******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.11.3 (Release date: Fri Feb 19 13:23:06 2016 -0800) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org . 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-suite.org . ******************************************************************************** ******************************************************************************** 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= common/INO_up800.s ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ CHO1 1.0000 800 CHO2 1.0000 800 FAS1 1.0000 800 FAS2 1.0000 800 ACC1 1.0000 800 INO1 1.0000 800 OPI3 1.0000 800 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme common/INO_up800.s -oc results/meme8 -mod zoops -dna -revcomp -bfile common/yeast.nc.6.freq -x_branch -nmotifs 2 -minw 8 -nostatus model: mod= zoops nmotifs= 2 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 50 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 7 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 global: substring= yes branching= yes wbranch= no bfactor= 3 heapsize= 64 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 5600 N= 7 shuffle= -1 strands: + - sample: seed= 0 ctfrac= -1 maxwords= -1 Letter frequencies in dataset: A 0.304 C 0.196 G 0.196 T 0.304 Background letter frequencies (from common/yeast.nc.6.freq): A 0.324 C 0.176 G 0.176 T 0.324 ******************************************************************************** ******************************************************************************** MOTIF KGSKGCATGTGAAAABT MEME-1 width = 17 sites = 7 llr = 117 E-value = 2.6e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif KGSKGCATGTGAAAABT MEME-1 Description -------------------------------------------------------------------------------- Simplified A :1:1::a::1:9a77:: pos.-specific C 1:4:3a:::::::::3: probability G 69467:::a:a1:3141 matrix T 3:13:::a:9::::139 bits 2.5 * * * 2.3 * * * 2.0 * * * 1.8 * ** * * Relative 1.5 * ***** * * Entropy 1.3 * ***** *** * (24.1 bits) 1.0 ** ********** * 0.8 ************** ** 0.5 ***************** 0.3 ***************** 0.0 ----------------- Multilevel GGCGGCATGTGAAAAGT consensus T GTC G C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGSKGCATGTGAAAABT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----------------- INO1 + 619 4.64e-10 GGCGGCTAAA TGCGGCATGTGAAAAGT ATTGTCTATT FAS1 - 91 6.11e-09 TGCTTGGCTG GGCGGCATGTGAAGTTT TTGGCCGTCG CHO2 - 350 6.52e-09 GAATAATGAA TGCGGCATGAGAAAAGT GTGGCAATTG ACC1 - 79 1.20e-08 CGCGCGCGGC CGGGCCATGTGAAGATT TTAACGGGCG CHO1 - 636 1.20e-08 ATCTTTAGAT GGGTCCATGTGAAAGCT CAAAGGCGTG OPI3 + 584 3.84e-08 GTGTCAATGA GAGTGCATGTGGAAAGT TGCACCGGTT FAS2 - 563 5.67e-08 AGGCGAATGA GGTAGCATGTGAAAACG CGGGAGATAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGSKGCATGTGAAAABT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- INO1 4.6e-10 618_[+1]_165 FAS1 6.1e-09 90_[-1]_693 CHO2 6.5e-09 349_[-1]_434 ACC1 1.2e-08 78_[-1]_705 CHO1 1.2e-08 635_[-1]_148 OPI3 3.8e-08 583_[+1]_200 FAS2 5.7e-08 562_[-1]_221 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGSKGCATGTGAAAABT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF KGSKGCATGTGAAAABT width=17 seqs=7 INO1 ( 619) TGCGGCATGTGAAAAGT 1 FAS1 ( 91) GGCGGCATGTGAAGTTT 1 CHO2 ( 350) TGCGGCATGAGAAAAGT 1 ACC1 ( 79) CGGGCCATGTGAAGATT 1 CHO1 ( 636) GGGTCCATGTGAAAGCT 1 OPI3 ( 584) GAGTGCATGTGGAAAGT 1 FAS2 ( 563) GGTAGCATGTGAAAACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGSKGCATGTGAAAABT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 17 n= 5488 bayes= 9.61287 E= 2.6e-002 -945 -30 170 -18 -118 -945 229 -945 -945 129 129 -118 -118 -945 170 -18 -945 70 202 -945 -945 251 -945 -945 162 -945 -945 -945 -945 -945 -945 162 -945 -945 251 -945 -118 -945 -945 140 -945 -945 251 -945 140 -945 -30 -945 162 -945 -945 -945 114 -945 70 -945 114 -945 -30 -118 -945 70 129 -18 -945 -945 -30 140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGSKGCATGTGAAAABT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 17 nsites= 7 E= 2.6e-002 0.000000 0.142857 0.571429 0.285714 0.142857 0.000000 0.857143 0.000000 0.000000 0.428571 0.428571 0.142857 0.142857 0.000000 0.571429 0.285714 0.000000 0.285714 0.714286 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.000000 1.000000 0.000000 0.857143 0.000000 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.714286 0.000000 0.285714 0.000000 0.714286 0.000000 0.142857 0.142857 0.000000 0.285714 0.428571 0.285714 0.000000 0.000000 0.142857 0.857143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGSKGCATGTGAAAABT MEME-1 regular expression -------------------------------------------------------------------------------- [GT]G[CG][GT][GC]CATGTGAA[AG]A[GCT]T -------------------------------------------------------------------------------- Time 3.11 secs. ******************************************************************************** ******************************************************************************** MOTIF CAMGSSCNCATCRCYACTSTC MEME-2 width = 21 sites = 6 llr = 108 E-value = 8.3e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAMGSSCNCATCRCYACTSTC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :85:2223:7::7::8::::: pos.-specific C 8:32357382:8:852a2328 probability G 222853222:::322:::522 matrix T :::::::2:2a2::3::827: bits 2.5 * 2.3 * 2.0 * 1.8 * * * * * * * Relative 1.5 * * * ** * * * Entropy 1.3 * * * ** * * * (26.0 bits) 1.0 ** **** * **** **** * 0.8 ** **** * *********** 0.5 ******* ************* 0.3 ********************* 0.0 --------------------- Multilevel CAAGGCCACATCACCACTGTC consensus C CG C G T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAMGSSCNCATCRCYACTSTC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------------- FAS2 + 710 1.81e-11 GAAGGTTACA CAAGACCACATCACCACTGTC GTGCTTTTCT INO1 - 369 5.01e-10 TGTTGTCCAT CAAGGGCACATCGGCACCGGC CTCATCGTCT OPI3 - 504 8.36e-10 CGAATTATAC GGCGGCGCCATCACTACTGTC GTCCCACCTG ACC1 + 135 5.28e-09 AGTCGAAATT CAACCGCTCATTGCCACTCTC TCTACTGCTT CHO1 + 615 1.83e-08 TGAACGTTCA CACGGCACCCTCACGCCTTTG AGCTTTCACA FAS1 + 45 2.47e-08 ACACGAGGTG CAGGCACGGTTCACTACTCCC CTGGCCTCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAMGSSCNCATCRCYACTSTC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- FAS2 1.8e-11 709_[+2]_70 INO1 5e-10 368_[-2]_411 OPI3 8.4e-10 503_[-2]_276 ACC1 5.3e-09 134_[+2]_645 CHO1 1.8e-08 614_[+2]_165 FAS1 2.5e-08 44_[+2]_735 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAMGSSCNCATCRCYACTSTC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAMGSSCNCATCRCYACTSTC width=21 seqs=6 FAS2 ( 710) CAAGACCACATCACCACTGTC 1 INO1 ( 369) CAAGGGCACATCGGCACCGGC 1 OPI3 ( 504) GGCGGCGCCATCACTACTGTC 1 ACC1 ( 135) CAACCGCTCATTGCCACTCTC 1 CHO1 ( 615) CACGGCACCCTCACGCCTTTG 1 FAS1 ( 45) CAGGCACGGTTCACTACTCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAMGSSCNCATCRCYACTSTC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5460 bayes= 10.276 E= 8.3e+001 -923 224 -7 -923 136 -923 -7 -923 62 92 -7 -923 -923 -7 224 -923 -96 92 151 -923 -96 151 92 -923 -96 192 -7 -923 4 92 -7 -96 -923 224 -7 -923 104 -7 -923 -96 -923 -923 -923 162 -923 224 -923 -96 104 -923 92 -923 -923 224 -7 -923 -923 151 -7 4 136 -7 -923 -923 -923 251 -923 -923 -923 -7 -923 136 -923 92 151 -96 -923 -7 -7 104 -923 224 -7 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAMGSSCNCATCRCYACTSTC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 8.3e+001 0.000000 0.833333 0.166667 0.000000 0.833333 0.000000 0.166667 0.000000 0.500000 0.333333 0.166667 0.000000 0.000000 0.166667 0.833333 0.000000 0.166667 0.333333 0.500000 0.000000 0.166667 0.500000 0.333333 0.000000 0.166667 0.666667 0.166667 0.000000 0.333333 0.333333 0.166667 0.166667 0.000000 0.833333 0.166667 0.000000 0.666667 0.166667 0.000000 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.833333 0.000000 0.166667 0.666667 0.000000 0.333333 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.500000 0.166667 0.333333 0.833333 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.333333 0.500000 0.166667 0.000000 0.166667 0.166667 0.666667 0.000000 0.833333 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAMGSSCNCATCRCYACTSTC MEME-2 regular expression -------------------------------------------------------------------------------- CA[AC]G[GC][CG]C[AC]CATC[AG]C[CT]ACT[GC]TC -------------------------------------------------------------------------------- Time 6.21 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CHO1 1.20e-08 614_[+2(1.83e-08)]_[-1(1.20e-08)]_\ 148 CHO2 9.89e-05 349_[-1(6.52e-09)]_434 FAS1 8.38e-09 44_[+2(2.47e-08)]_25_[-1(6.11e-09)]_\ 16_[-2(5.76e-05)]_656 FAS2 6.93e-11 562_[-1(5.67e-08)]_130_\ [+2(1.81e-11)]_70 ACC1 3.64e-09 34_[+2(3.28e-05)]_[+2(7.06e-05)]_2_\ [-1(1.20e-08)]_39_[+2(5.28e-09)]_645 INO1 1.66e-11 239_[-2(8.16e-05)]_108_\ [-2(5.01e-10)]_159_[+1(9.62e-05)]_4_[+1(5.31e-05)]_32_[+1(4.64e-10)]_165 OPI3 1.90e-09 503_[-2(8.36e-10)]_59_\ [+1(3.84e-08)]_32_[-1(3.61e-05)]_151 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-iMac.rd.unr.edu ********************************************************************************