******************************************************************************** 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/258/258.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10814 1.0000 500 23428 1.0000 500 263097 1.0000 500 263299 1.0000 500 264577 1.0000 500 269307 1.0000 500 34442 1.0000 500 bd1124 1.0000 500 bd1125 1.0000 500 bd909 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/258/258.seqs.fa -oc motifs/258 -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 0.272 C 0.240 G 0.217 T 0.271 Background letter frequencies (from dataset with add-one prior applied): A 0.272 C 0.240 G 0.217 T 0.271 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 6 llr = 100 E-value = 2.7e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::a7a3752:aa:: pos.-specific C :::a:::5:::a:::a probability G :22::::2::::::2: matrix T a88::3::358:::8: bits 2.2 2.0 * ** * *** * 1.8 * ** * *** * 1.5 * ** * *** * Relative 1.3 ***** * ****** Entropy 1.1 ***** * ****** (24.0 bits) 0.9 ******* ******** 0.7 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel TTTCAAACAATCAATC consensus T ATT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- bd1125 442 1.07e-09 CCTTTTGTTC TTTCAAACAATCAATC AATACACTAC bd1124 442 1.07e-09 CCTTTTGTTC TTTCAAACAATCAATC AATACACTAA 269307 359 1.85e-08 TGGTTCAGCC TTTCATAATTTCAATC CTCGAAGGGA 263299 211 1.85e-08 TGGTTCAGCC TTTCATAATTTCAATC CTCGAAGGGA 10814 252 4.16e-08 AAATCACACC TTGCAAACAATCAAGC TTGAACGAGT 34442 194 8.48e-08 ATATCACTTG TGTCAAAGATACAATC GACCGGGCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1125 1.1e-09 441_[+1]_43 bd1124 1.1e-09 441_[+1]_43 269307 1.8e-08 358_[+1]_126 263299 1.8e-08 210_[+1]_274 10814 4.2e-08 251_[+1]_233 34442 8.5e-08 193_[+1]_291 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=6 bd1125 ( 442) TTTCAAACAATCAATC 1 bd1124 ( 442) TTTCAAACAATCAATC 1 269307 ( 359) TTTCATAATTTCAATC 1 263299 ( 211) TTTCATAATTTCAATC 1 10814 ( 252) TTGCAAACAATCAAGC 1 34442 ( 194) TGTCAAAGATACAATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 4850 bayes= 9.31551 E= 2.7e-002 -923 -923 -923 188 -923 -923 -38 162 -923 -923 -38 162 -923 206 -923 -923 188 -923 -923 -923 129 -923 -923 30 188 -923 -923 -923 29 106 -38 -923 129 -923 -923 30 88 -923 -923 88 -71 -923 -923 162 -923 206 -923 -923 188 -923 -923 -923 188 -923 -923 -923 -923 -923 -38 162 -923 206 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 6 E= 2.7e-002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.166667 0.833333 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 0.333333 0.500000 0.166667 0.000000 0.666667 0.000000 0.000000 0.333333 0.500000 0.000000 0.000000 0.500000 0.166667 0.000000 0.000000 0.833333 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 0.000000 0.166667 0.833333 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TTTCA[AT]A[CA][AT][AT]TCAATC -------------------------------------------------------------------------------- Time 0.91 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 6 llr = 113 E-value = 2.1e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A a22:::::::82:2:785::2 pos.-specific C :27:7::::::3::::::::: probability G :7:2:a33aa2522a22552: matrix T ::283:77::::87:2::588 bits 2.2 * ** * 2.0 * * ** * 1.8 * * ** * 1.5 * * ** * Relative 1.3 * * * *** * * * ** Entropy 1.1 * ******** * * ***** (27.3 bits) 0.9 ** ******** * * ***** 0.7 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel AGCTCGTTGGAGTTGAAAGTT consensus T GG C GT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- bd1124 282 5.83e-13 TCAATCGGAT AGCTCGTTGGAGTTGAAAGTT TGTGATGTTG bd1125 282 1.55e-11 TCAATCGGAT AGCTCGTTGGAGTTGAGAGTT TGTGATGTTG bd909 20 3.48e-09 TGAACGAGAG AGCTCGTTGGAATGGGAATTA CATTACACAA 34442 30 4.28e-09 ACAGTGCATG ACCTCGGGGGGCTTGTAGTTT GGTAGTGATG 264577 8 5.93e-09 ACCCGGG AATGTGGGGGAGTTGAAGGTT GATTTGGAAG 23428 274 1.13e-08 GTGATCAGAA AGATTGTTGGACGAGAAGTGT GGAGTTTGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1124 5.8e-13 281_[+2]_198 bd1125 1.6e-11 281_[+2]_198 bd909 3.5e-09 19_[+2]_460 34442 4.3e-09 29_[+2]_450 264577 5.9e-09 7_[+2]_472 23428 1.1e-08 273_[+2]_206 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=6 bd1124 ( 282) AGCTCGTTGGAGTTGAAAGTT 1 bd1125 ( 282) AGCTCGTTGGAGTTGAGAGTT 1 bd909 ( 20) AGCTCGTTGGAATGGGAATTA 1 34442 ( 30) ACCTCGGGGGGCTTGTAGTTT 1 264577 ( 8) AATGTGGGGGAGTTGAAGGTT 1 23428 ( 274) AGATTGTTGGACGAGAAGTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4800 bayes= 9.30053 E= 2.1e-002 188 -923 -923 -923 -71 -52 161 -923 -71 147 -923 -70 -923 -923 -38 162 -923 147 -923 30 -923 -923 220 -923 -923 -923 62 130 -923 -923 62 130 -923 -923 220 -923 -923 -923 220 -923 161 -923 -38 -923 -71 48 120 -923 -923 -923 -38 162 -71 -923 -38 130 -923 -923 220 -923 129 -923 -38 -70 161 -923 -38 -923 88 -923 120 -923 -923 -923 120 88 -923 -923 -38 162 -71 -923 -923 162 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 2.1e-002 1.000000 0.000000 0.000000 0.000000 0.166667 0.166667 0.666667 0.000000 0.166667 0.666667 0.000000 0.166667 0.000000 0.000000 0.166667 0.833333 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.166667 0.333333 0.500000 0.000000 0.000000 0.000000 0.166667 0.833333 0.166667 0.000000 0.166667 0.666667 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.166667 0.166667 0.833333 0.000000 0.166667 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.166667 0.833333 0.166667 0.000000 0.000000 0.833333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- AGCT[CT]G[TG][TG]GGA[GC]TTGAA[AG][GT]TT -------------------------------------------------------------------------------- Time 1.81 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 5 llr = 103 E-value = 3.6e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 224:4:6:2::2:a:::::2: pos.-specific C :8::62::::8:::28242:: probability G 8:6a:84a68::a:8::66:a matrix T ::::::::2228:::28:28: bits 2.2 * * * * 2.0 * * ** * 1.8 * * ** * 1.5 * * * *** * Relative 1.3 ** * * * ** **** * Entropy 1.1 ******** ********* ** (29.6 bits) 0.9 ******** ********* ** 0.7 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GCGGCGAGGGCTGAGCTGGTG consensus AAA ACG ATTA CTCCCA sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- bd1125 171 9.58e-14 ACGTTCTGCT GCGGCGGGGGCTGAGCTGGTG AACCACTTGT bd1124 171 9.58e-14 ACGTTCTGCT GCGGCGGGGGCTGAGCTGGTG AACCACTTGT bd909 133 1.64e-09 AAGAGTGAGA GAAGAGAGAGCAGAGCTCCTG CAATTTCTCA 23428 370 2.84e-09 AACAACCAAA ACGGCCAGGGCTGACTTCTTG TTTGGCATTA 269307 178 3.59e-09 AACCTAGATT GCAGAGAGTTTTGAGCCGGAG CGGCCCTCAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1125 9.6e-14 170_[+3]_309 bd1124 9.6e-14 170_[+3]_309 bd909 1.6e-09 132_[+3]_347 23428 2.8e-09 369_[+3]_110 269307 3.6e-09 177_[+3]_302 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=5 bd1125 ( 171) GCGGCGGGGGCTGAGCTGGTG 1 bd1124 ( 171) GCGGCGGGGGCTGAGCTGGTG 1 bd909 ( 133) GAAGAGAGAGCAGAGCTCCTG 1 23428 ( 370) ACGGCCAGGGCTGACTTCTTG 1 269307 ( 178) GCAGAGAGTTTTGAGCCGGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4800 bayes= 10.8495 E= 3.6e-002 -44 -897 188 -897 -44 174 -897 -897 55 -897 146 -897 -897 -897 220 -897 55 132 -897 -897 -897 -26 188 -897 114 -897 88 -897 -897 -897 220 -897 -44 -897 146 -44 -897 -897 188 -44 -897 174 -897 -44 -44 -897 -897 156 -897 -897 220 -897 188 -897 -897 -897 -897 -26 188 -897 -897 174 -897 -44 -897 -26 -897 156 -897 74 146 -897 -897 -26 146 -44 -44 -897 -897 156 -897 -897 220 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 3.6e-002 0.200000 0.000000 0.800000 0.000000 0.200000 0.800000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.600000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.800000 0.000000 0.200000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.200000 0.000000 0.800000 0.000000 0.400000 0.600000 0.000000 0.000000 0.200000 0.600000 0.200000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA][CA][GA]G[CA][GC][AG]G[GAT][GT][CT][TA]GA[GC][CT][TC][GC][GCT][TA]G -------------------------------------------------------------------------------- Time 2.68 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10814 8.35e-05 251_[+1(4.16e-08)]_233 23428 1.10e-09 273_[+2(1.13e-08)]_75_\ [+3(2.84e-09)]_110 263097 2.72e-01 500 263299 5.40e-04 210_[+1(1.85e-08)]_274 264577 5.98e-05 7_[+2(5.93e-09)]_472 269307 3.77e-09 177_[+3(3.59e-09)]_160_\ [+1(1.85e-08)]_126 34442 1.64e-08 29_[+2(4.28e-09)]_143_\ [+1(8.48e-08)]_291 bd1124 1.25e-23 37_[+3(9.83e-05)]_112_\ [+3(9.58e-14)]_90_[+2(5.83e-13)]_139_[+1(1.07e-09)]_43 bd1125 2.98e-22 37_[+3(9.83e-05)]_112_\ [+3(9.58e-14)]_90_[+2(1.55e-11)]_139_[+1(1.07e-09)]_43 bd909 3.03e-10 19_[+2(3.48e-09)]_92_[+3(1.64e-09)]_\ 347 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************