******************************************************************************** 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 89 2 1.0000 160 3 1.0000 110 4 1.0000 110 5 1.0000 110 6 1.0000 110 ******************************************************************************** ******************************************************************************** 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_out3 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= 689 N= 6 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.276 C 0.164 G 0.228 T 0.332 Background letter frequencies (from dataset with add-one prior applied): A 0.276 C 0.165 G 0.228 T 0.332 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 14 sites = 5 llr = 65 E-value = 2.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 8::86a:2aa62:2 pos.-specific C :a22::8:::22:: probability G ::::2::8::2:28 matrix T 2:8:2:2::::68: bits 2.6 * 2.3 * 2.1 * 1.8 * * ** Relative 1.6 * ** ** Entropy 1.3 * * ***** * (18.7 bits) 1.0 **** ***** ** 0.8 **** ****** ** 0.5 ************** 0.3 ************** 0.0 -------------- Multilevel ACTAAACGAAATTG consensus T CCG TA CAGA sequence T GC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 2 146 1.98e-07 TTTAGTTAAT ACTAAATGAAATTG A 4 84 2.61e-07 CAGATGTTCA ACTCGACGAACTTG AATATGCTTC 5 90 3.61e-07 ATTATTGATG TCTAAACGAAAATG GCTAATG 6 91 3.83e-07 TTTAGTATAA ACTAAACAAAATGG CCTCTG 3 65 2.85e-06 CTAGATTACA ACCATACGAAGCTA TTGAAAAGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2 2e-07 145_[1]_1 4 2.6e-07 83_[1]_13 5 3.6e-07 89_[1]_7 6 3.8e-07 90_[1]_6 3 2.8e-06 64_[1]_32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=14 seqs=5 2 ( 146) ACTAAATGAAATTG 1 4 ( 84) ACTCGACGAACTTG 1 5 ( 90) TCTAAACGAAAATG 1 6 ( 91) ACTAAACAAAATGG 1 3 ( 65) ACCATACGAAGCTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 611 bayes= 6.92125 E= 2.5e+000 154 -897 -897 -73 -897 260 -897 -897 -897 28 -897 127 154 28 -897 -897 112 -897 -19 -73 186 -897 -897 -897 -897 228 -897 -73 -46 -897 181 -897 186 -897 -897 -897 186 -897 -897 -897 112 28 -19 -897 -46 28 -897 85 -897 -897 -19 127 -46 -897 181 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 5 E= 2.5e+000 0.800000 0.000000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.800000 0.200000 0.000000 0.000000 0.600000 0.000000 0.200000 0.200000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.200000 0.200000 0.000000 0.200000 0.200000 0.000000 0.600000 0.000000 0.000000 0.200000 0.800000 0.200000 0.000000 0.800000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT]C[TC][AC][AGT]A[CT][GA]AA[ACG][TAC][TG][GA] -------------------------------------------------------------------------------- Time 0.20 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 21 sites = 5 llr = 78 E-value = 4.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::22282::6a228:44:2:8 pos.-specific C 8:2222:2a::42:6:242a2 probability G :2:62:28:2:4::4:464:: matrix T 286:4:6::2::62:6::2:: bits 2.6 * * 2.3 * * 2.1 * * 1.8 * * * Relative 1.6 * ** * * * Entropy 1.3 * * ** * * * ** (22.5 bits) 1.0 ** * ** * ** * ** 0.8 ** * * ** ** *** * ** 0.5 **** * *********** ** 0.3 **** **************** 0.0 --------------------- Multilevel CTTGTATGCAACTACTAGGCA consensus TGAAACAC G GATGAGCA C sequence CCC G T AC C C G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 2 2 4.31e-09 G TTTGCATGCAAGCACAAGGCA ACGGTTGTTG 6 21 3.68e-08 CTAAATATGG CGACTATGCTACTACTGGACA TTCAAATGAT 5 54 4.38e-08 GTCTATAAGT CTTATATGCAAATAGAACCCC TTCCTATTAT 1 57 5.17e-08 TTCTGTCACA CTTGAAGCCGACAACTGCTCA GTATGGCAAG 4 35 7.08e-08 TATGTCTTTA CTCGGCAGCAAGTTGTCGGCA TTGTAAATTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2 4.3e-09 1_[2]_138 6 3.7e-08 20_[2]_69 5 4.4e-08 53_[2]_36 1 5.2e-08 56_[2]_12 4 7.1e-08 34_[2]_55 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 2 ( 2) TTTGCATGCAAGCACAAGGCA 1 6 ( 21) CGACTATGCTACTACTGGACA 1 5 ( 54) CTTATATGCAAATAGAACCCC 1 1 ( 57) CTTGAAGCCGACAACTGCTCA 1 4 ( 35) CTCGGCAGCAAGTTGTCGGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 569 bayes= 6.81762 E= 4.2e+001 -897 228 -897 -73 -897 -897 -19 127 -46 28 -897 85 -46 28 139 -897 -46 28 -19 27 154 28 -897 -897 -46 -897 -19 85 -897 28 181 -897 -897 260 -897 -897 112 -897 -19 -73 186 -897 -897 -897 -46 128 81 -897 -46 28 -897 85 154 -897 -897 -73 -897 186 81 -897 54 -897 -897 85 54 28 81 -897 -897 128 139 -897 -46 28 81 -73 -897 260 -897 -897 154 28 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 4.2e+001 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.200000 0.800000 0.200000 0.200000 0.000000 0.600000 0.200000 0.200000 0.600000 0.000000 0.200000 0.200000 0.200000 0.400000 0.800000 0.200000 0.000000 0.000000 0.200000 0.000000 0.200000 0.600000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.000000 0.200000 0.200000 1.000000 0.000000 0.000000 0.000000 0.200000 0.400000 0.400000 0.000000 0.200000 0.200000 0.000000 0.600000 0.800000 0.000000 0.000000 0.200000 0.000000 0.600000 0.400000 0.000000 0.400000 0.000000 0.000000 0.600000 0.400000 0.200000 0.400000 0.000000 0.000000 0.400000 0.600000 0.000000 0.200000 0.200000 0.400000 0.200000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT][TG][TAC][GAC][TACGA][AC][TAG][GC]C[AGT]A[CGA][TAC][AT][CG][TA][AGC][GC][GACTA]C[AC] -------------------------------------------------------------------------------- Time 0.36 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 8 sites = 6 llr = 44 E-value = 2.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A a::::::2 pos.-specific C ::3:25:: probability G :a3:8:3: matrix T ::3a:578 bits 2.6 2.3 2.1 * 1.8 ** Relative 1.6 ** ** Entropy 1.3 ** ** (10.6 bits) 1.0 ** *** * 0.8 ** ***** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AGCTGCTT consensus G TG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- 1 29 5.74e-05 CCGTCTGGTG AGGTGCGT GGATAGTGTG 5 10 1.15e-04 TTGTAGCAG AGCTGTTT ATACTCCTGT 4 2 1.15e-04 G AGCTGTTT AATGGACACT 2 90 1.15e-04 AGGAGTGGAA AGTTGCTT GTTAGAGGTT 6 69 3.87e-04 CAGATAGTGA AGTTGTGT TACATTTAGT 3 50 8.09e-04 GTTGTTGTAA AGGTCCTA GATTACAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1 5.7e-05 28_[3]_53 5 0.00011 9_[3]_93 4 0.00011 1_[3]_101 2 0.00011 89_[3]_63 6 0.00039 68_[3]_34 3 0.00081 49_[3]_53 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=8 seqs=6 1 ( 29) AGGTGCGT 1 5 ( 10) AGCTGTTT 1 4 ( 2) AGCTGTTT 1 2 ( 90) AGTTGCTT 1 6 ( 69) AGTTGTGT 1 3 ( 50) AGGTCCTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 647 bayes= 6.94747 E= 2.6e+003 186 -923 -923 -923 -923 -923 213 -923 -923 102 55 1 -923 -923 -923 159 -923 2 187 -923 -923 160 -923 59 -923 -923 55 101 -72 -923 -923 133 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 2.6e+003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.333333 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.333333 0.666667 0.166667 0.000000 0.000000 0.833333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- AG[CGT]TG[CT][TG]T -------------------------------------------------------------------------------- Time 0.46 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1 2.92e-06 28_[3(5.74e-05)]_20_[2(5.17e-08)]_12 2 1.36e-10 1_[2(4.31e-09)]_123_[1(1.98e-07)]_1 3 1.12e-03 64_[1(2.85e-06)]_32 4 7.45e-10 34_[2(7.08e-08)]_28_[1(2.61e-07)]_13 5 6.45e-10 53_[2(4.38e-08)]_15_[1(3.61e-07)]_7 6 1.77e-09 20_[2(3.68e-08)]_49_[1(3.83e-07)]_6 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo ********************************************************************************