******************************************************************************** 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/7/7.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 9231 1.0000 500 36719 1.0000 500 36721 1.0000 500 21198 1.0000 500 13566 1.0000 500 39131 1.0000 500 42373 1.0000 500 10363 1.0000 500 45182 1.0000 500 37202 1.0000 500 44657 1.0000 500 37176 1.0000 500 50181 1.0000 500 43681 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/7/7.seqs.fa -oc motifs/7 -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= 14 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= 7000 N= 14 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.282 C 0.238 G 0.225 T 0.255 Background letter frequencies (from dataset with add-one prior applied): A 0.282 C 0.238 G 0.225 T 0.255 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 10 llr = 125 E-value = 1.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :6:11:::1::14:52 pos.-specific C 33:3::31925:6::: probability G 7132:92:::58::17 matrix T ::749159:8:1:a41 bits 2.2 1.9 * 1.7 * * 1.5 ** ** * Relative 1.3 * ** *** * Entropy 1.1 * * ** ******* (18.0 bits) 0.9 * * ** ******* * 0.6 *** ************ 0.4 *** ************ 0.2 **************** 0.0 ---------------- Multilevel GATTTGTTCTCGCTAG consensus CCGC C CG A TA sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 36719 336 2.88e-09 ACAGTCAAAA GCTTTGTTCTGGCTTG ACTGTGAATC 44657 118 1.78e-07 GGATGTATGC GATGTGTTCTGTCTAG CTAGGCTGCT 50181 61 2.00e-07 AGAGTGTACA CATATGCTCTCGCTAG CGGCAGCATT 43681 23 3.01e-07 CCATCAATTT CCGTTGCTCTCGATTG TCTAAAAGTA 36721 63 7.59e-07 TTTATGAAAC GATCTGTTCCCACTTG ACCTCACAAG 37176 323 8.24e-07 GGGGATATAT CGTCTGTTCTGGCTAA TGTAAAGGGG 21198 120 1.15e-06 GCCAGTGATG GAGTTGCTCTGGCTGT AATTCACGAA 37202 225 1.44e-06 TAAAAACTCG GATTTGGCCCGGATAG GGGAATTGCG 42373 243 2.09e-06 TCTACTAGTG GCGCTGGTATCGATAG GGACAGCCTT 10363 11 1.04e-05 GAGAGCGACG GATGATTTCTCGATTA GAATCTCACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36719 2.9e-09 335_[+1]_149 44657 1.8e-07 117_[+1]_367 50181 2e-07 60_[+1]_424 43681 3e-07 22_[+1]_462 36721 7.6e-07 62_[+1]_422 37176 8.2e-07 322_[+1]_162 21198 1.2e-06 119_[+1]_365 37202 1.4e-06 224_[+1]_260 42373 2.1e-06 242_[+1]_242 10363 1e-05 10_[+1]_474 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=10 36719 ( 336) GCTTTGTTCTGGCTTG 1 44657 ( 118) GATGTGTTCTGTCTAG 1 50181 ( 61) CATATGCTCTCGCTAG 1 43681 ( 23) CCGTTGCTCTCGATTG 1 36721 ( 63) GATCTGTTCCCACTTG 1 37176 ( 323) CGTCTGTTCTGGCTAA 1 21198 ( 120) GAGTTGCTCTGGCTGT 1 37202 ( 225) GATTTGGCCCGGATAG 1 42373 ( 243) GCGCTGGTATCGATAG 1 10363 ( 11) GATGATTTCTCGATTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6790 bayes= 9.65702 E= 1.2e+001 -997 33 164 -997 109 33 -117 -997 -997 -997 42 145 -149 33 -17 65 -149 -997 -997 182 -997 -997 200 -135 -997 33 -17 97 -997 -125 -997 182 -149 192 -997 -997 -997 -25 -997 165 -997 107 115 -997 -149 -997 183 -135 50 133 -997 -997 -997 -997 -997 197 83 -997 -117 65 -49 -997 164 -135 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 1.2e+001 0.000000 0.300000 0.700000 0.000000 0.600000 0.300000 0.100000 0.000000 0.000000 0.000000 0.300000 0.700000 0.100000 0.300000 0.200000 0.400000 0.100000 0.000000 0.000000 0.900000 0.000000 0.000000 0.900000 0.100000 0.000000 0.300000 0.200000 0.500000 0.000000 0.100000 0.000000 0.900000 0.100000 0.900000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.500000 0.500000 0.000000 0.100000 0.000000 0.800000 0.100000 0.400000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.100000 0.400000 0.200000 0.000000 0.700000 0.100000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GC][AC][TG][TCG]TG[TCG]TC[TC][CG]G[CA]T[AT][GA] -------------------------------------------------------------------------------- Time 1.67 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 9 llr = 103 E-value = 1.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::2::1:3::68 pos.-specific C :1::12:4:9:2 probability G a9::::22:1:: matrix T ::8a978:a:4: bits 2.2 * 1.9 * * * 1.7 ** * * 1.5 ** ** ** Relative 1.3 ** ** * ** Entropy 1.1 ***** * ** * (16.5 bits) 0.9 ***** * **** 0.6 ******* **** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GGTTTTTCTCAA consensus A CGA TC sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 37176 445 1.94e-07 TGTCATTTCA GGTTTTTATCAA ATTGAAAGAC 36721 189 3.74e-07 CGGCGATCTC GGTTTTTGTCTA TCTTTACAGT 10363 204 5.40e-07 CAAGGACGAT GGTTTCTCTCAA AAGATCACGC 39131 237 8.23e-07 CCCAAATTGT GGATTTTCTCTA AAAAATGAAC 21198 308 1.36e-06 TAAATGACTC GGTTTTGGTCAA AAAATCATCC 45182 46 1.58e-06 CAAACAAACC GGATTTTATCAA ATCCACCCAT 9231 348 1.05e-05 TTCCATGGTA GGTTCATCTCAA GGAAATAAAC 50181 333 1.42e-05 CACCGCAATA GCTTTCTCTCTC TCATTTGGCC 36719 50 1.69e-05 TAAATATTTG GGTTTTGATGTC GGTCTACTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37176 1.9e-07 444_[+2]_44 36721 3.7e-07 188_[+2]_300 10363 5.4e-07 203_[+2]_285 39131 8.2e-07 236_[+2]_252 21198 1.4e-06 307_[+2]_181 45182 1.6e-06 45_[+2]_443 9231 1e-05 347_[+2]_141 50181 1.4e-05 332_[+2]_156 36719 1.7e-05 49_[+2]_439 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=9 37176 ( 445) GGTTTTTATCAA 1 36721 ( 189) GGTTTTTGTCTA 1 10363 ( 204) GGTTTCTCTCAA 1 39131 ( 237) GGATTTTCTCTA 1 21198 ( 308) GGTTTTGGTCAA 1 45182 ( 46) GGATTTTATCAA 1 9231 ( 348) GGTTCATCTCAA 1 50181 ( 333) GCTTTCTCTCTC 1 36719 ( 50) GGTTTTGATGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6846 bayes= 9.70369 E= 1.9e+001 -982 -982 215 -982 -982 -110 198 -982 -34 -982 -982 161 -982 -982 -982 197 -982 -110 -982 180 -134 -10 -982 138 -982 -982 -2 161 24 90 -2 -982 -982 -982 -982 197 -982 190 -102 -982 98 -982 -982 80 146 -10 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 9 E= 1.9e+001 0.000000 0.000000 1.000000 0.000000 0.000000 0.111111 0.888889 0.000000 0.222222 0.000000 0.000000 0.777778 0.000000 0.000000 0.000000 1.000000 0.000000 0.111111 0.000000 0.888889 0.111111 0.222222 0.000000 0.666667 0.000000 0.000000 0.222222 0.777778 0.333333 0.444444 0.222222 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.888889 0.111111 0.000000 0.555556 0.000000 0.000000 0.444444 0.777778 0.222222 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GG[TA]TT[TC][TG][CAG]TC[AT][AC] -------------------------------------------------------------------------------- Time 3.36 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 13 sites = 9 llr = 106 E-value = 5.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A a43:2:a:6:::8 pos.-specific C ::17:a:9::191 probability G :4:::::1:a6:: matrix T :1638:::4:311 bits 2.2 * * 1.9 * * 1.7 * ** * 1.5 * *** * * Relative 1.3 * *** * * Entropy 1.1 * ***** * * (17.0 bits) 0.9 * ******* ** 0.6 ************* 0.4 ************* 0.2 ************* 0.0 ------------- Multilevel AATCTCACAGGCA consensus GATA T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------- 10363 28 6.45e-08 TCTCGATTAG AATCTCACTGGCA GGAGGAGGGC 39131 461 2.20e-07 CTCCATTGAA AGTTTCACTGGCA CGTCATCTTA 42373 39 5.33e-07 ACGATACGGG AATCACACAGGCA AGACAGACAT 43681 271 9.31e-07 TGACCTGTAA AGACACACTGGCA CTTACGTAGT 45182 471 1.53e-06 GAGGATCTGC AACCTCACAGTCA GGGATACGGA 21198 166 1.94e-06 AAAAGGCTTT AGTTTCACAGGCT TTTTGAAGGT 36719 320 4.56e-06 CACGGCTTTA ATATTCACAGTCA AAAGCTTTGT 37202 482 7.11e-06 TTACAGTTTA AGACTCACTGCCC TGGTCT 50181 114 1.26e-05 ACGAGCGAGC AATCTCAGAGTTA GGGATAGACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10363 6.4e-08 27_[+3]_460 39131 2.2e-07 460_[+3]_27 42373 5.3e-07 38_[+3]_449 43681 9.3e-07 270_[+3]_217 45182 1.5e-06 470_[+3]_17 21198 1.9e-06 165_[+3]_322 36719 4.6e-06 319_[+3]_168 37202 7.1e-06 481_[+3]_6 50181 1.3e-05 113_[+3]_374 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=13 seqs=9 10363 ( 28) AATCTCACTGGCA 1 39131 ( 461) AGTTTCACTGGCA 1 42373 ( 39) AATCACACAGGCA 1 43681 ( 271) AGACACACTGGCA 1 45182 ( 471) AACCTCACAGTCA 1 21198 ( 166) AGTTTCACAGGCT 1 36719 ( 320) ATATTCACAGTCA 1 37202 ( 482) AGACTCACTGCCC 1 50181 ( 114) AATCTCAGAGTTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 6832 bayes= 9.70074 E= 5.0e+001 183 -982 -982 -982 66 -982 98 -120 24 -110 -982 112 -982 149 -982 38 -34 -982 -982 161 -982 207 -982 -982 183 -982 -982 -982 -982 190 -102 -982 98 -982 -982 80 -982 -982 215 -982 -982 -110 130 38 -982 190 -982 -120 146 -110 -982 -120 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 9 E= 5.0e+001 1.000000 0.000000 0.000000 0.000000 0.444444 0.000000 0.444444 0.111111 0.333333 0.111111 0.000000 0.555556 0.000000 0.666667 0.000000 0.333333 0.222222 0.000000 0.000000 0.777778 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.888889 0.111111 0.000000 0.555556 0.000000 0.000000 0.444444 0.000000 0.000000 1.000000 0.000000 0.000000 0.111111 0.555556 0.333333 0.000000 0.888889 0.000000 0.111111 0.777778 0.111111 0.000000 0.111111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- A[AG][TA][CT][TA]CAC[AT]G[GT]CA -------------------------------------------------------------------------------- Time 4.85 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9231 4.41e-02 347_[+2(1.05e-05)]_141 36719 8.23e-09 49_[+2(1.69e-05)]_258_\ [+3(4.56e-06)]_3_[+1(2.88e-09)]_149 36721 9.49e-06 62_[+1(7.59e-07)]_110_\ [+2(3.74e-07)]_300 21198 9.12e-08 119_[+1(1.15e-06)]_30_\ [+3(1.94e-06)]_129_[+2(1.36e-06)]_181 13566 8.11e-01 500 39131 5.38e-06 236_[+2(8.23e-07)]_212_\ [+3(2.20e-07)]_27 42373 1.41e-05 38_[+3(5.33e-07)]_191_\ [+1(2.09e-06)]_242 10363 1.30e-08 10_[+1(1.04e-05)]_1_[+3(6.45e-08)]_\ 163_[+2(5.40e-07)]_285 45182 6.60e-05 45_[+2(1.58e-06)]_413_\ [+3(1.53e-06)]_17 37202 1.27e-04 224_[+1(1.44e-06)]_241_\ [+3(7.11e-06)]_6 44657 9.86e-04 117_[+1(1.78e-07)]_367 37176 1.36e-06 322_[+1(8.24e-07)]_106_\ [+2(1.94e-07)]_44 50181 8.50e-07 60_[+1(2.00e-07)]_37_[+3(1.26e-05)]_\ 206_[+2(1.42e-05)]_156 43681 3.18e-06 6_[+1(8.71e-05)]_[+1(3.01e-07)]_232_\ [+3(9.31e-07)]_217 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************