******************************************************************************** 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/263/263.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 51404 1.0000 500 15577 1.0000 500 16875 1.0000 500 12368 1.0000 500 4016 1.0000 500 47226 1.0000 500 40603 1.0000 500 47927 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/263/263.seqs.fa -oc motifs/263 -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= 8 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= 4000 N= 8 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.254 C 0.246 G 0.257 T 0.242 Background letter frequencies (from dataset with add-one prior applied): A 0.254 C 0.247 G 0.257 T 0.243 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 3 llr = 54 E-value = 3.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :3:::::::::::::: pos.-specific C :73:7:3:a::3a37: probability G ::7::::::::::::a matrix T a::a3a7a:aa7:73: bits 2.0 * * * **** * * 1.8 * * * **** * * 1.6 * * * **** * * 1.4 * * * **** * * Relative 1.2 * * * **** * * Entropy 1.0 **************** (26.0 bits) 0.8 **************** 0.6 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel TCGTCTTTCTTTCTCG consensus AC T C C CT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 15577 71 1.44e-09 TTCTGCTGAC TCGTCTCTCTTTCTCG AAACTGGATG 12368 405 7.47e-09 CTTACGGTTG TCCTCTTTCTTTCCTG ACAAGAAGCT 51404 148 1.07e-08 GAGGCGCTCC TAGTTTTTCTTCCTCG CCGATCCCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 15577 1.4e-09 70_[+1]_414 12368 7.5e-09 404_[+1]_80 51404 1.1e-08 147_[+1]_337 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=3 15577 ( 71) TCGTCTCTCTTTCTCG 1 12368 ( 405) TCCTCTTTCTTTCCTG 1 51404 ( 148) TAGTTTTTCTTCCTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 3880 bayes= 9.99443 E= 3.1e+002 -823 -823 -823 204 39 143 -823 -823 -823 43 137 -823 -823 -823 -823 204 -823 143 -823 46 -823 -823 -823 204 -823 43 -823 146 -823 -823 -823 204 -823 202 -823 -823 -823 -823 -823 204 -823 -823 -823 204 -823 43 -823 146 -823 202 -823 -823 -823 43 -823 146 -823 143 -823 46 -823 -823 196 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 3 E= 3.1e+002 0.000000 0.000000 0.000000 1.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[CA][GC]T[CT]T[TC]TCTT[TC]C[TC][CT]G -------------------------------------------------------------------------------- Time 0.59 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 14 sites = 5 llr = 70 E-value = 9.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :2:::a:::a:2:: pos.-specific C :8284::22:8::: probability G :::24:::6:2:8: matrix T a:8:2:a82::82a bits 2.0 * ** * * 1.8 * ** * * 1.6 * ** * * 1.4 * ** * * Relative 1.2 **** *** ***** Entropy 1.0 **** *** ***** (20.2 bits) 0.8 **** *** ***** 0.6 **** ********* 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel TCTCCATTGACTGT consensus ACGG CC GAT sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 16875 367 2.57e-08 AGCTGTGAAC TCTCCATTGACTTT TTGGAATCCG 47226 5 9.92e-08 CATG TCTGTATTGACTGT GAATTGAGCG 51404 168 1.24e-07 TCCTCGCCGA TCCCCATTCACTGT AATTTCGACT 40603 449 1.90e-07 CGCATCTACC TCTCGATTTACAGT AGTTATAGGA 47927 202 9.57e-07 GGGACGGCTC TATCGATCGAGTGT GTCTGTGAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 16875 2.6e-08 366_[+2]_120 47226 9.9e-08 4_[+2]_482 51404 1.2e-07 167_[+2]_319 40603 1.9e-07 448_[+2]_38 47927 9.6e-07 201_[+2]_285 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=14 seqs=5 16875 ( 367) TCTCCATTGACTTT 1 47226 ( 5) TCTGTATTGACTGT 1 51404 ( 168) TCCCCATTCACTGT 1 40603 ( 449) TCTCGATTTACAGT 1 47927 ( 202) TATCGATCGAGTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 3896 bayes= 9.85583 E= 9.6e+001 -897 -897 -897 204 -34 170 -897 -897 -897 -30 -897 172 -897 170 -36 -897 -897 70 64 -28 197 -897 -897 -897 -897 -897 -897 204 -897 -30 -897 172 -897 -30 122 -28 197 -897 -897 -897 -897 170 -36 -897 -34 -897 -897 172 -897 -897 164 -28 -897 -897 -897 204 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 5 E= 9.6e+001 0.000000 0.000000 0.000000 1.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.800000 0.200000 0.000000 0.000000 0.400000 0.400000 0.200000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.200000 0.600000 0.200000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[CA][TC][CG][CGT]AT[TC][GCT]A[CG][TA][GT]T -------------------------------------------------------------------------------- Time 1.17 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 4 llr = 53 E-value = 6.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::a:::::::: pos.-specific C :83:38:5::3: probability G ::8::3:5:::: matrix T a3::8:a:aa8a bits 2.0 * * * ** * 1.8 * * * ** * 1.6 * * * ** * 1.4 * * * ** * Relative 1.2 ******* **** Entropy 1.0 ************ (19.2 bits) 0.8 ************ 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TCGATCTCTTTT consensus TC CG G C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 47927 279 1.00e-07 AACAGCGGCA TCGATCTCTTTT CCCTTGGACT 15577 489 1.97e-07 AGTGATAGAA TCCATCTCTTTT 47226 88 1.62e-06 CAAGTTTGGG TTGATGTGTTTT TACTGTTAAC 12368 281 1.62e-06 CTGGAGTGTG TCGACCTGTTCT GGCCACCAGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47927 1e-07 278_[+3]_210 15577 2e-07 488_[+3] 47226 1.6e-06 87_[+3]_401 12368 1.6e-06 280_[+3]_208 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=4 47927 ( 279) TCGATCTCTTTT 1 15577 ( 489) TCCATCTCTTTT 1 47226 ( 88) TTGATGTGTTTT 1 12368 ( 281) TCGACCTGTTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 3912 bayes= 10.6698 E= 6.7e+002 -865 -865 -865 204 -865 160 -865 4 -865 2 154 -865 197 -865 -865 -865 -865 2 -865 163 -865 160 -4 -865 -865 -865 -865 204 -865 102 96 -865 -865 -865 -865 204 -865 -865 -865 204 -865 2 -865 163 -865 -865 -865 204 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 4 E= 6.7e+002 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.250000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[CT][GC]A[TC][CG]T[CG]TT[TC]T -------------------------------------------------------------------------------- Time 1.83 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 51404 4.30e-08 147_[+1(1.07e-08)]_4_[+2(1.24e-07)]_\ 319 15577 4.83e-09 70_[+1(1.44e-09)]_17_[+3(4.66e-06)]_\ 373_[+3(1.97e-07)] 16875 2.82e-05 366_[+2(2.57e-08)]_120 12368 5.56e-07 280_[+3(1.62e-06)]_112_\ [+1(7.47e-09)]_80 4016 8.17e-01 500 47226 1.89e-06 4_[+2(9.92e-08)]_69_[+3(1.62e-06)]_\ 401 40603 2.98e-03 448_[+2(1.90e-07)]_38 47927 3.35e-07 201_[+2(9.57e-07)]_63_\ [+3(1.00e-07)]_210 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************