******************************************************************************** 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/436/436.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 13004 1.0000 500 13096 1.0000 500 52108 1.0000 500 37572 1.0000 500 18280 1.0000 500 49849 1.0000 500 16991 1.0000 500 41615 1.0000 500 34088 1.0000 500 36093 1.0000 500 49029 1.0000 500 45338 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/436/436.seqs.fa -oc motifs/436 -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= 12 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= 6000 N= 12 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.282 C 0.227 G 0.227 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.282 C 0.227 G 0.227 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 14 sites = 8 llr = 100 E-value = 8.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 41131::1::aa:: pos.-specific C 69:8:6:3:3::18 probability G ::8:::53:8:::: matrix T ::1:9454a:::93 bits 2.1 1.9 * ** 1.7 * ** 1.5 * * *** Relative 1.3 * ** ****** Entropy 1.1 ******* ****** (18.1 bits) 0.9 ******* ****** 0.6 ******* ****** 0.4 ******* ****** 0.2 ************** 0.0 -------------- Multilevel CCGCTCGTTGAATC consensus A A TTC C T sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 16991 28 1.92e-08 TAACTTTGAT CCGCTTGTTGAATC GGAAGTTTTC 37572 125 3.25e-07 AAATCTAACA ACGATCGCTGAATC GTGTCCAAAT 36093 191 4.28e-07 TTCATTTGAA ACGCTTGATGAATC CTTGGTTAAT 13004 112 7.21e-07 ACCAGAAGCG CCGCTCTTTCAACC AGTTTCACGA 18280 260 1.30e-06 CGGATTGCAA CAGCTCGCTCAATC TAACAGAAGT 49029 237 1.40e-06 GCCCAAACTG CCACTCTGTGAATT GGGAGAAAGT 34088 299 1.85e-06 AGAACATGAA ACGATTTTTGAATT TGACACCGAC 41615 124 2.66e-06 AGGTCTCCCA CCTCACTGTGAATC TCAACTGGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 16991 1.9e-08 27_[+1]_459 37572 3.2e-07 124_[+1]_362 36093 4.3e-07 190_[+1]_296 13004 7.2e-07 111_[+1]_375 18280 1.3e-06 259_[+1]_227 49029 1.4e-06 236_[+1]_250 34088 1.9e-06 298_[+1]_188 41615 2.7e-06 123_[+1]_363 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=14 seqs=8 16991 ( 28) CCGCTTGTTGAATC 1 37572 ( 125) ACGATCGCTGAATC 1 36093 ( 191) ACGCTTGATGAATC 1 13004 ( 112) CCGCTCTTTCAACC 1 18280 ( 260) CAGCTCGCTCAATC 1 49029 ( 237) CCACTCTGTGAATT 1 34088 ( 299) ACGATTTTTGAATT 1 41615 ( 124) CCTCACTGTGAATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 5844 bayes= 9.51076 E= 8.0e+001 41 146 -965 -965 -117 194 -965 -965 -117 -965 172 -107 -17 172 -965 -965 -117 -965 -965 173 -965 146 -965 51 -965 -965 114 92 -117 14 14 51 -965 -965 -965 192 -965 14 172 -965 183 -965 -965 -965 183 -965 -965 -965 -965 -86 -965 173 -965 172 -965 -8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 8 E= 8.0e+001 0.375000 0.625000 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 0.125000 0.000000 0.750000 0.125000 0.250000 0.750000 0.000000 0.000000 0.125000 0.000000 0.000000 0.875000 0.000000 0.625000 0.000000 0.375000 0.000000 0.000000 0.500000 0.500000 0.125000 0.250000 0.250000 0.375000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.875000 0.000000 0.750000 0.000000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA]CG[CA]T[CT][GT][TCG]T[GC]AAT[CT] -------------------------------------------------------------------------------- Time 1.43 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 5 llr = 92 E-value = 4.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::2:22:424::8:2:::: pos.-specific C ::::::2::::2:8:88::2: probability G 8::28642:68282:2:2:88 matrix T 2aa8:426a::22:2::8a:2 bits 2.1 1.9 ** * * 1.7 ** * * 1.5 ** * * * ** Relative 1.3 ***** * * ** ****** Entropy 1.1 ****** *** ********* (26.6 bits) 0.9 ****** *** ********* 0.6 ****** **** ********* 0.4 ****** **** ********* 0.2 *********** ********* 0.0 --------------------- Multilevel GTTTGGGTTGGAGCACCTTGG consensus T GATAA AACTGTGAG CT sequence CG G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 13096 349 7.73e-11 CACAATTTTT GTTTGGTTTGGGTCACCTTGG CAATCACCGT 18280 282 3.07e-10 TCTAACAGAA GTTTGTAGTGGAGCACCTTCG TGTCCAGGCC 37572 330 8.36e-10 GTTGTCCTCC GTTTGGCTTGATGCACATTGG ACATCCGTGC 34088 122 9.96e-09 GAAATATACC GTTTATGTTAGAGGAGCTTGT TTCTCTAGAT 45338 67 1.41e-08 AAGGACGTGA TTTGGGGATAGCGCTCCGTGG TTCAATTCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 13096 7.7e-11 348_[+2]_131 18280 3.1e-10 281_[+2]_198 37572 8.4e-10 329_[+2]_150 34088 1e-08 121_[+2]_358 45338 1.4e-08 66_[+2]_413 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 13096 ( 349) GTTTGGTTTGGGTCACCTTGG 1 18280 ( 282) GTTTGTAGTGGAGCACCTTCG 1 37572 ( 330) GTTTGGCTTGATGCACATTGG 1 34088 ( 122) GTTTATGTTAGAGGAGCTTGT 1 45338 ( 67) TTTGGGGATAGCGCTCCGTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5760 bayes= 10.4204 E= 4.3e+002 -897 -897 181 -40 -897 -897 -897 192 -897 -897 -897 192 -897 -897 -18 160 -49 -897 181 -897 -897 -897 140 60 -49 -18 81 -40 -49 -897 -18 118 -897 -897 -897 192 50 -897 140 -897 -49 -897 181 -897 50 -18 -18 -40 -897 -897 181 -40 -897 181 -18 -897 150 -897 -897 -40 -897 181 -18 -897 -49 181 -897 -897 -897 -897 -18 160 -897 -897 -897 192 -897 -18 181 -897 -897 -897 181 -40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 4.3e+002 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 0.600000 0.400000 0.200000 0.200000 0.400000 0.200000 0.200000 0.000000 0.200000 0.600000 0.000000 0.000000 0.000000 1.000000 0.400000 0.000000 0.600000 0.000000 0.200000 0.000000 0.800000 0.000000 0.400000 0.200000 0.200000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.800000 0.200000 0.000000 0.800000 0.000000 0.000000 0.200000 0.000000 0.800000 0.200000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.800000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT]TT[TG][GA][GT][GACT][TAG]T[GA][GA][ACGT][GT][CG][AT][CG][CA][TG]T[GC][GT] -------------------------------------------------------------------------------- Time 2.67 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 7 llr = 84 E-value = 7.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 7:::73a:::4: pos.-specific C ::1::6:::16: probability G 1::a3::a:6:: matrix T 1a9::1::a3:a bits 2.1 * * 1.9 * * *** * 1.7 * * *** * 1.5 * * *** * Relative 1.3 *** *** * Entropy 1.1 **** *** ** (17.4 bits) 0.9 **** *** ** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel ATTGACAGTGCT consensus GA TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 45338 193 1.47e-07 GACAAAACAA ATTGACAGTGAT GCCCAACATT 41615 226 3.58e-07 CCATTTTAAA ATTGAAAGTGCT CGAGAATCTC 49029 263 5.19e-07 GAGAAAGTCA ATTGACAGTTAT GCCTTTCTCC 37572 298 1.80e-06 GACAAGTACA ATCGACAGTGAT GTAAAATGCT 16991 311 2.66e-06 GGCGACTATG ATTGGAAGTTCT TATGCATCCC 49849 171 4.07e-06 GCCGTGCTTT TTTGACAGTCCT CAACGAGCAT 52108 29 6.67e-06 TGCAGCATTC GTTGGTAGTGCT TCCCAACCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45338 1.5e-07 192_[+3]_296 41615 3.6e-07 225_[+3]_263 49029 5.2e-07 262_[+3]_226 37572 1.8e-06 297_[+3]_191 16991 2.7e-06 310_[+3]_178 49849 4.1e-06 170_[+3]_318 52108 6.7e-06 28_[+3]_460 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=7 45338 ( 193) ATTGACAGTGAT 1 41615 ( 226) ATTGAAAGTGCT 1 49029 ( 263) ATTGACAGTTAT 1 37572 ( 298) ATCGACAGTGAT 1 16991 ( 311) ATTGGAAGTTCT 1 49849 ( 171) TTTGACAGTCCT 1 52108 ( 29) GTTGGTAGTGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5868 bayes= 9.55326 E= 7.0e+002 134 -945 -67 -88 -945 -945 -945 192 -945 -67 -945 170 -945 -945 214 -945 134 -945 33 -945 2 133 -945 -88 183 -945 -945 -945 -945 -945 214 -945 -945 -945 -945 192 -945 -67 133 12 60 133 -945 -945 -945 -945 -945 192 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 7.0e+002 0.714286 0.000000 0.142857 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.142857 0.000000 0.857143 0.000000 0.000000 1.000000 0.000000 0.714286 0.000000 0.285714 0.000000 0.285714 0.571429 0.000000 0.142857 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.142857 0.571429 0.285714 0.428571 0.571429 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- ATTG[AG][CA]AGT[GT][CA]T -------------------------------------------------------------------------------- Time 4.00 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 13004 1.16e-02 111_[+1(7.21e-07)]_375 13096 9.47e-07 348_[+2(7.73e-11)]_131 52108 4.01e-02 28_[+3(6.67e-06)]_460 37572 2.77e-11 124_[+1(3.25e-07)]_159_\ [+3(1.80e-06)]_20_[+2(8.36e-10)]_150 18280 1.16e-08 259_[+1(1.30e-06)]_8_[+2(3.07e-10)]_\ 198 49849 1.34e-02 170_[+3(4.07e-06)]_318 16991 2.20e-06 27_[+1(1.92e-08)]_269_\ [+3(2.66e-06)]_178 41615 2.23e-05 123_[+1(2.66e-06)]_88_\ [+3(3.58e-07)]_263 34088 3.11e-07 121_[+2(9.96e-09)]_156_\ [+1(1.85e-06)]_38_[+2(2.89e-05)]_129 36093 1.65e-03 190_[+1(4.28e-07)]_296 49029 2.69e-06 236_[+1(1.40e-06)]_12_\ [+3(5.19e-07)]_226 45338 1.07e-07 66_[+2(1.41e-08)]_105_\ [+3(1.47e-07)]_296 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************