******************************************************************************** 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/101/101.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 32237 1.0000 500 13578 1.0000 500 28497 1.0000 500 21501 1.0000 500 14096 1.0000 500 47589 1.0000 500 14472 1.0000 500 15399 1.0000 500 7528 1.0000 500 51541 1.0000 500 32929 1.0000 500 15688 1.0000 500 49158 1.0000 500 23164 1.0000 500 40080 1.0000 500 16786 1.0000 500 10724 1.0000 500 45135 1.0000 500 34938 1.0000 500 12810 1.0000 500 33194 1.0000 500 34631 1.0000 500 46418 1.0000 500 40031 1.0000 500 45036 1.0000 500 44430 1.0000 500 41157 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/101/101.seqs.fa -oc motifs/101 -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= 27 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= 13500 N= 27 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.269 C 0.240 G 0.234 T 0.257 Background letter frequencies (from dataset with add-one prior applied): A 0.269 C 0.240 G 0.234 T 0.257 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 15 llr = 171 E-value = 1.2e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :12191::::87 pos.-specific C 4:69:9:::::: probability G :1::1:9:9a13 matrix T 6821::1a1:11 bits 2.1 * 1.9 * * 1.7 *** * 1.5 ****** Relative 1.3 ******* Entropy 1.0 ** ******** (16.4 bits) 0.8 ** ********* 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTCCACGTGGAA consensus C A G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 45036 326 1.64e-07 AGAGAACGCA TTCCACGTGGAG ACGAACAAAC 34631 320 1.64e-07 AGAGAACGCA TTCCACGTGGAG ACGAACGAAC 16786 8 4.60e-07 AGGAAAT CTACACGTGGAA ACTCCACTCA 49158 324 5.64e-07 TCCACTCTCC TTCCACGTGGGA CCGCCCCTGG 47589 280 6.83e-07 AGCCCCATGC TTCCACGTTGAA CACCAGATTT 10724 21 1.00e-06 TTTGTCTGTG CTCCACGTTGAA GCGTGCGTCT 44430 179 1.68e-06 TGTCAGTGAG TTCCAAGTGGAA CAGCGTTGAA 23164 281 2.51e-06 CCCGACGAGG CTCCACTTGGAA TCTGGAGTTG 15688 110 2.90e-06 TGCGTGGAAC TTCCACGTGGTG GTTCAACGGG 40031 15 3.90e-06 AGTGACGGCT TTTCACGTGGGG TCATCATCGT 46418 416 5.14e-06 ACGCAACGGC CTACACGTGGAT TGATCCAATG 40080 292 6.03e-06 TAAAACAGAC CAACACGTGGAA GTTTGCACCC 7528 487 6.35e-06 ACCACAGATG CTTTACGTGGAA AG 15399 159 6.83e-06 ACGTGCAGAC TGCCGCGTGGAA GAGTGCCAAT 28497 376 1.66e-05 CTCTTATATT TGTAACGTGGAA CTGCCTCGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45036 1.6e-07 325_[+1]_163 34631 1.6e-07 319_[+1]_169 16786 4.6e-07 7_[+1]_481 49158 5.6e-07 323_[+1]_165 47589 6.8e-07 279_[+1]_209 10724 1e-06 20_[+1]_468 44430 1.7e-06 178_[+1]_310 23164 2.5e-06 280_[+1]_208 15688 2.9e-06 109_[+1]_379 40031 3.9e-06 14_[+1]_474 46418 5.1e-06 415_[+1]_73 40080 6e-06 291_[+1]_197 7528 6.4e-06 486_[+1]_2 15399 6.8e-06 158_[+1]_330 28497 1.7e-05 375_[+1]_113 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=15 45036 ( 326) TTCCACGTGGAG 1 34631 ( 320) TTCCACGTGGAG 1 16786 ( 8) CTACACGTGGAA 1 49158 ( 324) TTCCACGTGGGA 1 47589 ( 280) TTCCACGTTGAA 1 10724 ( 21) CTCCACGTTGAA 1 44430 ( 179) TTCCAAGTGGAA 1 23164 ( 281) CTCCACTTGGAA 1 15688 ( 110) TTCCACGTGGTG 1 40031 ( 15) TTTCACGTGGGG 1 46418 ( 416) CTACACGTGGAT 1 40080 ( 292) CAACACGTGGAA 1 7528 ( 487) CTTTACGTGGAA 1 15399 ( 159) TGCCGCGTGGAA 1 28497 ( 376) TGTAACGTGGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13203 bayes= 10.4549 E= 1.2e-005 -1055 74 -1055 122 -201 -1055 -81 164 -43 132 -1055 -36 -201 185 -1055 -194 179 -1055 -181 -1055 -201 196 -1055 -1055 -1055 -1055 200 -194 -1055 -1055 -1055 196 -1055 -1055 189 -94 -1055 -1055 210 -1055 157 -1055 -81 -194 131 -1055 19 -194 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 15 E= 1.2e-005 0.000000 0.400000 0.000000 0.600000 0.066667 0.000000 0.133333 0.800000 0.200000 0.600000 0.000000 0.200000 0.066667 0.866667 0.000000 0.066667 0.933333 0.000000 0.066667 0.000000 0.066667 0.933333 0.000000 0.000000 0.000000 0.000000 0.933333 0.066667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.866667 0.133333 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.133333 0.066667 0.666667 0.000000 0.266667 0.066667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TC]T[CAT]CACGTGGA[AG] -------------------------------------------------------------------------------- Time 7.82 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 14 llr = 173 E-value = 8.4e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :7:45329:9:1:a96 pos.-specific C a:93418:6::19:12 probability G ::11:2:14:611:1: matrix T :3:114:::146:::2 bits 2.1 * 1.9 * * 1.7 * * * 1.5 * * * * ** Relative 1.3 * * ** * *** Entropy 1.0 *** ***** *** (17.8 bits) 0.8 *** ***** *** 0.6 *** * ***** **** 0.4 *** * ********** 0.2 **************** 0.0 ---------------- Multilevel CACAATCACAGTCAAA consensus T CCAA G T C sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 32929 341 3.37e-10 CCAACGTCAA CACAATCACAGTCAAA GGGCGAGAGC 15688 150 1.23e-08 AGTCCAATAT CACGCTCACAGTCAAA TACCGGGAGA 45036 396 1.91e-07 ATAAGCAATA CACACAAAGATTCAAA TACGGGCCAT 34631 396 1.91e-07 ATTAGCAATA CACACAAAGATTCAAA TACGGGCCAT 49158 145 4.20e-07 TACAAGTCAA CACAAACACATACAAC ACAACTCAGT 21501 447 6.80e-07 TGAACAACTT CACCAGCAGATGCAAA TATCCAACGA 45135 221 1.26e-06 CGGGAATTTT CACTATCACAGTCAGT CACATGAAGA 28497 420 1.37e-06 GAACAACGAT CTCCATCACAGTCACT GTCAGTGACA 41157 187 1.48e-06 AACGCTGCGT CTGCATCACAGTCAAC GATCGCTGCG 16786 24 2.17e-06 GTGGAAACTC CACTCACGCAGTCAAT TCGAACGGAA 47589 414 2.89e-06 TTTGCATTTA CACGACCACATCCAAC GAAGTGTAAG 32237 473 3.31e-06 AGCACACGAC CTCCCGCAGAGAGAAA TTCTGTTCCC 51541 238 3.79e-06 GCCTTTGTGC CTCACTCAGTTCCAAA AGCTCCACCA 34938 401 4.90e-06 TTGCCATCAG CACATGAAGAGTGAAA CGGCTGGATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 32929 3.4e-10 340_[+2]_144 15688 1.2e-08 149_[+2]_335 45036 1.9e-07 395_[+2]_89 34631 1.9e-07 395_[+2]_89 49158 4.2e-07 144_[+2]_340 21501 6.8e-07 446_[+2]_38 45135 1.3e-06 220_[+2]_264 28497 1.4e-06 419_[+2]_65 41157 1.5e-06 186_[+2]_298 16786 2.2e-06 23_[+2]_461 47589 2.9e-06 413_[+2]_71 32237 3.3e-06 472_[+2]_12 51541 3.8e-06 237_[+2]_247 34938 4.9e-06 400_[+2]_84 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=14 32929 ( 341) CACAATCACAGTCAAA 1 15688 ( 150) CACGCTCACAGTCAAA 1 45036 ( 396) CACACAAAGATTCAAA 1 34631 ( 396) CACACAAAGATTCAAA 1 49158 ( 145) CACAAACACATACAAC 1 21501 ( 447) CACCAGCAGATGCAAA 1 45135 ( 221) CACTATCACAGTCAGT 1 28497 ( 420) CTCCATCACAGTCACT 1 41157 ( 187) CTGCATCACAGTCAAC 1 16786 ( 24) CACTCACGCAGTCAAT 1 47589 ( 414) CACGACCACATCCAAC 1 32237 ( 473) CTCCCGCAGAGAGAAA 1 51541 ( 238) CTCACTCAGTTCCAAA 1 34938 ( 401) CACATGAAGAGTGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13095 bayes= 9.71153 E= 8.4e-003 -1045 206 -1045 -1045 141 -1045 -1045 15 -1045 195 -171 -1045 67 25 -71 -84 89 84 -1045 -184 8 -175 -13 74 -33 171 -1045 -1045 178 -1045 -171 -1045 -1045 125 87 -1045 178 -1045 -1045 -184 -1045 -1045 129 74 -91 -75 -171 132 -1045 184 -71 -1045 189 -1045 -1045 -1045 167 -175 -171 -1045 108 -16 -1045 -26 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 14 E= 8.4e-003 0.000000 1.000000 0.000000 0.000000 0.714286 0.000000 0.000000 0.285714 0.000000 0.928571 0.071429 0.000000 0.428571 0.285714 0.142857 0.142857 0.500000 0.428571 0.000000 0.071429 0.285714 0.071429 0.214286 0.428571 0.214286 0.785714 0.000000 0.000000 0.928571 0.000000 0.071429 0.000000 0.000000 0.571429 0.428571 0.000000 0.928571 0.000000 0.000000 0.071429 0.000000 0.000000 0.571429 0.428571 0.142857 0.142857 0.071429 0.642857 0.000000 0.857143 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.857143 0.071429 0.071429 0.000000 0.571429 0.214286 0.000000 0.214286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[AT]C[AC][AC][TAG][CA]A[CG]A[GT]TCAA[ACT] -------------------------------------------------------------------------------- Time 15.57 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 6 llr = 118 E-value = 7.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :7aa22a225:3:878::782 pos.-specific C a3:::2::2::5:2::2:::: probability G ::::77:8:582a:3:8a328 matrix T ::::2:::7:2::::2::::: bits 2.1 * * * 1.9 * ** * * * 1.7 * ** * * * 1.5 * ** ** * * ** * Relative 1.3 * ** ** * ** *** ** Entropy 1.0 **** ** ** ********* (28.4 bits) 0.8 ******** ** ********* 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CAAAGGAGTAGCGAAAGGAAG consensus C G A G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 45036 425 2.35e-12 GGGCCATCGT CAAAGGAGTAGCGAAAGGGAG AGAATCATTT 34631 425 2.35e-12 GGGCCATCGT CAAAGGAGTAGCGAAAGGGAG AGAATAATTT 32237 113 7.37e-11 CGACCCCCCC CAAAGGAGTGTAGAGAGGAAG GAAAGGCTTC 41157 434 2.62e-09 TGGTTTCTCA CAAATCAATGGCGAAAGGAGG TTGGTTGTCT 15399 388 6.77e-09 CTCACAATGG CCAAGAAGAAGAGCAAGGAAA ACGAGACGCC 40031 285 9.90e-09 CGGTGGAACA CCAAAGAGCGGGGAGTCGAAG GAATATTAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45036 2.3e-12 424_[+3]_55 34631 2.3e-12 424_[+3]_55 32237 7.4e-11 112_[+3]_367 41157 2.6e-09 433_[+3]_46 15399 6.8e-09 387_[+3]_92 40031 9.9e-09 284_[+3]_195 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=6 45036 ( 425) CAAAGGAGTAGCGAAAGGGAG 1 34631 ( 425) CAAAGGAGTAGCGAAAGGGAG 1 32237 ( 113) CAAAGGAGTGTAGAGAGGAAG 1 41157 ( 434) CAAATCAATGGCGAAAGGAGG 1 15399 ( 388) CCAAGAAGAAGAGCAAGGAAA 1 40031 ( 285) CCAAAGAGCGGGGAGTCGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12960 bayes= 11.5238 E= 7.4e-001 -923 206 -923 -923 131 47 -923 -923 189 -923 -923 -923 189 -923 -923 -923 -69 -923 151 -62 -69 -52 151 -923 189 -923 -923 -923 -69 -923 183 -923 -69 -52 -923 138 89 -923 109 -923 -923 -923 183 -62 31 106 -49 -923 -923 -923 209 -923 163 -52 -923 -923 131 -923 51 -923 163 -923 -923 -62 -923 -52 183 -923 -923 -923 209 -923 131 -923 51 -923 163 -923 -49 -923 -69 -923 183 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 7.4e-001 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.666667 0.166667 0.166667 0.166667 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.166667 0.166667 0.000000 0.666667 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 0.833333 0.166667 0.333333 0.500000 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.833333 0.000000 0.000000 0.166667 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.833333 0.000000 0.166667 0.000000 0.166667 0.000000 0.833333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[AC]AAGGAGT[AG]G[CA]GA[AG]AGG[AG]AG -------------------------------------------------------------------------------- Time 22.67 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 32237 8.87e-09 37_[+3(5.63e-06)]_54_[+3(7.37e-11)]_\ 82_[+3(4.60e-05)]_236_[+2(3.31e-06)]_12 13578 1.06e-01 180_[+1(9.28e-05)]_308 28497 1.77e-04 375_[+1(1.66e-05)]_32_\ [+2(1.37e-06)]_65 21501 1.44e-03 446_[+2(6.80e-07)]_38 14096 3.62e-01 500 47589 4.01e-05 279_[+1(6.83e-07)]_122_\ [+2(2.89e-06)]_71 14472 9.54e-01 500 15399 1.97e-06 158_[+1(6.83e-06)]_217_\ [+3(6.77e-09)]_92 7528 2.75e-03 486_[+1(6.35e-06)]_2 51541 7.80e-03 237_[+2(3.79e-06)]_247 32929 2.89e-06 340_[+2(3.37e-10)]_144 15688 2.43e-07 96_[+1(4.78e-05)]_1_[+1(2.90e-06)]_\ 28_[+2(1.23e-08)]_335 49158 1.85e-06 144_[+2(4.20e-07)]_163_\ [+1(5.64e-07)]_165 23164 2.95e-02 280_[+1(2.51e-06)]_208 40080 6.70e-03 291_[+1(6.03e-06)]_197 16786 8.76e-06 7_[+1(4.60e-07)]_4_[+2(2.17e-06)]_\ 461 10724 3.53e-04 20_[+1(1.00e-06)]_468 45135 7.95e-03 220_[+2(1.26e-06)]_264 34938 1.04e-02 176_[+2(3.99e-05)]_208_\ [+2(4.90e-06)]_84 12810 6.04e-01 500 33194 4.86e-01 500 34631 6.82e-15 319_[+1(1.64e-07)]_64_\ [+2(1.91e-07)]_13_[+3(2.35e-12)]_55 46418 9.65e-03 415_[+1(5.14e-06)]_73 40031 1.28e-06 14_[+1(3.90e-06)]_258_\ [+3(9.90e-09)]_195 45036 6.82e-15 325_[+1(1.64e-07)]_58_\ [+2(1.91e-07)]_13_[+3(2.35e-12)]_55 44430 1.45e-03 178_[+1(1.68e-06)]_310 41157 8.58e-08 186_[+2(1.48e-06)]_231_\ [+3(2.62e-09)]_46 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************