******************************************************************************** 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/238/238.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10419 1.0000 500 10774 1.0000 500 20589 1.0000 500 23444 1.0000 500 24167 1.0000 500 24988 1.0000 500 260933 1.0000 500 261694 1.0000 500 270013 1.0000 500 2890 1.0000 500 31256 1.0000 500 33203 1.0000 500 34058 1.0000 500 5677 1.0000 500 5992 1.0000 500 6711 1.0000 500 8159 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/238/238.seqs.fa -oc motifs/238 -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 0.265 C 0.248 G 0.232 T 0.255 Background letter frequencies (from dataset with add-one prior applied): A 0.265 C 0.248 G 0.232 T 0.255 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 13 llr = 141 E-value = 1.8e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1a2381:92:8: pos.-specific C 9:86:5a149:9 probability G :::::1:::1:1 matrix T :::123::5:2: bits 2.1 * 1.9 * * 1.7 ** * * * 1.5 *** ** * * Relative 1.3 *** ** * * Entropy 1.1 *** * ** *** (15.7 bits) 0.8 ***** ** *** 0.6 ***** ** *** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CACCACCATCAC consensus ATT C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 2890 265 3.68e-07 ATCTCACAAC CACAACCATCAC GTGAAGCAAC 10419 404 5.83e-07 ATAGAGTACA CACCTCCATCAC CCATGGCCGA 270013 98 2.13e-06 ACAAGCTGCT CACCAGCACCAC TCATAACCTC 261694 488 2.13e-06 AAACACTTAT CACTACCATCAC A 20589 444 2.13e-06 GCCTGCCAGC CACCAACATCAC CCACTGCATC 33203 199 2.49e-06 GATGATGATG CACCACCAACTC CATACGGACC 23444 137 2.83e-06 GCAGCACGTC CACCTCCACCTC TGCCACGTCC 260933 288 3.96e-06 TGACCTTCCA CAAAACCACCAC AGCACCAAAC 24167 354 6.64e-06 ACCAGTGTCG CACCATCACGAC CTACCAACCG 8159 378 8.24e-06 GATTGATGAA CAACTTCATCAC ATGGTCATTG 24988 477 9.68e-06 GCCCACAGTC CACCACCCCCTC CGCTCTCCAA 5992 253 1.19e-05 GCTGTTTCAA AACAATCATCAC CTCCATGTAG 6711 134 2.48e-05 TAGTTGCTTG CACAATCAACAG CTCTATTAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2890 3.7e-07 264_[+1]_224 10419 5.8e-07 403_[+1]_85 270013 2.1e-06 97_[+1]_391 261694 2.1e-06 487_[+1]_1 20589 2.1e-06 443_[+1]_45 33203 2.5e-06 198_[+1]_290 23444 2.8e-06 136_[+1]_352 260933 4e-06 287_[+1]_201 24167 6.6e-06 353_[+1]_135 8159 8.2e-06 377_[+1]_111 24988 9.7e-06 476_[+1]_12 5992 1.2e-05 252_[+1]_236 6711 2.5e-05 133_[+1]_355 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=13 2890 ( 265) CACAACCATCAC 1 10419 ( 404) CACCTCCATCAC 1 270013 ( 98) CACCAGCACCAC 1 261694 ( 488) CACTACCATCAC 1 20589 ( 444) CACCAACATCAC 1 33203 ( 199) CACCACCAACTC 1 23444 ( 137) CACCTCCACCTC 1 260933 ( 288) CAAAACCACCAC 1 24167 ( 354) CACCATCACGAC 1 8159 ( 378) CAACTTCATCAC 1 24988 ( 477) CACCACCCCCTC 1 5992 ( 253) AACAATCATCAC 1 6711 ( 134) CACAATCAACAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 8313 bayes= 9.84967 E= 1.8e-003 -178 190 -1035 -1035 191 -1035 -1035 -1035 -79 177 -1035 -1035 21 131 -1035 -173 153 -1035 -1035 -15 -178 112 -159 27 -1035 201 -1035 -1035 180 -168 -1035 -1035 -79 64 -1035 85 -1035 190 -159 -1035 153 -1035 -1035 -15 -1035 190 -159 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 13 E= 1.8e-003 0.076923 0.923077 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.153846 0.846154 0.000000 0.000000 0.307692 0.615385 0.000000 0.076923 0.769231 0.000000 0.000000 0.230769 0.076923 0.538462 0.076923 0.307692 0.000000 1.000000 0.000000 0.000000 0.923077 0.076923 0.000000 0.000000 0.153846 0.384615 0.000000 0.461538 0.000000 0.923077 0.076923 0.000000 0.769231 0.000000 0.000000 0.230769 0.000000 0.923077 0.076923 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CAC[CA][AT][CT]CA[TC]C[AT]C -------------------------------------------------------------------------------- Time 2.67 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 8 llr = 117 E-value = 9.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 3:::1::6311::8:: pos.-specific C 8:::5:::::::1::: probability G ::94469:8919913a matrix T :a16:414::81:18: bits 2.1 * 1.9 * * 1.7 * * 1.5 ** * * ** * Relative 1.3 *** * ** ** ** Entropy 1.1 **** ***** ** ** (21.0 bits) 0.8 **** *********** 0.6 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CTGTCGGAGGTGGATG consensus A GGT TA G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 6711 343 9.04e-09 TGATGATGTG CTGTGTGAAGTGGATG TCACGTCGGA 31256 85 1.12e-08 AGCCGAGGCA CTGGCGGAGGTGGTTG AAGTTGATGA 34058 405 3.03e-08 TGAGGTCGGT ATGTGGGTGGTGGAGG GCGACGATTG 10419 94 3.39e-08 TTTTATTTGA CTGGCTGAGGTTGATG GTAAAGCAGC 10774 157 3.97e-08 CGTCATCTTT ATGTCGGAGGTGCATG TAGTAAATAT 23444 224 3.06e-07 GAGCTTGTGA CTGTGGGTGGAGGGGG CACTGCCCCA 20589 284 3.99e-07 GTCTCTCTGT CTGTCTGAAAGGGATG AAATTTGTCC 5677 18 7.69e-07 GTCGTTGACG CTTGAGTTGGTGGATG CTTTGGGTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6711 9e-09 342_[+2]_142 31256 1.1e-08 84_[+2]_400 34058 3e-08 404_[+2]_80 10419 3.4e-08 93_[+2]_391 10774 4e-08 156_[+2]_328 23444 3.1e-07 223_[+2]_261 20589 4e-07 283_[+2]_201 5677 7.7e-07 17_[+2]_467 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=8 6711 ( 343) CTGTGTGAAGTGGATG 1 31256 ( 85) CTGGCGGAGGTGGTTG 1 34058 ( 405) ATGTGGGTGGTGGAGG 1 10419 ( 94) CTGGCTGAGGTTGATG 1 10774 ( 157) ATGTCGGAGGTGCATG 1 23444 ( 224) CTGTGGGTGGAGGGGG 1 20589 ( 284) CTGTCTGAAAGGGATG 1 5677 ( 18) CTTGAGTTGGTGGATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 10.7454 E= 9.5e-002 -9 160 -965 -965 -965 -965 -965 197 -965 -965 192 -103 -965 -965 69 129 -108 101 69 -965 -965 -965 143 55 -965 -965 192 -103 123 -965 -965 55 -9 -965 169 -965 -108 -965 192 -965 -108 -965 -89 155 -965 -965 192 -103 -965 -98 192 -965 150 -965 -89 -103 -965 -965 11 155 -965 -965 211 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 8 E= 9.5e-002 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.375000 0.625000 0.125000 0.500000 0.375000 0.000000 0.000000 0.000000 0.625000 0.375000 0.000000 0.000000 0.875000 0.125000 0.625000 0.000000 0.000000 0.375000 0.250000 0.000000 0.750000 0.000000 0.125000 0.000000 0.875000 0.000000 0.125000 0.000000 0.125000 0.750000 0.000000 0.000000 0.875000 0.125000 0.000000 0.125000 0.875000 0.000000 0.750000 0.000000 0.125000 0.125000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CA]TG[TG][CG][GT]G[AT][GA]GTGGA[TG]G -------------------------------------------------------------------------------- Time 5.26 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 15 llr = 167 E-value = 6.9e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :72434163:1117:5 pos.-specific C :11:13::11:::32: probability G a1:6618::9:69:75 matrix T :17:12145:931:11 bits 2.1 * 1.9 * 1.7 * * 1.5 * ** * Relative 1.3 * * ** * Entropy 1.1 * * ** ** *** (16.1 bits) 0.8 * * ** ****** 0.6 ***** ********** 0.4 ***** ********** 0.2 **************** 0.0 ---------------- Multilevel GATGGAGATGTGGAGA consensus AAAC TA T CCG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 34058 195 1.85e-08 GGAGTGTCAT GATGGTGATGTGGCGG CGGTGCATGA 31256 240 2.22e-08 AGAGGAGGAG GATGGGGATGTGGAGG AGGATAGGAG 20589 117 1.44e-07 GAGTGGGCCT GATAAAGAAGTTGAGA CGACGTACTC 10774 448 1.12e-06 GCTCACTTCC GACGTCGTTGTGGAGG TAGTCTCACT 6711 195 1.83e-06 AGCGGCGAAC GACGGAGTTCTGGAGA GAAGCAGTAA 23444 433 2.41e-06 AGACAATTAT GAAAAAGTAGTGGACA ACTGCATCCT 270013 21 2.65e-06 TTGTTTTTTC GGTAGATAAGTGGAGA GCTAACTCCA 260933 144 2.65e-06 CATGAGTAAA GAAAGAGATGTTTAGA TGAGAGTACA 5677 155 2.90e-06 CCTTCTTCAT GGTGCCGTTGTGGCGG TTTAAATTAT 33203 183 6.16e-06 AGCGGCAGAC GATGACGATGATGATG CACCACCAAC 10419 10 7.22e-06 CAAAACTAT GCTGGCGATGATGACG ACGGTCGTCC 24988 9 7.79e-06 GGAGATAG GTTAGAGAAGTGACGA AAGAGCGGTG 2890 193 8.41e-06 TTCGCAGTGG GAAAGCAACGTGGACG TGAGGCTTCA 24167 403 1.13e-05 GGATCTCAGT GTTGGTGTCGTTGAGT GTTTGCACTC 8159 74 2.39e-05 AGTTACTTGC GATGATATAGTAGCGA GTTGATAGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 34058 1.9e-08 194_[+3]_290 31256 2.2e-08 239_[+3]_245 20589 1.4e-07 116_[+3]_368 10774 1.1e-06 447_[+3]_37 6711 1.8e-06 194_[+3]_290 23444 2.4e-06 432_[+3]_52 270013 2.6e-06 20_[+3]_464 260933 2.6e-06 143_[+3]_341 5677 2.9e-06 154_[+3]_330 33203 6.2e-06 182_[+3]_302 10419 7.2e-06 9_[+3]_475 24988 7.8e-06 8_[+3]_476 2890 8.4e-06 192_[+3]_292 24167 1.1e-05 402_[+3]_82 8159 2.4e-05 73_[+3]_411 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=15 34058 ( 195) GATGGTGATGTGGCGG 1 31256 ( 240) GATGGGGATGTGGAGG 1 20589 ( 117) GATAAAGAAGTTGAGA 1 10774 ( 448) GACGTCGTTGTGGAGG 1 6711 ( 195) GACGGAGTTCTGGAGA 1 23444 ( 433) GAAAAAGTAGTGGACA 1 270013 ( 21) GGTAGATAAGTGGAGA 1 260933 ( 144) GAAAGAGATGTTTAGA 1 5677 ( 155) GGTGCCGTTGTGGCGG 1 33203 ( 183) GATGACGATGATGATG 1 10419 ( 10) GCTGGCGATGATGACG 1 24988 ( 9) GTTAGAGAAGTGACGA 1 2890 ( 193) GAAAGCAACGTGGACG 1 24167 ( 403) GTTGGTGTCGTTGAGT 1 8159 ( 74) GATGATATAGTAGCGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 9.775 E= 6.9e-002 -1055 -1055 211 -1055 133 -189 -80 -94 -41 -89 -1055 138 59 -1055 137 -1055 1 -189 137 -193 59 43 -180 -35 -99 -1055 179 -193 118 -1055 -1055 65 33 -89 -1055 106 -1055 -189 201 -1055 -99 -1055 -1055 176 -199 -1055 137 38 -199 -1055 190 -193 147 11 -1055 -1055 -1055 -31 166 -193 81 -1055 101 -193 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 15 E= 6.9e-002 0.000000 0.000000 1.000000 0.000000 0.666667 0.066667 0.133333 0.133333 0.200000 0.133333 0.000000 0.666667 0.400000 0.000000 0.600000 0.000000 0.266667 0.066667 0.600000 0.066667 0.400000 0.333333 0.066667 0.200000 0.133333 0.000000 0.800000 0.066667 0.600000 0.000000 0.000000 0.400000 0.333333 0.133333 0.000000 0.533333 0.000000 0.066667 0.933333 0.000000 0.133333 0.000000 0.000000 0.866667 0.066667 0.000000 0.600000 0.333333 0.066667 0.000000 0.866667 0.066667 0.733333 0.266667 0.000000 0.000000 0.000000 0.200000 0.733333 0.066667 0.466667 0.000000 0.466667 0.066667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GA[TA][GA][GA][ACT]G[AT][TA]GT[GT]G[AC][GC][AG] -------------------------------------------------------------------------------- Time 7.83 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10419 5.47e-09 9_[+3(7.22e-06)]_68_[+2(3.39e-08)]_\ 294_[+1(5.83e-07)]_85 10774 1.44e-06 102_[+3(4.11e-05)]_38_\ [+2(3.97e-08)]_275_[+3(1.12e-06)]_37 20589 4.75e-09 116_[+3(1.44e-07)]_151_\ [+2(3.99e-07)]_144_[+1(2.13e-06)]_45 23444 6.45e-08 136_[+1(2.83e-06)]_75_\ [+2(3.06e-07)]_193_[+3(2.41e-06)]_52 24167 1.66e-04 353_[+1(6.64e-06)]_37_\ [+3(1.13e-05)]_82 24988 7.64e-04 8_[+3(7.79e-06)]_145_[+1(8.87e-05)]_\ 295_[+1(9.68e-06)]_12 260933 8.68e-05 143_[+3(2.65e-06)]_128_\ [+1(3.96e-06)]_201 261694 8.42e-03 487_[+1(2.13e-06)]_1 270013 1.34e-04 20_[+3(2.65e-06)]_61_[+1(2.13e-06)]_\ 391 2890 4.32e-05 192_[+3(8.41e-06)]_56_\ [+1(3.68e-07)]_224 31256 1.24e-09 84_[+2(1.12e-08)]_139_\ [+3(2.22e-08)]_245 33203 3.33e-04 182_[+3(6.16e-06)]_[+1(2.49e-06)]_\ 290 34058 2.97e-08 79_[+3(3.06e-05)]_99_[+3(1.85e-08)]_\ 194_[+2(3.03e-08)]_80 5677 1.95e-05 1_[+3(3.67e-05)]_[+2(7.69e-07)]_121_\ [+3(2.90e-06)]_330 5992 2.12e-02 252_[+1(1.19e-05)]_236 6711 1.45e-08 133_[+1(2.48e-05)]_49_\ [+3(1.83e-06)]_132_[+2(9.04e-09)]_142 8159 1.07e-03 73_[+3(2.39e-05)]_288_\ [+1(8.24e-06)]_111 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************