******************************************************************************** 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/165/165.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1172 1.0000 500 11797 1.0000 500 1471 1.0000 500 21994 1.0000 500 22513 1.0000 500 23937 1.0000 500 24693 1.0000 500 264332 1.0000 500 264610 1.0000 500 269844 1.0000 500 270071 1.0000 500 29496 1.0000 500 5388 1.0000 500 5743 1.0000 500 7880 1.0000 500 9695 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/165/165.seqs.fa -oc motifs/165 -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= 16 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= 8000 N= 16 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.251 C 0.229 G 0.239 T 0.281 Background letter frequencies (from dataset with add-one prior applied): A 0.251 C 0.229 G 0.239 T 0.281 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 11 llr = 165 E-value = 1.1e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 5:87:35:12::41::11::2 pos.-specific C :111122::::32::2::2:: probability G :9::912a389:37:671592 matrix T 5:12:51:6:1722a228416 bits 2.1 * 1.9 * * 1.7 * * * * * * 1.5 * * * * * * Relative 1.3 * * * ** * * Entropy 1.1 ** * * *** * * * (21.6 bits) 0.8 ***** * *** ** ** * 0.6 ***** ***** ***** ** 0.4 ***** ****** ******** 0.2 ************ ******** 0.0 --------------------- Multilevel AGAAGTAGTGGTAGTGGTGGT consensus T A G CG T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 7880 437 1.05e-09 ACACTAGAGA AGAAGTAGTAGTAGTTGTTGT TGCTATTTAA 24693 97 7.67e-09 CGGTAGAGGA AGCAGAGGTGGCCGTGGTGGT TTCTTCCTTT 270071 301 8.54e-09 AGTTCAGTGA TGAAGAAGGGTTTGTGGTTGT GTTTTGGTTG 29496 31 1.05e-08 TGCATCGAGG TGAAGGAGTGGTGGTGGAGGA TGGACCCTCC 5388 461 5.65e-08 GAGGAGATAA AGACGACGTGGTGTTGTTGGT TCACCCACAA 5743 387 6.14e-08 TCTTTGTGGA AGAAGTAGGGGCGATTGTTGA GGGTGCGAGA 264332 69 6.69e-08 GAGCCTGAGG AGAAGTAGTAGTAGTGAGGGG GGAATGGTTG 9695 305 1.00e-07 GTTCATCGTT TGATGTTGGGGTCGTCGTGGG TGGGTAGGTC 23937 10 1.27e-07 TCGAAGCGT TCAACTCGTGGTAGTCGTTGT CGTCGTATTT 22513 75 1.72e-07 GCGTCCACGT TGATGCGGAGGCTGTGGTCGT CGTCACTGTA 21994 82 6.24e-07 TAGGCTGCGG AGTAGCAGTGGTATTGTTCTT CGAATTTTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7880 1.1e-09 436_[+1]_43 24693 7.7e-09 96_[+1]_383 270071 8.5e-09 300_[+1]_179 29496 1e-08 30_[+1]_449 5388 5.6e-08 460_[+1]_19 5743 6.1e-08 386_[+1]_93 264332 6.7e-08 68_[+1]_411 9695 1e-07 304_[+1]_175 23937 1.3e-07 9_[+1]_470 22513 1.7e-07 74_[+1]_405 21994 6.2e-07 81_[+1]_398 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=11 7880 ( 437) AGAAGTAGTAGTAGTTGTTGT 1 24693 ( 97) AGCAGAGGTGGCCGTGGTGGT 1 270071 ( 301) TGAAGAAGGGTTTGTGGTTGT 1 29496 ( 31) TGAAGGAGTGGTGGTGGAGGA 1 5388 ( 461) AGACGACGTGGTGTTGTTGGT 1 5743 ( 387) AGAAGTAGGGGCGATTGTTGA 1 264332 ( 69) AGAAGTAGTAGTAGTGAGGGG 1 9695 ( 305) TGATGTTGGGGTCGTCGTGGG 1 23937 ( 10) TCAACTCGTGGTAGTCGTTGT 1 22513 ( 75) TGATGCGGAGGCTGTGGTCGT 1 21994 ( 82) AGTAGCAGTGGTATTGTTCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7680 bayes= 9.80094 E= 1.1e-004 112 -1010 -1010 70 -1010 -133 193 -1010 170 -133 -1010 -162 153 -133 -1010 -63 -1010 -133 193 -1010 12 -33 -139 70 112 -33 -39 -162 -1010 -1010 206 -1010 -146 -1010 19 118 -46 -1010 177 -1010 -1010 -1010 193 -162 -1010 25 -1010 137 53 -33 19 -63 -146 -1010 160 -63 -1010 -1010 -1010 183 -1010 -33 141 -63 -146 -1010 160 -63 -146 -1010 -139 154 -1010 -33 93 37 -1010 -1010 193 -162 -46 -1010 -39 118 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 11 E= 1.1e-004 0.545455 0.000000 0.000000 0.454545 0.000000 0.090909 0.909091 0.000000 0.818182 0.090909 0.000000 0.090909 0.727273 0.090909 0.000000 0.181818 0.000000 0.090909 0.909091 0.000000 0.272727 0.181818 0.090909 0.454545 0.545455 0.181818 0.181818 0.090909 0.000000 0.000000 1.000000 0.000000 0.090909 0.000000 0.272727 0.636364 0.181818 0.000000 0.818182 0.000000 0.000000 0.000000 0.909091 0.090909 0.000000 0.272727 0.000000 0.727273 0.363636 0.181818 0.272727 0.181818 0.090909 0.000000 0.727273 0.181818 0.000000 0.000000 0.000000 1.000000 0.000000 0.181818 0.636364 0.181818 0.090909 0.000000 0.727273 0.181818 0.090909 0.000000 0.090909 0.818182 0.000000 0.181818 0.454545 0.363636 0.000000 0.000000 0.909091 0.090909 0.181818 0.000000 0.181818 0.636364 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT]GAAG[TA]AG[TG]GG[TC][AG]GTGGT[GT]GT -------------------------------------------------------------------------------- Time 2.77 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 7 llr = 119 E-value = 2.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 319:::::4::411941:1:1 pos.-specific C 66:4aa:939:3191:74669 probability G 13:::::1:1:::::::133: matrix T ::16::a:3:a37::614:1: bits 2.1 ** 1.9 *** * 1.7 *** * 1.5 **** ** ** * Relative 1.3 * **** ** ** * Entropy 1.1 ****** ** ** * (24.6 bits) 0.8 ****** ** ***** * 0.6 ******** ** ********* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CCATCCTCACTATCATCCCCC consensus AG C C C A TGG sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 21994 447 2.31e-11 GTAGGCTTGA CCACCCTCACTCTCATCTGCC TTCATCACCG 270071 472 2.42e-10 CTCCCCCCTC CCATCCTCCCTAACATCCCGC GCTCGTCC 1172 436 2.74e-09 CTTCTCTTCG CCACCCTCTCTCTCCACCACC ACCTGATACC 9695 478 2.22e-08 GCGTCTGCTA GGATCCTCACTATCATACGTC AC 264332 428 3.33e-08 ACGATGATGT ACATCCTGTCTACCAACTCCA ACTATCCGTT 269844 198 4.04e-08 GTAAACAGAA CGTCCCTCACTTTCATTGCGC TTCTTTATGC 1471 449 4.57e-08 AAACATCTCC AAATCCTCCGTTTAAACTCCC ACAACACATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21994 2.3e-11 446_[+2]_33 270071 2.4e-10 471_[+2]_8 1172 2.7e-09 435_[+2]_44 9695 2.2e-08 477_[+2]_2 264332 3.3e-08 427_[+2]_52 269844 4e-08 197_[+2]_282 1471 4.6e-08 448_[+2]_31 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=7 21994 ( 447) CCACCCTCACTCTCATCTGCC 1 270071 ( 472) CCATCCTCCCTAACATCCCGC 1 1172 ( 436) CCACCCTCTCTCTCCACCACC 1 9695 ( 478) GGATCCTCACTATCATACGTC 1 264332 ( 428) ACATCCTGTCTACCAACTCCA 1 269844 ( 198) CGTCCCTCACTTTCATTGCGC 1 1471 ( 449) AAATCCTCCGTTTAAACTCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7680 bayes= 11.3214 E= 2.3e+000 19 132 -74 -945 -81 132 26 -945 177 -945 -945 -97 -945 90 -945 102 -945 212 -945 -945 -945 212 -945 -945 -945 -945 -945 183 -945 190 -74 -945 77 32 -945 3 -945 190 -74 -945 -945 -945 -945 183 77 32 -945 3 -81 -68 -945 135 -81 190 -945 -945 177 -68 -945 -945 77 -945 -945 102 -81 164 -945 -97 -945 90 -74 61 -81 132 26 -945 -945 132 26 -97 -81 190 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 2.3e+000 0.285714 0.571429 0.142857 0.000000 0.142857 0.571429 0.285714 0.000000 0.857143 0.000000 0.000000 0.142857 0.000000 0.428571 0.000000 0.571429 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 0.857143 0.142857 0.000000 0.428571 0.285714 0.000000 0.285714 0.000000 0.857143 0.142857 0.000000 0.000000 0.000000 0.000000 1.000000 0.428571 0.285714 0.000000 0.285714 0.142857 0.142857 0.000000 0.714286 0.142857 0.857143 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.428571 0.000000 0.000000 0.571429 0.142857 0.714286 0.000000 0.142857 0.000000 0.428571 0.142857 0.428571 0.142857 0.571429 0.285714 0.000000 0.000000 0.571429 0.285714 0.142857 0.142857 0.857143 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CA][CG]A[TC]CCTC[ACT]CT[ACT]TCA[TA]C[CT][CG][CG]C -------------------------------------------------------------------------------- Time 5.49 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 15 llr = 144 E-value = 3.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 193:52:51:55 pos.-specific C 9:3a:38:3a:3 probability G ::::5::5::5: matrix T :13::52:6::2 bits 2.1 * * 1.9 * * 1.7 * * * 1.5 ** * * Relative 1.3 ** * * * Entropy 1.1 ** ** ** ** (13.8 bits) 0.8 ** ** ** ** 0.6 ** ** ***** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CAACATCGTCAA consensus C GCTAC GC sequence T A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 24693 358 1.89e-06 AGTGGTGAAT CATCATCGTCGA CGTACTTCAA 269844 274 3.31e-06 ATGAAAGCAT CATCACCATCAA ACCACTACAA 21994 470 3.31e-06 CATCTGCCTT CATCACCGTCAC GAGCGCACCG 29496 482 4.85e-06 GCCAGCTCTC CACCGCCGCCAA AGAATGG 264610 483 5.57e-06 TCGATTCGAT CACCATCACCGA TCACCG 1471 480 7.76e-06 ACAACACATC CACCGTCACCAC TTCACCATA 270071 208 9.00e-06 AAACAACAGG CAACGTCGTCAT CATGCCGGTG 7880 307 1.11e-05 GGAAGGAGCA CAACATCATCGT ATCTTACCTC 264332 221 1.87e-05 TATGTCTGCT CACCGCCGACGC AGTTCTCTTC 1172 206 4.16e-05 GGCCCCTCAG CAACGATATCGA TCGTTGCGTC 5388 411 4.76e-05 CGACACGAGA CTACGACGTCGA CGTCGATACC 23937 427 4.76e-05 ATCGGAAGAA CATCATTGTCGT TCACAAGAGA 11797 208 5.38e-05 ACATCAATCC AATCGTCGTCAA TCATCATGAA 9695 45 6.37e-05 GAGTAGGAAG CAACAATACCAC TCGCATCTGG 22513 121 8.26e-05 CTCCAATGTG CTCCACCAACAC GTTCGCATCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24693 1.9e-06 357_[+3]_131 269844 3.3e-06 273_[+3]_215 21994 3.3e-06 469_[+3]_19 29496 4.8e-06 481_[+3]_7 264610 5.6e-06 482_[+3]_6 1471 7.8e-06 479_[+3]_9 270071 9e-06 207_[+3]_281 7880 1.1e-05 306_[+3]_182 264332 1.9e-05 220_[+3]_268 1172 4.2e-05 205_[+3]_283 5388 4.8e-05 410_[+3]_78 23937 4.8e-05 426_[+3]_62 11797 5.4e-05 207_[+3]_281 9695 6.4e-05 44_[+3]_444 22513 8.3e-05 120_[+3]_368 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=15 24693 ( 358) CATCATCGTCGA 1 269844 ( 274) CATCACCATCAA 1 21994 ( 470) CATCACCGTCAC 1 29496 ( 482) CACCGCCGCCAA 1 264610 ( 483) CACCATCACCGA 1 1471 ( 480) CACCGTCACCAC 1 270071 ( 208) CAACGTCGTCAT 1 7880 ( 307) CAACATCATCGT 1 264332 ( 221) CACCGCCGACGC 1 1172 ( 206) CAACGATATCGA 1 5388 ( 411) CTACGACGTCGA 1 23937 ( 427) CATCATTGTCGT 1 11797 ( 208) AATCGTCGTCAA 1 9695 ( 45) CAACAATACCAC 1 22513 ( 121) CTCCACCAACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7824 bayes= 10.3003 E= 3.9e+000 -191 202 -1055 -1055 179 -1055 -1055 -107 41 54 -1055 25 -1055 212 -1055 -1055 109 -1055 96 -1055 -33 54 -1055 73 -1055 180 -1055 -49 89 -1055 116 -1055 -91 22 -1055 110 -1055 212 -1055 -1055 109 -1055 96 -1055 89 54 -1055 -49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 15 E= 3.9e+000 0.066667 0.933333 0.000000 0.000000 0.866667 0.000000 0.000000 0.133333 0.333333 0.333333 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.533333 0.000000 0.466667 0.000000 0.200000 0.333333 0.000000 0.466667 0.000000 0.800000 0.000000 0.200000 0.466667 0.000000 0.533333 0.000000 0.133333 0.266667 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 0.533333 0.000000 0.466667 0.000000 0.466667 0.333333 0.000000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CA[ACT]C[AG][TCA][CT][GA][TC]C[AG][ACT] -------------------------------------------------------------------------------- Time 8.08 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1172 2.96e-06 205_[+3(4.16e-05)]_218_\ [+2(2.74e-09)]_44 11797 4.73e-02 207_[+3(5.38e-05)]_281 1471 2.83e-06 448_[+2(4.57e-08)]_10_\ [+3(7.76e-06)]_9 21994 3.09e-12 81_[+1(6.24e-07)]_117_\ [+1(2.97e-05)]_206_[+2(2.31e-11)]_2_[+3(3.31e-06)]_19 22513 5.28e-05 74_[+1(1.72e-07)]_25_[+3(8.26e-05)]_\ 368 23937 1.33e-04 9_[+1(1.27e-07)]_19_[+1(3.74e-05)]_\ 356_[+3(4.76e-05)]_62 24693 6.25e-07 96_[+1(7.67e-09)]_240_\ [+3(1.89e-06)]_131 264332 1.72e-09 68_[+1(6.69e-08)]_131_\ [+3(1.87e-05)]_195_[+2(3.33e-08)]_52 264610 8.96e-03 482_[+3(5.57e-06)]_6 269844 1.23e-06 197_[+2(4.04e-08)]_55_\ [+3(3.31e-06)]_215 270071 1.27e-12 207_[+3(9.00e-06)]_81_\ [+1(8.54e-09)]_150_[+2(2.42e-10)]_8 29496 6.79e-07 30_[+1(1.05e-08)]_282_\ [+3(6.70e-05)]_136_[+3(4.85e-06)]_7 5388 1.87e-05 410_[+3(4.76e-05)]_38_\ [+1(5.65e-08)]_19 5743 1.37e-03 89_[+1(9.83e-05)]_276_\ [+1(6.14e-08)]_93 7880 3.96e-07 173_[+1(2.20e-05)]_112_\ [+3(1.11e-05)]_118_[+1(1.05e-09)]_43 9695 5.29e-09 44_[+3(6.37e-05)]_248_\ [+1(1.00e-07)]_152_[+2(2.22e-08)]_2 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************