******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.3.0 (Release date: Sat Sep 26 01:51:56 PDT 2009) 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= out3.fasta ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1 1.0000 39 2 1.0000 150 3 1.0000 95 4 1.0000 40 5 1.0000 20 6 1.0000 20 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -dna -mod zoops -minsites 5 -nmotifs 3 -minw 6 -o meme_out2 out3.fasta model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 6 maxw= 50 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 5 maxsites= 6 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= 364 N= 6 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.297 C 0.154 G 0.212 T 0.338 Background letter frequencies (from dataset with add-one prior applied): A 0.296 C 0.155 G 0.212 T 0.337 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 11 sites = 6 llr = 57 E-value = 3.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 78:2738:5a7 pos.-specific C 2:833::a::3 probability G 2:2::52:5:: matrix T :2:5:2::::: bits 2.7 * 2.4 * 2.2 * 1.9 * * * Relative 1.6 * * * Entropy 1.3 * * * (13.7 bits) 1.1 ** * ***** 0.8 *** * ***** 0.5 *********** 0.3 *********** 0.0 ----------- Multilevel AACTAGACAAA consensus CCA G C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- 4 23 1.19e-06 ACAGATGTTC AACTCGACGAA CTTGAAT 6 10 7.54e-06 TTTAGTATA AACTAAACAAA 3 59 7.95e-06 CCTAGATTAC AACCATACGAA GCTATTGAAA 1 21 1.94e-05 GTCACACTTG AAGCCGACAAC TGCTCAGT 2 14 6.85e-05 TGCATGCAAG CACAAGGCAAC GGTTGTTGTT 5 9 7.49e-05 TTATTGAT GTCTAAACGAA A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4 1.2e-06 22_[1]_7 6 7.5e-06 9_[1] 3 8e-06 58_[1]_26 1 1.9e-05 20_[1]_8 2 6.8e-05 13_[1]_126 5 7.5e-05 8_[1]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=11 seqs=6 4 ( 23) AACTCGACGAA 1 6 ( 10) AACTAAACAAA 1 3 ( 59) AACCATACGAA 1 1 ( 21) AAGCCGACAAC 1 2 ( 14) CACAAGGCAAC 1 5 ( 9) GTCTAAACGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 304 bayes= 5.63421 E= 3.5e-002 117 11 -35 -923 149 -923 -923 -101 -923 243 -35 -923 -83 110 -923 57 117 110 -923 -923 17 -923 124 -101 149 -923 -35 -923 -923 269 -923 -923 75 -923 124 -923 175 -923 -923 -923 117 110 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 6 E= 3.5e-002 0.666667 0.166667 0.166667 0.000000 0.833333 0.000000 0.000000 0.166667 0.000000 0.833333 0.166667 0.000000 0.166667 0.333333 0.000000 0.500000 0.666667 0.333333 0.000000 0.000000 0.333333 0.000000 0.500000 0.166667 0.833333 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- AAC[TC][AC][GA]AC[AG]A[AC] -------------------------------------------------------------------------------- Time 0.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 11 sites = 5 llr = 36 E-value = 3.5e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::26:6:422 pos.-specific C :::2:624::: probability G :6:242:4::8 matrix T a4a4:22268: bits 2.7 2.4 2.2 1.9 Relative 1.6 * * Entropy 1.3 * * * (10.4 bits) 1.1 *** ** * 0.8 *** ** **** 0.5 *** ******* 0.3 *** ******* 0.0 ----------- Multilevel TGTTACACTTG consensus T AGGCGAAA sequence C TTT G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- 1 10 1.89e-07 AGTGTGTTC TGTCACACTTG AAGCCGACAA 4 9 3.66e-05 AATTCTAA TTTTACAGATG TTCAACTCGA 2 67 5.39e-05 CAGATTTAGT TGTTAGCCTTG TTAGGAGTGG 3 7 6.05e-05 GGCTGT TGTGGCTGTTG TGCTTCTTGT 6 1 2.64e-03 . TTTAGTATAAA CTAAACAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1 1.9e-07 9_[2]_19 4 3.7e-05 8_[2]_21 2 5.4e-05 66_[2]_73 3 6e-05 6_[2]_78 6 0.0026 [2]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=11 seqs=5 1 ( 10) TGTCACACTTG 1 4 ( 9) TTTTACAGATG 1 2 ( 67) TGTTAGCCTTG 1 3 ( 7) TGTGGCTGTTG 1 6 ( 1) TTTAGTATAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 304 bayes= 5.90207 E= 3.5e+005 -897 -897 -897 157 -897 -897 150 25 -897 -897 -897 157 -57 37 -8 25 102 -897 91 -897 -897 195 -8 -75 102 37 -897 -75 -897 137 91 -75 43 -897 -897 83 -57 -897 -897 125 -57 -897 191 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 5 E= 3.5e+005 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.000000 1.000000 0.200000 0.200000 0.200000 0.400000 0.600000 0.000000 0.400000 0.000000 0.000000 0.600000 0.200000 0.200000 0.600000 0.200000 0.000000 0.200000 0.000000 0.400000 0.400000 0.200000 0.400000 0.000000 0.000000 0.600000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.800000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[GT]T[TACGA][AG][CGT][ACT][CGT][TA][TA][GA] -------------------------------------------------------------------------------- Time 0.10 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 6 sites = 5 llr = 25 E-value = 7.5e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::2:24 pos.-specific C ::8:2: probability G :4:::6 matrix T a6:a6: bits 2.7 2.4 2.2 1.9 * Relative 1.6 * ** Entropy 1.3 * ** (7.3 bits) 1.1 * ** * 0.8 **** * 0.5 ****** 0.3 ****** 0.0 ------ Multilevel TTCTTG consensus GA AA sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ 2 93 2.67e-04 AGTGGAAAGT TGCTTG TTAGAGGTTC 3 21 6.90e-04 GCTGTTGTGC TTCTTG TTTAACTGGT 1 32 2.75e-03 AGCCGACAAC TGCTCA GT 4 3 3.87e-03 AA TTCTAA TTTTACAGAT 5 1 5.19e-03 . TTATTG ATGTCTAAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2 0.00027 92_[3]_52 3 0.00069 20_[3]_69 1 0.0027 31_[3]_2 4 0.0039 2_[3]_32 5 0.0052 [3]_14 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=6 seqs=5 2 ( 93) TGCTTG 1 3 ( 21) TTCTTG 1 1 ( 32) TGCTCA 1 4 ( 3) TTCTAA 1 5 ( 1) TTATTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 334 bayes= 6.04002 E= 7.5e+004 -897 -897 -897 157 -897 -897 91 83 -57 237 -897 -897 -897 -897 -897 157 -57 37 -897 83 43 -897 150 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 5 E= 7.5e+004 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.400000 0.600000 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.200000 0.200000 0.000000 0.600000 0.400000 0.000000 0.600000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[TG][CA]T[TAC][GA] -------------------------------------------------------------------------------- Time 0.12 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1 7.32e-08 9_[2(1.89e-07)]_[1(1.94e-05)]_8 2 2.61e-04 13_[1(6.85e-05)]_42_[2(5.39e-05)]_73 3 2.81e-05 6_[2(6.05e-05)]_41_[1(7.95e-06)]_26 4 1.01e-06 8_[2(3.66e-05)]_3_[1(1.19e-06)]_7 5 9.10e-04 8_[1(7.49e-05)]_1 6 1.43e-04 9_[1(7.54e-06)] -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo ********************************************************************************