******************************************************************************** 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/308/308.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 21279 1.0000 500 23615 1.0000 500 24565 1.0000 500 24568 1.0000 500 25065 1.0000 500 25121 1.0000 500 25246 1.0000 500 263459 1.0000 500 37495 1.0000 500 5885 1.0000 500 6368 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/308/308.seqs.fa -oc motifs/308 -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= 11 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= 5500 N= 11 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.256 C 0.247 G 0.239 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.256 C 0.247 G 0.239 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 11 llr = 123 E-value = 3.7e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :124:9:::5:5116 pos.-specific C ::15::51:1:4::: probability G 825:a1:99181493 matrix T 2721::5:14215:1 bits 2.1 * 1.9 * 1.7 * ** * 1.4 * ** ** * * Relative 1.2 * ** ** * * Entropy 1.0 * ***** * * (16.1 bits) 0.8 ** ***** * ** 0.6 ** ****** * *** 0.4 ********* ***** 0.2 *************** 0.0 --------------- Multilevel GTGCGACGGAGATGA consensus A T T CG G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 23615 110 7.48e-08 GGAGTTCGGT GTACGATGGAGAGGA TAATATGTAT 6368 276 6.76e-07 ATCGAGGAGG GGGCGACGGGGAGGA AGGATGCTGG 5885 175 6.76e-07 GTAGCACGGA GTACGACGGAGCAGA GAGTAACGCA 37495 256 1.14e-06 AGTACAATAA GTGCGATGGTTGTGA AGGAGATAAT 263459 199 1.14e-06 ACAGCCTGCT GTTAGACGGAGTGGA CGTGGTTGCG 25246 68 1.14e-06 ACATTTAGTT GTGCGATGTTGATGG CTCGGGGAAG 25121 301 1.14e-06 AGACGTACAT TTTAGATGGAGCTGA ATTGTCGTAT 21279 467 2.04e-06 TGTGTGGATT GAGTGACGGTGATGA CGTGCACCGC 24565 225 1.80e-05 TGGTCAACTT GTCCGACGGAGAGAT GAGACGAAAG 24568 250 1.91e-05 ATTCCTCTGT GGGAGACCGCGCTGG GCTTCTTGAC 25065 320 2.86e-05 TATCTGGTGC TTGAGGTGGTTCTGG GAGGTCAGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23615 7.5e-08 109_[+1]_376 6368 6.8e-07 275_[+1]_210 5885 6.8e-07 174_[+1]_311 37495 1.1e-06 255_[+1]_230 263459 1.1e-06 198_[+1]_287 25246 1.1e-06 67_[+1]_418 25121 1.1e-06 300_[+1]_185 21279 2e-06 466_[+1]_19 24565 1.8e-05 224_[+1]_261 24568 1.9e-05 249_[+1]_236 25065 2.9e-05 319_[+1]_166 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=11 23615 ( 110) GTACGATGGAGAGGA 1 6368 ( 276) GGGCGACGGGGAGGA 1 5885 ( 175) GTACGACGGAGCAGA 1 37495 ( 256) GTGCGATGGTTGTGA 1 263459 ( 199) GTTAGACGGAGTGGA 1 25246 ( 68) GTGCGATGTTGATGG 1 25121 ( 301) TTTAGATGGAGCTGA 1 21279 ( 467) GAGTGACGGTGATGA 1 24565 ( 225) GTCCGACGGAGAGAT 1 24568 ( 250) GGGAGACCGCGCTGG 1 25065 ( 320) TTGAGGTGGTTCTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 5346 bayes= 9.27758 E= 3.7e-001 -1010 -1010 178 -51 -149 -1010 -39 149 -49 -144 119 -51 51 114 -1010 -150 -1010 -1010 207 -1010 183 -1010 -139 -1010 -1010 114 -1010 81 -1010 -144 193 -1010 -1010 -1010 193 -150 83 -144 -139 49 -1010 -1010 178 -51 83 56 -139 -150 -149 -1010 61 108 -149 -1010 193 -1010 131 -1010 19 -150 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 11 E= 3.7e-001 0.000000 0.000000 0.818182 0.181818 0.090909 0.000000 0.181818 0.727273 0.181818 0.090909 0.545455 0.181818 0.363636 0.545455 0.000000 0.090909 0.000000 0.000000 1.000000 0.000000 0.909091 0.000000 0.090909 0.000000 0.000000 0.545455 0.000000 0.454545 0.000000 0.090909 0.909091 0.000000 0.000000 0.000000 0.909091 0.090909 0.454545 0.090909 0.090909 0.363636 0.000000 0.000000 0.818182 0.181818 0.454545 0.363636 0.090909 0.090909 0.090909 0.000000 0.363636 0.545455 0.090909 0.000000 0.909091 0.000000 0.636364 0.000000 0.272727 0.090909 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GTG[CA]GA[CT]GG[AT]G[AC][TG]G[AG] -------------------------------------------------------------------------------- Time 1.12 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 7 llr = 97 E-value = 1.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 4:3119116:1:a:: pos.-specific C 6a:99:79:a66:a: probability G ::3::1:::::4::9 matrix T ::4:::1:4:3:::1 bits 2.1 * * ** 1.9 * * ** 1.7 * * ** 1.4 * *** * * *** Relative 1.2 * *** * * *** Entropy 1.0 ** *** *** **** (20.1 bits) 0.8 ** ******* **** 0.6 ** ************ 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel CCTCCACCACCCACG consensus A A T TG sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 24565 361 8.74e-10 TCGGCCTTTT CCTCCACCACCCACG ACTGTCTCCG 263459 263 7.70e-09 TGCTCGACGA CCGCCACCACCGACG AAGACGTCCT 6368 473 2.48e-07 CACCGTAACA ACACCAACTCCGACG AAGAGAACCG 21279 230 3.81e-07 CACTCTCGCT ACGCAACCTCTCACG CAGGGCTTGA 25065 190 4.48e-07 TTTATGACAT CCTACATCACCGACG CCACCCGACA 24568 280 7.87e-07 TTGACACTCG ACACCACATCACACG ATGAACTTTC 23615 381 7.87e-07 CTCACGTTCT CCTCCGCCACTCACT GAAAATCCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24565 8.7e-10 360_[+2]_125 263459 7.7e-09 262_[+2]_223 6368 2.5e-07 472_[+2]_13 21279 3.8e-07 229_[+2]_256 25065 4.5e-07 189_[+2]_296 24568 7.9e-07 279_[+2]_206 23615 7.9e-07 380_[+2]_105 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=7 24565 ( 361) CCTCCACCACCCACG 1 263459 ( 263) CCGCCACCACCGACG 1 6368 ( 473) ACACCAACTCCGACG 1 21279 ( 230) ACGCAACCTCTCACG 1 25065 ( 190) CCTACATCACCGACG 1 24568 ( 280) ACACCACATCACACG 1 23615 ( 381) CCTCCGCCACTCACT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 5346 bayes= 10.1814 E= 1.7e+001 74 121 -945 -945 -945 202 -945 -945 16 -945 26 73 -84 179 -945 -945 -84 179 -945 -945 174 -945 -74 -945 -84 153 -945 -85 -84 179 -945 -945 116 -945 -945 73 -945 202 -945 -945 -84 121 -945 15 -945 121 84 -945 196 -945 -945 -945 -945 202 -945 -945 -945 -945 184 -85 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 7 E= 1.7e+001 0.428571 0.571429 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.000000 0.285714 0.428571 0.142857 0.857143 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.142857 0.714286 0.000000 0.142857 0.142857 0.857143 0.000000 0.000000 0.571429 0.000000 0.000000 0.428571 0.000000 1.000000 0.000000 0.000000 0.142857 0.571429 0.000000 0.285714 0.000000 0.571429 0.428571 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.857143 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CA]C[TAG]CCACC[AT]C[CT][CG]ACG -------------------------------------------------------------------------------- Time 2.19 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 14 sites = 11 llr = 119 E-value = 1.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :85::13::3:21: pos.-specific C 8:15:1::12::4: probability G 2155:84:93a:55 matrix T :1:1a:4a:3:815 bits 2.1 * 1.9 * * * 1.7 * ** * 1.4 * ** * Relative 1.2 * ** ** ** Entropy 1.0 ** ** ** ** * (15.7 bits) 0.8 ** ** ** ** * 0.6 ****** ** ** * 0.4 ********* **** 0.2 ********* **** 0.0 -------------- Multilevel CAACTGGTGAGTGG consensus GG T G CT sequence A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 25065 345 1.75e-08 GAGGTCAGTT CAGGTGTTGGGTGG TGCTCCAGTG 25121 366 1.88e-07 GAAGAATTGC CAAGTGGTGAGTGT GTCGGAGGTT 5885 271 3.82e-07 CAATGCTGCA CAGCTGATGGGTGT ATCATCAATT 23615 272 1.33e-06 CTCTTACCTC CAGCTGGTGTGACG CCGCCTACCG 24565 179 1.88e-06 TGATGGCGGA GAGGTGATGTGTCG CCTGATTTGA 25246 435 3.10e-06 TTCCCCAAAC CACCTGTTGTGTCT GTTGCTCCAC 6368 18 4.61e-06 ACTAAATCAC CAGTTGTTGCGTCT TGGCCTCGAA 24568 437 1.09e-05 ACGCCAGTTC CAAGTGATGAGAAT GCACCGTCAT 263459 411 2.25e-05 TTCACTTCAA CTACTGGTCGGTGG TGGCTGCCTT 21279 314 2.70e-05 CTTCATTGGG CGAGTATTGCGTGG CGACGGCAGT 37495 153 3.57e-05 CGTCGGAACT GAACTCGTGAGTTG TGAGAGAGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25065 1.8e-08 344_[+3]_142 25121 1.9e-07 365_[+3]_121 5885 3.8e-07 270_[+3]_216 23615 1.3e-06 271_[+3]_215 24565 1.9e-06 178_[+3]_308 25246 3.1e-06 434_[+3]_52 6368 4.6e-06 17_[+3]_469 24568 1.1e-05 436_[+3]_50 263459 2.2e-05 410_[+3]_76 21279 2.7e-05 313_[+3]_173 37495 3.6e-05 152_[+3]_334 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=14 seqs=11 25065 ( 345) CAGGTGTTGGGTGG 1 25121 ( 366) CAAGTGGTGAGTGT 1 5885 ( 271) CAGCTGATGGGTGT 1 23615 ( 272) CAGCTGGTGTGACG 1 24565 ( 179) GAGGTGATGTGTCG 1 25246 ( 435) CACCTGTTGTGTCT 1 6368 ( 18) CAGTTGTTGCGTCT 1 24568 ( 437) CAAGTGATGAGAAT 1 263459 ( 411) CTACTGGTCGGTGG 1 21279 ( 314) CGAGTATTGCGTGG 1 37495 ( 153) GAACTCGTGAGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 5357 bayes= 8.92481 E= 1.6e+000 -1010 173 -39 -1010 168 -1010 -139 -150 83 -144 93 -1010 -1010 88 93 -150 -1010 -1010 -1010 195 -149 -144 178 -1010 9 -1010 61 49 -1010 -1010 -1010 195 -1010 -144 193 -1010 9 -44 19 8 -1010 -1010 207 -1010 -49 -1010 -1010 166 -149 56 93 -150 -1010 -1010 119 81 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 11 E= 1.6e+000 0.000000 0.818182 0.181818 0.000000 0.818182 0.000000 0.090909 0.090909 0.454545 0.090909 0.454545 0.000000 0.000000 0.454545 0.454545 0.090909 0.000000 0.000000 0.000000 1.000000 0.090909 0.090909 0.818182 0.000000 0.272727 0.000000 0.363636 0.363636 0.000000 0.000000 0.000000 1.000000 0.000000 0.090909 0.909091 0.000000 0.272727 0.181818 0.272727 0.272727 0.000000 0.000000 1.000000 0.000000 0.181818 0.000000 0.000000 0.818182 0.090909 0.363636 0.454545 0.090909 0.000000 0.000000 0.545455 0.454545 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CA[AG][CG]TG[GTA]TG[AGT]GT[GC][GT] -------------------------------------------------------------------------------- Time 3.25 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21279 5.23e-07 229_[+2(3.81e-07)]_69_\ [+3(2.70e-05)]_139_[+1(2.04e-06)]_19 23615 3.16e-09 109_[+1(7.48e-08)]_147_\ [+3(1.33e-06)]_95_[+2(7.87e-07)]_105 24565 1.27e-09 178_[+3(1.88e-06)]_32_\ [+1(1.80e-05)]_121_[+2(8.74e-10)]_125 24568 3.31e-06 249_[+1(1.91e-05)]_15_\ [+2(7.87e-07)]_142_[+3(1.09e-05)]_50 25065 8.26e-09 189_[+2(4.48e-07)]_115_\ [+1(2.86e-05)]_10_[+3(1.75e-08)]_142 25121 4.18e-06 300_[+1(1.14e-06)]_50_\ [+3(1.88e-07)]_121 25246 8.98e-05 67_[+1(1.14e-06)]_352_\ [+3(3.10e-06)]_52 263459 7.37e-09 198_[+1(1.14e-06)]_49_\ [+2(7.70e-09)]_133_[+3(2.25e-05)]_76 37495 4.59e-04 152_[+3(3.57e-05)]_89_\ [+1(1.14e-06)]_230 5885 2.78e-06 174_[+1(6.76e-07)]_81_\ [+3(3.82e-07)]_216 6368 2.59e-08 17_[+3(4.61e-06)]_244_\ [+1(6.76e-07)]_182_[+2(2.48e-07)]_13 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************