******************************************************************************** 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/324/324.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10671 1.0000 500 17651 1.0000 500 1783 1.0000 500 18076 1.0000 500 22699 1.0000 500 23345 1.0000 500 23548 1.0000 500 23800 1.0000 500 24412 1.0000 500 24462 1.0000 500 262083 1.0000 500 264690 1.0000 500 269690 1.0000 500 39143 1.0000 500 41829 1.0000 500 4352 1.0000 500 7420 1.0000 500 9045 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/324/324.seqs.fa -oc motifs/324 -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= 18 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= 9000 N= 18 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.267 C 0.232 G 0.225 T 0.276 Background letter frequencies (from dataset with add-one prior applied): A 0.267 C 0.232 G 0.225 T 0.276 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 7 llr = 128 E-value = 2.3e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 919:111a::a1a71791::: pos.-specific C 1:141::::::::3:::14:1 probability G :3:4497:aa:9::731:11: matrix T :6:13:1:::::::1::7499 bits 2.1 ** 1.9 **** * 1.7 **** * 1.5 * ****** Relative 1.3 * * * ****** * ** Entropy 1.1 * * * ******* ** ** (26.5 bits) 0.9 * * ************ ** 0.6 **** **************** 0.4 **** **************** 0.2 ********************* 0.0 --------------------- Multilevel ATACGGGAGGAGAAGAATCTT consensus G GT C G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 9045 121 4.64e-13 GGGAAACCGG ATACGGGAGGAGAAGAATCTT GCTGTCCATT 24462 326 4.64e-13 GGGAAACCGG ATACGGGAGGAGAAGAATCTT GCTGTCCATT 4352 380 6.43e-09 CTACCAGTGC AGAGCAGAGGAGACGGATGTT CATAGTCACT 23345 322 6.90e-09 AGATTTGGCA ATCTTGGAGGAGAATGATTTT GCCAGAAGAC 264690 179 9.61e-09 GATCAGTGGA AAAGAGGAGGAAACGAACCTT GTCATCTCCT 24412 190 1.23e-08 GAAAGTGACA CTACGGTAGGAGAAAAGTTTT CGATTGTGTT 18076 33 2.19e-08 GTGGAAGATG AGAGTGAAGGAGAAGAAATGC CGTTAGGTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9045 4.6e-13 120_[+1]_359 24462 4.6e-13 325_[+1]_154 4352 6.4e-09 379_[+1]_100 23345 6.9e-09 321_[+1]_158 264690 9.6e-09 178_[+1]_301 24412 1.2e-08 189_[+1]_290 18076 2.2e-08 32_[+1]_447 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=7 9045 ( 121) ATACGGGAGGAGAAGAATCTT 1 24462 ( 326) ATACGGGAGGAGAAGAATCTT 1 4352 ( 380) AGAGCAGAGGAGACGGATGTT 1 23345 ( 322) ATCTTGGAGGAGAATGATTTT 1 264690 ( 179) AAAGAGGAGGAAACGAACCTT 1 24412 ( 190) CTACGGTAGGAGAAAAGTTTT 1 18076 ( 33) AGAGTGAAGGAGAAGAAATGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 8640 bayes= 10.112 E= 2.3e-003 168 -70 -945 -945 -90 -945 34 105 168 -70 -945 -945 -945 89 93 -95 -90 -70 93 5 -90 -945 193 -945 -90 -945 166 -95 190 -945 -945 -945 -945 -945 215 -945 -945 -945 215 -945 190 -945 -945 -945 -90 -945 193 -945 190 -945 -945 -945 142 30 -945 -945 -90 -945 166 -95 142 -945 34 -945 168 -945 -66 -945 -90 -70 -945 137 -945 89 -66 64 -945 -945 -66 163 -945 -70 -945 163 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 2.3e-003 0.857143 0.142857 0.000000 0.000000 0.142857 0.000000 0.285714 0.571429 0.857143 0.142857 0.000000 0.000000 0.000000 0.428571 0.428571 0.142857 0.142857 0.142857 0.428571 0.285714 0.142857 0.000000 0.857143 0.000000 0.142857 0.000000 0.714286 0.142857 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 0.142857 0.000000 0.857143 0.000000 1.000000 0.000000 0.000000 0.000000 0.714286 0.285714 0.000000 0.000000 0.142857 0.000000 0.714286 0.142857 0.714286 0.000000 0.285714 0.000000 0.857143 0.000000 0.142857 0.000000 0.142857 0.142857 0.000000 0.714286 0.000000 0.428571 0.142857 0.428571 0.000000 0.000000 0.142857 0.857143 0.000000 0.142857 0.000000 0.857143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[TG]A[CG][GT]GGAGGAGA[AC]G[AG]AT[CT]TT -------------------------------------------------------------------------------- Time 3.10 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 4 llr = 93 E-value = 2.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A a:8a::::8a::::3:::5:: pos.-specific C ::3:a8:33:a3:a:8aa5:8 probability G :a:::388:::3::::::::3 matrix T ::::::3::::5a:83:::a: bits 2.1 * * * * ** 1.9 ** ** ** ** ** * 1.7 ** ** ** ** ** * 1.5 ** ** ** ** ** * Relative 1.3 ** ***** ** ** *** ** Entropy 1.1 *********** ********* (33.4 bits) 0.9 *********** ********* 0.6 *********** ********* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel AGAACCGGAACTTCTCCCATC consensus C GTCC C AT C G sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 9045 251 3.76e-13 TAAAGAGTCC AGAACCGGAACTTCTCCCATC CATCAACCAC 24462 456 3.76e-13 TAAAGAGTCC AGAACCGGAACTTCTCCCATC CATCAACCAC 23800 292 1.24e-10 TCCGAGCGGA AGAACGGCCACGTCACCCCTC ATTCTTACGA 1783 353 1.56e-10 CTACTTTGAT AGCACCTGAACCTCTTCCCTG CTTCCACTTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9045 3.8e-13 250_[+2]_229 24462 3.8e-13 455_[+2]_24 23800 1.2e-10 291_[+2]_188 1783 1.6e-10 352_[+2]_127 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=4 9045 ( 251) AGAACCGGAACTTCTCCCATC 1 24462 ( 456) AGAACCGGAACTTCTCCCATC 1 23800 ( 292) AGAACGGCCACGTCACCCCTC 1 1783 ( 353) AGCACCTGAACCTCTTCCCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 8640 bayes= 11.0761 E= 2.4e+000 190 -865 -865 -865 -865 -865 215 -865 149 11 -865 -865 190 -865 -865 -865 -865 211 -865 -865 -865 169 15 -865 -865 -865 173 -14 -865 11 173 -865 149 11 -865 -865 190 -865 -865 -865 -865 211 -865 -865 -865 11 15 86 -865 -865 -865 186 -865 211 -865 -865 -10 -865 -865 144 -865 169 -865 -14 -865 211 -865 -865 -865 211 -865 -865 90 111 -865 -865 -865 -865 -865 186 -865 169 15 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 2.4e+000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.250000 0.750000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.750000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.250000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- AG[AC]AC[CG][GT][GC][AC]AC[TCG]TC[TA][CT]CC[AC]T[CG] -------------------------------------------------------------------------------- Time 6.25 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 6 llr = 109 E-value = 5.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :5::::::2233:a8:8:2: pos.-specific C ::3:::2:2:2:2::::7:: probability G 8::88a:a73578::823:8 matrix T 25722:8::5::::22::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 GATGGGTGGTGGGAAGACTG consensus TC GAA G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 9045 20 4.00e-12 GAGGAAAGAA GTTGGGTGGTAGGAAGACTG TTGTTTGTAG 24462 225 4.00e-12 GAGGAAAGAA GTTGGGTGGTAGGAAGACTG TTGTTTGTAG 4352 459 7.15e-09 TTGTGGTTGT GACTGGTGAGCGGAAGAGTG ACGTGACGCG 269690 94 1.13e-08 TGGAATTAGG TATGGGTGCTGACAAGAGTG AAAATGCTGG 262083 119 1.93e-08 GAAGAATACG GTTGTGTGGGGGGATGACAT TGACGTCGAG 23345 350 2.04e-08 TTTGCCAGAA GACGGGCGGAGAGAATGCTG GCATTGTTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9045 4e-12 19_[+3]_461 24462 4e-12 224_[+3]_256 4352 7.1e-09 458_[+3]_22 269690 1.1e-08 93_[+3]_387 262083 1.9e-08 118_[+3]_362 23345 2e-08 349_[+3]_131 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=6 9045 ( 20) GTTGGGTGGTAGGAAGACTG 1 24462 ( 225) GTTGGGTGGTAGGAAGACTG 1 4352 ( 459) GACTGGTGAGCGGAAGAGTG 1 269690 ( 94) TATGGGTGCTGACAAGAGTG 1 262083 ( 119) GTTGTGTGGGGGGATGACAT 1 23345 ( 350) GACGGGCGGAGAGAATGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 8658 bayes= 10.9416 E= 5.1e+000 -923 -923 189 -72 90 -923 -923 86 -923 52 -923 127 -923 -923 189 -72 -923 -923 189 -72 -923 -923 215 -923 -923 -47 -923 159 -923 -923 215 -923 -68 -47 156 -923 -68 -923 56 86 32 -47 115 -923 32 -923 156 -923 -923 -47 189 -923 190 -923 -923 -923 164 -923 -923 -72 -923 -923 189 -72 164 -923 -43 -923 -923 152 56 -923 -68 -923 -923 159 -923 -923 189 -72 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 5.1e+000 0.000000 0.000000 0.833333 0.166667 0.500000 0.000000 0.000000 0.500000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 1.000000 0.000000 0.166667 0.166667 0.666667 0.000000 0.166667 0.000000 0.333333 0.500000 0.333333 0.166667 0.500000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.166667 0.833333 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.000000 0.000000 0.833333 0.166667 0.833333 0.000000 0.166667 0.000000 0.000000 0.666667 0.333333 0.000000 0.166667 0.000000 0.000000 0.833333 0.000000 0.000000 0.833333 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[AT][TC]GGGTGG[TG][GA][GA]GAAGA[CG]TG -------------------------------------------------------------------------------- Time 9.72 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10671 4.06e-01 500 17651 1.43e-01 308_[+3(4.49e-05)]_172 1783 1.85e-07 352_[+2(1.56e-10)]_127 18076 4.96e-05 32_[+1(2.19e-08)]_447 22699 2.72e-01 500 23345 3.41e-09 321_[+1(6.90e-09)]_7_[+3(2.04e-08)]_\ 131 23548 2.97e-01 500 23800 4.54e-07 291_[+2(1.24e-10)]_188 24412 6.87e-05 189_[+1(1.23e-08)]_290 24462 1.67e-25 224_[+3(4.00e-12)]_81_\ [+1(4.64e-13)]_109_[+2(3.76e-13)]_24 262083 5.19e-04 118_[+3(1.93e-08)]_362 264690 3.06e-05 178_[+1(9.61e-09)]_301 269690 1.71e-04 93_[+3(1.13e-08)]_387 39143 3.06e-01 81_[+3(7.41e-05)]_399 41829 5.99e-01 500 4352 3.02e-09 379_[+1(6.43e-09)]_58_\ [+3(7.15e-09)]_22 7420 6.90e-01 500 9045 1.67e-25 19_[+3(4.00e-12)]_81_[+1(4.64e-13)]_\ 109_[+2(3.76e-13)]_229 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************