******************************************************************************** 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/14/14.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 15442 1.0000 500 39573 1.0000 500 46087 1.0000 500 41393 1.0000 500 39571 1.0000 500 39572 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/14/14.seqs.fa -oc motifs/14 -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= 6 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= 3000 N= 6 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.301 C 0.215 G 0.200 T 0.284 Background letter frequencies (from dataset with add-one prior applied): A 0.301 C 0.215 G 0.200 T 0.284 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 5 llr = 90 E-value = 2.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :62:::::2::26a6:2::26 pos.-specific C 6:4::2::28624:28::8:4 probability G 4::8::::224::::28::8: matrix T :442a8aa4::6::2::a2:: bits 2.3 2.1 1.9 * ** * 1.6 * ** * * * * Relative 1.4 * ** ** ** * ***** Entropy 1.2 * ***** ** * ***** (25.8 bits) 0.9 * ***** ** ** ****** 0.7 ** ***** ** ** ****** 0.5 ******** ************ 0.2 ******** ************ 0.0 --------------------- Multilevel CACGTTTTTCCTAAACGTCGA consensus GTTT C AGGAC CGA TAC sequence A C C T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 39571 366 1.24e-10 CGATACGAGT CTTGTCTTTCCTAAACGTCGA CACTATACCT 46087 385 4.67e-10 CTTAGGTGCA GTCGTTTTGCGAAAACGTCGA ATATTGTAAT 39573 323 2.37e-09 GCGTTGGAAT CACTTTTTTCCTCAACATCGC AACGTGCGAC 39572 415 4.94e-09 TGTCTCAACC GATGTTTTACCTCATCGTCAC TCACAATCAC 41393 213 4.78e-08 TCTTTTATAT CAAGTTTTCGGCAACGGTTGA GACGTGTATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 39571 1.2e-10 365_[+1]_114 46087 4.7e-10 384_[+1]_95 39573 2.4e-09 322_[+1]_157 39572 4.9e-09 414_[+1]_65 41393 4.8e-08 212_[+1]_267 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=5 39571 ( 366) CTTGTCTTTCCTAAACGTCGA 1 46087 ( 385) GTCGTTTTGCGAAAACGTCGA 1 39573 ( 323) CACTTTTTTCCTCAACATCGC 1 39572 ( 415) GATGTTTTACCTCATCGTCAC 1 41393 ( 213) CAAGTTTTCGGCAACGGTTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2880 bayes= 9.41936 E= 2.5e+001 -897 148 100 -897 100 -897 -897 49 -59 89 -897 49 -897 -897 199 -50 -897 -897 -897 181 -897 -10 -897 149 -897 -897 -897 181 -897 -897 -897 181 -59 -10 0 49 -897 189 0 -897 -897 148 100 -897 -59 -10 -897 108 100 89 -897 -897 173 -897 -897 -897 100 -10 -897 -50 -897 189 0 -897 -59 -897 199 -897 -897 -897 -897 181 -897 189 -897 -50 -59 -897 199 -897 100 89 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 2.5e+001 0.000000 0.600000 0.400000 0.000000 0.600000 0.000000 0.000000 0.400000 0.200000 0.400000 0.000000 0.400000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.200000 0.200000 0.200000 0.400000 0.000000 0.800000 0.200000 0.000000 0.000000 0.600000 0.400000 0.000000 0.200000 0.200000 0.000000 0.600000 0.600000 0.400000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.200000 0.000000 0.200000 0.000000 0.800000 0.200000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.200000 0.000000 0.800000 0.000000 0.600000 0.400000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG][AT][CTA][GT]T[TC]TT[TACG][CG][CG][TAC][AC]A[ACT][CG][GA]T[CT][GA][AC] -------------------------------------------------------------------------------- Time 0.48 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 6 llr = 97 E-value = 1.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::7:7382:::27::2:232a pos.-specific C ::35:2:8:::7:a5::23:: probability G 5a:52:2:5272::::22:7: matrix T 5:::25::583:3:588532: bits 2.3 * * 2.1 * * 1.9 * * 1.6 * * * Relative 1.4 * * * * Entropy 1.2 ** * ***** * ** * (23.3 bits) 0.9 **** *********** ** 0.7 ***** *********** ** 0.5 ***************** ** 0.2 ********************* 0.0 --------------------- Multilevel GGACATACGTGCACCTTTAGA consensus T CG A T T T T C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 15442 376 4.74e-11 CTTTGATCAC GGAGGTACTTGCACCTTTCGA CCAAACCCTC 46087 3 2.58e-10 GG TGACAAACGTGCACCTTCAGA CGCGTTTTCC 39572 113 2.39e-08 TTTAGCAGAC GGAGACACTTGCACCAGACGA AGCAGGCCAT 39573 374 4.86e-08 CATGCGTCCT TGACATGCGTGGTCTTTTTTA TGGCTATAGA 41393 77 5.61e-08 CGGTCGGTCG GGCGAAACGGTATCTTTTTGA CAGTGACTGT 39571 77 3.12e-07 ACCCTGGCAT TGCCTTAATTTCACTTTGAAA ATTGAGTCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 15442 4.7e-11 375_[+2]_104 46087 2.6e-10 2_[+2]_477 39572 2.4e-08 112_[+2]_367 39573 4.9e-08 373_[+2]_106 41393 5.6e-08 76_[+2]_403 39571 3.1e-07 76_[+2]_403 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=6 15442 ( 376) GGAGGTACTTGCACCTTTCGA 1 46087 ( 3) TGACAAACGTGCACCTTCAGA 1 39572 ( 113) GGAGACACTTGCACCAGACGA 1 39573 ( 374) TGACATGCGTGGTCTTTTTTA 1 41393 ( 77) GGCGAAACGGTATCTTTTTGA 1 39571 ( 77) TGCCTTAATTTCACTTTGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2880 bayes= 8.90388 E= 1.3e+002 -923 -923 132 82 -923 -923 232 -923 115 63 -923 -923 -923 122 132 -923 115 -923 -27 -77 15 -37 -923 82 147 -923 -27 -923 -85 195 -923 -923 -923 -923 132 82 -923 -923 -27 155 -923 -923 173 23 -85 163 -27 -923 115 -923 -923 23 -923 222 -923 -923 -923 122 -923 82 -85 -923 -923 155 -923 -923 -27 155 -85 -37 -27 82 15 63 -923 23 -85 -923 173 -77 173 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 1.3e+002 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.666667 0.000000 0.166667 0.166667 0.333333 0.166667 0.000000 0.500000 0.833333 0.000000 0.166667 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.666667 0.333333 0.166667 0.666667 0.166667 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.166667 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.833333 0.166667 0.166667 0.166667 0.500000 0.333333 0.333333 0.000000 0.333333 0.166667 0.000000 0.666667 0.166667 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT]G[AC][CG]A[TA]AC[GT]T[GT]C[AT]C[CT]TTT[ACT]GA -------------------------------------------------------------------------------- Time 0.87 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 4 llr = 64 E-value = 4.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :5:a:5:a::585a: pos.-specific C a::::3::::5:5:: probability G :5a:::a:::::::3 matrix T ::::a3::aa:3::8 bits 2.3 * * * 2.1 * * * 1.9 * * * * ** 1.6 * *** **** * Relative 1.4 * *** **** * Entropy 1.2 * *** **** ** (22.9 bits) 0.9 ***** ********* 0.7 ***** ********* 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel CAGATAGATTAAAAT consensus G C CTC G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 15442 349 7.69e-09 CGTAATCTAA CGGATCGATTCACAT TTCTTTGATC 39572 44 3.99e-08 CAATTGATTT CGGATAGATTCTCAT CCGACCGTCT 39571 479 7.32e-08 CATCAAGTTG CAGATTGATTAAAAT TAACAGA 46087 229 8.81e-08 CGACACGACA CAGATAGATTAAAAG ACATGCGTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 15442 7.7e-09 348_[+3]_137 39572 4e-08 43_[+3]_442 39571 7.3e-08 478_[+3]_7 46087 8.8e-08 228_[+3]_257 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=4 15442 ( 349) CGGATCGATTCACAT 1 39572 ( 44) CGGATAGATTCTCAT 1 39571 ( 479) CAGATTGATTAAAAT 1 46087 ( 229) CAGATAGATTAAAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 2916 bayes= 9.50779 E= 4.2e+002 -865 221 -865 -865 73 -865 132 -865 -865 -865 232 -865 173 -865 -865 -865 -865 -865 -865 181 73 22 -865 -18 -865 -865 232 -865 173 -865 -865 -865 -865 -865 -865 181 -865 -865 -865 181 73 122 -865 -865 132 -865 -865 -18 73 122 -865 -865 173 -865 -865 -865 -865 -865 32 140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 4 E= 4.2e+002 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.250000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.500000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[AG]GAT[ACT]GATT[AC][AT][AC]A[TG] -------------------------------------------------------------------------------- Time 1.31 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 15442 1.63e-11 348_[+3(7.69e-09)]_12_\ [+2(4.74e-11)]_104 39573 6.39e-09 322_[+1(2.37e-09)]_30_\ [+2(4.86e-08)]_106 46087 1.06e-15 2_[+2(2.58e-10)]_205_[+3(8.81e-08)]_\ 141_[+1(4.67e-10)]_95 41393 1.03e-07 76_[+2(5.61e-08)]_115_\ [+1(4.78e-08)]_267 39571 2.13e-13 76_[+2(3.12e-07)]_268_\ [+1(1.24e-10)]_92_[+3(7.32e-08)]_7 39572 3.45e-13 43_[+3(3.99e-08)]_54_[+2(2.39e-08)]_\ 281_[+1(4.94e-09)]_65 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************