******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.5.1 (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= house_keeping_promoters.txt CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ dnaA 1.0000 100 dnaX 1.0000 100 yaaO 1.0000 100 ispE 1.0000 100 glmU 1.0000 100 mfd 1.0000 100 yabM 1.0000 100 coaX 1.0000 100 pabB 1.0000 100 ctsR 1.0000 100 rpmGB 1.0000 100 rpoB 1.0000 100 rpsJ 1.0000 100 ecfA 1.0000 100 ybbC 1.0000 100 sigW 1.0000 100 ybzH 1.0000 100 gamR 1.0000 100 kdgD 1.0000 100 lmrB 1.0000 100 yceJ 1.0000 100 ycgE 1.0000 100 ycgK 1.0000 100 hxlR 1.0000 100 srfAA 1.0000 100 srfAC 1.0000 100 ycxD 1.0000 100 tcyC 1.0000 100 ycnB 1.0000 100 yczG 1.0000 100 gabR 1.0000 100 cutI 1.0000 100 pxpA 1.0000 100 mtlR 1.0000 100 ydaF 1.0000 100 lrpC 1.0000 100 ndoAI 1.0000 100 rsbRA 1.0000 100 cds-YP_009513945.1 1.0000 100 tex 1.0000 100 ydcL 1.0000 100 lrpA 1.0000 100 lrpB 1.0000 100 cdnL 1.0000 100 ydeF 1.0000 100 ydeL 1.0000 100 ydzF 1.0000 100 ydeP 1.0000 100 ydeS 1.0000 100 aseR 1.0000 100 ydfD 1.0000 100 ydfF 1.0000 100 ydfK 1.0000 100 ydgC 1.0000 100 ydgI 1.0000 100 ydhC 1.0000 100 gmuB 1.0000 100 yezC 1.0000 100 yerO 1.0000 100 yezE 1.0000 100 flvL 1.0000 100 spmH 1.0000 100 copP 1.0000 100 treP 1.0000 100 acoA 1.0000 100 malA 1.0000 100 padR 1.0000 100 yfiR 1.0000 100 yfiU 1.0000 100 rpsNB 1.0000 100 ygaO 1.0000 100 yhbI 1.0000 100 nsrR 1.0000 100 citR 1.0000 100 yhdI 1.0000 100 asiMB 1.0000 100 cueR 1.0000 100 yhgD 1.0000 100 comK 1.0000 100 ntdR 1.0000 100 yisR 1.0000 100 yisV 1.0000 100 yizB 1.0000 100 tenA 1.0000 100 yjcK 1.0000 100 yjcP 1.0000 100 manR 1.0000 100 yjdG 1.0000 100 uxaC 1.0000 100 xre 1.0000 100 xpf 1.0000 100 ykkA 1.0000 100 ohrR 1.0000 100 tnrA 1.0000 100 ykoM 1.0000 100 mtnA 1.0000 100 mhqR 1.0000 100 ykvN 1.0000 100 ykvZ 1.0000 100 ccpC 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 house_keeping_promoters.txt -dna -mod zoops -nmotifs 3 -minw 6 -maxw 50 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= 100 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= 10000 N= 100 sample: seed= 0 hsfrac= 0 searchsize= 10000 norand= no csites= 1000 Letter frequencies in dataset: A 0.347 C 0.14 G 0.194 T 0.32 Background letter frequencies (from file dataset with add-one prior applied): A 0.347 C 0.14 G 0.194 T 0.32 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AGGAGG MEME-1 width = 6 sites = 45 llr = 337 E-value = 1.9e-016 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGGAGG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 7::8:: pos.-specific C 1::::: probability G 1aa2aa matrix T 1::::: bits 2.8 2.6 2.3 ** ** 2.0 ** ** Relative 1.7 ** ** Entropy 1.4 ** ** (10.8 bits) 1.1 ***** 0.9 ***** 0.6 ***** 0.3 ****** 0.0 ------ Multilevel AGGAGG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGAGG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ ccpC 90 1.71e-04 GATAACAAAA AGGAGG ACGAC mtnA 46 1.71e-04 CTCTCTGAGA AGGAGG CTTTTTTACG ykkA 85 1.71e-04 GTACCTAGTT AGGAGG GGAACTGAAC xpf 87 1.71e-04 GCCAAAAATG AGGAGG ATCATAGA yisR 86 1.71e-04 CGACTTAAAA AGGAGG ATGATTCAA yfiR 88 1.71e-04 TTTAATAATC AGGAGG ATGAATC malA 88 1.71e-04 AACGTTATCA AGGAGG TCGTCAT acoA 87 1.71e-04 CCTAAATAGA AGGAGG CGCACAAA yezE 85 1.71e-04 CATTTGTTTC AGGAGG TGATCATTTT ydfK 90 1.71e-04 GCAGTTTTAT AGGAGG AAAAA ydfF 89 1.71e-04 TATGAATGTA AGGAGG AAAATC aseR 88 1.71e-04 TGATTTGGGA AGGAGG AGCTCAT ydzF 85 1.71e-04 TACTTAAAAA AGGAGG TTTGATTACA mtlR 87 1.71e-04 AAGATTGGCT AGGAGG TCTTTTTT pxpA 89 1.71e-04 TTGCTTTGGC AGGAGG GATTCT tcyC 86 1.71e-04 AGGTATGATA AGGAGG CGCTTTCTT kdgD 87 1.71e-04 CACAAATAAC AGGAGG TTATGTTG ecfA 85 1.71e-04 ATTAGCTGAG AGGAGG CCGGTTTTCC rpsJ 88 1.71e-04 GTAGGCGAAA AGGAGG GAAAATA ctsR 88 1.71e-04 AAGTCAGTAA AGGAGG GGGTTGA mfd 89 1.71e-04 GGAAACAGAG AGGAGG GGCCAT dnaX 87 1.71e-04 TGAATAACGG AGGAGG GCAAACCC dnaA 82 1.71e-04 TTCTAAGAAA AGGAGG GACGTGCCGG rpsNB 86 2.66e-04 TCGATTTAAA GGGAGG CTATGTGAC ydgI 43 2.66e-04 TTTATGCGCT GGGAGG TTGTTCAAAA rsbRA 86 2.66e-04 GTTTTTTATT GGGAGG TAAGCGAAT srfAA 86 2.66e-04 TAAAGATTAG GGGAGG TATGACAAT ycgE 87 2.66e-04 CGATTTTATA GGGAGG ACTGTCAG gamR 34 2.66e-04 CTTTCATATT GGGAGG GCAAATGGTA tenA 87 3.61e-04 TTATTTTCAG AGGGGG AATGATTT yisV 93 3.61e-04 TGTGTAAAAA AGGGGG GC copP 88 3.61e-04 GAAACGGCGA AGGGGG ATTTACC gmuB 87 3.61e-04 TTTTAATAAC AGGGGG GATAGCAG ycxD 88 3.61e-04 GGTACAAAAC AGGGGG AGAAGGC hxlR 86 3.61e-04 AAGGTTACTA AGGGGG GGGATTCTA ybbC 88 3.61e-04 ATTTTAAAAC AGGGGG CATCCTC padR 90 4.30e-04 CAGCCAGACA CGGAGG ATAGC treP 88 4.30e-04 AAAACGGATA CGGAGG GGTTGGC ycnB 87 4.30e-04 CGCATAACGA CGGAGG AGATTTAC comK 88 5.87e-04 AGAAAAAGGA TGGAGG CCATAAT cdnL 87 5.87e-04 ATACCATATA TGGAGG TGGATGAT tex 85 5.87e-04 ACGACAAAAT TGGAGG CTTTGGTTAC ndoAI 85 5.87e-04 GTAAGTTTGG TGGAGG TGTATGTTTT ycgK 90 5.87e-04 GTTCAACCTA TGGAGG CTGAA glmU 88 5.87e-04 AAAGGGATAT TGGAGG CCAATAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGAGG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ccpC 0.00017 89_[+1]_5 mtnA 0.00017 45_[+1]_49 ykkA 0.00017 84_[+1]_10 xpf 0.00017 86_[+1]_8 yisR 0.00017 85_[+1]_9 yfiR 0.00017 87_[+1]_7 malA 0.00017 87_[+1]_7 acoA 0.00017 86_[+1]_8 yezE 0.00017 84_[+1]_10 ydfK 0.00017 89_[+1]_5 ydfF 0.00017 88_[+1]_6 aseR 0.00017 87_[+1]_7 ydzF 0.00017 84_[+1]_10 mtlR 0.00017 86_[+1]_8 pxpA 0.00017 88_[+1]_6 tcyC 0.00017 85_[+1]_9 kdgD 0.00017 86_[+1]_8 ecfA 0.00017 84_[+1]_10 rpsJ 0.00017 87_[+1]_7 ctsR 0.00017 87_[+1]_7 mfd 0.00017 88_[+1]_6 dnaX 0.00017 86_[+1]_8 dnaA 0.00017 81_[+1]_13 rpsNB 0.00027 85_[+1]_9 ydgI 0.00027 42_[+1]_52 rsbRA 0.00027 85_[+1]_9 srfAA 0.00027 85_[+1]_9 ycgE 0.00027 86_[+1]_8 gamR 0.00027 33_[+1]_61 tenA 0.00036 86_[+1]_8 yisV 0.00036 92_[+1]_2 copP 0.00036 87_[+1]_7 gmuB 0.00036 86_[+1]_8 ycxD 0.00036 87_[+1]_7 hxlR 0.00036 85_[+1]_9 ybbC 0.00036 87_[+1]_7 padR 0.00043 89_[+1]_5 treP 0.00043 87_[+1]_7 ycnB 0.00043 86_[+1]_8 comK 0.00059 87_[+1]_7 cdnL 0.00059 86_[+1]_8 tex 0.00059 84_[+1]_10 ndoAI 0.00059 84_[+1]_10 ycgK 0.00059 89_[+1]_5 glmU 0.00059 87_[+1]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGAGG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGGAGG width=6 seqs=45 ccpC ( 90) AGGAGG 1 mtnA ( 46) AGGAGG 1 ykkA ( 85) AGGAGG 1 xpf ( 87) AGGAGG 1 yisR ( 86) AGGAGG 1 yfiR ( 88) AGGAGG 1 malA ( 88) AGGAGG 1 acoA ( 87) AGGAGG 1 yezE ( 85) AGGAGG 1 ydfK ( 90) AGGAGG 1 ydfF ( 89) AGGAGG 1 aseR ( 88) AGGAGG 1 ydzF ( 85) AGGAGG 1 mtlR ( 87) AGGAGG 1 pxpA ( 89) AGGAGG 1 tcyC ( 86) AGGAGG 1 kdgD ( 87) AGGAGG 1 ecfA ( 85) AGGAGG 1 rpsJ ( 88) AGGAGG 1 ctsR ( 88) AGGAGG 1 mfd ( 89) AGGAGG 1 dnaX ( 87) AGGAGG 1 dnaA ( 82) AGGAGG 1 rpsNB ( 86) GGGAGG 1 ydgI ( 43) GGGAGG 1 rsbRA ( 86) GGGAGG 1 srfAA ( 86) GGGAGG 1 ycgE ( 87) GGGAGG 1 gamR ( 34) GGGAGG 1 tenA ( 87) AGGGGG 1 yisV ( 93) AGGGGG 1 copP ( 88) AGGGGG 1 gmuB ( 87) AGGGGG 1 ycxD ( 88) AGGGGG 1 hxlR ( 86) AGGGGG 1 ybbC ( 88) AGGGGG 1 padR ( 90) CGGAGG 1 treP ( 88) CGGAGG 1 ycnB ( 87) CGGAGG 1 comK ( 88) TGGAGG 1 cdnL ( 87) TGGAGG 1 tex ( 85) TGGAGG 1 ndoAI ( 85) TGGAGG 1 ycgK ( 90) TGGAGG 1 glmU ( 88) TGGAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGAGG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 9500 bayes= 8.76414 E= 1.9e-016 94 -107 -54 -126 -1214 -1214 236 -1214 -1214 -1214 236 -1214 128 -1214 -32 -1214 -1214 -1214 236 -1214 -1214 -1214 236 -1214 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGAGG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 45 E= 1.9e-016 0.666667 0.066667 0.133333 0.133333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.844444 0.000000 0.155556 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGAGG MEME-1 regular expression -------------------------------------------------------------------------------- AGGAGG -------------------------------------------------------------------------------- Time 6.24 secs. ******************************************************************************** ******************************************************************************** MOTIF BCTYYTTTYTTKTNW MEME-2 width = 15 sites = 45 llr = 367 E-value = 3.2e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif BCTYYTTTYTTKTNW MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1::1:1::23::123 pos.-specific C 472461:2421::21 probability G 2::1:::1::14:4: matrix T 337447a74686926 bits 2.8 2.6 2.3 2.0 Relative 1.7 * * Entropy 1.4 * * * (11.8 bits) 1.1 * * * * * 0.9 ** * * * * 0.6 ******** *** 0.3 *************** 0.0 --------------- Multilevel CCTTCTTTCTTTTGT consensus TTCCT CTA G AA sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BCTYYTTTYTTKTNW MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- rpoB 10 8.76e-08 ATTAGAAAC CCTTTTTTCTTTTGT CTTGTAAAAG yceJ 36 8.24e-07 GAATTGAATT CCTCCTTCCTCTTAT GACTTCCTGC dnaA 33 1.55e-06 AGCGCCATTT GCTCTTTTTTTGTGT TCTATAACAG cds-YP_009513945.1 19 1.84e-06 TGGACATCCG GCTTCTTTTTTTTGC GGTTGACTAT citR 1 2.16e-06 . CCCCTATCCTTTTCT GTTATTATAG yhbI 38 2.16e-06 CTTTGACAAA TCTTCTTTCATTTAT TAATATTTTA yhdI 1 3.52e-06 . CCCCTTTCCTTTCGT TACAATGATC ykkA 33 4.73e-06 TGTAATGAGA GCTTTTTTCTTTTTT AAAGGGAATT padR 3 4.73e-06 TC CCTTCCTCCCTTTTC TATAATAAGG mtnA 29 8.06e-06 AGATGTTAAG CCTCCTTCTCTCTGA GAAGGAGGCT tcyC 1 8.06e-06 . TCTGCTTTCATTTCA ATCATACTCC yfiR 3 9.38e-06 CT TCTCCTTTATTTTAC AAGAAAAAGA ykvN 41 1.07e-05 ATCGGAAGTA CCCACTTTTTTGTGA TATAGTAACT tex 29 1.39e-05 GCGCCAGCTG TCTTTTTTTATGTGT TTTTTTCGGT ycxD 18 1.39e-05 GCGCCGGTCG CTCCCTTTATTGTAT GGCCGCGGTC ydeS 30 1.56e-05 TAAATGGATT TCTGTTTTCTTTTTT TATTCAATTT ydzF 4 1.56e-05 GCG GCCCCTTTCACTTCA GATCGTGAAT ydfK 67 2.22e-05 ATAGAGCACT CCTATTTTTTTGTGC AGTTTTATAG ydfF 16 2.22e-05 GTCCAACGTT TTTTCCTCCTTGTCA CGCTTACATT yezE 39 2.51e-05 TGTTTTTTTA GCTTTTTTCTTGACT GTTCAGTCTG copP 13 4.86e-05 ATGCTGCTCG TCTTTTTTATTGTTT TTTAAAACTT yisR 23 5.37e-05 TTAAAGTGTA CCTCCATTTCCTTAT AATAAAAAGG nsrR 32 5.96e-05 ATGTTTTTTA ATTCCTTTTTTTTCA TTTTTCAATC tnrA 45 6.64e-05 CAAGCGTCAG GTTTTTTCTCTTTGT TTTTTATATA yjdG 2 8.12e-05 A TCCCCCTCAATTTTT TCATCTTTCT acoA 52 8.12e-05 AGACTGGCAC ACTTCTTGCATTTAT AATGGTGAAC yabM 33 9.79e-05 GTATAATAAC CTCGTTTTTATTTGT GCCGCGGTAA xpf 64 1.07e-04 TGATTGGTGT CCGTTTTTTATTTGC CAAAAATGAG ydaF 32 1.41e-04 GCTTAACAGC CCATCCTTTTTGTAT TGAAAAAAAC mfd 60 1.41e-04 CTAGACCAAA GCGTTTTTCTGTTCT CGCAGGAAAC ykvZ 2 1.68e-04 T TCTCCTTTCAGCTAA AAACACAAAA tenA 71 1.68e-04 CGGGAAAGTG GTTTTTTTATTTTCA GAGGGGGAAT cutI 33 1.68e-04 TTTTTTATCA TCCACTTACTTGTCT CCGTCTCTAA manR 1 1.84e-04 . TCTCTATGATTTTGT TTTATAATGT yfiU 37 1.99e-04 TTTCTGCTCA CTTTCTTTCAGGAGT GAAAATCGAG rpsNB 30 2.34e-04 AAGCGGTATG CTTGCTTTTTTGAAT GGTGAATGAT lrpB 75 2.34e-04 ATTTTGTAAA ACTTTTTCACTGTGA AAGGAGTTAC rsbRA 17 2.53e-04 AATAGAGCAA CTTTTTTTGTTTTCA AAAAACATAA gabR 2 3.21e-04 A TCCCCCTGTCGGTAT TTTCTTATCA ykoM 59 3.47e-04 TATGTAAGGG TTTTCATTATTTTTT TATAAAAATC asiMB 32 3.47e-04 GTATAAAAAA GCCGTTTGCATGTAA TGTGCAACTT flvL 51 3.47e-04 GCGTTATGGT TTTCCCTCCTTTATA ATCGTGTCAC yezC 61 4.95e-04 ATCAAAGGAA TTTTCATTCATTCGC CTAAATATGT yizB 14 6.11e-04 AGTATGAGAA ATTCCATTTTTGTTA AAAGGAAAAA ycgE 3 6.11e-04 CT CTTACTTTTCTATGT AAGTTCTGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BCTYYTTTYTTKTNW MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- rpoB 8.8e-08 9_[+2]_76 yceJ 8.2e-07 35_[+2]_50 dnaA 1.5e-06 32_[+2]_53 cds-YP_009513945.1 1.8e-06 18_[+2]_67 citR 2.2e-06 [+2]_85 yhbI 2.2e-06 37_[+2]_48 yhdI 3.5e-06 [+2]_85 ykkA 4.7e-06 32_[+2]_53 padR 4.7e-06 2_[+2]_83 mtnA 8.1e-06 28_[+2]_57 tcyC 8.1e-06 [+2]_85 yfiR 9.4e-06 2_[+2]_83 ykvN 1.1e-05 40_[+2]_45 tex 1.4e-05 28_[+2]_57 ycxD 1.4e-05 17_[+2]_68 ydeS 1.6e-05 29_[+2]_56 ydzF 1.6e-05 3_[+2]_82 ydfK 2.2e-05 66_[+2]_19 ydfF 2.2e-05 15_[+2]_70 yezE 2.5e-05 38_[+2]_47 copP 4.9e-05 12_[+2]_73 yisR 5.4e-05 22_[+2]_63 nsrR 6e-05 31_[+2]_54 tnrA 6.6e-05 44_[+2]_41 yjdG 8.1e-05 1_[+2]_84 acoA 8.1e-05 51_[+2]_34 yabM 9.8e-05 32_[+2]_53 xpf 0.00011 63_[+2]_22 ydaF 0.00014 31_[+2]_54 mfd 0.00014 59_[+2]_26 ykvZ 0.00017 1_[+2]_84 tenA 0.00017 70_[+2]_15 cutI 0.00017 32_[+2]_53 manR 0.00018 [+2]_85 yfiU 0.0002 36_[+2]_49 rpsNB 0.00023 29_[+2]_56 lrpB 0.00023 74_[+2]_11 rsbRA 0.00025 16_[+2]_69 gabR 0.00032 1_[+2]_84 ykoM 0.00035 58_[+2]_27 asiMB 0.00035 31_[+2]_54 flvL 0.00035 50_[+2]_35 yezC 0.0005 60_[+2]_25 yizB 0.00061 13_[+2]_72 ycgE 0.00061 2_[+2]_83 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BCTYYTTTYTTKTNW MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF BCTYYTTTYTTKTNW width=15 seqs=45 rpoB ( 10) CCTTTTTTCTTTTGT 1 yceJ ( 36) CCTCCTTCCTCTTAT 1 dnaA ( 33) GCTCTTTTTTTGTGT 1 cds-YP_009513945.1 ( 19) GCTTCTTTTTTTTGC 1 citR ( 1) CCCCTATCCTTTTCT 1 yhbI ( 38) TCTTCTTTCATTTAT 1 yhdI ( 1) CCCCTTTCCTTTCGT 1 ykkA ( 33) GCTTTTTTCTTTTTT 1 padR ( 3) CCTTCCTCCCTTTTC 1 mtnA ( 29) CCTCCTTCTCTCTGA 1 tcyC ( 1) TCTGCTTTCATTTCA 1 yfiR ( 3) TCTCCTTTATTTTAC 1 ykvN ( 41) CCCACTTTTTTGTGA 1 tex ( 29) TCTTTTTTTATGTGT 1 ycxD ( 18) CTCCCTTTATTGTAT 1 ydeS ( 30) TCTGTTTTCTTTTTT 1 ydzF ( 4) GCCCCTTTCACTTCA 1 ydfK ( 67) CCTATTTTTTTGTGC 1 ydfF ( 16) TTTTCCTCCTTGTCA 1 yezE ( 39) GCTTTTTTCTTGACT 1 copP ( 13) TCTTTTTTATTGTTT 1 yisR ( 23) CCTCCATTTCCTTAT 1 nsrR ( 32) ATTCCTTTTTTTTCA 1 tnrA ( 45) GTTTTTTCTCTTTGT 1 yjdG ( 2) TCCCCCTCAATTTTT 1 acoA ( 52) ACTTCTTGCATTTAT 1 yabM ( 33) CTCGTTTTTATTTGT 1 xpf ( 64) CCGTTTTTTATTTGC 1 ydaF ( 32) CCATCCTTTTTGTAT 1 mfd ( 60) GCGTTTTTCTGTTCT 1 ykvZ ( 2) TCTCCTTTCAGCTAA 1 tenA ( 71) GTTTTTTTATTTTCA 1 cutI ( 33) TCCACTTACTTGTCT 1 manR ( 1) TCTCTATGATTTTGT 1 yfiU ( 37) CTTTCTTTCAGGAGT 1 rpsNB ( 30) CTTGCTTTTTTGAAT 1 lrpB ( 75) ACTTTTTCACTGTGA 1 rsbRA ( 17) CTTTTTTTGTTTTCA 1 gabR ( 2) TCCCCCTGTCGGTAT 1 ykoM ( 59) TTTTCATTATTTTTT 1 asiMB ( 32) GCCGTTTGCATGTAA 1 flvL ( 51) TTTCCCTCCTTTATA 1 yezC ( 61) TTTTCATTCATTCGC 1 yizB ( 14) ATTCCATTTTTGTTA 1 ycgE ( 3) CTTACTTTTCTATGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BCTYYTTTYTTKTNW MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 8600 bayes= 7.9516 E= 3.2e-008 -196 144 4 6 -1214 230 -1214 -4 -396 67 -213 115 -196 135 -81 48 -1214 205 -1214 40 -138 -7 -1214 120 -1214 -1214 -1214 165 -396 67 -113 106 -96 167 -313 15 -38 16 -1214 85 -1214 -107 -113 140 -396 -165 87 85 -196 -165 -1214 144 -50 67 87 -85 -26 -7 -1214 85 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BCTYYTTTYTTKTNW MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 45 E= 3.2e-008 0.088889 0.377778 0.200000 0.333333 0.000000 0.688889 0.000000 0.311111 0.022222 0.222222 0.044444 0.711111 0.088889 0.355556 0.111111 0.444444 0.000000 0.577778 0.000000 0.422222 0.133333 0.133333 0.000000 0.733333 0.000000 0.000000 0.000000 1.000000 0.022222 0.222222 0.088889 0.666667 0.177778 0.444444 0.022222 0.355556 0.266667 0.155556 0.000000 0.577778 0.000000 0.066667 0.088889 0.844444 0.022222 0.044444 0.355556 0.577778 0.088889 0.044444 0.000000 0.866667 0.244444 0.222222 0.355556 0.177778 0.288889 0.133333 0.000000 0.577778 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BCTYYTTTYTTKTNW MEME-2 regular expression -------------------------------------------------------------------------------- [CTG][CT][TC][TC][CT]TT[TC][CT][TA]T[TG]T[GAC][TA] -------------------------------------------------------------------------------- Time 11.76 secs. ******************************************************************************** ******************************************************************************** MOTIF MYCRRCHRMWTTDCYTTRCGR MEME-3 width = 21 sites = 9 llr = 140 E-value = 8.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif MYCRRCHRMWTTDCYTTRCGR MEME-3 Description -------------------------------------------------------------------------------- Simplified A 4:267:3633::2:11:4116 pos.-specific C 677::9417:11:84::172: probability G :::33::3:1::4:1::4174 matrix T :311:12::6993239a:1:: bits 2.8 2.6 2.3 * 2.0 * Relative 1.7 * * * Entropy 1.4 * * * * * (22.4 bits) 1.1 *** * * ** * ** ** 0.9 *** ** * ** * ** *** 0.6 ********* ** ******** 0.3 ********************* 0.0 --------------------- Multilevel CCCAACCACTTTGCCTTACGA consensus ATAGG AGAA TTT G CG sequence T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MYCRRCHRMWTTDCYTTRCGR MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- tenA 43 1.78e-11 TATGCCAATT CCAAACCACTTTTCCTTGCGG GAAAGTGGTT rpsJ 16 9.37e-10 TGCTGACACA CCCGGCCGCTTTGCCATGGCA AGGTGTTCAG yezC 31 4.41e-09 ATGAAGTTAA ATCAACAGCATTACCTTACGA TCAAAGGAAT mtlR 41 1.31e-08 TCTCTATATC CTCTACTGCATCTCCTTGCGA CTTCATCCGC ydfD 69 8.72e-08 TAGATTTTGA CCCAACCAATTTATTTTAAGG AGACCGATTC padR 57 1.19e-07 ACAGTTGAGC ACCGGCTCATCTGTTTTGCGA AACAGCCAGA flvL 29 1.28e-07 TCAATCATCT CCAAGCCAAGTTGCGTTATGG TTTTCCCTCC pabB 41 1.49e-07 CACTTTTTTC ACTAACAACATTGCTTTACAA TTAAAAACAA yjcP 53 5.45e-07 CAAATTGTTA ATCGATAACTTTTCATTCCCG ATATTAAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MYCRRCHRMWTTDCYTTRCGR MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- tenA 1.8e-11 42_[+3]_37 rpsJ 9.4e-10 15_[+3]_64 yezC 4.4e-09 30_[+3]_49 mtlR 1.3e-08 40_[+3]_39 ydfD 8.7e-08 68_[+3]_11 padR 1.2e-07 56_[+3]_23 flvL 1.3e-07 28_[+3]_51 pabB 1.5e-07 40_[+3]_39 yjcP 5.5e-07 52_[+3]_27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MYCRRCHRMWTTDCYTTRCGR MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF MYCRRCHRMWTTDCYTTRCGR width=21 seqs=9 tenA ( 43) CCAAACCACTTTTCCTTGCGG 1 rpsJ ( 16) CCCGGCCGCTTTGCCATGGCA 1 yezC ( 31) ATCAACAGCATTACCTTACGA 1 mtlR ( 41) CTCTACTGCATCTCCTTGCGA 1 ydfD ( 69) CCCAACCAATTTATTTTAAGG 1 padR ( 57) ACCGGCTCATCTGTTTTGCGA 1 flvL ( 29) CCAAGCCAAGTTGCGTTATGG 1 pabB ( 41) ACTAACAACATTGCTTTACAA 1 yjcP ( 53) ATCGATAACTTTTCATTCCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MYCRRCHRMWTTDCYTTRCGR MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 8000 bayes= 9.92868 E= 8.2e+000 36 199 -982 -982 -982 225 -982 6 -64 225 -982 -152 68 -982 78 -152 94 -982 78 -982 -982 267 -982 -152 -6 167 -982 -52 68 -33 78 -982 -6 225 -982 -982 -6 -982 -81 80 -982 -33 -982 147 -982 -33 -982 147 -64 -982 119 6 -982 248 -982 -52 -164 167 -81 6 -164 -982 -982 147 -982 -982 -982 164 36 -33 119 -982 -164 225 -81 -152 -164 67 178 -982 68 -982 119 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MYCRRCHRMWTTDCYTTRCGR MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 8.2e+000 0.444444 0.555556 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.222222 0.666667 0.000000 0.111111 0.555556 0.000000 0.333333 0.111111 0.666667 0.000000 0.333333 0.000000 0.000000 0.888889 0.000000 0.111111 0.333333 0.444444 0.000000 0.222222 0.555556 0.111111 0.333333 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.000000 0.111111 0.555556 0.000000 0.111111 0.000000 0.888889 0.000000 0.111111 0.000000 0.888889 0.222222 0.000000 0.444444 0.333333 0.000000 0.777778 0.000000 0.222222 0.111111 0.444444 0.111111 0.333333 0.111111 0.000000 0.000000 0.888889 0.000000 0.000000 0.000000 1.000000 0.444444 0.111111 0.444444 0.000000 0.111111 0.666667 0.111111 0.111111 0.111111 0.222222 0.666667 0.000000 0.555556 0.000000 0.444444 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MYCRRCHRMWTTDCYTTRCGR MEME-3 regular expression -------------------------------------------------------------------------------- [CA][CT][CA][AG][AG]C[CAT][AG][CA][TA]TT[GTA][CT][CT]TT[AG]C[GC][AG] -------------------------------------------------------------------------------- Time 16.44 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- dnaA 9.03e-05 32_[+2(1.55e-06)]_53 dnaX 7.76e-02 100 yaaO 2.48e-01 100 ispE 5.08e-01 100 glmU 9.18e-02 100 mfd 2.38e-03 100 yabM 5.46e-02 32_[+2(9.79e-05)]_53 coaX 9.45e-01 100 pabB 1.14e-04 40_[+3(1.49e-07)]_39 ctsR 1.72e-01 100 rpmGB 6.69e-01 100 rpoB 9.68e-05 9_[+2(8.76e-08)]_76 rpsJ 9.68e-08 15_[+3(9.37e-10)]_64 ecfA 3.44e-02 100 ybbC 1.49e-01 100 sigW 7.38e-01 100 ybzH 8.51e-01 100 gamR 1.33e-01 100 kdgD 6.63e-02 100 lmrB 1.31e-01 100 yceJ 1.18e-03 35_[+2(8.24e-07)]_50 ycgE 7.53e-03 100 ycgK 4.02e-01 100 hxlR 3.35e-01 100 srfAA 2.55e-01 100 srfAC 5.08e-01 100 ycxD 9.86e-04 17_[+2(1.39e-05)]_68 tcyC 4.17e-04 [+2(8.06e-06)]_85 ycnB 7.19e-03 100 yczG 6.14e-01 100 gabR 4.87e-02 100 cutI 4.66e-02 100 pxpA 8.64e-02 100 mtlR 3.37e-07 40_[+3(1.31e-08)]_39 ydaF 1.53e-02 100 lrpC 3.58e-01 100 ndoAI 1.12e-01 100 rsbRA 1.29e-03 100 cds-YP_009513945.1 3.94e-05 18_[+2(1.84e-06)]_67 tex 2.47e-03 28_[+2(1.39e-05)]_57 ydcL 4.44e-01 100 lrpA 3.35e-01 100 lrpB 7.92e-02 100 cdnL 2.38e-01 100 ydeF 3.34e-01 100 ydeL 3.66e-01 100 ydzF 5.80e-04 3_[+2(1.56e-05)]_82 ydeP 4.40e-01 100 ydeS 1.15e-02 29_[+2(1.56e-05)]_56 aseR 6.41e-02 100 ydfD 9.97e-05 68_[+3(8.72e-08)]_11 ydfF 8.87e-04 15_[+2(2.22e-05)]_70 ydfK 5.50e-04 66_[+2(2.22e-05)]_19 ydgC 8.84e-01 100 ydgI 1.30e-01 100 ydhC 1.42e-01 100 gmuB 1.47e-01 100 yezC 9.21e-07 30_[+3(4.41e-09)]_49 yerO 7.80e-01 100 yezE 3.41e-04 38_[+2(2.51e-05)]_47 flvL 1.84e-05 28_[+3(1.28e-07)]_51 spmH 6.54e-01 100 copP 5.96e-03 12_[+2(4.86e-05)]_73 treP 7.43e-02 100 acoA 4.67e-03 51_[+2(8.12e-05)]_34 malA 2.07e-02 100 padR 4.31e-08 2_[+2(4.73e-06)]_39_[+3(1.19e-07)]_\ 23 yfiR 2.94e-04 2_[+2(9.38e-06)]_83 yfiU 1.14e-02 100 rpsNB 8.78e-03 100 ygaO 2.95e-01 100 yhbI 1.64e-03 37_[+2(2.16e-06)]_48 nsrR 2.34e-02 31_[+2(5.96e-05)]_54 citR 1.82e-03 [+2(2.16e-06)]_85 yhdI 1.54e-03 [+2(3.52e-06)]_85 asiMB 9.58e-02 100 cueR 8.68e-01 100 yhgD 5.01e-01 100 comK 8.64e-02 100 ntdR 2.39e-01 100 yisR 1.66e-03 22_[+2(5.37e-05)]_63 yisV 1.12e-01 100 yizB 1.36e-01 100 tenA 2.91e-10 42_[+3(1.78e-11)]_37 yjcK 2.19e-01 100 yjcP 3.49e-04 52_[+3(5.45e-07)]_27 manR 2.08e-02 100 yjdG 8.49e-03 1_[+2(8.12e-05)]_84 uxaC 8.62e-01 100 xre 5.54e-01 100 xpf 1.99e-03 100 ykkA 4.90e-04 32_[+2(4.73e-06)]_53 ohrR 7.72e-01 100 tnrA 3.27e-02 44_[+2(6.64e-05)]_41 ykoM 1.12e-01 100 mtnA 3.10e-04 28_[+2(8.06e-06)]_57 mhqR 1.80e-01 100 ykvN 9.05e-03 40_[+2(1.07e-05)]_45 ykvZ 5.33e-02 100 ccpC 1.61e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************