******************************************************************************** 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/184/184.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 25189 1.0000 500 261867 1.0000 500 34306 1.0000 500 6964 1.0000 500 723 1.0000 500 7827 1.0000 500 843 1.0000 500 bd663 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/184/184.seqs.fa -oc motifs/184 -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 0.268 C 0.245 G 0.216 T 0.271 Background letter frequencies (from dataset with add-one prior applied): A 0.268 C 0.246 G 0.216 T 0.271 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 8 llr = 115 E-value = 8.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :393:35615463199:343: pos.-specific C :8:38653946:69:1a6549 probability G 5::31::::::41:::::13: matrix T 5:1311:1:1::::1::1:11 bits 2.2 2.0 * 1.8 * 1.5 * * * * Relative 1.3 * * **** * Entropy 1.1 *** * ** **** * (20.7 bits) 0.9 *** * * * ** **** * 0.7 *** ***** ********* * 0.4 *** *************** * 0.2 *** ***************** 0.0 --------------------- Multilevel GCAACCAACACACCAACCCCC consensus TA C ACC CAGA AAA sequence G G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 261867 439 1.88e-11 ATTGCTACAC GCATCCCACACACCAACCCAC GCAACCCCAC bd663 469 5.42e-09 GAAACCGGAA GAAGCCAACCAGCCAACCAAC GCAATGCAAC 6964 391 9.10e-08 TTTGCCAACC TCAATCCACAAACCACCCAGC CCTCTCGCTT 34306 367 9.10e-08 CCGCCGCACC GCAGGCAACCCGGCAACAAGC AAACGCTCAC 7827 446 1.39e-07 ATCATACCTT TCACCCATCACACAAACTCCC CCATCACTCC 25189 390 3.22e-07 GGAATTTGGA GAAACACCCTCAACAACCGCC AACTTCAAGA 723 474 5.20e-07 CCCCTCCGCC TCACCACAAACAACAACACCT CCAACA 843 186 2.03e-06 TCGTCCAGGT TCTTCTACCCAGCCTACCCTC CAAATTGGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 261867 1.9e-11 438_[+1]_41 bd663 5.4e-09 468_[+1]_11 6964 9.1e-08 390_[+1]_89 34306 9.1e-08 366_[+1]_113 7827 1.4e-07 445_[+1]_34 25189 3.2e-07 389_[+1]_90 723 5.2e-07 473_[+1]_6 843 2e-06 185_[+1]_294 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=8 261867 ( 439) GCATCCCACACACCAACCCAC 1 bd663 ( 469) GAAGCCAACCAGCCAACCAAC 1 6964 ( 391) TCAATCCACAAACCACCCAGC 1 34306 ( 367) GCAGGCAACCCGGCAACAAGC 1 7827 ( 446) TCACCCATCACACAAACTCCC 1 25189 ( 390) GAAACACCCTCAACAACCGCC 1 723 ( 474) TCACCACAAACAACAACACCT 1 843 ( 186) TCTTCTACCCAGCCTACCCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3840 bayes= 8.90388 E= 8.0e+001 -965 -965 121 88 -10 161 -965 -965 171 -965 -965 -111 -10 3 21 -11 -965 161 -79 -111 -10 135 -965 -111 90 103 -965 -965 122 3 -965 -111 -110 183 -965 -965 90 61 -965 -111 49 135 -965 -965 122 -965 79 -965 -10 135 -79 -965 -110 183 -965 -965 171 -965 -965 -111 171 -97 -965 -965 -965 202 -965 -965 -10 135 -965 -111 49 103 -79 -965 -10 61 21 -111 -965 183 -965 -111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 8.0e+001 0.000000 0.000000 0.500000 0.500000 0.250000 0.750000 0.000000 0.000000 0.875000 0.000000 0.000000 0.125000 0.250000 0.250000 0.250000 0.250000 0.000000 0.750000 0.125000 0.125000 0.250000 0.625000 0.000000 0.125000 0.500000 0.500000 0.000000 0.000000 0.625000 0.250000 0.000000 0.125000 0.125000 0.875000 0.000000 0.000000 0.500000 0.375000 0.000000 0.125000 0.375000 0.625000 0.000000 0.000000 0.625000 0.000000 0.375000 0.000000 0.250000 0.625000 0.125000 0.000000 0.125000 0.875000 0.000000 0.000000 0.875000 0.000000 0.000000 0.125000 0.875000 0.125000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.625000 0.000000 0.125000 0.375000 0.500000 0.125000 0.000000 0.250000 0.375000 0.250000 0.125000 0.000000 0.875000 0.000000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GT][CA]A[ACGT]C[CA][AC][AC]C[AC][CA][AG][CA]CAAC[CA][CA][CAG]C -------------------------------------------------------------------------------- Time 0.56 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 14 sites = 3 llr = 50 E-value = 3.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::::::3::::: pos.-specific C :::3:::33:a::: probability G :3a73aa7:a:aa: matrix T a7::7:::3::::a bits 2.2 * ** * ** 2.0 * * ** ***** 1.8 * * ** ***** 1.5 * * ** ***** Relative 1.3 * ** *** ***** Entropy 1.1 ******** ***** (24.0 bits) 0.9 ******** ***** 0.7 ******** ***** 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel TTGGTGGGAGCGGT consensus G CG CC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 34306 223 4.94e-09 GGTCGCGTGT TTGGTGGGTGCGGT TGGCGGGCGG 843 51 2.50e-08 TTCACCCGTC TTGGTGGCAGCGGT ACCTCCTGGA 261867 307 5.37e-08 GACTTTTGCA TGGCGGGGCGCGGT GCTTTCTCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 34306 4.9e-09 222_[+2]_264 843 2.5e-08 50_[+2]_436 261867 5.4e-08 306_[+2]_180 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=14 seqs=3 34306 ( 223) TTGGTGGGTGCGGT 1 843 ( 51) TTGGTGGCAGCGGT 1 261867 ( 307) TGGCGGGGCGCGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 3896 bayes= 10.0004 E= 3.2e+002 -823 -823 -823 188 -823 -823 62 130 -823 -823 221 -823 -823 44 162 -823 -823 -823 62 130 -823 -823 221 -823 -823 -823 221 -823 -823 44 162 -823 32 44 -823 30 -823 -823 221 -823 -823 202 -823 -823 -823 -823 221 -823 -823 -823 221 -823 -823 -823 -823 188 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 3 E= 3.2e+002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.333333 0.333333 0.000000 0.333333 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 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[TG]G[GC][TG]GG[GC][ACT]GCGGT -------------------------------------------------------------------------------- Time 1.08 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 7 llr = 93 E-value = 2.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :9::6:6:3::1a319 pos.-specific C 1::::::64:33:6:1 probability G 713a3a4::4:6::9: matrix T 1:7:1::4367::1:: bits 2.2 * * 2.0 * * * 1.8 * * * 1.5 * * * * Relative 1.3 * * * * ** Entropy 1.1 *** ** ** * ** (19.1 bits) 0.9 **** *** ** * ** 0.7 ******** ******* 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel GATGAGACCTTGACGA consensus G G GTAGCC A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 25189 170 5.65e-09 GATCAAAACC GATGAGGCCTTCACGA AGTGGTCCCG 843 97 5.81e-08 CCGAAGTAAA GAGGAGACTGCGACGA TTGAGCCAGT 34306 88 1.59e-07 GTTGGTAACT GATGAGGTCGTCATGA CAGAACTGCC bd663 293 1.82e-07 GTGCTTGACT TATGGGACATTGACGA AGAAGTCCCC 261867 122 7.40e-07 GTACGAGTGT GATGGGGTCTCAAAGA AGGTACTAGA 6964 132 2.18e-06 GGTGGTGATG GAGGTGATAGTGAAGC AAAAGCTGGT 723 377 2.65e-06 TTGGAAGAAA CGTGAGACTTTGACAA TATTTACTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25189 5.6e-09 169_[+3]_315 843 5.8e-08 96_[+3]_388 34306 1.6e-07 87_[+3]_397 bd663 1.8e-07 292_[+3]_192 261867 7.4e-07 121_[+3]_363 6964 2.2e-06 131_[+3]_353 723 2.7e-06 376_[+3]_108 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=7 25189 ( 170) GATGAGGCCTTCACGA 1 843 ( 97) GAGGAGACTGCGACGA 1 34306 ( 88) GATGAGGTCGTCATGA 1 bd663 ( 293) TATGGGACATTGACGA 1 261867 ( 122) GATGGGGTCTCAAAGA 1 6964 ( 132) GAGGTGATAGTGAAGC 1 723 ( 377) CGTGAGACTTTGACAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 3880 bayes= 9.7185 E= 2.4e+002 -945 -78 172 -92 168 -945 -60 -945 -945 -945 40 140 -945 -945 221 -945 109 -945 40 -92 -945 -945 221 -945 109 -945 99 -945 -945 122 -945 66 9 80 -945 8 -945 -945 99 108 -945 22 -945 140 -90 22 140 -945 190 -945 -945 -945 9 122 -945 -92 -90 -945 199 -945 168 -78 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 7 E= 2.4e+002 0.000000 0.142857 0.714286 0.142857 0.857143 0.000000 0.142857 0.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 1.000000 0.000000 0.571429 0.000000 0.285714 0.142857 0.000000 0.000000 1.000000 0.000000 0.571429 0.000000 0.428571 0.000000 0.000000 0.571429 0.000000 0.428571 0.285714 0.428571 0.000000 0.285714 0.000000 0.000000 0.428571 0.571429 0.000000 0.285714 0.000000 0.714286 0.142857 0.285714 0.571429 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.571429 0.000000 0.142857 0.142857 0.000000 0.857143 0.000000 0.857143 0.142857 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GA[TG]G[AG]G[AG][CT][CAT][TG][TC][GC]A[CA]GA -------------------------------------------------------------------------------- Time 1.71 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25189 9.73e-08 169_[+3(5.65e-09)]_204_\ [+1(3.22e-07)]_90 261867 6.11e-14 121_[+3(7.40e-07)]_169_\ [+2(5.37e-08)]_118_[+1(1.88e-11)]_41 34306 4.54e-12 87_[+3(1.59e-07)]_119_\ [+2(4.94e-09)]_130_[+1(9.10e-08)]_113 6964 3.78e-06 131_[+3(2.18e-06)]_243_\ [+1(9.10e-08)]_89 723 1.22e-05 376_[+3(2.65e-06)]_81_\ [+1(5.20e-07)]_6 7827 1.33e-04 445_[+1(1.39e-07)]_34 843 1.48e-10 50_[+2(2.50e-08)]_32_[+3(5.81e-08)]_\ 73_[+1(2.03e-06)]_294 bd663 1.76e-08 292_[+3(1.82e-07)]_160_\ [+1(5.42e-09)]_11 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************