******************************************************************************** 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/275/275.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 49118 1.0000 500 15913 1.0000 500 50292 1.0000 500 43799 1.0000 500 46067 1.0000 500 5702 1.0000 500 31636 1.0000 500 47105 1.0000 500 32553 1.0000 500 36107 1.0000 500 36988 1.0000 500 37220 1.0000 500 37240 1.0000 500 35540 1.0000 500 34603 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/275/275.seqs.fa -oc motifs/275 -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= 15 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= 7500 N= 15 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.276 C 0.235 G 0.212 T 0.277 Background letter frequencies (from dataset with add-one prior applied): A 0.276 C 0.235 G 0.212 T 0.277 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 4 llr = 116 E-value = 1.4e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :a:a:::::a:a::3:::a:: pos.-specific C a:a::aaaa:a:::8aa::a: probability G ::::a:::::::a:::::::a matrix T :::::::::::::a:::a::: bits 2.2 * * * 2.0 * * ***** * * ** ** 1.8 ************** ****** 1.6 ************** ****** Relative 1.3 ************** ****** Entropy 1.1 ********************* (41.8 bits) 0.9 ********************* 0.7 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CACAGCCCCACAGTCCCTACG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 37220 315 1.41e-13 CACAACAAAT CACAGCCCCACAGTCCCTACG AATATCCAAG 32553 315 1.41e-13 CACAACGAAT CACAGCCCCACAGTCCCTACG AATATCCAAG 49118 290 1.41e-13 CACAACGAAT CACAGCCCCACAGTCCCTACG AATATCCAAG 36988 315 3.07e-13 CACAACAAAT CACAGCCCCACAGTACCTACG AATATCCATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37220 1.4e-13 314_[+1]_165 32553 1.4e-13 314_[+1]_165 49118 1.4e-13 289_[+1]_190 36988 3.1e-13 314_[+1]_165 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=4 37220 ( 315) CACAGCCCCACAGTCCCTACG 1 32553 ( 315) CACAGCCCCACAGTCCCTACG 1 49118 ( 290) CACAGCCCCACAGTCCCTACG 1 36988 ( 315) CACAGCCCCACAGTACCTACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7200 bayes= 10.813 E= 1.4e-009 -865 209 -865 -865 185 -865 -865 -865 -865 209 -865 -865 185 -865 -865 -865 -865 -865 223 -865 -865 209 -865 -865 -865 209 -865 -865 -865 209 -865 -865 -865 209 -865 -865 185 -865 -865 -865 -865 209 -865 -865 185 -865 -865 -865 -865 -865 223 -865 -865 -865 -865 185 -14 167 -865 -865 -865 209 -865 -865 -865 209 -865 -865 -865 -865 -865 185 185 -865 -865 -865 -865 209 -865 -865 -865 -865 223 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 1.4e-009 0.000000 1.000000 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CACAGCCCCACAGT[CA]CCTACG -------------------------------------------------------------------------------- Time 1.93 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 4 llr = 113 E-value = 3.3e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A a::a:a8::::::a::a:aa: pos.-specific C ::::a::a::a:8:aa::::: probability G :aa:::3:a::::::::a::a matrix T :::::::::a:a3:::::::: bits 2.2 ** * * * 2.0 ** * ** * ** * * 1.8 ****** ***** ******** 1.6 ****** ***** ******** Relative 1.3 ****** ***** ******** Entropy 1.1 ********************* (40.7 bits) 0.9 ********************* 0.7 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel AGGACAACGTCTCACCAGAAG consensus G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 37220 241 1.86e-13 ACTCCTGGTA AGGACAACGTCTCACCAGAAG TTCAATCGCC 36988 241 1.86e-13 ACTCCATGTA AGGACAACGTCTCACCAGAAG TTCAATCGCG 32553 241 1.86e-13 ACTTCTGGTA AGGACAACGTCTCACCAGAAG TTCAATCGCC 49118 216 7.18e-13 ACTCCTGGTA AGGACAGCGTCTTACCAGAAG TTCAATCGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37220 1.9e-13 240_[+2]_239 36988 1.9e-13 240_[+2]_239 32553 1.9e-13 240_[+2]_239 49118 7.2e-13 215_[+2]_264 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=4 37220 ( 241) AGGACAACGTCTCACCAGAAG 1 36988 ( 241) AGGACAACGTCTCACCAGAAG 1 32553 ( 241) AGGACAACGTCTCACCAGAAG 1 49118 ( 216) AGGACAGCGTCTTACCAGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7200 bayes= 10.813 E= 3.3e-008 185 -865 -865 -865 -865 -865 223 -865 -865 -865 223 -865 185 -865 -865 -865 -865 209 -865 -865 185 -865 -865 -865 144 -865 24 -865 -865 209 -865 -865 -865 -865 223 -865 -865 -865 -865 185 -865 209 -865 -865 -865 -865 -865 185 -865 167 -865 -15 185 -865 -865 -865 -865 209 -865 -865 -865 209 -865 -865 185 -865 -865 -865 -865 -865 223 -865 185 -865 -865 -865 185 -865 -865 -865 -865 -865 223 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 3.3e-008 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 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 0.750000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 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 0.750000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- AGGACA[AG]CGTCT[CT]ACCAGAAG -------------------------------------------------------------------------------- Time 3.58 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 7 llr = 140 E-value = 5.4e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :991a:a63:7139a1:9a:: pos.-specific C 71:::1::71:61:::a::7a probability G ::1::9:4:33:61:9:1::: matrix T 3::9:::::6:3:::::::3: bits 2.2 2.0 * * 1.8 * * * * * * 1.6 *** *** * * Relative 1.3 ****** ****** * Entropy 1.1 ********* * ******** (28.9 bits) 0.9 ********* * ******** 0.7 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CAATAGAACTACGAAGCAACC consensus T GAGGTA T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 36988 422 5.58e-13 TTGTGTTCAT CAATAGAACTACGAAGCAACC TAAGCGTCTC 32553 421 5.58e-13 TTGTGTTCAT CAATAGAACTACGAAGCAACC CCTCCGTCTT 49118 397 5.58e-13 TTGTGTTCTT CAATAGAACTACGAAGCAACC CCTCCGTCTT 37220 421 2.80e-12 TTGTGTTCAT CAATAGAACTACAAAGCAACC CCCCCGTCTT 46067 157 8.34e-09 ACTTTACTGT TAGTAGAGCGGAGAAACAATC CTTTATTTGA 5702 190 1.26e-08 CCAGTACATA TAATAGAGAGGTAGAGCGATC AAGTAGCTGC 37240 90 1.57e-08 CGGAACTTAC CCAAACAGACATCAAGCAACC CAGTGAAAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36988 5.6e-13 421_[+3]_58 32553 5.6e-13 420_[+3]_59 49118 5.6e-13 396_[+3]_83 37220 2.8e-12 420_[+3]_59 46067 8.3e-09 156_[+3]_323 5702 1.3e-08 189_[+3]_290 37240 1.6e-08 89_[+3]_390 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=7 36988 ( 422) CAATAGAACTACGAAGCAACC 1 32553 ( 421) CAATAGAACTACGAAGCAACC 1 49118 ( 397) CAATAGAACTACGAAGCAACC 1 37220 ( 421) CAATAGAACTACAAAGCAACC 1 46067 ( 157) TAGTAGAGCGGAGAAACAATC 1 5702 ( 190) TAATAGAGAGGTAGAGCGATC 1 37240 ( 90) CCAAACAGACATCAAGCAACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7200 bayes= 10.6112 E= 5.4e-008 -945 160 -945 5 163 -71 -945 -945 163 -945 -57 -945 -95 -945 -945 163 185 -945 -945 -945 -945 -71 201 -945 185 -945 -945 -945 105 -945 101 -945 5 160 -945 -945 -945 -71 43 104 137 -945 43 -945 -95 128 -945 5 5 -71 143 -945 163 -945 -57 -945 185 -945 -945 -945 -95 -945 201 -945 -945 209 -945 -945 163 -945 -57 -945 185 -945 -945 -945 -945 160 -945 5 -945 209 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 5.4e-008 0.000000 0.714286 0.000000 0.285714 0.857143 0.142857 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.142857 0.000000 0.000000 0.857143 1.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.857143 0.000000 1.000000 0.000000 0.000000 0.000000 0.571429 0.000000 0.428571 0.000000 0.285714 0.714286 0.000000 0.000000 0.000000 0.142857 0.285714 0.571429 0.714286 0.000000 0.285714 0.000000 0.142857 0.571429 0.000000 0.285714 0.285714 0.142857 0.571429 0.000000 0.857143 0.000000 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.857143 0.000000 0.000000 1.000000 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.714286 0.000000 0.285714 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT]AATAGA[AG][CA][TG][AG][CT][GA]AAGCAA[CT]C -------------------------------------------------------------------------------- Time 5.41 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49118 1.46e-26 215_[+2(7.18e-13)]_53_\ [+1(1.41e-13)]_86_[+3(5.58e-13)]_21_[+1(1.48e-05)]_41 15913 3.86e-01 500 50292 1.70e-01 456_[+1(5.32e-05)]_23 43799 9.94e-01 500 46067 2.73e-04 156_[+3(8.34e-09)]_323 5702 6.35e-05 189_[+3(1.26e-08)]_290 31636 2.54e-01 500 47105 9.99e-01 500 32553 3.94e-27 240_[+2(1.86e-13)]_53_\ [+1(1.41e-13)]_85_[+3(5.58e-13)]_59 36107 2.15e-01 500 36988 8.38e-27 240_[+2(1.86e-13)]_53_\ [+1(3.07e-13)]_86_[+3(5.58e-13)]_58 37220 1.88e-26 140_[+3(1.70e-05)]_79_\ [+2(1.86e-13)]_53_[+1(1.41e-13)]_85_[+3(2.80e-12)]_59 37240 1.68e-04 89_[+3(1.57e-08)]_390 35540 5.65e-01 500 34603 2.23e-01 293_[+3(8.34e-05)]_186 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************