******************************************************************************** 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= all_upstream.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ NC_006577.2:106-205 1.0000 100 NC_006577.2:21673-21772 1.0000 100 NC_006577.2:22842-22941 1.0000 100 NC_006577.2:26951-27050 1.0000 100 NC_006577.2:27273-27372 1.0000 100 NC_006577.2:27533-27632 1.0000 100 NC_006577.2:28220-28319 1.0000 100 NC_006577.2:28242-28341 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 all_upstream.fasta -dna -oc . -nostatus -time 18000 -mod zoops -nmotifs 3 -minw 5 -maxw 50 -objfun classic -minsites 2 -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= 5 maxw= 50 nsites: minsites= 2 maxsites= 8 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= 800 N= 8 sample: seed= 0 hsfrac= 0 searchsize= 800 norand= no csites= 1000 Letter frequencies in dataset: A 0.273 C 0.155 G 0.174 T 0.399 Background letter frequencies (from file dataset with add-one prior applied): A 0.273 C 0.155 G 0.174 T 0.399 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AWSWSMTTAAATCTAAAC MEME-1 width = 18 sites = 5 llr = 102 E-value = 3.0e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif AWSWSMTTAAATCTAAAC MEME-1 Description -------------------------------------------------------------------------------- Simplified A a4:4:6::aaa:::aaa: pos.-specific C ::6:64::::::a::::a probability G ::4:4::::::::::::: matrix T :6:6::aa:::a:a:::: bits 2.7 * * 2.4 * * 2.2 * * 1.9 * *** * **** Relative 1.6 * * * *** * **** Entropy 1.3 * * ************** (29.5 bits) 1.1 * * ************** 0.8 * * ************** 0.5 ****************** 0.3 ****************** 0.0 ------------------ Multilevel ATCTCATTAAATCTAAAC consensus AGAGC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWSWSMTTAAATCTAAAC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ NC_006577.2:26951-27050 76 3.10e-10 CTCTTGTCAG ATCTCATTAAATCTAAAC TTTATTT NC_006577.2:22842-22941 83 3.10e-10 ATAACGATAA ATCTCATTAAATCTAAAC NC_006577.2:21673-21772 82 3.10e-10 TACTTGTTAG ATCTCATTAAATCTAAAC T NC_006577.2:28242-28341 54 1.15e-09 CTGCCTTGTT AAGAGCTTAAATCTAAAC TATTAGGATG NC_006577.2:28220-28319 76 1.15e-09 CTGCCTTGTT AAGAGCTTAAATCTAAAC TATTAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWSWSMTTAAATCTAAAC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- NC_006577.2:26951-27050 3.1e-10 75_[+1]_7 NC_006577.2:22842-22941 3.1e-10 82_[+1] NC_006577.2:21673-21772 3.1e-10 81_[+1]_1 NC_006577.2:28242-28341 1.1e-09 53_[+1]_29 NC_006577.2:28220-28319 1.1e-09 75_[+1]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWSWSMTTAAATCTAAAC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AWSWSMTTAAATCTAAAC width=18 seqs=5 NC_006577.2:26951-27050 ( 76) ATCTCATTAAATCTAAAC 1 NC_006577.2:22842-22941 ( 83) ATCTCATTAAATCTAAAC 1 NC_006577.2:21673-21772 ( 82) ATCTCATTAAATCTAAAC 1 NC_006577.2:28242-28341 ( 54) AAGAGCTTAAATCTAAAC 1 NC_006577.2:28220-28319 ( 76) AAGAGCTTAAATCTAAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWSWSMTTAAATCTAAAC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 664 bayes= 7.2955 E= 3.0e-010 187 -897 -897 -897 55 -897 -897 59 -897 195 120 -897 55 -897 -897 59 -897 195 120 -897 114 137 -897 -897 -897 -897 -897 132 -897 -897 -897 132 187 -897 -897 -897 187 -897 -897 -897 187 -897 -897 -897 -897 -897 -897 132 -897 269 -897 -897 -897 -897 -897 132 187 -897 -897 -897 187 -897 -897 -897 187 -897 -897 -897 -897 269 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWSWSMTTAAATCTAAAC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 5 E= 3.0e-010 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.600000 0.000000 0.600000 0.400000 0.000000 0.400000 0.000000 0.000000 0.600000 0.000000 0.600000 0.400000 0.000000 0.600000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 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 AWSWSMTTAAATCTAAAC MEME-1 regular expression -------------------------------------------------------------------------------- A[TA][CG][TA][CG][AC]TTAAATCTAAAC -------------------------------------------------------------------------------- Time 0.21 secs. ******************************************************************************** ******************************************************************************** MOTIF GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC MEME-2 width = 48 sites = 2 llr = 135 E-value = 7.6e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::aa::a::::::a::::::a::aaa:::a:::::a:::a:a::::: pos.-specific C :::::a:::a:::::aa::a:::::::aa::::::::::::::a::aa probability G aa::::::::a::::::a::::a::::::::a:aa:::aa:::::a:: matrix T ::a:::a:a::aaa::::a:a::a:::::a::a::a:a:::a::a::: bits 2.7 * * ** * ** * ** 2.4 ** * ** *** * * ** * ** ** * *** 2.2 ** * ** *** * * ** * ** ** * *** 1.9 ** *** * ** **** * ** ***** ** ** * *** ** *** Relative 1.6 ** *** * ** **** * ** ***** ** ** * *** ** *** Entropy 1.3 ************************************************ (97.1 bits) 1.1 ************************************************ 0.8 ************************************************ 0.5 ************************************************ 0.3 ************************************************ 0.0 ------------------------------------------------ Multilevel GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------------------------ NC_006577.2:28242-28341 1 6.01e-30 . GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC TTGTTAAGAG NC_006577.2:28220-28319 23 6.01e-30 GTCTAAAGTT GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC TTGTTAAGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- NC_006577.2:28242-28341 6e-30 [+2]_52 NC_006577.2:28220-28319 6e-30 22_[+2]_30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC width=48 seqs=2 NC_006577.2:28242-28341 ( 1) GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC 1 NC_006577.2:28220-28319 ( 23) GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 48 n= 424 bayes= 7.7211 E= 7.6e-007 -765 -765 252 -765 -765 -765 252 -765 -765 -765 -765 132 187 -765 -765 -765 187 -765 -765 -765 -765 268 -765 -765 -765 -765 -765 132 187 -765 -765 -765 -765 -765 -765 132 -765 268 -765 -765 -765 -765 252 -765 -765 -765 -765 132 -765 -765 -765 132 -765 -765 -765 132 187 -765 -765 -765 -765 268 -765 -765 -765 268 -765 -765 -765 -765 252 -765 -765 -765 -765 132 -765 268 -765 -765 -765 -765 -765 132 187 -765 -765 -765 -765 -765 252 -765 -765 -765 -765 132 187 -765 -765 -765 187 -765 -765 -765 187 -765 -765 -765 -765 268 -765 -765 -765 268 -765 -765 -765 -765 -765 132 187 -765 -765 -765 -765 -765 252 -765 -765 -765 -765 132 -765 -765 252 -765 -765 -765 252 -765 -765 -765 -765 132 187 -765 -765 -765 -765 -765 -765 132 -765 -765 252 -765 -765 -765 252 -765 187 -765 -765 -765 -765 -765 -765 132 187 -765 -765 -765 -765 268 -765 -765 -765 -765 -765 132 -765 -765 252 -765 -765 268 -765 -765 -765 268 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 48 nsites= 2 E= 7.6e-007 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC MEME-2 regular expression -------------------------------------------------------------------------------- GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC -------------------------------------------------------------------------------- Time 0.38 secs. ******************************************************************************** ******************************************************************************** MOTIF CCWCCCA MEME-3 width = 7 sites = 2 llr = 22 E-value = 3.8e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCWCCCA MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::5:::a pos.-specific C aa:aaa: probability G ::::::: matrix T ::5:::: bits 2.7 ** *** 2.4 ** *** 2.2 ** *** 1.9 ** **** Relative 1.6 ** **** Entropy 1.3 ** **** (15.9 bits) 1.1 ** **** 0.8 ** **** 0.5 ******* 0.3 ******* 0.0 ------- Multilevel CCACCCA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCWCCCA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------- NC_006577.2:27533-27632 63 6.62e-06 ACAAGTTATA CCACCCA CTTCAGATTA NC_006577.2:106-205 85 1.63e-05 CCTCAGCGTC CCTCCCA TAGGTCGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCWCCCA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- NC_006577.2:27533-27632 6.6e-06 62_[+3]_31 NC_006577.2:106-205 1.6e-05 84_[+3]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCWCCCA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCWCCCA width=7 seqs=2 NC_006577.2:27533-27632 ( 63) CCACCCA 1 NC_006577.2:106-205 ( 85) CCTCCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCWCCCA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 752 bayes= 8.55075 E= 3.8e+001 -765 268 -765 -765 -765 268 -765 -765 87 -765 -765 33 -765 268 -765 -765 -765 268 -765 -765 -765 268 -765 -765 187 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCWCCCA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 2 E= 3.8e+001 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCWCCCA MEME-3 regular expression -------------------------------------------------------------------------------- CC[AT]CCCA -------------------------------------------------------------------------------- Time 0.54 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- NC_006577.2:106-205 9.54e-03 84_[+3(1.63e-05)]_9 NC_006577.2:21673-21772 2.60e-06 81_[+1(3.10e-10)]_1 NC_006577.2:22842-22941 3.44e-06 82_[+1(3.10e-10)] NC_006577.2:26951-27050 6.05e-07 75_[+1(3.10e-10)]_7 NC_006577.2:27273-27372 9.08e-01 100 NC_006577.2:27533-27632 5.49e-04 62_[+3(6.62e-06)]_31 NC_006577.2:28220-28319 5.99e-32 22_[+2(6.01e-30)]_5_[+1(1.15e-09)]_\ 7 NC_006577.2:28242-28341 1.72e-32 [+2(6.01e-30)]_5_[+1(1.15e-09)]_29 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: ip-172-31-12-214 ********************************************************************************