******************************************************************************** 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/269/269.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 46559 1.0000 500 47315 1.0000 500 47944 1.0000 500 35493 1.0000 500 45555 1.0000 500 49551 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/269/269.seqs.fa -oc motifs/269 -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= 6 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= 3000 N= 6 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.283 C 0.221 G 0.207 T 0.290 Background letter frequencies (from dataset with add-one prior applied): A 0.283 C 0.221 G 0.207 T 0.290 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 6 llr = 78 E-value = 1.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 3aa57:7a33:::28 pos.-specific C :::23:2::2:585: probability G 7::3:a2:::a3::2 matrix T ::::::::75:223: bits 2.3 * * 2.0 * * 1.8 ** * * * 1.6 ** * * * Relative 1.4 ** * * * * Entropy 1.1 *** ** * * * * (18.7 bits) 0.9 *** ** ** * * * 0.7 ********* *** * 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GAAAAGAATTGCCCA consensus A GC AA G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 47315 265 6.82e-09 TAGGTATTTC GAAACGAATTGCCCA TGAAATCGGG 35493 151 7.21e-08 AAATGTAAAG GAACAGAATTGCCTA TCGGCATAAA 47944 334 3.56e-07 GACGGCTTGC GAAGAGAAAAGCCAA CCAATTCGAC 49551 46 1.04e-06 TCGGAACAAT GAAAAGCATTGGCTG AAATGCCACA 46559 131 2.24e-06 TAAATCCTAA AAAGCGGATAGTCCA TCAGGTTTTG 45555 6 2.87e-06 GGACC AAAAAGAAACGGTCA AACCTTAGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47315 6.8e-09 264_[+1]_221 35493 7.2e-08 150_[+1]_335 47944 3.6e-07 333_[+1]_152 49551 1e-06 45_[+1]_440 46559 2.2e-06 130_[+1]_355 45555 2.9e-06 5_[+1]_480 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=6 47315 ( 265) GAAACGAATTGCCCA 1 35493 ( 151) GAACAGAATTGCCTA 1 47944 ( 334) GAAGAGAAAAGCCAA 1 49551 ( 46) GAAAAGCATTGGCTG 1 46559 ( 131) AAAGCGGATAGTCCA 1 45555 ( 6) AAAAAGAAACGGTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 2916 bayes= 8.92184 E= 1.2e+002 24 -923 169 -923 182 -923 -923 -923 182 -923 -923 -923 82 -40 69 -923 124 59 -923 -923 -923 -923 227 -923 124 -40 -31 -923 182 -923 -923 -923 24 -923 -923 120 24 -40 -923 79 -923 -923 227 -923 -923 118 69 -80 -923 192 -923 -80 -76 118 -923 20 156 -923 -31 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 6 E= 1.2e+002 0.333333 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.166667 0.333333 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.166667 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.333333 0.166667 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.333333 0.166667 0.000000 0.833333 0.000000 0.166667 0.166667 0.500000 0.000000 0.333333 0.833333 0.000000 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GA]AA[AG][AC]GAA[TA][TA]G[CG]C[CT]A -------------------------------------------------------------------------------- Time 0.48 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 6 llr = 94 E-value = 2.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::22:a:527::2253:3 pos.-specific C 72::57:::22:7a:733a: probability G :23:32a::3:2::7::2:: matrix T 377a::::a:723:2222:7 bits 2.3 * * * 2.0 * * * 1.8 * *** * * 1.6 * *** * * Relative 1.4 * *** * * Entropy 1.1 * ** *** ** * (22.5 bits) 0.9 * ** **** **** ** 0.7 **************** ** 0.5 ***************** ** 0.2 ***************** ** 0.0 -------------------- Multilevel CTTTCCGATATACCGCAACT consensus T G G G T CC A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 35493 237 5.27e-09 TCTCGTCACT TTTTGCGATGCATCGCACCT ACCGTACACA 49551 189 1.41e-08 CTATCCGCGC CTGTCCGATATACCTCTACA GACAACCTCT 47315 376 1.56e-08 GGGTCCAATG CCTTACGATGTGCCGCCGCT CCCCAAAAGT 46559 475 3.63e-08 CCCGAATTGA CTGTGAGATCTACCGAAACT CGAACA 45555 418 4.71e-08 CTTAGACTGT CTTTCGGATAAACCACATCT CTTTTGTCGT 47944 122 2.07e-07 TGGCTAGCAC TGTTCCGATATTTCGTCCCA TTCTTTACCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35493 5.3e-09 236_[+2]_244 49551 1.4e-08 188_[+2]_292 47315 1.6e-08 375_[+2]_105 46559 3.6e-08 474_[+2]_6 45555 4.7e-08 417_[+2]_63 47944 2.1e-07 121_[+2]_359 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=6 35493 ( 237) TTTTGCGATGCATCGCACCT 1 49551 ( 189) CTGTCCGATATACCTCTACA 1 47315 ( 376) CCTTACGATGTGCCGCCGCT 1 46559 ( 475) CTGTGAGATCTACCGAAACT 1 45555 ( 418) CTTTCGGATAAACCACATCT 1 47944 ( 122) TGTTCCGATATTTCGTCCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 2886 bayes= 8.90689 E= 2.5e+002 -923 159 -923 20 -923 -40 -31 120 -923 -923 69 120 -923 -923 -923 178 -76 118 69 -923 -76 159 -31 -923 -923 -923 227 -923 182 -923 -923 -923 -923 -923 -923 178 82 -40 69 -923 -76 -40 -923 120 124 -923 -31 -80 -923 159 -923 20 -923 218 -923 -923 -76 -923 169 -80 -76 159 -923 -80 82 59 -923 -80 24 59 -31 -80 -923 218 -923 -923 24 -923 -923 120 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 2.5e+002 0.000000 0.666667 0.000000 0.333333 0.000000 0.166667 0.166667 0.666667 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.166667 0.500000 0.333333 0.000000 0.166667 0.666667 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.166667 0.333333 0.000000 0.166667 0.166667 0.000000 0.666667 0.666667 0.000000 0.166667 0.166667 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.166667 0.000000 0.666667 0.166667 0.166667 0.666667 0.000000 0.166667 0.500000 0.333333 0.000000 0.166667 0.333333 0.333333 0.166667 0.166667 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT]T[TG]T[CG]CGAT[AG]TA[CT]CGC[AC][AC]C[TA] -------------------------------------------------------------------------------- Time 0.85 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 6 llr = 93 E-value = 4.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2a8:232:7::7:2::::22 pos.-specific C 8:27:55:2a::3:55::28 probability G :::25:282::353:3::5: matrix T :::23222::a:2552aa2: bits 2.3 * 2.0 * 1.8 * ** ** 1.6 * * ** ** Relative 1.4 ** * ** ** * Entropy 1.1 *** * *** ** * (22.3 bits) 0.9 **** * *** * ** * 0.7 ***** ****** **** * 0.5 ****** *********** * 0.2 ******************** 0.0 -------------------- Multilevel CAACGCCGACTAGTCCTTGC consensus TA GCGTG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 49551 87 4.17e-09 GGGCAAAAGT CAACGAGGACTACATGTTGC CAGCTTTTTG 45555 388 1.10e-08 AGTTTGAACC CAATTTCGACTGGGCGTTGC CTTAGACTGT 47944 71 1.10e-08 CGCCAGTCTT CAACGCCGCCTAGTCCTTTA GAATCCTTCA 46559 182 3.70e-08 AGGCTTCTTT CAACTCCGACTGTTTTTTAC ATATGGACAT 35493 276 7.59e-08 AGATCCATCA CACGACAGACTACTTCTTGC AGGATTCATC 47315 443 3.64e-07 CGTTTCCCCC AAACGATTGCTAGGCCTTCC AGTTAGGATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49551 4.2e-09 86_[+3]_394 45555 1.1e-08 387_[+3]_93 47944 1.1e-08 70_[+3]_410 46559 3.7e-08 181_[+3]_299 35493 7.6e-08 275_[+3]_205 47315 3.6e-07 442_[+3]_38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=6 49551 ( 87) CAACGAGGACTACATGTTGC 1 45555 ( 388) CAATTTCGACTGGGCGTTGC 1 47944 ( 71) CAACGCCGCCTAGTCCTTTA 1 46559 ( 182) CAACTCCGACTGTTTTTTAC 1 35493 ( 276) CACGACAGACTACTTCTTGC 1 47315 ( 443) AAACGATTGCTAGGCCTTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 2886 bayes= 8.90689 E= 4.8e+002 -76 192 -923 -923 182 -923 -923 -923 156 -40 -923 -923 -923 159 -31 -80 -76 -923 127 20 24 118 -923 -80 -76 118 -31 -80 -923 -923 201 -80 124 -40 -31 -923 -923 218 -923 -923 -923 -923 -923 178 124 -923 69 -923 -923 59 127 -80 -76 -923 69 79 -923 118 -923 79 -923 118 69 -80 -923 -923 -923 178 -923 -923 -923 178 -76 -40 127 -80 -76 192 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 4.8e+002 0.166667 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.666667 0.166667 0.166667 0.166667 0.000000 0.500000 0.333333 0.333333 0.500000 0.000000 0.166667 0.166667 0.500000 0.166667 0.166667 0.000000 0.000000 0.833333 0.166667 0.666667 0.166667 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.333333 0.500000 0.166667 0.166667 0.000000 0.333333 0.500000 0.000000 0.500000 0.000000 0.500000 0.000000 0.500000 0.333333 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.166667 0.166667 0.500000 0.166667 0.166667 0.833333 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CAAC[GT][CA]CGACT[AG][GC][TG][CT][CG]TTGC -------------------------------------------------------------------------------- Time 1.19 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46559 1.49e-10 130_[+1(2.24e-06)]_36_\ [+3(3.70e-08)]_273_[+2(3.63e-08)]_6 47315 2.53e-12 264_[+1(6.82e-09)]_96_\ [+2(1.56e-08)]_47_[+3(3.64e-07)]_38 47944 4.41e-11 70_[+3(1.10e-08)]_31_[+2(2.07e-07)]_\ 192_[+1(3.56e-07)]_152 35493 1.91e-12 150_[+1(7.21e-08)]_71_\ [+2(5.27e-09)]_19_[+3(7.59e-08)]_37_[+2(1.53e-05)]_148 45555 7.76e-11 5_[+1(2.87e-06)]_193_[+1(8.17e-05)]_\ 159_[+3(1.10e-08)]_10_[+2(4.71e-08)]_63 49551 3.90e-12 45_[+1(1.04e-06)]_26_[+3(4.17e-09)]_\ 82_[+2(1.41e-08)]_206_[+2(5.56e-05)]_66 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************