******************************************************************************** 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/166/166.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 21117 1.0000 500 21751 1.0000 500 22871 1.0000 500 23904 1.0000 500 24856 1.0000 500 2526 1.0000 500 25374 1.0000 500 261531 1.0000 500 263310 1.0000 500 35266 1.0000 500 35771 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/166/166.seqs.fa -oc motifs/166 -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 0.287 C 0.229 G 0.231 T 0.253 Background letter frequencies (from dataset with add-one prior applied): A 0.287 C 0.229 G 0.231 T 0.253 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 11 llr = 120 E-value = 1.0e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :4::71:::::1 pos.-specific C 42:2::::::63 probability G 33:8311:a::6 matrix T 42a::89a:a4: bits 2.1 * 1.9 * *** 1.7 * *** 1.5 ** **** Relative 1.3 ** **** Entropy 1.1 ********* (15.7 bits) 0.9 ********** 0.6 ********** 0.4 * ********** 0.2 * ********** 0.0 ------------ Multilevel CATGATTTGTCG consensus TG G TC sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 21117 285 5.66e-07 TTCGTTTGTG CATGATTTGTTG AGTAGAAATA 23904 162 7.72e-07 TGACATTGTG TATGATTTGTTG TATAATTACC 263310 489 1.01e-06 CGAGGTTTAC CATGATTTGTCC 24856 239 2.46e-06 AGCAGGAGCG GCTGGTTTGTCG GTGAGGGTGC 21751 123 2.85e-06 AAGCCGAGAT GCTGATTTGTCC TGCTTCATCT 261531 167 6.43e-06 AGTCTAGGCT TGTCGTTTGTCG TTCTTCTCTC 25374 261 6.43e-06 ACCCCGCTGT CGTGAATTGTCG TCGGTTTGCC 35771 111 8.58e-06 GAAGCTCGTG TTTGATTTGTCA AATGAGAAGG 35266 242 1.07e-05 CTTGGATTCT GATGAGTTGTTG GGAGAAGATC 22871 311 1.32e-05 GGAGAGTGGT TGTCGTTTGTCC GGGAGGAGAT 2526 4 1.44e-05 TGG CTTGATGTGTTG GTTGTTGAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21117 5.7e-07 284_[+1]_204 23904 7.7e-07 161_[+1]_327 263310 1e-06 488_[+1] 24856 2.5e-06 238_[+1]_250 21751 2.9e-06 122_[+1]_366 261531 6.4e-06 166_[+1]_322 25374 6.4e-06 260_[+1]_228 35771 8.6e-06 110_[+1]_378 35266 1.1e-05 241_[+1]_247 22871 1.3e-05 310_[+1]_178 2526 1.4e-05 3_[+1]_485 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=11 21117 ( 285) CATGATTTGTTG 1 23904 ( 162) TATGATTTGTTG 1 263310 ( 489) CATGATTTGTCC 1 24856 ( 239) GCTGGTTTGTCG 1 21751 ( 123) GCTGATTTGTCC 1 261531 ( 167) TGTCGTTTGTCG 1 25374 ( 261) CGTGAATTGTCG 1 35771 ( 111) TTTGATTTGTCA 1 35266 ( 242) GATGAGTTGTTG 1 22871 ( 311) TGTCGTTTGTCC 1 2526 ( 4) CTTGATGTGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5379 bayes= 8.93074 E= 1.0e-003 -1010 67 24 52 34 -33 24 -48 -1010 -1010 -1010 198 -1010 -33 182 -1010 134 -1010 24 -1010 -166 -1010 -135 169 -1010 -1010 -135 184 -1010 -1010 -1010 198 -1010 -1010 211 -1010 -1010 -1010 -1010 198 -1010 148 -1010 52 -166 25 146 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 11 E= 1.0e-003 0.000000 0.363636 0.272727 0.363636 0.363636 0.181818 0.272727 0.181818 0.000000 0.000000 0.000000 1.000000 0.000000 0.181818 0.818182 0.000000 0.727273 0.000000 0.272727 0.000000 0.090909 0.000000 0.090909 0.818182 0.000000 0.000000 0.090909 0.909091 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.636364 0.000000 0.363636 0.090909 0.272727 0.636364 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CTG][AG]TG[AG]TTTGT[CT][GC] -------------------------------------------------------------------------------- Time 1.28 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 6 llr = 107 E-value = 5.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :28:2:::2::::2::3:2:: pos.-specific C 28235:a2523838:a73887 probability G ::::::::28323:2::3::: matrix T 8::73a:82:3:3:8::3:23 bits 2.1 * * 1.9 ** * 1.7 ** * 1.5 * ** * * * * ** Relative 1.3 *** *** * * *** ** Entropy 1.1 **** *** * * **** *** (25.8 bits) 0.9 **** *** * * **** *** 0.6 ******** * * **** *** 0.4 ******** ************ 0.2 ********************* 0.0 --------------------- Multilevel TCATCTCTCGCCCCTCCCCCC consensus CT G G AG T sequence T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 263310 293 3.54e-11 ATTCTCACAT TCCTCTCTCGGCGCTCCTCCC GTCTTCGTCC 35771 441 4.53e-10 AACCGACGGA TCATCTCTTGCCCATCCCCCC TCCCCACACA 2526 225 3.58e-09 CATCATATCA TCACTTCTCGTCTCTCACACT AACTGCTTCA 21751 282 8.16e-09 AATCTGCCAC TCACCTCTCCTCTCGCCTCTC TCTCGTGAAC 24856 352 1.14e-08 ATCCATAACA TAATTTCTGGGGGCTCAGCCC AACAGAGGGG 22871 227 1.56e-08 TGGATTTCCA CCATATCCAGCCCCTCCGCCT CCTCCGTATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263310 3.5e-11 292_[+2]_187 35771 4.5e-10 440_[+2]_39 2526 3.6e-09 224_[+2]_255 21751 8.2e-09 281_[+2]_198 24856 1.1e-08 351_[+2]_128 22871 1.6e-08 226_[+2]_253 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=6 263310 ( 293) TCCTCTCTCGGCGCTCCTCCC 1 35771 ( 441) TCATCTCTTGCCCATCCCCCC 1 2526 ( 225) TCACTTCTCGTCTCTCACACT 1 21751 ( 282) TCACCTCTCCTCTCGCCTCTC 1 24856 ( 352) TAATTTCTGGGGGCTCAGCCC 1 22871 ( 227) CCATATCCAGCCCCTCCGCCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5280 bayes= 10.2276 E= 5.3e+000 -923 -45 -923 172 -78 186 -923 -923 154 -45 -923 -923 -923 54 -923 139 -78 113 -923 40 -923 -923 -923 198 -923 213 -923 -923 -923 -45 -923 172 -78 113 -47 -60 -923 -45 185 -923 -923 54 53 40 -923 186 -47 -923 -923 54 53 40 -78 186 -923 -923 -923 -923 -47 172 -923 213 -923 -923 22 154 -923 -923 -923 54 53 40 -78 186 -923 -923 -923 186 -923 -60 -923 154 -923 40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 5.3e+000 0.000000 0.166667 0.000000 0.833333 0.166667 0.833333 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.166667 0.500000 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.166667 0.500000 0.166667 0.166667 0.000000 0.166667 0.833333 0.000000 0.000000 0.333333 0.333333 0.333333 0.000000 0.833333 0.166667 0.000000 0.000000 0.333333 0.333333 0.333333 0.166667 0.833333 0.000000 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.333333 0.333333 0.333333 0.166667 0.833333 0.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.666667 0.000000 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TCA[TC][CT]TCTCG[CGT]C[CGT]CTC[CA][CGT]CC[CT] -------------------------------------------------------------------------------- Time 2.57 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 7 llr = 93 E-value = 6.3e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A a::3::1::1::13: pos.-specific C :a4193::63a7::9 probability G :::3::7::4::::1 matrix T ::63171a41:397: bits 2.1 * * 1.9 * * * 1.7 ** * * 1.5 ** * * * * Relative 1.3 ** * * *** * Entropy 1.1 *** ** ** ***** (19.2 bits) 0.9 *** ***** ***** 0.6 *** ***** ***** 0.4 *** ***** ***** 0.2 *** *********** 0.0 --------------- Multilevel ACTACTGTCGCCTTC consensus CG C TC T A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 21751 344 5.69e-09 TCACCCCCAC ACTTCTGTTGCCTTC TCTGCACCTG 261531 281 9.87e-08 CCACCTCACA ACCCCTGTCTCCTTC AAGAACTTTG 2526 408 2.36e-07 ACGGCTACAA ACCACCGTCCCTTTC TTGCTACGTC 24856 39 4.44e-07 TAGCTGAGGT ACTGCTATTGCCTAC ACTGCCACGT 35266 439 6.23e-07 CTCCAAACGA ACCGCTGTTGCCAAC GCCTCCTTTC 22871 393 1.02e-06 TGAGTTTGGT ACTTTTGTCCCCTTG ACAACGAAAT 263310 202 1.98e-06 CCAACTGAGT ACTACCTTCACTTTC TAGCTCATGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21751 5.7e-09 343_[+3]_142 261531 9.9e-08 280_[+3]_205 2526 2.4e-07 407_[+3]_78 24856 4.4e-07 38_[+3]_447 35266 6.2e-07 438_[+3]_47 22871 1e-06 392_[+3]_93 263310 2e-06 201_[+3]_284 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=7 21751 ( 344) ACTTCTGTTGCCTTC 1 261531 ( 281) ACCCCTGTCTCCTTC 1 2526 ( 408) ACCACCGTCCCTTTC 1 24856 ( 39) ACTGCTATTGCCTAC 1 35266 ( 439) ACCGCTGTTGCCAAC 1 22871 ( 393) ACTTTTGTCCCCTTG 1 263310 ( 202) ACTACCTTCACTTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 5346 bayes= 10.1814 E= 6.3e+001 180 -945 -945 -945 -945 213 -945 -945 -945 91 -945 117 -1 -68 30 17 -945 191 -945 -82 -945 32 -945 149 -100 -945 163 -82 -945 -945 -945 198 -945 132 -945 76 -100 32 89 -82 -945 213 -945 -945 -945 164 -945 17 -100 -945 -945 176 -1 -945 -945 149 -945 191 -69 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 7 E= 6.3e+001 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.428571 0.000000 0.571429 0.285714 0.142857 0.285714 0.285714 0.000000 0.857143 0.000000 0.142857 0.000000 0.285714 0.000000 0.714286 0.142857 0.000000 0.714286 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.571429 0.000000 0.428571 0.142857 0.285714 0.428571 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.714286 0.000000 0.285714 0.142857 0.000000 0.000000 0.857143 0.285714 0.000000 0.000000 0.714286 0.000000 0.857143 0.142857 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- AC[TC][AGT]C[TC]GT[CT][GC]C[CT]T[TA]C -------------------------------------------------------------------------------- Time 3.78 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21117 7.40e-03 284_[+1(5.66e-07)]_204 21751 8.14e-12 122_[+1(2.85e-06)]_147_\ [+2(8.16e-09)]_41_[+3(5.69e-09)]_142 22871 7.77e-09 226_[+2(1.56e-08)]_63_\ [+1(1.32e-05)]_70_[+3(1.02e-06)]_93 23904 1.24e-02 161_[+1(7.72e-07)]_39_\ [+1(6.43e-05)]_276 24856 5.70e-10 38_[+3(4.44e-07)]_185_\ [+1(2.46e-06)]_101_[+2(1.14e-08)]_128 2526 5.54e-10 3_[+1(1.44e-05)]_209_[+2(3.58e-09)]_\ 162_[+3(2.36e-07)]_78 25374 2.23e-02 260_[+1(6.43e-06)]_228 261531 2.58e-06 166_[+1(6.43e-06)]_102_\ [+3(9.87e-08)]_205 263310 4.53e-12 201_[+3(1.98e-06)]_76_\ [+2(3.54e-11)]_175_[+1(1.01e-06)] 35266 2.36e-05 241_[+1(1.07e-05)]_185_\ [+3(6.23e-07)]_47 35771 1.02e-07 110_[+1(8.58e-06)]_318_\ [+2(4.53e-10)]_39 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************