******************************************************************************** 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/158/158.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10894 1.0000 500 1884 1.0000 500 20978 1.0000 500 21498 1.0000 500 22969 1.0000 500 23205 1.0000 500 2407 1.0000 500 261778 1.0000 500 261829 1.0000 500 263033 1.0000 500 31132 1.0000 500 34590 1.0000 500 3592 1.0000 500 3744 1.0000 500 5894 1.0000 500 6537 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/158/158.seqs.fa -oc motifs/158 -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= 16 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= 8000 N= 16 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.256 C 0.226 G 0.244 T 0.274 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.226 G 0.244 T 0.274 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 15 llr = 150 E-value = 7.0e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::a4:73::4:3 pos.-specific C 9a::9::82:9: probability G 1::1:21:7::4 matrix T :::511621613 bits 2.1 * 1.9 ** 1.7 ** 1.5 *** * * Relative 1.3 *** * * * Entropy 1.1 *** * * * (14.4 bits) 0.9 *** ** **** 0.6 *********** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CCATCATCGTCG consensus A GATCA T sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 21498 65 1.87e-07 CGCCTCCGGT CCATCATCGACG TCGCCTCTTG 34590 466 4.64e-07 CCCTGATCAA CCATCAACGTCG GTCTCCTGCT 6537 462 7.72e-07 GTGAAAGGTC CCAACATCGACA TCCATCACGT 1884 318 1.34e-06 CTCAACTGTT CCATCATCCTCA GCATTGCTCG 10894 310 1.48e-06 TCTCTGGACT CCATCGTCGTCT CCTCATTGGT 5894 276 3.69e-06 AGCCTCTCTT CCATCAACCTCA CAGCATATAC 3744 467 1.14e-05 TCGAAACCAT CCAACAGCCTCA CATTTCATAT 263033 182 1.36e-05 GTTTCTTCTC CCATCAGTGTCT CTTCTACCAT 261829 189 1.36e-05 GTCGTCTTTG CCAACAACGATG GGGAATGCAG 31132 399 1.50e-05 TTTCCGCTCT CCAACTTCGACT GGATTTTTGA 20978 124 2.07e-05 CGTTGATGGA GCAACATTGTCG CTGGAGGTCG 22969 479 2.45e-05 TTGTTTACAC GCATCATCTACG CCTCATCCTC 23205 61 2.65e-05 TCTTTCCAAG CCAGCATCTTCT GAGGAGAAGG 261778 370 5.09e-05 ACAGCTACGA CCAATGACGACT TAAGTTTCAG 3592 392 1.51e-04 GTTGACGACT CCATTGTTGTTG TTCTATTGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21498 1.9e-07 64_[+1]_424 34590 4.6e-07 465_[+1]_23 6537 7.7e-07 461_[+1]_27 1884 1.3e-06 317_[+1]_171 10894 1.5e-06 309_[+1]_179 5894 3.7e-06 275_[+1]_213 3744 1.1e-05 466_[+1]_22 263033 1.4e-05 181_[+1]_307 261829 1.4e-05 188_[+1]_300 31132 1.5e-05 398_[+1]_90 20978 2.1e-05 123_[+1]_365 22969 2.4e-05 478_[+1]_10 23205 2.7e-05 60_[+1]_428 261778 5.1e-05 369_[+1]_119 3592 0.00015 391_[+1]_97 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=15 21498 ( 65) CCATCATCGACG 1 34590 ( 466) CCATCAACGTCG 1 6537 ( 462) CCAACATCGACA 1 1884 ( 318) CCATCATCCTCA 1 10894 ( 310) CCATCGTCGTCT 1 5894 ( 276) CCATCAACCTCA 1 3744 ( 467) CCAACAGCCTCA 1 263033 ( 182) CCATCAGTGTCT 1 261829 ( 189) CCAACAACGATG 1 31132 ( 399) CCAACTTCGACT 1 20978 ( 124) GCAACATTGTCG 1 22969 ( 479) GCATCATCTACG 1 23205 ( 61) CCAGCATCTTCT 1 261778 ( 370) CCAATGACGACT 1 3592 ( 392) CCATTGTTGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7824 bayes= 9.6993 E= 7.0e-003 -1055 194 -87 -1055 -1055 215 -1055 -1055 197 -1055 -1055 -1055 65 -1055 -187 96 -1055 194 -1055 -104 152 -1055 -29 -204 6 -1055 -87 113 -1055 182 -1055 -46 -1055 -18 145 -104 65 -1055 -1055 113 -1055 194 -1055 -104 6 -1055 71 28 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 15 E= 7.0e-003 0.000000 0.866667 0.133333 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.066667 0.533333 0.000000 0.866667 0.000000 0.133333 0.733333 0.000000 0.200000 0.066667 0.266667 0.000000 0.133333 0.600000 0.000000 0.800000 0.000000 0.200000 0.000000 0.200000 0.666667 0.133333 0.400000 0.000000 0.000000 0.600000 0.000000 0.866667 0.000000 0.133333 0.266667 0.000000 0.400000 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CCA[TA]C[AG][TA][CT][GC][TA]C[GTA] -------------------------------------------------------------------------------- Time 2.67 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 16 llr = 167 E-value = 5.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :81321:9318:15:1 pos.-specific C :::::6:1:1:261:1 probability G 9:9442a:36:63141 matrix T 13:342::4232:468 bits 2.1 1.9 * 1.7 * ** 1.5 * * ** Relative 1.3 * * ** Entropy 1.1 *** ** * (15.0 bits) 0.9 *** ** * * ** 0.6 *** ** *** ** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel GAGGTCGATGAGCATT consensus T TG A T GTG sequence A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 2407 127 3.43e-08 AAGCTTGGTA GAGGGCGAAGAGGAGT GCGTAGAGTA 22969 74 9.98e-08 TCTACGATGG GAGTGGGAGGAGCAGT AGGTCGTTTG 6537 322 2.06e-07 GATGATCCGT GAGAGCGAAGACCTTT GCCCCCCCCC 3744 91 5.19e-07 TGCGTCATCG GAGGACGATGAGCGGT GAAGTCCGGT 261778 70 7.70e-07 TGTTGATGGT GAGGTCGAGGAGGCTT TGCAGGAAGA 263033 397 9.79e-07 CTCTCTGGGT GAGTTCGATGTTCTTT TTTCAATTGA 1884 158 3.47e-06 TTCAACGATG GAGTGAGATCAGCATT GGTGATGGAT 261829 156 4.63e-06 CGTCGGCTTC GAGATTGAAGTCCTTT CTTCTGTGTC 21498 161 4.63e-06 TCAGTTCTGC GTAGGCGAGTAGCAGT GAAGGAAGGA 23205 293 8.51e-06 ACCAATACTG GTGATGGATAAGCATT AAAAAGTAGT 20978 139 1.50e-05 ATTGTCGCTG GAGGTCGATGTTGATG GAGACGAGTC 10894 235 2.49e-05 GGAGGTGCCG GAGGATGAAGAGAAGA GGCACCACAG 34590 195 2.85e-05 GCCGAGAGAT GTGGTGGAGCAGCTTC CTGTGAACGA 5894 235 3.96e-05 TGGTATGATG TTGTTCGAGTACCAGT TAGTGAGTTC 31132 296 4.48e-05 TGCAGTGAAT GAATGCGCTGAGATTT ACTTTCGGCT 3592 40 7.54e-05 ATGGGTGTGT GAGAATGAATTTGTGT TGTGTTGAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2407 3.4e-08 126_[+2]_358 22969 1e-07 73_[+2]_411 6537 2.1e-07 321_[+2]_163 3744 5.2e-07 90_[+2]_394 261778 7.7e-07 69_[+2]_415 263033 9.8e-07 396_[+2]_88 1884 3.5e-06 157_[+2]_327 261829 4.6e-06 155_[+2]_329 21498 4.6e-06 160_[+2]_324 23205 8.5e-06 292_[+2]_192 20978 1.5e-05 138_[+2]_346 10894 2.5e-05 234_[+2]_250 34590 2.9e-05 194_[+2]_290 5894 4e-05 234_[+2]_250 31132 4.5e-05 295_[+2]_189 3592 7.5e-05 39_[+2]_445 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=16 2407 ( 127) GAGGGCGAAGAGGAGT 1 22969 ( 74) GAGTGGGAGGAGCAGT 1 6537 ( 322) GAGAGCGAAGACCTTT 1 3744 ( 91) GAGGACGATGAGCGGT 1 261778 ( 70) GAGGTCGAGGAGGCTT 1 263033 ( 397) GAGTTCGATGTTCTTT 1 1884 ( 158) GAGTGAGATCAGCATT 1 261829 ( 156) GAGATTGAAGTCCTTT 1 21498 ( 161) GTAGGCGAGTAGCAGT 1 23205 ( 293) GTGATGGATAAGCATT 1 20978 ( 139) GAGGTCGATGTTGATG 1 10894 ( 235) GAGGATGAAGAGAAGA 1 34590 ( 195) GTGGTGGAGCAGCTTC 1 5894 ( 235) TTGTTCGAGTACCAGT 1 31132 ( 296) GAATGCGCTGAGATTT 1 3592 ( 40) GAGAATGAATTTGTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 7760 bayes= 8.91886 E= 5.5e-001 -1064 -1064 194 -213 155 -1064 -1064 -13 -103 -1064 184 -1064 -3 -1064 84 19 -45 -1064 62 67 -203 132 -38 -55 -1064 -1064 203 -1064 187 -185 -1064 -1064 29 -1064 35 45 -203 -85 135 -55 155 -1064 -1064 -13 -1064 -27 135 -55 -103 147 3 -1064 97 -185 -196 45 -1064 -1064 84 104 -203 -185 -196 157 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 16 E= 5.5e-001 0.000000 0.000000 0.937500 0.062500 0.750000 0.000000 0.000000 0.250000 0.125000 0.000000 0.875000 0.000000 0.250000 0.000000 0.437500 0.312500 0.187500 0.000000 0.375000 0.437500 0.062500 0.562500 0.187500 0.187500 0.000000 0.000000 1.000000 0.000000 0.937500 0.062500 0.000000 0.000000 0.312500 0.000000 0.312500 0.375000 0.062500 0.125000 0.625000 0.187500 0.750000 0.000000 0.000000 0.250000 0.000000 0.187500 0.625000 0.187500 0.125000 0.625000 0.250000 0.000000 0.500000 0.062500 0.062500 0.375000 0.000000 0.000000 0.437500 0.562500 0.062500 0.062500 0.062500 0.812500 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[AT]G[GTA][TG]CGA[TAG]G[AT]G[CG][AT][TG]T -------------------------------------------------------------------------------- Time 5.39 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 10 llr = 126 E-value = 1.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 9715:aa:6735243 pos.-specific C 1252a::a3373167 probability G :143::::::::6:: matrix T ::::::::1::21:: bits 2.1 * * 1.9 **** 1.7 **** 1.5 * **** Relative 1.3 * **** * * Entropy 1.1 * **** ** ** (18.2 bits) 0.9 ** **** ** ** 0.6 *********** ** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel AACACAACAACAGCC consensus CGG CCACAAA sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 23205 407 5.81e-10 TGTTGCATGA AACACAACAACAGCC CGCCGTAGTC 20978 289 4.52e-09 ACAAAAACAG AAGACAACAACCGCC AATAGAGGGC 6537 349 1.92e-07 CCCCCCCCCC AACGCAACACCCGCA TTATCATCTC 21498 349 3.45e-07 AACCTTCAGC AGCACAACAACAGCA ACTACATCAA 5894 409 7.17e-07 AGAGTTGGTA AACCCAACACCCAAC ACCCATCGTC 3744 396 1.22e-06 ACACAAATGC AACGCAACTACAAAC ACTGACTTCG 10894 462 2.23e-06 GTTTGCACCA CCGACAACCCCAGCC ATCTCTGCCC 261829 337 2.56e-06 GTACTGTAAA AAGACAACAAAATAA TCAAACAACG 1884 294 2.91e-06 TTGTGTTTAC AAACCAACCAATGCC TCAACTGTTC 31132 464 7.16e-06 TCGGGCGAAC ACGGCAACCAATCAC CCCCTCTGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23205 5.8e-10 406_[+3]_79 20978 4.5e-09 288_[+3]_197 6537 1.9e-07 348_[+3]_137 21498 3.5e-07 348_[+3]_137 5894 7.2e-07 408_[+3]_77 3744 1.2e-06 395_[+3]_90 10894 2.2e-06 461_[+3]_24 261829 2.6e-06 336_[+3]_149 1884 2.9e-06 293_[+3]_192 31132 7.2e-06 463_[+3]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=10 23205 ( 407) AACACAACAACAGCC 1 20978 ( 289) AAGACAACAACCGCC 1 6537 ( 349) AACGCAACACCCGCA 1 21498 ( 349) AGCACAACAACAGCA 1 5894 ( 409) AACCCAACACCCAAC 1 3744 ( 396) AACGCAACTACAAAC 1 10894 ( 462) CCGACAACCCCAGCC 1 261829 ( 337) AAGACAACAAAATAA 1 1884 ( 294) AAACCAACCAATGCC 1 31132 ( 464) ACGGCAACCAATCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 7776 bayes= 10.5453 E= 1.2e+000 182 -117 -997 -997 145 -18 -129 -997 -135 115 71 -997 97 -18 30 -997 -997 215 -997 -997 197 -997 -997 -997 197 -997 -997 -997 -997 215 -997 -997 123 41 -997 -145 145 41 -997 -997 23 163 -997 -997 97 41 -997 -45 -35 -117 129 -145 65 141 -997 -997 23 163 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 1.2e+000 0.900000 0.100000 0.000000 0.000000 0.700000 0.200000 0.100000 0.000000 0.100000 0.500000 0.400000 0.000000 0.500000 0.200000 0.300000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.300000 0.000000 0.100000 0.700000 0.300000 0.000000 0.000000 0.300000 0.700000 0.000000 0.000000 0.500000 0.300000 0.000000 0.200000 0.200000 0.100000 0.600000 0.100000 0.400000 0.600000 0.000000 0.000000 0.300000 0.700000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- A[AC][CG][AGC]CAAC[AC][AC][CA][ACT][GA][CA][CA] -------------------------------------------------------------------------------- Time 7.82 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10894 1.80e-06 234_[+2(2.49e-05)]_59_\ [+1(1.48e-06)]_140_[+3(2.23e-06)]_24 1884 3.52e-07 157_[+2(3.47e-06)]_120_\ [+3(2.91e-06)]_9_[+1(1.34e-06)]_171 20978 4.45e-08 123_[+1(2.07e-05)]_3_[+2(1.50e-05)]_\ 134_[+3(4.52e-09)]_197 21498 1.09e-08 64_[+1(1.87e-07)]_84_[+2(4.63e-06)]_\ 124_[+3(1.72e-05)]_33_[+3(3.45e-07)]_137 22969 5.19e-05 73_[+2(9.98e-08)]_369_\ [+2(3.49e-05)]_4_[+1(2.45e-05)]_10 23205 5.05e-09 60_[+1(2.65e-05)]_71_[+3(8.75e-05)]_\ 134_[+2(8.51e-06)]_98_[+3(5.81e-10)]_79 2407 9.32e-05 126_[+2(3.43e-08)]_181_\ [+2(1.39e-05)]_161 261778 4.06e-04 51_[+2(3.96e-05)]_2_[+2(7.70e-07)]_\ 284_[+1(5.09e-05)]_119 261829 3.27e-06 155_[+2(4.63e-06)]_17_\ [+1(1.36e-05)]_136_[+3(2.56e-06)]_149 263033 5.44e-05 181_[+1(1.36e-05)]_203_\ [+2(9.79e-07)]_88 31132 6.50e-05 295_[+2(4.48e-05)]_87_\ [+1(1.50e-05)]_53_[+3(7.16e-06)]_22 34590 7.66e-05 194_[+2(2.85e-05)]_255_\ [+1(4.64e-07)]_23 3592 6.18e-02 39_[+2(7.54e-05)]_445 3744 2.00e-07 90_[+2(5.19e-07)]_289_\ [+3(1.22e-06)]_56_[+1(1.14e-05)]_22 5894 2.22e-06 234_[+2(3.96e-05)]_25_\ [+1(3.69e-06)]_121_[+3(7.17e-07)]_77 6537 1.32e-09 84_[+3(1.98e-05)]_222_\ [+2(2.06e-07)]_11_[+3(1.92e-07)]_98_[+1(7.72e-07)]_27 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************