******************************************************************************** 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/16/16.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 18080 1.0000 500 49388 1.0000 500 26336 1.0000 500 45623 1.0000 500 45624 1.0000 500 44332 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/16/16.seqs.fa -oc motifs/16 -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 0.256 C 0.293 G 0.230 T 0.221 Background letter frequencies (from dataset with add-one prior applied): A 0.256 C 0.293 G 0.230 T 0.221 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 18 sites = 6 llr = 88 E-value = 1.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 2::3:2:2:525:823:: pos.-specific C 8::2a222:5:::22::8 probability G :::2:35:3:852:5:a2 matrix T :aa3:3377:::8:27:: bits 2.2 ** * 2.0 ** * 1.7 ** * * 1.5 ** * * * * Relative 1.3 ** * * * ** * Entropy 1.1 *** * * **** *** (21.1 bits) 0.9 *** * ******* *** 0.7 *** * ******** *** 0.4 *** * ******** *** 0.2 ****************** 0.0 ------------------ Multilevel CTTACGGTTAGATAGTGC consensus T TT GC G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ 45624 303 9.49e-10 TTCATATTTA CTTACTGTTAGGTATTGC AATCCGAATC 44332 391 3.06e-09 TTGGAAAGGT CTTTCGGTTCGGTCGTGC CCGTGTCGTA 26336 306 2.61e-08 GAATGAATAC CTTACCTATCGGTAGTGC TAGTCTCTGC 18080 9 1.16e-07 AGCAGCAG CTTCCGTTGAGATACAGC AGTAGTGACA 49388 244 5.49e-07 AAACTAGGGC CTTTCAGTTAAATAAAGG CTGGACCAAA 45623 463 1.34e-06 CGAAAGGTTC ATTGCTCCGCGAGAGTGC AATCCTCTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45624 9.5e-10 302_[+1]_180 44332 3.1e-09 390_[+1]_92 26336 2.6e-08 305_[+1]_177 18080 1.2e-07 8_[+1]_474 49388 5.5e-07 243_[+1]_239 45623 1.3e-06 462_[+1]_20 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=18 seqs=6 45624 ( 303) CTTACTGTTAGGTATTGC 1 44332 ( 391) CTTTCGGTTCGGTCGTGC 1 26336 ( 306) CTTACCTATCGGTAGTGC 1 18080 ( 9) CTTCCGTTGAGATACAGC 1 49388 ( 244) CTTTCAGTTAAATAAAGG 1 45623 ( 463) ATTGCTCCGCGAGAGTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 2898 bayes= 8.91289 E= 1.5e+001 -62 151 -923 -923 -923 -923 -923 218 -923 -923 -923 218 38 -81 -46 59 -923 177 -923 -923 -62 -81 54 59 -923 -81 112 59 -62 -81 -923 159 -923 -923 54 159 96 77 -923 -923 -62 -923 186 -923 96 -923 112 -923 -923 -923 -46 191 170 -81 -923 -923 -62 -81 112 -41 38 -923 -923 159 -923 -923 212 -923 -923 151 -46 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 6 E= 1.5e+001 0.166667 0.833333 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.166667 0.166667 0.333333 0.000000 1.000000 0.000000 0.000000 0.166667 0.166667 0.333333 0.333333 0.000000 0.166667 0.500000 0.333333 0.166667 0.166667 0.000000 0.666667 0.000000 0.000000 0.333333 0.666667 0.500000 0.500000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 0.166667 0.833333 0.833333 0.166667 0.000000 0.000000 0.166667 0.166667 0.500000 0.166667 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.833333 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CTT[AT]C[GT][GT]T[TG][AC]G[AG]TAG[TA]GC -------------------------------------------------------------------------------- Time 0.36 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 6 llr = 79 E-value = 2.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :3:::2::232:3227 pos.-specific C 8::a2::a3:3a37:3 probability G :2::::2:5:2:::8: matrix T 25a:888::73:32:: bits 2.2 * 2.0 * 1.7 ** * * 1.5 ****** * * Relative 1.3 ****** * * Entropy 1.1 * ****** * * ** (19.0 bits) 0.9 * ****** * * ** 0.7 ******** * * *** 0.4 ********** ***** 0.2 ********** ***** 0.0 ---------------- Multilevel CTTCTTTCGTCCACGA consensus A CAT C C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 26336 358 1.40e-08 CTTCTTCTGA CATCTTTCCTCCTCGA CTCTTCCTCG 18080 278 7.82e-08 TGGCCCGGGT CATCTTTCGTACACGC CAAGCCCGTC 45623 137 1.88e-07 AAGGTTATGC CGTCTTGCGTTCCCGA GGACTGCAAG 45624 23 6.43e-07 AGGCTTGTTC CTTCTTTCAAGCTAGA GGTGATACCC 49388 359 1.55e-06 CGGGGGTATC TTTCTATCCTTCCTGA CCTTATTTAT 44332 197 2.29e-06 TCCGTGGACG CTTCCTTCGACCACAC GGGTATAGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 26336 1.4e-08 357_[+2]_127 18080 7.8e-08 277_[+2]_207 45623 1.9e-07 136_[+2]_348 45624 6.4e-07 22_[+2]_462 49388 1.5e-06 358_[+2]_126 44332 2.3e-06 196_[+2]_288 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=6 26336 ( 358) CATCTTTCCTCCTCGA 1 18080 ( 278) CATCTTTCGTACACGC 1 45623 ( 137) CGTCTTGCGTTCCCGA 1 45624 ( 23) CTTCTTTCAAGCTAGA 1 49388 ( 359) TTTCTATCCTTCCTGA 1 44332 ( 197) CTTCCTTCGACCACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 2910 bayes= 8.91886 E= 2.1e+002 -923 151 -923 -41 38 -923 -46 118 -923 -923 -923 218 -923 177 -923 -923 -923 -81 -923 191 -62 -923 -923 191 -923 -923 -46 191 -923 177 -923 -923 -62 19 112 -923 38 -923 -923 159 -62 19 -46 59 -923 177 -923 -923 38 19 -923 59 -62 119 -923 -41 -62 -923 186 -923 138 19 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 6 E= 2.1e+002 0.000000 0.833333 0.000000 0.166667 0.333333 0.000000 0.166667 0.500000 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 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.833333 0.000000 1.000000 0.000000 0.000000 0.166667 0.333333 0.500000 0.000000 0.333333 0.000000 0.000000 0.666667 0.166667 0.333333 0.166667 0.333333 0.000000 1.000000 0.000000 0.000000 0.333333 0.333333 0.000000 0.333333 0.166667 0.666667 0.000000 0.166667 0.166667 0.000000 0.833333 0.000000 0.666667 0.333333 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[TA]TCTTTC[GC][TA][CT]C[ACT]CG[AC] -------------------------------------------------------------------------------- Time 0.68 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 6 llr = 81 E-value = 2.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::52::::::a3752: pos.-specific C :8552::577:::2:2 probability G a:::2:2::3:::2:: matrix T :2:37a853::73288 bits 2.2 * * 2.0 * * * 1.7 * * * 1.5 * ** * ** Relative 1.3 * ** * ** Entropy 1.1 ** ** * *** ** (19.6 bits) 0.9 *** ********* ** 0.7 *** ********* ** 0.4 ************* ** 0.2 **************** 0.0 ---------------- Multilevel GCACTTTCCCATAATT consensus CT TTG AT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 18080 137 5.69e-09 AAGCCGAATC GCCCTTTCCCATTATT ACGCTGCCCA 26336 384 8.86e-08 CTCTTCCTCG GTCCTTTTTCATTATT CCTGTTCCTC 45624 286 2.65e-07 AAACGTACAA GCCTCTTTTCATATTT ACTTACTGTT 49388 61 2.89e-07 TAAGAAAACC GCATTTGCCGAAAATT CCGAAATTTC 45623 353 5.91e-07 GTGTTCCCAT GCAATTTTCCATACAT GTCTGGTGCG 44332 125 2.09e-06 TGACTTCCAG GCACGTTCCGAAAGTC CATTGCCATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 18080 5.7e-09 136_[+3]_348 26336 8.9e-08 383_[+3]_101 45624 2.7e-07 285_[+3]_199 49388 2.9e-07 60_[+3]_424 45623 5.9e-07 352_[+3]_132 44332 2.1e-06 124_[+3]_360 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=6 18080 ( 137) GCCCTTTCCCATTATT 1 26336 ( 384) GTCCTTTTTCATTATT 1 45624 ( 286) GCCTCTTTTCATATTT 1 49388 ( 61) GCATTTGCCGAAAATT 1 45623 ( 353) GCAATTTTCCATACAT 1 44332 ( 125) GCACGTTCCGAAAGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 2910 bayes= 10.02 E= 2.8e+002 -923 -923 212 -923 -923 151 -923 -41 96 77 -923 -923 -62 77 -923 59 -923 -81 -46 159 -923 -923 -923 218 -923 -923 -46 191 -923 77 -923 118 -923 119 -923 59 -923 119 54 -923 196 -923 -923 -923 38 -923 -923 159 138 -923 -923 59 96 -81 -46 -41 -62 -923 -923 191 -923 -81 -923 191 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 6 E= 2.8e+002 0.000000 0.000000 1.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.500000 0.500000 0.000000 0.000000 0.166667 0.500000 0.000000 0.333333 0.000000 0.166667 0.166667 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.500000 0.000000 0.500000 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.666667 0.000000 0.000000 0.333333 0.500000 0.166667 0.166667 0.166667 0.166667 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.833333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GC[AC][CT]TTT[CT][CT][CG]A[TA][AT]ATT -------------------------------------------------------------------------------- Time 1.03 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 18080 3.35e-12 8_[+1(1.16e-07)]_110_[+3(5.69e-09)]_\ 125_[+2(7.82e-08)]_207 49388 8.96e-09 60_[+3(2.89e-07)]_167_\ [+1(5.49e-07)]_97_[+2(1.55e-06)]_126 26336 2.16e-12 305_[+1(2.61e-08)]_34_\ [+2(1.40e-08)]_10_[+3(8.86e-08)]_101 45623 5.66e-09 136_[+2(1.88e-07)]_200_\ [+3(5.91e-07)]_94_[+1(1.34e-06)]_20 45624 9.80e-12 22_[+2(6.43e-07)]_213_\ [+3(7.10e-05)]_18_[+3(2.65e-07)]_1_[+1(9.49e-10)]_180 44332 6.59e-10 124_[+3(2.09e-06)]_56_\ [+2(2.29e-06)]_178_[+1(3.06e-09)]_92 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************