+2(6.16e-08)]_355 40475 2.41e-04 154_[+1(1.28e-06)]_134_\ [+3(1.06e-05)]_184 46732 5.54e-06 200_[+1(2.11e-07)]_170_\ [+2(9.51e-05)]_55_[+3(1.48e-05)]_32 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************