******************************************************************************** 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/468/468.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 41365 1.0000 500 11472 1.0000 500 31400 1.0000 387 41388 1.0000 500 1800 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/468/468.seqs.fa -oc motifs/468 -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= 5 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= 2387 N= 5 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.257 C 0.273 G 0.206 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.257 C 0.273 G 0.206 T 0.263 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 14 sites = 4 llr = 62 E-value = 6.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 3:58:838:::::: pos.-specific C :::3a::::a:::: probability G 8a:::38:8::8aa matrix T ::5::::33:a3:: bits 2.3 * ** 2.1 * ** 1.8 * * ** ** 1.6 * * ** ** Relative 1.4 ** * * ****** Entropy 1.1 ** *********** (22.5 bits) 0.9 ************** 0.7 ************** 0.5 ************** 0.2 ************** 0.0 -------------- Multilevel GGAACAGAGCTGGG consensus A TC GATT T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 11472 340 2.72e-09 GCTTTCACTT GGTACAGAGCTGGG CGCTTCACTT 1800 420 1.06e-08 GGCAGAGCTC GGTCCAGAGCTGGG TACCGAACTG 41365 19 1.11e-07 TACCATGGAA GGAACGATGCTGGG TATCCTGAGG 41388 110 2.35e-07 AAAAAGAACC AGAACAGATCTTGG TTCGCGCCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11472 2.7e-09 339_[+1]_147 1800 1.1e-08 419_[+1]_67 41365 1.1e-07 18_[+1]_468 41388 2.3e-07 109_[+1]_377 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=14 seqs=4 11472 ( 340) GGTACAGAGCTGGG 1 1800 ( 420) GGTCCAGAGCTGGG 1 41365 ( 19) GGAACGATGCTGGG 1 41388 ( 110) AGAACAGATCTTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 2322 bayes= 9.17866 E= 6.1e+000 -4 -865 186 -865 -865 -865 228 -865 96 -865 -865 92 154 -13 -865 -865 -865 187 -865 -865 154 -865 28 -865 -4 -865 186 -865 154 -865 -865 -8 -865 -865 186 -8 -865 187 -865 -865 -865 -865 -865 192 -865 -865 186 -8 -865 -865 228 -865 -865 -865 228 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 4 E= 6.1e+000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.250000 0.000000 0.750000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GA]G[AT][AC]C[AG][GA][AT][GT]CT[GT]GG -------------------------------------------------------------------------------- Time 0.28 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 5 llr = 89 E-value = 1.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :8428::466:::846:2::: pos.-specific C ::2::224::aa::2:::::8 probability G a22822:2:2::a2:46:4:: matrix T ::2::68:42::::4:486a2 bits 2.3 * * 2.1 * * 1.8 * *** * 1.6 * * *** * Relative 1.4 ** ** **** * Entropy 1.1 ** ** * **** ****** (25.7 bits) 0.9 ** ** * * **** ****** 0.7 ** **** ****** ****** 0.5 ** ****************** 0.2 ** ****************** 0.0 --------------------- Multilevel GAAGATTAAACCGAAAGTTTC consensus GCAGCCCTG GTGTAG T sequence G G G T C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 41365 174 1.62e-09 CCCGAGCAAT GATGAGTATACCGGTAGTTTC CTTCACGGTC 41388 427 1.96e-09 TCACTTTTCT GAAAATTCATCCGAAATTTTC CGAAATACCG 31400 346 1.96e-09 CGTGAATGCC GAGGATTATACCGATGTTGTT GGTCAGCTTG 1800 104 7.93e-09 GATATTCCGT GGAGATCCAACCGACAGATTC AGTCTGCTTC 11472 445 9.19e-09 GGGAGTAGCA GACGGCTGAGCCGAAGGTGTC GCACTGGGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41365 1.6e-09 173_[+2]_306 41388 2e-09 426_[+2]_53 31400 2e-09 345_[+2]_21 1800 7.9e-09 103_[+2]_376 11472 9.2e-09 444_[+2]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 41365 ( 174) GATGAGTATACCGGTAGTTTC 1 41388 ( 427) GAAAATTCATCCGAAATTTTC 1 31400 ( 346) GAGGATTATACCGATGTTGTT 1 1800 ( 104) GGAGATCCAACCGACAGATTC 1 11472 ( 445) GACGGCTGAGCCGAAGGTGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2287 bayes= 9.0862 E= 1.2e+001 -897 -897 228 -897 164 -897 -4 -897 64 -45 -4 -40 -36 -897 195 -897 164 -897 -4 -897 -897 -45 -4 119 -897 -45 -897 160 64 55 -4 -897 122 -897 -897 60 122 -897 -4 -40 -897 187 -897 -897 -897 187 -897 -897 -897 -897 228 -897 164 -897 -4 -897 64 -45 -897 60 122 -897 95 -897 -897 -897 154 60 -36 -897 -897 160 -897 -897 95 119 -897 -897 -897 192 -897 155 -897 -40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 1.2e+001 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.400000 0.200000 0.200000 0.200000 0.200000 0.000000 0.800000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.200000 0.200000 0.600000 0.000000 0.200000 0.000000 0.800000 0.400000 0.400000 0.200000 0.000000 0.600000 0.000000 0.000000 0.400000 0.600000 0.000000 0.200000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.400000 0.200000 0.000000 0.400000 0.600000 0.000000 0.400000 0.000000 0.000000 0.000000 0.600000 0.400000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[AG][ACGT][GA][AG][TCG][TC][ACG][AT][AGT]CCG[AG][ATC][AG][GT][TA][TG]T[CT] -------------------------------------------------------------------------------- Time 0.53 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 4 llr = 55 E-value = 7.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::35:::::a:a pos.-specific C :58::::::::: probability G 85::a:3aa:8: matrix T 3::5:a8:::3: bits 2.3 * ** 2.1 * *** * 1.8 ** *** * 1.6 ** *** * Relative 1.4 * ** ***** Entropy 1.1 *** ******** (19.7 bits) 0.9 ************ 0.7 ************ 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel GCCAGTTGGAGA consensus TGAT G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 11472 381 4.96e-08 TCTCTCCTTC GGCTGTTGGAGA GAGGCTAGGA 41365 488 3.14e-07 TCCCGTACCA GCAAGTTGGAGA C 1800 86 6.08e-07 GTGAATCTTC GCCTGTTGGATA TTCCGTGGAG 41388 89 7.92e-07 GTGTGATCCG TGCAGTGGGAGA AAAAGAACCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11472 5e-08 380_[+3]_108 41365 3.1e-07 487_[+3]_1 1800 6.1e-07 85_[+3]_403 41388 7.9e-07 88_[+3]_400 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=4 11472 ( 381) GGCTGTTGGAGA 1 41365 ( 488) GCAAGTTGGAGA 1 1800 ( 86) GCCTGTTGGATA 1 41388 ( 89) TGCAGTGGGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 2332 bayes= 9.18488 E= 7.2e+001 -865 -865 186 -8 -865 87 128 -865 -4 146 -865 -865 96 -865 -865 92 -865 -865 228 -865 -865 -865 -865 192 -865 -865 28 151 -865 -865 228 -865 -865 -865 228 -865 196 -865 -865 -865 -865 -865 186 -8 196 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 4 E= 7.2e+001 0.000000 0.000000 0.750000 0.250000 0.000000 0.500000 0.500000 0.000000 0.250000 0.750000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 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 0.750000 0.250000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GT][CG][CA][AT]GT[TG]GGA[GT]A -------------------------------------------------------------------------------- Time 0.78 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41365 3.68e-12 18_[+1(1.11e-07)]_141_\ [+2(1.62e-09)]_293_[+3(3.14e-07)]_1 11472 9.97e-14 339_[+1(2.72e-09)]_27_\ [+3(4.96e-08)]_52_[+2(9.19e-09)]_35 31400 3.75e-05 345_[+2(1.96e-09)]_21 41388 2.11e-11 88_[+3(7.92e-07)]_9_[+1(2.35e-07)]_\ 303_[+2(1.96e-09)]_53 1800 3.33e-12 85_[+3(6.08e-07)]_6_[+2(7.93e-09)]_\ 223_[+1(1.56e-05)]_58_[+1(1.06e-08)]_46_[+1(1.76e-05)]_7 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************