******************************************************************************** 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/425/425.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 32852 1.0000 500 49362 1.0000 500 45033 1.0000 500 43847 1.0000 500 45406 1.0000 500 36628 1.0000 500 49794 1.0000 500 49890 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/425/425.seqs.fa -oc motifs/425 -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= 8 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= 4000 N= 8 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.255 C 0.251 G 0.227 T 0.267 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.251 G 0.227 T 0.267 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 19 sites = 5 llr = 87 E-value = 4.3e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4:2::4::62::::::::: pos.-specific C ::2a:24::::2:::8:a: probability G 6a6:a228:::684::8:8 matrix T :::::24248a226a22:2 bits 2.1 * * 1.9 * ** * * * 1.7 * ** * * * 1.5 * ** * * * Relative 1.3 * ** * ** * ***** Entropy 1.1 ** ** **** ******* (25.1 bits) 0.9 ** ** **** ******* 0.6 ***** ************ 0.4 ***** ************* 0.2 ***** ************* 0.0 ------------------- Multilevel GGGCGACGATTGGTTCGCG consensus A A CTTTA CTG TT T sequence C GG T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 45406 107 1.63e-10 TAATTGGACA GGGCGCTGTTTGGGTCGCG GTAGTCCATT 32852 157 3.30e-09 AAAAAAATCC AGGCGACGAATGGTTCGCT TGTCGATACA 43847 90 9.73e-09 ACAATTGCAT AGGCGGCTTTTCGTTCGCG CTCCGGTTCT 49794 239 1.49e-08 TTATCGCGTC GGCCGTTGATTTGTTTGCG AAGGACCGCT 49890 165 2.07e-08 CCACATAGCC GGACGAGGATTGTGTCTCG ACACACGTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45406 1.6e-10 106_[+1]_375 32852 3.3e-09 156_[+1]_325 43847 9.7e-09 89_[+1]_392 49794 1.5e-08 238_[+1]_243 49890 2.1e-08 164_[+1]_317 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=19 seqs=5 45406 ( 107) GGGCGCTGTTTGGGTCGCG 1 32852 ( 157) AGGCGACGAATGGTTCGCT 1 43847 ( 90) AGGCGGCTTTTCGTTCGCG 1 49794 ( 239) GGCCGTTGATTTGTTTGCG 1 49890 ( 165) GGACGAGGATTGTGTCTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 3856 bayes= 9.84093 E= 4.3e+001 65 -897 140 -897 -897 -897 214 -897 -35 -33 140 -897 -897 199 -897 -897 -897 -897 214 -897 65 -33 -18 -41 -897 67 -18 58 -897 -897 182 -41 123 -897 -897 58 -35 -897 -897 158 -897 -897 -897 190 -897 -33 140 -41 -897 -897 182 -41 -897 -897 82 117 -897 -897 -897 190 -897 167 -897 -41 -897 -897 182 -41 -897 199 -897 -897 -897 -897 182 -41 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 5 E= 4.3e+001 0.400000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.200000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.200000 0.200000 0.200000 0.000000 0.400000 0.200000 0.400000 0.000000 0.000000 0.800000 0.200000 0.600000 0.000000 0.000000 0.400000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.600000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GA]G[GAC]CG[ACGT][CTG][GT][AT][TA]T[GCT][GT][TG]T[CT][GT]C[GT] -------------------------------------------------------------------------------- Time 0.52 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 8 llr = 101 E-value = 4.3e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::44:::::36::: pos.-specific C 3::4116:6:961::4 probability G ::333::a1:1:31:: matrix T 8a84354:3a:1:9a6 bits 2.1 * 1.9 * * * * 1.7 * * * * 1.5 * * ** ** Relative 1.3 * * ** ** Entropy 1.1 *** ** ** *** (18.1 bits) 0.9 *** ** ** *** 0.6 *** *********** 0.4 **** *********** 0.2 **** *********** 0.0 ---------------- Multilevel TTTCATCGCTCCATTT consensus C GTGAT T AG C sequence GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 43847 344 2.79e-08 ACAAGTGGAA TTTTAACGCTCAATTT CCAGAGCATC 45406 292 3.38e-08 CGACGTACCA TTTTATCGCTCCGTTC GGTATTAACA 36628 148 2.66e-07 TGCAAGCGCG TTGCATTGTTCCATTT GTCAGGACCA 49362 90 6.99e-07 GGTCTGTAGA TTTCGCTGCTCAATTT TCATTTGCAA 32852 342 1.78e-06 GATTCATTGG CTTGTACGCTCTATTC CCAGCCAATG 49794 374 2.05e-06 GTGTATTGCC TTTGTTCGCTGCCTTT CTCTGAAACA 49890 101 2.68e-06 ATTTCCGTTT TTTCCACGGTCCAGTT TGTCAAACAC 45033 107 3.83e-06 CATCGTACTA CTGTGTTGTTCCGTTC CATGAGTGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43847 2.8e-08 343_[+2]_141 45406 3.4e-08 291_[+2]_193 36628 2.7e-07 147_[+2]_337 49362 7e-07 89_[+2]_395 32852 1.8e-06 341_[+2]_143 49794 2.1e-06 373_[+2]_111 49890 2.7e-06 100_[+2]_384 45033 3.8e-06 106_[+2]_378 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=8 43847 ( 344) TTTTAACGCTCAATTT 1 45406 ( 292) TTTTATCGCTCCGTTC 1 36628 ( 148) TTGCATTGTTCCATTT 1 49362 ( 90) TTTCGCTGCTCAATTT 1 32852 ( 342) CTTGTACGCTCTATTC 1 49794 ( 374) TTTGTTCGCTGCCTTT 1 49890 ( 101) TTTCCACGGTCCAGTT 1 45033 ( 107) CTGTGTTGTTCCGTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 3880 bayes= 8.91886 E= 4.3e+001 -965 -1 -965 149 -965 -965 -965 191 -965 -965 14 149 -965 58 14 49 55 -101 14 -9 55 -101 -965 91 -965 131 -965 49 -965 -965 214 -965 -965 131 -86 -9 -965 -965 -965 191 -965 180 -86 -965 -3 131 -965 -109 129 -101 14 -965 -965 -965 -86 171 -965 -965 -965 191 -965 58 -965 123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 8 E= 4.3e+001 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.375000 0.250000 0.375000 0.375000 0.125000 0.250000 0.250000 0.375000 0.125000 0.000000 0.500000 0.000000 0.625000 0.000000 0.375000 0.000000 0.000000 1.000000 0.000000 0.000000 0.625000 0.125000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.875000 0.125000 0.000000 0.250000 0.625000 0.000000 0.125000 0.625000 0.125000 0.250000 0.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 0.000000 1.000000 0.000000 0.375000 0.000000 0.625000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TC]T[TG][CTG][AGT][TA][CT]G[CT]TC[CA][AG]TT[TC] -------------------------------------------------------------------------------- Time 1.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 19 sites = 6 llr = 94 E-value = 1.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :8:::3:38:3253:72:: pos.-specific C :2:2a::22a:3:3:3:28 probability G a:5::5a:::523:a:7:2 matrix T ::58:2:5::2323::28: bits 2.1 * * * 1.9 * * * * * 1.7 * * * * * 1.5 * * * * * Relative 1.3 ** ** * ** * ** Entropy 1.1 ***** * ** ** ** (22.5 bits) 0.9 ***** * ** ***** 0.6 ******* *** * ***** 0.4 *********** ******* 0.2 *********** ******* 0.0 ------------------- Multilevel GAGTCGGTACGCAAGAGTC consensus T A A ATGC C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 45033 312 1.45e-09 TCCTTGAAGA GATTCAGTACGGGAGAGTC CTGTCCTCTT 36628 264 1.98e-09 CAGAGAGAGT GAGTCGGAACTTATGAGTC ACGTGTCTTA 43847 378 1.05e-08 TCCAGCAGTA GATTCAGTCCATACGAGTC CACAAGAGTC 49890 317 4.81e-08 TTGGATAGCA GAGCCGGAACGCAAGCGTG TAGACAAGGT 49362 284 2.16e-07 GTAAGTTGAC GAGTCTGCACGATTGATTC CGGCTAAGTT 49794 455 2.75e-07 CTCACCCCTC GCTTCGGTACACGCGCACC TTTCTTCGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45033 1.4e-09 311_[+3]_170 36628 2e-09 263_[+3]_218 43847 1.1e-08 377_[+3]_104 49890 4.8e-08 316_[+3]_165 49362 2.2e-07 283_[+3]_198 49794 2.8e-07 454_[+3]_27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=19 seqs=6 45033 ( 312) GATTCAGTACGGGAGAGTC 1 36628 ( 264) GAGTCGGAACTTATGAGTC 1 43847 ( 378) GATTCAGTCCATACGAGTC 1 49890 ( 317) GAGCCGGAACGCAAGCGTG 1 49362 ( 284) GAGTCTGCACGATTGATTC 1 49794 ( 455) GCTTCGGTACACGCGCACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 3856 bayes= 9.77374 E= 1.7e+002 -923 -923 214 -923 171 -59 -923 -923 -923 -923 114 91 -923 -59 -923 164 -923 199 -923 -923 38 -923 114 -68 -923 -923 214 -923 38 -59 -923 91 171 -59 -923 -923 -923 199 -923 -923 38 -923 114 -68 -61 41 -44 32 97 -923 55 -68 38 41 -923 32 -923 -923 214 -923 138 41 -923 -923 -61 -923 155 -68 -923 -59 -923 164 -923 173 -44 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 6 E= 1.7e+002 0.000000 0.000000 1.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.166667 0.000000 0.833333 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.500000 0.166667 0.000000 0.000000 1.000000 0.000000 0.333333 0.166667 0.000000 0.500000 0.833333 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.500000 0.166667 0.166667 0.333333 0.166667 0.333333 0.500000 0.000000 0.333333 0.166667 0.333333 0.333333 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.166667 0.000000 0.666667 0.166667 0.000000 0.166667 0.000000 0.833333 0.000000 0.833333 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GA[GT]TC[GA]G[TA]AC[GA][CT][AG][ACT]G[AC]GTC -------------------------------------------------------------------------------- Time 1.57 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 32852 2.84e-07 156_[+1(3.30e-09)]_166_\ [+2(1.78e-06)]_143 49362 1.26e-06 89_[+2(6.99e-07)]_178_\ [+3(2.16e-07)]_198 45033 4.12e-08 106_[+2(3.83e-06)]_189_\ [+3(1.45e-09)]_170 43847 2.17e-13 89_[+1(9.73e-09)]_235_\ [+2(2.79e-08)]_18_[+3(1.05e-08)]_104 45406 3.84e-10 106_[+1(1.63e-10)]_166_\ [+2(3.38e-08)]_193 36628 1.65e-08 147_[+2(2.66e-07)]_100_\ [+3(1.98e-09)]_218 49794 3.91e-10 238_[+1(1.49e-08)]_116_\ [+2(2.05e-06)]_65_[+3(2.75e-07)]_27 49890 1.34e-10 100_[+2(2.68e-06)]_48_\ [+1(2.07e-08)]_133_[+3(4.81e-08)]_165 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************