******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.0 (Release date: Tue Mar 9 17:38:20 2021 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://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 ******************************************************************************** PRIMARY SEQUENCES= common/INO_up800.s CONTROL SEQUENCES= --none-- 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/meme11 -mod zoops -dna -revcomp -bfile common/yeast.nc.6.freq -nmotifs 2 -objfun classic -minw 8 -nostatus -mpi model: mod= zoops nmotifs= 2 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + - width: minw= 8 maxw= 50 nsites: minsites= 2 maxsites= 7 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 5600 N= 7 sample: seed= 0 hsfrac= 0 searchsize= 5600 norand= no csites= 1000 Letter frequencies in dataset: A 0.304 C 0.196 G 0.196 T 0.304 Background letter frequencies (from file common/yeast.nc.6.freq): A 0.324 C 0.176 G 0.176 T 0.324 Background model order: 5 ******************************************************************************** ******************************************************************************** MOTIF GSKGCATGTGAAA MEME-1 width = 13 sites = 7 llr = 101 E-value = 1.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GSKGCATGTGAAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 1:1::a::1:9a7 pos.-specific C :4:3a:::::::: probability G 9467:::a:a1:3 matrix T :13:::a:9:::: bits 2.5 * * * 2.3 * * * 2.0 * * * 1.8 * ** * * Relative 1.5 * ***** * * Entropy 1.3 * ***** *** (20.7 bits) 1.0 ** ********** 0.8 ************* 0.5 ************* 0.3 ************* 0.0 ------------- Multilevel GCGGCATGTGAAA consensus GTC G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSKGCATGTGAAA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------- INO1 + 620 1.21e-08 GCGGCTAAAT GCGGCATGTGAAA AGTATTGTCT FAS1 - 94 1.87e-08 GCTTGGCTGG GCGGCATGTGAAG TTTTTGGCCG ACC1 - 82 6.62e-08 GCGCGCGGCC GGGCCATGTGAAG ATTTTAACGG CHO2 - 353 1.05e-07 AATAATGAAT GCGGCATGAGAAA AGTGTGGCAA CHO1 - 639 1.69e-07 TCTTTAGATG GGTCCATGTGAAA GCTCAAAGGC FAS2 - 566 5.62e-07 GGCGAATGAG GTAGCATGTGAAA ACGCGGGAGA OPI3 + 585 1.08e-06 TGTCAATGAG AGTGCATGTGGAA AGTTGCACCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSKGCATGTGAAA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- INO1 1.2e-08 619_[+1]_168 FAS1 1.9e-08 93_[-1]_694 ACC1 6.6e-08 81_[-1]_706 CHO2 1.1e-07 352_[-1]_435 CHO1 1.7e-07 638_[-1]_149 FAS2 5.6e-07 565_[-1]_222 OPI3 1.1e-06 584_[+1]_203 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSKGCATGTGAAA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GSKGCATGTGAAA width=13 seqs=7 INO1 ( 620) GCGGCATGTGAAA 1 FAS1 ( 94) GCGGCATGTGAAG 1 ACC1 ( 82) GGGCCATGTGAAG 1 CHO2 ( 353) GCGGCATGAGAAA 1 CHO1 ( 639) GGTCCATGTGAAA 1 FAS2 ( 566) GTAGCATGTGAAA 1 OPI3 ( 585) AGTGCATGTGGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSKGCATGTGAAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 5516 bayes= 9.62022 E= 1.9e-001 -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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSKGCATGTGAAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 7 E= 1.9e-001 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSKGCATGTGAAA MEME-1 regular expression -------------------------------------------------------------------------------- G[CG][GT][GC]CATGTGAA[AG] -------------------------------------------------------------------------------- Time 0.43 secs. ******************************************************************************** ******************************************************************************** MOTIF TTGACWCYTGCYCWG MEME-2 width = 15 sites = 7 llr = 99 E-value = 5.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTGACWCYTGCYCWG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::9:63::11:13: pos.-specific C ::3:a:76:19471: probability G ::7::1::17::11a matrix T aa:1:3:49::6:4: bits 2.5 * * 2.3 * * 2.0 * * 1.8 * * * * Relative 1.5 *** * * * * Entropy 1.3 *** * ***** * * (20.3 bits) 1.0 ***** ******* * 0.8 ***** ******* * 0.5 ***** ******* * 0.3 ************* * 0.0 --------------- Multilevel TTGACACCTGCTCTG consensus C TAT C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGACWCYTGCYCWG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------- CHO2 + 104 7.20e-10 AGTTCTTACT TTGACACCTGCCCAG ATCCAAAGTT OPI3 - 566 2.56e-08 TGCACTCTCA TTGACACCTACCCTG GTCATCAAGG ACC1 - 585 1.59e-07 GGGAAGTTTC TTGTCTCTTGCTCTG AATCTGAATT CHO1 + 30 2.05e-07 ACAATATTAT TTGACACTTGATCAG CAGCAAAATA FAS1 + 54 3.85e-07 GCAGGCACGG TTCACTACTCCCCTG GCCTCCAACA FAS2 - 272 5.11e-07 TTAACGCGTT TTGACAACGGCTGGG ACAACAACGA INO1 + 214 8.01e-07 CCAGCAATCA TTCACGCTTGCTACG TTGTATATGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGACWCYTGCYCWG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CHO2 7.2e-10 103_[+2]_682 OPI3 2.6e-08 565_[-2]_220 ACC1 1.6e-07 584_[-2]_201 CHO1 2e-07 29_[+2]_756 FAS1 3.8e-07 53_[+2]_732 FAS2 5.1e-07 271_[-2]_514 INO1 8e-07 213_[+2]_572 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGACWCYTGCYCWG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTGACWCYTGCYCWG width=15 seqs=7 CHO2 ( 104) TTGACACCTGCCCAG 1 OPI3 ( 566) TTGACACCTACCCTG 1 ACC1 ( 585) TTGTCTCTTGCTCTG 1 CHO1 ( 30) TTGACACTTGATCAG 1 FAS1 ( 54) TTCACTACTCCCCTG 1 FAS2 ( 272) TTGACAACGGCTGGG 1 INO1 ( 214) TTCACGCTTGCTACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGACWCYTGCYCWG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 5502 bayes= 9.61655 E= 5.4e+001 -945 -945 -945 162 -945 -945 -945 162 -945 70 202 -945 140 -945 -945 -118 -945 251 -945 -945 82 -945 -30 -18 -18 202 -945 -945 -945 170 -945 40 -945 -945 -30 140 -118 -30 202 -945 -118 229 -945 -945 -945 129 -945 82 -118 202 -30 -945 -18 -30 -30 40 -945 -945 251 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGACWCYTGCYCWG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 7 E= 5.4e+001 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.285714 0.714286 0.000000 0.857143 0.000000 0.000000 0.142857 0.000000 1.000000 0.000000 0.000000 0.571429 0.000000 0.142857 0.285714 0.285714 0.714286 0.000000 0.000000 0.000000 0.571429 0.000000 0.428571 0.000000 0.000000 0.142857 0.857143 0.142857 0.142857 0.714286 0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 0.428571 0.000000 0.571429 0.142857 0.714286 0.142857 0.000000 0.285714 0.142857 0.142857 0.428571 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGACWCYTGCYCWG MEME-2 regular expression -------------------------------------------------------------------------------- TT[GC]AC[AT][CA][CT]TGC[TC]C[TA]G -------------------------------------------------------------------------------- Time 0.82 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CHO1 1.48e-06 29_[+2(2.05e-07)]_594_\ [-1(1.69e-07)]_149 CHO2 4.39e-09 103_[+2(7.20e-10)]_234_\ [-1(1.05e-07)]_435 FAS1 3.35e-07 53_[+2(3.85e-07)]_25_[-1(1.87e-08)]_\ 694 FAS2 1.08e-05 271_[-2(5.11e-07)]_279_\ [-1(5.62e-07)]_222 ACC1 4.83e-07 81_[-1(6.62e-08)]_490_\ [-2(1.59e-07)]_201 INO1 4.45e-07 213_[+2(8.01e-07)]_342_\ [+1(1.52e-05)]_36_[+1(1.21e-08)]_53_[-1(5.60e-06)]_102 OPI3 1.20e-06 314_[-1(3.24e-05)]_238_\ [-2(2.56e-08)]_4_[+1(1.08e-06)]_203 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************