******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 3.5.1 (Release date: 2005/12/14 00:00:05) 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= MCM1.fasta ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ MCM1_1 1.0000 18 MCM1_2 1.0000 18 MCM1_3 1.0000 18 MCM1_4 1.0000 18 MCM1_5 1.0000 18 MCM1_6 1.0000 18 MCM1_7 1.0000 18 MCM1_8 1.0000 18 MCM1_9 1.0000 18 MCM1_10 1.0000 18 MCM1_11 1.0000 18 MCM1_12 1.0000 18 MCM1_13 1.0000 18 MCM1_14 1.0000 18 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -revcomp -dna MCM1.fasta model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 18 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 14 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 252 N= 14 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.317 C 0.183 G 0.183 T 0.317 Background letter frequencies (from dataset with add-one prior applied): A 0.316 C 0.184 G 0.184 T 0.316 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 13 sites = 14 llr = 152 E-value = 2.4e-028 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :11::3676321: pos.-specific C :::a922::22:: probability G ::::::11:169a matrix T a99:151244::: bits 2.4 * * 2.2 * * 2.0 * ** 1.7 * ** ** Information 1.5 * ** ** content 1.2 ** ** ** (15.6 bits) 1.0 ***** *** 0.7 ***** ** *** 0.5 ***** *** *** 0.2 ********* *** 0.0 ------------- Multilevel TTTCCTAAATGGG consensus ACTTAA sequence C CC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------- MCM1_6 + 1 1.22e-08 . TTTCCTAAACGGG CTCAA MCM1_3 - 4 3.18e-07 TT TTTCCAAATCGGG TCA MCM1_14 + 1 6.77e-07 . TTTCCTAAAGCGG GAAAT MCM1_11 - 4 7.73e-07 TT TTTCCTAAACAGG TTA MCM1_13 - 4 1.65e-06 TA TTTCCCAAAAAGG AAA MCM1_7 + 1 1.93e-06 . TTTCCTCTTTGGG CAAGT MCM1_5 - 4 1.93e-06 TT TTTCCTCTTTGGG CGG MCM1_10 - 4 2.64e-06 AT TTTCCCGATTGGG GTG MCM1_2 - 4 3.15e-06 TT TTACCAAAAAGGG CAA MCM1_9 - 4 5.25e-06 CT TTTCCAATAGCGG TAA MCM1_8 + 1 5.25e-06 . TTACCACAAAGGG TAAAA MCM1_4 - 4 2.35e-05 AT TTTCTTTATTGGG TTT MCM1_1 + 1 5.34e-05 . TATCTCAAAACGG CAAAA MCM1_12 - 4 6.58e-05 AA TTTCCTAGTTAAG AAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- MCM1_6 1.2e-08 [+1]_5 MCM1_3 3.2e-07 3_[-1]_2 MCM1_14 6.8e-07 [+1]_5 MCM1_11 7.7e-07 3_[-1]_2 MCM1_13 1.7e-06 3_[-1]_2 MCM1_7 1.9e-06 [+1]_5 MCM1_5 1.9e-06 3_[-1]_2 MCM1_10 2.6e-06 3_[-1]_2 MCM1_2 3.2e-06 3_[-1]_2 MCM1_9 5.2e-06 3_[-1]_2 MCM1_8 5.2e-06 [+1]_5 MCM1_4 2.4e-05 3_[-1]_2 MCM1_1 5.3e-05 [+1]_5 MCM1_12 6.6e-05 3_[-1]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=13 seqs=14 MCM1_6 ( 1) TTTCCTAAACGGG 1 MCM1_3 ( 4) TTTCCAAATCGGG 1 MCM1_14 ( 1) TTTCCTAAAGCGG 1 MCM1_11 ( 4) TTTCCTAAACAGG 1 MCM1_13 ( 4) TTTCCCAAAAAGG 1 MCM1_7 ( 1) TTTCCTCTTTGGG 1 MCM1_5 ( 4) TTTCCTCTTTGGG 1 MCM1_10 ( 4) TTTCCCGATTGGG 1 MCM1_2 ( 4) TTACCAAAAAGGG 1 MCM1_9 ( 4) TTTCCAATAGCGG 1 MCM1_8 ( 1) TTACCACAAAGGG 1 MCM1_4 ( 4) TTTCTTTATTGGG 1 MCM1_1 ( 1) TATCTCAAAACGG 1 MCM1_12 ( 4) TTTCCTAGTTAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 84 bayes= 2.32193 E= 2.4e-028 -1826 -1748 -1748 166 -214 -1748 -1748 155 -114 -1748 -1748 143 -1826 244 -1748 -1826 -1826 221 -1748 -114 -14 21 -1748 66 102 21 -136 -214 117 -1748 -136 -56 85 -1748 -1748 43 -14 21 -36 17 -56 21 163 -1826 -214 -1748 233 -1826 -1826 -1748 244 -1826 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 14 E= 2.4e-028 0.000000 0.000000 0.000000 1.000000 0.071429 0.000000 0.000000 0.928571 0.142857 0.000000 0.000000 0.857143 0.000000 1.000000 0.000000 0.000000 0.000000 0.857143 0.000000 0.142857 0.285714 0.214286 0.000000 0.500000 0.642857 0.214286 0.071429 0.071429 0.714286 0.000000 0.071429 0.214286 0.571429 0.000000 0.000000 0.428571 0.285714 0.214286 0.142857 0.357143 0.214286 0.214286 0.571429 0.000000 0.071429 0.000000 0.928571 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- Time 0.11 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- MCM1_1 6.41e-04 [+1(5.34e-05)]_5 MCM1_2 3.78e-05 3_[-1(3.15e-06)]_2 MCM1_3 3.82e-06 3_[-1(3.18e-07)]_2 MCM1_4 2.82e-04 3_[-1(2.35e-05)]_2 MCM1_5 2.32e-05 3_[-1(1.93e-06)]_2 MCM1_6 1.46e-07 [+1(1.22e-08)]_5 MCM1_7 2.32e-05 [+1(1.93e-06)]_5 MCM1_8 6.30e-05 [+1(5.25e-06)]_5 MCM1_9 6.30e-05 3_[-1(5.25e-06)]_2 MCM1_10 3.17e-05 3_[-1(2.64e-06)]_2 MCM1_11 9.28e-06 3_[-1(7.73e-07)]_2 MCM1_12 7.89e-04 3_[-1(6.58e-05)]_2 MCM1_13 1.98e-05 3_[-1(1.65e-06)]_2 MCM1_14 8.13e-06 [+1(6.77e-07)]_5 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: uracil.gs.washington.edu ********************************************************************************