******************************************************************************** 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/116/116.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11024 1.0000 500 11235 1.0000 500 11239 1.0000 500 12079 1.0000 500 1309 1.0000 500 22663 1.0000 500 24602 1.0000 500 24958 1.0000 500 25005 1.0000 500 25477 1.0000 500 261283 1.0000 500 264532 1.0000 500 3869 1.0000 500 4075 1.0000 500 4076 1.0000 500 9438 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/116/116.seqs.fa -oc motifs/116 -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= 16 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= 8000 N= 16 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.281 C 0.238 G 0.222 T 0.260 Background letter frequencies (from dataset with add-one prior applied): A 0.281 C 0.238 G 0.222 T 0.260 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 7 llr = 122 E-value = 7.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 161::::41::7:131a93: pos.-specific C 91:3:a66:77169:9:171 probability G ::::::1::3:::::::::: matrix T :397a:3:9:314:7::::9 bits 2.2 * 2.0 ** 1.7 ** * 1.5 * ** * ** Relative 1.3 * * ** ** * *** * Entropy 1.1 * **** **** ******** (25.2 bits) 0.9 * **** **** ******** 0.7 * ****************** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel CATTTCCCTCCACCTCAACT consensus T C TA GT T A A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 4075 434 9.47e-12 AGAAAAAGCT CATTTCCATCCATCTCAACT ACTTGCACGT 4076 434 1.30e-11 AGAAACAGCT CTTTTCCCTCCATCTCAACT ACTTGCACAT 9438 248 2.20e-09 TCTACCAAAC CATTTCTCTCCATCAAAACT TCTTGCTACG 264532 393 2.46e-09 GAAGCTAGTA CTTTTCTCTGCACATCAACT TCCCGTAACT 24958 129 1.93e-08 CATCGTGTAC CCTCTCCATCTACCTCACAT GACATCGATC 3869 380 5.01e-08 ATATAGTGTG AATTTCGCACCCCCTCAAAT AGGGCCGGGC 261283 51 1.38e-07 TAGGACTCAC CAACTCCATGTTCCACAACC AAGGCTACTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4075 9.5e-12 433_[+1]_47 4076 1.3e-11 433_[+1]_47 9438 2.2e-09 247_[+1]_233 264532 2.5e-09 392_[+1]_88 24958 1.9e-08 128_[+1]_352 3869 5e-08 379_[+1]_101 261283 1.4e-07 50_[+1]_430 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=7 4075 ( 434) CATTTCCATCCATCTCAACT 1 4076 ( 434) CTTTTCCCTCCATCTCAACT 1 9438 ( 248) CATTTCTCTCCATCAAAACT 1 264532 ( 393) CTTTTCTCTGCACATCAACT 1 24958 ( 129) CCTCTCCATCTACCTCACAT 1 3869 ( 380) AATTTCGCACCCCCTCAAAT 1 261283 ( 51) CAACTCCATGTTCCACAACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 7696 bayes= 9.94496 E= 7.4e-001 -97 185 -945 -945 102 -74 -945 14 -97 -945 -945 172 -945 26 -945 146 -945 -945 -945 194 -945 207 -945 -945 -945 126 -63 14 61 126 -945 -945 -97 -945 -945 172 -945 158 37 -945 -945 158 -945 14 135 -74 -945 -86 -945 126 -945 72 -97 185 -945 -945 3 -945 -945 146 -97 185 -945 -945 183 -945 -945 -945 161 -74 -945 -945 3 158 -945 -945 -945 -74 -945 172 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 7 E= 7.4e-001 0.142857 0.857143 0.000000 0.000000 0.571429 0.142857 0.000000 0.285714 0.142857 0.000000 0.000000 0.857143 0.000000 0.285714 0.000000 0.714286 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.571429 0.142857 0.285714 0.428571 0.571429 0.000000 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.714286 0.285714 0.000000 0.000000 0.714286 0.000000 0.285714 0.714286 0.142857 0.000000 0.142857 0.000000 0.571429 0.000000 0.428571 0.142857 0.857143 0.000000 0.000000 0.285714 0.000000 0.000000 0.714286 0.142857 0.857143 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 0.000000 0.142857 0.000000 0.857143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AT]T[TC]TC[CT][CA]T[CG][CT]A[CT]C[TA]CAA[CA]T -------------------------------------------------------------------------------- Time 2.61 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 6 llr = 110 E-value = 8.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 235::::::33:23:::::2: pos.-specific C :2::2:77:::23:2:::::8 probability G 853:85:3a7:2338::7:8: matrix T ::2a:53:::7723:aa3a:2 bits 2.2 * 2.0 * * ** * 1.7 * * ** * 1.5 * ** * *** ** Relative 1.3 * ** * *** *** Entropy 1.1 * ******** ******* (26.3 bits) 0.9 * ******** ******* 0.7 ** ********* ******* 0.4 ************ ******** 0.2 ********************* 0.0 --------------------- Multilevel GGATGGCCGGTTCAGTTGTGC consensus AG TTG AA GG T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 4076 374 1.54e-12 AGATTCATTA GGATGTCCGGTTCTGTTGTGC CGACCAACAA 4075 374 1.37e-11 AGATTCATTG GGGTGTTCGGTTCGGTTGTGC CGACCAACAA 1309 188 1.87e-09 ACCATAAGAT GGTTGTCCGATTGAGTTGTAC ACTTGCTCCT 11235 383 1.50e-08 CCCCCACTTC GAATGGCCGAACAACTTGTGC AACCCCCCCT 12079 311 1.85e-08 AAATGACCCG AAATGGCGGGAGTGGTTTTGC CGATGCCTCC 261283 290 2.23e-08 GGAGGACGCT GCGTCGTGGGTTGTGTTTTGT GTTTTGGATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4076 1.5e-12 373_[+2]_106 4075 1.4e-11 373_[+2]_106 1309 1.9e-09 187_[+2]_292 11235 1.5e-08 382_[+2]_97 12079 1.8e-08 310_[+2]_169 261283 2.2e-08 289_[+2]_190 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=6 4076 ( 374) GGATGTCCGGTTCTGTTGTGC 1 4075 ( 374) GGGTGTTCGGTTCGGTTGTGC 1 1309 ( 188) GGTTGTCCGATTGAGTTGTAC 1 11235 ( 383) GAATGGCCGAACAACTTGTGC 1 12079 ( 311) AAATGGCGGGAGTGGTTTTGC 1 261283 ( 290) GCGTCGTGGGTTGTGTTTTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7680 bayes= 10.7686 E= 8.1e+000 -75 -923 191 -923 25 -51 117 -923 83 -923 59 -64 -923 -923 -923 194 -923 -51 191 -923 -923 -923 117 94 -923 148 -923 36 -923 148 59 -923 -923 -923 217 -923 25 -923 159 -923 25 -923 -923 136 -923 -51 -41 136 -75 49 59 -64 25 -923 59 36 -923 -51 191 -923 -923 -923 -923 194 -923 -923 -923 194 -923 -923 159 36 -923 -923 -923 194 -75 -923 191 -923 -923 181 -923 -64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 8.1e+000 0.166667 0.000000 0.833333 0.000000 0.333333 0.166667 0.500000 0.000000 0.500000 0.000000 0.333333 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.166667 0.166667 0.666667 0.166667 0.333333 0.333333 0.166667 0.333333 0.000000 0.333333 0.333333 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.833333 0.000000 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[GA][AG]TG[GT][CT][CG]G[GA][TA]T[CG][AGT]GTT[GT]TGC -------------------------------------------------------------------------------- Time 5.18 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 6 llr = 104 E-value = 4.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :52:2:5::272:3:::322 pos.-specific C 33:7::::::2::2:::::: probability G 7:8:82::a8:8838a8558 matrix T :2:3:85a::2:222:223: bits 2.2 * * 2.0 ** * 1.7 ** * 1.5 * * *** ** *** * Relative 1.3 * * ** *** ** *** * Entropy 1.1 * **** *** ** *** * (25.0 bits) 0.9 * ******** ** *** * 0.7 * *********** ****** 0.4 ************* ****** 0.2 ************* ****** 0.0 -------------------- Multilevel GAGCGTATGGAGGAGGGGGG consensus CC T T G AT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 9438 383 4.85e-13 TCCCAGGTTC GAGCGTATGGAGGGGGGGGG GGCGCCGTAA 11239 28 7.31e-09 CCCCATCTTG GAATGTATGGCGGAGGGTGG TCTAATGAAC 24602 182 9.13e-09 AGGTAGCGCG GTGTGTTTGGAGGTGGGATA GTTTCATCTC 264532 274 1.23e-08 GTGGTTGAAA CAGCATTTGGAGGAGGTGAG CCGCAATAGA 3869 239 1.73e-08 GTTTGGTTGC CCGCGGTTGGTGTCGGGGGG ACAGCCAATA 1309 278 2.89e-08 CATTCTGGTT GCGCGTATGAAAGGTGGATG GTAAGGTTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9438 4.9e-13 382_[+3]_98 11239 7.3e-09 27_[+3]_453 24602 9.1e-09 181_[+3]_299 264532 1.2e-08 273_[+3]_207 3869 1.7e-08 238_[+3]_242 1309 2.9e-08 277_[+3]_203 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=6 9438 ( 383) GAGCGTATGGAGGGGGGGGG 1 11239 ( 28) GAATGTATGGCGGAGGGTGG 1 24602 ( 182) GTGTGTTTGGAGGTGGGATA 1 264532 ( 274) CAGCATTTGGAGGAGGTGAG 1 3869 ( 239) CCGCGGTTGGTGTCGGGGGG 1 1309 ( 278) GCGCGTATGAAAGGTGGATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 7696 bayes= 10.7716 E= 4.9e+000 -923 49 159 -923 83 49 -923 -64 -75 -923 191 -923 -923 148 -923 36 -75 -923 191 -923 -923 -923 -41 168 83 -923 -923 94 -923 -923 -923 194 -923 -923 217 -923 -75 -923 191 -923 125 -51 -923 -64 -75 -923 191 -923 -923 -923 191 -64 25 -51 59 -64 -923 -923 191 -64 -923 -923 217 -923 -923 -923 191 -64 25 -923 117 -64 -75 -923 117 36 -75 -923 191 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 4.9e+000 0.000000 0.333333 0.666667 0.000000 0.500000 0.333333 0.000000 0.166667 0.166667 0.000000 0.833333 0.000000 0.000000 0.666667 0.000000 0.333333 0.166667 0.000000 0.833333 0.000000 0.000000 0.000000 0.166667 0.833333 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.666667 0.166667 0.000000 0.166667 0.166667 0.000000 0.833333 0.000000 0.000000 0.000000 0.833333 0.166667 0.333333 0.166667 0.333333 0.166667 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.333333 0.000000 0.500000 0.166667 0.166667 0.000000 0.500000 0.333333 0.166667 0.000000 0.833333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC][AC]G[CT]GT[AT]TGGAGG[AG]GGG[GA][GT]G -------------------------------------------------------------------------------- Time 7.69 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11024 6.84e-01 500 11235 2.64e-04 382_[+2(1.50e-08)]_97 11239 8.55e-05 27_[+3(7.31e-09)]_453 12079 3.22e-05 310_[+2(1.85e-08)]_169 1309 4.00e-09 187_[+2(1.87e-09)]_69_\ [+3(2.89e-08)]_203 22663 5.67e-01 500 24602 2.90e-04 181_[+3(9.13e-09)]_299 24958 5.38e-04 128_[+1(1.93e-08)]_11_\ [+1(5.37e-05)]_321 25005 8.24e-01 500 25477 3.58e-01 500 261283 1.44e-07 50_[+1(1.38e-07)]_219_\ [+2(2.23e-08)]_190 264532 2.50e-10 273_[+3(1.23e-08)]_99_\ [+1(2.46e-09)]_88 3869 5.41e-08 238_[+3(1.73e-08)]_121_\ [+1(5.01e-08)]_101 4075 1.34e-14 373_[+2(1.37e-11)]_39_\ [+1(9.47e-12)]_47 4076 2.25e-15 373_[+2(1.54e-12)]_39_\ [+1(1.30e-11)]_47 9438 1.34e-13 247_[+1(2.20e-09)]_115_\ [+3(4.85e-13)]_98 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************