******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.1.1 (Release date: Wed Jan 29 15:00:42 2020 -0800) For further information on how to interpret please access http://meme-suite.org/. To get a copy of the MEME software please access 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 ******************************************************************************** PRIMARY SEQUENCES= upstream.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Gene_1 1.0000 293 Gene_2 1.0000 100 Gene_3 1.0000 100 Gene_4 1.0000 100 Gene_5 1.0000 100 Gene_6 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 upstream.fasta -dna -oc . -nostatus -time 18000 -mod zoops -nmotifs 3 -minw 6 -maxw 50 -objfun classic -markov_order 0 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= 50 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= 793 N= 6 sample: seed= 0 hsfrac= 0 searchsize= 793 norand= no csites= 1000 Letter frequencies in dataset: A 0.269 C 0.175 G 0.214 T 0.342 Background letter frequencies (from file dataset with add-one prior applied): A 0.269 C 0.175 G 0.214 T 0.342 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF RATTCAAC MEME-1 width = 8 sites = 6 llr = 58 E-value = 5.2e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif RATTCAAC MEME-1 Description -------------------------------------------------------------------------------- Simplified A 78:::aa: pos.-specific C :2:2a::a probability G 3::::::: matrix T ::a8:::: bits 2.5 * * 2.3 * * 2.0 **** 1.8 **** Relative 1.5 * **** Entropy 1.3 ** **** (13.9 bits) 1.0 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AATTCAAC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RATTCAAC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- Gene_5 58 1.88e-05 CTTATATGCG AATTCAAC CCTTGACATC Gene_2 90 1.88e-05 CCACTTGGTA AATTCAAC CAA Gene_4 84 3.37e-05 GTTTTGAGGA GATTCAAC TAGACGAAT Gene_1 62 3.37e-05 TTGTCTACTC GATTCAAC TAAACGAAAT Gene_6 40 4.33e-05 TGCTGCTGCG AATCCAAC AGAGGTTGTA Gene_3 59 5.55e-05 GTGGAACTAA ACTTCAAC ATTACGAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RATTCAAC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Gene_5 1.9e-05 57_[+1]_35 Gene_2 1.9e-05 89_[+1]_3 Gene_4 3.4e-05 83_[+1]_9 Gene_1 3.4e-05 61_[+1]_224 Gene_6 4.3e-05 39_[+1]_53 Gene_3 5.5e-05 58_[+1]_34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RATTCAAC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RATTCAAC width=8 seqs=6 Gene_5 ( 58) AATTCAAC 1 Gene_2 ( 90) AATTCAAC 1 Gene_4 ( 84) GATTCAAC 1 Gene_1 ( 62) GATTCAAC 1 Gene_6 ( 40) AATCCAAC 1 Gene_3 ( 59) ACTTCAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RATTCAAC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 751 bayes= 7.40669 E= 5.2e-003 131 -923 64 -923 163 -7 -923 -923 -923 -923 -923 155 -923 -7 -923 128 -923 251 -923 -923 189 -923 -923 -923 189 -923 -923 -923 -923 251 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RATTCAAC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 5.2e-003 0.666667 0.000000 0.333333 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.000000 0.833333 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RATTCAAC MEME-1 regular expression -------------------------------------------------------------------------------- [AG]ATTCAAC -------------------------------------------------------------------------------- Time 0.20 secs. ******************************************************************************** ******************************************************************************** MOTIF ARGTTGT MEME-2 width = 7 sites = 6 llr = 47 E-value = 1.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif ARGTTGT MEME-2 Description -------------------------------------------------------------------------------- Simplified A a3::::: pos.-specific C :2::2:: probability G :5a::a: matrix T :::a8:a bits 2.5 2.3 * * 2.0 * * * 1.8 * * * Relative 1.5 * ** ** Entropy 1.3 * ** ** (11.2 bits) 1.0 * ***** 0.8 ******* 0.5 ******* 0.3 ******* 0.0 ------- Multilevel AGGTTGT consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGTTGT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------- Gene_6 50 1.05e-04 AATCCAACAG AGGTTGT AACAGATAGT Gene_3 38 1.05e-04 CTTGTTTCTC AGGTTGT TGTCGTGGAA Gene_1 242 1.05e-04 TTTTGTCTGC AGGTTGT GTGGAAAGTC Gene_2 36 2.38e-04 GAAAAATGGT AAGTTGT TGATTAGAAA Gene_5 3 3.24e-04 TA ACGTTGT TTATAAGCCT Gene_4 50 4.46e-04 TCCAGTTGTC AAGTCGT TGGTGTTACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGTTGT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Gene_6 0.00011 49_[+2]_44 Gene_3 0.00011 37_[+2]_56 Gene_1 0.00011 241_[+2]_45 Gene_2 0.00024 35_[+2]_58 Gene_5 0.00032 2_[+2]_91 Gene_4 0.00045 49_[+2]_44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGTTGT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ARGTTGT width=7 seqs=6 Gene_6 ( 50) AGGTTGT 1 Gene_3 ( 38) AGGTTGT 1 Gene_1 ( 242) AGGTTGT 1 Gene_2 ( 36) AAGTTGT 1 Gene_5 ( 3) ACGTTGT 1 Gene_4 ( 50) AAGTCGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGTTGT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 757 bayes= 7.41824 E= 1.4e+001 189 -923 -923 -923 31 -7 122 -923 -923 -923 222 -923 -923 -923 -923 155 -923 -7 -923 128 -923 -923 222 -923 -923 -923 -923 155 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGTTGT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 6 E= 1.4e+001 1.000000 0.000000 0.000000 0.000000 0.333333 0.166667 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGTTGT MEME-2 regular expression -------------------------------------------------------------------------------- A[GA]GTTGT -------------------------------------------------------------------------------- Time 0.37 secs. ******************************************************************************** ******************************************************************************** MOTIF AAWMGAAA MEME-3 width = 8 sites = 6 llr = 47 E-value = 8.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAWMGAAA MEME-3 Description -------------------------------------------------------------------------------- Simplified A a755:aa8 pos.-specific C ::25:::: probability G :2::a::: matrix T :23::::2 bits 2.5 2.3 * 2.0 * *** 1.8 * *** Relative 1.5 * *** Entropy 1.3 * ***** (11.4 bits) 1.0 * ***** 0.8 ** ***** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AAAAGAAA consensus TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWMGAAA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- Gene_5 93 1.42e-05 ATTCAAGTAT AAACGAAA Gene_1 71 1.42e-05 CGATTCAACT AAACGAAA TTTTGTCCTT Gene_6 90 1.05e-04 ATTTAGTCTA AACAGAAA CTT Gene_3 77 1.05e-04 ATTACGAACC AATAGAAA AGGTTCATGT Gene_2 45 4.03e-04 TAAGTTGTTG ATTAGAAA TAATGGTGTT Gene_4 93 4.71e-04 AGATTCAACT AGACGAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWMGAAA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Gene_5 1.4e-05 92_[+3] Gene_1 1.4e-05 70_[+3]_215 Gene_6 0.00011 89_[+3]_3 Gene_3 0.00011 76_[+3]_16 Gene_2 0.0004 44_[+3]_48 Gene_4 0.00047 92_[+3] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWMGAAA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAWMGAAA width=8 seqs=6 Gene_5 ( 93) AAACGAAA 1 Gene_1 ( 71) AAACGAAA 1 Gene_6 ( 90) AACAGAAA 1 Gene_3 ( 77) AATAGAAA 1 Gene_2 ( 45) ATTAGAAA 1 Gene_4 ( 93) AGACGAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWMGAAA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 751 bayes= 7.40669 E= 8.2e+001 189 -923 -923 -923 131 -923 -36 -103 90 -7 -923 -4 90 151 -923 -923 -923 -923 222 -923 189 -923 -923 -923 189 -923 -923 -923 163 -923 -923 -103 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWMGAAA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 8.2e+001 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.166667 0.166667 0.500000 0.166667 0.000000 0.333333 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWMGAAA MEME-3 regular expression -------------------------------------------------------------------------------- AA[AT][AC]GAAA -------------------------------------------------------------------------------- Time 0.51 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Gene_1 1.25e-04 61_[+1(3.37e-05)]_1_[+3(1.42e-05)]_\ 215 Gene_2 1.49e-04 89_[+1(1.88e-05)]_3 Gene_3 5.98e-05 58_[+1(5.55e-05)]_34 Gene_4 4.76e-04 83_[+1(3.37e-05)]_9 Gene_5 1.06e-05 57_[+1(1.88e-05)]_27_[+3(1.42e-05)] Gene_6 4.81e-05 39_[+1(4.33e-05)]_53 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: ip-172-31-6-99 ********************************************************************************