******************************************************************************** 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/355/355.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 31433 1.0000 500 46707 1.0000 500 46867 1.0000 500 39392 1.0000 500 43313 1.0000 500 23497 1.0000 500 50141 1.0000 500 18572 1.0000 500 34132 1.0000 500 45509 1.0000 500 35939 1.0000 500 20677 1.0000 500 36276 1.0000 500 49612 1.0000 500 49482 1.0000 500 48899 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/355/355.seqs.fa -oc motifs/355 -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= 16 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= 8000 N= 16 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.281 C 0.235 G 0.220 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.281 C 0.235 G 0.220 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 8 llr = 97 E-value = 2.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4:5:a:1aa:a: pos.-specific C 3538:::::a:9 probability G :1:3:a9::::1 matrix T 443::::::::: bits 2.2 * * 2.0 * * 1.7 ** **** 1.5 ******** Relative 1.3 ********* Entropy 1.1 ********* (17.5 bits) 0.9 ********* 0.7 * ********* 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel ACACAGGAACAC consensus TTCG sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 36276 321 1.41e-07 TCATGAGAAC ACACAGGAACAC ACATATCACG 46707 336 2.78e-07 ACGGACTCCG TTACAGGAACAC CGTGGATGTT 46867 313 3.60e-07 GTGGCGCTGG ATACAGGAACAC AAAATTGTTC 31433 94 5.42e-07 TCCGTGGAAT TCTCAGGAACAC AGATGCTTCC 43313 396 3.03e-06 CTGTAGGCGT ACACAGAAACAC GACTCTAGCG 48899 321 3.34e-06 CAAACGTGTT CTCGAGGAACAC GTTCGATCTG 35939 248 3.60e-06 TCGCCAGAGT TCCCAGGAACAG TCTTCAAAAA 20677 345 6.33e-06 GGTTGAATTT CGTGAGGAACAC TTTCGAACTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36276 1.4e-07 320_[+1]_168 46707 2.8e-07 335_[+1]_153 46867 3.6e-07 312_[+1]_176 31433 5.4e-07 93_[+1]_395 43313 3e-06 395_[+1]_93 48899 3.3e-06 320_[+1]_168 35939 3.6e-06 247_[+1]_241 20677 6.3e-06 344_[+1]_144 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=8 36276 ( 321) ACACAGGAACAC 1 46707 ( 336) TTACAGGAACAC 1 46867 ( 313) ATACAGGAACAC 1 31433 ( 94) TCTCAGGAACAC 1 43313 ( 396) ACACAGAAACAC 1 48899 ( 321) CTCGAGGAACAC 1 35939 ( 248) TCCCAGGAACAG 1 20677 ( 345) CGTGAGGAACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7824 bayes= 9.93221 E= 2.0e+001 42 9 -965 51 -965 109 -81 51 83 9 -965 -8 -965 167 18 -965 183 -965 -965 -965 -965 -965 218 -965 -117 -965 199 -965 183 -965 -965 -965 183 -965 -965 -965 -965 209 -965 -965 183 -965 -965 -965 -965 190 -81 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 8 E= 2.0e+001 0.375000 0.250000 0.000000 0.375000 0.000000 0.500000 0.125000 0.375000 0.500000 0.250000 0.000000 0.250000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.125000 0.000000 0.875000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.875000 0.125000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [ATC][CT][ACT][CG]AGGAACAC -------------------------------------------------------------------------------- Time 2.03 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 19 sites = 9 llr = 131 E-value = 2.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A a8942866:7:2:6aa3:9 pos.-specific C :1:2:21:621214::2:: probability G :1138::241167::::a1 matrix T ::::::32::8:2:::4:: bits 2.2 * 2.0 * 1.7 * ** * 1.5 * ** * Relative 1.3 * * * ** ** Entropy 1.1 * * ** * ** ** (21.0 bits) 0.9 *** ** * * **** ** 0.7 *** ** ******** ** 0.4 ******************* 0.2 ******************* 0.0 ------------------- Multilevel AAAAGAAACATGGAAATGA consensus GACTGGC ATC A sequence C T C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 20677 232 1.84e-09 AGTTGCATAA AAAAGAAACATAGCAAAGA GAAAGTATTG 43313 84 1.08e-08 ATGAACTTGA AAAGGACAGCTGGCAATGA TCACGTGATC 46707 189 5.30e-08 CGAAGGATTC AAACGATACGTGTCAATGA TGTCACGCGT 39392 348 6.45e-08 TAAGGAACAG AGAGGAAGCATCGAAACGA GTTTCCAACT 50141 53 1.03e-07 GACCCGGCAA ACAAGAAAGCTAGAAAAGA TACGCTTTTG 34132 65 1.57e-07 CGGATGTGCC AAAGAAATCACGGAAACGA GGGCGCTGAC 35939 430 2.33e-07 GACCTATGTT AAAAAAAGGATCCAAATGA ATGTAGTGGC 45509 41 3.82e-07 TTGCTGAGAA AAGCGCTAGAGGGAAATGA GACCCAGAGA 31433 308 4.08e-07 ATACGAGAAA AAAAGCTTCATGTCAAAGG AATATAGGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20677 1.8e-09 231_[+2]_250 43313 1.1e-08 83_[+2]_398 46707 5.3e-08 188_[+2]_293 39392 6.5e-08 347_[+2]_134 50141 1e-07 52_[+2]_429 34132 1.6e-07 64_[+2]_417 35939 2.3e-07 429_[+2]_52 45509 3.8e-07 40_[+2]_441 31433 4.1e-07 307_[+2]_174 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=19 seqs=9 20677 ( 232) AAAAGAAACATAGCAAAGA 1 43313 ( 84) AAAGGACAGCTGGCAATGA 1 46707 ( 189) AAACGATACGTGTCAATGA 1 39392 ( 348) AGAGGAAGCATCGAAACGA 1 50141 ( 53) ACAAGAAAGCTAGAAAAGA 1 34132 ( 65) AAAGAAATCACGGAAACGA 1 35939 ( 430) AAAAAAAGGATCCAAATGA 1 45509 ( 41) AAGCGCTAGAGGGAAATGA 1 31433 ( 308) AAAAGCTTCATGTCAAAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 7712 bayes= 9.87573 E= 2.6e+001 183 -982 -982 -982 147 -108 -98 -982 166 -982 -98 -982 66 -8 60 -982 -34 -982 182 -982 147 -8 -982 -982 98 -108 -982 34 98 -982 2 -25 -982 124 101 -982 125 -8 -98 -982 -982 -108 -98 156 -34 -8 134 -982 -982 -108 160 -25 98 92 -982 -982 183 -982 -982 -982 183 -982 -982 -982 25 -8 -982 75 -982 -982 218 -982 166 -982 -98 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 9 E= 2.6e+001 1.000000 0.000000 0.000000 0.000000 0.777778 0.111111 0.111111 0.000000 0.888889 0.000000 0.111111 0.000000 0.444444 0.222222 0.333333 0.000000 0.222222 0.000000 0.777778 0.000000 0.777778 0.222222 0.000000 0.000000 0.555556 0.111111 0.000000 0.333333 0.555556 0.000000 0.222222 0.222222 0.000000 0.555556 0.444444 0.000000 0.666667 0.222222 0.111111 0.000000 0.000000 0.111111 0.111111 0.777778 0.222222 0.222222 0.555556 0.000000 0.000000 0.111111 0.666667 0.222222 0.555556 0.444444 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.222222 0.000000 0.444444 0.000000 0.000000 1.000000 0.000000 0.888889 0.000000 0.111111 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- AAA[AGC][GA][AC][AT][AGT][CG][AC]T[GAC][GT][AC]AA[TAC]GA -------------------------------------------------------------------------------- Time 4.25 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 4 llr = 84 E-value = 5.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::3:8::::38:::::::3:: pos.-specific C 8a::3a:::::3::83:::3a probability G :::a::3aa83835333:38: matrix T 3:8:::8:::::85:58a5:: bits 2.2 * * * ** * 2.0 * * * ** * * 1.7 * * * ** * * 1.5 * * * ** * * Relative 1.3 ** * * *** * * * ** Entropy 1.1 *************** ** ** (30.1 bits) 0.9 *************** ** ** 0.7 *************** ** ** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CCTGACTGGGAGTGCTTTTGC consensus T A C G AGCGTGCG AC sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 23497 306 5.54e-11 AAATCTCTCT CCAGCCTGGGAGTGCCTTTGC CTTTTGGATC 31433 253 1.43e-10 GCTGTTTGTC TCTGACTGGGAGTTGGTTGGC GCTCGTCTGC 46867 243 3.12e-10 TTTTTTTCTT CCTGACTGGGGCTGCTGTTCC AAACGAACAA 43313 183 3.63e-10 AAAAGGGTGT CCTGACGGGAAGGTCTTTAGC TCTCCAAATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23497 5.5e-11 305_[+3]_174 31433 1.4e-10 252_[+3]_227 46867 3.1e-10 242_[+3]_237 43313 3.6e-10 182_[+3]_297 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=4 23497 ( 306) CCAGCCTGGGAGTGCCTTTGC 1 31433 ( 253) TCTGACTGGGAGTTGGTTGGC 1 46867 ( 243) CCTGACTGGGGCTGCTGTTCC 1 43313 ( 183) CCTGACGGGAAGGTCTTTAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7680 bayes= 10.9061 E= 5.5e+002 -865 167 -865 -8 -865 209 -865 -865 -17 -865 -865 150 -865 -865 218 -865 141 9 -865 -865 -865 209 -865 -865 -865 -865 18 150 -865 -865 218 -865 -865 -865 218 -865 -17 -865 177 -865 141 -865 18 -865 -865 9 177 -865 -865 -865 18 150 -865 -865 118 92 -865 167 18 -865 -865 9 18 92 -865 -865 18 150 -865 -865 -865 192 -17 -865 18 92 -865 9 177 -865 -865 209 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 5.5e+002 0.000000 0.750000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.500000 0.500000 0.000000 0.750000 0.250000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.250000 0.500000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT]C[TA]G[AC]C[TG]GG[GA][AG][GC][TG][GT][CG][TCG][TG]T[TAG][GC]C -------------------------------------------------------------------------------- Time 6.36 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31433 2.10e-12 93_[+1(5.42e-07)]_147_\ [+3(1.43e-10)]_34_[+2(4.08e-07)]_174 46707 4.72e-07 188_[+2(5.30e-08)]_128_\ [+1(2.78e-07)]_153 46867 1.87e-09 55_[+3(7.99e-05)]_166_\ [+3(3.12e-10)]_49_[+1(3.60e-07)]_176 39392 2.70e-04 347_[+2(6.45e-08)]_134 43313 8.31e-13 83_[+2(1.08e-08)]_80_[+3(3.63e-10)]_\ 192_[+1(3.03e-06)]_93 23497 1.11e-06 305_[+3(5.54e-11)]_174 50141 5.00e-04 52_[+2(1.03e-07)]_429 18572 7.72e-01 500 34132 1.16e-03 64_[+2(1.57e-07)]_417 45509 1.60e-03 40_[+2(3.82e-07)]_441 35939 1.18e-06 247_[+1(3.60e-06)]_112_\ [+3(6.38e-05)]_37_[+2(2.33e-07)]_52 20677 1.81e-07 231_[+2(1.84e-09)]_94_\ [+1(6.33e-06)]_144 36276 1.91e-03 320_[+1(1.41e-07)]_168 49612 7.23e-01 500 49482 7.96e-01 500 48899 2.07e-02 320_[+1(3.34e-06)]_168 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************