1******************************************************************************** 2MEME - Motif discovery tool 3******************************************************************************** 4MEME version 3.5.7 (Release date: 2007-12-17 16:56:19 -0800 (Mon, 17 Dec 2007)) 5 6For further information on how to interpret these results or to get 7a copy of the MEME software please access http://meme.nbcr.net. 8 9This file may be used as input to the MAST algorithm for searching 10sequence databases for matches to groups of motifs. MAST is available 11for interactive use and downloading at http://meme.nbcr.net. 12******************************************************************************** 13 14 15******************************************************************************** 16REFERENCE 17******************************************************************************** 18If you use this program in your research, please cite: 19 20Timothy L. Bailey and Charles Elkan, 21"Fitting a mixture model by expectation maximization to discover 22motifs in biopolymers", Proceedings of the Second International 23Conference on Intelligent Systems for Molecular Biology, pp. 28-36, 24AAAI Press, Menlo Park, California, 1994. 25******************************************************************************** 26 27 28******************************************************************************** 29TRAINING SET 30******************************************************************************** 31DATAFILE= test.fa 32ALPHABET= ACGT 33Sequence name Weight Length Sequence name Weight Length 34------------- ------ ------ ------------- ------ ------ 35SEQ1; 1.0000 200 SEQ2; 1.0000 200 36SEQ3; 1.0000 200 SEQ4; 1.0000 200 37SEQ5; 1.0000 200 SEQ6; 1.0000 200 38SEQ7; 1.0000 200 SEQ8; 1.0000 200 39SEQ9; 1.0000 200 SEQ10; 1.0000 200 40******************************************************************************** 41 42******************************************************************************** 43COMMAND LINE SUMMARY 44******************************************************************************** 45This information can also be useful in the event you wish to report a 46problem with the MEME software. 47 48command: meme test.fa -dna -w 10 -dir /home/bartek/MetaMotif/meme 49 50model: mod= zoops nmotifs= 1 evt= inf 51object function= E-value of product of p-values 52width: minw= 10 maxw= 10 minic= 0.00 53width: wg= 11 ws= 1 endgaps= yes 54nsites: minsites= 2 maxsites= 10 wnsites= 0.8 55theta: prob= 1 spmap= uni spfuzz= 0.5 56em: prior= dirichlet b= 0.01 maxiter= 50 57 distance= 1e-05 58data: n= 2000 N= 10 59strands: + 60sample: seed= 0 seqfrac= 1 61Letter frequencies in dataset: 62A 0.255 C 0.235 G 0.261 T 0.249 63Background letter frequencies (from dataset with add-one prior applied): 64A 0.255 C 0.236 G 0.260 T 0.249 65******************************************************************************** 66 67 68******************************************************************************** 69MOTIF 1 width = 10 sites = 10 llr = 140 E-value = 1.1e-022 70******************************************************************************** 71-------------------------------------------------------------------------------- 72 Motif 1 Description 73-------------------------------------------------------------------------------- 74Simplified A :::aa::::a 75pos.-specific C a:a:::a::: 76probability G :::::::a:: 77matrix T :a:::a::a: 78 79 bits 2.1 *** ** * 80 1.9 ********** 81 1.7 ********** 82 1.5 ********** 83Information 1.3 ********** 84content 1.0 ********** 85(20.1 bits) 0.8 ********** 86 0.6 ********** 87 0.4 ********** 88 0.2 ********** 89 0.0 ---------- 90 91Multilevel CTCAATCGTA 92consensus 93sequence 94 95-------------------------------------------------------------------------------- 96 97-------------------------------------------------------------------------------- 98 Motif 1 sites sorted by position p-value 99-------------------------------------------------------------------------------- 100Sequence name Start P-value Site 101------------- ----- --------- ---------- 102SEQ10; 3 8.71e-07 TT CTCAATCGTA GAGTATGCTT 103SEQ9; 93 8.71e-07 CGCCTAGAAA CTCAATCGTA GAGTATCACG 104SEQ8; 172 8.71e-07 CCCGGAGTAT CTCAATCGTA GATGAATACC 105SEQ7; 177 8.71e-07 AAGTCTTTGA CTCAATCGTA GACCCAACAC 106SEQ6; 105 8.71e-07 GTCAGCCGGT CTCAATCGTA GATCAGAGGC 107SEQ5; 185 8.71e-07 ACGGGCAAGC CTCAATCGTA GAGGAT 108SEQ4; 173 8.71e-07 GTTCGAGAGC CTCAATCGTA GATAACCTCT 109SEQ3; 112 8.71e-07 GTTATATTGG CTCAATCGTA GATGAAACCA 110SEQ2; 172 8.71e-07 AAGCGTCGTG CTCAATCGTA GATAACAGAG 111SEQ1; 52 8.71e-07 CTTTACTCGG CTCAATCGTA GAGGCGGTGC 112-------------------------------------------------------------------------------- 113 114-------------------------------------------------------------------------------- 115 Motif 1 block diagrams 116-------------------------------------------------------------------------------- 117SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM 118------------- ---------------- ------------- 119SEQ10; 8.7e-07 2_[1]_188 120SEQ9; 8.7e-07 92_[1]_98 121SEQ8; 8.7e-07 171_[1]_19 122SEQ7; 8.7e-07 176_[1]_14 123SEQ6; 8.7e-07 104_[1]_86 124SEQ5; 8.7e-07 184_[1]_6 125SEQ4; 8.7e-07 172_[1]_18 126SEQ3; 8.7e-07 111_[1]_79 127SEQ2; 8.7e-07 171_[1]_19 128SEQ1; 8.7e-07 51_[1]_139 129-------------------------------------------------------------------------------- 130 131-------------------------------------------------------------------------------- 132 Motif 1 in BLOCKS format 133-------------------------------------------------------------------------------- 134BL MOTIF 1 width=10 seqs=10 135SEQ10; ( 3) CTCAATCGTA 1 136SEQ9; ( 93) CTCAATCGTA 1 137SEQ8; ( 172) CTCAATCGTA 1 138SEQ7; ( 177) CTCAATCGTA 1 139SEQ6; ( 105) CTCAATCGTA 1 140SEQ5; ( 185) CTCAATCGTA 1 141SEQ4; ( 173) CTCAATCGTA 1 142SEQ3; ( 112) CTCAATCGTA 1 143SEQ2; ( 172) CTCAATCGTA 1 144SEQ1; ( 52) CTCAATCGTA 1 145// 146 147-------------------------------------------------------------------------------- 148 149-------------------------------------------------------------------------------- 150 Motif 1 position-specific scoring matrix 151-------------------------------------------------------------------------------- 152log-odds matrix: alength= 4 w= 10 n= 1910 bayes= 8.51691 E= 1.1e-022 153 -997 208 -997 -997 154 -997 -997 -997 200 155 -997 208 -997 -997 156 197 -997 -997 -997 157 197 -997 -997 -997 158 -997 -997 -997 200 159 -997 208 -997 -997 160 -997 -997 194 -997 161 -997 -997 -997 200 162 197 -997 -997 -997 163-------------------------------------------------------------------------------- 164 165-------------------------------------------------------------------------------- 166 Motif 1 position-specific probability matrix 167-------------------------------------------------------------------------------- 168letter-probability matrix: alength= 4 w= 10 nsites= 10 E= 1.1e-022 169 0.000000 1.000000 0.000000 0.000000 170 0.000000 0.000000 0.000000 1.000000 171 0.000000 1.000000 0.000000 0.000000 172 1.000000 0.000000 0.000000 0.000000 173 1.000000 0.000000 0.000000 0.000000 174 0.000000 0.000000 0.000000 1.000000 175 0.000000 1.000000 0.000000 0.000000 176 0.000000 0.000000 1.000000 0.000000 177 0.000000 0.000000 0.000000 1.000000 178 1.000000 0.000000 0.000000 0.000000 179-------------------------------------------------------------------------------- 180 181-------------------------------------------------------------------------------- 182 Motif 1 regular expression 183-------------------------------------------------------------------------------- 184CTCAATCGTA 185-------------------------------------------------------------------------------- 186 187 188 189 190Time 0.26 secs. 191 192******************************************************************************** 193 194 195******************************************************************************** 196SUMMARY OF MOTIFS 197******************************************************************************** 198 199-------------------------------------------------------------------------------- 200 Combined block diagrams: non-overlapping sites with p-value < 0.0001 201-------------------------------------------------------------------------------- 202SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM 203------------- ---------------- ------------- 204SEQ1; 1.66e-04 51_[1(8.71e-07)]_139 205SEQ2; 1.66e-04 171_[1(8.71e-07)]_19 206SEQ3; 1.66e-04 111_[1(8.71e-07)]_79 207SEQ4; 1.66e-04 172_[1(8.71e-07)]_18 208SEQ5; 1.66e-04 184_[1(8.71e-07)]_6 209SEQ6; 1.66e-04 104_[1(8.71e-07)]_86 210SEQ7; 1.66e-04 176_[1(8.71e-07)]_14 211SEQ8; 1.66e-04 171_[1(8.71e-07)]_19 212SEQ9; 1.66e-04 92_[1(8.71e-07)]_98 213SEQ10; 1.66e-04 2_[1(8.71e-07)]_188 214-------------------------------------------------------------------------------- 215 216******************************************************************************** 217 218 219******************************************************************************** 220Stopped because nmotifs = 1 reached. 221******************************************************************************** 222 223CPU: pc-arendt9 224 225******************************************************************************** 226