******************************************************************************** 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/347/347.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11404 1.0000 500 262844 1.0000 500 264634 1.0000 500 268167 1.0000 500 30854 1.0000 500 32481 1.0000 500 3876 1.0000 500 7423 1.0000 500 8149 1.0000 500 8692 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/347/347.seqs.fa -oc motifs/347 -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= 10 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= 5000 N= 10 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.266 C 0.233 G 0.231 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.266 C 0.233 G 0.231 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 8 llr = 104 E-value = 1.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 8858:4a::5:1::: pos.-specific C ::3:94:1a:a11aa probability G :1:311:6::::3:: matrix T 313::1:3:5:86:: bits 2.1 * * ** 1.9 * * * ** 1.7 * * * ** 1.5 * * * * ** Relative 1.3 * * * * ** Entropy 1.1 * ** * * * ** (18.8 bits) 0.8 ** ** ****** ** 0.6 ** ** ********* 0.4 ***** ********* 0.2 *************** 0.0 --------------- Multilevel AAAACAAGCACTTCC consensus T CG C T T G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 8149 421 4.12e-09 ATAATGTGAT AAAACAAGCACTTCC TTCCGATCTT 11404 406 2.08e-07 AAAGATTTGC AATACCATCACTGCC TCATATCACG 268167 268 2.95e-07 AGCAGTAGCT ATAGCCAGCTCTTCC TTCTCTCTCC 8692 346 4.31e-07 GAATGACAGA TAAACAAGCTCATCC CGTTTTCATC 7423 432 5.28e-07 GCACCAAGCA AACACGAGCACCTCC AATCTTCTTC 30854 254 7.25e-07 GCAACATAAG AACACTATCACTGCC TATTCCAAAC 32481 476 1.05e-06 CTACTACAGT AGTACCACCTCTTCC ATTTGCAACC 264634 439 3.52e-06 ATTGAGATGC TAAGGAAGCTCTCCC ACCCAACATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8149 4.1e-09 420_[+1]_65 11404 2.1e-07 405_[+1]_80 268167 3e-07 267_[+1]_218 8692 4.3e-07 345_[+1]_140 7423 5.3e-07 431_[+1]_54 30854 7.2e-07 253_[+1]_232 32481 1e-06 475_[+1]_10 264634 3.5e-06 438_[+1]_47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=8 8149 ( 421) AAAACAAGCACTTCC 1 11404 ( 406) AATACCATCACTGCC 1 268167 ( 268) ATAGCCAGCTCTTCC 1 8692 ( 346) TAAACAAGCTCATCC 1 7423 ( 432) AACACGAGCACCTCC 1 30854 ( 254) AACACTATCACTGCC 1 32481 ( 476) AGTACCACCTCTTCC 1 264634 ( 439) TAAGGAAGCTCTCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 4860 bayes= 9.24436 E= 1.2e+000 149 -965 -965 -11 149 -965 -89 -111 91 10 -965 -11 149 -965 11 -965 -965 191 -89 -965 49 69 -89 -111 191 -965 -965 -965 -965 -90 143 -11 -965 210 -965 -965 91 -965 -965 89 -965 210 -965 -965 -109 -90 -965 147 -965 -90 11 121 -965 210 -965 -965 -965 210 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 8 E= 1.2e+000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 0.125000 0.125000 0.500000 0.250000 0.000000 0.250000 0.750000 0.000000 0.250000 0.000000 0.000000 0.875000 0.125000 0.000000 0.375000 0.375000 0.125000 0.125000 1.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.625000 0.250000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.125000 0.125000 0.000000 0.750000 0.000000 0.125000 0.250000 0.625000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT]A[ACT][AG]C[AC]A[GT]C[AT]CT[TG]CC -------------------------------------------------------------------------------- Time 0.86 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 14 sites = 10 llr = 114 E-value = 8.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 71::32::6:16:: pos.-specific C ::371:::1a:::: probability G 15715:2a3:81:9 matrix T 24:2188:::13a1 bits 2.1 * * 1.9 * * * 1.7 * * ** 1.5 * * ** Relative 1.3 * *** * ** Entropy 1.1 * *** ** ** (16.5 bits) 0.8 * ** *** ** ** 0.6 **** ********* 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel AGGCGTTGACGATG consensus TTCTAAG G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 264634 13 1.08e-07 AATGGTGAGA AGGCGTGGGCGATG AGTCCATCCA 8692 305 1.13e-06 GTAGATTTGA AGCGATTGACGATG GAGATTAAAG 8149 397 1.13e-06 GACGTCAGAT TTGCTTTGACGATG ATAATGTGAT 7423 150 1.13e-06 AATAGGAGTA TGGCGTTGACAATG ACTGATATCT 268167 123 1.38e-06 TCTTTGTTGG GTGTGTTGACGATG ATGGCTGTAT 262844 135 2.20e-06 AAGATGTGTT ATCCAATGACGTTG ATGAAATGAA 3876 220 2.86e-06 TCTCCTGCGT AGGCCATGGCGTTG GTTGTAGGTT 11404 463 2.86e-06 AATCACGCCC ATCCATTGCCGTTG CTTCATCATT 32481 177 3.96e-06 GATGCCGTGA AAGCGTGGACGGTG CGAAGGCGCT 30854 179 1.73e-05 TGAGAAAGAC AGGTGTTGGCTATT CGTTGAGTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 264634 1.1e-07 12_[+2]_474 8692 1.1e-06 304_[+2]_182 8149 1.1e-06 396_[+2]_90 7423 1.1e-06 149_[+2]_337 268167 1.4e-06 122_[+2]_364 262844 2.2e-06 134_[+2]_352 3876 2.9e-06 219_[+2]_267 11404 2.9e-06 462_[+2]_24 32481 4e-06 176_[+2]_310 30854 1.7e-05 178_[+2]_308 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=14 seqs=10 264634 ( 13) AGGCGTGGGCGATG 1 8692 ( 305) AGCGATTGACGATG 1 8149 ( 397) TTGCTTTGACGATG 1 7423 ( 150) TGGCGTTGACAATG 1 268167 ( 123) GTGTGTTGACGATG 1 262844 ( 135) ATCCAATGACGTTG 1 3876 ( 220) AGGCCATGGCGTTG 1 11404 ( 463) ATCCATTGCCGTTG 1 32481 ( 177) AAGCGTGGACGGTG 1 30854 ( 179) AGGTGTTGGCTATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 4870 bayes= 9.17683 E= 8.5e-001 139 -997 -121 -43 -141 -997 111 57 -997 37 160 -997 -997 159 -121 -43 17 -122 111 -143 -41 -997 -997 157 -997 -997 -21 157 -997 -997 211 -997 117 -122 38 -997 -997 210 -997 -997 -141 -997 179 -143 117 -997 -121 15 -997 -997 -997 189 -997 -997 196 -143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 10 E= 8.5e-001 0.700000 0.000000 0.100000 0.200000 0.100000 0.000000 0.500000 0.400000 0.000000 0.300000 0.700000 0.000000 0.000000 0.700000 0.100000 0.200000 0.300000 0.100000 0.500000 0.100000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.600000 0.100000 0.300000 0.000000 0.000000 1.000000 0.000000 0.000000 0.100000 0.000000 0.800000 0.100000 0.600000 0.000000 0.100000 0.300000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.900000 0.100000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AT][GT][GC][CT][GA][TA][TG]G[AG]CG[AT]TG -------------------------------------------------------------------------------- Time 1.77 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 10 llr = 103 E-value = 9.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :74:24:a5:76 pos.-specific C a3:882a::9:1 probability G ::11:::::::: matrix T ::51:4::5133 bits 2.1 * * 1.9 * ** 1.7 * ** * 1.5 * ** * Relative 1.3 * * ** * Entropy 1.1 ** ** ** ** (14.8 bits) 0.8 ** ** ***** 0.6 ***** ****** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CATCCACAACAA consensus CA AT T TT sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 7423 474 2.67e-07 CTACGTCCAA CATCCTCAACAA TAATCAATTA 8149 179 2.03e-06 ACAGCTCAGA CCACCACAACAA ACGGCCTCTC 262844 29 2.30e-06 ATTGCGGCTG CAACCACATCTA CTGCGGGGGG 11404 443 3.32e-06 GTCACTATCA CAGCCTCAACAA TCACGCCCAT 268167 369 6.57e-06 CTCCGATGTC CATGCTCATCAA CATTGCCATT 30854 437 1.26e-05 AATACACTTT CAACCACAATAA CAACACAAAG 32481 448 1.35e-05 CCAAGCTACA CATCACCATCAT CTGTCGCTAC 3876 83 1.73e-05 TTCCTTCTTG CCACCCCATCTT TTCCAGCTGA 264634 317 2.72e-05 TGAGTGCTGC CCTTCACATCAT GGCTTATTTG 8692 367 3.84e-05 ATCCCGTTTT CATCATCAACTC ACGTTTCCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7423 2.7e-07 473_[+3]_15 8149 2e-06 178_[+3]_310 262844 2.3e-06 28_[+3]_460 11404 3.3e-06 442_[+3]_46 268167 6.6e-06 368_[+3]_120 30854 1.3e-05 436_[+3]_52 32481 1.4e-05 447_[+3]_41 3876 1.7e-05 82_[+3]_406 264634 2.7e-05 316_[+3]_172 8692 3.8e-05 366_[+3]_122 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=10 7423 ( 474) CATCCTCAACAA 1 8149 ( 179) CCACCACAACAA 1 262844 ( 29) CAACCACATCTA 1 11404 ( 443) CAGCCTCAACAA 1 268167 ( 369) CATGCTCATCAA 1 30854 ( 437) CAACCACAATAA 1 32481 ( 448) CATCACCATCAT 1 3876 ( 83) CCACCCCATCTT 1 264634 ( 317) CCTTCACATCAT 1 8692 ( 367) CATCATCAACTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 4890 bayes= 8.93074 E= 9.1e+001 -997 210 -997 -997 139 37 -997 -997 59 -997 -121 89 -997 178 -121 -143 -41 178 -997 -997 59 -22 -997 57 -997 210 -997 -997 191 -997 -997 -997 91 -997 -997 89 -997 195 -997 -143 139 -997 -997 15 117 -122 -997 15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 10 E= 9.1e+001 0.000000 1.000000 0.000000 0.000000 0.700000 0.300000 0.000000 0.000000 0.400000 0.000000 0.100000 0.500000 0.000000 0.800000 0.100000 0.100000 0.200000 0.800000 0.000000 0.000000 0.400000 0.200000 0.000000 0.400000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.900000 0.000000 0.100000 0.700000 0.000000 0.000000 0.300000 0.600000 0.100000 0.000000 0.300000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[AC][TA]C[CA][ATC]CA[AT]C[AT][AT] -------------------------------------------------------------------------------- Time 2.67 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11404 6.17e-08 405_[+1(2.08e-07)]_22_\ [+3(3.32e-06)]_8_[+2(2.86e-06)]_24 262844 1.25e-04 28_[+3(2.30e-06)]_94_[+2(2.20e-06)]_\ 352 264634 2.77e-07 12_[+2(1.08e-07)]_290_\ [+3(2.72e-05)]_110_[+1(3.52e-06)]_47 268167 8.11e-08 122_[+2(1.38e-06)]_131_\ [+1(2.95e-07)]_86_[+3(6.57e-06)]_120 30854 3.21e-06 178_[+2(1.73e-05)]_61_\ [+1(7.25e-07)]_168_[+3(1.26e-05)]_52 32481 1.28e-06 176_[+2(3.96e-06)]_257_\ [+3(1.35e-05)]_16_[+1(1.05e-06)]_10 3876 3.36e-04 82_[+3(1.73e-05)]_125_\ [+2(2.86e-06)]_267 7423 6.12e-09 149_[+2(1.13e-06)]_268_\ [+1(5.28e-07)]_27_[+3(2.67e-07)]_15 8149 4.48e-10 178_[+3(2.03e-06)]_206_\ [+2(1.13e-06)]_10_[+1(4.12e-09)]_65 8692 4.74e-07 304_[+2(1.13e-06)]_27_\ [+1(4.31e-07)]_6_[+3(3.84e-05)]_122 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************