******************************************************************************** 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/218/218.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11228 1.0000 500 12166 1.0000 500 20014 1.0000 500 20916 1.0000 500 21811 1.0000 500 22958 1.0000 500 261228 1.0000 500 261904 1.0000 500 263396 1.0000 500 2649 1.0000 500 2895 1.0000 500 31510 1.0000 500 37739 1.0000 500 42380 1.0000 500 5938 1.0000 500 8121 1.0000 500 9023 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/218/218.seqs.fa -oc motifs/218 -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 0.275 C 0.231 G 0.236 T 0.259 Background letter frequencies (from dataset with add-one prior applied): A 0.275 C 0.231 G 0.236 T 0.259 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 16 llr = 167 E-value = 2.0e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :11:131:11:4:41 pos.-specific C 3834815a2936a19 probability G :12:1:1:3:21:3: matrix T 8156:63:5:6::3: bits 2.1 * * 1.9 * * 1.7 * * * 1.5 * * * * Relative 1.3 * * * * * * Entropy 1.1 * ** * * * * (15.0 bits) 0.8 ** ** * * ** * 0.6 ** *** * **** * 0.4 ** ***** **** * 0.2 ************* * 0.0 --------------- Multilevel TCTTCTCCTCTCCAC consensus C CC AT G CA G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 22958 472 6.73e-10 TACAGGTAAC TCTTCTCCTCTCCAC ATCCACAAAA 2649 424 5.50e-08 GAGACCTCCA TCTTCACCGCTCCAC ACTCAAAGGC 12166 111 4.10e-07 GCAGTCATAA TCTTCTGCTCCCCGC CAATCTCGAG 2895 7 1.88e-06 AAGGCC TCGCCACCGCGCCGC CACTTAATCA 21811 450 3.51e-06 AAAAAGCAAC CTTCCTCCTCCCCTC TTCAAAACAC 31510 271 5.15e-06 TTCTTCTTAT CCTTCTTCACTACGC GACGAGGGCC 42380 458 5.65e-06 CACATTTTCC TTTTCTGCGCTACAC GTCTTCACTA 9023 43 7.39e-06 ACAACCGCGT TCGTATCCCCTACTC AAAAGGATTC 37739 14 8.03e-06 TTGGGCCTCG CCGCCATCTCCCCCC TTTGGAGTGA 11228 370 1.03e-05 CTACCCGCGG TCTCCACCTCTGCAA ATACAGTCAA 20014 80 1.12e-05 CCAGTATTTC TCCCCCTCTCGACTC TTCATCTTCG 263396 356 1.22e-05 TCCCTCTCCT CCCCCTTCTCTCCCA ACCGACTGTA 8121 445 2.06e-05 TTACAAGACC TCACATTCTCCCCTC TAATTGAAAA 261228 420 2.06e-05 GCGGTAACGA TCCTGTCCCCGACGC CGATAGGCGA 20916 234 2.37e-05 TAAACATGGC TACTCTACGCTCCAC TTCAATGCTG 5938 286 6.51e-05 CCCGAACACC TGTTCACCCATACAC TACCACCGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22958 6.7e-10 471_[+1]_14 2649 5.5e-08 423_[+1]_62 12166 4.1e-07 110_[+1]_375 2895 1.9e-06 6_[+1]_479 21811 3.5e-06 449_[+1]_36 31510 5.1e-06 270_[+1]_215 42380 5.6e-06 457_[+1]_28 9023 7.4e-06 42_[+1]_443 37739 8e-06 13_[+1]_472 11228 1e-05 369_[+1]_116 20014 1.1e-05 79_[+1]_406 263396 1.2e-05 355_[+1]_130 8121 2.1e-05 444_[+1]_41 261228 2.1e-05 419_[+1]_66 20916 2.4e-05 233_[+1]_252 5938 6.5e-05 285_[+1]_200 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=16 22958 ( 472) TCTTCTCCTCTCCAC 1 2649 ( 424) TCTTCACCGCTCCAC 1 12166 ( 111) TCTTCTGCTCCCCGC 1 2895 ( 7) TCGCCACCGCGCCGC 1 21811 ( 450) CTTCCTCCTCCCCTC 1 31510 ( 271) CCTTCTTCACTACGC 1 42380 ( 458) TTTTCTGCGCTACAC 1 9023 ( 43) TCGTATCCCCTACTC 1 37739 ( 14) CCGCCATCTCCCCCC 1 11228 ( 370) TCTCCACCTCTGCAA 1 20014 ( 80) TCCCCCTCTCGACTC 1 263396 ( 356) CCCCCTTCTCTCCCA 1 8121 ( 445) TCACATTCTCCCCTC 1 261228 ( 420) TCCTGTCCCCGACGC 1 20916 ( 234) TACTCTACGCTCCAC 1 5938 ( 286) TGTTCACCCATACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 8262 bayes= 9.00948 E= 2.0e-002 -1064 12 -1064 154 -214 170 -191 -105 -214 12 -33 95 -1064 92 -1064 112 -114 182 -191 -1064 18 -188 -1064 127 -214 112 -91 27 -1064 212 -1064 -1064 -214 -30 9 95 -214 202 -1064 -1064 -1064 12 -33 112 45 129 -191 -1064 -1064 212 -1064 -1064 45 -88 9 -5 -114 192 -1064 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 16 E= 2.0e-002 0.000000 0.250000 0.000000 0.750000 0.062500 0.750000 0.062500 0.125000 0.062500 0.250000 0.187500 0.500000 0.000000 0.437500 0.000000 0.562500 0.125000 0.812500 0.062500 0.000000 0.312500 0.062500 0.000000 0.625000 0.062500 0.500000 0.125000 0.312500 0.000000 1.000000 0.000000 0.000000 0.062500 0.187500 0.250000 0.500000 0.062500 0.937500 0.000000 0.000000 0.000000 0.250000 0.187500 0.562500 0.375000 0.562500 0.062500 0.000000 0.000000 1.000000 0.000000 0.000000 0.375000 0.125000 0.250000 0.250000 0.125000 0.875000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TC]C[TC][TC]C[TA][CT]C[TG]C[TC][CA]C[AGT]C -------------------------------------------------------------------------------- Time 3.27 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 11 llr = 139 E-value = 6.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :129::a16:a1:25: pos.-specific C 33::5::12::2:15: probability G 748129:6:a:3a3:9 matrix T :3::31:22::5:511 bits 2.1 * * 1.9 * ** * 1.7 ** ** * * 1.5 * ** ** * * Relative 1.3 * ** ** ** * * Entropy 1.1 * ** ** ** * * (18.2 bits) 0.8 * ** ** ** * * 0.6 * ********* * ** 0.4 * ********* * ** 0.2 **************** 0.0 ---------------- Multilevel GGGACGAGAGATGTAG consensus CC T G GC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 2895 257 8.41e-10 CTGCCCTTGG GTGACGAGAGATGTCG ATGGCGTTAA 31510 77 8.42e-09 CCAGCACCCA GGGATGAGAGAGGTCG ACATCCGCTG 261228 172 1.01e-08 ACCGCATGCA GCGACGAGAGAGGGAG AGTTTAAGGC 20014 291 9.67e-08 TTGAAAGGTG GGGATGATAGATGGCG GAGTTGCTCT 261904 4 9.92e-07 AAG GCGACGAGAGAAGTAT TGAGAATGAG 263396 13 1.36e-06 ACAGTGTAAT GAGGCGAGAGATGAAG AAGAATGAAA 21811 317 2.12e-06 AAGTGTTGTG CTGATGAGTGATGGTG GGATTTTGCC 20916 291 3.15e-06 TCGTAAATGG CGAAGGAGAGAGGCAG TGATGCTGTG 8121 141 3.79e-06 GGCCAGGAAG GGAAGGATCGACGTCG TCGTCGTCGT 2649 256 3.79e-06 TCTCATGCCG CCGACGACCGACGACG AAACGAGTTC 37739 439 4.02e-06 TAAGTGCAAA GTGACTAATGATGTAG ACAAAATGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2895 8.4e-10 256_[+2]_228 31510 8.4e-09 76_[+2]_408 261228 1e-08 171_[+2]_313 20014 9.7e-08 290_[+2]_194 261904 9.9e-07 3_[+2]_481 263396 1.4e-06 12_[+2]_472 21811 2.1e-06 316_[+2]_168 20916 3.2e-06 290_[+2]_194 8121 3.8e-06 140_[+2]_344 2649 3.8e-06 255_[+2]_229 37739 4e-06 438_[+2]_46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=11 2895 ( 257) GTGACGAGAGATGTCG 1 31510 ( 77) GGGATGAGAGAGGTCG 1 261228 ( 172) GCGACGAGAGAGGGAG 1 20014 ( 291) GGGATGATAGATGGCG 1 261904 ( 4) GCGACGAGAGAAGTAT 1 263396 ( 13) GAGGCGAGAGATGAAG 1 21811 ( 317) CTGATGAGTGATGGTG 1 20916 ( 291) CGAAGGAGAGAGGCAG 1 8121 ( 141) GGAAGGATCGACGTCG 1 2649 ( 256) CCGACGACCGACGACG 1 37739 ( 439) GTGACTAATGATGTAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 9.90346 E= 6.5e-002 -1010 24 163 -1010 -160 24 63 8 -60 -1010 180 -1010 172 -1010 -137 -1010 -1010 124 -37 8 -1010 -1010 195 -151 186 -1010 -1010 -1010 -160 -134 143 -51 121 -34 -1010 -51 -1010 -1010 208 -1010 186 -1010 -1010 -1010 -160 -34 21 81 -1010 -1010 208 -1010 -60 -134 21 81 72 98 -1010 -151 -1010 -1010 195 -151 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 11 E= 6.5e-002 0.000000 0.272727 0.727273 0.000000 0.090909 0.272727 0.363636 0.272727 0.181818 0.000000 0.818182 0.000000 0.909091 0.000000 0.090909 0.000000 0.000000 0.545455 0.181818 0.272727 0.000000 0.000000 0.909091 0.090909 1.000000 0.000000 0.000000 0.000000 0.090909 0.090909 0.636364 0.181818 0.636364 0.181818 0.000000 0.181818 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.090909 0.181818 0.272727 0.454545 0.000000 0.000000 1.000000 0.000000 0.181818 0.090909 0.272727 0.454545 0.454545 0.454545 0.000000 0.090909 0.000000 0.000000 0.909091 0.090909 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GC][GCT]GA[CT]GAGAGA[TG]G[TG][AC]G -------------------------------------------------------------------------------- Time 6.29 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 12 llr = 142 E-value = 7.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :8:6a128633585:8 pos.-specific C a3a4:9:133331191 probability G ::::::3211::2:1: matrix T ::::::6:1452:4:1 bits 2.1 * * 1.9 * * * 1.7 * * ** * 1.5 * * ** * Relative 1.3 * * ** * Entropy 1.1 ****** ** (17.1 bits) 0.8 ****** * * ** 0.6 ******** **** 0.4 ********* ****** 0.2 **************** 0.0 ---------------- Multilevel CACAACTAATTAAACA consensus C C G CAAC T sequence CC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 31510 454 9.34e-09 ACACATTGTC CACAACTAATCAATCA AACCCGTTCT 2895 396 8.20e-08 TGCTTCGATA CACAACAAAATAAACA TACGTGACCC 42380 241 5.24e-07 TTAGCGACTG CCCCACTAACTAACCA ACTAAACAAA 261228 446 5.85e-07 GATAGGCGAG CACAACGAAGTTAACA TGAGTGTTGC 5938 336 6.47e-07 ATACTTGATA CACCACAACACAAACA CAAACAACTA 20014 470 9.63e-07 CAAACAACGG CACAACGAACACGTCA ACAACACAAC 2649 233 1.96e-06 CTACCTTCAA CCCCACTAAATCATCT CATGCCGCCG 20916 144 2.13e-06 GAGTCATGTC CACAACTGGTACATCA TCGTCGACGA 11228 252 3.42e-06 GTCAATACCC CACCACTAATTTGTCC AGATTATTGA 12166 450 4.56e-06 TTGATCATCT CACAACTGCCAACACA TTTTCACTTC 21811 478 6.38e-06 AAAACACAAC CCCCACTCTTCAAACA CCCAATC 261904 156 1.22e-05 CGCATGCTGT CACAAAGACTTCAAGA GTGCAAAGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31510 9.3e-09 453_[+3]_31 2895 8.2e-08 395_[+3]_89 42380 5.2e-07 240_[+3]_244 261228 5.8e-07 445_[+3]_39 5938 6.5e-07 335_[+3]_149 20014 9.6e-07 469_[+3]_15 2649 2e-06 232_[+3]_252 20916 2.1e-06 143_[+3]_341 11228 3.4e-06 251_[+3]_233 12166 4.6e-06 449_[+3]_35 21811 6.4e-06 477_[+3]_7 261904 1.2e-05 155_[+3]_329 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=12 31510 ( 454) CACAACTAATCAATCA 1 2895 ( 396) CACAACAAAATAAACA 1 42380 ( 241) CCCCACTAACTAACCA 1 261228 ( 446) CACAACGAAGTTAACA 1 5938 ( 336) CACCACAACACAAACA 1 20014 ( 470) CACAACGAACACGTCA 1 2649 ( 233) CCCCACTAAATCATCT 1 20916 ( 144) CACAACTGGTACATCA 1 11228 ( 252) CACCACTAATTTGTCC 1 12166 ( 450) CACAACTGCCAACACA 1 21811 ( 478) CCCCACTCTTCAAACA 1 261904 ( 156) CACAAAGACTTCAAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 9.87026 E= 7.1e+000 -1023 212 -1023 -1023 145 12 -1023 -1023 -1023 212 -1023 -1023 108 85 -1023 -1023 186 -1023 -1023 -1023 -172 199 -1023 -1023 -72 -1023 9 117 145 -147 -50 -1023 108 12 -150 -163 -14 12 -150 69 -14 12 -1023 95 86 53 -1023 -63 145 -147 -50 -1023 86 -147 -1023 69 -1023 199 -150 -1023 160 -147 -1023 -163 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 12 E= 7.1e+000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.583333 0.416667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.083333 0.916667 0.000000 0.000000 0.166667 0.000000 0.250000 0.583333 0.750000 0.083333 0.166667 0.000000 0.583333 0.250000 0.083333 0.083333 0.250000 0.250000 0.083333 0.416667 0.250000 0.250000 0.000000 0.500000 0.500000 0.333333 0.000000 0.166667 0.750000 0.083333 0.166667 0.000000 0.500000 0.083333 0.000000 0.416667 0.000000 0.916667 0.083333 0.000000 0.833333 0.083333 0.000000 0.083333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[AC]C[AC]AC[TG]A[AC][TAC][TAC][AC]A[AT]CA -------------------------------------------------------------------------------- Time 9.44 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11228 6.63e-04 251_[+3(3.42e-06)]_102_\ [+1(1.03e-05)]_116 12166 5.40e-05 110_[+1(4.10e-07)]_139_\ [+1(4.10e-07)]_170_[+3(4.56e-06)]_35 20014 3.40e-08 79_[+1(1.12e-05)]_196_\ [+2(9.67e-08)]_163_[+3(9.63e-07)]_15 20916 3.22e-06 143_[+3(2.13e-06)]_74_\ [+1(2.37e-05)]_42_[+2(3.15e-06)]_194 21811 1.09e-06 316_[+2(2.12e-06)]_117_\ [+1(3.51e-06)]_13_[+3(6.38e-06)]_7 22958 1.40e-06 130_[+2(4.69e-05)]_325_\ [+1(6.73e-10)]_14 261228 4.70e-09 171_[+2(1.01e-08)]_232_\ [+1(2.06e-05)]_11_[+3(5.85e-07)]_39 261904 2.71e-04 3_[+2(9.92e-07)]_136_[+3(1.22e-05)]_\ 329 263396 1.18e-04 12_[+2(1.36e-06)]_327_\ [+1(1.22e-05)]_130 2649 1.44e-08 232_[+3(1.96e-06)]_7_[+2(3.79e-06)]_\ 152_[+1(5.50e-08)]_62 2895 7.99e-12 6_[+1(1.88e-06)]_235_[+2(8.41e-10)]_\ 123_[+3(8.20e-08)]_89 31510 2.32e-11 76_[+2(8.42e-09)]_178_\ [+1(5.15e-06)]_168_[+3(9.34e-09)]_31 37739 5.91e-04 13_[+1(8.03e-06)]_410_\ [+2(4.02e-06)]_46 42380 6.11e-05 240_[+3(5.24e-07)]_201_\ [+1(5.65e-06)]_28 5938 7.68e-04 285_[+1(6.51e-05)]_35_\ [+3(6.47e-07)]_149 8121 1.28e-03 140_[+2(3.79e-06)]_288_\ [+1(2.06e-05)]_41 9023 2.08e-02 42_[+1(7.39e-06)]_443 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************