******************************************************************************** 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/264/264.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10173 1.0000 500 2065 1.0000 500 20971 1.0000 500 21021 1.0000 500 2327 1.0000 500 23989 1.0000 500 24815 1.0000 500 261018 1.0000 500 263332 1.0000 500 3785 1.0000 500 5510 1.0000 500 6547 1.0000 500 9342 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/264/264.seqs.fa -oc motifs/264 -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= 13 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= 6500 N= 13 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.267 C 0.223 G 0.244 T 0.267 Background letter frequencies (from dataset with add-one prior applied): A 0.267 C 0.223 G 0.244 T 0.267 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 13 llr = 169 E-value = 7.9e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 2:::1:2:::331122::5:: pos.-specific C 1:12:2::111::8:1:1:21 probability G :86364:72:52625119:28 matrix T 8235358379253:369:551 bits 2.2 2.0 1.7 * 1.5 * ** Relative 1.3 * * ** * Entropy 1.1 * ** * * ** * (18.8 bits) 0.9 *** **** * *** * 0.7 ***** **** *** *** * 0.4 ********** ********** 0.2 ********************* 0.0 --------------------- Multilevel TGGTGTTGTTGTGCGTTGATG consensus TTGTGATG AAT TA TC sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 23989 388 1.17e-10 CGTACAGCGT TGGTGGTGTTAAGCGTTGACG AGATGATGGC 5510 274 7.59e-10 ACAGCGACGA TGTTGTTGTTGTGCTATGTTG CACAACATCC 2327 215 3.15e-09 AGCTTTTGGT TTGGGTTGTTGGGCGATGATG GTGATGATGC 2065 266 2.57e-08 GATGATTGCC TGTTGCTGTTGAGCTCTGATG ATACAGTGGA 6547 76 7.04e-08 GTGAGTTGTT TGGTTGTGTTGGAGGTTGTTG CGACGATGAC 261018 445 2.11e-07 CGGCTTTGTC TGCCTTTTTTGTTCGTTGTCG CCGTCACGCT 263332 27 2.31e-07 GAGTTGTGGT TGGGGGAGGTTGGGGTTGTTG ATTGGGGGTC 20971 58 1.14e-06 GAGAGGAAGG AGTGTGTGTTATGAATTGATG GCCAAGACAA 10173 250 3.07e-06 GAATTTGTAT TTTGTTATGTATGCAATGATG TGAGGGAAGT 21021 69 3.49e-06 GTTGTACATA TGGCGTATTCCTTCTTTGAGG GCTTGGCTTT 9342 470 4.22e-06 CTGGTTGTAA AGGTGTTGTTAATCTTGGTCT CGCGAGTATC 3785 295 5.08e-06 GTGGAAGAGG TTGTGGTTGTTAGCGGTGAGC TGGATTGATG 24815 159 1.24e-05 ATGTGTGCCA CGGTACTGCTGTTCGTTCTGG CAATTTGTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23989 1.2e-10 387_[+1]_92 5510 7.6e-10 273_[+1]_206 2327 3.2e-09 214_[+1]_265 2065 2.6e-08 265_[+1]_214 6547 7e-08 75_[+1]_404 261018 2.1e-07 444_[+1]_35 263332 2.3e-07 26_[+1]_453 20971 1.1e-06 57_[+1]_422 10173 3.1e-06 249_[+1]_230 21021 3.5e-06 68_[+1]_411 9342 4.2e-06 469_[+1]_10 3785 5.1e-06 294_[+1]_185 24815 1.2e-05 158_[+1]_321 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=13 23989 ( 388) TGGTGGTGTTAAGCGTTGACG 1 5510 ( 274) TGTTGTTGTTGTGCTATGTTG 1 2327 ( 215) TTGGGTTGTTGGGCGATGATG 1 2065 ( 266) TGTTGCTGTTGAGCTCTGATG 1 6547 ( 76) TGGTTGTGTTGGAGGTTGTTG 1 261018 ( 445) TGCCTTTTTTGTTCGTTGTCG 1 263332 ( 27) TGGGGGAGGTTGGGGTTGTTG 1 20971 ( 58) AGTGTGTGTTATGAATTGATG 1 10173 ( 250) TTTGTTATGTATGCAATGATG 1 21021 ( 69) TGGCGTATTCCTTCTTTGAGG 1 9342 ( 470) AGGTGTTGTTAATCTTGGTCT 1 3785 ( 295) TTGTGGTTGTTAGCGGTGAGC 1 24815 ( 159) CGGTACTGCTGTTCGTTCTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6240 bayes= 8.90388 E= 7.9e-003 -79 -153 -1035 153 -1035 -1035 165 -21 -1035 -153 133 21 -1035 -53 33 101 -179 -1035 133 21 -1035 -53 66 79 -21 -1035 -1035 153 -1035 -1035 150 21 -1035 -153 -8 138 -1035 -153 -1035 179 21 -153 92 -79 21 -1035 -8 79 -179 -1035 133 21 -179 179 -67 -1035 -79 -1035 114 21 -21 -153 -166 121 -1035 -1035 -166 179 -1035 -153 192 -1035 101 -1035 -1035 79 -1035 5 -8 101 -1035 -153 179 -179 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 7.9e-003 0.153846 0.076923 0.000000 0.769231 0.000000 0.000000 0.769231 0.230769 0.000000 0.076923 0.615385 0.307692 0.000000 0.153846 0.307692 0.538462 0.076923 0.000000 0.615385 0.307692 0.000000 0.153846 0.384615 0.461538 0.230769 0.000000 0.000000 0.769231 0.000000 0.000000 0.692308 0.307692 0.000000 0.076923 0.230769 0.692308 0.000000 0.076923 0.000000 0.923077 0.307692 0.076923 0.461538 0.153846 0.307692 0.000000 0.230769 0.461538 0.076923 0.000000 0.615385 0.307692 0.076923 0.769231 0.153846 0.000000 0.153846 0.000000 0.538462 0.307692 0.230769 0.076923 0.076923 0.615385 0.000000 0.000000 0.076923 0.923077 0.000000 0.076923 0.923077 0.000000 0.538462 0.000000 0.000000 0.461538 0.000000 0.230769 0.230769 0.538462 0.000000 0.076923 0.846154 0.076923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[GT][GT][TG][GT][TG][TA][GT][TG]T[GA][TAG][GT]C[GT][TA]TG[AT][TCG]G -------------------------------------------------------------------------------- Time 1.53 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 13 llr = 166 E-value = 2.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 931961282281668261282 pos.-specific C :45:271155:8312217318 probability G :151227:121112:62152: matrix T 12:::::12:1::1::121:: bits 2.2 2.0 1.7 1.5 * * * Relative 1.3 * * * * * Entropy 1.1 * * * * ** * * (18.4 bits) 0.9 * ** *** ** * ** 0.7 * ****** **** ** * ** 0.4 * **************** ** 0.2 ********************* 0.0 --------------------- Multilevel ACCAACGACCACAAAGACGAC consensus AG GGA TA CG AG C sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 263332 301 2.50e-10 CGACCACTTC AAGAGCGAACACAAAGACGAC GTCGAAGTGA 24815 359 4.82e-08 GGAAGAAGAC AACAACAACAACAACAACAAC AACAGTCAAG 2065 84 6.58e-08 CGAGACACCG ACGAACGTTCACAAAGGCCAA GTTGGATGGC 3785 67 7.28e-08 GACGAAGTCA ATGAACGAGCAGCAAGGCGAC CGCTGCTGCT 10173 450 8.06e-08 CGTCGCAGAC AACAACCATGGCAAAGACGAC GAAGAAGAGC 20971 92 1.20e-07 AAGACAAATG ATGACCGAACACCGAGAGGAC ACTTAAGTCG 261018 111 7.27e-07 CTCCGATATG AGCAGCAACCAACGAGACAAC GAGGATTATC 2327 476 8.57e-07 CAAGTTTCCG ACGACGGACGACACACTCCAC CACG 5510 468 9.30e-07 AACATTCTCA ACCAACGACCACATAGCTTGC TCTGGTTACC 21021 454 1.89e-06 AGAACGCAGC ACCAAAGACAACAGACAACGC GTTTCACATC 9342 176 3.17e-06 GGTTCAGACA ACAAGGAACAACCAAAGCGAA TGAGTCGATG 6547 271 3.40e-06 AGCCCAACAA ATGGAGGACGACGACGATGAC TCTACGATGA 23989 82 1.13e-05 CAATACATGA TACAACGCTCTCAAAAACCCC TCATCCTGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263332 2.5e-10 300_[+2]_179 24815 4.8e-08 358_[+2]_121 2065 6.6e-08 83_[+2]_396 3785 7.3e-08 66_[+2]_413 10173 8.1e-08 449_[+2]_30 20971 1.2e-07 91_[+2]_388 261018 7.3e-07 110_[+2]_369 2327 8.6e-07 475_[+2]_4 5510 9.3e-07 467_[+2]_12 21021 1.9e-06 453_[+2]_26 9342 3.2e-06 175_[+2]_304 6547 3.4e-06 270_[+2]_209 23989 1.1e-05 81_[+2]_398 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=13 263332 ( 301) AAGAGCGAACACAAAGACGAC 1 24815 ( 359) AACAACAACAACAACAACAAC 1 2065 ( 84) ACGAACGTTCACAAAGGCCAA 1 3785 ( 67) ATGAACGAGCAGCAAGGCGAC 1 10173 ( 450) AACAACCATGGCAAAGACGAC 1 20971 ( 92) ATGACCGAACACCGAGAGGAC 1 261018 ( 111) AGCAGCAACCAACGAGACAAC 1 2327 ( 476) ACGACGGACGACACACTCCAC 1 5510 ( 468) ACCAACGACCACATAGCTTGC 1 21021 ( 454) ACCAAAGACAACAGACAACGC 1 9342 ( 176) ACAAGGAACAACCAAAGCGAA 1 6547 ( 271) ATGGAGGACGACGACGATGAC 1 23989 ( 82) TACAACGCTCTCAAAAACCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6240 bayes= 9.43532 E= 2.4e-001 179 -1035 -1035 -179 21 79 -166 -21 -179 105 92 -1035 179 -1035 -166 -1035 121 -53 -8 -1035 -179 164 -8 -1035 -21 -153 150 -1035 167 -153 -1035 -179 -79 127 -166 -21 -21 127 -8 -1035 167 -1035 -166 -179 -179 193 -166 -1035 121 47 -166 -1035 121 -153 -8 -179 167 -53 -1035 -1035 -21 -53 133 -1035 121 -153 -8 -179 -179 164 -166 -79 -79 47 92 -179 153 -153 -67 -1035 -79 193 -1035 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 2.4e-001 0.923077 0.000000 0.000000 0.076923 0.307692 0.384615 0.076923 0.230769 0.076923 0.461538 0.461538 0.000000 0.923077 0.000000 0.076923 0.000000 0.615385 0.153846 0.230769 0.000000 0.076923 0.692308 0.230769 0.000000 0.230769 0.076923 0.692308 0.000000 0.846154 0.076923 0.000000 0.076923 0.153846 0.538462 0.076923 0.230769 0.230769 0.538462 0.230769 0.000000 0.846154 0.000000 0.076923 0.076923 0.076923 0.846154 0.076923 0.000000 0.615385 0.307692 0.076923 0.000000 0.615385 0.076923 0.230769 0.076923 0.846154 0.153846 0.000000 0.000000 0.230769 0.153846 0.615385 0.000000 0.615385 0.076923 0.230769 0.076923 0.076923 0.692308 0.076923 0.153846 0.153846 0.307692 0.461538 0.076923 0.769231 0.076923 0.153846 0.000000 0.153846 0.846154 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- A[CAT][CG]A[AG][CG][GA]A[CT][CAG]AC[AC][AG]A[GA][AG]C[GC]AC -------------------------------------------------------------------------------- Time 3.08 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 11 llr = 117 E-value = 5.8e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :264:::31:1: pos.-specific C a54645a:7a:3 probability G :1::4::::::7 matrix T :2::35:72:9: bits 2.2 * * * 2.0 * * * 1.7 * * * 1.5 * * ** Relative 1.3 * * *** Entropy 1.1 * ** ******* (15.3 bits) 0.9 * ** ******* 0.7 * ** ******* 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CCACCCCTCCTG consensus CAGT A C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 23989 24 1.59e-06 GAAACTCCCT CCCAGTCTCCTG ACAAGTCAAC 261018 10 2.01e-06 CACCCGAAT CAACTCCTCCTG ACTATTGGGA 263332 333 2.52e-06 TCGAAGTGAC CGACGCCTCCTG TTTTTAACAG 6547 240 2.97e-06 ACAAAGCAAT CCAACTCACCTG TGTGAAGCGA 9342 422 3.47e-06 ACAGACAACC CTACCCCTCCTC CCTCGTCTAC 2327 176 3.47e-06 GAGTAGCCTG CCCAGCCTCCTC CGATGACAAC 21021 372 4.19e-06 CTAAACACAG CCACCCCTCCAG CGGCACCCGA 20971 149 5.21e-06 ACGTCCCTCA CCAATTCACCTG CCACCTTCAC 10173 399 1.57e-05 CATACATCTT CCCCCCCAACTG TTCTATCTTG 5510 145 1.69e-05 AGAGGTCAAC CACCGTCTTCTG ACGGATGCCG 2065 424 2.87e-05 GGCTTCATCA CTACTTCTTCTC CATCGAAACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23989 1.6e-06 23_[+3]_465 261018 2e-06 9_[+3]_479 263332 2.5e-06 332_[+3]_156 6547 3e-06 239_[+3]_249 9342 3.5e-06 421_[+3]_67 2327 3.5e-06 175_[+3]_313 21021 4.2e-06 371_[+3]_117 20971 5.2e-06 148_[+3]_340 10173 1.6e-05 398_[+3]_90 5510 1.7e-05 144_[+3]_344 2065 2.9e-05 423_[+3]_65 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=11 23989 ( 24) CCCAGTCTCCTG 1 261018 ( 10) CAACTCCTCCTG 1 263332 ( 333) CGACGCCTCCTG 1 6547 ( 240) CCAACTCACCTG 1 9342 ( 422) CTACCCCTCCTC 1 2327 ( 176) CCCAGCCTCCTC 1 21021 ( 372) CCACCCCTCCAG 1 20971 ( 149) CCAATTCACCTG 1 10173 ( 399) CCCCCCCAACTG 1 5510 ( 145) CACCGTCTTCTG 1 2065 ( 424) CTACTTCTTCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6357 bayes= 10.1999 E= 5.8e+000 -1010 217 -1010 -1010 -55 129 -142 -55 125 71 -1010 -1010 45 151 -1010 -1010 -1010 71 57 3 -1010 129 -1010 77 -1010 217 -1010 -1010 3 -1010 -1010 145 -155 171 -1010 -55 -1010 217 -1010 -1010 -155 -1010 -1010 177 -1010 29 157 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 11 E= 5.8e+000 0.000000 1.000000 0.000000 0.000000 0.181818 0.545455 0.090909 0.181818 0.636364 0.363636 0.000000 0.000000 0.363636 0.636364 0.000000 0.000000 0.000000 0.363636 0.363636 0.272727 0.000000 0.545455 0.000000 0.454545 0.000000 1.000000 0.000000 0.000000 0.272727 0.000000 0.000000 0.727273 0.090909 0.727273 0.000000 0.181818 0.000000 1.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.909091 0.000000 0.272727 0.727273 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CC[AC][CA][CGT][CT]C[TA]CCT[GC] -------------------------------------------------------------------------------- Time 4.50 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10173 1.11e-07 249_[+1(3.07e-06)]_128_\ [+3(1.57e-05)]_39_[+2(8.06e-08)]_30 2065 1.97e-09 83_[+2(6.58e-08)]_161_\ [+1(2.57e-08)]_81_[+1(6.92e-05)]_35_[+3(2.87e-05)]_65 20971 2.36e-08 57_[+1(1.14e-06)]_13_[+2(1.20e-07)]_\ 36_[+3(5.21e-06)]_340 21021 6.60e-07 68_[+1(3.49e-06)]_282_\ [+3(4.19e-06)]_70_[+2(1.89e-06)]_26 2327 4.32e-10 175_[+3(3.47e-06)]_27_\ [+1(3.15e-09)]_4_[+1(7.94e-05)]_215_[+2(8.57e-07)]_4 23989 1.07e-10 23_[+3(1.59e-06)]_46_[+2(1.13e-05)]_\ 285_[+1(1.17e-10)]_92 24815 1.06e-05 158_[+1(1.24e-05)]_179_\ [+2(4.82e-08)]_121 261018 1.09e-08 9_[+3(2.01e-06)]_89_[+2(7.27e-07)]_\ 313_[+1(2.11e-07)]_35 263332 8.79e-12 26_[+1(2.31e-07)]_253_\ [+2(2.50e-10)]_11_[+3(2.52e-06)]_156 3785 8.46e-06 66_[+2(7.28e-08)]_207_\ [+1(5.08e-06)]_93_[+2(6.31e-05)]_71 5510 5.37e-10 144_[+3(1.69e-05)]_117_\ [+1(7.59e-10)]_173_[+2(9.30e-07)]_12 6547 2.36e-08 75_[+1(7.04e-08)]_25_[+1(8.78e-05)]_\ 97_[+3(2.97e-06)]_19_[+2(3.40e-06)]_209 9342 1.05e-06 175_[+2(3.17e-06)]_225_\ [+3(3.47e-06)]_36_[+1(4.22e-06)]_10 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************