******************************************************************************** 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/381/381.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 46434 1.0000 500 46470 1.0000 500 49989 1.0000 500 54319 1.0000 500 54510 1.0000 500 46475 1.0000 500 50594 1.0000 500 46502 1.0000 500 45275 1.0000 500 45288 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/381/381.seqs.fa -oc motifs/381 -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= 10 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= 5000 N= 10 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.250 C 0.254 G 0.225 T 0.271 Background letter frequencies (from dataset with add-one prior applied): A 0.250 C 0.254 G 0.225 T 0.271 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 10 llr = 117 E-value = 1.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :83::61813:93::: pos.-specific C 1:42:232:1:12::2 probability G 81::7:2:8:a:3:7: matrix T 1138324:16::2a38 bits 2.2 * 1.9 * * 1.7 * * 1.5 ** * Relative 1.3 * * ** ** ** Entropy 1.1 ** ** ** ** *** (16.8 bits) 0.9 ** ** ** ** *** 0.6 ** *** ***** *** 0.4 ****** ***** *** 0.2 ************ *** 0.0 ---------------- Multilevel GACTGATAGTGAATGT consensus ACTCCC A G TC sequence T TG C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 50594 369 2.89e-09 ATAATCCCAG GATTGACAGTGAGTGT TCCAATCGCA 46502 467 1.61e-08 CGAAGGCGAC GACTGACAGTGAATTT ACCAAGGGCG 45288 75 1.08e-07 TCCGTGCCCC GATTGAAAGAGAATGT GCATCACTTT 54510 190 2.79e-07 GTTTCCTGTG GACCGATAGTGATTGC CTCTACCGTC 45275 430 1.04e-06 CGAGGAAGTT GATCGTTCGTGAGTGT GGATTTCAAA 54319 246 4.24e-06 AAAGCTCATA GAATTAGAATGACTTT TAGAAAAAAT 46475 32 4.55e-06 GATTGTCGAA CAATGATCGAGAATTT TTTTCAGGGG 46434 335 1.02e-05 CCTATTGGGA GGATTCTAGCGATTGT TGCTCGAGTC 46470 327 1.71e-05 TCAATTGCAC TACTTCCATTGACTGT CTGTCTCCTG 49989 324 2.34e-05 GTAAATCCGA GTCTGTGAGAGCGTGC GGCGCATCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50594 2.9e-09 368_[+1]_116 46502 1.6e-08 466_[+1]_18 45288 1.1e-07 74_[+1]_410 54510 2.8e-07 189_[+1]_295 45275 1e-06 429_[+1]_55 54319 4.2e-06 245_[+1]_239 46475 4.6e-06 31_[+1]_453 46434 1e-05 334_[+1]_150 46470 1.7e-05 326_[+1]_158 49989 2.3e-05 323_[+1]_161 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=10 50594 ( 369) GATTGACAGTGAGTGT 1 46502 ( 467) GACTGACAGTGAATTT 1 45288 ( 75) GATTGAAAGAGAATGT 1 54510 ( 190) GACCGATAGTGATTGC 1 45275 ( 430) GATCGTTCGTGAGTGT 1 54319 ( 246) GAATTAGAATGACTTT 1 46475 ( 32) CAATGATCGAGAATTT 1 46434 ( 335) GGATTCTAGCGATTGT 1 46470 ( 327) TACTTCCATTGACTGT 1 49989 ( 324) GTCTGTGAGAGCGTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 4850 bayes= 8.91886 E= 1.1e+001 -997 -134 183 -144 168 -997 -117 -144 27 65 -997 14 -997 -35 -997 156 -997 -997 164 14 126 -35 -997 -44 -132 24 -17 56 168 -35 -997 -997 -132 -997 183 -144 27 -134 -997 114 -997 -997 215 -997 185 -134 -997 -997 27 -35 42 -44 -997 -997 -997 188 -997 -997 164 14 -997 -35 -997 156 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 1.1e+001 0.000000 0.100000 0.800000 0.100000 0.800000 0.000000 0.100000 0.100000 0.300000 0.400000 0.000000 0.300000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.700000 0.300000 0.600000 0.200000 0.000000 0.200000 0.100000 0.300000 0.200000 0.400000 0.800000 0.200000 0.000000 0.000000 0.100000 0.000000 0.800000 0.100000 0.300000 0.100000 0.000000 0.600000 0.000000 0.000000 1.000000 0.000000 0.900000 0.100000 0.000000 0.000000 0.300000 0.200000 0.300000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.700000 0.300000 0.000000 0.200000 0.000000 0.800000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GA[CAT][TC][GT][ACT][TCG][AC]G[TA]GA[AGCT]T[GT][TC] -------------------------------------------------------------------------------- Time 0.93 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 7 llr = 85 E-value = 1.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 63:4::9:6:a: pos.-specific C ::::::19:::1 probability G 17::a3:14a:9 matrix T 3:a6:7:::::: bits 2.2 * * 1.9 * * ** 1.7 * * ** 1.5 * * ** *** Relative 1.3 ** * ** *** Entropy 1.1 ** ******** (17.5 bits) 0.9 *********** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel AGTTGTACAGAG consensus TA A G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 46475 344 1.43e-07 CTACCGGTAG AGTAGTACAGAG AGACTTCCTT 46434 184 1.43e-07 CTAGAGCGCT AGTAGTACAGAG CTAGTAGTTA 45288 164 5.15e-07 CGCTACGTGC TGTTGTACGGAG TATTAGCAAG 54510 112 1.54e-06 TGTTGGGTGT AATTGGACGGAG AGACTCACGC 46470 301 2.86e-06 GGCACGGCAC TGTTGTACAGAC TGTTTCAATT 49989 143 5.03e-06 AACACACATA GGTAGTAGGGAG GAGTCATCAG 45275 205 5.38e-06 TCTGCCGAAA AATTGGCCAGAG GCGTTGAGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46475 1.4e-07 343_[+2]_145 46434 1.4e-07 183_[+2]_305 45288 5.1e-07 163_[+2]_325 54510 1.5e-06 111_[+2]_377 46470 2.9e-06 300_[+2]_188 49989 5e-06 142_[+2]_346 45275 5.4e-06 204_[+2]_284 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=7 46475 ( 344) AGTAGTACAGAG 1 46434 ( 184) AGTAGTACAGAG 1 45288 ( 164) TGTTGTACGGAG 1 54510 ( 112) AATTGGACGGAG 1 46470 ( 301) TGTTGTACAGAC 1 49989 ( 143) GGTAGTAGGGAG 1 45275 ( 205) AATTGGCCAGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 4890 bayes= 9.02018 E= 1.2e+001 119 -945 -65 7 19 -945 167 -945 -945 -945 -945 188 78 -945 -945 107 -945 -945 215 -945 -945 -945 35 139 178 -83 -945 -945 -945 175 -65 -945 119 -945 93 -945 -945 -945 215 -945 200 -945 -945 -945 -945 -83 193 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 1.2e+001 0.571429 0.000000 0.142857 0.285714 0.285714 0.000000 0.714286 0.000000 0.000000 0.000000 0.000000 1.000000 0.428571 0.000000 0.000000 0.571429 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.714286 0.857143 0.142857 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.571429 0.000000 0.428571 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.857143 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AT][GA]T[TA]G[TG]AC[AG]GAG -------------------------------------------------------------------------------- Time 1.81 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 8 llr = 105 E-value = 2.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :9:4:33:1:1:3::: pos.-specific C 81:188:::1:85::: probability G ::1:3:19:::311:3 matrix T 3:95::61999:19a8 bits 2.2 1.9 * 1.7 * 1.5 * * * Relative 1.3 ** * ***** ** Entropy 1.1 *** ** ***** *** (19.0 bits) 0.9 *** ** ***** *** 0.6 *** ******** *** 0.4 ************ *** 0.2 **************** 0.0 ---------------- Multilevel CATTCCTGTTTCCTTT consensus T AGAA GA G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 45288 225 3.98e-08 CTTTCAAAGG CATCGCTGTTTCCTTT GATTCGAAGA 54510 7 7.58e-08 CGTTTC CATTGCTGTTACCTTT CAATCATGTA 46475 59 1.56e-07 TTTCAGGGGC TATACCAGTTTCGTTT CCCGCTACTC 54319 416 1.70e-07 CGTATGCCCC CATACCAGATTCATTT CATAATTTTT 50594 80 2.24e-07 GGTGAGCAGT CATTCATGTTTGATTG CCCTGTCAAA 46434 377 4.13e-07 TGTTCGTATT CCTACATGTTTCCTTG CTTTGCAAGA 49989 162 1.40e-06 GAGGAGTCAT CAGTCCTTTTTCCGTT ATGACGCGTT 46502 403 3.50e-06 GCAATTTCCC TATTCCGGTCTGTTTT TGGTATAGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45288 4e-08 224_[+3]_260 54510 7.6e-08 6_[+3]_478 46475 1.6e-07 58_[+3]_426 54319 1.7e-07 415_[+3]_69 50594 2.2e-07 79_[+3]_405 46434 4.1e-07 376_[+3]_108 49989 1.4e-06 161_[+3]_323 46502 3.5e-06 402_[+3]_82 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=8 45288 ( 225) CATCGCTGTTTCCTTT 1 54510 ( 7) CATTGCTGTTACCTTT 1 46475 ( 59) TATACCAGTTTCGTTT 1 54319 ( 416) CATACCAGATTCATTT 1 50594 ( 80) CATTCATGTTTGATTG 1 46434 ( 377) CCTACATGTTTCCTTG 1 49989 ( 162) CAGTCCTTTTTCCGTT 1 46502 ( 403) TATTCCGGTCTGTTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 4850 bayes= 9.24139 E= 2.2e+001 -965 156 -965 -12 181 -102 -965 -965 -965 -965 -84 169 59 -102 -965 88 -965 156 15 -965 0 156 -965 -965 0 -965 -84 120 -965 -965 196 -112 -100 -965 -965 169 -965 -102 -965 169 -100 -965 -965 169 -965 156 15 -965 0 97 -84 -112 -965 -965 -84 169 -965 -965 -965 188 -965 -965 15 147 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 8 E= 2.2e+001 0.000000 0.750000 0.000000 0.250000 0.875000 0.125000 0.000000 0.000000 0.000000 0.000000 0.125000 0.875000 0.375000 0.125000 0.000000 0.500000 0.000000 0.750000 0.250000 0.000000 0.250000 0.750000 0.000000 0.000000 0.250000 0.000000 0.125000 0.625000 0.000000 0.000000 0.875000 0.125000 0.125000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.875000 0.125000 0.000000 0.000000 0.875000 0.000000 0.750000 0.250000 0.000000 0.250000 0.500000 0.125000 0.125000 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT]AT[TA][CG][CA][TA]GTTT[CG][CA]TT[TG] -------------------------------------------------------------------------------- Time 2.70 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46434 2.05e-08 183_[+2(1.43e-07)]_139_\ [+1(1.02e-05)]_26_[+3(4.13e-07)]_108 46470 8.51e-04 300_[+2(2.86e-06)]_14_\ [+1(1.71e-05)]_158 49989 3.33e-06 142_[+2(5.03e-06)]_7_[+3(1.40e-06)]_\ 146_[+1(2.34e-05)]_161 54319 1.15e-05 245_[+1(4.24e-06)]_154_\ [+3(1.70e-07)]_69 54510 1.40e-09 6_[+3(7.58e-08)]_89_[+2(1.54e-06)]_\ 66_[+1(2.79e-07)]_295 46475 4.01e-09 31_[+1(4.55e-06)]_11_[+3(1.56e-07)]_\ 238_[+2(5.67e-05)]_19_[+2(1.43e-07)]_145 50594 1.59e-08 79_[+3(2.24e-07)]_273_\ [+1(2.89e-09)]_116 46502 1.22e-06 402_[+3(3.50e-06)]_48_\ [+1(1.61e-08)]_18 45275 9.90e-05 204_[+2(5.38e-06)]_213_\ [+1(1.04e-06)]_55 45288 1.15e-10 74_[+1(1.08e-07)]_73_[+2(5.15e-07)]_\ 49_[+3(3.98e-08)]_260 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************