******************************************************************************** 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/3/3.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11282 1.0000 500 11761 1.0000 500 261272 1.0000 500 261447 1.0000 500 263105 1.0000 500 3275 1.0000 500 3893 1.0000 500 4844 1.0000 500 5114 1.0000 500 5500 1.0000 500 6625 1.0000 500 7325 1.0000 500 7417 1.0000 500 7595 1.0000 500 7885 1.0000 500 9689 1.0000 500 bd930 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/3/3.seqs.fa -oc motifs/3 -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= 17 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= 8500 N= 17 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.286 C 0.233 G 0.225 T 0.256 Background letter frequencies (from dataset with add-one prior applied): A 0.286 C 0.233 G 0.225 T 0.256 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 17 llr = 174 E-value = 2.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4:9:a9:41184:53: pos.-specific C 2112::8486:16245 probability G :8:8:112:324241: matrix T 51:::1111::12:25 bits 2.1 1.9 1.7 * 1.5 ** Relative 1.3 ****** * Entropy 1.1 ****** * * * (14.7 bits) 0.9 ****** * * * 0.6 ****** *** * * 0.4 ******* *** ** * 0.2 **************** 0.0 ---------------- Multilevel TGAGAACCCCAACACC consensus A A GGGGGAT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 3893 428 5.04e-08 GTGTCATCGA TGAGAACCCGAGCCCC CTCCTCGAAA 7885 421 6.48e-07 AGTAGAAGAT TGCGAACCCCACCACC TTCACCTGAC 11282 163 6.48e-07 AGTTGCGGGA AGAGAACCCCATTGCC ATCTGTCGAG 3275 342 1.17e-06 AACATCACGA TGAGAAGCCGAACGAC AGCATCGACA 261447 222 1.46e-06 GAGTACGATG AGAGAACACCACGAAT CGCAGTCATT 4844 444 2.24e-06 CATCTCTCAA AGCGAACCCGAAGGCC AGTCCAGTTG 5500 341 2.76e-06 AAACAACCGA AGAGAACCCAGGCGTC AGCTTCGAAG 7595 169 4.46e-06 TTGTGGTCAG TGAGATCACCATCGCT GCCAGTAGTG 5114 467 4.90e-06 TCGTCGCTAA TGAGAACTCCAGTATT CTTTCAGCTA 7417 282 5.88e-06 ATTCATCCAT CGACAACGCCAGCAGT TCGAGTTCAC 11761 332 8.37e-06 TGTCATCCAA CGAGAACGCCAATCTT TTATTTTGGC 9689 452 2.32e-05 AACGCTTTCA ACAGAACATCAACCAC CCCCCCACTA 263105 240 2.50e-05 GTCGAGACGA CGAGAATACGGACGAC CACTTGCCAC 7325 108 3.77e-05 ACTGGCAACA AGAGAGCAACAGCAAT GCACCCAATG 261272 261 3.77e-05 CCACGGCTGC TGACAACCTCGGGAGT TCTCAAGTTT 6625 27 4.03e-05 TCCATCCGCT TTAGAAGACGAAGACT TCTCACCAAC bd930 366 4.88e-05 CATTCACATA TCACAACGCAGACACC ACGACAAGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3893 5e-08 427_[+1]_57 7885 6.5e-07 420_[+1]_64 11282 6.5e-07 162_[+1]_322 3275 1.2e-06 341_[+1]_143 261447 1.5e-06 221_[+1]_263 4844 2.2e-06 443_[+1]_41 5500 2.8e-06 340_[+1]_144 7595 4.5e-06 168_[+1]_316 5114 4.9e-06 466_[+1]_18 7417 5.9e-06 281_[+1]_203 11761 8.4e-06 331_[+1]_153 9689 2.3e-05 451_[+1]_33 263105 2.5e-05 239_[+1]_245 7325 3.8e-05 107_[+1]_377 261272 3.8e-05 260_[+1]_224 6625 4e-05 26_[+1]_458 bd930 4.9e-05 365_[+1]_119 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=17 3893 ( 428) TGAGAACCCGAGCCCC 1 7885 ( 421) TGCGAACCCCACCACC 1 11282 ( 163) AGAGAACCCCATTGCC 1 3275 ( 342) TGAGAAGCCGAACGAC 1 261447 ( 222) AGAGAACACCACGAAT 1 4844 ( 444) AGCGAACCCGAAGGCC 1 5500 ( 341) AGAGAACCCAGGCGTC 1 7595 ( 169) TGAGATCACCATCGCT 1 5114 ( 467) TGAGAACTCCAGTATT 1 7417 ( 282) CGACAACGCCAGCAGT 1 11761 ( 332) CGAGAACGCCAATCTT 1 9689 ( 452) ACAGAACATCAACCAC 1 263105 ( 240) CGAGAATACGGACGAC 1 7325 ( 108) AGAGAGCAACAGCAAT 1 261272 ( 261) TGACAACCTCGGGAGT 1 6625 ( 27) TTAGAAGACGAAGACT 1 bd930 ( 366) TCACAACGCAGACACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 9.71481 E= 2.4e-001 30 -40 -1073 88 -1073 -98 187 -212 162 -98 -1073 -1073 -1073 -40 187 -1073 180 -1073 -1073 -1073 162 -1073 -194 -212 -1073 182 -94 -212 30 82 -35 -212 -228 182 -1073 -112 -128 134 38 -1073 142 -1073 6 -1073 53 -98 65 -112 -1073 134 6 -53 72 -40 65 -1073 4 82 -94 -53 -1073 118 -1073 88 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 17 E= 2.4e-001 0.352941 0.176471 0.000000 0.470588 0.000000 0.117647 0.823529 0.058824 0.882353 0.117647 0.000000 0.000000 0.000000 0.176471 0.823529 0.000000 1.000000 0.000000 0.000000 0.000000 0.882353 0.000000 0.058824 0.058824 0.000000 0.823529 0.117647 0.058824 0.352941 0.411765 0.176471 0.058824 0.058824 0.823529 0.000000 0.117647 0.117647 0.588235 0.294118 0.000000 0.764706 0.000000 0.235294 0.000000 0.411765 0.117647 0.352941 0.117647 0.000000 0.588235 0.235294 0.176471 0.470588 0.176471 0.352941 0.000000 0.294118 0.411765 0.117647 0.176471 0.000000 0.529412 0.000000 0.470588 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TA]GAGAAC[CA]C[CG][AG][AG][CG][AG][CA][CT] -------------------------------------------------------------------------------- Time 2.66 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 6 llr = 106 E-value = 1.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :55:73:a7:722:::723: pos.-specific C 2:2:::::2:::::2:2::3 probability G 853a27a:2a37278a2877 matrix T ::::2::::::273:::::: bits 2.1 * * * * 1.9 * * * * 1.7 * ** * * 1.5 * * ** * ** * Relative 1.3 * * ** * ** * * Entropy 1.1 ** * *** ** *** *** (25.4 bits) 0.9 ** * *** *** *** *** 0.6 ** ***************** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GAAGAGGAAGAGTGGGAGGG consensus GG A G T AC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- bd930 231 6.69e-11 AAGGAGAGGG GGAGAAGAAGAGTGGGAGAG TCACTCATGA 3275 289 1.85e-09 GGGAGGGGAG GAGGAGGAGGAGGGGGGGGG ATAAAGACGA 7595 300 3.84e-09 ACGAAGTGTT CGGGAGGACGGGTGGGCGGG CGTGATATTT 261447 188 9.97e-09 AGAAAAGTCT GAAGGAGAAGAATTGGAGGC ATTCGAGTAC 6625 108 1.33e-08 CCACGAGACG GACGAGGAAGAGAGCGAGAC TTTGCCTCAA 3893 81 1.41e-08 CGCATTGGAA GGAGTGGAAGGTTTGGAAGG AAGGGTGTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd930 6.7e-11 230_[+2]_250 3275 1.9e-09 288_[+2]_192 7595 3.8e-09 299_[+2]_181 261447 1e-08 187_[+2]_293 6625 1.3e-08 107_[+2]_373 3893 1.4e-08 80_[+2]_400 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=6 bd930 ( 231) GGAGAAGAAGAGTGGGAGAG 1 3275 ( 289) GAGGAGGAGGAGGGGGGGGG 1 7595 ( 300) CGGGAGGACGGGTGGGCGGG 1 261447 ( 188) GAAGGAGAAGAATTGGAGGC 1 6625 ( 108) GACGAGGAAGAGAGCGAGAC 1 3893 ( 81) GGAGTGGAAGGTTTGGAAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 8177 bayes= 10.07 E= 1.6e+001 -923 -48 188 -923 80 -923 115 -923 80 -48 56 -923 -923 -923 215 -923 122 -923 -43 -62 22 -923 156 -923 -923 -923 215 -923 180 -923 -923 -923 122 -48 -43 -923 -923 -923 215 -923 122 -923 56 -923 -78 -923 156 -62 -78 -923 -43 138 -923 -923 156 38 -923 -48 188 -923 -923 -923 215 -923 122 -48 -43 -923 -78 -923 188 -923 22 -923 156 -923 -923 52 156 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 1.6e+001 0.000000 0.166667 0.833333 0.000000 0.500000 0.000000 0.500000 0.000000 0.500000 0.166667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.166667 0.166667 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.166667 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.166667 0.000000 0.666667 0.166667 0.166667 0.000000 0.166667 0.666667 0.000000 0.000000 0.666667 0.333333 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.166667 0.166667 0.000000 0.166667 0.000000 0.833333 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.333333 0.666667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[AG][AG]GA[GA]GAAG[AG]GT[GT]GGAG[GA][GC] -------------------------------------------------------------------------------- Time 5.29 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 7 llr = 117 E-value = 2.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1a:4::::1:6:6114393:3 pos.-specific C 7:a3:71a:7:149:47:477 probability G :::19::::13:::3::1:3: matrix T 1::1139:9119::61::3:: bits 2.1 * * 1.9 * * 1.7 ** * 1.5 ** * * * Relative 1.3 ** ***** * * * * Entropy 1.1 ** ***** * * ** ** (24.2 bits) 0.9 *** ****** *** ** ** 0.6 *** *********** ** ** 0.4 *** ***************** 0.2 ********************* 0.0 --------------------- Multilevel CACAGCTCTCATACTACACCC consensus C T G C GCA AGA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 6625 3 1.57e-11 AT CACCGCTCTCGTCCTCCATCC GCTTTAGAAG 5114 10 2.20e-09 ACAACGTTC CACGGCTCTGATACTACAAGC TGTAACAGAG 9689 287 1.37e-08 TTGACGTCGA CACTGCTCTCGTACGTCGCCA TCCATCGCAT 7595 458 1.73e-08 ACCACCAACA AACAGTTCTTTTACTACACCC AATCAGAGGT 3893 462 2.01e-08 AAGCACGTCG CACCGCTCACATCATAAAACC AACAAAGCAC 11761 377 2.91e-08 GTAGGCTAAG TACAGTTCTCATCCGCAACGA AAGATTTGTG bd930 461 5.65e-08 CCAATCGTAT CACATCCCTCACACACCATCC TGCCATAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6625 1.6e-11 2_[+3]_477 5114 2.2e-09 9_[+3]_470 9689 1.4e-08 286_[+3]_193 7595 1.7e-08 457_[+3]_22 3893 2e-08 461_[+3]_18 11761 2.9e-08 376_[+3]_103 bd930 5.6e-08 460_[+3]_19 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=7 6625 ( 3) CACCGCTCTCGTCCTCCATCC 1 5114 ( 10) CACGGCTCTGATACTACAAGC 1 9689 ( 287) CACTGCTCTCGTACGTCGCCA 1 7595 ( 458) AACAGTTCTTTTACTACACCC 1 3893 ( 462) CACCGCTCACATCATAAAACC 1 11761 ( 377) TACAGTTCTCATCCGCAACGA 1 bd930 ( 461) CACATCCCTCACACACCATCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 8160 bayes= 10.0295 E= 2.4e+002 -100 162 -945 -84 180 -945 -945 -945 -945 210 -945 -945 58 29 -66 -84 -945 -945 193 -84 -945 162 -945 16 -945 -70 -945 174 -945 210 -945 -945 -100 -945 -945 174 -945 162 -66 -84 100 -945 34 -84 -945 -70 -945 174 100 88 -945 -945 -100 188 -945 -945 -100 -945 34 116 58 88 -945 -84 0 162 -945 -945 158 -945 -66 -945 0 88 -945 16 -945 162 34 -945 0 162 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 2.4e+002 0.142857 0.714286 0.000000 0.142857 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.428571 0.285714 0.142857 0.142857 0.000000 0.000000 0.857143 0.142857 0.000000 0.714286 0.000000 0.285714 0.000000 0.142857 0.000000 0.857143 0.000000 1.000000 0.000000 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.714286 0.142857 0.142857 0.571429 0.000000 0.285714 0.142857 0.000000 0.142857 0.000000 0.857143 0.571429 0.428571 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.142857 0.000000 0.285714 0.571429 0.428571 0.428571 0.000000 0.142857 0.285714 0.714286 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.285714 0.428571 0.000000 0.285714 0.000000 0.714286 0.285714 0.000000 0.285714 0.714286 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CAC[AC]G[CT]TCTC[AG]T[AC]C[TG][AC][CA]A[CAT][CG][CA] -------------------------------------------------------------------------------- Time 8.12 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11282 3.89e-03 162_[+1(6.48e-07)]_322 11761 8.33e-06 331_[+1(8.37e-06)]_29_\ [+3(2.91e-08)]_103 261272 2.92e-03 107_[+2(1.43e-05)]_133_\ [+1(3.77e-05)]_224 261447 2.31e-07 187_[+2(9.97e-09)]_14_\ [+1(1.46e-06)]_263 263105 1.37e-01 239_[+1(2.50e-05)]_245 3275 9.45e-08 288_[+2(1.85e-09)]_33_\ [+1(1.17e-06)]_143 3893 9.88e-13 80_[+2(1.41e-08)]_327_\ [+1(5.04e-08)]_18_[+3(2.01e-08)]_18 4844 8.41e-03 443_[+1(2.24e-06)]_41 5114 1.60e-07 9_[+3(2.20e-09)]_436_[+1(4.90e-06)]_\ 18 5500 1.30e-03 340_[+1(2.76e-06)]_144 6625 5.91e-13 2_[+3(1.57e-11)]_3_[+1(4.03e-05)]_\ 65_[+2(1.33e-08)]_373 7325 1.31e-01 107_[+1(3.77e-05)]_377 7417 4.69e-02 281_[+1(5.88e-06)]_203 7595 1.70e-11 168_[+1(4.46e-06)]_115_\ [+2(3.84e-09)]_138_[+3(1.73e-08)]_22 7885 1.70e-04 420_[+1(6.48e-07)]_64 9689 9.75e-06 286_[+3(1.37e-08)]_144_\ [+1(2.32e-05)]_33 bd930 1.08e-11 230_[+2(6.69e-11)]_115_\ [+1(4.88e-05)]_79_[+3(5.65e-08)]_19 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************