******************************************************************************** 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/192/192.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1856 1.0000 500 2069 1.0000 500 20763 1.0000 500 21288 1.0000 500 22739 1.0000 500 33625 1.0000 500 35182 1.0000 500 37962 1.0000 500 39539 1.0000 500 4842 1.0000 500 5552 1.0000 500 6982 1.0000 500 8432 1.0000 500 8527 1.0000 500 8776 1.0000 500 9520 1.0000 500 bd870 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/192/192.seqs.fa -oc motifs/192 -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 0.248 C 0.237 G 0.250 T 0.266 Background letter frequencies (from dataset with add-one prior applied): A 0.248 C 0.237 G 0.250 T 0.266 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 16 llr = 183 E-value = 1.2e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1411::14:::::7:: pos.-specific C :11::::11:::1::1 probability G 8476238:5a:67:59 matrix T 211388164:a4335: bits 2.1 * 1.9 ** 1.7 ** 1.5 ** * Relative 1.2 * ** * Entropy 1.0 * *** *** *** (16.5 bits) 0.8 * *** ******* 0.6 * ************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel GAGGTTGTGGTGGAGG consensus G T G AT TTTT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 22739 415 2.45e-09 GAAGGTTGAC GAGGTTGTGGTTGATG TTGCAGCAGA 20763 153 1.23e-08 GTTGTTGGAT GAGGTTGATGTTGAGG TGGACGACGT 21288 201 2.36e-08 TCCACTGGGC GAGGTTGTCGTGGAGG ACGTTGCTTT 8432 216 2.24e-07 TGAACTCTCT GGAGTTGAGGTTGATG GCAGAGACAG 9520 326 4.61e-07 GGTGGCAAAC GGAGTTGTGGTTGTTG GTTGTGTGAA 1856 293 6.48e-07 CATGGTTGCT GTGGTTGCGGTGGAGG TCGGGTTGGA 35182 450 1.77e-06 CTCTTATTGA GAGTTGAAGGTTGATG GTTCACATTA 8776 207 2.77e-06 AGAAGTCATT GTCTTTGTTGTGGATG TTCTTTCTCC 6982 300 3.29e-06 CTTTAACGGT TGGTTGGATGTGGTGG TGGGGAGAAG bd870 179 3.88e-06 TCTCTAATGT GGTATTGATGTGGTTG TTCGTCGTTG 5552 72 3.88e-06 ATGAAGCGGT TGGTTGGTTGTTTAGG GCAGTGCAGA 4842 325 6.66e-06 CTTCATGTTG GGTGGTGTTGTGTTGG TGCCGCAGGC 37962 196 6.66e-06 TGGCATCGAC GAGGTGTTGGTGTTGG CGGCAAAGTT 33625 286 8.26e-06 CGTTTGGCTT GAGAGTGTGGTGTATC GTGAGTCCCT 2069 455 3.06e-05 GATGCAGACG ACGGTTGACGTGGAGC TCAAAAGCAA 8527 80 3.54e-05 GTCTTGAGTC TAGTGTATGGTTCATG AAGCCTCCTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22739 2.4e-09 414_[+1]_70 20763 1.2e-08 152_[+1]_332 21288 2.4e-08 200_[+1]_284 8432 2.2e-07 215_[+1]_269 9520 4.6e-07 325_[+1]_159 1856 6.5e-07 292_[+1]_192 35182 1.8e-06 449_[+1]_35 8776 2.8e-06 206_[+1]_278 6982 3.3e-06 299_[+1]_185 bd870 3.9e-06 178_[+1]_306 5552 3.9e-06 71_[+1]_413 4842 6.7e-06 324_[+1]_160 37962 6.7e-06 195_[+1]_289 33625 8.3e-06 285_[+1]_199 2069 3.1e-05 454_[+1]_30 8527 3.5e-05 79_[+1]_405 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=16 22739 ( 415) GAGGTTGTGGTTGATG 1 20763 ( 153) GAGGTTGATGTTGAGG 1 21288 ( 201) GAGGTTGTCGTGGAGG 1 8432 ( 216) GGAGTTGAGGTTGATG 1 9520 ( 326) GGAGTTGTGGTTGTTG 1 1856 ( 293) GTGGTTGCGGTGGAGG 1 35182 ( 450) GAGTTGAAGGTTGATG 1 8776 ( 207) GTCTTTGTTGTGGATG 1 6982 ( 300) TGGTTGGATGTGGTGG 1 bd870 ( 179) GGTATTGATGTGGTTG 1 5552 ( 72) TGGTTGGTTGTTTAGG 1 4842 ( 325) GGTGGTGTTGTGTTGG 1 37962 ( 196) GAGGTGTTGGTGTTGG 1 33625 ( 286) GAGAGTGTGGTGTATC 1 2069 ( 455) ACGGTTGACGTGGAGC 1 8527 ( 80) TAGTGTATGGTTCATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 9.74459 E= 1.2e-005 -198 -1064 158 -50 82 -192 58 -109 -99 -192 146 -109 -99 -1064 117 23 -1064 -1064 -42 161 -1064 -1064 0 150 -99 -1064 170 -208 60 -192 -1064 108 -1064 -92 100 50 -1064 -1064 200 -1064 -1064 -1064 -1064 191 -1064 -1064 117 72 -1064 -192 146 -9 147 -1064 -1064 23 -1064 -1064 100 91 -1064 -92 181 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 16 E= 1.2e-005 0.062500 0.000000 0.750000 0.187500 0.437500 0.062500 0.375000 0.125000 0.125000 0.062500 0.687500 0.125000 0.125000 0.000000 0.562500 0.312500 0.000000 0.000000 0.187500 0.812500 0.000000 0.000000 0.250000 0.750000 0.125000 0.000000 0.812500 0.062500 0.375000 0.062500 0.000000 0.562500 0.000000 0.125000 0.500000 0.375000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.562500 0.437500 0.000000 0.062500 0.687500 0.250000 0.687500 0.000000 0.000000 0.312500 0.000000 0.000000 0.500000 0.500000 0.000000 0.125000 0.875000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[AG]G[GT]T[TG]G[TA][GT]GT[GT][GT][AT][GT]G -------------------------------------------------------------------------------- Time 2.72 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 13 llr = 156 E-value = 1.7e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 3:83:8::6::8132: pos.-specific C 5a158:55:7a:951a probability G ::::113:22:2:24: matrix T 2:22122522::::3: bits 2.1 * * * 1.9 * * * 1.7 * * * * 1.5 * * * * Relative 1.2 * * *** * Entropy 1.0 ** ** * *** * (17.3 bits) 0.8 ** ** * **** * 0.6 ** ********** * 0.4 ************** * 0.2 **************** 0.0 ---------------- Multilevel CCACCACCACCACCGC consensus A A GTT G AT sequence T T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 21288 467 9.35e-10 CGACAGCACA CCACCACCACCACCAC CACCACCAAA 5552 292 1.59e-07 AGCTGCGAAA CCAACAGTTCCACAGC TTTATTTTAA 37962 138 2.55e-07 TGTCAATCAC ACAACAGTAGCACCGC TCTCTCAATC 8776 462 3.97e-07 CTCTTCTCTC ACACCACCATCACCCC CGACCGACGT 39539 440 5.46e-07 TCCCCGCCCC CCCCCACCTCCACAGC AACCCTTCAA 8432 96 7.40e-07 ATCACTAGAT CCATCGGCACCACCAC ATCTTATTCT 33625 482 8.15e-07 GCCCACGTGT TCACCATCACCGCATC ACA 8527 387 1.42e-06 TCATCAACAC ACATCACTGTCACCTC ATGCTCAAGT 1856 483 1.42e-06 CCCGTCATAA CCATTACTACCGCCGC CC bd870 477 4.03e-06 AACTGCCGCC ACTACACTACCAAAGC AAACCACC 6982 448 4.34e-06 GAGAGGAAAC CCTCCTTCTCCACCTC ATTCTTCCCT 2069 73 1.07e-05 CAACAATCCT TCACGAGCAGCACGAC GAGACTTTCT 4842 375 1.13e-05 GTTTTCGGCT TCAACTCTGCCGCGTC CCCATTTTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21288 9.4e-10 466_[+2]_18 5552 1.6e-07 291_[+2]_193 37962 2.5e-07 137_[+2]_347 8776 4e-07 461_[+2]_23 39539 5.5e-07 439_[+2]_45 8432 7.4e-07 95_[+2]_389 33625 8.2e-07 481_[+2]_3 8527 1.4e-06 386_[+2]_98 1856 1.4e-06 482_[+2]_2 bd870 4e-06 476_[+2]_8 6982 4.3e-06 447_[+2]_37 2069 1.1e-05 72_[+2]_412 4842 1.1e-05 374_[+2]_110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=13 21288 ( 467) CCACCACCACCACCAC 1 5552 ( 292) CCAACAGTTCCACAGC 1 37962 ( 138) ACAACAGTAGCACCGC 1 8776 ( 462) ACACCACCATCACCCC 1 39539 ( 440) CCCCCACCTCCACAGC 1 8432 ( 96) CCATCGGCACCACCAC 1 33625 ( 482) TCACCATCACCGCATC 1 8527 ( 387) ACATCACTGTCACCTC 1 1856 ( 483) CCATTACTACCGCCGC 1 bd870 ( 477) ACTACACTACCAAAGC 1 6982 ( 448) CCTCCTTCTCCACCTC 1 2069 ( 73) TCACGAGCAGCACGAC 1 4842 ( 375) TCAACTCTGCCGCGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 10.4722 E= 1.7e-002 31 96 -1035 -20 -1035 208 -1035 -1035 163 -162 -1035 -79 31 96 -1035 -20 -1035 184 -170 -178 163 -1035 -170 -79 -1035 119 30 -79 -1035 119 -1035 80 131 -1035 -70 -20 -1035 155 -70 -79 -1035 208 -1035 -1035 163 -1035 -12 -1035 -168 196 -1035 -1035 31 119 -70 -1035 -10 -162 62 21 -1035 208 -1035 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 13 E= 1.7e-002 0.307692 0.461538 0.000000 0.230769 0.000000 1.000000 0.000000 0.000000 0.769231 0.076923 0.000000 0.153846 0.307692 0.461538 0.000000 0.230769 0.000000 0.846154 0.076923 0.076923 0.769231 0.000000 0.076923 0.153846 0.000000 0.538462 0.307692 0.153846 0.000000 0.538462 0.000000 0.461538 0.615385 0.000000 0.153846 0.230769 0.000000 0.692308 0.153846 0.153846 0.000000 1.000000 0.000000 0.000000 0.769231 0.000000 0.230769 0.000000 0.076923 0.923077 0.000000 0.000000 0.307692 0.538462 0.153846 0.000000 0.230769 0.076923 0.384615 0.307692 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CAT]CA[CAT]CA[CG][CT][AT]CC[AG]C[CA][GTA]C -------------------------------------------------------------------------------- Time 5.38 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 9 llr = 107 E-value = 1.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:6aa319:998 pos.-specific C 891::39:a112 probability G ::3::::::::: matrix T 11:::3:1:::: bits 2.1 ** * 1.9 ** * 1.7 ** * * 1.5 * ** ***** Relative 1.2 * ** ****** Entropy 1.0 ** ** ****** (17.2 bits) 0.8 ** ** ****** 0.6 ***** ****** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CCAAAACACAAA consensus G C C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 21288 419 8.83e-08 GGGGACAACT CCAAAACACAAA CGACGAAGAG 8432 489 1.37e-07 TTTCGACAGA CCAAATCACAAA 9520 464 1.17e-06 ACAGTTTTGC CCAAACCTCAAA TTAGGCCAGC 22739 237 1.46e-06 TCTCGCTTCA TCAAATCACAAA AACACGGCAA 20763 477 1.46e-06 TAAATTTCAA CCAAAAAACAAA CACAAACAAT 33625 33 2.51e-06 CCCGACCTTC CCGAATCACCAA TGGATCCCCT 39539 470 2.70e-06 CTTCAAACCT CCCAAACACAAC ACACAACACC 8527 237 5.43e-06 GATAAAATCA CTGAACCACAAC CAAGCCGACG 5552 260 8.74e-06 ACTAACTCGA ACGAACCACACA ACCCGCAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21288 8.8e-08 418_[+3]_70 8432 1.4e-07 488_[+3] 9520 1.2e-06 463_[+3]_25 22739 1.5e-06 236_[+3]_252 20763 1.5e-06 476_[+3]_12 33625 2.5e-06 32_[+3]_456 39539 2.7e-06 469_[+3]_19 8527 5.4e-06 236_[+3]_252 5552 8.7e-06 259_[+3]_229 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=9 21288 ( 419) CCAAAACACAAA 1 8432 ( 489) CCAAATCACAAA 1 9520 ( 464) CCAAACCTCAAA 1 22739 ( 237) TCAAATCACAAA 1 20763 ( 477) CCAAAAAACAAA 1 33625 ( 33) CCGAATCACCAA 1 39539 ( 470) CCCAAACACAAC 1 8527 ( 237) CTGAACCACAAC 1 5552 ( 260) ACGAACCACACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 8313 bayes= 10.6984 E= 1.3e+000 -115 172 -982 -125 -982 191 -982 -125 116 -109 41 -982 201 -982 -982 -982 201 -982 -982 -982 43 49 -982 33 -115 191 -982 -982 184 -982 -982 -125 -982 208 -982 -982 184 -109 -982 -982 184 -109 -982 -982 165 -9 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 9 E= 1.3e+000 0.111111 0.777778 0.000000 0.111111 0.000000 0.888889 0.000000 0.111111 0.555556 0.111111 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.333333 0.000000 0.333333 0.111111 0.888889 0.000000 0.000000 0.888889 0.000000 0.000000 0.111111 0.000000 1.000000 0.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.777778 0.222222 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CC[AG]AA[ACT]CACAA[AC] -------------------------------------------------------------------------------- Time 8.02 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1856 1.29e-06 292_[+1(6.48e-07)]_147_\ [+3(6.25e-05)]_15_[+2(1.42e-06)]_2 2069 1.55e-03 72_[+2(1.07e-05)]_366_\ [+1(3.06e-05)]_30 20763 8.61e-07 152_[+1(1.23e-08)]_308_\ [+3(1.46e-06)]_12 21288 1.54e-13 200_[+1(2.36e-08)]_5_[+1(3.54e-05)]_\ 181_[+3(8.83e-08)]_36_[+2(9.35e-10)]_18 22739 1.24e-07 236_[+3(1.46e-06)]_166_\ [+1(2.45e-09)]_70 33625 4.31e-07 32_[+3(2.51e-06)]_241_\ [+1(8.26e-06)]_180_[+2(8.15e-07)]_3 35182 2.51e-02 449_[+1(1.77e-06)]_35 37962 1.07e-05 137_[+2(2.55e-07)]_42_\ [+1(6.66e-06)]_289 39539 3.32e-05 439_[+2(5.46e-07)]_14_\ [+3(2.70e-06)]_19 4842 6.17e-05 119_[+3(6.04e-05)]_193_\ [+1(6.66e-06)]_34_[+2(1.13e-05)]_110 5552 1.52e-07 71_[+1(3.88e-06)]_172_\ [+3(8.74e-06)]_20_[+2(1.59e-07)]_193 6982 2.61e-04 299_[+1(3.29e-06)]_132_\ [+2(4.34e-06)]_37 8432 9.99e-10 95_[+2(7.40e-07)]_104_\ [+1(2.24e-07)]_257_[+3(1.37e-07)] 8527 5.21e-06 79_[+1(3.54e-05)]_141_\ [+3(5.43e-06)]_138_[+2(1.42e-06)]_98 8776 2.24e-05 206_[+1(2.77e-06)]_239_\ [+2(3.97e-07)]_23 9520 1.51e-05 325_[+1(4.61e-07)]_122_\ [+3(1.17e-06)]_25 bd870 2.08e-04 178_[+1(3.88e-06)]_282_\ [+2(4.03e-06)]_8 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************