******************************************************************************** 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/10/10.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 43087 1.0000 500 47752 1.0000 500 48128 1.0000 500 38966 1.0000 500 48867 1.0000 500 44994 1.0000 500 44995 1.0000 500 8282 1.0000 500 48379 1.0000 500 43971 1.0000 500 34433 1.0000 500 39443 1.0000 500 33704 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/10/10.seqs.fa -oc motifs/10 -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= 13 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= 6500 N= 13 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.298 C 0.214 G 0.204 T 0.285 Background letter frequencies (from dataset with add-one prior applied): A 0.298 C 0.214 G 0.204 T 0.285 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 19 sites = 9 llr = 127 E-value = 2.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::427::7689:7248a pos.-specific C ::1331:6a:1219213:: probability G :::4::14:33::1:121: matrix T aa92272:::::::16:1: bits 2.3 * 2.1 * 1.8 ** * * * 1.6 ** * * * Relative 1.4 *** ** ** * Entropy 1.1 *** ** *** * (20.4 bits) 0.9 *** *** *** ** 0.7 **** ********** ** 0.5 *************** *** 0.2 ******************* 0.0 ------------------- Multilevel TTTGATACCAAAACATAAA consensus CCATG GGC CAC sequence TT G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 44994 415 3.79e-10 TGCAGATGAA TTTGATAGCAGAACATAAA ATCAGTTGTG 38966 458 2.93e-08 TTCACAATTT TTTTCTACCGAAACAGCAA ACCAGGAAAA 47752 31 2.93e-08 CGATGTCGGT TTTCTTTGCGGAACATCAA AATCGCGAAA 44995 411 3.29e-08 TCTCAGATGA TTTTATGCCAGAACATAAA AGTCGATTGG 33704 179 1.56e-07 TCCACCGTAC TTTGCATCCAAAACTTAAA TTGGAAACTT 48379 169 3.81e-07 CTCTTGCCTA TTTCTTAGCAAAACCAATA GTCAATCTTT 34433 430 7.86e-07 GAGCACACAA TTTCCAACCAACCCACGAA AATACCATTT 48867 365 8.33e-07 CCATGAAGAC TTCGACAGCAAAAGATGAA AAGGCTCGTC 43087 219 8.33e-07 TAGCGAATCA TTTGATACCGCCACCACGA CTGTTTTCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44994 3.8e-10 414_[+1]_67 38966 2.9e-08 457_[+1]_24 47752 2.9e-08 30_[+1]_451 44995 3.3e-08 410_[+1]_71 33704 1.6e-07 178_[+1]_303 48379 3.8e-07 168_[+1]_313 34433 7.9e-07 429_[+1]_52 48867 8.3e-07 364_[+1]_117 43087 8.3e-07 218_[+1]_263 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=19 seqs=9 44994 ( 415) TTTGATAGCAGAACATAAA 1 38966 ( 458) TTTTCTACCGAAACAGCAA 1 47752 ( 31) TTTCTTTGCGGAACATCAA 1 44995 ( 411) TTTTATGCCAGAACATAAA 1 33704 ( 179) TTTGCATCCAAAACTTAAA 1 48379 ( 169) TTTCTTAGCAAAACCAATA 1 34433 ( 430) TTTCCAACCAACCCACGAA 1 48867 ( 365) TTCGACAGCAAAAGATGAA 1 43087 ( 219) TTTGATACCGCCACCACGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 6266 bayes= 9.57582 E= 2.0e+001 -982 -982 -982 181 -982 -982 -982 181 -982 -94 -982 164 -982 64 112 -36 58 64 -982 -36 -42 -94 -982 123 116 -982 -88 -36 -982 138 112 -982 -982 222 -982 -982 116 -982 71 -982 90 -94 71 -982 139 6 -982 -982 158 -94 -982 -982 -982 206 -88 -982 116 6 -982 -136 -42 -94 -88 96 58 64 12 -982 139 -982 -88 -136 175 -982 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 9 E= 2.0e+001 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.111111 0.000000 0.888889 0.000000 0.333333 0.444444 0.222222 0.444444 0.333333 0.000000 0.222222 0.222222 0.111111 0.000000 0.666667 0.666667 0.000000 0.111111 0.222222 0.000000 0.555556 0.444444 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.555556 0.111111 0.333333 0.000000 0.777778 0.222222 0.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.000000 0.888889 0.111111 0.000000 0.666667 0.222222 0.000000 0.111111 0.222222 0.111111 0.111111 0.555556 0.444444 0.333333 0.222222 0.000000 0.777778 0.000000 0.111111 0.111111 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TTT[GCT][ACT][TA][AT][CG]C[AG][AG][AC]AC[AC][TA][ACG]AA -------------------------------------------------------------------------------- Time 1.60 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 6 llr = 108 E-value = 6.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 3::3::::3:727835:328: pos.-specific C ::::2:7a:8:822::7:22: probability G 7:7:383::2::2:7:377:: matrix T :a3752::7:3::::5::::a bits 2.3 * 2.1 * 1.8 * * * 1.6 * * * * * * Relative 1.4 * *** * * * * Entropy 1.1 *** *** * * ** ** ** (25.9 bits) 0.9 **** ******* ** ***** 0.7 ********************* 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GTGTTGCCTCACAAGACGGAT consensus A TAG G A T ATGA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 44995 466 4.55e-12 CTTTCGTGTA GTGTTGCCTCACAAGTCAGAT TCTAAACGGC 43087 441 6.61e-10 CCGAGCATCG GTGTGTGCTCACAAAACGGAT TGCAAGGGGC 33704 75 1.95e-09 AGACGCTTCC GTTACGGCTCACAAGACGGCT CGTCATGATG 43971 87 5.75e-09 AACCTTGGTC ATTATGCCTCTCAAGAGGCAT AGTTAGATTT 47752 311 1.09e-08 GCACCGAATA GTGTGGCCAGACCAATCGAAT CGGTCGACGG 48867 398 4.65e-08 CTCGTCCCAT ATGTTGCCACTAGCGTGAGAT TTGAAAATCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44995 4.5e-12 465_[+2]_14 43087 6.6e-10 440_[+2]_39 33704 1.9e-09 74_[+2]_405 43971 5.7e-09 86_[+2]_393 47752 1.1e-08 310_[+2]_169 48867 4.7e-08 397_[+2]_82 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=6 44995 ( 466) GTGTTGCCTCACAAGTCAGAT 1 43087 ( 441) GTGTGTGCTCACAAAACGGAT 1 33704 ( 75) GTTACGGCTCACAAGACGGCT 1 43971 ( 87) ATTATGCCTCTCAAGAGGCAT 1 47752 ( 311) GTGTGGCCAGACCAATCGAAT 1 48867 ( 398) ATGTTGCCACTAGCGTGAGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6240 bayes= 10.4688 E= 6.6e+001 16 -923 171 -923 -923 -923 -923 181 -923 -923 171 23 16 -923 -923 123 -923 -36 71 81 -923 -923 203 -77 -923 164 71 -923 -923 222 -923 -923 16 -923 -923 123 -923 196 -29 -923 116 -923 -923 23 -83 196 -923 -923 116 -36 -29 -923 148 -36 -923 -923 16 -923 171 -923 75 -923 -923 81 -923 164 71 -923 16 -923 171 -923 -83 -36 171 -923 148 -36 -923 -923 -923 -923 -923 181 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 6.6e+001 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.333333 0.000000 0.000000 0.666667 0.000000 0.166667 0.333333 0.500000 0.000000 0.000000 0.833333 0.166667 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.833333 0.166667 0.000000 0.666667 0.000000 0.000000 0.333333 0.166667 0.833333 0.000000 0.000000 0.666667 0.166667 0.166667 0.000000 0.833333 0.166667 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.666667 0.333333 0.000000 0.333333 0.000000 0.666667 0.000000 0.166667 0.166667 0.666667 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA]T[GT][TA][TG]G[CG]C[TA]C[AT]CAA[GA][AT][CG][GA]GAT -------------------------------------------------------------------------------- Time 2.98 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 8 llr = 91 E-value = 6.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::511::::a1 pos.-specific C ::a113:41a:1 probability G 3::1::a6:::: matrix T 8a:386::9::8 bits 2.3 * * * 2.1 * * * 1.8 ** * ** 1.6 ** * ** Relative 1.4 ** ***** Entropy 1.1 *** ***** (16.4 bits) 0.9 *** ***** 0.7 *** ******** 0.5 *** ******** 0.2 ************ 0.0 ------------ Multilevel TTCATTGGTCAT consensus G T C C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 43087 383 9.07e-08 GAAGATTAGG TTCATTGGTCAT TGATTGCACC 44994 208 4.68e-07 CCAATAATAA TTCGTTGGTCAT TCAAGCACGA 39443 14 1.87e-06 TTTCTTCGTC GTCATCGCTCAT GGTGAACTCC 34433 82 4.64e-06 TTTTTTTATT TTCTTTGCTCAC ATTATTGTCA 48379 120 4.64e-06 ACATGATTTT GTCAATGGTCAT TTTACGACCA 48128 381 4.64e-06 AGTTCCGCCC TTCATCGCCCAT TTTTTTGCGT 48867 448 5.73e-06 CGATCTTATA TTCCTTGGTCAA CAAGATCGGG 33704 283 1.13e-05 AGTAAGCTTT TTCTCAGGTCAT TCTGGAACGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43087 9.1e-08 382_[+3]_106 44994 4.7e-07 207_[+3]_281 39443 1.9e-06 13_[+3]_475 34433 4.6e-06 81_[+3]_407 48379 4.6e-06 119_[+3]_369 48128 4.6e-06 380_[+3]_108 48867 5.7e-06 447_[+3]_41 33704 1.1e-05 282_[+3]_206 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=8 43087 ( 383) TTCATTGGTCAT 1 44994 ( 208) TTCGTTGGTCAT 1 39443 ( 14) GTCATCGCTCAT 1 34433 ( 82) TTCTTTGCTCAC 1 48379 ( 120) GTCAATGGTCAT 1 48128 ( 381) TTCATCGCCCAT 1 48867 ( 448) TTCCTTGGTCAA 1 33704 ( 283) TTCTCAGGTCAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6357 bayes= 9.63231 E= 6.2e+002 -965 -965 29 140 -965 -965 -965 181 -965 222 -965 -965 75 -77 -71 -19 -125 -77 -965 140 -125 23 -965 113 -965 -965 229 -965 -965 81 161 -965 -965 -77 -965 162 -965 222 -965 -965 175 -965 -965 -965 -125 -77 -965 140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 8 E= 6.2e+002 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.125000 0.125000 0.250000 0.125000 0.125000 0.000000 0.750000 0.125000 0.250000 0.000000 0.625000 0.000000 0.000000 1.000000 0.000000 0.000000 0.375000 0.625000 0.000000 0.000000 0.125000 0.000000 0.875000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.125000 0.125000 0.000000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TG]TC[AT]T[TC]G[GC]TCAT -------------------------------------------------------------------------------- Time 4.42 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43087 3.23e-12 36_[+2(9.94e-05)]_161_\ [+1(8.33e-07)]_145_[+3(9.07e-08)]_46_[+2(6.61e-10)]_39 47752 1.48e-08 30_[+1(2.93e-08)]_261_\ [+2(1.09e-08)]_169 48128 5.23e-02 380_[+3(4.64e-06)]_108 38966 7.03e-04 457_[+1(2.93e-08)]_24 48867 8.11e-09 364_[+1(8.33e-07)]_14_\ [+2(4.65e-08)]_29_[+3(5.73e-06)]_41 44994 7.92e-09 207_[+3(4.68e-07)]_195_\ [+1(3.79e-10)]_47_[+1(9.91e-05)]_1 44995 1.42e-11 410_[+1(3.29e-08)]_36_\ [+2(4.55e-12)]_14 8282 8.94e-01 500 48379 3.43e-05 119_[+3(4.64e-06)]_37_\ [+1(3.81e-07)]_313 43971 3.89e-05 86_[+2(5.75e-09)]_393 34433 2.63e-05 81_[+3(4.64e-06)]_336_\ [+1(7.86e-07)]_52 39443 1.11e-02 13_[+3(1.87e-06)]_475 33704 1.70e-10 74_[+2(1.95e-09)]_83_[+1(1.56e-07)]_\ 85_[+3(1.13e-05)]_206 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************