******************************************************************************** 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/202/202.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 19141 1.0000 500 28635 1.0000 500 30921 1.0000 500 35637 1.0000 500 6395 1.0000 500 bd1754 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/202/202.seqs.fa -oc motifs/202 -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 0.252 C 0.227 G 0.272 T 0.249 Background letter frequencies (from dataset with add-one prior applied): A 0.252 C 0.227 G 0.272 T 0.249 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 4 llr = 89 E-value = 6.4e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::a8:8:3::3::3::33:a: pos.-specific C 8a:3a:38a:5::858888:a probability G :::::35:::::::5:::::: matrix T 3:::::3::a3aa::3::3:: bits 2.1 * * * * 1.9 ** * ** ** ** 1.7 ** * ** ** ** 1.5 ** * ** ** ** Relative 1.3 ***** *** *** ****** Entropy 1.1 ****** *** ********** (32.0 bits) 0.9 ****** *** ********** 0.6 ****** ************** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CCAACAGCCTCTTCCCCCCAC consensus T C GCA A AGTAAT sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 28635 462 1.58e-13 TCTTTTCGAT CCAACAGCCTCTTCGCCCCAC CACACATTCT 19141 462 1.58e-13 TCTTTTCGAT CCAACAGCCTCTTCGCCCCAC CACACATTCT 35637 362 4.08e-10 CCGACCGCCA TCAACACACTATTCCTCCTAC AACAGGGAGC 6395 459 6.46e-10 TCTAGGTTCA CCACCGTCCTTTTACCAACAC CCATCACAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 28635 1.6e-13 461_[+1]_18 19141 1.6e-13 461_[+1]_18 35637 4.1e-10 361_[+1]_118 6395 6.5e-10 458_[+1]_21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=4 28635 ( 462) CCAACAGCCTCTTCGCCCCAC 1 19141 ( 462) CCAACAGCCTCTTCGCCCCAC 1 35637 ( 362) TCAACACACTATTCCTCCTAC 1 6395 ( 459) CCACCGTCCTTTTACCAACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2880 bayes= 9.48985 E= 6.4e-003 -865 172 -865 0 -865 214 -865 -865 199 -865 -865 -865 157 14 -865 -865 -865 214 -865 -865 157 -865 -12 -865 -865 14 88 0 -1 172 -865 -865 -865 214 -865 -865 -865 -865 -865 200 -1 114 -865 0 -865 -865 -865 200 -865 -865 -865 200 -1 172 -865 -865 -865 114 88 -865 -865 172 -865 0 -1 172 -865 -865 -1 172 -865 -865 -865 172 -865 0 199 -865 -865 -865 -865 214 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 6.4e-003 0.000000 0.750000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.250000 0.500000 0.250000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.500000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.750000 0.000000 0.250000 0.250000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT]CA[AC]C[AG][GCT][CA]CT[CAT]TT[CA][CG][CT][CA][CA][CT]AC -------------------------------------------------------------------------------- Time 0.32 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 19 sites = 5 llr = 91 E-value = 2.3e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :a464:::::4:::::::: pos.-specific C a:242822:8::a2:a:2a probability G ::2::2:8::42:8::26: matrix T ::2:4:8:a228::a:82: bits 2.1 * * * * 1.9 ** * * ** * 1.7 ** * * ** * 1.5 ** ** * ** * Relative 1.3 ** ***** ****** * Entropy 1.1 ** * ***** ****** * (26.2 bits) 0.9 ** * ***** ****** * 0.6 ** * ***** ******** 0.4 ** **************** 0.2 ** **************** 0.0 ------------------- Multilevel CAAAACTGTCATCGTCTGC consensus CCTGCC TGG C GC sequence G C T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 28635 262 2.10e-11 CGGTGCATCC CAACTCTGTCGTCGTCTGC GTCTCGTTTG 19141 262 2.10e-11 CGGTGCATCC CAACTCTGTCGTCGTCTGC GTCTCGTTTG 6395 61 1.06e-08 TCTACCAAAG CACAACCGTCATCCTCGGC TGCAACCGAC bd1754 425 1.13e-08 GTGGCTGTTA CAGAACTGTTAGCGTCTTC AGGACAAGTA 30921 45 2.11e-08 ACACATAATT CATACGTCTCTTCGTCTCC ATCAACTTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 28635 2.1e-11 261_[+2]_220 19141 2.1e-11 261_[+2]_220 6395 1.1e-08 60_[+2]_421 bd1754 1.1e-08 424_[+2]_57 30921 2.1e-08 44_[+2]_437 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=19 seqs=5 28635 ( 262) CAACTCTGTCGTCGTCTGC 1 19141 ( 262) CAACTCTGTCGTCGTCTGC 1 6395 ( 61) CACAACCGTCATCCTCGGC 1 bd1754 ( 425) CAGAACTGTTAGCGTCTTC 1 30921 ( 45) CATACGTCTCTTCGTCTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 2892 bayes= 8.9589 E= 2.3e-002 -897 214 -897 -897 199 -897 -897 -897 67 -18 -44 -32 125 82 -897 -897 67 -18 -897 68 -897 182 -44 -897 -897 -18 -897 168 -897 -18 155 -897 -897 -897 -897 200 -897 182 -897 -32 67 -897 55 -32 -897 -897 -44 168 -897 214 -897 -897 -897 -18 155 -897 -897 -897 -897 200 -897 214 -897 -897 -897 -897 -44 168 -897 -18 114 -32 -897 214 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 5 E= 2.3e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.200000 0.200000 0.200000 0.600000 0.400000 0.000000 0.000000 0.400000 0.200000 0.000000 0.400000 0.000000 0.800000 0.200000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.400000 0.000000 0.400000 0.200000 0.000000 0.000000 0.200000 0.800000 0.000000 1.000000 0.000000 0.000000 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 0.200000 0.800000 0.000000 0.200000 0.600000 0.200000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CA[ACGT][AC][ATC][CG][TC][GC]T[CT][AGT][TG]C[GC]TC[TG][GCT]C -------------------------------------------------------------------------------- Time 0.72 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 6 llr = 102 E-value = 3.2e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :3:::85:2::2283:53:a pos.-specific C 2:a:::2:::558:35:38: probability G 87:a32:a::5:::22::2: matrix T ::::7:3:8a:3:22353:: bits 2.1 * 1.9 ** * * * 1.7 ** * * * 1.5 ** * * * ** Relative 1.3 * ** * *** ** ** Entropy 1.1 ****** **** ** * ** (24.5 bits) 0.9 ****** **** ** * ** 0.6 ************** ** ** 0.4 ************** ***** 0.2 ************** ***** 0.0 -------------------- Multilevel GGCGTAAGTTCCCAACAACA consensus A G T GT CTTC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 28635 203 7.19e-11 TGGGTTGGAT GGCGTATGTTGCCAACAACA GAAAGGAGGT 19141 203 7.19e-11 TGGGTTGGAT GGCGTATGTTGCCAACAACA GAAAGGAGGT 35637 323 7.68e-10 GCGGGCGGTG GGCGGAAGTTCTCACTTTCA AACACAACGC 30921 446 3.08e-08 GCTGCGGTTT GACGTGAGTTCTCTCTTTCA CCATCCTCCC bd1754 156 4.41e-08 TTAGCCATTC CACGGAAGATGCCATCTCCA ATATTGAGCA 6395 148 1.63e-07 ACAAAACACG GGCGTACGTTCAAAGGACGA CTCCAAGAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 28635 7.2e-11 202_[+3]_278 19141 7.2e-11 202_[+3]_278 35637 7.7e-10 322_[+3]_158 30921 3.1e-08 445_[+3]_35 bd1754 4.4e-08 155_[+3]_325 6395 1.6e-07 147_[+3]_333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=6 28635 ( 203) GGCGTATGTTGCCAACAACA 1 19141 ( 203) GGCGTATGTTGCCAACAACA 1 35637 ( 323) GGCGGAAGTTCTCACTTTCA 1 30921 ( 446) GACGTGAGTTCTCTCTTTCA 1 bd1754 ( 156) CACGGAAGATGCCATCTCCA 1 6395 ( 148) GGCGTACGTTCAAAGGACGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 2886 bayes= 8.90689 E= 3.2e-001 -923 -44 161 -923 40 -923 129 -923 -923 214 -923 -923 -923 -923 187 -923 -923 -923 29 142 173 -923 -71 -923 99 -44 -923 42 -923 -923 187 -923 -59 -923 -923 174 -923 -923 -923 200 -923 114 88 -923 -59 114 -923 42 -59 188 -923 -923 173 -923 -923 -58 40 56 -71 -58 -923 114 -71 42 99 -923 -923 100 40 56 -923 42 -923 188 -71 -923 199 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 3.2e-001 0.000000 0.166667 0.833333 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.833333 0.000000 0.166667 0.000000 0.500000 0.166667 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.166667 0.000000 0.000000 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.166667 0.500000 0.000000 0.333333 0.166667 0.833333 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.333333 0.333333 0.166667 0.166667 0.000000 0.500000 0.166667 0.333333 0.500000 0.000000 0.000000 0.500000 0.333333 0.333333 0.000000 0.333333 0.000000 0.833333 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[GA]CG[TG]A[AT]GTT[CG][CT]CA[AC][CT][AT][ACT]CA -------------------------------------------------------------------------------- Time 1.02 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 19141 4.78e-23 202_[+3(7.19e-11)]_39_\ [+2(2.10e-11)]_181_[+1(1.58e-13)]_18 28635 4.78e-23 202_[+3(7.19e-11)]_39_\ [+2(2.10e-11)]_181_[+1(1.58e-13)]_18 30921 9.12e-09 17_[+2(4.20e-05)]_8_[+2(2.11e-08)]_\ 382_[+3(3.08e-08)]_35 35637 1.06e-11 322_[+3(7.68e-10)]_19_\ [+1(4.08e-10)]_118 6395 8.82e-14 60_[+2(1.06e-08)]_68_[+3(1.63e-07)]_\ 65_[+1(9.18e-05)]_205_[+1(6.46e-10)]_21 bd1754 3.21e-08 155_[+3(4.41e-08)]_249_\ [+2(1.13e-08)]_57 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************