******************************************************************************** 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/466/466.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 36570 1.0000 500 51110 1.0000 500 9664 1.0000 500 39885 1.0000 500 41581 1.0000 500 32453 1.0000 500 38410 1.0000 500 37064 1.0000 500 47974 1.0000 500 37241 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/466/466.seqs.fa -oc motifs/466 -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 0.273 C 0.239 G 0.215 T 0.274 Background letter frequencies (from dataset with add-one prior applied): A 0.273 C 0.239 G 0.215 T 0.274 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 4 llr = 86 E-value = 1.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :3:3::::3:::::a83::8: pos.-specific C :3::::a:8:3:38::3:::3 probability G a5a::a::::8a3::3538:8 matrix T :::8a::a:a::53:::833: bits 2.2 * * * * 2.0 * * ** * 1.8 * * **** * * * 1.6 * * **** * * * Relative 1.3 * * **** *** * * * Entropy 1.1 * ********** *** **** (31.0 bits) 0.9 * ********** *** **** 0.7 ************ ******** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GGGTTGCTCTGGTCAAGTGAG consensus A A A C CT GAGTTC sequence C G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 38410 207 1.15e-13 TCGTGATTAC GGGTTGCTCTGGTCAAGTGAG GTAGAAATAC 32453 208 1.15e-13 TCGTGAATAC GGGTTGCTCTGGTCAAGTGAG GTAGAGATAC 47974 147 1.08e-09 CAAAGAGGAC GAGATGCTATGGGTAGATGAG TAATCTCGAA 41581 464 1.54e-09 ATCATCGCTG GCGTTGCTCTCGCCAACGTTC TTACTTTACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38410 1.2e-13 206_[+1]_273 32453 1.2e-13 207_[+1]_272 47974 1.1e-09 146_[+1]_333 41581 1.5e-09 463_[+1]_16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=4 38410 ( 207) GGGTTGCTCTGGTCAAGTGAG 1 32453 ( 208) GGGTTGCTCTGGTCAAGTGAG 1 47974 ( 147) GAGATGCTATGGGTAGATGAG 1 41581 ( 464) GCGTTGCTCTCGCCAACGTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4800 bayes= 10.2276 E= 1.4e+001 -865 -865 221 -865 -13 7 122 -865 -865 -865 221 -865 -13 -865 -865 145 -865 -865 -865 187 -865 -865 221 -865 -865 206 -865 -865 -865 -865 -865 187 -13 165 -865 -865 -865 -865 -865 187 -865 7 180 -865 -865 -865 221 -865 -865 7 22 87 -865 165 -865 -13 187 -865 -865 -865 146 -865 22 -865 -13 7 122 -865 -865 -865 22 145 -865 -865 180 -13 146 -865 -865 -13 -865 7 180 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 1.4e+001 0.000000 0.000000 1.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.750000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.750000 0.250000 0.750000 0.000000 0.000000 0.250000 0.000000 0.250000 0.750000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[GAC]G[TA]TGCT[CA]T[GC]G[TCG][CT]A[AG][GAC][TG][GT][AT][GC] -------------------------------------------------------------------------------- Time 0.85 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 5 llr = 96 E-value = 1.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :2::2:8882:4:4::::a:: pos.-specific C 2::a6:222844842:::::: probability G 8:8::a::::2:::24aa:a4 matrix T :82:2:::::422266::::6 bits 2.2 * ** * 2.0 * * ** * 1.8 * * **** 1.6 * * * **** Relative 1.3 * ** * * * **** Entropy 1.1 **** ***** * ****** (27.7 bits) 0.9 **** ***** * ****** 0.7 ********** * ******* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GTGCCGAAACCACATTGGAGT consensus CAT A CCCATCTCCG G sequence T GT TG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 32453 151 1.38e-13 GGAGTCGCCG GTGCCGAAACCCCCTTGGAGT CTTCAGGGTT 38410 150 1.37e-11 GGAGTTGCCG GTGCCGAACCCCCCTTGGAGT CTTCAGGGCT 9664 64 2.29e-09 GGGTACCTCT GTGCTGACACTATATGGGAGG ATGCAACCAT 47974 74 5.17e-09 GAAACAATAC GAGCAGCAACGACAGTGGAGG TACAGATCCA 51110 424 1.43e-08 GGTTGTTTCA CTTCCGAAAATTCTCGGGAGT CGTAGTTCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 32453 1.4e-13 150_[+2]_329 38410 1.4e-11 149_[+2]_330 9664 2.3e-09 63_[+2]_416 47974 5.2e-09 73_[+2]_406 51110 1.4e-08 423_[+2]_56 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 32453 ( 151) GTGCCGAAACCCCCTTGGAGT 1 38410 ( 150) GTGCCGAACCCCCCTTGGAGT 1 9664 ( 64) GTGCTGACACTATATGGGAGG 1 47974 ( 74) GAGCAGCAACGACAGTGGAGG 1 51110 ( 424) CTTCCGAAAATTCTCGGGAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4800 bayes= 10.1572 E= 1.4e+001 -897 -25 189 -897 -45 -897 -897 155 -897 -897 189 -45 -897 207 -897 -897 -45 133 -897 -45 -897 -897 222 -897 155 -25 -897 -897 155 -25 -897 -897 155 -25 -897 -897 -45 174 -897 -897 -897 74 -10 55 55 74 -897 -45 -897 174 -897 -45 55 74 -897 -45 -897 -25 -10 113 -897 -897 89 113 -897 -897 222 -897 -897 -897 222 -897 187 -897 -897 -897 -897 -897 222 -897 -897 -897 89 113 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 1.4e+001 0.000000 0.200000 0.800000 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.200000 0.600000 0.000000 0.200000 0.000000 0.000000 1.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.400000 0.200000 0.400000 0.400000 0.400000 0.000000 0.200000 0.000000 0.800000 0.000000 0.200000 0.400000 0.400000 0.000000 0.200000 0.000000 0.200000 0.200000 0.600000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.600000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GC][TA][GT]C[CAT]G[AC][AC][AC][CA][CTG][ACT][CT][ACT][TCG][TG]GGAG[TG] -------------------------------------------------------------------------------- Time 1.69 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 5 llr = 98 E-value = 2.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :48:::a:::6:68224a::: pos.-specific C 8::4::::6::24:::2:::: probability G 22::6a:84:28::8:4:a:8 matrix T :4264::2:a2::2:8:::a2 bits 2.2 * * 2.0 * * 1.8 ** * *** 1.6 ** * * *** Relative 1.3 * *** * * * **** Entropy 1.1 * * ****** * *** **** (28.2 bits) 0.9 * ******** ***** **** 0.7 * ************** **** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CAATGGAGCTAGAAGTAAGTG consensus GTTCT TG GCCTAAG T sequence G T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 38410 349 3.66e-12 AGGACACTAC CTACGGAGGTAGAAGTGAGTG TACCAGTGCG 32453 349 3.66e-12 AGGACACTGC CTACGGAGGTAGAAGTGAGTG TACCAGTGCT 37241 294 1.28e-09 TCAACGGTTC CGTTTGAGCTAGCTGTAAGTG GCATGTGCCA 36570 210 3.39e-09 GACAGTGGTC GAATGGAGCTGCCAGAAAGTG AAGTTATTTA 41581 208 9.70e-09 GATCAGTTGA CAATTGATCTTGAAATCAGTT AAGTAAAATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38410 3.7e-12 348_[+3]_131 32453 3.7e-12 348_[+3]_131 37241 1.3e-09 293_[+3]_186 36570 3.4e-09 209_[+3]_270 41581 9.7e-09 207_[+3]_272 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=5 38410 ( 349) CTACGGAGGTAGAAGTGAGTG 1 32453 ( 349) CTACGGAGGTAGAAGTGAGTG 1 37241 ( 294) CGTTTGAGCTAGCTGTAAGTG 1 36570 ( 210) GAATGGAGCTGCCAGAAAGTG 1 41581 ( 208) CAATTGATCTTGAAATCAGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4800 bayes= 10.1572 E= 2.6e+001 -897 174 -10 -897 55 -897 -10 55 155 -897 -897 -45 -897 74 -897 113 -897 -897 148 55 -897 -897 222 -897 187 -897 -897 -897 -897 -897 189 -45 -897 133 89 -897 -897 -897 -897 187 114 -897 -10 -45 -897 -25 189 -897 114 74 -897 -897 155 -897 -897 -45 -45 -897 189 -897 -45 -897 -897 155 55 -25 89 -897 187 -897 -897 -897 -897 -897 222 -897 -897 -897 -897 187 -897 -897 189 -45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 2.6e+001 0.000000 0.800000 0.200000 0.000000 0.400000 0.000000 0.200000 0.400000 0.800000 0.000000 0.000000 0.200000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.600000 0.400000 0.000000 0.000000 0.000000 0.000000 1.000000 0.600000 0.000000 0.200000 0.200000 0.000000 0.200000 0.800000 0.000000 0.600000 0.400000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.200000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.800000 0.400000 0.200000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG][ATG][AT][TC][GT]GA[GT][CG]T[AGT][GC][AC][AT][GA][TA][AGC]AGT[GT] -------------------------------------------------------------------------------- Time 2.76 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36570 7.21e-05 209_[+3(3.39e-09)]_270 51110 4.01e-04 423_[+2(1.43e-08)]_56 9664 3.14e-05 63_[+2(2.29e-09)]_416 39885 9.70e-01 500 41581 6.66e-10 207_[+3(9.70e-09)]_235_\ [+1(1.54e-09)]_16 32453 1.50e-26 150_[+2(1.38e-13)]_36_\ [+1(1.15e-13)]_120_[+3(3.66e-12)]_131 38410 1.30e-24 149_[+2(1.37e-11)]_36_\ [+1(1.15e-13)]_121_[+3(3.66e-12)]_131 37064 5.45e-01 500 47974 3.81e-10 73_[+2(5.17e-09)]_52_[+1(1.08e-09)]_\ 333 37241 4.30e-05 293_[+3(1.28e-09)]_186 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************