******************************************************************************** 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/73/73.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10358 1.0000 500 10378 1.0000 500 11079 1.0000 500 1397 1.0000 500 1587 1.0000 500 1869 1.0000 500 1870 1.0000 500 21789 1.0000 500 23935 1.0000 500 262946 1.0000 500 27564 1.0000 500 3384 1.0000 500 37280 1.0000 500 7229 1.0000 500 7542 1.0000 500 9742 1.0000 500 bd1071 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/73/73.seqs.fa -oc motifs/73 -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 0.264 C 0.241 G 0.242 T 0.253 Background letter frequencies (from dataset with add-one prior applied): A 0.264 C 0.241 G 0.242 T 0.253 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 12 llr = 149 E-value = 1.3e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::3::::222113: pos.-specific C 123::1:1:2::1::: probability G 33:95:84938189:a matrix T 6581392513:81:8: bits 2.1 * 1.8 * 1.6 * * * * * 1.4 * ** * * * * Relative 1.2 ** ** * * *** Entropy 1.0 ** ** * ** *** (17.9 bits) 0.8 * ** ** * ****** 0.6 **** **** ****** 0.4 ********* ****** 0.2 ********* ****** 0.0 ---------------- Multilevel TTTGGTGTGGGTGGTG consensus GGC A G T A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 7542 338 1.60e-08 ATTCCACACT TTTGTTGTGAGTGGTG TGGTTAGTGT 1587 150 2.18e-08 CTGCTGGCAG TTTGGTGCGTGTGGTG CGACCCCTCT 10358 284 2.15e-07 AATTGGAGAG GTCGGTGTGCGTGGAG GAAAGACGAT 262946 57 2.97e-07 TGAGCTTCAT TGTGGTGTGGAAGGTG TTGAAGTGTG 21789 89 3.86e-07 ATGTCTGAAT GTTGATGGGTGTGATG TGATGTGGAA 7229 345 5.68e-07 GGCTGGATTG GGTGGTGGTAGTGGTG CTACTGCCGT 9742 52 6.15e-07 CCAACCTCTG TGTGGTGGGGGAAGTG CGAAGTGTCT 1397 363 6.15e-07 CGCTCTTTGC TTTGTTGGGTGTTGAG GGTCGAGGAG bd1071 83 7.34e-07 CTGTTGTTGC GGCGATTGGGGTGGTG ATGGCGGCGT 23935 329 1.79e-06 TCCTGGTGTT CCTTGTGTGTGTGGTG GCTATTCACG 37280 333 8.60e-06 TGAAAGACGT TCTGATGTGCAGGGAG AAAAATACTG 11079 219 1.25e-05 CAGGCAGGTG TTCGTCTTGGGTCGTG GGCAAGTAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7542 1.6e-08 337_[+1]_147 1587 2.2e-08 149_[+1]_335 10358 2.1e-07 283_[+1]_201 262946 3e-07 56_[+1]_428 21789 3.9e-07 88_[+1]_396 7229 5.7e-07 344_[+1]_140 9742 6.2e-07 51_[+1]_433 1397 6.2e-07 362_[+1]_122 bd1071 7.3e-07 82_[+1]_402 23935 1.8e-06 328_[+1]_156 37280 8.6e-06 332_[+1]_152 11079 1.3e-05 218_[+1]_266 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=12 7542 ( 338) TTTGTTGTGAGTGGTG 1 1587 ( 150) TTTGGTGCGTGTGGTG 1 10358 ( 284) GTCGGTGTGCGTGGAG 1 262946 ( 57) TGTGGTGTGGAAGGTG 1 21789 ( 89) GTTGATGGGTGTGATG 1 7229 ( 345) GGTGGTGGTAGTGGTG 1 9742 ( 52) TGTGGTGGGGGAAGTG 1 1397 ( 363) TTTGTTGGGTGTTGAG 1 bd1071 ( 83) GGCGATTGGGGTGGTG 1 23935 ( 329) CCTTGTGTGTGTGGTG 1 37280 ( 333) TCTGATGTGCAGGGAG 1 11079 ( 219) TTCGTCTTGGGTCGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 9.87026 E= 1.3e-002 -1023 -153 46 120 -1023 -53 46 98 -1023 5 -1023 157 -1023 -1023 192 -160 -8 -1023 105 -2 -1023 -153 -1023 186 -1023 -1023 178 -60 -1023 -153 78 98 -1023 -1023 192 -160 -66 -53 46 40 -66 -1023 178 -1023 -66 -1023 -154 157 -166 -153 163 -160 -166 -1023 192 -1023 -8 -1023 -1023 157 -1023 -1023 205 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 12 E= 1.3e-002 0.000000 0.083333 0.333333 0.583333 0.000000 0.166667 0.333333 0.500000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.916667 0.083333 0.250000 0.000000 0.500000 0.250000 0.000000 0.083333 0.000000 0.916667 0.000000 0.000000 0.833333 0.166667 0.000000 0.083333 0.416667 0.500000 0.000000 0.000000 0.916667 0.083333 0.166667 0.166667 0.333333 0.333333 0.166667 0.000000 0.833333 0.000000 0.166667 0.000000 0.083333 0.750000 0.083333 0.083333 0.750000 0.083333 0.083333 0.000000 0.916667 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TG][TG][TC]G[GAT]TG[TG]G[GT]GTGG[TA]G -------------------------------------------------------------------------------- Time 2.94 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 17 llr = 160 E-value = 4.3e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 196:7515178: pos.-specific C 9:193:918219 probability G :1:::2:1:::: matrix T ::31:4:41111 bits 2.1 1.8 1.6 * * 1.4 ** * * * Relative 1.2 ** * * * * Entropy 1.0 ** ** * * * (13.5 bits) 0.8 ***** * **** 0.6 ***** * **** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CAACAACACAAC consensus T CT T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 21789 437 7.27e-08 CCATCCCACC CAACAACACAAC CTAACAACAC 10358 453 8.08e-07 ATTTCACAAC CAACCACTCAAC AATCATCACC 262946 326 3.13e-06 TTCGCTCCAT CATCATCACCAC AGTCACGATT 27564 454 8.73e-06 ACAAGGCAAC CAACAGCAAAAC CATGAGAATA 1397 455 8.73e-06 GGAATTGCGT CAACAACTTAAC ACCTCTGCTC 1870 302 1.25e-05 TAGGTAAAGA CAACAACGCAAT CTGGAAATTC 7542 488 1.41e-05 TGCACACAAA CAACAAAGCAAC G 3384 463 1.41e-05 CTGCTTAAAA CAACATCTCCCC CCCCCCTCGC 37280 459 1.50e-05 GCCGTCGCCA CAACCGCACATC GGTAGACTTT 1587 408 1.71e-05 CTACTCAAGA AATCCACACAAC CAGAGCACAG 7229 97 1.91e-05 GGATACTGGC CAACCACCCCAC CGCCAGGATG 10378 483 2.47e-05 ACTCTCGTGT CGTCATCTCAAC AAAACC bd1071 368 3.83e-05 ACAGCCAGCT CATCCGAACAAC ACAGCGGCGG 9742 434 5.17e-05 ACTATTCAAT CAATATCACATC ACCAAGCCTC 23935 413 5.17e-05 TGTTCCCCAG AACCATCTCAAC TCAATTGGTC 1869 223 6.55e-05 TCTTGGCAAA CAACAACAACAT GCCTAGATGA 11079 335 9.07e-05 GAGAGCACCA CATCATCTCTCC GCATTGTTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21789 7.3e-08 436_[+2]_52 10358 8.1e-07 452_[+2]_36 262946 3.1e-06 325_[+2]_163 27564 8.7e-06 453_[+2]_35 1397 8.7e-06 454_[+2]_34 1870 1.3e-05 301_[+2]_187 7542 1.4e-05 487_[+2]_1 3384 1.4e-05 462_[+2]_26 37280 1.5e-05 458_[+2]_30 1587 1.7e-05 407_[+2]_81 7229 1.9e-05 96_[+2]_392 10378 2.5e-05 482_[+2]_6 bd1071 3.8e-05 367_[+2]_121 9742 5.2e-05 433_[+2]_55 23935 5.2e-05 412_[+2]_76 1869 6.6e-05 222_[+2]_266 11079 9.1e-05 334_[+2]_154 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=17 21789 ( 437) CAACAACACAAC 1 10358 ( 453) CAACCACTCAAC 1 262946 ( 326) CATCATCACCAC 1 27564 ( 454) CAACAGCAAAAC 1 1397 ( 455) CAACAACTTAAC 1 1870 ( 302) CAACAACGCAAT 1 7542 ( 488) CAACAAAGCAAC 1 3384 ( 463) CAACATCTCCCC 1 37280 ( 459) CAACCGCACATC 1 1587 ( 408) AATCCACACAAC 1 7229 ( 97) CAACCACCCCAC 1 10378 ( 483) CGTCATCTCAAC 1 bd1071 ( 368) CATCCGAACAAC 1 9742 ( 434) CAATATCACATC 1 23935 ( 413) AACCATCTCAAC 1 1869 ( 223) CAACAACAACAT 1 11079 ( 335) CATCATCTCTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 8313 bayes= 9.00042 E= 4.3e-002 -116 187 -1073 -1073 183 -1073 -204 -1073 129 -203 -1073 22 -1073 196 -1073 -210 142 29 -1073 -1073 83 -1073 -46 48 -116 187 -1073 -1073 83 -203 -104 48 -116 177 -1073 -210 142 -3 -1073 -210 153 -103 -1073 -110 -1073 187 -1073 -110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 17 E= 4.3e-002 0.117647 0.882353 0.000000 0.000000 0.941176 0.000000 0.058824 0.000000 0.647059 0.058824 0.000000 0.294118 0.000000 0.941176 0.000000 0.058824 0.705882 0.294118 0.000000 0.000000 0.470588 0.000000 0.176471 0.352941 0.117647 0.882353 0.000000 0.000000 0.470588 0.058824 0.117647 0.352941 0.117647 0.823529 0.000000 0.058824 0.705882 0.235294 0.000000 0.058824 0.764706 0.117647 0.000000 0.117647 0.000000 0.882353 0.000000 0.117647 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CA[AT]C[AC][AT]C[AT]C[AC]AC -------------------------------------------------------------------------------- Time 5.68 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 17 llr = 149 E-value = 2.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :1:1::3::1:: pos.-specific C 2427:9219113 probability G 61:1::1:12:2 matrix T 1581a159:595 bits 2.1 * 1.8 * 1.6 ** * 1.4 ** ** * Relative 1.2 * ** ** * Entropy 1.0 * ** ** * (12.6 bits) 0.8 * * ** ** * 0.6 * **** ** * 0.4 ****** ** ** 0.2 ************ 0.0 ------------ Multilevel GTTCTCTTCTTT consensus CCC A G C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 11079 352 5.69e-08 TCTCCGCATT GTTCTCTTCTTT GAAGGCAACG 27564 246 1.99e-06 GAGTTGAACA GTTCTCCTCTTG AGAACGTCTC 3384 342 5.17e-06 TCTTGCTGCC GTTTTCTTCTTC CACGACGTCT 21789 482 5.17e-06 CCAACCCAAA GCTCTCATCATT CCTCATC 9742 133 1.54e-05 TTGAAGTAAC GCCGTCTTCTTT GGCATTCCGA 37280 192 2.71e-05 GACGTATGTT TTTCTCTTCCTC TGGGTTTCCC 262946 372 3.00e-05 ACCGTCGCTT GCTCTCGTCGTG AATCGTCCTC 23935 41 3.29e-05 CCTTCAAAGA TTCCTCATCTTC AAGTTAATCG 1397 301 3.29e-05 TAATGTGGTG GTTTTCATCGTG GATAGGGGCA 1870 445 3.57e-05 TGTTTCATCT GTTATCATCGTT CCATCATAAA 1869 206 3.92e-05 CAAGGGGTGG GACCTCTTCTTG GCAAACAACA 10378 349 5.84e-05 TACAGTACTT GCTGTCATCCTC TCTCTGAAAC 10358 426 8.01e-05 CGCGGACCCC CTTCTCCTCGCT ACAACATTTC 7229 67 9.20e-05 CACACACAAC CCTCTTCTCTTT ATCAGATTGG 1587 169 1.06e-04 TGTGGTGCGA CCCCTCTTGTTT GTGACTCTCT bd1071 438 1.58e-04 ATTCAAACAC GGTCTCTCCATT CATTTCAAAT 7542 444 1.58e-04 CAACACCGGA CCTCTCTCCTCC GGTTGCGCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11079 5.7e-08 351_[+3]_137 27564 2e-06 245_[+3]_243 3384 5.2e-06 341_[+3]_147 21789 5.2e-06 481_[+3]_7 9742 1.5e-05 132_[+3]_356 37280 2.7e-05 191_[+3]_297 262946 3e-05 371_[+3]_117 23935 3.3e-05 40_[+3]_448 1397 3.3e-05 300_[+3]_188 1870 3.6e-05 444_[+3]_44 1869 3.9e-05 205_[+3]_283 10378 5.8e-05 348_[+3]_140 10358 8e-05 425_[+3]_63 7229 9.2e-05 66_[+3]_422 1587 0.00011 168_[+3]_320 bd1071 0.00016 437_[+3]_51 7542 0.00016 443_[+3]_45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=17 11079 ( 352) GTTCTCTTCTTT 1 27564 ( 246) GTTCTCCTCTTG 1 3384 ( 342) GTTTTCTTCTTC 1 21789 ( 482) GCTCTCATCATT 1 9742 ( 133) GCCGTCTTCTTT 1 37280 ( 192) TTTCTCTTCCTC 1 262946 ( 372) GCTCTCGTCGTG 1 23935 ( 41) TTCCTCATCTTC 1 1397 ( 301) GTTTTCATCGTG 1 1870 ( 445) GTTATCATCGTT 1 1869 ( 206) GACCTCTTCTTG 1 10378 ( 349) GCTGTCATCCTC 1 10358 ( 426) CTTCTCCTCGCT 1 7229 ( 67) CCTCTTCTCTTT 1 1587 ( 169) CCCCTCTTGTTT 1 bd1071 ( 438) GGTCTCTCCATT 1 7542 ( 444) CCTCTCTCCTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 8313 bayes= 9.00042 E= 2.1e+002 -1073 -3 142 -110 -216 77 -204 90 -1073 -3 -1073 160 -216 155 -104 -110 -1073 -1073 -1073 198 -1073 196 -1073 -210 16 -45 -204 90 -1073 -103 -1073 180 -1073 196 -204 -1073 -116 -103 -4 107 -1073 -103 -1073 180 -1073 29 -4 90 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 17 E= 2.1e+002 0.000000 0.235294 0.647059 0.117647 0.058824 0.411765 0.058824 0.470588 0.000000 0.235294 0.000000 0.764706 0.058824 0.705882 0.117647 0.117647 0.000000 0.000000 0.000000 1.000000 0.000000 0.941176 0.000000 0.058824 0.294118 0.176471 0.058824 0.470588 0.000000 0.117647 0.000000 0.882353 0.000000 0.941176 0.058824 0.000000 0.117647 0.117647 0.235294 0.529412 0.000000 0.117647 0.000000 0.882353 0.000000 0.294118 0.235294 0.470588 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC][TC][TC]CTC[TA]TC[TG]T[TCG] -------------------------------------------------------------------------------- Time 8.33 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10358 3.58e-07 283_[+1(2.15e-07)]_126_\ [+3(8.01e-05)]_15_[+2(8.08e-07)]_19_[+2(6.15e-05)]_5 10378 4.96e-03 348_[+3(5.84e-05)]_122_\ [+2(2.47e-05)]_6 11079 1.43e-06 218_[+1(1.25e-05)]_100_\ [+2(9.07e-05)]_5_[+3(5.69e-08)]_137 1397 3.56e-06 296_[+1(3.02e-05)]_50_\ [+1(6.15e-07)]_76_[+2(8.73e-06)]_34 1587 9.10e-07 149_[+1(2.18e-08)]_242_\ [+2(1.71e-05)]_81 1869 2.03e-02 205_[+3(3.92e-05)]_5_[+2(6.55e-05)]_\ 266 1870 4.30e-03 301_[+2(1.25e-05)]_131_\ [+3(3.57e-05)]_44 21789 5.61e-09 88_[+1(3.86e-07)]_332_\ [+2(7.27e-08)]_33_[+3(5.17e-06)]_7 23935 4.37e-05 40_[+3(3.29e-05)]_276_\ [+1(1.79e-06)]_68_[+2(5.17e-05)]_76 262946 6.79e-07 56_[+1(2.97e-07)]_253_\ [+2(3.13e-06)]_34_[+3(3.00e-05)]_117 27564 2.14e-04 245_[+3(1.99e-06)]_165_\ [+3(8.01e-05)]_19_[+2(8.73e-06)]_35 3384 4.21e-04 341_[+3(5.17e-06)]_109_\ [+2(1.41e-05)]_26 37280 4.96e-05 191_[+3(2.71e-05)]_129_\ [+1(8.60e-06)]_110_[+2(1.50e-05)]_30 7229 1.63e-05 66_[+3(9.20e-05)]_18_[+2(1.91e-05)]_\ 140_[+1(1.02e-05)]_80_[+1(5.68e-07)]_140 7542 8.22e-07 337_[+1(1.60e-08)]_134_\ [+2(1.41e-05)]_1 9742 8.77e-06 51_[+1(6.15e-07)]_65_[+3(1.54e-05)]_\ 289_[+2(5.17e-05)]_55 bd1071 5.93e-05 82_[+1(7.34e-07)]_269_\ [+2(3.83e-05)]_121 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************