******************************************************************************** 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/438/438.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 46476 1.0000 500 2089 1.0000 500 3267 1.0000 500 38271 1.0000 500 48903 1.0000 500 44189 1.0000 500 11169 1.0000 500 45097 1.0000 500 45386 1.0000 500 7966 1.0000 500 4021 1.0000 500 34529 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/438/438.seqs.fa -oc motifs/438 -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= 12 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= 6000 N= 12 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.259 C 0.234 G 0.223 T 0.284 Background letter frequencies (from dataset with add-one prior applied): A 0.259 C 0.234 G 0.223 T 0.284 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 14 sites = 8 llr = 96 E-value = 1.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A a:53::3:51:89: pos.-specific C :931:a531693:: probability G :116::1813:::a matrix T ::1:a:1:3:1:1: bits 2.2 * * 1.9 * * * 1.7 * ** * 1.5 ** ** * * Relative 1.3 ** ** * * ** Entropy 1.1 ** ** * **** (17.3 bits) 0.9 ** *** * ***** 0.6 ** *** * ***** 0.4 ** *** * ***** 0.2 ************** 0.0 -------------- Multilevel ACAGTCCGACCAAG consensus CA ACTG C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 2089 352 1.06e-08 ACCACTGTTG ACAGTCCGTCCAAG TTCGCCACCT 11169 346 9.64e-08 TATCAGAAGC ACAATCCGAGCAAG ATTGATTCGG 48903 125 5.36e-07 AATTGGTTTC ACAGTCAGCCCCAG TAACAGCCGA 3267 25 1.52e-06 ATTATATCTC ACGGTCACTCCAAG GAGAGGGAAT 34529 419 2.67e-06 CAATATCACG ACCCTCCCGCCAAG GTCTATACGA 45386 350 3.31e-06 CAATTTCAAT AGAGTCCGAGCATG CTTTGATTGT 7966 218 4.65e-06 AGGAAGATGG ACCGTCTGACTCAG AATATATACT 45097 74 5.98e-06 CGACACGGGT ACTATCGGAACAAG ATAGACCGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2089 1.1e-08 351_[+1]_135 11169 9.6e-08 345_[+1]_141 48903 5.4e-07 124_[+1]_362 3267 1.5e-06 24_[+1]_462 34529 2.7e-06 418_[+1]_68 45386 3.3e-06 349_[+1]_137 7966 4.7e-06 217_[+1]_269 45097 6e-06 73_[+1]_413 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=14 seqs=8 2089 ( 352) ACAGTCCGTCCAAG 1 11169 ( 346) ACAATCCGAGCAAG 1 48903 ( 125) ACAGTCAGCCCCAG 1 3267 ( 25) ACGGTCACTCCAAG 1 34529 ( 419) ACCCTCCCGCCAAG 1 45386 ( 350) AGAGTCCGAGCATG 1 7966 ( 218) ACCGTCTGACTCAG 1 45097 ( 74) ACTATCGGAACAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 5844 bayes= 9.51076 E= 1.7e+002 195 -965 -965 -965 -965 190 -83 -965 95 10 -83 -118 -5 -90 149 -965 -965 -965 -965 181 -965 210 -965 -965 -5 110 -83 -118 -965 10 175 -965 95 -90 -83 -19 -105 142 16 -965 -965 190 -965 -118 153 10 -965 -965 176 -965 -965 -118 -965 -965 216 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 8 E= 1.7e+002 1.000000 0.000000 0.000000 0.000000 0.000000 0.875000 0.125000 0.000000 0.500000 0.250000 0.125000 0.125000 0.250000 0.125000 0.625000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.500000 0.125000 0.125000 0.000000 0.250000 0.750000 0.000000 0.500000 0.125000 0.125000 0.250000 0.125000 0.625000 0.250000 0.000000 0.000000 0.875000 0.000000 0.125000 0.750000 0.250000 0.000000 0.000000 0.875000 0.000000 0.000000 0.125000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- AC[AC][GA]TC[CA][GC][AT][CG]C[AC]AG -------------------------------------------------------------------------------- Time 1.30 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 12 llr = 113 E-value = 5.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::2:12:::18 pos.-specific C :9:732321a8: probability G ::326:383::2 matrix T a17:183:6:2: bits 2.2 * 1.9 * 1.7 ** * 1.5 ** * * Relative 1.3 ** * * * Entropy 1.1 *** * *** (13.6 bits) 0.9 ****** * *** 0.6 ****** ***** 0.4 ****** ***** 0.2 ****** ***** 0.0 ------------ Multilevel TCTCGTTGTCCA consensus G C C G sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 4021 337 1.86e-07 TCATTGTTGC TCTCGTGGTCCA GCGCTTTATC 7966 411 3.68e-06 TACTTTACCC TCTAGTCGGCCA AGTCTCAATG 44189 129 4.14e-06 GACACAGTGC TCTCCCTGTCCA CGCGTCTTTT 45097 379 6.33e-06 CGCATCAGTG TCGCGTTGTCTA CACTGCTCGA 34529 81 8.11e-06 TCCTCTCCTT TCTCCTGCTCCA CGTGATGTTC 38271 71 1.08e-05 CCCCGTTCAA TCGCGAGGTCCA ACGTCCCGAA 2089 301 1.08e-05 GATCAAGCCG TCGCGCAGGCCA CACCATCCAC 45386 435 2.94e-05 TTAAACGTGT TCTGCTTGCCCA TCTTGAGCAT 48903 381 4.84e-05 TCGAAGGGAC TCGGCTCGGCCG TTCCTGCCAT 46476 462 5.98e-05 TGCGTTTGCG TCTAGTAGTCAA TCAGTCAGTC 11169 267 6.78e-05 GGATGAAGTA TTTCGTCCGCCA AAGAATGCTA 3267 197 1.14e-04 ATTTTAGGTT TCTCTTTGTCTG TAGTAGAAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4021 1.9e-07 336_[+2]_152 7966 3.7e-06 410_[+2]_78 44189 4.1e-06 128_[+2]_360 45097 6.3e-06 378_[+2]_110 34529 8.1e-06 80_[+2]_408 38271 1.1e-05 70_[+2]_418 2089 1.1e-05 300_[+2]_188 45386 2.9e-05 434_[+2]_54 48903 4.8e-05 380_[+2]_108 46476 6e-05 461_[+2]_27 11169 6.8e-05 266_[+2]_222 3267 0.00011 196_[+2]_292 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=12 4021 ( 337) TCTCGTGGTCCA 1 7966 ( 411) TCTAGTCGGCCA 1 44189 ( 129) TCTCCCTGTCCA 1 45097 ( 379) TCGCGTTGTCTA 1 34529 ( 81) TCTCCTGCTCCA 1 38271 ( 71) TCGCGAGGTCCA 1 2089 ( 301) TCGCGCAGGCCA 1 45386 ( 435) TCTGCTTGCCCA 1 48903 ( 381) TCGGCTCGGCCG 1 46476 ( 462) TCTAGTAGTCAA 1 11169 ( 267) TTTCGTCCGCCA 1 3267 ( 197) TCTCTTTGTCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5868 bayes= 9.37898 E= 5.9e+002 -1023 -1023 -1023 181 -1023 197 -1023 -177 -1023 -1023 58 123 -63 151 -42 -1023 -1023 51 139 -177 -163 -49 -1023 140 -63 10 16 23 -1023 -49 190 -1023 -1023 -149 58 104 -1023 210 -1023 -1023 -163 168 -1023 -77 169 -1023 -42 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 12 E= 5.9e+002 0.000000 0.000000 0.000000 1.000000 0.000000 0.916667 0.000000 0.083333 0.000000 0.000000 0.333333 0.666667 0.166667 0.666667 0.166667 0.000000 0.000000 0.333333 0.583333 0.083333 0.083333 0.166667 0.000000 0.750000 0.166667 0.250000 0.250000 0.333333 0.000000 0.166667 0.833333 0.000000 0.000000 0.083333 0.333333 0.583333 0.000000 1.000000 0.000000 0.000000 0.083333 0.750000 0.000000 0.166667 0.833333 0.000000 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TC[TG]C[GC]T[TCG]G[TG]CCA -------------------------------------------------------------------------------- Time 2.68 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 8 llr = 102 E-value = 1.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 61:65:3341:41:: pos.-specific C 3::::4:1:1::::: probability G :9a4:6656::::a9 matrix T 1:::5:11:8a69:1 bits 2.2 * * 1.9 * * 1.7 * * * 1.5 ** * ** Relative 1.3 ** * *** Entropy 1.1 *** * * * *** (18.3 bits) 0.9 ****** ******* 0.6 ******* ******* 0.4 ******* ******* 0.2 *************** 0.0 --------------- Multilevel AGGAAGGGGTTTTGG consensus C GTCAAA A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 48903 181 2.04e-09 GTACAGGCAC AGGGAGGGGTTTTGG GGAGAATTTC 44189 309 3.54e-08 TCACGTCCAC AGGGTGAGGTTTTGG CATCCTCAGT 34529 323 8.41e-07 TCCTCCACGA AGGATCGAGTTAAGG TTGTCCCCGT 4021 175 8.41e-07 GCAGGCTTCT TGGAAGGCATTTTGG AAGGTCTGAT 11169 400 1.36e-06 TATGCAGGAA AGGAAGAGATTATGT TTCAAAAGCT 45097 482 1.46e-06 GGACGTGTCG AAGATCGTGTTTTGG TTTC 38271 200 1.94e-06 CTTCACGGAA CGGATCGAAATTTGG ATTGATTTAG 7966 302 2.38e-06 CTAATCTGTG CGGGAGTGGCTATGG CTCGATAGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48903 2e-09 180_[+3]_305 44189 3.5e-08 308_[+3]_177 34529 8.4e-07 322_[+3]_163 4021 8.4e-07 174_[+3]_311 11169 1.4e-06 399_[+3]_86 45097 1.5e-06 481_[+3]_4 38271 1.9e-06 199_[+3]_286 7966 2.4e-06 301_[+3]_184 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=8 48903 ( 181) AGGGAGGGGTTTTGG 1 44189 ( 309) AGGGTGAGGTTTTGG 1 34529 ( 323) AGGATCGAGTTAAGG 1 4021 ( 175) TGGAAGGCATTTTGG 1 11169 ( 400) AGGAAGAGATTATGT 1 45097 ( 482) AAGATCGTGTTTTGG 1 38271 ( 200) CGGATCGAAATTTGG 1 7966 ( 302) CGGGAGTGGCTATGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 5832 bayes= 10.8309 E= 1.8e+002 127 10 -965 -118 -105 -965 197 -965 -965 -965 216 -965 127 -965 75 -965 95 -965 -965 81 -965 68 149 -965 -5 -965 149 -118 -5 -90 116 -118 53 -965 149 -965 -105 -90 -965 140 -965 -965 -965 181 53 -965 -965 114 -105 -965 -965 162 -965 -965 216 -965 -965 -965 197 -118 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 8 E= 1.8e+002 0.625000 0.250000 0.000000 0.125000 0.125000 0.000000 0.875000 0.000000 0.000000 0.000000 1.000000 0.000000 0.625000 0.000000 0.375000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.375000 0.625000 0.000000 0.250000 0.000000 0.625000 0.125000 0.250000 0.125000 0.500000 0.125000 0.375000 0.000000 0.625000 0.000000 0.125000 0.125000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.375000 0.000000 0.000000 0.625000 0.125000 0.000000 0.000000 0.875000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.875000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AC]GG[AG][AT][GC][GA][GA][GA]TT[TA]TGG -------------------------------------------------------------------------------- Time 3.87 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46476 3.38e-02 461_[+2(5.98e-05)]_27 2089 4.49e-06 300_[+2(1.08e-05)]_39_\ [+1(1.06e-08)]_135 3267 1.18e-03 24_[+1(1.52e-06)]_462 38271 2.65e-04 70_[+2(1.08e-05)]_117_\ [+3(1.94e-06)]_286 48903 2.19e-09 124_[+1(5.36e-07)]_42_\ [+3(2.04e-09)]_185_[+2(4.84e-05)]_108 44189 4.51e-06 128_[+2(4.14e-06)]_168_\ [+3(3.54e-08)]_177 11169 2.38e-07 266_[+2(6.78e-05)]_67_\ [+1(9.64e-08)]_40_[+3(1.36e-06)]_86 45097 1.26e-06 73_[+1(5.98e-06)]_291_\ [+2(6.33e-06)]_91_[+3(1.46e-06)]_4 45386 9.02e-04 349_[+1(3.31e-06)]_71_\ [+2(2.94e-05)]_54 7966 9.58e-07 217_[+1(4.65e-06)]_70_\ [+3(2.38e-06)]_94_[+2(3.68e-06)]_78 4021 4.55e-06 174_[+3(8.41e-07)]_147_\ [+2(1.86e-07)]_152 34529 4.65e-07 80_[+2(8.11e-06)]_230_\ [+3(8.41e-07)]_81_[+1(2.67e-06)]_68 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************