******************************************************************************** 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/358/358.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 48375 1.0000 500 49223 1.0000 500 49728 1.0000 500 52684 1.0000 500 43817 1.0000 500 44482 1.0000 500 54412 1.0000 500 49140 1.0000 500 46963 1.0000 500 48552 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/358/358.seqs.fa -oc motifs/358 -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 0.267 C 0.230 G 0.213 T 0.290 Background letter frequencies (from dataset with add-one prior applied): A 0.267 C 0.230 G 0.213 T 0.290 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 10 llr = 124 E-value = 2.6e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :113a4:32521:::7 pos.-specific C 2:9::2:17::34:72 probability G 81:7::6615:15a31 matrix T :8:::44:::851::: bits 2.2 * 2.0 * * 1.8 * * 1.6 * * * * Relative 1.3 * *** ** Entropy 1.1 * *** * ** ** (17.9 bits) 0.9 ***** ***** **** 0.7 ***** ***** **** 0.4 *********** **** 0.2 **************** 0.0 ---------------- Multilevel GTCGAAGGCATTGGCA consensus C A TTAAGACC GC sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 54412 411 1.81e-09 CGTATTCACG GTCGATGGCGTCCGCA GCCTAACCGT 52684 411 1.81e-09 CGTATTCACG GTCGATGGCGTCCGCA GCCTAACCGT 49223 419 1.38e-07 ACTGCAAGCC GTCGATGGCAAGGGCA CCATGACGAT 48552 341 2.18e-07 CATGAGCATC GTCAATTGCATTGGCC TCGCTAGAGT 48375 181 4.55e-07 AATTTAATGT GTCGAATCCATCGGGA TCAATATAAT 49728 185 3.01e-06 TCACATTTTC CTCGACGAGGTTCGGA TTGGCTCGAA 49140 31 4.16e-06 TCCCACGATG CTCAACGGAATAGGCA CTTACGGTTT 46963 314 4.43e-06 GTCTTAAAAA GAAGAATACATTGGCA GTGAGGGGAA 43817 394 4.99e-06 CCTACTTTCC GGCAAAGGCGTTTGCG TTGACTGTGA 44482 412 5.61e-06 ATAGTACACA GTCGAATAAGATCGGC GATAATCTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 54412 1.8e-09 410_[+1]_74 52684 1.8e-09 410_[+1]_74 49223 1.4e-07 418_[+1]_66 48552 2.2e-07 340_[+1]_144 48375 4.5e-07 180_[+1]_304 49728 3e-06 184_[+1]_300 49140 4.2e-06 30_[+1]_454 46963 4.4e-06 313_[+1]_171 43817 5e-06 393_[+1]_91 44482 5.6e-06 411_[+1]_73 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=10 54412 ( 411) GTCGATGGCGTCCGCA 1 52684 ( 411) GTCGATGGCGTCCGCA 1 49223 ( 419) GTCGATGGCAAGGGCA 1 48552 ( 341) GTCAATTGCATTGGCC 1 48375 ( 181) GTCGAATCCATCGGGA 1 49728 ( 185) CTCGACGAGGTTCGGA 1 49140 ( 31) CTCAACGGAATAGGCA 1 46963 ( 314) GAAGAATACATTGGCA 1 43817 ( 394) GGCAAAGGCGTTTGCG 1 44482 ( 412) GTCGAATAAGATCGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 4850 bayes= 9.17088 E= 2.6e-002 -997 -20 191 -997 -141 -997 -109 146 -141 197 -997 -997 17 -997 171 -997 191 -997 -997 -997 58 -20 -997 46 -997 -997 149 46 17 -120 149 -997 -42 160 -109 -997 91 -997 123 -997 -42 -997 -997 146 -141 38 -109 79 -997 80 123 -153 -997 -997 223 -997 -997 160 49 -997 139 -20 -109 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 2.6e-002 0.000000 0.200000 0.800000 0.000000 0.100000 0.000000 0.100000 0.800000 0.100000 0.900000 0.000000 0.000000 0.300000 0.000000 0.700000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.200000 0.000000 0.400000 0.000000 0.000000 0.600000 0.400000 0.300000 0.100000 0.600000 0.000000 0.200000 0.700000 0.100000 0.000000 0.500000 0.000000 0.500000 0.000000 0.200000 0.000000 0.000000 0.800000 0.100000 0.300000 0.100000 0.500000 0.000000 0.400000 0.500000 0.100000 0.000000 0.000000 1.000000 0.000000 0.000000 0.700000 0.300000 0.000000 0.700000 0.200000 0.100000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GC]TC[GA]A[ATC][GT][GA][CA][AG][TA][TC][GC]G[CG][AC] -------------------------------------------------------------------------------- Time 0.88 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 4 llr = 89 E-value = 3.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A aaa:a::::a8::3:::5:3: pos.-specific C :::8:a585::::88::3::: probability G :::3:::3::::a:::a:388 matrix T ::::::5:5:3a::3a:38:3 bits 2.2 * * * 2.0 *** ** * * * 1.8 *** ** * ** ** 1.6 *** ** * ** ** Relative 1.3 ****** * * ****** ** Entropy 1.1 ****** * ******** *** (32.0 bits) 0.9 ***************** *** 0.7 ***************** *** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel AAACACCCCAATGCCTGATGG consensus G TGT T AT CGAT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 54412 52 1.65e-13 AAAATCCATC AAACACCCCAATGCCTGATGG AGGAGGCTTC 52684 52 1.65e-13 AAAATCCATC AAACACCCCAATGCCTGATGG AGGAGGCTTC 44482 99 4.79e-10 ACGTCGTGTA AAAGACTGTAATGCTTGCTGT TAATGCAGAT 49223 296 4.79e-10 TTGAGCGTTA AAACACTCTATTGACTGTGAG TTCCTTGCGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 54412 1.7e-13 51_[+2]_428 52684 1.7e-13 51_[+2]_428 44482 4.8e-10 98_[+2]_381 49223 4.8e-10 295_[+2]_184 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=4 54412 ( 52) AAACACCCCAATGCCTGATGG 1 52684 ( 52) AAACACCCCAATGCCTGATGG 1 44482 ( 99) AAAGACTGTAATGCTTGCTGT 1 49223 ( 296) AAACACTCTATTGACTGTGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4800 bayes= 10.2276 E= 3.4e+000 190 -865 -865 -865 190 -865 -865 -865 190 -865 -865 -865 -865 170 23 -865 190 -865 -865 -865 -865 212 -865 -865 -865 112 -865 79 -865 170 23 -865 -865 112 -865 79 190 -865 -865 -865 149 -865 -865 -21 -865 -865 -865 178 -865 -865 223 -865 -9 170 -865 -865 -865 170 -865 -21 -865 -865 -865 178 -865 -865 223 -865 90 12 -865 -21 -865 -865 23 137 -9 -865 181 -865 -865 -865 181 -21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 3.4e+000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.750000 0.250000 0.000000 0.000000 0.500000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.250000 0.000000 0.250000 0.000000 0.000000 0.250000 0.750000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 0.750000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- AAA[CG]AC[CT][CG][CT]A[AT]TG[CA][CT]TG[ACT][TG][GA][GT] -------------------------------------------------------------------------------- Time 1.75 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 3 llr = 74 E-value = 1.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :a:a:::::::::::::a:: pos.-specific C 3:::a3:3a::a7::::::a probability G 7:a::737:3a:3::aa::: matrix T ::::::7::7:::aa:::a: bits 2.2 * * * ** ** * 2.0 **** * ** *** * 1.8 **** * ** ******* 1.6 **** * ** ******* Relative 1.3 ****** ** ********** Entropy 1.1 ******************** (35.6 bits) 0.9 ******************** 0.7 ******************** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GAGACGTGCTGCCTTGGATC consensus C CGC G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 54412 338 5.00e-13 ATGTTATTTT GAGACGTGCTGCCTTGGATC ATTGGCGATA 52684 338 5.00e-13 ATGTTATTTT GAGACGTGCTGCCTTGGATC ATTGGCGATA 48552 463 2.61e-11 GTAACTGTAT CAGACCGCCGGCGTTGGATC CGTGCCTTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 54412 5e-13 337_[+3]_143 52684 5e-13 337_[+3]_143 48552 2.6e-11 462_[+3]_18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=3 54412 ( 338) GAGACGTGCTGCCTTGGATC 1 52684 ( 338) GAGACGTGCTGCCTTGGATC 1 48552 ( 463) CAGACCGCCGGCGTTGGATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 4810 bayes= 11.0937 E= 1.7e+000 -823 53 164 -823 190 -823 -823 -823 -823 -823 222 -823 190 -823 -823 -823 -823 212 -823 -823 -823 53 164 -823 -823 -823 64 120 -823 53 164 -823 -823 212 -823 -823 -823 -823 64 120 -823 -823 222 -823 -823 212 -823 -823 -823 153 64 -823 -823 -823 -823 178 -823 -823 -823 178 -823 -823 222 -823 -823 -823 222 -823 190 -823 -823 -823 -823 -823 -823 178 -823 212 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 3 E= 1.7e+000 0.000000 0.333333 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC]AGAC[GC][TG][GC]C[TG]GC[CG]TTGGATC -------------------------------------------------------------------------------- Time 2.55 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48375 2.20e-03 180_[+1(4.55e-07)]_304 49223 5.13e-09 295_[+2(4.79e-10)]_79_\ [+2(3.83e-05)]_2_[+1(1.38e-07)]_66 49728 9.78e-03 184_[+1(3.01e-06)]_300 52684 3.06e-23 51_[+2(1.65e-13)]_265_\ [+3(5.00e-13)]_53_[+1(1.81e-09)]_74 43817 4.09e-02 393_[+1(4.99e-06)]_91 44482 1.49e-07 98_[+2(4.79e-10)]_292_\ [+1(5.61e-06)]_73 54412 3.06e-23 51_[+2(1.65e-13)]_265_\ [+3(5.00e-13)]_53_[+1(1.81e-09)]_74 49140 1.50e-02 30_[+1(4.16e-06)]_454 46963 8.67e-03 313_[+1(4.43e-06)]_171 48552 4.79e-10 340_[+1(2.18e-07)]_106_\ [+3(2.61e-11)]_18 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************