******************************************************************************** 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/339/339.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10042 1.0000 500 11028 1.0000 500 12122 1.0000 500 12188 1.0000 500 25771 1.0000 500 264767 1.0000 500 3321 1.0000 500 3591 1.0000 500 5209 1.0000 500 5768 1.0000 500 6359 1.0000 500 7649 1.0000 500 8137 1.0000 500 8206 1.0000 500 8235 1.0000 500 8321 1.0000 500 8795 1.0000 500 8896 1.0000 500 9532 1.0000 500 bd853 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/339/339.seqs.fa -oc motifs/339 -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= 20 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= 10000 N= 20 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.273 C 0.227 G 0.231 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.273 C 0.227 G 0.231 T 0.268 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 4 llr = 105 E-value = 1.6e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::a::a3a::::8:8::3:a: pos.-specific C aa:aa:8::::a::3aa8::a probability G ::::::::a8a::8::::::: matrix T :::::::::3::33::::a:: bits 2.1 ** ** * ** ** * 1.9 ****** ** ** ** *** 1.7 ****** ** ** ** *** 1.5 ****** ** ** ** *** Relative 1.3 ************ * ****** Entropy 1.1 ********************* (37.9 bits) 0.9 ********************* 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CCACCACAGGGCAGACCCTAC consensus A T TTC A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8235 461 1.15e-13 AGAAAGACCT CCACCACAGGGCAGACCCTAC CGGAACAACA 25771 464 1.15e-13 AGAAAGACTG CCACCACAGGGCAGACCCTAC CGGAAAAACT 12122 461 1.15e-13 AGAAAGACTT CCACCACAGGGCAGACCCTAC CGGAAAAACA 264767 251 9.83e-12 ACGCTCACAG CCACCAAAGTGCTTCCCATAC TCAAGATGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8235 1.1e-13 460_[+1]_19 25771 1.1e-13 463_[+1]_16 12122 1.1e-13 460_[+1]_19 264767 9.8e-12 250_[+1]_229 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=4 8235 ( 461) CCACCACAGGGCAGACCCTAC 1 25771 ( 464) CCACCACAGGGCAGACCCTAC 1 12122 ( 461) CCACCACAGGGCAGACCCTAC 1 264767 ( 251) CCACCAAAGTGCTTCCCATAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 9600 bayes= 11.2282 E= 1.6e-005 -865 213 -865 -865 -865 213 -865 -865 187 -865 -865 -865 -865 213 -865 -865 -865 213 -865 -865 187 -865 -865 -865 -13 172 -865 -865 187 -865 -865 -865 -865 -865 211 -865 -865 -865 170 -10 -865 -865 211 -865 -865 213 -865 -865 146 -865 -865 -10 -865 -865 170 -10 146 14 -865 -865 -865 213 -865 -865 -865 213 -865 -865 -13 172 -865 -865 -865 -865 -865 189 187 -865 -865 -865 -865 213 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 1.6e-005 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 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 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.250000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CCACCA[CA]AG[GT]GC[AT][GT][AC]CC[CA]TAC -------------------------------------------------------------------------------- Time 3.66 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 4 llr = 102 E-value = 3.8e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A a::a::8a:::a::a:a:83: pos.-specific C ::8:a3::a:a::a:a:3:8a probability G :8:::8:::a::a::::8::: matrix T :33:::3:::::::::::3:: bits 2.1 * *** ** * * 1.9 * ** ********** * 1.7 * ** ********** * 1.5 * ** ********** * Relative 1.3 ****** *********** ** Entropy 1.1 ********************* (36.8 bits) 0.9 ********************* 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel AGCACGAACGCAGCACAGACC consensus TT CT CTA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8235 296 1.43e-13 ATCTGTGCGT AGCACGAACGCAGCACAGACC GTATTTATCC 25771 298 1.43e-13 ATCTGTGCGT AGCACGAACGCAGCACAGACC GTATTTTTTC 12122 296 7.05e-13 ATCTGTGCGA AGCACGTACGCAGCACAGACC GAATTTATTC 5209 180 2.27e-11 GCATCTTGAT ATTACCAACGCAGCACACTAC TTCTGCTTAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8235 1.4e-13 295_[+2]_184 25771 1.4e-13 297_[+2]_182 12122 7.1e-13 295_[+2]_184 5209 2.3e-11 179_[+2]_300 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=4 8235 ( 296) AGCACGAACGCAGCACAGACC 1 25771 ( 298) AGCACGAACGCAGCACAGACC 1 12122 ( 296) AGCACGTACGCAGCACAGACC 1 5209 ( 180) ATTACCAACGCAGCACACTAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 9600 bayes= 11.2282 E= 3.8e-004 187 -865 -865 -865 -865 -865 170 -10 -865 172 -865 -10 187 -865 -865 -865 -865 213 -865 -865 -865 14 170 -865 146 -865 -865 -10 187 -865 -865 -865 -865 213 -865 -865 -865 -865 211 -865 -865 213 -865 -865 187 -865 -865 -865 -865 -865 211 -865 -865 213 -865 -865 187 -865 -865 -865 -865 213 -865 -865 187 -865 -865 -865 -865 14 170 -865 146 -865 -865 -10 -13 172 -865 -865 -865 213 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 3.8e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.750000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.750000 0.000000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.750000 0.000000 0.000000 0.250000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- A[GT][CT]AC[GC][AT]ACGCAGCACA[GC][AT][CA]C -------------------------------------------------------------------------------- Time 7.02 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 4 llr = 101 E-value = 1.7e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::a:3a::33a::::a:: pos.-specific C :8:a::88:::::::a:::a: probability G :3a:a:3::3a8:::::8::: matrix T a::::::::8::8:a:a3::a bits 2.1 *** * * * 1.9 * **** * * **** *** 1.7 * **** * * **** *** 1.5 * **** * * **** *** Relative 1.3 ********* ** ******** Entropy 1.1 ********************* (36.4 bits) 0.9 ********************* 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TCGCGACCATGGTATCTGACT consensus G GA G AA T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8235 400 1.85e-13 CTTTCTAACG TCGCGACCATGGTATCTGACT ACTAGGCTTA 25771 402 1.85e-13 CTTTCTAACG TCGCGACCATGGTATCTGACT ACTAGGCTTT 12122 400 1.85e-13 CTTTCTAACG TCGCGACCATGGTATCTGACT ACTAGGCTTA 8795 235 4.37e-11 GTCTGGTAGC TGGCGAGAAGGAAATCTTACT AGTTTATCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8235 1.9e-13 399_[+3]_80 25771 1.9e-13 401_[+3]_78 12122 1.9e-13 399_[+3]_80 8795 4.4e-11 234_[+3]_245 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=4 8235 ( 400) TCGCGACCATGGTATCTGACT 1 25771 ( 402) TCGCGACCATGGTATCTGACT 1 12122 ( 400) TCGCGACCATGGTATCTGACT 1 8795 ( 235) TGGCGAGAAGGAAATCTTACT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 9600 bayes= 11.2282 E= 1.7e-003 -865 -865 -865 189 -865 172 11 -865 -865 -865 211 -865 -865 213 -865 -865 -865 -865 211 -865 187 -865 -865 -865 -865 172 11 -865 -13 172 -865 -865 187 -865 -865 -865 -865 -865 11 148 -865 -865 211 -865 -13 -865 170 -865 -13 -865 -865 148 187 -865 -865 -865 -865 -865 -865 189 -865 213 -865 -865 -865 -865 -865 189 -865 -865 170 -10 187 -865 -865 -865 -865 213 -865 -865 -865 -865 -865 189 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 1.7e-003 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.750000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[CG]GCGA[CG][CA]A[TG]G[GA][TA]ATCT[GT]ACT -------------------------------------------------------------------------------- Time 10.28 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10042 9.90e-01 500 11028 4.71e-01 500 12122 4.01e-27 295_[+2(7.05e-13)]_28_\ [+1(6.84e-06)]_34_[+3(1.85e-13)]_40_[+1(1.15e-13)]_19 12188 1.60e-01 278_[+2(7.85e-05)]_201 25771 8.52e-28 297_[+2(1.43e-13)]_28_\ [+1(5.58e-05)]_34_[+3(1.85e-13)]_41_[+1(1.15e-13)]_16 264767 5.97e-07 250_[+1(9.83e-12)]_229 3321 4.64e-01 500 3591 1.24e-01 500 5209 1.72e-07 179_[+2(2.27e-11)]_300 5768 1.58e-01 500 6359 7.83e-01 500 7649 3.95e-01 500 8137 4.88e-01 500 8206 7.65e-01 500 8235 8.52e-28 295_[+2(1.43e-13)]_83_\ [+3(1.85e-13)]_40_[+1(1.15e-13)]_19 8321 3.77e-02 500 8795 1.81e-06 234_[+3(4.37e-11)]_245 8896 8.25e-02 351_[+2(7.85e-05)]_128 9532 3.85e-01 500 bd853 9.91e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************