******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.5.2 (Release date: Sun Jan 29 10:33:12 2023 -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= GSM4240099_JH4_Rad21degron_IAA_a_rep1_meme-chip/seqs-centered CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr12:113434675-11343507 1.0000 100 chr12:113457333-11345773 1.0000 100 chr12:113489363-11348976 1.0000 100 chr12:113451873-11345227 1.0000 100 chr12:113476311-11347671 1.0000 100 chr12:113449198-11344959 1.0000 100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme GSM4240099_JH4_Rad21degron_IAA_a_rep1_meme-chip/seqs-centered -oc GSM4240099_JH4_Rad21degron_IAA_a_rep1_meme-chip/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 15 -bfile GSM4240099_JH4_Rad21degron_IAA_a_rep1_meme-chip/background -dna -searchsize 100000 -revcomp -nostatus -mpi model: mod= zoops nmotifs= 3 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + - width: minw= 6 maxw= 15 nsites: minsites= 2 maxsites= 6 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= 600 N= 6 sample: seed= 0 hsfrac= 0 searchsize= 600 norand= no csites= 1000 Letter frequencies in dataset: A 0.273 C 0.227 G 0.227 T 0.273 Background letter frequencies (from file GSM4240099_JH4_Rad21degron_IAA_a_rep1_meme-chip/background): A 0.275 C 0.225 G 0.225 T 0.275 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF GCWTSAG MEME-1 width = 7 sites = 6 llr = 49 E-value = 3.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCWTSAG MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::7::8: pos.-specific C :a::7:: probability G a:::3:a matrix T ::3a:2: bits 2.2 ** * 1.9 ** * * 1.7 ** * * 1.5 ** * * Relative 1.3 ** **** Entropy 1.1 ** **** (11.7 bits) 0.9 ******* 0.6 ******* 0.4 ******* 0.2 ******* 0.0 ------- Multilevel GCATCAG consensus T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWTSAG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------- chr12:113449198-11344959 + 63 5.33e-05 AATAGAGATT GCATCAG TATGGCTAGA chr12:113457333-11345773 + 40 5.33e-05 GTTCTTCCTA GCATCAG GACTGAGGCC chr12:113434675-11343507 + 78 1.07e-04 ggcttttttg gcttcag attttttttc chr12:113451873-11345227 - 89 1.60e-04 TCTGG GCATGAG TGTGCCCGAT chr12:113489363-11348976 + 71 1.60e-04 CTGACCTGGG GCATGAG GCTAGTGGAA chr12:113476311-11347671 + 40 3.20e-04 TCTGCTTGCT GCTTCTG AGCTCTACCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWTSAG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:113449198-11344959 5.3e-05 62_[+1]_31 chr12:113457333-11345773 5.3e-05 39_[+1]_54 chr12:113434675-11343507 0.00011 77_[+1]_16 chr12:113451873-11345227 0.00016 88_[-1]_5 chr12:113489363-11348976 0.00016 70_[+1]_23 chr12:113476311-11347671 0.00032 39_[+1]_54 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWTSAG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCWTSAG width=7 seqs=6 chr12:113449198-11344959 ( 63) GCATCAG 1 chr12:113457333-11345773 ( 40) GCATCAG 1 chr12:113434675-11343507 ( 78) GCTTCAG 1 chr12:113451873-11345227 ( 89) GCATGAG 1 chr12:113489363-11348976 ( 71) GCATGAG 1 chr12:113476311-11347671 ( 40) GCTTCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWTSAG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 564 bayes= 6.53916 E= 3.0e+002 -923 -923 215 -923 -923 215 -923 -923 127 -923 -923 28 -923 -923 -923 186 -923 157 57 -923 160 -923 -923 -72 -923 -923 215 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWTSAG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 6 E= 3.0e+002 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.333333 0.000000 0.833333 0.000000 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWTSAG MEME-1 regular expression -------------------------------------------------------------------------------- GC[AT]T[CG]AG -------------------------------------------------------------------------------- Time 0.76 secs. ******************************************************************************** ******************************************************************************** MOTIF CAGAACTTGG MEME-2 width = 10 sites = 4 llr = 47 E-value = 3.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAGAACTTGG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :a:a8::::: pos.-specific C 8::::a:::3 probability G 3:a:::3:a8 matrix T ::::3:8a:: bits 2.2 * * * 1.9 *** * ** 1.7 *** * ** 1.5 *** * ** Relative 1.3 **** * *** Entropy 1.1 ********** (16.9 bits) 0.9 ********** 0.6 ********** 0.4 ********** 0.2 ********** 0.0 ---------- Multilevel CAGAACTTGG consensus G T G C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGAACTTGG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- chr12:113449198-11344959 + 81 9.07e-07 ATGGCTAGAC CAGAACTTGG GAATCTCAAT chr12:113476311-11347671 - 24 9.07e-07 AAGCAGCAAG CAGAACTTGG GCTAACAGAA chr12:113457333-11345773 - 64 6.60e-06 GAGAACCACA CAGAACGTGC TGCTAATGGC chr12:113434675-11343507 - 25 8.41e-06 CAAGTATCAT GAGATCTTGG CTGGGAGGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGAACTTGG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:113449198-11344959 9.1e-07 80_[+2]_10 chr12:113476311-11347671 9.1e-07 23_[-2]_67 chr12:113457333-11345773 6.6e-06 63_[-2]_27 chr12:113434675-11343507 8.4e-06 24_[-2]_66 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGAACTTGG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAGAACTTGG width=10 seqs=4 chr12:113449198-11344959 ( 81) CAGAACTTGG 1 chr12:113476311-11347671 ( 24) CAGAACTTGG 1 chr12:113457333-11345773 ( 64) CAGAACGTGC 1 chr12:113434675-11343507 ( 25) GAGATCTTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGAACTTGG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 546 bayes= 7.82337 E= 3.7e+002 -865 174 15 -865 186 -865 -865 -865 -865 -865 215 -865 186 -865 -865 -865 144 -865 -865 -14 -865 215 -865 -865 -865 -865 15 144 -865 -865 -865 186 -865 -865 215 -865 -865 15 174 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGAACTTGG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 4 E= 3.7e+002 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGAACTTGG MEME-2 regular expression -------------------------------------------------------------------------------- [CG]AGA[AT]C[TG]TG[GC] -------------------------------------------------------------------------------- Time 5.01 secs. ******************************************************************************** ******************************************************************************** MOTIF GKGGGSACTG MEME-3 width = 10 sites = 4 llr = 45 E-value = 1.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GKGGGSACTG MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::::8::: pos.-specific C ::::35:a:: probability G a5a8853::a matrix T :5:3::::a: bits 2.2 * * * * 1.9 * * *** 1.7 * * *** 1.5 * * *** Relative 1.3 * *** *** Entropy 1.1 ********** (16.4 bits) 0.9 ********** 0.6 ********** 0.4 ********** 0.2 ********** 0.0 ---------- Multilevel GGGGGCACTG consensus T TCGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKGGGSACTG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- chr12:113449198-11344959 + 7 9.93e-07 GTTGGT GGGGGCACTG GAGAGGCCAA chr12:113476311-11347671 - 85 3.02e-06 CAGGAG GGGGGGGCTG AAAGGCAGAC chr12:113489363-11348976 - 16 7.44e-06 TCCCTCTGCT GTGGCCACTG CCTGGTCTAG chr12:113451873-11345227 + 42 8.92e-06 AAGGCGATGA GTGTggactg gaaatgcatc -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKGGGSACTG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:113449198-11344959 9.9e-07 6_[+3]_84 chr12:113476311-11347671 3e-06 84_[-3]_6 chr12:113489363-11348976 7.4e-06 15_[-3]_75 chr12:113451873-11345227 8.9e-06 41_[+3]_49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKGGGSACTG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GKGGGSACTG width=10 seqs=4 chr12:113449198-11344959 ( 7) GGGGGCACTG 1 chr12:113476311-11347671 ( 85) GGGGGGGCTG 1 chr12:113489363-11348976 ( 16) GTGGCCACTG 1 chr12:113451873-11345227 ( 42) GTGTGGACTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKGGGSACTG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 546 bayes= 7.08215 E= 1.4e+003 -865 -865 215 -865 -865 -865 115 86 -865 -865 215 -865 -865 -865 174 -14 -865 15 174 -865 -865 115 115 -865 144 -865 15 -865 -865 215 -865 -865 -865 -865 -865 186 -865 -865 215 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKGGGSACTG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 4 E= 1.4e+003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.250000 0.750000 0.000000 0.000000 0.500000 0.500000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKGGGSACTG MEME-3 regular expression -------------------------------------------------------------------------------- G[GT]G[GT][GC][CG][AG]CTG -------------------------------------------------------------------------------- Time 5.86 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:113434675-11343507 1.95e-03 24_[-2(8.41e-06)]_66 chr12:113457333-11345773 7.40e-04 39_[+1(5.33e-05)]_17_[-2(6.60e-06)]_\ 27 chr12:113489363-11348976 1.05e-03 15_[-3(7.44e-06)]_75 chr12:113451873-11345227 2.80e-03 41_[+3(8.92e-06)]_49 chr12:113476311-11347671 1.07e-06 23_[-2(9.07e-07)]_51_[-3(3.02e-06)]_\ 6 chr12:113449198-11344959 7.84e-08 6_[+3(9.93e-07)]_46_[+1(5.33e-05)]_\ 11_[+2(9.07e-07)]_10 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: bnode001.sibcb.ac.cn ********************************************************************************