******************************************************************************** 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/325/325.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 47097 1.0000 500 37793 1.0000 500 39093 1.0000 500 43321 1.0000 500 32772 1.0000 500 6066 1.0000 500 33535 1.0000 500 45601 1.0000 500 42488 1.0000 500 46377 1.0000 500 36381 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/325/325.seqs.fa -oc motifs/325 -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= 11 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= 5500 N= 11 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.266 C 0.241 G 0.233 T 0.259 Background letter frequencies (from dataset with add-one prior applied): A 0.266 C 0.241 G 0.233 T 0.259 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 10 llr = 111 E-value = 8.6e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 8:11a:2:::95 pos.-specific C :7:5:a:::514 probability G 2::2:::a:2:1 matrix T :392::8:a3:: bits 2.1 * * 1.9 ** ** 1.7 ** ** 1.5 * ** ** * Relative 1.3 * * ***** * Entropy 1.0 *** ***** * (16.0 bits) 0.8 *** ***** * 0.6 *** ******** 0.4 *** ******** 0.2 ************ 0.0 ------------ Multilevel ACTCACTGTCAA consensus GT G A T C sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 39093 430 6.84e-08 GGTCTCACTC ACTCACTGTCAA CTTGAGATTG 45601 344 1.30e-07 GGATCAATTC ACTCACTGTCAC TCCAAAATCA 47097 443 7.36e-07 GGTTTGCCGA ATTCACTGTCAC AGTCAGTTGC 43321 446 1.69e-06 TAACGAACAC ACTAACTGTCAA TAAATCCCCC 33535 287 4.10e-06 ACACACCGGT ATTCACAGTCAA TTCGAGTCCA 36381 344 6.07e-06 GTGGAAGTAT GCTTACTGTTAA TTCCATGCTT 46377 61 7.42e-06 TAAAGTGTAC ACTTACAGTTAA ATCAGGTGGC 32772 340 9.02e-06 TTTTTCGTTG ACTGACTGTGAG GAATCATACA 37793 356 1.51e-05 AAAAGATTTT GTTGACTGTGAC AACGATCGCC 6066 482 2.60e-05 CCAACGCGAG ACACACTGTTCC GCGCACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 39093 6.8e-08 429_[+1]_59 45601 1.3e-07 343_[+1]_145 47097 7.4e-07 442_[+1]_46 43321 1.7e-06 445_[+1]_43 33535 4.1e-06 286_[+1]_202 36381 6.1e-06 343_[+1]_145 46377 7.4e-06 60_[+1]_428 32772 9e-06 339_[+1]_149 37793 1.5e-05 355_[+1]_133 6066 2.6e-05 481_[+1]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=10 39093 ( 430) ACTCACTGTCAA 1 45601 ( 344) ACTCACTGTCAC 1 47097 ( 443) ATTCACTGTCAC 1 43321 ( 446) ACTAACTGTCAA 1 33535 ( 287) ATTCACAGTCAA 1 36381 ( 344) GCTTACTGTTAA 1 46377 ( 61) ACTTACAGTTAA 1 32772 ( 340) ACTGACTGTGAG 1 37793 ( 356) GTTGACTGTGAC 1 6066 ( 482) ACACACTGTTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5379 bayes= 9.32048 E= 8.6e-002 159 -997 -22 -997 -997 154 -997 21 -141 -997 -997 179 -141 105 -22 -38 191 -997 -997 -997 -997 205 -997 -997 -41 -997 -997 162 -997 -997 210 -997 -997 -997 -997 195 -997 105 -22 21 176 -127 -997 -997 91 73 -122 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 10 E= 8.6e-002 0.800000 0.000000 0.200000 0.000000 0.000000 0.700000 0.000000 0.300000 0.100000 0.000000 0.000000 0.900000 0.100000 0.500000 0.200000 0.200000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.200000 0.300000 0.900000 0.100000 0.000000 0.000000 0.500000 0.400000 0.100000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AG][CT]T[CGT]AC[TA]GT[CTG]A[AC] -------------------------------------------------------------------------------- Time 1.18 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 7 llr = 114 E-value = 5.3e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 3::734::77194:1:3::3: pos.-specific C 66:37:a::14:::73::71: probability G 149::1:a3131::1:6::47 matrix T ::1::4::::1:6a:71a313 bits 2.1 ** 1.9 ** * * 1.7 ** * * 1.5 * ** * * Relative 1.3 * ** * * ** * Entropy 1.0 **** *** *** * ** * (23.6 bits) 0.8 **** **** ***** ** * 0.6 ***** **** ******** * 0.4 ********** ******** * 0.2 ********************* 0.0 --------------------- Multilevel CCGACACGAACATTCTGTCGG consensus AG CAT G G A CA TAT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 46377 167 2.90e-10 CAATACAACG CCGACTCGGATATTCTGTCAG TCTTTTGTGA 47097 27 7.95e-10 AAGGCAGGAA AGGACTCGGACAATCCGTCGG AAGCCCAGTC 39093 396 1.09e-08 TTGTCGCGAC AGGCAACGAACATTCTTTCAG AGCGGTCTCA 33535 222 2.22e-08 TCAGACGCTA CCGAAACGAAGAATCCATCTT GTCGTCACCA 36381 61 3.30e-08 GTAATTGTCC CGTCCACGACGATTCTGTTGG AAGTTTCCGC 42488 323 5.11e-08 AACCAGCCCT CCGACTCGAGAAATATATTGG AGGCACGTAA 43321 164 1.28e-07 GTCGACGTCA GCGACGCGAACGTTGTGTCCT GACCATTCGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46377 2.9e-10 166_[+2]_313 47097 7.9e-10 26_[+2]_453 39093 1.1e-08 395_[+2]_84 33535 2.2e-08 221_[+2]_258 36381 3.3e-08 60_[+2]_419 42488 5.1e-08 322_[+2]_157 43321 1.3e-07 163_[+2]_316 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=7 46377 ( 167) CCGACTCGGATATTCTGTCAG 1 47097 ( 27) AGGACTCGGACAATCCGTCGG 1 39093 ( 396) AGGCAACGAACATTCTTTCAG 1 33535 ( 222) CCGAAACGAAGAATCCATCTT 1 36381 ( 61) CGTCCACGACGATTCTGTTGG 1 42488 ( 323) CCGACTCGAGAAATATATTGG 1 43321 ( 164) GCGACGCGAACGTTGTGTCCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5280 bayes= 9.40072 E= 5.3e+001 10 124 -71 -945 -945 124 88 -945 -945 -945 188 -86 142 25 -945 -945 10 157 -945 -945 69 -945 -71 72 -945 205 -945 -945 -945 -945 210 -945 142 -945 29 -945 142 -75 -71 -945 -90 83 29 -86 168 -945 -71 -945 69 -945 -945 114 -945 -945 -945 194 -90 157 -71 -945 -945 25 -945 146 10 -945 129 -86 -945 -945 -945 194 -945 157 -945 14 10 -75 88 -86 -945 -945 161 14 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 5.3e+001 0.285714 0.571429 0.142857 0.000000 0.000000 0.571429 0.428571 0.000000 0.000000 0.000000 0.857143 0.142857 0.714286 0.285714 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 0.428571 0.000000 0.142857 0.428571 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.714286 0.000000 0.285714 0.000000 0.714286 0.142857 0.142857 0.000000 0.142857 0.428571 0.285714 0.142857 0.857143 0.000000 0.142857 0.000000 0.428571 0.000000 0.000000 0.571429 0.000000 0.000000 0.000000 1.000000 0.142857 0.714286 0.142857 0.000000 0.000000 0.285714 0.000000 0.714286 0.285714 0.000000 0.571429 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.714286 0.000000 0.285714 0.285714 0.142857 0.428571 0.142857 0.000000 0.000000 0.714286 0.285714 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CA][CG]G[AC][CA][AT]CG[AG]A[CG]A[TA]TC[TC][GA]T[CT][GA][GT] -------------------------------------------------------------------------------- Time 2.26 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 8 llr = 89 E-value = 1.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :9::::::1155 pos.-specific C 1:::a1:9::1: probability G 91:::9:15631 matrix T ::aa::a:4314 bits 2.1 * 1.9 *** * 1.7 *** * 1.5 ******** Relative 1.3 ******** Entropy 1.0 ******** (16.0 bits) 0.8 ******** * 0.6 ********** * 0.4 ********** * 0.2 ************ 0.0 ------------ Multilevel GATTCGTCGGAA consensus TTGT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 36381 16 3.30e-07 GGGTGCGGCA GATTCGTCGGGT TGATCCGCGT 33535 188 3.30e-07 CAGGCACGCC GATTCGTCGGGT AGCGGATGCC 45601 455 4.47e-07 TCGGTTTATT GATTCGTCGTAA TCAATCTTTT 46377 111 1.24e-06 TAAGCCAGGA GATTCGTCTGTA ATGAAACAAC 39093 319 4.61e-06 TCCGAAAAGA GGTTCGTCGTAA GGCTTCGCGT 42488 130 7.55e-06 CTGCGATCTG GATTCGTCTAAG CGACAGAGAC 47097 339 1.50e-05 TCTATTACTT GATTCCTGTGAA GATTTGTAGC 37793 454 2.48e-05 TTCCGCACCG CATTCGTCAGCT TGAATCTATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36381 3.3e-07 15_[+3]_473 33535 3.3e-07 187_[+3]_301 45601 4.5e-07 454_[+3]_34 46377 1.2e-06 110_[+3]_378 39093 4.6e-06 318_[+3]_170 42488 7.5e-06 129_[+3]_359 47097 1.5e-05 338_[+3]_150 37793 2.5e-05 453_[+3]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=8 36381 ( 16) GATTCGTCGGGT 1 33535 ( 188) GATTCGTCGGGT 1 45601 ( 455) GATTCGTCGTAA 1 46377 ( 111) GATTCGTCTGTA 1 39093 ( 319) GGTTCGTCGTAA 1 42488 ( 130) GATTCGTCTAAG 1 47097 ( 339) GATTCCTGTGAA 1 37793 ( 454) CATTCGTCAGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5379 bayes= 10.7142 E= 1.5e+002 -965 -94 191 -965 171 -965 -90 -965 -965 -965 -965 195 -965 -965 -965 195 -965 205 -965 -965 -965 -94 191 -965 -965 -965 -965 195 -965 186 -90 -965 -109 -965 110 53 -109 -965 142 -5 91 -94 10 -105 91 -965 -90 53 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 8 E= 1.5e+002 0.000000 0.125000 0.875000 0.000000 0.875000 0.000000 0.125000 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 0.125000 0.875000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.875000 0.125000 0.000000 0.125000 0.000000 0.500000 0.375000 0.125000 0.000000 0.625000 0.250000 0.500000 0.125000 0.250000 0.125000 0.500000 0.000000 0.125000 0.375000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GATTCGTC[GT][GT][AG][AT] -------------------------------------------------------------------------------- Time 3.49 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47097 4.11e-10 26_[+2(7.95e-10)]_199_\ [+1(2.05e-05)]_80_[+3(1.50e-05)]_92_[+1(7.36e-07)]_46 37793 2.26e-03 355_[+1(1.51e-05)]_86_\ [+3(2.48e-05)]_35 39093 1.73e-10 168_[+1(9.77e-05)]_138_\ [+3(4.61e-06)]_65_[+2(1.09e-08)]_13_[+1(6.84e-08)]_59 43321 3.78e-07 163_[+2(1.28e-07)]_87_\ [+3(6.91e-05)]_162_[+1(1.69e-06)]_43 32772 1.52e-02 339_[+1(9.02e-06)]_149 6066 5.51e-02 481_[+1(2.60e-05)]_7 33535 1.29e-09 187_[+3(3.30e-07)]_22_\ [+2(2.22e-08)]_44_[+1(4.10e-06)]_111_[+1(9.18e-05)]_79 45601 2.34e-06 343_[+1(1.30e-07)]_99_\ [+3(4.47e-07)]_34 42488 5.30e-06 129_[+3(7.55e-06)]_181_\ [+2(5.11e-08)]_157 46377 1.36e-10 60_[+1(7.42e-06)]_38_[+3(1.24e-06)]_\ 44_[+2(2.90e-10)]_313 36381 2.69e-09 15_[+3(3.30e-07)]_33_[+2(3.30e-08)]_\ 262_[+1(6.07e-06)]_145 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************