******************************************************************************** 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/167/167.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 13794 1.0000 500 17952 1.0000 500 18220 1.0000 500 2124 1.0000 500 22666 1.0000 500 23031 1.0000 500 24795 1.0000 500 25364 1.0000 500 261627 1.0000 500 33348 1.0000 500 38780 1.0000 500 bd1193 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/167/167.seqs.fa -oc motifs/167 -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= 12 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= 6000 N= 12 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.262 C 0.247 G 0.242 T 0.249 Background letter frequencies (from dataset with add-one prior applied): A 0.262 C 0.247 G 0.242 T 0.249 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 12 llr = 120 E-value = 1.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 5::21:2::::: pos.-specific C 1:::5:3::1:: probability G 448:2a:2a:68 matrix T :6383:58:943 bits 2.0 * * 1.8 * * 1.6 * ** 1.4 * * *** Relative 1.2 ** * *** * Entropy 1.0 *** * ***** (14.4 bits) 0.8 *** * ***** 0.6 **** ******* 0.4 **** ******* 0.2 ************ 0.0 ------------ Multilevel ATGTCGTTGTGG consensus GGT T C TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 22666 287 2.99e-07 GCCTCCTGCC ATGTCGCTGTGG AGGTGTGGAA 38780 99 3.95e-07 CTCAGGTAGT GTGTCGTTGTTG ACAACGGGGG 33348 69 6.41e-07 GGAGGAGGAT GGGTCGTTGTTG TTGTTGTTCG 25364 246 1.35e-06 GGCCCGTGAC ATGTTGTTGTTG TGTTGCCGCA 18220 58 9.67e-06 TATCGGACGA AGGTTGCTGTGT TCGTACCTCT 2124 235 1.20e-05 CAACAAGGCT GTGTGGCTGTGT GAAGGAGTTA 17952 180 1.69e-05 CAGGGGTGAT ATTTTGTTGTGT GGGCACCACC 23031 170 1.96e-05 CAACATCGGC ATGACGATGTTG CGTCGAAGAT bd1193 12 2.06e-05 AATTGAGGGG GTTACGTTGTTG TGCTCTCTGT 13794 24 2.92e-05 CGTTTCAAAG GGGTAGTGGTGG TAGCAGTGCG 24795 112 6.15e-05 GTTAGAGCGG AGGTGGATGCGG CTGCGGTGCC 261627 410 7.09e-05 GGTTCTTCTT CGTTCGCGGTGG AGCGAAATAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22666 3e-07 286_[+1]_202 38780 3.9e-07 98_[+1]_390 33348 6.4e-07 68_[+1]_420 25364 1.3e-06 245_[+1]_243 18220 9.7e-06 57_[+1]_431 2124 1.2e-05 234_[+1]_254 17952 1.7e-05 179_[+1]_309 23031 2e-05 169_[+1]_319 bd1193 2.1e-05 11_[+1]_477 13794 2.9e-05 23_[+1]_465 24795 6.1e-05 111_[+1]_377 261627 7.1e-05 409_[+1]_79 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=12 22666 ( 287) ATGTCGCTGTGG 1 38780 ( 99) GTGTCGTTGTTG 1 33348 ( 69) GGGTCGTTGTTG 1 25364 ( 246) ATGTTGTTGTTG 1 18220 ( 58) AGGTTGCTGTGT 1 2124 ( 235) GTGTGGCTGTGT 1 17952 ( 180) ATTTTGTTGTGT 1 23031 ( 170) ATGACGATGTTG 1 bd1193 ( 12) GTTACGTTGTTG 1 13794 ( 24) GGGTAGTGGTGG 1 24795 ( 112) AGGTGGATGCGG 1 261627 ( 410) CGTTCGCGGTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5868 bayes= 8.93074 E= 1.0e+000 93 -156 78 -1023 -1023 -1023 78 123 -1023 -1023 163 1 -65 -1023 -1023 174 -165 102 -54 1 -1023 -1023 204 -1023 -65 43 -1023 101 -1023 -1023 -54 174 -1023 -1023 204 -1023 -1023 -156 -1023 188 -1023 -1023 127 74 -1023 -1023 163 1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 12 E= 1.0e+000 0.500000 0.083333 0.416667 0.000000 0.000000 0.000000 0.416667 0.583333 0.000000 0.000000 0.750000 0.250000 0.166667 0.000000 0.000000 0.833333 0.083333 0.500000 0.166667 0.250000 0.000000 0.000000 1.000000 0.000000 0.166667 0.333333 0.000000 0.500000 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 0.083333 0.000000 0.916667 0.000000 0.000000 0.583333 0.416667 0.000000 0.000000 0.750000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AG][TG][GT]T[CT]G[TC]TGT[GT][GT] -------------------------------------------------------------------------------- Time 1.56 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 6 llr = 106 E-value = 1.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 8:a:8::35528523a:2:7: pos.-specific C 22:::2:22:3:::3:::52: probability G :5:a:8a23552583:a82:a matrix T :3::2::3::::::::::32: bits 2.0 * * * * 1.8 ** * ** * 1.6 ** * ** * 1.4 ** ** * *** * Relative 1.2 * ***** * * *** * Entropy 1.0 * ***** * *** *** * (25.5 bits) 0.8 * ***** * *** *** * 0.6 ******* ****** ****** 0.4 ******* ************* 0.2 ******* ************* 0.0 --------------------- Multilevel AGAGAGGAAAGAAGAAGGCAG consensus T TGGC G C T sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 25364 212 1.59e-11 AGAAAGCACC ATAGAGGAAGGAGGGAGGCAG GGTGGCCCGT 17952 124 4.72e-10 GGTTCCAAAA AGAGAGGCAAGAAGAAGGGAG GAAAGTAGTC 2124 146 1.13e-09 CCCGATGAGA AGAGAGGGAGGAAGAAGGTTG TCAAGCCAAG 261627 214 8.17e-09 AGGATCACGT ACAGACGACACAGGCAGGCAG CCAAGCTCTC bd1193 455 2.67e-08 TCCTCTGCAA CGAGAGGTGACAGACAGACAG CTCTTGCCGT 24795 171 4.83e-08 TGCGAAGGTG ATAGTGGTGGAGAGGAGGTCG AGAAGATGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25364 1.6e-11 211_[+2]_268 17952 4.7e-10 123_[+2]_356 2124 1.1e-09 145_[+2]_334 261627 8.2e-09 213_[+2]_266 bd1193 2.7e-08 454_[+2]_25 24795 4.8e-08 170_[+2]_309 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=6 25364 ( 212) ATAGAGGAAGGAGGGAGGCAG 1 17952 ( 124) AGAGAGGCAAGAAGAAGGGAG 1 2124 ( 146) AGAGAGGGAGGAAGAAGGTTG 1 261627 ( 214) ACAGACGACACAGGCAGGCAG 1 bd1193 ( 455) CGAGAGGTGACAGACAGACAG 1 24795 ( 171) ATAGTGGTGGAGAGGAGGTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5760 bayes= 10.3532 E= 1.5e+001 167 -56 -923 -923 -923 -56 104 42 193 -923 -923 -923 -923 -923 204 -923 167 -923 -923 -58 -923 -56 178 -923 -923 -923 204 -923 35 -56 -54 42 93 -56 46 -923 93 -923 104 -923 -65 43 104 -923 167 -923 -54 -923 93 -923 104 -923 -65 -923 178 -923 35 43 46 -923 193 -923 -923 -923 -923 -923 204 -923 -65 -923 178 -923 -923 102 -54 42 135 -56 -923 -58 -923 -923 204 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 1.5e+001 0.833333 0.166667 0.000000 0.000000 0.000000 0.166667 0.500000 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.166667 0.166667 0.333333 0.500000 0.166667 0.333333 0.000000 0.500000 0.000000 0.500000 0.000000 0.166667 0.333333 0.500000 0.000000 0.833333 0.000000 0.166667 0.000000 0.500000 0.000000 0.500000 0.000000 0.166667 0.000000 0.833333 0.000000 0.333333 0.333333 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.500000 0.166667 0.333333 0.666667 0.166667 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- A[GT]AGAGG[AT][AG][AG][GC]A[AG]G[ACG]AGG[CT]AG -------------------------------------------------------------------------------- Time 3.13 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 11 llr = 136 E-value = 1.6e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :71257::35:151211:1: pos.-specific C 8:9512a:353::133416: probability G :::43::92:5635435::a matrix T 23::11:13:332424:93: bits 2.0 * * 1.8 * * 1.6 * ** * * 1.4 * * ** * * Relative 1.2 * * ** * * Entropy 1.0 *** ** * * * (17.8 bits) 0.8 *** *** * * *** 0.6 **** *** * ** **** 0.4 ******** ***** **** 0.2 ******** ***** ***** 0.0 -------------------- Multilevel CACCAACGAAGGAGGTGTCG consensus T GG CCCTGTCCC T sequence T T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 25364 47 3.61e-08 CCACAATTTG CACCAACGCATGAAATGTCG ATGGCAGCTG 22666 79 4.14e-08 GCTCAAAGAA TACGGACGCAGGATCGGTCG GTGTGTTGTC 24795 64 8.97e-08 GTGGCGAAGC CTCCACCGAAGGAGAGCTCG GCTGCGTTTT 13794 272 2.24e-07 AACAAACCAA CACCTCCGAAGGATCGCTCG TTCACAACTC 261627 434 7.91e-07 CGAAATAGGA CACAGACGACGTGGGCATCG GCATCTCTTC 33348 161 8.63e-07 CGGCGACGGG CACGGACGGACGGGGTGCTG CGTTGAGTGC 18220 114 1.31e-06 CTGAAACATG TTCCAACGGCTTATTTCTCG CAACTACCAG bd1193 44 1.42e-06 ACAACGTGGA CACCAACGTCCAGTGTCTAG TGTCTAACGA 38780 363 1.66e-06 TCCCCCCATC CAAGAACGCACGTGTCGTTG ATGGTCGTAG 23031 230 5.34e-06 CTGATGCTCG CACACTCGTCGTTGCCGTCG CAGTCAACCT 2124 179 8.02e-06 AAGCCAAGGA CTCGAACTTCTGACGAGTTG TAAGATCATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25364 3.6e-08 46_[+3]_434 22666 4.1e-08 78_[+3]_402 24795 9e-08 63_[+3]_417 13794 2.2e-07 271_[+3]_209 261627 7.9e-07 433_[+3]_47 33348 8.6e-07 160_[+3]_320 18220 1.3e-06 113_[+3]_367 bd1193 1.4e-06 43_[+3]_437 38780 1.7e-06 362_[+3]_118 23031 5.3e-06 229_[+3]_251 2124 8e-06 178_[+3]_302 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=11 25364 ( 47) CACCAACGCATGAAATGTCG 1 22666 ( 79) TACGGACGCAGGATCGGTCG 1 24795 ( 64) CTCCACCGAAGGAGAGCTCG 1 13794 ( 272) CACCTCCGAAGGATCGCTCG 1 261627 ( 434) CACAGACGACGTGGGCATCG 1 33348 ( 161) CACGGACGGACGGGGTGCTG 1 18220 ( 114) TTCCAACGGCTTATTTCTCG 1 bd1193 ( 44) CACCAACGTCCAGTGTCTAG 1 38780 ( 363) CAAGAACGCACGTGTCGTTG 1 23031 ( 230) CACACTCGTCGTTGCCGTCG 1 2124 ( 179) CTCGAACTTCTGACGAGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 5772 bayes= 9.38837 E= 1.6e+002 -1010 173 -1010 -45 147 -1010 -1010 13 -153 188 -1010 -1010 -53 88 59 -1010 106 -144 17 -145 147 -44 -1010 -145 -1010 202 -1010 -1010 -1010 -1010 191 -145 6 14 -41 13 106 88 -1010 -1010 -1010 14 91 13 -153 -1010 139 13 106 -1010 17 -45 -153 -144 91 55 -53 14 59 -45 -153 14 17 55 -153 56 117 -1010 -1010 -144 -1010 187 -153 137 -1010 13 -1010 -1010 204 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 11 E= 1.6e+002 0.000000 0.818182 0.000000 0.181818 0.727273 0.000000 0.000000 0.272727 0.090909 0.909091 0.000000 0.000000 0.181818 0.454545 0.363636 0.000000 0.545455 0.090909 0.272727 0.090909 0.727273 0.181818 0.000000 0.090909 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.909091 0.090909 0.272727 0.272727 0.181818 0.272727 0.545455 0.454545 0.000000 0.000000 0.000000 0.272727 0.454545 0.272727 0.090909 0.000000 0.636364 0.272727 0.545455 0.000000 0.272727 0.181818 0.090909 0.090909 0.454545 0.363636 0.181818 0.272727 0.363636 0.181818 0.090909 0.272727 0.272727 0.363636 0.090909 0.363636 0.545455 0.000000 0.000000 0.090909 0.000000 0.909091 0.090909 0.636364 0.000000 0.272727 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[AT]C[CG][AG]ACG[ACT][AC][GCT][GT][AG][GT][GC][TCG][GC]T[CT]G -------------------------------------------------------------------------------- Time 4.68 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 13794 5.72e-06 23_[+1(2.92e-05)]_236_\ [+3(2.24e-07)]_140_[+2(4.75e-05)]_48 17952 3.90e-07 123_[+2(4.72e-10)]_35_\ [+1(1.69e-05)]_309 18220 2.15e-04 57_[+1(9.67e-06)]_44_[+3(1.31e-06)]_\ 367 2124 4.16e-09 145_[+2(1.13e-09)]_12_\ [+3(8.02e-06)]_36_[+1(1.20e-05)]_254 22666 4.86e-07 78_[+3(4.14e-08)]_188_\ [+1(2.99e-07)]_202 23031 1.41e-03 169_[+1(1.96e-05)]_48_\ [+3(5.34e-06)]_251 24795 9.45e-09 63_[+3(8.97e-08)]_28_[+1(6.15e-05)]_\ 47_[+2(4.83e-08)]_309 25364 6.29e-14 46_[+3(3.61e-08)]_145_\ [+2(1.59e-11)]_13_[+1(1.35e-06)]_243 261627 1.55e-08 213_[+2(8.17e-09)]_175_\ [+1(7.09e-05)]_12_[+3(7.91e-07)]_47 33348 9.18e-07 68_[+1(6.41e-07)]_80_[+3(8.63e-07)]_\ 40_[+1(5.25e-05)]_268 38780 1.34e-05 98_[+1(3.95e-07)]_252_\ [+3(1.66e-06)]_118 bd1193 2.56e-08 11_[+1(2.06e-05)]_20_[+3(1.42e-06)]_\ 391_[+2(2.67e-08)]_25 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************