******************************************************************************** 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/261/261.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 20404 1.0000 500 24073 1.0000 500 24454 1.0000 500 260879 1.0000 500 260880 1.0000 500 26140 1.0000 500 261453 1.0000 500 262104 1.0000 500 262171 1.0000 500 262322 1.0000 500 262527 1.0000 500 262585 1.0000 500 262645 1.0000 500 262747 1.0000 500 262826 1.0000 500 263482 1.0000 500 263734 1.0000 500 263859 1.0000 500 264679 1.0000 500 264792 1.0000 500 27435 1.0000 500 32522 1.0000 500 36249 1.0000 500 3635 1.0000 500 37366 1.0000 500 8253 1.0000 500 8255 1.0000 500 8657 1.0000 500 9678 1.0000 500 bd1878 1.0000 500 ThpsCt024 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/261/261.seqs.fa -oc motifs/261 -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= 31 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= 15500 N= 31 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.273 C 0.224 G 0.228 T 0.275 Background letter frequencies (from dataset with add-one prior applied): A 0.273 C 0.224 G 0.228 T 0.275 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 19 sites = 24 llr = 275 E-value = 2.5e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 246358348165253:861 pos.-specific C 32275273:73:824a:38 probability G 53:::::3:213:12:2:1 matrix T :12:::::2::1:21:::: bits 2.2 * 1.9 * 1.7 * 1.5 * Relative 1.3 * * * ** * Entropy 1.1 ** * * ** * (16.6 bits) 0.9 **** ** * **** 0.6 * **** *** * **** 0.4 * *********** **** 0.2 ******************* 0.0 ------------------- Multilevel GAACAACAACAACACCAAC consensus CGCAC AC CGACA C sequence A T G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 20404 61 6.19e-10 ACCACAACCA CAACCACAACAACAACAAC CTTGCATTTT 24073 362 9.89e-09 TTCGGTTCGC CGCCAACAACAACAACAAC ACGGTGTCTT 26140 2 4.36e-08 G CAACAACAACAACGGCAAC GGCATGATGA 27435 314 1.56e-07 CTCATTGGGT GAACCACCTCCACAACGAC GAATAAGGAT 260880 246 1.56e-07 AGAGCTGGGT GGTACACCACAACTGCAAC CTGGTAAGAA 260879 252 1.56e-07 AGAGCTGGGT GGTACACCACAACTGCAAC CTGGTAAGAA 262747 423 2.60e-07 AAGAACGAAA GCAACACAACACCAACAAC CCACCAACAC 37366 11 2.94e-07 AATGCATCAC AATCAACAACAACATCACC CGACGGCAGT 264679 122 3.32e-07 ATTAGCAAAA AGACCAAAAGAACAACACC AGGGATTCCA 262322 294 9.17e-07 ACCAGTACAT GAACAAAAAAAGAACCACC ATGGGCCTCC 3635 356 1.39e-06 ATCCATCGCG GTACCAACACCAAGCCAAC AAACCGGTCT 263859 319 1.53e-06 CTGACGGATA GTCCCACGAGGGCACCAAC GATTCCAATT 262585 323 2.05e-06 ACGCCCTCGA AACCAACGTCATCAGCAAC GAACGGCACA bd1878 422 2.71e-06 GAACCTTCTT CAACCAAGACCGCCCCACG CCCAACCCAT 263734 456 2.97e-06 CTGTGAATAG CATCAACAACCTACCCACC AGTGAACCCT 262645 426 3.55e-06 CTCCCAGCCC AAACAAACACCACTCCACG CTAGATTCTT 8657 460 5.44e-06 TAAAAAGAAC GCACAACCACAACCTCGAA CCTTGTAGAA 32522 463 5.44e-06 TGTGGTTGTT GTAAACACTCAGCACCACC ATTGGCAGCT 8253 164 5.90e-06 CTCAATCCGT GCACTCCAACAGCTGCACC CTCGCTCAGT 263482 475 1.36e-05 AGTGTGCTCC CGCAACCCACATCACCATC TCTTGCC 262826 65 1.92e-05 CAGATTCCTC GCTTCACAAACGCCACAAC TCAATTATTG 24454 402 2.81e-05 ACGACGTGGT GGAAAGAGAAAACCCCGAC GCGTCGGCAA 264792 419 2.99e-05 TATGCGAAAA GGACAACGTGGAAACCAAA CCTTCCAAAA 262527 159 5.00e-05 CGGTGATGTA AACACCCGAGCGAAACGAC AGGCGACCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20404 6.2e-10 60_[+1]_421 24073 9.9e-09 361_[+1]_120 26140 4.4e-08 1_[+1]_480 27435 1.6e-07 313_[+1]_168 260880 1.6e-07 245_[+1]_236 260879 1.6e-07 251_[+1]_230 262747 2.6e-07 422_[+1]_59 37366 2.9e-07 10_[+1]_471 264679 3.3e-07 121_[+1]_360 262322 9.2e-07 293_[+1]_188 3635 1.4e-06 355_[+1]_126 263859 1.5e-06 318_[+1]_163 262585 2e-06 322_[+1]_159 bd1878 2.7e-06 421_[+1]_60 263734 3e-06 455_[+1]_26 262645 3.6e-06 425_[+1]_56 8657 5.4e-06 459_[+1]_22 32522 5.4e-06 462_[+1]_19 8253 5.9e-06 163_[+1]_318 263482 1.4e-05 474_[+1]_7 262826 1.9e-05 64_[+1]_417 24454 2.8e-05 401_[+1]_80 264792 3e-05 418_[+1]_63 262527 5e-05 158_[+1]_323 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=19 seqs=24 20404 ( 61) CAACCACAACAACAACAAC 1 24073 ( 362) CGCCAACAACAACAACAAC 1 26140 ( 2) CAACAACAACAACGGCAAC 1 27435 ( 314) GAACCACCTCCACAACGAC 1 260880 ( 246) GGTACACCACAACTGCAAC 1 260879 ( 252) GGTACACCACAACTGCAAC 1 262747 ( 423) GCAACACAACACCAACAAC 1 37366 ( 11) AATCAACAACAACATCACC 1 264679 ( 122) AGACCAAAAGAACAACACC 1 262322 ( 294) GAACAAAAAAAGAACCACC 1 3635 ( 356) GTACCAACACCAAGCCAAC 1 263859 ( 319) GTCCCACGAGGGCACCAAC 1 262585 ( 323) AACCAACGTCATCAGCAAC 1 bd1878 ( 422) CAACCAAGACCGCCCCACG 1 263734 ( 456) CATCAACAACCTACCCACC 1 262645 ( 426) AAACAAACACCACTCCACG 1 8657 ( 460) GCACAACCACAACCTCGAA 1 32522 ( 463) GTAAACACTCAGCACCACC 1 8253 ( 164) GCACTCCAACAGCTGCACC 1 263482 ( 475) CGCAACCCACATCACCATC 1 262826 ( 65) GCTTCACAAACGCCACAAC 1 24454 ( 402) GGAAAGAGAAAACCCCGAC 1 264792 ( 419) GGACAACGTGGAAACCAAA 1 262527 ( 159) AACACCCGAGCGAAACGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 14942 bayes= 9.72788 E= 2.5e-010 -39 16 125 -1123 61 -42 35 -114 109 -10 -1123 -40 10 158 -1123 -272 87 104 -1123 -272 154 -42 -245 -1123 10 166 -1123 -1123 61 58 13 -1123 161 -1123 -1123 -72 -113 166 -45 -1123 119 38 -145 -1123 99 -242 35 -114 -39 182 -1123 -1123 99 -10 -145 -72 10 90 -13 -172 -1123 216 -1123 -1123 161 -1123 -45 -1123 119 58 -1123 -272 -171 190 -145 -1123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 24 E= 2.5e-010 0.208333 0.250000 0.541667 0.000000 0.416667 0.166667 0.291667 0.125000 0.583333 0.208333 0.000000 0.208333 0.291667 0.666667 0.000000 0.041667 0.500000 0.458333 0.000000 0.041667 0.791667 0.166667 0.041667 0.000000 0.291667 0.708333 0.000000 0.000000 0.416667 0.333333 0.250000 0.000000 0.833333 0.000000 0.000000 0.166667 0.125000 0.708333 0.166667 0.000000 0.625000 0.291667 0.083333 0.000000 0.541667 0.041667 0.291667 0.125000 0.208333 0.791667 0.000000 0.000000 0.541667 0.208333 0.083333 0.166667 0.291667 0.416667 0.208333 0.083333 0.000000 1.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.625000 0.333333 0.000000 0.041667 0.083333 0.833333 0.083333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GCA][AG][ACT][CA][AC]A[CA][ACG]AC[AC][AG][CA][AC][CAG]CA[AC]C -------------------------------------------------------------------------------- Time 7.18 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 5 llr = 125 E-value = 5.0e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :6:a::::aa::::a:::2a2 pos.-specific C a2a::::2::2a28:2aa8:8 probability G :2::a::8:::::2:8::::: matrix T :::::aa:::8:8:::::::: bits 2.2 * * * * ** 1.9 * ***** ** * * ** * 1.7 * ***** ** * * ** * 1.5 * ******** * ***** * Relative 1.3 * ******************* Entropy 1.1 * ******************* (36.1 bits) 0.9 * ******************* 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CACAGTTGAATCTCAGCCCAC consensus C C C CG C A A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 261453 480 1.78e-13 AGATCACAGG CACAGTTGAATCTCAGCCCAC 260880 474 1.78e-13 TAGATCCAGG CACAGTTGAATCTCAGCCCAC CAGTAC 260879 480 1.78e-13 TAGATCCAGG CACAGTTGAATCTCAGCCCAC 262322 480 4.72e-13 TGTTATAGAT CGCAGTTGAATCTCAGCCCAC 36249 14 4.17e-10 TCGTCGTCGC CCCAGTTCAACCCGACCCAAA CATCGGTACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 261453 1.8e-13 479_[+2] 260880 1.8e-13 473_[+2]_6 260879 1.8e-13 479_[+2] 262322 4.7e-13 479_[+2] 36249 4.2e-10 13_[+2]_466 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 261453 ( 480) CACAGTTGAATCTCAGCCCAC 1 260880 ( 474) CACAGTTGAATCTCAGCCCAC 1 260879 ( 480) CACAGTTGAATCTCAGCCCAC 1 262322 ( 480) CGCAGTTGAATCTCAGCCCAC 1 36249 ( 14) CCCAGTTCAACCCGACCCAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14880 bayes= 12.4823 E= 5.0e-009 -897 216 -897 -897 113 -16 -19 -897 -897 216 -897 -897 187 -897 -897 -897 -897 -897 213 -897 -897 -897 -897 186 -897 -897 -897 186 -897 -16 181 -897 187 -897 -897 -897 187 -897 -897 -897 -897 -16 -897 154 -897 216 -897 -897 -897 -16 -897 154 -897 184 -19 -897 187 -897 -897 -897 -897 -16 181 -897 -897 216 -897 -897 -897 216 -897 -897 -45 184 -897 -897 187 -897 -897 -897 -45 184 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 5.0e-009 0.000000 1.000000 0.000000 0.000000 0.600000 0.200000 0.200000 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[ACG]CAGTT[GC]AA[TC]C[TC][CG]A[GC]CC[CA]A[CA] -------------------------------------------------------------------------------- Time 14.07 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 4 llr = 112 E-value = 6.9e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::aaaaa::a::::a:a: pos.-specific C ::::a:::::::::::::::: probability G a:::::::::a:::a:::::a matrix T :aaa:::::::a:a:aa:a:: bits 2.2 * * * * * 1.9 ********************* 1.7 ********************* 1.5 ********************* Relative 1.3 ********************* Entropy 1.1 ********************* (40.6 bits) 0.9 ********************* 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GTTTCAAAAAGTATGTTATAG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 262322 457 6.11e-13 TGACTGTTTA GTTTCAAAAAGTATGTTATAG ATCGCAGTTG 261453 451 6.11e-13 TAATAACTCA GTTTCAAAAAGTATGTTATAG ATCACAGGCA 260880 446 6.11e-13 GTGTATTTTA GTTTCAAAAAGTATGTTATAG ATCCAGGCAC 260879 452 6.11e-13 GTGTATTTTA GTTTCAAAAAGTATGTTATAG ATCCAGGCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 262322 6.1e-13 456_[+3]_23 261453 6.1e-13 450_[+3]_29 260880 6.1e-13 445_[+3]_34 260879 6.1e-13 451_[+3]_28 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=4 262322 ( 457) GTTTCAAAAAGTATGTTATAG 1 261453 ( 451) GTTTCAAAAAGTATGTTATAG 1 260880 ( 446) GTTTCAAAAAGTATGTTATAG 1 260879 ( 452) GTTTCAAAAAGTATGTTATAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14880 bayes= 11.8607 E= 6.9e-006 -865 -865 213 -865 -865 -865 -865 186 -865 -865 -865 186 -865 -865 -865 186 -865 216 -865 -865 187 -865 -865 -865 187 -865 -865 -865 187 -865 -865 -865 187 -865 -865 -865 187 -865 -865 -865 -865 -865 213 -865 -865 -865 -865 186 187 -865 -865 -865 -865 -865 -865 186 -865 -865 213 -865 -865 -865 -865 186 -865 -865 -865 186 187 -865 -865 -865 -865 -865 -865 186 187 -865 -865 -865 -865 -865 213 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 6.9e-006 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 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GTTTCAAAAAGTATGTTATAG -------------------------------------------------------------------------------- Time 21.34 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20404 3.16e-06 27_[+1(1.05e-09)]_14_[+1(6.19e-10)]_\ 421 24073 1.46e-05 361_[+1(9.89e-09)]_31_\ [+1(2.19e-05)]_70 24454 3.12e-02 401_[+1(2.81e-05)]_80 260879 2.92e-21 251_[+1(1.56e-07)]_181_\ [+3(6.11e-13)]_7_[+2(1.78e-13)] 260880 2.92e-21 245_[+1(1.56e-07)]_181_\ [+3(6.11e-13)]_7_[+2(1.78e-13)]_6 26140 7.44e-04 1_[+1(4.36e-08)]_480 261453 2.35e-17 450_[+3(6.11e-13)]_8_[+2(1.78e-13)] 262104 8.02e-01 500 262171 3.19e-01 500 262322 4.11e-20 293_[+1(9.17e-07)]_144_\ [+3(6.11e-13)]_2_[+2(4.72e-13)] 262527 6.58e-02 158_[+1(5.00e-05)]_323 262585 7.79e-04 322_[+1(2.05e-06)]_72_\ [+2(5.57e-05)]_66 262645 5.93e-03 425_[+1(3.55e-06)]_56 262747 9.03e-04 422_[+1(2.60e-07)]_7_[+1(4.60e-06)]_\ 33 262826 1.18e-01 64_[+1(1.92e-05)]_417 263482 1.20e-02 474_[+1(1.36e-05)]_7 263734 1.25e-02 455_[+1(2.97e-06)]_26 263859 1.09e-02 318_[+1(1.53e-06)]_163 264679 2.63e-03 121_[+1(3.32e-07)]_360 264792 5.34e-02 418_[+1(2.99e-05)]_63 27435 2.03e-03 15_[+1(7.16e-05)]_279_\ [+1(1.56e-07)]_168 32522 1.98e-02 462_[+1(5.44e-06)]_19 36249 2.76e-06 13_[+2(4.17e-10)]_466 3635 5.43e-03 355_[+1(1.39e-06)]_100_\ [+1(9.07e-05)]_7 37366 3.25e-03 10_[+1(2.94e-07)]_471 8253 1.68e-02 163_[+1(5.90e-06)]_318 8255 7.57e-01 500 8657 5.30e-02 459_[+1(5.44e-06)]_22 9678 9.82e-01 500 bd1878 7.14e-03 421_[+1(2.71e-06)]_60 ThpsCt024 4.92e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************