******************************************************************************** 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/242/242.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 9475 1.0000 500 42866 1.0000 500 31982 1.0000 500 9259 1.0000 500 46736 1.0000 500 7553 1.0000 500 28577 1.0000 500 14444 1.0000 500 47824 1.0000 500 15508 1.0000 500 49459 1.0000 500 50598 1.0000 500 44623 1.0000 500 51708 1.0000 500 26980 1.0000 500 12305 1.0000 500 46257 1.0000 500 42879 1.0000 500 39357 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/242/242.seqs.fa -oc motifs/242 -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= 19 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= 9500 N= 19 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.257 C 0.254 G 0.240 T 0.248 Background letter frequencies (from dataset with add-one prior applied): A 0.257 C 0.254 G 0.240 T 0.248 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 18 llr = 165 E-value = 2.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::::::1::: pos.-specific C 252311::2:2: probability G :2:7::354164 matrix T 838:99753936 bits 2.1 1.9 1.6 * * 1.4 * ** * Relative 1.2 * ***** * Entropy 1.0 * ****** * * (13.2 bits) 0.8 * ****** * * 0.6 * ****** *** 0.4 ******** *** 0.2 ************ 0.0 ------------ Multilevel TCTGTTTGGTGT consensus TCC GTT TG sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 39357 454 9.89e-08 TAGAAATTGG TCTGTTTTGTGT CTGCCTGTCT 46736 477 1.17e-06 TGAGTCCCTC TCTGTTGTGTGT AGCTTTGTCG 12305 21 2.27e-06 GACAGACTTG TCCGTTTGGTGT CACGTATGTC 31982 21 4.18e-06 TTGTCAGGCA TCTGTTTTATGG AGCTGTCCAT 9475 392 4.77e-06 TTGGGCGTTC TCTGTTTTCTTT AGAAAACCAA 47824 314 5.58e-06 CCATTCGCCG TTTGTTTGGTCT TCCAAAGGCC 51708 90 1.30e-05 CCGAAATGCT TGTGTTGTTTGG AATATGCTAC 44623 143 1.70e-05 TCAGCTTCTC TCTCTTTGCTTT ACCAGTGTCA 49459 408 2.06e-05 ATACACCACA TCTCTTTGTTCG ACAACGTTTT 50598 181 3.88e-05 GGGTTTTATC TCCGTTTGATTT TCCCGACCCA 14444 167 3.88e-05 GATAAATCGG CCTCTTTTGTTG GTTGCTGTTT 42879 218 4.12e-05 TGAAAACGCA TTTGTTTTGGGG GCGGTTTTCG 15508 285 5.59e-05 CCTCGCCAAT CTTGTTGGTTGG TACATGATTT 28577 308 6.42e-05 TGGCAAAGCG TTCGCTTTGTGG GAAGACCCGG 26980 437 8.38e-05 GGAACTGTCT CGTCTTTGCTGT TAAGACGCAC 42866 312 8.38e-05 CACACAGTTG TGTGTCTGGTTG GTACTTTTTG 7553 277 9.46e-05 GATTCGAGCT TTCGTTGTTTCT GCTACTTTGC 9259 33 1.39e-04 CAGCCTTCGT TGTCCTGGTTGT TTCATCACGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 39357 9.9e-08 453_[+1]_35 46736 1.2e-06 476_[+1]_12 12305 2.3e-06 20_[+1]_468 31982 4.2e-06 20_[+1]_468 9475 4.8e-06 391_[+1]_97 47824 5.6e-06 313_[+1]_175 51708 1.3e-05 89_[+1]_399 44623 1.7e-05 142_[+1]_346 49459 2.1e-05 407_[+1]_81 50598 3.9e-05 180_[+1]_308 14444 3.9e-05 166_[+1]_322 42879 4.1e-05 217_[+1]_271 15508 5.6e-05 284_[+1]_204 28577 6.4e-05 307_[+1]_181 26980 8.4e-05 436_[+1]_52 42866 8.4e-05 311_[+1]_177 7553 9.5e-05 276_[+1]_212 9259 0.00014 32_[+1]_456 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=18 39357 ( 454) TCTGTTTTGTGT 1 46736 ( 477) TCTGTTGTGTGT 1 12305 ( 21) TCCGTTTGGTGT 1 31982 ( 21) TCTGTTTTATGG 1 9475 ( 392) TCTGTTTTCTTT 1 47824 ( 314) TTTGTTTGGTCT 1 51708 ( 90) TGTGTTGTTTGG 1 44623 ( 143) TCTCTTTGCTTT 1 49459 ( 408) TCTCTTTGTTCG 1 50598 ( 181) TCCGTTTGATTT 1 14444 ( 167) CCTCTTTTGTTG 1 42879 ( 218) TTTGTTTTGGGG 1 15508 ( 285) CTTGTTGGTTGG 1 28577 ( 308) TTCGCTTTGTGG 1 26980 ( 437) CGTCTTTGCTGT 1 42866 ( 312) TGTGTCTGGTTG 1 7553 ( 277) TTCGTTGTTTCT 1 9259 ( 33) TGTCCTGGTTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 9291 bayes= 9.85814 E= 2.7e+000 -1081 -61 -1081 175 -1081 98 -11 16 -1081 -19 -1081 165 -1081 13 159 -1081 -1081 -119 -1081 184 -1081 -219 -1081 193 -1081 -1081 21 154 -1081 -1081 106 101 -121 -61 89 16 -1081 -1081 -211 193 -1081 -61 121 16 -1081 -1081 89 116 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 2.7e+000 0.000000 0.166667 0.000000 0.833333 0.000000 0.500000 0.222222 0.277778 0.000000 0.222222 0.000000 0.777778 0.000000 0.277778 0.722222 0.000000 0.000000 0.111111 0.000000 0.888889 0.000000 0.055556 0.000000 0.944444 0.000000 0.000000 0.277778 0.722222 0.000000 0.000000 0.500000 0.500000 0.111111 0.166667 0.444444 0.277778 0.000000 0.000000 0.055556 0.944444 0.000000 0.166667 0.555556 0.277778 0.000000 0.000000 0.444444 0.555556 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[CTG][TC][GC]TT[TG][GT][GT]T[GT][TG] -------------------------------------------------------------------------------- Time 3.37 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 5 llr = 93 E-value = 1.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::62:::::::a6::224:: pos.-specific C :::2:2:4:a:::46:::82 probability G aa:288a66:a::6288::8 matrix T ::442:::4:::4:2::62: bits 2.1 ** * *** 1.9 ** * *** 1.6 ** * *** 1.4 ** * *** Relative 1.2 ** *** *** ** ** Entropy 1.0 *** ********** ***** (26.9 bits) 0.8 *** ********** ***** 0.6 *** **************** 0.4 *** **************** 0.2 *** **************** 0.0 -------------------- Multilevel GGATGGGGGCGAAGCGGTCG consensus TATC CT TCGAAATC sequence C T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 42866 238 8.77e-11 CTGTAGGATG GGATGGGGTCGATCCGGACG TAAGGCACCC 47824 144 4.28e-10 AGTTCAACAG GGTGGGGGGCGAACGGGTCG GATGCGGCGG 39357 171 1.25e-09 GTAACGGTAT GGATTGGGGCGAAGCGAACG GGAGCGACGG 14444 432 4.23e-09 TAATATTGTT GGTAGCGCGCGAAGCAGTCG TCGCAATGGC 15508 97 1.08e-08 GTCAGGTTTC GGACGGGCTCGATGTGGTTC CCGTGTCGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42866 8.8e-11 237_[+2]_243 47824 4.3e-10 143_[+2]_337 39357 1.3e-09 170_[+2]_310 14444 4.2e-09 431_[+2]_49 15508 1.1e-08 96_[+2]_384 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=5 42866 ( 238) GGATGGGGTCGATCCGGACG 1 47824 ( 144) GGTGGGGGGCGAACGGGTCG 1 39357 ( 171) GGATTGGGGCGAAGCGAACG 1 14444 ( 432) GGTAGCGCGCGAAGCAGTCG 1 15508 ( 97) GGACGGGCTCGATGTGGTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 9139 bayes= 11.0868 E= 1.7e+002 -897 -897 205 -897 -897 -897 205 -897 122 -897 -897 69 -36 -35 -27 69 -897 -897 173 -31 -897 -35 173 -897 -897 -897 205 -897 -897 65 132 -897 -897 -897 132 69 -897 197 -897 -897 -897 -897 205 -897 196 -897 -897 -897 122 -897 -897 69 -897 65 132 -897 -897 124 -27 -31 -36 -897 173 -897 -36 -897 173 -897 64 -897 -897 127 -897 165 -897 -31 -897 -35 173 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 5 E= 1.7e+002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.000000 0.000000 0.400000 0.200000 0.200000 0.200000 0.400000 0.000000 0.000000 0.800000 0.200000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 0.600000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.400000 0.000000 0.400000 0.600000 0.000000 0.000000 0.600000 0.200000 0.200000 0.200000 0.000000 0.800000 0.000000 0.200000 0.000000 0.800000 0.000000 0.400000 0.000000 0.000000 0.600000 0.000000 0.800000 0.000000 0.200000 0.000000 0.200000 0.800000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GG[AT][TACG][GT][GC]G[GC][GT]CGA[AT][GC][CGT][GA][GA][TA][CT][GC] -------------------------------------------------------------------------------- Time 6.65 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 19 llr = 164 E-value = 4.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 16372226aaa8 pos.-specific C 32:24384:::: probability G 327:44:1:::: matrix T 41:1:2:::::2 bits 2.1 *** 1.9 *** 1.6 *** 1.4 *** Relative 1.2 * * **** Entropy 1.0 ** * **** (12.5 bits) 0.8 ** ****** 0.6 *** ****** 0.4 **** ****** 0.2 ************ 0.0 ------------ Multilevel TAGACGCAAAAA consensus G ACGCAC T sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 44623 224 1.75e-06 GACGTTGACG TAGAGACAAAAA ATGAACAGTT 49459 214 2.84e-06 CGAACCGATT CAGAGTCAAAAA AATACTGTGG 50598 22 3.71e-06 AGGAAGAGTT TGGACGCAAAAA GGCACCGATC 42879 135 4.79e-06 TGCTGACGGT GAGCCGCAAAAA CCAGTATTTG 47824 399 4.79e-06 AAAGGGACAC TAGACGAAAAAA GGAACGAACG 26980 285 5.62e-06 CTGCACTGCG TAGAGCCAAAAT ACTAACTGTA 9475 177 1.15e-05 GATGCCGGCG GAAACCCCAAAA TCGGCATCAA 15508 127 1.30e-05 CCGTGTCGTC GTGAGCCAAAAA TTCGGACAGA 46257 359 1.61e-05 CGCGACTCGT CCGACGCCAAAA GCATAATTCT 46736 2 2.29e-05 G GAAAGTCCAAAA TCTGGAACGA 12305 132 4.12e-05 CGAGGAACCT GAGCGCAAAAAA GCTCGTTCCC 39357 110 8.95e-05 ATTAGTGTCG AAGACGCCAAAT CAGAAATCCT 28577 120 8.95e-05 AGACGTGAAA CGAAAGCAAAAA GATTGCACTC 31982 310 8.95e-05 TCCCCGAAAA CCGCCCCCAAAA CAAATGCGTT 51708 75 1.04e-04 CCAAACCGAT GAGAGCCGAAAT GCTTGTGTTG 9259 262 1.77e-04 ATGGCTGCTT TCGAAACAAAAT CAGTGCCTAA 42866 331 2.23e-04 TTGGTACTTT TTGAATAAAAAA ACGGCAGTGA 14444 45 2.89e-04 GAAAAACCCT TGATGGCCAAAA GGGGTCACGA 7553 423 3.01e-04 GCCGGCGTCT CAACCAACAAAA ATGCAAGTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44623 1.8e-06 223_[+3]_265 49459 2.8e-06 213_[+3]_275 50598 3.7e-06 21_[+3]_467 42879 4.8e-06 134_[+3]_354 47824 4.8e-06 398_[+3]_90 26980 5.6e-06 284_[+3]_204 9475 1.1e-05 176_[+3]_312 15508 1.3e-05 126_[+3]_362 46257 1.6e-05 358_[+3]_130 46736 2.3e-05 1_[+3]_487 12305 4.1e-05 131_[+3]_357 39357 8.9e-05 109_[+3]_379 28577 8.9e-05 119_[+3]_369 31982 8.9e-05 309_[+3]_179 51708 0.0001 74_[+3]_414 9259 0.00018 261_[+3]_227 42866 0.00022 330_[+3]_158 14444 0.00029 44_[+3]_444 7553 0.0003 422_[+3]_66 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=19 44623 ( 224) TAGAGACAAAAA 1 49459 ( 214) CAGAGTCAAAAA 1 50598 ( 22) TGGACGCAAAAA 1 42879 ( 135) GAGCCGCAAAAA 1 47824 ( 399) TAGACGAAAAAA 1 26980 ( 285) TAGAGCCAAAAT 1 9475 ( 177) GAAACCCCAAAA 1 15508 ( 127) GTGAGCCAAAAA 1 46257 ( 359) CCGACGCCAAAA 1 46736 ( 2) GAAAGTCCAAAA 1 12305 ( 132) GAGCGCAAAAAA 1 39357 ( 110) AAGACGCCAAAT 1 28577 ( 120) CGAAAGCAAAAA 1 31982 ( 310) CCGCCCCCAAAA 1 51708 ( 75) GAGAGCCGAAAT 1 9259 ( 262) TCGAAACAAAAT 1 42866 ( 331) TTGAATAAAAAA 1 14444 ( 45) TGATGGCCAAAA 1 7553 ( 423) CAACCAACAAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 9291 bayes= 9.12593 E= 4.4e+002 -229 5 39 57 117 -69 -61 -124 3 -1089 162 -1089 152 -27 -1089 -223 -70 73 81 -1089 -70 31 62 -65 -29 163 -1089 -1089 117 54 -219 -1089 196 -1089 -1089 -1089 196 -1089 -1089 -1089 196 -1089 -1089 -1089 162 -1089 -1089 -24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 19 E= 4.4e+002 0.052632 0.263158 0.315789 0.368421 0.578947 0.157895 0.157895 0.105263 0.263158 0.000000 0.736842 0.000000 0.736842 0.210526 0.000000 0.052632 0.157895 0.421053 0.421053 0.000000 0.157895 0.315789 0.368421 0.157895 0.210526 0.789474 0.000000 0.000000 0.578947 0.368421 0.052632 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.789474 0.000000 0.000000 0.210526 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TGC]A[GA][AC][CG][GC][CA][AC]AAA[AT] -------------------------------------------------------------------------------- Time 9.94 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9475 9.60e-04 176_[+3(1.15e-05)]_203_\ [+1(4.77e-06)]_97 42866 4.82e-08 237_[+2(8.77e-11)]_54_\ [+1(8.38e-05)]_177 31982 3.60e-03 20_[+1(4.18e-06)]_277_\ [+3(8.95e-05)]_179 9259 8.22e-02 500 46736 4.87e-04 1_[+3(2.29e-05)]_267_[+1(7.36e-05)]_\ 184_[+1(1.17e-06)]_12 7553 1.13e-01 276_[+1(9.46e-05)]_212 28577 2.41e-02 119_[+3(8.95e-05)]_176_\ [+1(6.42e-05)]_181 14444 1.02e-06 166_[+1(3.88e-05)]_253_\ [+2(4.23e-09)]_49 47824 5.29e-10 143_[+2(4.28e-10)]_150_\ [+1(5.58e-06)]_73_[+3(4.79e-06)]_90 15508 2.12e-07 96_[+2(1.08e-08)]_10_[+3(1.30e-05)]_\ 146_[+1(5.59e-05)]_204 49459 5.78e-05 213_[+3(2.84e-06)]_182_\ [+1(2.06e-05)]_81 50598 2.09e-03 21_[+3(3.71e-06)]_147_\ [+1(3.88e-05)]_308 44623 5.34e-04 142_[+1(1.70e-05)]_69_\ [+3(1.75e-06)]_265 51708 7.21e-03 89_[+1(1.30e-05)]_399 26980 1.19e-03 284_[+3(5.62e-06)]_140_\ [+1(8.38e-05)]_52 12305 4.73e-04 20_[+1(2.27e-06)]_99_[+3(4.12e-05)]_\ 357 46257 1.85e-02 358_[+3(1.61e-05)]_130 42879 8.13e-04 134_[+3(4.79e-06)]_71_\ [+1(4.12e-05)]_271 39357 5.04e-10 109_[+3(8.95e-05)]_49_\ [+2(1.25e-09)]_132_[+1(9.46e-05)]_119_[+1(9.89e-08)]_35 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************