******************************************************************************** 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= housekeeping.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ dnaN 1.0000 100 rplI 1.0000 100 cds-WP_000373151.1 1.0000 100 merR 1.0000 100 mecI 1.0000 100 cds-WP_000427807.1 1.0000 100 cds-WP_000159127.1 1.0000 100 cds-WP_000414486.1 1.0000 100 sarS 1.0000 100 cds-WP_001793808.1 1.0000 100 cds-WP_041205521.1 1.0000 100 cds-WP_000181832.1 1.0000 100 cds-WP_001012724.1 1.0000 100 cds-WP_000922328.1 1.0000 100 cds-WP_020444620.1 1.0000 100 cds-WP_000291432.1 1.0000 100 cds-WP_000667382.1 1.0000 100 cds-WP_000954261.1 1.0000 100 mepR 1.0000 100 cds-WP_000467652.1 1.0000 100 cds-WP_041205307.1 1.0000 100 cds-WP_001079938.1 1.0000 100 cds-WP_001550052.1 1.0000 100 ychF 1.0000 100 rpsF 1.0000 100 rpsR 1.0000 100 cds-WP_000804879.1 1.0000 100 tet(M) 1.0000 100 cds-WP_000403916.1 1.0000 100 treR 1.0000 100 dnaX 1.0000 100 cds-WP_000344337.1 1.0000 100 cds-WP_000691766.1 1.0000 100 cds-WP_000157650.1 1.0000 100 mfd 1.0000 100 cds-WP_000021445.1 1.0000 100 cds-WP_000551762.1 1.0000 100 rpmG 1.0000 100 nusG 1.0000 100 rplK 1.0000 100 rplA 1.0000 100 rplJ 1.0000 100 rplL 1.0000 100 rpoB 1.0000 100 rpoC 1.0000 100 cds-WP_020444636.1 1.0000 100 rpsL 1.0000 100 rpsG 1.0000 100 fusA 1.0000 100 tuf 1.0000 100 cds-WP_000954654.1 1.0000 100 cds-WP_000638613.1 1.0000 100 mgrA 1.0000 100 cds-WP_000972699.1 1.0000 100 cds-WP_000654030.1 1.0000 100 cds-WP_001186979.1 1.0000 100 cds-WP_000560872.1 1.0000 100 dltA 1.0000 100 ygs 1.0000 100 cds-WP_000404422.1 1.0000 100 cds-WP_000287265.1 1.0000 100 cds-WP_000278010.1 1.0000 100 cds-WP_001031975.1 1.0000 100 cds-WP_001020625.1 1.0000 100 rpmF 1.0000 100 cds-WP_001055143.1 1.0000 100 cds-WP_000933363.1 1.0000 100 rpsA 1.0000 100 cds-WP_000361544.1 1.0000 100 cds-WP_000283016.1 1.0000 100 cds-WP_000356975.1 1.0000 100 cds-WP_000505015.1 1.0000 100 lexA 1.0000 100 rpsN 1.0000 100 rpmG_2 1.0000 100 cds-WP_000600812.1 1.0000 100 cds-WP_000624945.1 1.0000 100 cds-WP_001293307.1 1.0000 100 rpsO 1.0000 100 infB 1.0000 100 cds-WP_000020853.1 1.0000 100 cds-WP_000727423.1 1.0000 100 nusA 1.0000 100 cds-WP_020444698.1 1.0000 100 tsf 1.0000 100 rpsB 1.0000 100 codY 1.0000 100 trmFO 1.0000 100 rplS 1.0000 100 rpsP 1.0000 100 fapR 1.0000 100 rpmB 1.0000 100 rpoZ 1.0000 100 polX 1.0000 100 cds-WP_000278802.1 1.0000 100 cds-WP_000175001.1 1.0000 100 cds-WP_000333630.1 1.0000 100 scpB 1.0000 100 cds-WP_000256338.1 1.0000 100 nusB 1.0000 100 efp 1.0000 100 cds-WP_000161314.1 1.0000 100 rpmG_3 1.0000 100 rpoD 1.0000 100 rpsU 1.0000 100 prmA 1.0000 100 hrcA 1.0000 100 rpsT 1.0000 100 holA 1.0000 100 greA 1.0000 100 cds-WP_000704122.1 1.0000 100 rpmA 1.0000 100 cds-WP_016187883.1 1.0000 100 rplU 1.0000 100 rplT 1.0000 100 rpmI 1.0000 100 infC 1.0000 100 nrdR 1.0000 100 polA 1.0000 100 cds-WP_020444737.1 1.0000 100 cds-WP_000160435.1 1.0000 100 rpsD 1.0000 100 ccpA 1.0000 100 cds-WP_000757543.1 1.0000 100 cds-WP_000221179.1 1.0000 100 cds-WP_000375864.1 1.0000 100 cds-WP_000613733.1 1.0000 100 dinB 1.0000 100 cds-WP_000691584.1 1.0000 100 cds-WP_001208482.1 1.0000 100 cds-WP_000128898.1 1.0000 100 agrB 1.0000 100 cds-WP_000790330.1 1.0000 100 cds-WP_000370124.1 1.0000 100 sigB 1.0000 100 tenA 1.0000 100 cds-WP_001094394.1 1.0000 100 atpD 1.0000 100 atpG 1.0000 100 atpA 1.0000 100 cds-WP_000241351.1 1.0000 100 cds-WP_000140679.1 1.0000 100 atpE 1.0000 100 atpB 1.0000 100 cds-WP_000379888.1 1.0000 100 cds-WP_000808968.1 1.0000 100 rho 1.0000 100 cds-WP_000451438.1 1.0000 100 rpoE 1.0000 100 czrA 1.0000 100 cds-WP_000927363.1 1.0000 100 cds-WP_001793365.1 1.0000 100 cds-WP_000850011.1 1.0000 100 rpsI 1.0000 100 rplM 1.0000 100 rplQ 1.0000 100 cds-WP_020444776.1 1.0000 100 rpsK 1.0000 100 rpsM 1.0000 100 rpmJ 1.0000 100 infA 1.0000 100 rplO 1.0000 100 rpmD 1.0000 100 rpsE 1.0000 100 rplR 1.0000 100 rplF 1.0000 100 rpsH 1.0000 100 cds-WP_001140799.1 1.0000 100 rplE 1.0000 100 rplX 1.0000 100 rplN 1.0000 100 rpsQ 1.0000 100 rpmC 1.0000 100 rplP 1.0000 100 rpsC 1.0000 100 rplV 1.0000 100 rpsS 1.0000 100 rplB 1.0000 100 rplW 1.0000 100 rplD 1.0000 100 rplC 1.0000 100 rpsJ 1.0000 100 cds-WP_000951058.1 1.0000 100 cds-WP_000032855.1 1.0000 100 cds-WP_000831055.1 1.0000 100 cds-WP_001030125.1 1.0000 100 cds-WP_000073195.1 1.0000 100 cds-WP_000477992.1 1.0000 100 cds-WP_020444782.1 1.0000 100 cds-WP_000828570.1 1.0000 100 cds-WP_000238542.1 1.0000 100 cds-WP_000656771.1 1.0000 100 cds-WP_000289213.1 1.0000 100 cds-WP_000332063.1 1.0000 100 sarU 1.0000 100 cds-WP_000990133.1 1.0000 100 cds-WP_000074007.1 1.0000 100 cds-SABB_RS14155 1.0000 100 cds-WP_000376235.1 1.0000 100 cds-WP_000351761.1 1.0000 100 farR 1.0000 100 cds-WP_001791286.1 1.0000 100 cds-WP_001224184.1 1.0000 100 blaI 1.0000 100 cds-WP_000151114.1 1.0000 100 cds-WP_000198597.1 1.0000 100 cds-WP_000106185.1 1.0000 100 cds-WP_000887000.1 1.0000 100 sasF 1.0000 100 icaR 1.0000 100 cds-WP_000610969.1 1.0000 100 cds-WP_001054111.1 1.0000 100 cds-WP_000742839.1 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 housekeeping.fasta -dna -nmotifs 3 -minw 6 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= 213 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= 21300 N= 213 sample: seed= 0 hsfrac= 0 searchsize= 21300 norand= no csites= 1000 Letter frequencies in dataset: A 0.336 C 0.159 G 0.135 T 0.37 Background letter frequencies (from file dataset with add-one prior applied): A 0.336 C 0.159 G 0.135 T 0.37 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WWWWWTTCCTCC MEME-1 width = 12 sites = 95 llr = 743 E-value = 1.8e-044 ******************************************************************************** -------------------------------------------------------------------------------- Motif WWWWWTTCCTCC MEME-1 Description -------------------------------------------------------------------------------- Simplified A 4354411::::2 pos.-specific C :212:229a:a7 probability G 111::1:::::: matrix T 5433567::a:1 bits 2.9 2.6 * * 2.3 ** * 2.0 ** * Relative 1.7 ** * Entropy 1.4 ** * (11.3 bits) 1.2 ***** 0.9 ***** 0.6 ****** 0.3 * ******** 0.0 ------------ Multilevel TTAATTTCCTCC consensus AATTA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWWWTTCCTCC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ rplD 80 1.36e-06 TTATTATTCT TCACTTTCCTCC TTTACGTAT cds-WP_001140799.1 81 1.36e-06 CATTTATTAA TAAATTTCCTCC GATTAATT rpsE 80 1.36e-06 ATCTTAAAAT TAAATTTCCTCC CTGTTTATG atpD 81 1.36e-06 GAACTTATTA TAAATTTCCTCC TTTTATCG rpsO 80 3.14e-06 CATAAGTTTG TAAAATTCCTCC TTTAACTAA rpsH 80 4.33e-06 ATTTTTTCTC AGACTTTCCTCC GTTGTTAGT cds-WP_020444776.1 81 4.33e-06 ATTCAGCTGC ATATATTCCTCC TATAAATT rplQ 82 4.33e-06 TTTTCTTCTA ACTATTTCCTCC AATTGAG rpmI 80 6.20e-06 ATTAATTTCG ATAATGTCCTCC TGAATATAA rpsK 79 8.32e-06 TTTTTTATTA TCCATTTCCTCC GTTTAAAATT tenA 79 8.32e-06 CATCAAAAAA ATAAATCCCTCC TAAAAAATGT rpsQ 81 1.07e-05 AGTTATTAAT TCATTCTCCTCC AATGTTTT cds-WP_001186979.1 78 1.07e-05 TGTTATCCTA TAAATGTCCTCC TAACTATTTT rpsC 82 1.33e-05 CGAATTAATT GAAAATTCCTCC CTTATGA cds-WP_000159127.1 83 1.59e-05 TTGTCAGTAA ACTTATTCCTCC CATTAA rpsS 82 1.86e-05 TGCGTGTATT ATTCTTCCCTCC GCGGGTT rplV 81 1.86e-05 TTATAGATAA TTCATCTCCTCC TGTAGGAT rplN 81 1.86e-05 TGTTCAAATC TCTATTCCCTCC AAATTGAT rplF 80 1.86e-05 AACCATTATT TTTTATTCCTCC ACGGTATTG rpmJ 82 1.86e-05 CAGTGAGGTA TTATATCCCTCC ATATTTT cds-WP_000256338.1 82 1.86e-05 GTTACGTCTT TAATTGTCCTCC ACTAATT rplU 81 2.14e-05 CGCACTGAAT AATATGTCCTCC ACGTTTCA cds-WP_000283016.1 82 2.14e-05 TTATTCTAAG TTCATTCCCTCC TTATTGT rplW 79 2.41e-05 CGACGATTTT TTCAACTCCTCC ACGAGCCTAT rpmD 78 2.41e-05 TTCTTAATAT GTTAATTCCTCC CTTTTGATCA rpmG_3 82 2.41e-05 CATAAATCTT TACTATTCCTCC TTATTGG dinB 82 2.70e-05 TTTCATTTTT AATCATCCCTCC ACTCGTG cds-SABB_RS14155 76 3.01e-05 GCCAATTGAT TACTTCTCCTCC TTATTATCAC cds-WP_000074007.1 81 3.01e-05 GTTGATACCA TTAATATCCTCC ACCTTAGA efp 82 3.01e-05 TATTCGCACA TTTTACTCCTCC TTTGACT rpsJ 82 3.31e-05 ATTTACATCT GCTTATTCCTCC CTTTTAA rplX 82 3.31e-05 TGTTGGTTAT GTTTATTCCTCC ACGGGTG rplC 79 3.64e-05 ATATTATCTG TTAAAATCCTCC ACCTGAAAGC rplB 80 3.64e-05 TTTTGTTAAT GGTAATTCCTCC ATTCGCTGT rplM 80 3.64e-05 CTTCGTAAAT AAAAAATCCTCC TGTTAATAA tet(M) 81 4.28e-05 GAAAACCCAA AAACTTACCTCC TTTTAGTG cds-WP_001054111.1 80 4.67e-05 CTAACATGAT TAACTTACCTCC GCATACATT cds-WP_000151114.1 78 4.67e-05 AACAAATATT AGTAACCCCTCC TGAACTATGT rpsI 81 5.15e-05 ATGCACCAAT TAATCTTCCTCC TTTACTGA rpoD 82 5.74e-05 CAAGTATAAA TTTTAGCCCTCC GGCAAAG cds-WP_000278802.1 80 5.74e-05 TCGAATCTTT ACATTACCCTCC ATCACTGCA cds-WP_000610969.1 79 6.39e-05 CAGAAATTTA TCTTTATCCTCC CTCTGTAAAT cds-WP_000106185.1 82 6.39e-05 TCCAATTGCG AAACTTTCCTCA GTAGTAG rplE 81 6.39e-05 AATTATTGTT CAACTTTCCTCC TAGGGTGA atpE 79 6.39e-05 TTAATATATG TTAGTGTCCTCC TTTAATTTAA cds-WP_000140679.1 78 6.39e-05 GCTAATAAAA TTACTTTCCTCA CAGTACTTGG rpsU 80 6.39e-05 AGGCAACTAT AAACCTCCCTCC CTTTATGTC ccpA 84 7.77e-05 CTTATTTTGC AAATGTTCCTCC TTTAA scpB 78 7.77e-05 TATAATTGTA ATAATCTCCTCA CTTGATGGTA trmFO 83 7.77e-05 GTATTTACTG TTATTTTCCTCA TATCTT rplP 80 8.58e-05 GATTCTTGTG ATCACCTCCTCC TTTTATTAT rplO 82 8.58e-05 TCTTCTTTTT ATTAGTTCCTCC ACGGCTT cds-WP_000175001.1 82 8.58e-05 GAATTTATTA ATATATTCCTCA ATAATTA mgrA 80 8.58e-05 TTTGCCTATC ATACAGACCTCC TCTTGAAAT sasF 83 9.60e-05 TCCTTCATTC ACTCTTTCCTCA TATAAC cds-WP_000831055.1 82 9.60e-05 TACATTCCTT ATCATTTCCTCA CCACCCT cds-WP_000954261.1 81 9.60e-05 CGAATGTTAA TGTTTATCCTCC TATAATGC cds-WP_001030125.1 33 1.08e-04 AAAGATATTG AAAATGTCCTCA TTGTCACTCT rplR 83 1.08e-04 CTATTTGAGA TTTCTTTCCTCA TAACTT cds-WP_000933363.1 25 1.08e-04 CATAAGCAAG GAAATCACCTCC CAGTGTAGTG cds-WP_000922328.1 81 1.08e-04 AATGTCTGTT TCACTTTGCTCC TGTCTTAT cds-WP_001094394.1 81 1.20e-04 AACTTCATAT TGTTAATCCTCC TTACCTAT cds-WP_001079938.1 81 1.20e-04 AAATACCTTC AGTGTCTCCTCC TTATTTTA rplT 81 1.34e-04 GCCATCCTTA ATGGATTCCTCC TTAAAAAA cds-WP_020444698.1 75 1.34e-04 TTCATTAAAG ATAAATTCCACC ATTAACAGAA polA 81 1.48e-04 TATATATTTA ATCAAGACCTCC AATTTTAA rpsP 81 1.64e-04 AATTTTGTAC TGAATTTCCTCT AAAATATT cds-WP_000804879.1 40 1.81e-04 GCCCCGAATC ATACTTCCCTCT ATTTCTTCGT cds-WP_000951058.1 21 2.00e-04 TATATTGATT TCTAATTGCTCC CGTTTTATAA atpG 82 2.00e-04 TTTGTTCAAA TCATATTCCACC ACTCTAT rpsB 81 2.00e-04 CTCCATTAAT TGGTTATCCTCC TTAAATAT atpA 82 2.20e-04 AATTAATTAA TATTTCTCCTCA CTGTATC cds-WP_000287265.1 81 2.20e-04 AAATTTTGAA TTATTTCGCTCC AAAACGAA tsf 81 2.41e-04 ATTTTACTAT TGAATAACCTCC TTATTACT nusA 82 2.63e-04 TACTAAATTG CACTACTCCTCC TTTTTTG rpoZ 79 2.87e-04 ATATCTTTTT ACTAAAACCTCC GATTTTTTAT cds-WP_000624945.1 83 2.87e-04 TGTTCAAGTT TTCATCTCCTCT CCTTGT cds-WP_000238542.1 82 3.12e-04 TATTTTTATC ATTAATCCCTCT TTATTAA prmA 82 3.12e-04 GTTTTTCTAA GAAATTCCCTCT TATTTCA cds-WP_000403916.1 76 3.12e-04 TGTTTTGTGA GTAAAAACCTCC ACGGATATAG infB 83 3.37e-04 TATCTACTTA TAGTATTCCTCA CTAATA polX 83 3.64e-04 GGACCAGAAG AAAAATACCTCA CAATAA rplS 82 3.64e-04 TCTTGTATCC AACTTCTCCTCT TAAATAT cds-WP_000990133.1 82 3.93e-04 CATACAGCAC ATTACTTCCTCA CTGAAAC cds-WP_020444737.1 5 3.93e-04 GCTT ACGCAGTCCTCA AAGTCACCTG codY 82 3.93e-04 ATATTTTTAT ATGTTTTCCTCT TTTTAAG cds-WP_001293307.1 80 3.93e-04 TATCTAGAAT TATTACTGCTCC ACATTTTTT cds-WP_001055143.1 84 3.93e-04 TTTCAATTAG ACACTATCCTCT TTAAA cds-WP_000704122.1 82 4.25e-04 AGTTATAAGC TTAATTCACTCC AATATGT ygs 33 4.93e-04 TTGATGTTTT AATTAGTCCACC ATTTCGATTT cds-WP_000742839.1 80 5.29e-04 AATGTTGATT GTATTTTCCTCG CTTACCTAT rpmA 80 6.07e-04 AATCTAATTT AATATTCACTCC ACGTAAGGC rpsN 80 6.97e-04 ATGCTAAACT ATTTTTCACTCC ATTGATATA infC 27 8.94e-04 GTGTATTGAC ACATATTCCTTC TCGCCCATAA rpsM 81 1.27e-03 TTCCAATTAT TTTCTCTCCACA TTTAATTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWWWTTCCTCC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- rplD 1.4e-06 79_[+1]_9 cds-WP_001140799.1 1.4e-06 80_[+1]_8 rpsE 1.4e-06 79_[+1]_9 atpD 1.4e-06 80_[+1]_8 rpsO 3.1e-06 79_[+1]_9 rpsH 4.3e-06 79_[+1]_9 cds-WP_020444776.1 4.3e-06 80_[+1]_8 rplQ 4.3e-06 81_[+1]_7 rpmI 6.2e-06 79_[+1]_9 rpsK 8.3e-06 78_[+1]_10 tenA 8.3e-06 78_[+1]_10 rpsQ 1.1e-05 80_[+1]_8 cds-WP_001186979.1 1.1e-05 77_[+1]_11 rpsC 1.3e-05 81_[+1]_7 cds-WP_000159127.1 1.6e-05 82_[+1]_6 rpsS 1.9e-05 81_[+1]_7 rplV 1.9e-05 80_[+1]_8 rplN 1.9e-05 80_[+1]_8 rplF 1.9e-05 79_[+1]_9 rpmJ 1.9e-05 81_[+1]_7 cds-WP_000256338.1 1.9e-05 81_[+1]_7 rplU 2.1e-05 80_[+1]_8 cds-WP_000283016.1 2.1e-05 81_[+1]_7 rplW 2.4e-05 78_[+1]_10 rpmD 2.4e-05 77_[+1]_11 rpmG_3 2.4e-05 81_[+1]_7 dinB 2.7e-05 81_[+1]_7 cds-SABB_RS14155 3e-05 75_[+1]_13 cds-WP_000074007.1 3e-05 80_[+1]_8 efp 3e-05 81_[+1]_7 rpsJ 3.3e-05 81_[+1]_7 rplX 3.3e-05 81_[+1]_7 rplC 3.6e-05 78_[+1]_10 rplB 3.6e-05 79_[+1]_9 rplM 3.6e-05 79_[+1]_9 tet(M) 4.3e-05 80_[+1]_8 cds-WP_001054111.1 4.7e-05 79_[+1]_9 cds-WP_000151114.1 4.7e-05 77_[+1]_11 rpsI 5.1e-05 80_[+1]_8 rpoD 5.7e-05 81_[+1]_7 cds-WP_000278802.1 5.7e-05 79_[+1]_9 cds-WP_000610969.1 6.4e-05 78_[+1]_10 cds-WP_000106185.1 6.4e-05 81_[+1]_7 rplE 6.4e-05 80_[+1]_8 atpE 6.4e-05 78_[+1]_10 cds-WP_000140679.1 6.4e-05 77_[+1]_11 rpsU 6.4e-05 79_[+1]_9 ccpA 7.8e-05 83_[+1]_5 scpB 7.8e-05 77_[+1]_11 trmFO 7.8e-05 82_[+1]_6 rplP 8.6e-05 79_[+1]_9 rplO 8.6e-05 81_[+1]_7 cds-WP_000175001.1 8.6e-05 81_[+1]_7 mgrA 8.6e-05 79_[+1]_9 sasF 9.6e-05 82_[+1]_6 cds-WP_000831055.1 9.6e-05 81_[+1]_7 cds-WP_000954261.1 9.6e-05 80_[+1]_8 cds-WP_001030125.1 0.00011 32_[+1]_56 rplR 0.00011 82_[+1]_6 cds-WP_000933363.1 0.00011 24_[+1]_64 cds-WP_000922328.1 0.00011 80_[+1]_8 cds-WP_001094394.1 0.00012 80_[+1]_8 cds-WP_001079938.1 0.00012 80_[+1]_8 rplT 0.00013 80_[+1]_8 cds-WP_020444698.1 0.00013 74_[+1]_14 polA 0.00015 80_[+1]_8 rpsP 0.00016 80_[+1]_8 cds-WP_000804879.1 0.00018 39_[+1]_49 cds-WP_000951058.1 0.0002 20_[+1]_68 atpG 0.0002 81_[+1]_7 rpsB 0.0002 80_[+1]_8 atpA 0.00022 81_[+1]_7 cds-WP_000287265.1 0.00022 80_[+1]_8 tsf 0.00024 80_[+1]_8 nusA 0.00026 81_[+1]_7 rpoZ 0.00029 78_[+1]_10 cds-WP_000624945.1 0.00029 82_[+1]_6 cds-WP_000238542.1 0.00031 81_[+1]_7 prmA 0.00031 81_[+1]_7 cds-WP_000403916.1 0.00031 75_[+1]_13 infB 0.00034 82_[+1]_6 polX 0.00036 82_[+1]_6 rplS 0.00036 81_[+1]_7 cds-WP_000990133.1 0.00039 81_[+1]_7 cds-WP_020444737.1 0.00039 4_[+1]_84 codY 0.00039 81_[+1]_7 cds-WP_001293307.1 0.00039 79_[+1]_9 cds-WP_001055143.1 0.00039 83_[+1]_5 cds-WP_000704122.1 0.00042 81_[+1]_7 ygs 0.00049 32_[+1]_56 cds-WP_000742839.1 0.00053 79_[+1]_9 rpmA 0.00061 79_[+1]_9 rpsN 0.0007 79_[+1]_9 infC 0.00089 26_[+1]_62 rpsM 0.0013 80_[+1]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWWWTTCCTCC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF WWWWWTTCCTCC width=12 seqs=95 rplD ( 80) TCACTTTCCTCC 1 cds-WP_001140799.1 ( 81) TAAATTTCCTCC 1 rpsE ( 80) TAAATTTCCTCC 1 atpD ( 81) TAAATTTCCTCC 1 rpsO ( 80) TAAAATTCCTCC 1 rpsH ( 80) AGACTTTCCTCC 1 cds-WP_020444776.1 ( 81) ATATATTCCTCC 1 rplQ ( 82) ACTATTTCCTCC 1 rpmI ( 80) ATAATGTCCTCC 1 rpsK ( 79) TCCATTTCCTCC 1 tenA ( 79) ATAAATCCCTCC 1 rpsQ ( 81) TCATTCTCCTCC 1 cds-WP_001186979.1 ( 78) TAAATGTCCTCC 1 rpsC ( 82) GAAAATTCCTCC 1 cds-WP_000159127.1 ( 83) ACTTATTCCTCC 1 rpsS ( 82) ATTCTTCCCTCC 1 rplV ( 81) TTCATCTCCTCC 1 rplN ( 81) TCTATTCCCTCC 1 rplF ( 80) TTTTATTCCTCC 1 rpmJ ( 82) TTATATCCCTCC 1 cds-WP_000256338.1 ( 82) TAATTGTCCTCC 1 rplU ( 81) AATATGTCCTCC 1 cds-WP_000283016.1 ( 82) TTCATTCCCTCC 1 rplW ( 79) TTCAACTCCTCC 1 rpmD ( 78) GTTAATTCCTCC 1 rpmG_3 ( 82) TACTATTCCTCC 1 dinB ( 82) AATCATCCCTCC 1 cds-SABB_RS14155 ( 76) TACTTCTCCTCC 1 cds-WP_000074007.1 ( 81) TTAATATCCTCC 1 efp ( 82) TTTTACTCCTCC 1 rpsJ ( 82) GCTTATTCCTCC 1 rplX ( 82) GTTTATTCCTCC 1 rplC ( 79) TTAAAATCCTCC 1 rplB ( 80) GGTAATTCCTCC 1 rplM ( 80) AAAAAATCCTCC 1 tet(M) ( 81) AAACTTACCTCC 1 cds-WP_001054111.1 ( 80) TAACTTACCTCC 1 cds-WP_000151114.1 ( 78) AGTAACCCCTCC 1 rpsI ( 81) TAATCTTCCTCC 1 rpoD ( 82) TTTTAGCCCTCC 1 cds-WP_000278802.1 ( 80) ACATTACCCTCC 1 cds-WP_000610969.1 ( 79) TCTTTATCCTCC 1 cds-WP_000106185.1 ( 82) AAACTTTCCTCA 1 rplE ( 81) CAACTTTCCTCC 1 atpE ( 79) TTAGTGTCCTCC 1 cds-WP_000140679.1 ( 78) TTACTTTCCTCA 1 rpsU ( 80) AAACCTCCCTCC 1 ccpA ( 84) AAATGTTCCTCC 1 scpB ( 78) ATAATCTCCTCA 1 trmFO ( 83) TTATTTTCCTCA 1 rplP ( 80) ATCACCTCCTCC 1 rplO ( 82) ATTAGTTCCTCC 1 cds-WP_000175001.1 ( 82) ATATATTCCTCA 1 mgrA ( 80) ATACAGACCTCC 1 sasF ( 83) ACTCTTTCCTCA 1 cds-WP_000831055.1 ( 82) ATCATTTCCTCA 1 cds-WP_000954261.1 ( 81) TGTTTATCCTCC 1 cds-WP_001030125.1 ( 33) AAAATGTCCTCA 1 rplR ( 83) TTTCTTTCCTCA 1 cds-WP_000933363.1 ( 25) GAAATCACCTCC 1 cds-WP_000922328.1 ( 81) TCACTTTGCTCC 1 cds-WP_001094394.1 ( 81) TGTTAATCCTCC 1 cds-WP_001079938.1 ( 81) AGTGTCTCCTCC 1 rplT ( 81) ATGGATTCCTCC 1 cds-WP_020444698.1 ( 75) ATAAATTCCACC 1 polA ( 81) ATCAAGACCTCC 1 rpsP ( 81) TGAATTTCCTCT 1 cds-WP_000804879.1 ( 40) ATACTTCCCTCT 1 cds-WP_000951058.1 ( 21) TCTAATTGCTCC 1 atpG ( 82) TCATATTCCACC 1 rpsB ( 81) TGGTTATCCTCC 1 atpA ( 82) TATTTCTCCTCA 1 cds-WP_000287265.1 ( 81) TTATTTCGCTCC 1 tsf ( 81) TGAATAACCTCC 1 nusA ( 82) CACTACTCCTCC 1 rpoZ ( 79) ACTAAAACCTCC 1 cds-WP_000624945.1 ( 83) TTCATCTCCTCT 1 cds-WP_000238542.1 ( 82) ATTAATCCCTCT 1 prmA ( 82) GAAATTCCCTCT 1 cds-WP_000403916.1 ( 76) GTAAAAACCTCC 1 infB ( 83) TAGTATTCCTCA 1 polX ( 83) AAAAATACCTCA 1 rplS ( 82) AACTTCTCCTCT 1 cds-WP_000990133.1 ( 82) ATTACTTCCTCA 1 cds-WP_020444737.1 ( 5) ACGCAGTCCTCA 1 codY ( 82) ATGTTTTCCTCT 1 cds-WP_001293307.1 ( 80) TATTACTGCTCC 1 cds-WP_001055143.1 ( 84) ACACTATCCTCT 1 cds-WP_000704122.1 ( 82) TTAATTCACTCC 1 ygs ( 33) AATTAGTCCACC 1 cds-WP_000742839.1 ( 80) GTATTTTCCTCG 1 rpmA ( 80) AATATTCACTCC 1 rpsN ( 80) ATTTTTCACTCC 1 infC ( 27) ACATATTCCTTC 1 rpsM ( 81) TTTCTCTCCACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWWWTTCCTCC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 18957 bayes= 8.07169 E= 1.8e-044 36 -291 -51 29 -9 17 -51 15 56 -33 -136 -18 36 25 -210 -9 21 -192 -268 57 -141 8 -22 67 -183 17 -1321 97 -341 254 -168 -1321 -1321 265 -1321 -1321 -300 -1321 -1321 137 -1321 264 -1321 -513 -109 223 -368 -213 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWWWTTCCTCC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 95 E= 1.8e-044 0.431579 0.021053 0.094737 0.452632 0.315789 0.178947 0.094737 0.410526 0.494737 0.126316 0.052632 0.326316 0.431579 0.189474 0.031579 0.347368 0.389474 0.042105 0.021053 0.547368 0.126316 0.168421 0.115789 0.589474 0.094737 0.178947 0.000000 0.726316 0.031579 0.926316 0.042105 0.000000 0.000000 1.000000 0.000000 0.000000 0.042105 0.000000 0.000000 0.957895 0.000000 0.989474 0.000000 0.010526 0.157895 0.747368 0.010526 0.084211 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWWWTTCCTCC MEME-1 regular expression -------------------------------------------------------------------------------- [TA][TA][AT][AT][TA]TTCCTCC -------------------------------------------------------------------------------- Time 21.21 secs. ******************************************************************************** ******************************************************************************** MOTIF WAAGGAGGWGNAHD MEME-2 width = 14 sites = 42 llr = 419 E-value = 2.9e-025 ******************************************************************************** -------------------------------------------------------------------------------- Motif WAAGGAGGWGNAHD MEME-2 Description -------------------------------------------------------------------------------- Simplified A 586::a::423553 pos.-specific C 2::::::1::323: probability G ::189:a9:621:3 matrix T 32211:::612234 bits 2.9 * 2.6 ** 2.3 * ** 2.0 * ** Relative 1.7 ** ** Entropy 1.4 ***** (14.4 bits) 1.2 ***** * 0.9 ***** * 0.6 * ***** * 0.3 ********** ** 0.0 -------------- Multilevel AAAGGAGGTGCAAT consensus T T AAA TA sequence T CG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAGGAGGWGNAHD MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- rplK 85 2.91e-08 ATCACGATAT CAAGGAGGTGCACA TC rpsF 81 3.74e-08 GTATAGACCA CAAGGAGGTGCAAA TATAAA cds-WP_000373151.1 86 1.47e-07 TATATAACTT AAAGGAGGTGACAT A cds-WP_000404422.1 86 3.07e-07 CAGATAATAA AAAGGAGGAGTAAA G cds-WP_000887000.1 83 4.83e-07 AAAAATTTAG AAAGGAGGTACATG TTAA cds-WP_001208482.1 85 4.83e-07 GAAGTTATCA AACGGAGGTGCACT AA cds-WP_000654030.1 85 4.83e-07 TTTATAAATA TAAGGAGGAGGTAG TA rpsD 84 9.74e-07 AAAAAGAATT AAAGGAGGAGTCTT ATT rplJ 86 1.27e-06 CAAAAATTTA AATGGAGGTGTCTG A cds-WP_000198597.1 86 1.45e-06 CAAAATGATG TACGGAGGTGCAAT G rpsT 85 1.45e-06 GAACTCACTT TTAGGAGGTGACAG AA cds-WP_001030125.1 85 1.85e-06 ATATCATCTT TTAGGAGGTGGCTG TC rpmB 86 1.85e-06 TATATTTATT AAAGGAGGTACTCA T dnaX 86 2.41e-06 GGTAATTGTT TATGGAGGTGCTAA C cds-WP_001012724.1 86 2.68e-06 TCAGATGCTC AAAGGAGGATCGAA C rplA 85 3.04e-06 TAAAACCACT AAAGGAGGAACTAT AA cds-WP_000477992.1 87 3.45e-06 CATTTATTTT CAAGGAGGTTGAAT rpsR 84 3.82e-06 AAAAATTATC AAAGGAGGCACACA ATC cds-WP_000332063.1 83 5.98e-06 AAAAAATAAT AAATGAGGTGACTG AATT cds-WP_000656771.1 82 6.73e-06 TTCAATAACA CAAGGAGGTTGATT TATTT cds-WP_000157650.1 56 8.24e-06 GTTGATGGGT AAGTGAGGTGCTCG TTTTGAGCAA cds-WP_000927363.1 85 9.16e-06 TAAATTAAAA AATGGAGGATACCG CC cds-WP_001224184.1 86 1.02e-05 TAGAGAACTA TAAGTAGGTGGAAT C cds-WP_000333630.1 84 1.12e-05 CTATCAAGTA AAAGGAGCTGTATT ACG rpoC 58 1.37e-05 AATCTAAATT GAAGGAGGTAGGCT CCTTGATTGA rpsA 85 1.81e-05 ATGTAGTGTA TAAGGAGGCAAACA AG mepR 85 1.98e-05 CATCTAACGA AATGGTGGTGCAAT AA rpmF 86 2.57e-05 GTTTATAATC TAAGGAGGATATAT C rpsL 81 2.57e-05 TTAAAAAGTG AAGAGAGGAGGACA TATCAC cds-WP_020444782.1 86 3.05e-05 TCTATAAATA AAAGGAGCAAAACA C cds-WP_000954654.1 86 3.05e-05 TAGACAATGT ATGTGAGGTGAAAG T rplL 84 3.05e-05 AATTAAAAAT AATGGAGGAATTAT AAA agrB 79 3.31e-05 CGTATAATGA CAGTGAGGAGAGTG GTGTAAAA rplI 82 3.31e-05 ACAGAACAAT TAAGTAGGAGTGAA GATGC sarU 83 3.60e-05 ACATCAGAAA ATAGTAGGAGAATG TAAG cds-WP_000140679.1 36 3.60e-05 GTCATCCAGG ATTGGAGCAGCAAA AAAAGATATA cds-WP_000221179.1 87 3.92e-05 TATTTAACGT CTAGGAGGTATGTT merR 86 3.92e-05 TTATACTTTT TATTGAGGTGACAA T cds-WP_000560872.1 86 4.57e-05 ACATTTAGCG TGAGGAGGTGTTTT T rpsI 31 9.05e-05 ACCACCGCGA CTTGTAGGTGTGCG ACGTGTTGTT cds-WP_020444636.1 85 9.73e-05 CAAGCAGAAC TTTGGAGGATAAAT TA cds-WP_000414486.1 87 1.38e-04 AACAACGTTA AAAAGAGGAATATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAGGAGGWGNAHD MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- rplK 2.9e-08 84_[+2]_2 rpsF 3.7e-08 80_[+2]_6 cds-WP_000373151.1 1.5e-07 85_[+2]_1 cds-WP_000404422.1 3.1e-07 85_[+2]_1 cds-WP_000887000.1 4.8e-07 82_[+2]_4 cds-WP_001208482.1 4.8e-07 84_[+2]_2 cds-WP_000654030.1 4.8e-07 84_[+2]_2 rpsD 9.7e-07 83_[+2]_3 rplJ 1.3e-06 85_[+2]_1 cds-WP_000198597.1 1.4e-06 85_[+2]_1 rpsT 1.4e-06 84_[+2]_2 cds-WP_001030125.1 1.9e-06 84_[+2]_2 rpmB 1.9e-06 85_[+2]_1 dnaX 2.4e-06 85_[+2]_1 cds-WP_001012724.1 2.7e-06 85_[+2]_1 rplA 3e-06 84_[+2]_2 cds-WP_000477992.1 3.5e-06 86_[+2] rpsR 3.8e-06 83_[+2]_3 cds-WP_000332063.1 6e-06 82_[+2]_4 cds-WP_000656771.1 6.7e-06 81_[+2]_5 cds-WP_000157650.1 8.2e-06 55_[+2]_31 cds-WP_000927363.1 9.2e-06 84_[+2]_2 cds-WP_001224184.1 1e-05 85_[+2]_1 cds-WP_000333630.1 1.1e-05 83_[+2]_3 rpoC 1.4e-05 57_[+2]_29 rpsA 1.8e-05 84_[+2]_2 mepR 2e-05 84_[+2]_2 rpmF 2.6e-05 85_[+2]_1 rpsL 2.6e-05 80_[+2]_6 cds-WP_020444782.1 3.1e-05 85_[+2]_1 cds-WP_000954654.1 3.1e-05 85_[+2]_1 rplL 3.1e-05 83_[+2]_3 agrB 3.3e-05 78_[+2]_8 rplI 3.3e-05 81_[+2]_5 sarU 3.6e-05 82_[+2]_4 cds-WP_000140679.1 3.6e-05 35_[+2]_51 cds-WP_000221179.1 3.9e-05 86_[+2] merR 3.9e-05 85_[+2]_1 cds-WP_000560872.1 4.6e-05 85_[+2]_1 rpsI 9e-05 30_[+2]_56 cds-WP_020444636.1 9.7e-05 84_[+2]_2 cds-WP_000414486.1 0.00014 86_[+2] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAGGAGGWGNAHD MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF WAAGGAGGWGNAHD width=14 seqs=42 rplK ( 85) CAAGGAGGTGCACA 1 rpsF ( 81) CAAGGAGGTGCAAA 1 cds-WP_000373151.1 ( 86) AAAGGAGGTGACAT 1 cds-WP_000404422.1 ( 86) AAAGGAGGAGTAAA 1 cds-WP_000887000.1 ( 83) AAAGGAGGTACATG 1 cds-WP_001208482.1 ( 85) AACGGAGGTGCACT 1 cds-WP_000654030.1 ( 85) TAAGGAGGAGGTAG 1 rpsD ( 84) AAAGGAGGAGTCTT 1 rplJ ( 86) AATGGAGGTGTCTG 1 cds-WP_000198597.1 ( 86) TACGGAGGTGCAAT 1 rpsT ( 85) TTAGGAGGTGACAG 1 cds-WP_001030125.1 ( 85) TTAGGAGGTGGCTG 1 rpmB ( 86) AAAGGAGGTACTCA 1 dnaX ( 86) TATGGAGGTGCTAA 1 cds-WP_001012724.1 ( 86) AAAGGAGGATCGAA 1 rplA ( 85) AAAGGAGGAACTAT 1 cds-WP_000477992.1 ( 87) CAAGGAGGTTGAAT 1 rpsR ( 84) AAAGGAGGCACACA 1 cds-WP_000332063.1 ( 83) AAATGAGGTGACTG 1 cds-WP_000656771.1 ( 82) CAAGGAGGTTGATT 1 cds-WP_000157650.1 ( 56) AAGTGAGGTGCTCG 1 cds-WP_000927363.1 ( 85) AATGGAGGATACCG 1 cds-WP_001224184.1 ( 86) TAAGTAGGTGGAAT 1 cds-WP_000333630.1 ( 84) AAAGGAGCTGTATT 1 rpoC ( 58) GAAGGAGGTAGGCT 1 rpsA ( 85) TAAGGAGGCAAACA 1 mepR ( 85) AATGGTGGTGCAAT 1 rpmF ( 86) TAAGGAGGATATAT 1 rpsL ( 81) AAGAGAGGAGGACA 1 cds-WP_020444782.1 ( 86) AAAGGAGCAAAACA 1 cds-WP_000954654.1 ( 86) ATGTGAGGTGAAAG 1 rplL ( 84) AATGGAGGAATTAT 1 agrB ( 79) CAGTGAGGAGAGTG 1 rplI ( 82) TAAGTAGGAGTGAA 1 sarU ( 83) ATAGTAGGAGAATG 1 cds-WP_000140679.1 ( 36) ATTGGAGCAGCAAA 1 cds-WP_000221179.1 ( 87) CTAGGAGGTATGTT 1 merR ( 86) TATTGAGGTGACAA 1 cds-WP_000560872.1 ( 86) TGAGGAGGTGTTTT 1 rpsI ( 31) CTTGTAGGTGTGCG 1 cds-WP_020444636.1 ( 85) TTTGGAGGATAAAT 1 cds-WP_000414486.1 ( 87) AAAAGAGGAATATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAGGAGGWGNAHD MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 18531 bayes= 10.289 E= 2.9e-025 64 7 -250 -37 122 -1204 -250 -96 94 -174 -51 -79 -282 -1204 262 -163 -1204 -1204 274 -196 154 -1204 -1204 -395 -1204 -1204 289 -1204 -1204 -115 278 -1204 18 -174 -1204 63 -50 -1204 219 -137 -23 96 30 -63 50 26 8 -96 43 72 -1204 -37 -1 -1204 108 4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAGGAGGWGNAHD MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 42 E= 2.9e-025 0.523810 0.166667 0.023810 0.285714 0.785714 0.000000 0.023810 0.190476 0.642857 0.047619 0.095238 0.214286 0.047619 0.000000 0.833333 0.119048 0.000000 0.000000 0.904762 0.095238 0.976190 0.000000 0.000000 0.023810 0.000000 0.000000 1.000000 0.000000 0.000000 0.071429 0.928571 0.000000 0.380952 0.047619 0.000000 0.571429 0.238095 0.000000 0.619048 0.142857 0.285714 0.309524 0.166667 0.238095 0.476190 0.190476 0.142857 0.190476 0.452381 0.261905 0.000000 0.285714 0.333333 0.000000 0.285714 0.380952 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAGGAGGWGNAHD MEME-2 regular expression -------------------------------------------------------------------------------- [AT]A[AT]GGAGG[TA][GA][CAT]A[ATC][TAG] -------------------------------------------------------------------------------- Time 39.99 secs. ******************************************************************************** ******************************************************************************** MOTIF GTGGRASGGCAAARCNGADCCSHGAVAC MEME-3 width = 28 sites = 4 llr = 116 E-value = 2.3e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGGRASGGCAAARCNGADCCSHGAVAC MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::55::3:8aa5:3:83:::3:838: pos.-specific C :::::35::8::::833::8a553:3:a probability G 8:88535a833::5338:53:5:8:5:: matrix T 3a33:::::::::::3:33:::3:3:3: bits 2.9 * 2.6 * * * 2.3 * * * 2.0 * * * * ** * * Relative 1.7 * ** **** * * *** * * Entropy 1.4 **** **** ** * * *** * * (41.7 bits) 1.2 ***** ********* * *** * * 0.9 ***** ********* ** *** ***** 0.6 *************** ************ 0.3 *************** ************ 0.0 ---------------------------- Multilevel GTGGAACGGCAAAACAGAGCCCCGAGAC consensus T TTGCG AGG GGCCTAG GACTAT sequence G G T T C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGRASGGCAAARCNGADCCSHGAVAC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------------------- rpsJ 14 5.67e-16 CAATGACTGT GTGGGCCGGCGAAACGGTACCGCGACAC ATTCTATCAA rplK 44 6.44e-16 AATGTTAAGA GTGGGAGGGCAAAACTGAGCCCTGTGAC CACATCACGA cds-WP_000804879.1 12 5.28e-13 TAAATACGTT GTTTAGGGGGAAAGCACAGCCCCGAATC ATACTTCCCT cds-WP_000181832.1 52 8.04e-13 ACATATTTAT TTGGAACGACAAAGGCGATGCGACAGAC AGATTTGTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGRASGGCAAARCNGADCCSHGAVAC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- rpsJ 5.7e-16 13_[+3]_59 rplK 6.4e-16 43_[+3]_29 cds-WP_000804879.1 5.3e-13 11_[+3]_61 cds-WP_000181832.1 8e-13 51_[+3]_21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGRASGGCAAARCNGADCCSHGAVAC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTGGRASGGCAAARCNGADCCSHGAVAC width=28 seqs=4 rpsJ ( 14) GTGGGCCGGCGAAACGGTACCGCGACAC 1 rplK ( 44) GTGGGAGGGCAAAACTGAGCCCTGTGAC 1 cds-WP_000804879.1 ( 12) GTTTAGGGGGAAAGCACAGCCCCGAATC 1 cds-WP_000181832.1 ( 52) TTGGAACGACAAAGGCGATGCGACAGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGRASGGCAAARCNGADCCSHGAVAC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 28 n= 15549 bayes= 11.9242 E= 2.3e-003 -865 -865 247 -56 -865 -865 -865 143 -865 -865 247 -56 -865 -865 247 -56 57 -865 188 -865 57 65 88 -865 -865 165 188 -865 -865 -865 288 -865 -43 -865 247 -865 -865 224 88 -865 116 -865 88 -865 157 -865 -865 -865 157 -865 -865 -865 57 -865 188 -865 -865 224 88 -865 -43 65 88 -56 -865 65 247 -865 116 -865 -865 -56 -43 -865 188 -56 -865 224 88 -865 -865 265 -865 -865 -865 165 188 -865 -43 165 -865 -56 -865 65 247 -865 116 -865 -865 -56 -43 65 188 -865 116 -865 -865 -56 -865 265 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGRASGGCAAARCNGADCCSHGAVAC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 28 nsites= 4 E= 2.3e-003 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.250000 0.500000 0.000000 0.500000 0.000000 0.500000 0.250000 0.250000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.750000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.750000 0.250000 0.000000 0.250000 0.250000 0.250000 0.250000 0.000000 0.250000 0.750000 0.000000 0.750000 0.000000 0.000000 0.250000 0.250000 0.000000 0.500000 0.250000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.250000 0.500000 0.000000 0.250000 0.000000 0.250000 0.750000 0.000000 0.750000 0.000000 0.000000 0.250000 0.250000 0.250000 0.500000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGRASGGCAAARCNGADCCSHGAVAC MEME-3 regular expression -------------------------------------------------------------------------------- [GT]T[GT][GT][AG][ACG][CG]G[GA][CG][AG]AA[AG][CG][ACGT][GC][AT][GAT][CG]C[CG][CAT][GC][AT][GAC][AT]C -------------------------------------------------------------------------------- Time 57.99 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- dnaN 2.16e-01 100 rplI 6.89e-03 81_[+2(3.31e-05)]_5 cds-WP_000373151.1 6.47e-04 85_[+2(1.47e-07)]_1 merR 6.28e-02 85_[+2(3.92e-05)]_1 mecI 1.75e-02 19_[+3(3.63e-05)]_53 cds-WP_000427807.1 4.69e-01 100 cds-WP_000159127.1 1.26e-02 82_[+1(1.59e-05)]_6 cds-WP_000414486.1 1.43e-01 100 sarS 4.45e-01 100 cds-WP_001793808.1 3.34e-01 100 cds-WP_041205521.1 8.98e-01 100 cds-WP_000181832.1 6.67e-09 51_[+3(8.04e-13)]_21 cds-WP_001012724.1 3.06e-04 85_[+2(2.68e-06)]_1 cds-WP_000922328.1 6.90e-02 100 cds-WP_020444620.1 9.31e-01 100 cds-WP_000291432.1 9.97e-01 100 cds-WP_000667382.1 5.82e-01 100 cds-WP_000954261.1 6.63e-02 80_[+1(9.60e-05)]_8 mepR 3.97e-02 84_[+2(1.98e-05)]_2 cds-WP_000467652.1 3.52e-01 100 cds-WP_041205307.1 3.90e-01 100 cds-WP_001079938.1 9.08e-02 100 cds-WP_001550052.1 2.37e-01 100 ychF 1.17e-01 100 rpsF 6.38e-05 80_[+2(3.74e-08)]_6 rpsR 1.00e-02 83_[+2(3.82e-06)]_3 cds-WP_000804879.1 5.84e-11 11_[+3(5.28e-13)]_61 tet(M) 4.25e-02 80_[+1(4.28e-05)]_8 cds-WP_000403916.1 4.93e-02 100 treR 5.50e-01 100 dnaX 8.97e-03 85_[+2(2.41e-06)]_1 cds-WP_000344337.1 2.77e-01 100 cds-WP_000691766.1 6.81e-01 100 cds-WP_000157650.1 1.35e-03 55_[+2(8.24e-06)]_31 mfd 8.18e-01 100 cds-WP_000021445.1 8.17e-01 100 cds-WP_000551762.1 6.87e-01 100 rpmG 8.38e-01 100 nusG 2.06e-01 100 rplK 7.74e-17 43_[+3(6.44e-16)]_13_[+2(2.91e-08)]_\ 2 rplA 4.33e-04 84_[+2(3.04e-06)]_2 rplJ 1.41e-03 85_[+2(1.27e-06)]_1 rplL 2.13e-02 83_[+2(3.05e-05)]_3 rpoB 1.72e-01 100 rpoC 6.81e-03 57_[+2(1.37e-05)]_29 cds-WP_020444636.1 8.27e-02 84_[+2(9.73e-05)]_2 rpsL 1.11e-02 80_[+2(2.57e-05)]_6 rpsG 5.94e-01 100 fusA 1.84e-01 100 tuf 1.97e-01 100 cds-WP_000954654.1 6.09e-02 85_[+2(3.05e-05)]_1 cds-WP_000638613.1 3.26e-01 100 mgrA 8.61e-02 79_[+1(8.58e-05)]_9 cds-WP_000972699.1 1.84e-01 100 cds-WP_000654030.1 7.40e-05 84_[+2(4.83e-07)]_2 cds-WP_001186979.1 2.78e-02 77_[+1(1.07e-05)]_11 cds-WP_000560872.1 3.85e-02 85_[+2(4.57e-05)]_1 dltA 2.27e-01 100 ygs 1.00e-01 100 cds-WP_000404422.1 5.44e-04 85_[+2(3.07e-07)]_1 cds-WP_000287265.1 2.11e-01 100 cds-WP_000278010.1 5.04e-01 100 cds-WP_001031975.1 3.15e-01 100 cds-WP_001020625.1 1.47e-01 100 rpmF 5.72e-02 85_[+2(2.57e-05)]_1 cds-WP_001055143.1 2.89e-01 100 cds-WP_000933363.1 9.46e-03 100 rpsA 3.26e-02 84_[+2(1.81e-05)]_2 cds-WP_000361544.1 1.88e-01 100 cds-WP_000283016.1 4.04e-02 81_[+1(2.14e-05)]_7 cds-WP_000356975.1 5.18e-01 100 cds-WP_000505015.1 7.54e-01 100 lexA 8.73e-01 100 rpsN 1.57e-01 100 rpmG_2 3.96e-01 100 cds-WP_000600812.1 9.99e-01 100 cds-WP_000624945.1 1.75e-01 100 cds-WP_001293307.1 1.05e-01 100 rpsO 6.80e-04 79_[+1(3.14e-06)]_9 infB 2.79e-01 100 cds-WP_000020853.1 9.95e-01 100 cds-WP_000727423.1 7.88e-01 100 nusA 1.85e-01 100 cds-WP_020444698.1 8.60e-02 100 tsf 1.89e-01 100 rpsB 1.71e-01 100 codY 1.40e-01 100 trmFO 1.08e-01 82_[+1(7.77e-05)]_6 rplS 2.60e-01 100 rpsP 7.17e-02 100 fapR 1.83e-01 100 rpmB 2.86e-03 85_[+2(1.85e-06)]_1 rpoZ 2.44e-01 100 polX 1.92e-02 100 cds-WP_000278802.1 8.10e-02 79_[+1(5.74e-05)]_9 cds-WP_000175001.1 4.52e-02 81_[+1(8.58e-05)]_7 cds-WP_000333630.1 7.18e-03 83_[+2(1.12e-05)]_3 scpB 8.71e-02 77_[+1(7.77e-05)]_11 cds-WP_000256338.1 1.93e-02 81_[+1(1.86e-05)]_7 nusB 2.95e-01 100 efp 1.62e-02 81_[+1(3.01e-05)]_7 cds-WP_000161314.1 2.11e-01 100 rpmG_3 4.50e-02 81_[+1(2.41e-05)]_7 rpoD 3.32e-02 81_[+1(5.74e-05)]_7 rpsU 7.17e-02 79_[+1(6.39e-05)]_9 prmA 8.96e-02 100 hrcA 4.38e-01 100 rpsT 2.76e-03 84_[+2(1.45e-06)]_2 holA 3.84e-01 100 greA 4.15e-01 100 cds-WP_000704122.1 3.40e-02 100 rpmA 1.96e-01 100 cds-WP_016187883.1 7.95e-01 100 rplU 2.59e-03 80_[+1(2.14e-05)]_8 rplT 1.65e-01 100 rpmI 7.82e-03 79_[+1(6.20e-06)]_9 infC 6.01e-02 100 nrdR 4.33e-01 100 polA 1.05e-01 100 cds-WP_020444737.1 1.71e-01 100 cds-WP_000160435.1 3.62e-01 100 rpsD 1.85e-03 83_[+2(9.74e-07)]_3 ccpA 1.24e-01 83_[+1(7.77e-05)]_5 cds-WP_000757543.1 3.94e-02 100 cds-WP_000221179.1 2.03e-02 86_[+2(3.92e-05)] cds-WP_000375864.1 2.66e-01 100 cds-WP_000613733.1 8.60e-01 100 dinB 3.84e-02 81_[+1(2.70e-05)]_7 cds-WP_000691584.1 3.64e-01 100 cds-WP_001208482.1 1.95e-03 84_[+2(4.83e-07)]_2 cds-WP_000128898.1 5.38e-01 100 agrB 1.18e-02 78_[+2(3.31e-05)]_8 cds-WP_000790330.1 4.55e-01 100 cds-WP_000370124.1 6.45e-01 100 sigB 3.04e-01 100 tenA 1.25e-02 78_[+1(8.32e-06)]_10 cds-WP_001094394.1 1.31e-01 100 atpD 2.99e-03 80_[+1(1.36e-06)]_8 atpG 1.65e-01 100 atpA 1.57e-01 100 cds-WP_000241351.1 9.02e-01 100 cds-WP_000140679.1 4.95e-04 35_[+2(3.60e-05)]_28_[+1(6.39e-05)]_\ 11 atpE 7.94e-02 78_[+1(6.39e-05)]_10 atpB 8.61e-02 100 cds-WP_000379888.1 6.31e-01 100 cds-WP_000808968.1 2.92e-01 100 rho 4.29e-01 100 cds-WP_000451438.1 6.01e-01 100 rpoE 1.46e-01 100 czrA 6.26e-01 100 cds-WP_000927363.1 2.38e-02 84_[+2(9.16e-06)]_2 cds-WP_001793365.1 7.24e-01 100 cds-WP_000850011.1 8.34e-01 100 rpsI 5.56e-04 30_[+2(9.05e-05)]_36_[+1(5.15e-05)]_\ 8 rplM 2.08e-02 79_[+1(3.64e-05)]_9 rplQ 1.12e-02 81_[+1(4.33e-06)]_7 cds-WP_020444776.1 2.04e-03 80_[+1(4.33e-06)]_8 rpsK 4.96e-03 78_[+1(8.32e-06)]_10 rpsM 5.56e-01 100 rpmJ 9.89e-04 81_[+1(1.86e-05)]_7 infA 4.66e-01 100 rplO 4.90e-02 81_[+1(8.58e-05)]_7 rpmD 3.71e-02 77_[+1(2.41e-05)]_11 rpsE 5.27e-03 79_[+1(1.36e-06)]_9 rplR 1.05e-01 100 rplF 3.53e-02 79_[+1(1.86e-05)]_9 rpsH 1.71e-03 79_[+1(4.33e-06)]_9 cds-WP_001140799.1 2.77e-03 80_[+1(1.36e-06)]_8 rplE 5.61e-02 80_[+1(6.39e-05)]_8 rplX 2.01e-02 81_[+1(3.31e-05)]_7 rplN 3.20e-03 80_[+1(1.86e-05)]_8 rpsQ 2.65e-03 80_[+1(1.07e-05)]_8 rpmC 2.94e-01 100 rplP 3.49e-02 79_[+1(8.58e-05)]_9 rpsC 2.24e-03 81_[+1(1.33e-05)]_7 rplV 1.94e-03 80_[+1(1.86e-05)]_8 rpsS 1.62e-02 81_[+1(1.86e-05)]_7 rplB 1.07e-02 79_[+1(3.64e-05)]_9 rplW 3.85e-02 78_[+1(2.41e-05)]_10 rplD 1.60e-03 79_[+1(1.36e-06)]_9 rplC 1.30e-02 78_[+1(3.64e-05)]_10 rpsJ 8.38e-14 13_[+3(5.67e-16)]_40_[+1(3.31e-05)]_\ 7 cds-WP_000951058.1 8.30e-02 100 cds-WP_000032855.1 7.84e-01 100 cds-WP_000831055.1 1.42e-01 81_[+1(9.60e-05)]_7 cds-WP_001030125.1 1.47e-04 84_[+2(1.85e-06)]_2 cds-WP_000073195.1 2.25e-02 100 cds-WP_000477992.1 4.75e-03 86_[+2(3.45e-06)] cds-WP_020444782.1 1.63e-02 85_[+2(3.05e-05)]_1 cds-WP_000828570.1 2.49e-01 100 cds-WP_000238542.1 2.86e-01 100 cds-WP_000656771.1 2.86e-03 81_[+2(6.73e-06)]_5 cds-WP_000289213.1 8.91e-01 100 cds-WP_000332063.1 1.38e-02 82_[+2(5.98e-06)]_4 sarU 4.06e-02 82_[+2(3.60e-05)]_4 cds-WP_000990133.1 1.30e-01 100 cds-WP_000074007.1 3.45e-02 80_[+1(3.01e-05)]_8 cds-SABB_RS14155 5.53e-02 75_[+1(3.01e-05)]_13 cds-WP_000376235.1 6.39e-01 100 cds-WP_000351761.1 7.74e-01 100 farR 2.63e-01 100 cds-WP_001791286.1 5.13e-01 100 cds-WP_001224184.1 1.44e-02 85_[+2(1.02e-05)]_1 blaI 6.92e-01 100 cds-WP_000151114.1 8.65e-02 77_[+1(4.67e-05)]_11 cds-WP_000198597.1 4.04e-03 85_[+2(1.45e-06)]_1 cds-WP_000106185.1 4.79e-02 81_[+1(6.39e-05)]_7 cds-WP_000887000.1 1.18e-03 82_[+2(4.83e-07)]_4 sasF 1.24e-01 82_[+1(9.60e-05)]_6 icaR 4.21e-01 100 cds-WP_000610969.1 1.67e-02 78_[+1(6.39e-05)]_10 cds-WP_001054111.1 4.99e-02 79_[+1(4.67e-05)]_9 cds-WP_000742839.1 1.63e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************